Index

A acyltransferase 123 adduct formation 815, 822 α-helical segment 190 adenosine-5´-phosphosulfate (APS) 610, 613 α-ketobutyrate 613 adenosine-5´-phosphosulfate reductase 610, 611 α-Proteobacteria 780, 791 adenosyl-GDP-cobinamide 91 α/β heterodimer 137–139 adenosyl cobalamin 72, 73, 82, 91 α helix 511 adenosylcobinamide phosphate 91 α polypeptide 175, 188, 204 adenosylcobyric acid 90 αβ LH1 subunit 513 adenylylsulfate 610, 613 A-branch 301 adenylysulfate:phosphate adenylyltransferase (APAT) 610 A-side electron transfer 346 Adiantum capillus-veneris 814 aa3-type cytochrome c oxidase 407, 408, 541, 636, 788 AdoMet:diacylglycerol 3-amino-3-carboxypropyl transferase AAA+ 69, 748 128 AAA+ ATPases 749 ADP-inhibition 477 AAA proteins 69 ADP sulfurylase 610 AAA+ proteins 70 Aequoria victoria 845 AAnP. See aerobic anoxygenic phototrophs aerobic anoxygenic phototrophs 19, 31, 32–52, 599 AAP. See aerobic anoxygenic phototrophs carbon metabolism 40–41 ABC. See ATP-binding cassette (ABC) deep ocean absorbance spectra vertical distribution 50 in vivo 39 ecological roles 47–51 absorption maxima 431 environment 32 carotenoid 926 evolution 38–40 absorption transitions 200 marine 48–49 accA 122 morphology 35 accB 122 nutritional status 43 accC 122 phylogeny 33, 37 accD 122 taxonomy 37 acceptor pool 530 aerobic bacteria 112 acceptor quinone 379, 380–399 aerobic cobalamin biosynthetic pathway 84 reactions 382 aerobic conditions 58, 72, 112, 417 acceptor quinone complex 383 aerobic cyclization system 72 accessory phototrophy 50 aerobic pathway 84 Acetobacteraceae 603, 614 aerobic photosynthetic bacteria 98, 99, 112 3-acetoxychlorophyllide a 68 aerobic phototoxicity 38 acetyl carbonyl 204 aerobic phototrophic bacteria 19 Acidiphilium 34, 112, 113, 599, 608 aerobic purple bacteria 19–20 Acidiphilium acidophilum 599 aerobic repression Acidiphilium cryptum 603, 614 CrtJ 716–721 Acidiphilium cryptum JF-5 790, 791, 792 aerobic repressor 784, 785 Acidiphilium rubrum 112, 113 aerobic respiration 149 Acidisphaera 34 aerotaxis 651 Acidithiobacillus 459, 608 AerR 785, 791 Acidithiobacillus ferrooxidans 459, 666 aerR 785, 786, 789 acidophilic purple bacteria 11 affi nity chromatography 849 acid pocket 715 AFFM. See atomic force fl uorescence microscopy (AFFM) acpP 122 AFM. See atomic force microscopy (AFM) acpS 122 AFM topographs 164 ACP synthase 122 Agrobacteria 694 acrylic acid 546 Agrobacterium 702 AcsF 42, 72 Agrobacterium tumefaciens 805 acsF 44, 47, 51, 72, 794 ALA. See δ-aminolevulinate; See 5-aminolevulinic acid (ALA) actin fi lament 486 ALAD. See δ-aminolevulinic acid dehydratase action spectrum 871 ALA dehydratase 60 + – active P QB state 957, 961, 963 ALA synthase 778, 780, 782, 783, 786, 788, 791 acyl carrier protein (ACP) 122 Alcaligenes eutrophus 744 976 Index

Alcaligenes faecalis 635 hexagonally packed 945 alcohols 40 LH2 size heterogeneity 948 Alexandrium 48 packing density 946 algae 103 ring size 151 algal blooms 48 antenna absorption transition 203–205 Alkalilimnicola 600 antenna complex 146–151; See also light-harvesting 1 Alkalilimnicola ehrlichei 604, 615 complex; See also light-harvesting 2 complex alkaliphilic purple bacteria 10–11 artifi cial 861 Alkalispirillum 600 synthesis 147 Allochromation vinosum 612, 745 antenna connectivity 170 Allochromatium 8 antenna domain formation 944 Allochromatium minutissimum 607 antenna domains 257, 945, 946, 949 Allochromatium vinosum 3, 4, 6, 103, 384, 515, 596, 601, 604, antenna heterogeneity 944 606, 609, 610, 613, 615, 853 antenna proteins 200–201 Allochromatium warmingii 601 anthraquinone 304, 382, 391 allosteric 791 antibiotic resistance markers 842 alphaproteobacteria 5, 18–19, 59, 98, 99, 111, 112, 581, 597 antimycin 519 phototrophic 597 antimycin A 435, 455, 526 alternative nitrogenase 769 antioxidative 41 amidase 90 anti sigma factor FlgM 645 amino acid APAT 611 distribution 918, 920 APB. See aerobic phototrophic bacteria model sequence 920 apoCyt c 409 motifs 918, 920 apoCyt c heme binding 413 sequence contexts 922 apocytochrome c 407 amino acid sequence 921 apoptosis 527 model 916 AppA 652, 718, 719, 732, 785, 818, 831 5-aminolevulinic acid (ALA) 778, 780, 782, 783, 786, 788, light-responding antirepressor 718 791 regulatory role 718 aminopropanol 82 appA 785 aminopropyltriethoxysilane 862 apparent equilibrium constant 520, 524 ammonium transporter 769–770 apr 603 AmtB 769–770 APS kinase 613, 615 amphiphile 146 APS reductase 615 amphiphilic protein maquettes 905–907 APS reductase pathway 610 AmtB 769–770 Aquifex aeolicus 749 ammonium transporter 769–770 Arabidopsis thaliana 72, 612, 847 anaerobic ammonia oxidation 624 ArcB/ArcA 753 anaerobic aromatic compound ArcB sensor kinase 754 degradation 589–590 Archaea 609, 746 anaerobic benzoate degradation 580–589 Arhodomonas aquaeolei 600 anaerobic benzoate photometabolism 580 aromatic compounds 577–591 anaerobic conditions 72, 523 degradation 577–591 anaerobic respiration 149 aromatic residues 916, 918, 920, 922, 924 anaerobiosis 848 arrA 549 analogs 184 arrB 549 anaplerotic CO2 fi xation 40 ars determinants 662 anaplerotic CO2 incorporation 48 arsABC 673, 675 AnfA 769 arsC gene family 676 anfA 765 arsenate 549, 663 anfHDGK 769 arsenate reductase 676 anfHDK 761 arsenate respiration 549 anhydrorhodovibrin 929, 931 arsenic 548–550 anisotropy decay 243 arsenite 550 annihilation experiments 148 arsenite oxidase 459, 549, 552 Antarctica 4 arsenite oxidation 549, 664 antenna ars operon 663 clustering 945 Arsukibacterium ikkense 601 complex assembly 946 artifi cial antenna complex 861 domain formation 944 artifi cial LH1-type complex 873 heterogeneity 944 Aspergillus nidulans 847 Index 977 assembly 195 B core complexes 172 assembly factor β-barrel 416 LhaA 174 β-carotene 98, 113 assembly factor for LH2 174 β-carotene ketolase 113 assembly pathways 407 β-dodecyl maltoside 260 assembly protein β-galactosidase 780, 789 Surf1 545 β-hydroxydecanoyl-ACP dehydratase 122 assimilatory nitrate reductase (Nas) 548, 637 β-hydroxyl-ACP dehydratase 122 assimilatory sulfate reduction 610, 612–615, 613, 616 β-ketoacyl-ACP reductase 122 asymmetrical ζ-carotene 104 β-ketoacyl-ACP synthase I 122 AT-rich codons 850 β-ketoacyl-ACP synthase II 122 ATB binding β-ketoacyl-ACP synthase III 122 Walker A and B motifs 411 β-octyl-glucoside 185 ATCC17023 critical micelle concentration 185 wild-type strain 849 micelle 185 ATCC17025 780, 782, 791 β-octylglucoside (β-OG) 140, 146, 864 ATCC17029 780, 782 β-oxidation 580, 581, 584, 585, 586, 587 atomic force fl uorescence microscopy (AFFM) 270 β helix 511 atomic force microscopy (AFM) 137, 146, 150, 163, 165, 201, β mutant 338 254, 255, 257, 258, 262, 270, 286, 478, 513, 520, 528, β mutation 347 861, 862, 864–865, 941–951 β polypeptide 175, 188, 205 fast scanning 950 ‘b’ position 454, 456 scan range 950 B-branch 301, 306 tip as nano-dissector 950 electron transfer 348, 958 atomic level structural model B-branch electron transfer 348, 958 photosynthetic unit 287 B-side electron transfer 346–348 atomic models 950 b-type heme 452, 752 atovaquone analog 445 B1020 150 ATP 90, 613 B780 934 ATP-binding cassette (ABC) 410 B798-832 35, 46 ATP-binding cassette transporter complex 410 B800 142, 150, 203, 214, 225–226, 878, 882–885 ATP-synthase 475–493, 942 B800-814 46 ATP:sulfate adenylyltransferase 610 B800-820 46, 150 ATP analog 806 B800-830 148, 150 ATPase 419, 748 B800-850 46, 150 CPx-type 661 B800-B850 920 P-type 661 fl uorescence up-conversion 225 ATPase domain 69 B800 molecule 203 ATP binding site 69 B806 46 ATP dependent oligomers 70 B820 182, 188, 932, 934 ATP hydrolysis 66, 70 dimeric structure 186 ATP production 425 hydrophobic surface area 183 ATP regenerating system 67 NMR experiments 186 ATP regeneration system 74 oligomerization 187 ATP sulfurylase 610, 611, 613, 615, 616 reversible dissociation 183 ATP synthase 254, 262, 264, 279, 476–488, 510, 538 B820-type complex 188 proton translocation 476–488 minimal requirements 190 ATP synthesis 510 B820 complex 157, 175, 183 ATP synthesis/hydrolysis 478–486 chemically synthesized polypeptides 189 auto-induce 844 heterodimeric B820 189 auto-oxidization 438 homodimeric B820 189 autophosphorylation 800, 802, 806 membrane-spanning middle segment 189 RegB 713 N-terminus 189 Avena sativa 815 protein interactions 189 average excitation lifetime 280 proteolysis 189 avoided level crossings 283 shorter synthetic polypeptides 189 Azoarcus 581, 588 B850 142, 214, 878, 885–889 Azotobacter vinelandii 637 B850 ring azoxystobin 442 elliptical deformation 207 B870 934 978 Index

B875 150, 927 Mg coordination 184–188 B880 926, 932, 935 binding energy 185 B880 formation 931 modifi ed pigments 915 B890 150 molecule 204, 205 Bacillus 457, 669 distorted conformation 205 Bacillus PS3 479 monomer 338, 341 Bacillus selenitireducens 549, 664 π-π interactions 190 Bacillus subtilis 413, 813, 852 Qy-band 897 back-reaction 148 replacement 305 bacterial artifi cial chromosome (BAC) 45 spectra 897 bacterial plasma membrane 264 stereochemical aspects 915 bacteriochlorin 58, 897 surface area 897 bacteriochlorin exclusion 301 tetrapyrrole ring 42 bacteriochlorin replacement 302 transition dipoles 168 bacteriochlorin ring 141 water ligand 344 (bacterio)chlorophyll 916 bacteriochlorophyll-B850/protein interface 922 (bacterio)chlorophyll binding pocket 916 bacteriochlorophyll-binding proteins statistical analysis 916 synthetic 895, 896–907 binding 916 bacteriochlorophyll/protein interface 915, 916, 922 binding-motifs 916 packing interactions 923 binding pockets 919 bacteriochlorophyll/transmembrane helix interface 923 binding site bacteriochlorophyll a 42, 58, 65, 68, 112, 214, 338, 873 re-design 920 zinc-substituted 873

bioinformatics 916 bacteriochlorophyll aGG 68 Chl binding 918–919 bacteriochlorophyll b 58, 65, 112 hydrogen bonding 916, 918 bacteriochlorophyll b-containing B800-1020 46 interactions 917 bacteriochlorophyll biosynthesis 83 ligation 916, 918 cyclase enzyme 83 motifs 922 Mg chelatase 90 pigment-protein 916 bacteriochlorophyll dimer 337, 344 pockets 918 bacteriochlorophyll exchange substituent 918 light-harvesting 1 complex 928 interactions 918 bacteriochlorophyllide a 68 α-ligated states 918 bacteriochlorophyll molecules α-ligation 918 coordination to Mg 933 β-ligated 923 bacteriochlorophyll pathway 147 β-ligated states 918 bacteriochlorophyll protein β-ligation 918 assembly 918 bacteriochlorophyll (BChl) 21, 42, 58–75, 138, 182, 184, 186, bacteriochlorophyll protein platforms 202, 232, 337, 356, 699, 703, 778, 780, 783, 787, 794, de novo design 895, 896–907 895–907, 914, 916, 920; See also chlorophyll (Chl) bacteriochlorophyll synthase 67, 74, 147 aggregation 897 bacteriochlorophyll synthesis 83, 92 B800 142 bacteriopheophorbide 902 B850 142 Fe 902 bacteriochlorophyll-protein hydrogen bonds 186 Ni 902 (B)Chl ligation 915 Zn 902 binding 202, 919, 922 bacteriopheophytin (BPhe) 44, 193, 341, 356, 392 model 919 bacteriopheophytin a 338 binding pocket bacteriophytochrome 43, 267, 719, 728–730, 799–807, distribution 918 827–831 biosynthesis 58–75, 164, 787 Agrobacterium tumefaciens 805 C132 keto group 186 Bradyrhizobium ORS278 800 C3-acetyl group 139, 140, 144 CBD 805 C31 acetyl group 186 chromophore binding domain 803 exchange 915 Cph1 804 histidine ligand 185, 344 Deinococcus radiodurans 800, 805 isocyclic ring 915 dimerization domain 803 ligand 922 fl ash photolysis 805 ligation Fremyella displosiphon 800 α-type 915 GAF domain 803, 804, 805 β-type 915 Kineococcus radiotolerans 804 Index 979

PAS domain 803, 805 benzoate photometabolism 580 Pfr 804 benzoquinone 382 photocycle 829 benzoyl-CoA reductase 583 PHY domain 803 betaine 119 Pr 804 betaine lipid 120, 128–129 Rhodobacter sphaeroides 804 betaproteobacteria 5, 22, 23, 98, 100, 111, 112, 603

Rhodospirillum centenum 800 bH–bL heme distances 430

Synechocystis PCC 6803 800, 804 bH cytochrome 517 bacterioplankton 37 bilin 729, 804–805, 828 bacteriorubixanthinal 113 ATP analog 806 Badger-Bauer relationship 390 biliverdin IXα 804, 805 band shift 554 E-Z isomerization 804 Banff thermal springs 51 Lumi-F 804, 805 barrel 416 Lumi-R 804, 805 basal body 646 meta-Ra 805 base-catalyzed mechanism 815 meta-Rc 805 bc1:RC stoichiometric ratio 512 photo-isomerization 804 BchB 74 phycocyanobilin 804 bchB 74 phytochromobilin 804 BchC 73 Z-E isomerization 805 bchC 73 ZZZssa conformation 805 BchD 67, 717 bilin chromophore 828 bchD 787 biliverdin 829 BchE 42, 72 biliverdin IXα 804, 805 bchE 44, 47, 51, 72, 783, 794, 795 binding BchF 73 16-fold LH1 ring 163 bchF 73 binding change mechanism 477 BchG 268 binding energy 185 bchG 74 binding helix 902, 903, 917 BchH 67, 69, 71 binding motifs 916 protoporphyrin IX binding 70 binding pocket bchH 787 statistical analysis 924 BchI 67, 70, 717 binding site bchI 787 CrtJ 717 bchJ 72 RegA 715 BChl. See bacteriochlorophyll (BChl) binuclear iron-sulfur clusters 439 BchL 74 biodiversity 51 bchL 74 bioenergetic enzymes 703 BChl-B850 915, 923 biofi lm 51, 696, 701 BChl/BChl coupling 207 biofi lm formation 820, 824, 828 Bchla GG reductase 307 biogenesis 407, 408–421, 846 BChl synthase 268 core complexes 174–175 BChl triplet 300 cytochrome complex 415–421 BchM 71 intermediates 408 bchM 71 photosynthetic complexes 175 BchN 74 biogenesis pathway 408 bchN 74 biogeochemical cycling 51 bchP 74, 164 bioinformatics 916 BchX 74 biomass 50 bchX 74 biomass production 126 bchXYZ 73 bionanotechnology 862 BchY 74 biosynthesis bchY 74 antenna complex 147 BchZ 74 bacteriochlorophyll 787 bchZ 74 carotenoid 97–114 bciA 73 gene cluster 103 bd-type oxidase 540, 542, 543 genes 102 behavior 646–653 carotenoid gene cluster 101 behavioral responses 646–653 heme 415, 780 benzamidine 146 membrane lipid 119–132 benzene rings 577 spirilloxanthin 104–108 benzoate degradation 580–589, 591, 702 biotin carboxylase subunit of ACC 122 980 Index biotin carboxyl carrier protein subunit of ACC 122 bucket brigade hydrogen transfer 518 biphasic growth 600 buoyancy regulation 34 biphasic photooxidation 517 Burkholderiales 599 5-bisphosphate carboxylase/oxygenase (Rubisco) 41, 564 bypass reactions 460 bisphosphatidylglycerol 125 bL–c1 heme distances 430 C Blastochloris 440 Blastochloris sulfoviridis 7, 579, 597, 598 c position 456 Blastochloris viridis 9, 45, 104, 161, 239, 256, 258, 259, 296, C-5 pathway 59 299, 343, 356, 360, 380, 383, 384, 387, 388, 394, 397, c-di-GMP phosphodiesterase 820 512, 514, 518, 942–944, 960 c-ring 478 reaction center-light-harvesting 1 complexes 162, 258, 943 C-terminal reaction center X-ray structure 383, 386 light-harvesting 1 complex 871 Blastomonas 34 C-terminal processing 150 Blastomonas natatoria 34 C-terminal regions 187 Blastopirellula marina 458 C-terminus of LH1 α progressive deletion 165 bL cytochrome 517 blooms c-type apocytochromes 269 stratifi ed lakes 7–8 c-type cytochrome 409–415 BlrB 818, 821 maturation 436 BluB 91 pentaheme 547 BluE 92 C131 keto group 144 blue-shift 42, 45, 148, 188, 203, 204, 245–247, 306, 823, 827, C3-acetyl group 139, 140, 144 829, 922, 930, 932 bacteriochlorophyll 144 blue light photoreceptor 719 C30 molecule 41 blue light sensor 652 C4 pathway 778, 791 blue native polyacrylamide gel electrophoresis (BN-PAGE) C5 pathway 778, 791

418526 caa3-type enzyme 542 BluF 92 CadA/CadC resistance system 661 BLUF domain 731, 732–734, 811, 816–823 caldariellaquinone 469 crystal structure 733 Calvin-Benson-Bassham cycle 564–566, 568–570, 572 BLUF photocycle 818 Calvin Benson Bassham response regulators/sensor kinase BN-PAGE. See Blue-Native-polyacrylamide gel electrophore- system (CbbRRS) 572–574 sis (BN-PAGE) Calvin Cycle 19, 25, 27, 38 Bordetella bronchiseptica 415 Calyptogena magnifi ca 609 Bordetella parapertussis 415 Candidatus kuenenia 458 Bordetella pertussis 414 canthaxanthin synthesis 113 Born-Oppenheimer approximation 885 carbohydrates 40 Bos taurus 479 carbon-fi xation 24–27 Box I 439 carbon availability 789 Box II 439 carbon cycling 48 BPhe. See bacteriopheophytin (BPhe) carbon dioxide metabolism 564–575 BPhe replacement 306 carbon fi xation 707 Bradyrhizobiaceae 23, 603, 614 carbon metabolism Bradyrhizobium 19, 22–27, 100, 113, 439, 627, 667, 693, 720, aerobic anoxygenic phototrophs 40–41 721, 728, 729 carbon monoxide 752 PpsR2 719 carbon sources 40 Bradyrhizobium denitrifi cans 32 carbonyl 387, 389, 390, 392, 395, 396 Bradyrhizobium japonicum 418, 540, 581, 708, 709, 744, 766, carboxyltransferase subunit (CT-α) of Acetyl-CoA carboxylase 781 122 Bradyrhizobium sp. BTAi1 23, 627, 629, 630, 719, 789, 790, carboxyltransferase subunit of ACC 122 792 cardiolipin 120, 125, 526, 527 Bradyrizobium ORS278 102, 113, 699, 719, 729, 790, 800, carotenal pathway 108, 109, 112 branched four-helix bundle proteins 901–904 carotene isomerase 104 broad phonon side band (PSB) 884 carotenogenesis 92, 101–111 Brownian ratchet 485 pathways bta genes 120 table 99–101 btaA 121 carotenoid 41, 97–114, 138, 183, 193, 300, 340, 348, 699, btaB 121 700, 703, 914, 915, 916, 919, 921, 924 1 – Bu state 224, 227 absorption 915 energy transfer 224 absorption maxima 926 Index 981

acids 98 carotenoidless mutants 193, 926 acyclic 98 carotenoid pathways assembly 915 table 99–101 binding 916, 920, 924 carotenoid sulfate 98, 113, 114 aromatic residues 924 carotenoid sulfates 38 mutations 924 carotenoid synthesis 175, 800 statistical analysis 919 carotenoid triplet 298 binding-motifs 916 catalysis binding pockets 919, 924 Rieske/Cytochrome b complex (RB) 455–456 bioinformatics 916 cation-π interaction 329, 444 biosynthesis 97, 98–114, 800, 854 cation diffusion facilitator (CDF) 661 gene cluster 103, 113 cation diffusion facilitator system 661 genes 102 CBA effl ux pumps 658 carotenoid pathways 99 cbb 564–575

table 99–101 cbb3 cytochrome oxidase 700, 735, 754, 782, 788

composition 98 cbb3-Cox 415–420

conformations 924 cbb3-type cytochrome c oxidase 407, 540–541, 543, 545, 553, conjugation length 930 629, 636, 781

cyclic 98 cbbI operon 564–570, 572, 573

effect on LH1 formation 930 cbbII operon 564–570, 572, 573 energy transfer to BChl 915 cbbLS gene 564, 565, 573, 574 Erythrobacter-type 113, 114 cbbM gene 564, 566, 573 glucoside 98 CbbR 563–572 fatty acid ester 98 cbbR 564 glucoside fatty acid ester 98 cbbR 564–567, 569, 572 hydrophobic interactions 915, 924 CbbRRS. See Calvin Benson Bassham response regulators/ methoxy 98 sensor kinase system (CbbRRS) mutant 107 CbiE 89 non-photosynthetic 98, 113 CbiT 89 π-π 924 CC1HL 410 photoactive 38 CcdA 410 pigment-protein sites 916 ccdA 409 plant 113 Ccm-system I 407, 409–415 polyene chain 919, 924 CcmABCDEFGHI 409, 410 resonance Raman studies 924 CcmHIF-containing complex 414 role in assembly of RC-LH1 complexes 193 ccoGHIS operon 540 S* state 222–224 CcoN 540 energy transfer 222–224 CcoNOQP 419 S1 state 219–222 ccoNOQP 417, 781 energy transfer 219–222 ccoNOQP operon 540 S2 state 216–219 CcoO 540 energy transfer 216–219 CcoP 540 stabilizing effect on LH1 931 Ccs-system II 409–415 structural stabilization 915 CcsA 410 sulfates 98 CcsB 410 carotenoid-B820 interactions 933 CcsX 410 carotenoid-bacteriochlorophyll energy transfer 213–230, 927, cd1 surface helix 436

931, 933 cd1 type nitrite reductase 635 carotenoid-band shift 554 cd2 surface helix 436 carotenoid-less mutant 165 CDP-diacylglycerol 123 carotenoid-LH1 subunit interactions 931 cdsA 121 carotenoid acids 98 cell-free expression system 852 carotenoid binding in LH1 931 cellular BChl content 42 hydrophobic interactions 933 cellular redox 708 π-π stacking 933 cellulase 854 carotenoid biosynthesis genes 102 Cellulomonas fi mi 854 gene cluster 101 census techniques 47 carotenoid excited state 215–216 central metal carotenoid glucoside 98, 109–110 binding selectivity 902 carotenoid glucoside ester 109 coordination 898, 902 carotenoidless mutant 163 coordination number 904 982 Index cfp 649 chlorophyll binding proteins chaperone 411 synthetic 896–907 copper metallo 417 chlorophyll delivery 269 chaperones 701 chlorophyll geometries chaperonins 269 robustness and optimality 285 charge-transfer character 208 chlorophyllide 73, 74 charged residues 329, 331 chlorophyllide a 68 charge recombination 343, 345–347, 383 chlorophyll synthase ChlG 74 charge separation 136, 355, 356–370, 362 chlorophyll synthesis 800 reaction center 356–370 chloroplast 409, 476, 746 charge transfer 446 chloroxanthin 107 chelatase 58 chromate 663 chemiolithoautotrophic 564 Chromatiaceae 5, 380, 596, 600 chemoheterotrophic 564 Chromatiales 600 chemoheterotrophic culture 842, 844, 848 chromatic adaptation 260, 267, 800 chemoheterotrophic growth 267 Chromatium 8, 543, 666 chemosensory machinery 645 Chromatium okenii 6, 109 chemosensory pathway 643 Chromatium purpuratum 109, 183, 201, 220 chemosensory proteins 649 Chromatium salexigens 823 chemotaxis 646, 698 Chromatium tepidum 10, 201 Rhodobacter sphaeroides 647–651 Chromatium vinosum 103, 148–149, 356, 435, 441, 566, 581, chimeric RCs 298 745 Chlamydomonas 457, 814–815 Chromatium weissei 6 Chlamydomonas reinhardtii 72, 468, 813 chromatophore 71, 147, 257, 426, 484, 520, 521, 703 chloramphenicol 70 mini 484 chlorate reductase 550 chromatophore heterogeneity 520 Chlorella 65 chromatophore model 264 chloride 312 photosynthetic unit 287 chlorin 897 chromatophore vesicle 262 chlorin macrocycles 58 chromophore 207–208, 823 chlorin reductase 67, 73, 74 bilin 828 chlorobactene glucosyltransferase 110 biliverdin 829 chlorobactene lauroyltransferase 110 cyanophycobilin 831 Chlorobaculum tepidum 103, 110 fl avin adenine dinucleotide (FAD) 813, 816 chlorobenzoate 577 linear tetrapyrrole 827 3-chlorobenzoate 578 modifi ed 824 Chlorobiaceae 380, 596 phycocyanobilin 829 Chlorobium 746 phytochromobilin 827 Chlorobium chlorochromatii 676 ribofl avin 816 Chlorobium ferrooxidans 676 chromosome 780, 786, 791 Chlorobium limicola 103, 549 Chromosome 1 150 Chlorobium limicola DSM245 676 ChrR 737 Chlorobium phaeobacteroides 549 circadian clock 702–703 Chlorobium tepidum 73, 103, 110, 410, 676 circular chromosomes 692 Chlorobium vibrioforme 607 circular conformations 163 Chlorofl exaceae 380, 596 circular dichroism (CD) 183, 206, 237, 849, 921 Chlorofl exi 746 spectrum of iB873 933 Chlorofl exus 8, 679 citric acid cycle 41 Chlorofl exus aggregans DSM 9485 676 Citrobacter 669 Chlorofl exus aurantiacus 103, 385, 549, 550, 666, 813 Citromicrobium 40 Chlorofl exus aurantiacus J-10-fl 676 Citromicrobium bathyomarinum 34 chlorophyll (Chl) 67, 914, 918. See also bacteriochlorophyll clamp region 441 (BChl) climate change 40, 52 binding sites 898 closed ring 163 covalent binding 901 closed ring structure 160 induced protein structure 905 cls 121 spectra 897 cluster-to-cluster transfer rates 281, 288 stereochemistry 898 CO 752 chlorophyll-protein interactions 897–899, 898 co-crystallization 528 chlorophyll a 343 CO2 fi xation 563, 564 chlorophyll a´ 343 anaplerotic 40 Index 983

photoautotrophic 40 conformation-dependent cleavage 446 primary producers 2 conformational motion 235 coal refuse heaps 51 conformational relaxation 968 cob(II)yrinic acid a,c-diamide 90 conformational substates 207, 957 cobA 784, 787 conformation locking 967 cobA 787 Congregibacter litoralis 34 cobalamin 81, 81–92 Congregibacter litoralis KT71 24 cobalamin biosynthetic genes conjugal mating 850 Rhodobacter capsulatus 84 conjugated double-bond system 140 Rhodobacter sphaeroides 84 conjugated macrocycle 204 cobalamin biosynthetic operons 84 conjugation 851 cobalt 82, 90 conjugation length 931 cobalt insertion 84 consensus sequence 716 cobaltochelatase 89, 90 RegR 716 CobC 90 continuous assays 69 CobE 92 CooA 743, 752 CobG 86 CooLH hydrogenase 746 CobH 89 Rhodospirillum rubrum 746 CobJ 87 Coomassie Brilliant Blue 846 CobL 88 cooperative formation 934 CobN 89 cooperative formation of LH1 931 CobP 91 coordinate regulation 717 CobQ 90 coordination CobS 89 axial 408 CobT 89 Mg 139, 140 CobW 92 Mg2+ 144 cobyrinic acid a,c diamide synthase 609 out of plane 408 CobZ 87 coo regulon 752 codon usage 850 cop operon 662 cofactor copper-binding motif 420 functional assembly 924 copper-binding protein Cox11p 545 interactions 916 copper-containing Nor 634 reconstitution 924 copper binding site 418 cofactor-binding motif 935 copper metallochaperone 417 light-harvesting complex 935 copper transporter 420 cofactors 914 coproporphyrinogen III 60, 64, 785, 787, 788, 794 coherent energy transfer 882 coproporphyrinogen III oxidase 60, 64 cold habitat purple bacteria 11 core antenna 915 colloid theory 172 core complex 943, 946 Comamonadaceae 603, 614 assembly 172 combinatorial design 899–901 biogenesis 174–175 combinatorial synthesis 900 core dimers complementation rescue technique 66 phospholipid content 173 complex-specifi c assembly factors 268 quinone content 173 LhaA 268 core light-harvesting antenna complex. See light-harvesting 1 PucC 268 complex PuhB 268 corrinoid synthesis 784 PuhC 268 corrin ring 82, 84 PuhE 268 cosmid 782, 785, 789 Complex I 510, 526, 745 cosynthase 64 reverse electron transfer 512 coupling 345, 348 Complex III 526 coupling effi ciency 486 Complex IV 526 coupling strength 205 complex lipid composition 120 coxII promoter 853 complex organics 40 Cph1 804 compliance 485 CPO. See coproporphyrinogen III oxidase computational sequence analysis 918 CPx-type ATPases 661 computational studies 139 Craurococcus 34, 113 conductive atomic force microscopy (CAFM) 862, 863, crocacin analog 445 865–869 cross-sectional area 136 conformation 383 cross-transfer probabilities 281 984 Index cross-trapping probability 289 cysH 613, 614 CRP 752 CysI 613 crt genes 102, 104, 105 cysI 614 CrtA 102, 104, 105, 107, 108 CysJ 613 crtA 102 cysJ 614 CrtB 102, 105 cysPTWA 613, 614 crtB 717 cystathionine 613 CrtC 102, 104, 105, 107, 108 cystathionine γ-lyase 613 CrtD 102, 104, 105, 107, 108 cysteine 613 CrtE 102, 105 cysteine persulfi de 605 CrtF 102, 104, 105, 107, 108 cysteine sulfane 605 CrtH 104 Cyt. See cytochrome (Cyt) CrtI 102, 103, 105, 108, 113 cytidylyltransferase 124 crtI 717 cytochrome (Cyt) 45, 258, 408, 514, 700, 703 CrtISO 104 a-type 408 CrtJ 707, 708, 716–720, 785–787, 791, 795 b-type 408 aerobic repression 716–721 c-type 408 binding site 717 d-type 408 oxidized 717 o-type 408 recognition sequence 717 soluble 45 crtJ 785, 786, 787, 789 tetraheme 942, 943

CrtJ/PpsR 716, 719 cytochrome aa3-type terminal oxidase 541 phylogenetic analysis 719, 720 cytochrome b 426, 427, 431–436 CrtR 104 di-heme 745 CrtW 102, 104, 105, 113 surface 435 CrtY 102, 104, 105, 113 topology 432 crude oil 587 cytochrome b558/566 459 cryo-electron microscopy 254, 256, 286, 942, 947 cytochrome b561 270 cryo-EM projection map 169 cytochrome b6 432 cryptochrome 734 cytochrome b6 f complex 427, 432, 453 crystallization 140 evolution 456–458

lipidic cubic phases 140 cytochrome bc1 complex 46, 173, 254, 257, 259, 262–265, crystals 279, 425–447, 453–455, 509–530, 539, 625, 903, 907, Type II 146 942, 950 crystal structure dimeric structure 525, 528 protein maquette 904 distal niche 454 uroporphyrinogen III synthase 64 evolution 456–458 π CuA 542 extended -orbital system 445

CuA center 416, 418, 419 homodimeric organization 512 Cupriavidus metallidurans 612 large-scale domain movement 431 Cupriavidus necator 744 proximal niche 455 current-voltage curves Qi site 467–468 reaction center 867 Qo site 455 current-voltage measurements 863, 868 Rhodobacter current rectifi cation 868 mutants 428–430 curvature mismatch 173 Rhodobacter sphaeroides 455 CXXCH heme binding motif 408, 409 structure 427–446, 453–455 cyanide 82 subunit IV 262, 432, 453 cyanobacteria 103, 104, 267, 380, 384, 409, 596, 694 topology 432 phycobilisomes 384 cytochrome bd-type quinol oxidase 539–540 cyanobacterial phytochrome 800 cytochrome bH 453 cyano cobalamin 72, 82 cytochrome b hemes 452 cyanophycobilin 831 cytochrome bL 453, 455 cyclic electron fl ow 263 cytochrome c 408, 452, 625 cyclic electron transfer 266, 510, 512 large 437 cyclo-octasulfur 608 maturation 408 cyclohexanecarboxylate small 437 degradation 587–588 tetraheme 45 CydA 540 tethering 527 CysDN 613 cytochrome c heme lyase 409 cysDN 614 cytochrome c oxidase (COX) 131, 426, 527, 672 Index 985 cytochrome c synthetase 409 Debye-Waller factor 885 cytochrome c´ 408 Dechloromonas 415 cytochrome c1 263, 408, 426, 427, 436–438 deep ocean 50, 52 cytochrome c2 46, 173, 263, 279, 323–333, 345, 348, 408, aerobic anoxygenic phototrophs 426, 452, 456, 514–516, 527–528, 542–543, 703, 844 vertical distribution 50 co-crystallization 528 Dehalococcoides ethenogenes 746 confi nement 521 4-dehydrolycopene 112 diffusion and confi nement 527–528 Deinococcus radiodurans 800, 829, 831 Rhodobacter sphaeroides 323, 324–333 delay after laser fl ash (DAF) 964 soluble periplasmic 45 deletion strain cytochrome c2:reaction center complex 323–333 PUC705-BA 844, 846 distal conformation 516 PUF∆LMX21 844, 846 mutation effects 329–332 ∆∆11 844, 846 Rhodobacter sphaeroides 323–333 delocalization 234, 237–238, 238, 241 structure 325–327 denitrifi cation 624–636 cytochrome c2m 515 denitrifi cation gene clusters 628 cytochrome c3 458 de novo design cytochrome c4 458 bacteriochlorophyll protein platforms 895–907 cytochrome c8 514 de novo pigment proteins 895 cytochrome cbb3-type terminal oxidase 540–541 de novo polypeptides 915 cytochrome cbb3 oxidase 515, 713, 717 density-matrix 355, 368–370 cytochrome co 408 density functional theory 221, 393, 394 cytochrome complex 415–421 Deriphat 160 855 biogenesis 415–421 Deriphat 160-C 308 cytochrome cp 408 Desulfovibrio vulgaris 611 cytochrome cy 408, 426, 453, 456, 515, 517, 521, 527, detergent 145–146, 182, 855 542–543, 845, 846 detergent micelle 157 membrane-bound 542–543 detoxifi cation cytochrome f 458 enzymatic 662–665 cytochrome maturation detrapping probability 281 c-type 436 deuteroporphyrin IX 69 cytochrome oxidase 510, 521 Dexter energy transfer 218 cytochrome subunit 298 Dhp domain 806 cytoplasm 407, 409, 412, 413, 419, 420 di(acyl-glucosyl)-diapocarotene-dioate 110, 113 cytoplasmic membrane 147, 262, 264, 267, 409, 410, 412, di-heme cytochrome b 745 415, 418, 841, 846 diacylglycerol-N,N,N,-trimethylhomoserine 120, 128 invagination sites 267 diacylglycerol glycosyltransferase 121 CzcCBA system 658 diacylglycerolhomoserine 128 Czr system 675 diacylglycerolhomoserine N-methyltransferase 121 diacylglycerolhomoserine synthase 121 D diacylglycerol moiety 122 diagonal disorder 881, 883 δ-aminolevulinate 59 diapocarotenoic acid 113 δ-aminolevulinate synthase 57 4,4´-diapocarotene-4,4´-dioate 41 δ-aminolevulinic acid dehydratase 62. See also porphobilino- diazotroph 761 gen synthase diazotrophic growth 700 δ-aminolevulinic acid synthase 60 dicarboxylic acids 586 ∆ ~ µH+ See proton electrochemical potential difference dielectric effects 361 2-D photon echo 242 dielectric properties 203 damage dielectric response oxidative 545 + – P QA formation 967 dark growth 6, 7 dielectric screening 358 Davydov splitting 886 differential centrifugation 846, 855 DCCD 480 diffusion limit 328 DCCD-binding protein 480 diheme cytochrome c1 counterparts 436, 437 ddhA 547 diheptanoyl-sn-glycero-3-phosphocholine (DHPC) 170 ddhB 547 2-dihydro-3 112 ddhC 547 4-dihydroanhydrorhodovibrin 108 ddhD 547 2-dihydroneurosporene 112 deactivation channel 928 17,18-dihydroporphyrin 897. See also chlorin Dead Sea 10 3,4-dihydrospheroidene 107 986 Index

4-dihydrospirilloxanthin 108 DNase I footprinting 715 dihydroxylycopene diglucoside 110, 112 DNR/NNR 633 diketospirilloxanthin 111 domain mobility 469 2,2´-diketospirilloxanthin 108 dorA gene 547 dimeric core complex dorC 548 comparison with monomer core complex 169 dorC gene 547 excitation sharing in array 173 dor promoter 853 reaction center-light-harvesting 1-PufX complex 168–174 DOXP pathway 103 dimerization 419, 947 D pathway 544, 546 dimer of supercomplexes 529 DraG 767–768 dimers 946 DraT 767–768 dimethyl diselenide 674 DsbA-DsbB pathway 412 dimethyl ditelluride 674 DsbB link 674 dimethyl selenenyl sulfi de 674 dsbD 409 dimethyl selenide 674 DsbD 410 dimethyl sulfi de 40, 546, 600, 601 dsr genes 602, 603, 607, 608, 609 dimethylsulfoniopropionate (DMSP) 40, 546, 600 dsrAB 602, 609 dimethyl sulfoxide (DMSO) 546, 601, 780, 781, 788, 853 DsrAB 607, 609, 616 dimethyl sulfoxide reductase 547, 548, 552 DsrC 609 dimethyl telluride 674 dsrEFH 609 2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) 870 DsrEFH 609, 610 dinitrogenase reductase activating glycohydrolase (DraG) 767 DsrJ 609 dinitrogenase reductase ADP-ribosyl transferase (DraT) 767 DsrK 609 dinofl agellates 48 DsrL 609 Dinoroseobacter 34 DsrN 610 Dinoroseobacter shibae 41, 43, 603, 614, 627 DsrO 609 Dinoroseobacter shibae DFL 12 676 DsrP 609 dioleoyl-9 160 Dsr proteins 608, 610 dioxygenase 459 DsrR 609 diphenylamine 103 duroquinone 390 diphosphatidyl-glycerol 527 dynamic disorder 206, 207 dipole-dipole approximation 280 dynamic Stokes shift 239 dipyrromethane cofactor 63 directed modifi cation E reaction center 338–349 disorder 235, 237, 244, 246 ecological roles light-harvesting complexes 205–207 aerobic anoxygenic phototrophs 47–51 disordered exciton model 238, 240 Ectothiorhodosinus 600, 601 dispersed polaron theory 367 Ectothiorhodosinus mongolicum 600, 601 dispersive forces 203 Ectothiorhodospira 10, 46, 543, 549, 600, 601 disproportionation 607 Ectothiorhodospiracea 604, 615 dissipation probability 280 Ectothiorhodospiraceae 5, 112, 596, 600 dissociation constant 327 Ectothiorhodospira haloalkaliphila 600, 601 dissolved organic matter 50 Ectothiorhodospira halochloris 512 dissymmetry 528 Ectothiorhodospira halophila 652, 823 disulfi de 606 Ectothiorhodospira marina 601 disulfi de bond 413, 714 Ectothiorhodospira marismortui 600, 601 disulfi de bridge 438 Ectothiorhodospira mobilis 601 divinyl-protochlorophyllide 71, 72 Ectothiorhodospira shaposhnikovii 515, 600, 601 DMS dehydrogenase 548, 550 Ectothiorhodospira vacuolata 601, 853 DMSO. See dimethylsulfoxide (DMSO) effective Hamiltonian 279, 280 DMSO/DMS couple 547 light-harvesting assembly 279 DMSO/TMAO reductase 552 ef loop 436, 443 DMSO reductase 547, 548, 552 elastic coupling 485–486 DMSP-producing algae 50 elastic power transmission 485 DNA-binding activity 715 electrical charge separation 426 DNA binding motif 715 electric capacitance 484 DnaK 269 electric functionality 862 DNA recognition helix 716 electroabsorption 344 DNA recognition sequences 715 electrochemical proton gradient 269 Index 987 electrochromism 483 electron spin echo (ESE) 957 electrode 862, 863, 870 exponential dependence on distance 345 APS-ITO 870 fi rst order rate 327, 332 – → – PSU-assembled 870 low-temperature QA QB QAQB 957–959 – → – counter 870 QA QB QAQB 956 potential 871 reactions 327–329, 363–370 RC-assembled 871 second order rate 332–333 reference 870 sequential 963 working 870 surface-hopping model 363–367 electromotor 478–481 uphill steps 514 structure 478–481 electron transfer pathways electron-nuclear double resonance (ENDOR) 342, 380, 389, Rhodobacter sphaeroides 382 391, 393, 396, 954, 954–969 electron transport 426, 735 1H 959, 960 electron transport chain 674 2H 959 electrostatic confi nement 527 high-fi eld 396 electrostatic coupling 904 high-frequency 966 electrostatic environment 208 matrix high-frequency 960, 969 electrostatic forces 340 Mims-type 959, 960 electrostatic interaction 327, 341, 514, 528, 657 Q-band 396 elemental sulfur 596–597, 601, 602, 605–607, 616

spin-correlated radical pair (SCRP) 965, 966, 968 S7 rings 607

time-resolved 965, 967 S8 rings 607 time-resolved high-frequency 963, 968 ellipsis 944 electron-phonon coupling 884 elliptical deformation electron-phonon coupling strength 885 B850 ring 207 electron acceptors 41 elliptical LH116 assembly 945 electron crystallography 137 Em 438, 439, 445, 554 electron density map 140 encounter complex 527 electron donor 4, 41, 149, 597 endoplasmic reticulum (ER) 269 reaction center 514–515 endoprotease GluC 189 sulfur compounds 149 endosymbiosis 433 electron fl ow 46 energetic disorder 888 electronic absorption 207 correlated 888 electronic coupling 279, 343, 881 random 888

strong 881 energy-conserving H2 evolving membrane-associated hydrog- weak 881 enase 746 electronic coupling factor 361 energy barrier 944 electronic matrix element 345 energy conduits 147 electronic structure 342 energy dissipation 898 electronic transitions 200, 204, 208 energy transduction 41 electron injection barrier 868 energy transfer 149, 216–226, 233, 239, 258, 266, 862, 881, electron microscopy 844, 941 915, 943 1 – analysis 163 Bu state 224 negative stain analysis 168 carotenoid-bacteriochlorophyll 927 electron paramagnetic resonance (EPR) 183, 380, 389, 393, coherent 882 395, 439, 455, 955 domains 943 analysis 87 electronic coupling 881 high-frequency 955, 969 hopping 235, 243, 246 spectra 444, 445 incoherent 881 pulsed 955 light-harvesting 1 complex 226–227 time-resolved 955 light-harvesting 2 complex 216–226 electron spin densities 342 S* state 222–224 electron spin echo (ESE) 957 S1 state 219–222 electron spin echo envelope modulation (ESEEM) 393, 439 S2 state 216–219 electron transfer 39, 266, 287, 327–330, 337, 339–349, 355, single photosynthetic unit 889–891 366, 368, 370, 382, 396, 398, 413, 510, 674, 822, 868, energy transition 921, 954–973 tuning 205 –20 °C 521 energy trapping 243–244, 260 A-side 346 robustness B-branch 348, 958 graceful degradation 285 B-side 346–348 parameter insensitivity 285 988 Index

robustness and optimality 285 excitation sharing 173, 282, 289 optimization 173 dimer array 173 enoyl-ACP reductase I 122 PufX 172–174 ensemble averages 283 excitation spectra 921 ensemble reactions 950 excitation trap 928, 935 Enterobacter 669 excited state 206 Enterococcus hirae 661 excited triplet state 357 enumeration 47 exciton 232, 235–239 environmental limits to photosynthesis 12 exciton-phonon coupling 233, 237 enzymatic detoxifi cation 662–665 exciton delocalization 929 equilibrium constant 520 exciton dynamics ER. See endoplasmic reticulum (ER) wavelike motion 246 Erb-type. See Erythrobacter-type carotenoid excitonically-coupled systems 206 Erwinia herbicola 110, 854 BChl systems 204 carotenoid biosynthetic pathway 854 excitonic coupling 886 Erwinia uredovora 103 excitonic interactions 205, 207 Erythrobacter 34, 40, 113 light-harvesting complexes 205–207 Erythrobacter-type carotenoid 99, 113, 114 exciton migration 147 Erythrobacter litoralis 676 lake model 147 Erythrobacter longus 102, 104, 113 puddle model 147 Erythrobacter sp NAP1 19, 790, 792 exciton model 205 Erythromicrobium 40, 113 exciton relaxation 246 Erythromicrobium hydrolyticum 599 exciton spectra 235–239 Erythromicrobium ramosum 34 exciton state 233, 235, 238, 245 Erythromonas 34, 113 exciton transfer 45 erythroxanthin sulfate 41 expression plasmids 842, 844, 849 Escherichia 702 external sulfur uptake 607–608 Escherichia coli 21, 40, 66, 71, 74, 104, 108, 268, 411, 476, extra-cytoplasmatic function (ECF) 737 479, 588, 646–647, 695, 701, 744–757, 778, 781, 785, extracellular sequestration 665 786, 795, 820, 844, 847, 850, 852, 856 extracellular sulfur globules 600, 602, 608 Fnr protein 753 extreme environments 9–12, 51 genome 848 extremophilic purple bacteria 9–12 hemC mutants 63 extremophily 51, 52 hydroxymethylbilane synthase 63 extremotolerance 51 membrane proteome 848, 851 extrinsic domain 430 paradigm 646–647 YcgF 820 F Escherichia coli K-12 795 esterifying alcohol 187, 899 φ mutant 338 φ ethylbenzene dehydrogenase 547, 550 B mutant 346

8-ethyl group 58 F1 475

8-ethylidene 58 F1Fo ATP synthase 538 Euglena 817 fabA 122 Euglena gracilis 817, 820 fabB 122 eutectic model 949 fabD 122 eutectic phase behavior 945 fabF 122 Eutreptia 817 fabG 122 evolution fabH 122 aerobic anoxygenic phototrophs 38–40 fabI 122 fabZ 122 cytochrome b6 f complex 456–458 FAD. See fl avin adenine dinucleotide (FAD) cytochrome bc1 456–458 physical constraints of 284–286 farnesyl hydroxyethyl side chain 408 purple bacteria 17–28 farnesyl pyrophosphate 103 Rieske/Cytochrome b complex 456–458 fast exchange limit 328 transhydrogenase 497 fatty acid diesters 110 exchange chromatography 851 fatty acid ester excitation delocalization 935 carotenoid glucoside 98 excitation energy 136, 166, 206 fatty acids 122–123, 586 excitation energy transfer 170, 200, 205, 950 FccA 606 excitation relaxation 929 FccAB 602, 606 Index 989 fccAB 603 FnrL 721, 781–786, 790, 795 FccB 606 oxygen inactivation model 721 Fe-bacteriochlorophyll. See Fe-bacteriopheophorbide fnrL 781–786, 789, 794, 795 Fe-bacteriopheophorbide 902 mutant 721 Fe-removal/Zn-replacement 962, 965, 967 null mutant 722 Fe-S center 87, 539, 721, 794 See also iron-sulfur cluster Rubrivivax gelatinosus 722 [2Fe2S] cluster 438, 439, 452, 753 FnrN 753

Em7 value 439 FnrT 753 2+ [4Fe-4S] cluster 753 FOF1-ATP synthase 452, 475–488 [FeFe]-hydrogenase 744, 746 gearshift 479 [NiFe]-hydrogenase 743, 745–746, 754 rotary catalysis 476–478

H2-sensing 750 slip 486 femtosecond resonance Raman 227 torque 475 Fe removal 305 torsional spring constant 485 Fe replacement 304, 305 structure 476–478 fermentation 149 folding fermentative bacteria 591 membrane protein 914 ferredoxin 74, 581, 584 foreign gene expression 839–856 ferrochelatase 58, 86, 787 formate dehydrogenase 548 FhlA 752 Förster-type mechanism 218 fi lamentous anoxygenic phototrophs 596 Förster formula 233 fi nite temperature quantum theory 282 generalized 233 thermal disorder 282 Förster radius 276 fi rst order electron transfer rate 327, 332 Förster theory 242, 243, 280 fi x 781 fosmid library 51 fi xed nitrogen four-helix bundle 903, 904, 934 sensing 763–766 design 903 FixK1 753 lipophilic 906 FixK2 753 modeling 903 FixL 753 reorientation 905 fl agella 644 four-helix bundle proteins 895, 896, 899, 900, 901, 905 σ fl agellar-specifi c sigma factor ( 28) 645 Fourier transform infra-red spectroscopy (FTIR) 380, fl agellar helix 644 389–391, 397, 731, 957 fl agellar proteins 644 Franck-Condon factor 367 fl agellin 644 free-energy perturbation 358 fl ash photolysis 805 free energy 358, 359, 363 fl avin 87, 611 free energy calculations 255 fl avin adenine dinucleotide (FAD) 813, 816 free radical SAM 72 fl avin cofactor 539 free radical SAM enzymes 65 fl avin mononucleotide (FMN) 813, 816 freeze-fracture electron micrograph 262 fl avocytochrome c (FccAB) 602, 606, 616 freeze-fracture electron microscopy 168, 257, 260 fl avocytochrome c sulfi de dehydrogenase (FccAB) 606, 645 freeze-thaw sonication 261 fl avoprotein 90 freeze thawing 946 fl exible hinge region 157 Fremyella displosiphon 800 fl uorescence 233, 235, 237–240, 243–246, 357 French press 846 fl uorescence depolarization studies 205 Frenkel-excitons 880 fl uorescence emission 933 freshwater lakes 51 fl uorescence emission properties 928 fructose-1,6-bisphosphate 571 fl uorescence excitation spectra 207, 226, 882 fructose-6-phosphate 571 fl uorescence fl uctuations 244 fructose 1,6/sedoheptulose 1,7-bisphosphatase 566 fl uorescence properties 206 fructose 1,6/sedoheptulose 1,7-bisphosphate aldolase 566 fl uorescence resonance energy transfer (FRET) 478 Fth/FtsY 269 fl uorescence up-conversion 217, 225, 239, 240 Fulvimarina 19 B800-B850 225 Fulvimarina pelagi 24 FMN. See fl avin mononucleotide (FMN) fumarate-nitrate reduction (FNR) 708 Fnr 707, 721, 722, 752, 753, 781, 782 fungi 847 regulation by 721–722 funiculosin 455 Escherichia coli 753 FNR consensus-like sequences 781, 786, 787, 794, 795 FNR consensus sequence 781, 783 990 Index

G glycoglycerolipid 126–128 glycolipid 119 γ-carotene 113 glycosyltransferase 127 γ-carotene synthase 109 GMP-adenylyl-cyclase-FhlA (GAF) 728 G+C content 850 gold-coated silicon probe GAF domain 728 2-mercaptopyridine modifi ed 869 galactosyltransferase 127 gold substrate 861, 865–869 gammaproteobacteria 5, 24 graceful degradation 285 Gammaproteobacteria 22, 98, 100, 109, 112 Gram-positive bacteria 409 gas vesicle protein 702 grazing pressure 50 gel electrophoresis green fi lamentous bacteria 109 blue native polyacrylamide 526 green fl uorescent protein (GFP) 845, 846, 850 gel fi ltration 849 green nonsulfur bacteria 746 Geminicoccus 34 green plant 577 gene duplication 696 green sulfur bacteria 101–104, 109, 110, 596 gene expression 744–755, 799, 839–856 Chlorobium tepidum 410 auto-induction 848 GroEL 269 hydrogenase ground state conformation 383 regulation 743–755 ground state interaction 203–205 regulation 707, 707–722, 744–755 gene homologs 696–701 H general membrane assembly factors 268, 269 DnaK 269 H+ output 430 GroEL 269 1H ENDOR 959 SecA 269 2H ENDOR 959, 968 gene regulation H2 744–757

light-dependent 727–737 H2-regulation 754 gene split 457 H2-sensing [NiFe]-hydrogenase 750 gene transfer 45 H2-sensor 750

horizontal 45 H2-specifi c signal transduction system 747

lateral 38 H2 sensor 743, 745, 751 genome 691–704 H2 signal 750

architecture 692–696 H2 transduction 751 characteristics 692–696 habitats 7-9, 149 sequences 45, 101, 579 Halobacterium salinarum 851 sizes 692 Halochromatium 10 genomics 17, 18, 27, 28, 69–704 halophilic purple bacteria 10–11 structural 847 Halorhodospira 10, 110, 600, 601 geranylgeraniol 58, 74, 164, 306 Halorhodospira abdelmalekii 112, 600, 601 geranylgeranyl 187 Halorhodospira halochloris 112, 600, 601 geranylgeranyl pyrophosphate 74, 103 Halorhodospira halophila 600, 601, 604, 606, 609, 611, 615, geranylgeranyl pyrophosphate synthase 103 823, 827 geranylgeranyl reductase 67 Halorhodospira halophila SL1 790, 791, 792 German Collection of Microorganisms and Cell Cultures 150 Halorhodospira halophilum 24 GFP. See green fl uorescent protein (GFP) Halorhodospira halophilum SL1 24 GGDEF/EAL domain 728 Halorhodospira neutriphila 600, 601 glass substrate 864 Halorhodospira sp. SL1 19 GlnB 764 halotolerance 51 global fi tting data analysis 217, 223 Hamiltonian 206 global oxygenation 38 Hansenula polymorpha 852 global regulatory system 712, 716 HBA. See hydrogenobyrinic acid (HBA) glucosyltransferase 127 HbrL 789 glutamate-1-semialdehyde aminotransferase 778, 793 hbrL 789 glutamine 764 HCCS/CCHL 410 glutamyl-tRNA reductase 59, 778, 793 heat-shock response 701 glutamyl-tRNA synthetase 59 Helicobacter 414 glutathione 41, 608, 613 heliobacteria 109 glutathione amide 609 Heliobacteriaceae 380 glutathione selenopersulfi de 669 Heliobacterium chlorum 149 glyceraldehyde-3-phosphate dehydrogenase (cbbGII) 566 helix glycerol 3-phosphate 125 binding 902, 903 glycerol 3-phosphate 1-O- acyltransferase 121 shielding 902, 903 glycogenin 128 310 helix 137 Index 991 helix-helix interactions 137 HF Mims-type ENDOR 961 helix-hinge-helix solution 157 high-fequency 1H-ENDOR 961, 962 helix-turn-helix DNA binding domain 717 high-frequency EPR 955 helix-turn-helix motif 721 high-light 255, 945, 948 helix W 166 high-light light-harvesting 2 complex 255 HemA 780, 782, 789 high-potential 2Fe-2S Rieske protein 942 hemA 61, 780–783, 788, 789 high-potential iron sulfur protein (HiPIP) 514, 515, 543 HemB 783, 791, 794 high-resolution AFM 949 hemB 783, 784, 788, 789, 791 high aeration conditions 175 hemC 63, 784, 785, 787–789, 794 higher-throughput methodologies 851 hemC mutants higher plants 103, 104 Escherichia coli 63 high oxygen 780, 785, 786, 788 hemD 64 high performance liquid chromatography (HPLC) 49, 193, heme 407–420, 778, 780, 787, 789 927 attachment 269 hinge protein 438 stereo-selectivity 413 HiPIP. See high-potential iron sulfur proteins (HiPIP) biosynthesis 57, 58, 65, 415, 780 histidine 190, 344, 933 delivery pathway 412 histidine kinase 652, 751, 806

high-spin heme a3-CuB binuclear center 416 histidine protein kinase 708, 712

high-spin heme b3-CuB binuclear center 416 6-histidine tag 170 ligation 409 HMB. See hydroxymethylbilane low-spin heme a 416 HMBS. See hydroxymethylbilane synthase lyase 411 HMB synthase 60 periplasmic ligation 410 Hoefl ea phototrophica 34 reservoir 415 hole-burning 236, 361 transporter 412 holocomplex 147 vinyl-2 group 411 holocyt c production 408 hemE 784, 785, 788, 789, 794 holocytochrome 407 heme-binding protein 899 homocysteine 613 heme-copper oxidase 416, 540 homogeneous line shape 208 heme a 408, 409 homologous recombination 850 heme a3-CuB center 544 RegA 709–711 heme bH 431, 433 RegB 709–711 heme bL 431 Homo sapiens 479 heme ci 457, 468 horizontal gene transfer 45, 694 heme d 408, 409 HoxA 748, 751 heme macrocycle 438 hoxE 746 heme o 408 hoxF 746 heme reductase 410 hoxH 746 heme b 436 HoxJ 748 HemF 64, 65, 785, 786, 794 HoxJ/HoxA 750 hemF 64 hoxU 746 HemG 795 hoxY 746 hemG 65, 794 HQNO. See 2-n-heptyl-4-hydroxyquinoline-N-oxide (HQNO) hemH 787, 788, 794 Hückel molecular orbital model 342 HemN 64, 65, 785, 786, 794 hup locus 746 hemN 51, 64, 629 HupR 743, 748, 749, 751, 752 HemN-type coproporphyrinogen III oxidase 794 HupR/HoxA 747 HemN-type motif 794 hupR gene 749 hemomolybdoprotein 602 hupR mutants 750 HemT 780, 782 hupSLC genes 753 hemT 61, 780–782, 789 hupS promoter 754 hemY 65 HupT 743, 748, 750, 751, 752 HemZ 786 HupT/HoxJ 747 hemZ 64, 786, 788, 789, 794 HupT/HupR 750 heptane-1 146 hupT gene 749 heterodisulfi de reductase 609 hupT mutants 750 heterologous expression 847, 848, 850–852 hupTUV operon 749, 750 Heterosigma akashiwo 669 HupU 750 hexachlorobenzene 64 HupUV 743, 751, 752 hexameric rings 70 HupUV/HoxBC 747 992 Index

HupUV hydrogenase 750 Idiomarina loihiensis 824 HvrA 736 IHF. See integration host factor (IHF) hvrA 770 Ilyobacter tartaricus 478, 479 hybrid reconstitution 191 IMAC. See immobilized metal affi nity chromatography hybrid sensor kinase 572 (IMAC) hydride transfer 495 image processing 948 transhydrogenase 503 imidazole 815 hydrogenase 743–755 immobilized metal affi nity chromatography (IMAC) 842, 849 gene expression immunoblotting 846 regulation 743–755 inclusion bodies 69, 841, 842, 847, 852, 853 hydrogen bond 137, 140–143, 161, 186, 187, 203, 204, 330, incoherent energy transfer 881 340–345, 347, 349, 384, 385, 387, 390–394, 396, 915, incoherent hopping 206 916, 918, 922–924 indium tin oxide 862 network 175, 208 electrode 863 polypeptide 141 individual complexes 943 quinone binding sites 389 inducible ICMs 852 hydrogen evolution 744–757 induction 267 hydrogenobyrinic acid (HBA) 84, 89 infrared epifl uorescence microscopy (IREM) 47, 49 hydrogenobyrinic acid a,c-diamide 89 infrared fast repetition rate fl uorometry (IRFRR) 47,49 Hydrogenophilus thermoluteolus 566 infrared spectra 394, 396 hydrogenosome 746 inhibitors 70 hydrogen transfer 518 inorganic sulfur compounds 600 bucket brigade 518 integration host factor (IHF) 749, 752–754, 770 hydropathy analysis 148 interaction motif hydrophobic effect 900 prediction 916 hydrophobic groups 190 interactions hydrophobic interaction 327, 331, 915 cofactor 916 hydrophobic mismatch 267, 946 intercellular connective structures 34 hydrophobic mutations 331 intercomplex disorder 883 hydrophobic residues 329, 331 intercomplex heterogeneity 883 hydrophobic surface 183 intermediate iB873 932 hydrostatic pressure 208 intermediates of LH1 assembly 932, 933 hydrothermal vent 32, 39, 50 intermolecular disulfi de bond 714 hydrothermal vent plumes 47 internal transcribed spacer analysis 35 4-hydroxybenzoate 578, 579, 586–587 interspecifi c complementation 854 hydroxy chlorophyllide 73 intracellular sequestration 665 4-hydroxy cinnamic acid 823 intracellular sulfur globules 602, 607, 608 3-hydroxyethyl bacteriochlorophyllide a 68 intracomplex disorder 883 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase 67 intracomplex heterogeneity 883 3-hydroxyethyl chlorophyllide a 68 intracytoplasmic membrane (ICM) 136, 137, 147, 172, 200, hydroxymethylbilane 60 254, 257, 258, 264, 525, 841–860 hydroxymethylbilane synthase 63 biogenesis 846 Escherichia coli 63 domains 261 hydroxyneurosporene-O-methyltransferase 107 formation 267 hydroxyneurosporene synthase 107 inducible 852 hydroxy protochlorophyllide 73 induction of assembly 267 hynS 753 spherical vesicles 845 hyp 753 synthesis 844 hyperfi ne coupling 396 tubular membranes 844 hyperfi ne interactions 391, 393 ultrastructure 844 hypersaline springs 42, 51 inverse-Mollweide projection 287 hypersaline spring system 39 invertebrates 410 hyp genes 745 in vitro transcription-translation system 175 ion exchange chromatography 61, 849, 869, 926, 929 I ionic strength 516, 527, 950 IR difference spectroscopy 391 iB873 175, 932–934 iron 193, 415 CD spectrum 933 limitation 415 iB873 complex 934 iron-reducers 591 ICM. See intracytoplasmic membrane (ICM) iron-sulfur cluster 744–757; See also Fe-S center Index 993 iron-sulfur fl avoprotein 609 lauryldimethylamine oxide (LDAO) 140, 146, 300, 926, 929 iron-sulfur protein 426, 427, 431, 432, 438–441 LD. See linear dichroism (LD) extrinsic domain 432, 435 LDAO. See lauryldimethylamine oxide (LDAO) macro-movement 441 Leigh syndrome 418 topology 432 leucine zipper-like motif 414 iron-sulfur protein subunit 512 level of hydration 825 Isochromatium buderi 601 LH1. See light-harvesting 1 complex isocitrate dehydrogenase (ICDH) 500 LH1-only strain 161 isocyclic ring 898, 915 LH1α polypeptide 157 isocytochrome c2 542–543 N-terminal domain 175 isoelectric points 848 solution structure 157–158 isomerase 82 LH1β polypeptide isomerization 804, 825, 827, 829 NMR studies 157 isoprene 384, 387, 388 solution structure 157–158 isoprenoid alcohol 897 LH2. See light-harvesting 2 complex isoprenoid chain 518 LH2– mutant M21 263 iterative design 899–901 LH3. See light-harvesting 3 complex iterative redesign 904 LH4. See light-harvesting 4 complex IUPAC-IUB nomenclature 98 LhaA IUPAC numbering scheme 58 assembly factor 174 lhaA 148, 174 J liganding histidine 917 ligase 585, 586, 588, 589 Jannaschia 19, 440 ligation-independent cloning 842, 843, 851 Jannaschia sp. CCS1 790, 792, 819 light, oxygen or voltage (LOV) 813. See also LOV domain Juan de Fuca Ridge 50 photocycle 814 Jα helix 815 light-dark difference spectrum 193 light-dependent reversal of the electron fl ow 554 K light-driven proton gradient 175 light-harvesting keto carbonyl 204 absorption 922 Ketogulonicigenium 38 assembly 922 ketolation 108 BChl-B800 921 keystone consumer 50 BChl-B850 921, 923 KH2PO4 571 mutations 922 kinase activity 713 scanning permutagenesis 922 kinase domain 806 light-harvesting 1-PufX complex 524 Kineococcus radiotolerans 804 S-shaped chain 524 kinetic analysis 60, 74 light-harvesting complex 45–46, 511, 699, 703, 861–873, kinetic effi ciency 476 877–891, 913, 914–936. See also specifi c complex kinetic fl uorometry 49 artifi cial 862–873 kinetic mechanism 71 assembly on solid substrates 861–873 kinetic phase 515 assembly 913, 916, 920, 921, 924–935 kinetics 355 model systems 924–926 Klebsiella pneumoniae 748 carotenoid-binding 919, 920, 924-926 Kleinfeld effect 956 charge-transfer character 208 Km values 69, 462 cofactor-binding motif 935 K pathway 544, 546 design 913–924 disorder 205–207 L dynamic disorder 206 electronic transitions 208 laboratory culture electrostatic environment 208 ease of growth 4 energy transfer 921 Labrenzia 34 excitation energy 206 lacZ 780, 783, 785–787, 789 incoherent hopping 206 reporter activity 568 excitation spectra 921 Lake Fryxell 4 excited state 206 Lamprobacter modestohalophilus 667 excitonic interactions 205–207 Lamprocystis roseopersicina 108 homogeneous line shape 208 Langmuir-Blodgett fi lm 863, 864 hydrostatic pressure 208 lateral gene transfer 38 insertion of polypeptides 268 994 Index

membrane 268 effect on oligomers 161 model sequences 921 LH2 comparison 161 pigment tuning 935 role in quinone exchange 161

Qy transitions 208 hydrogen bond formation 187 solvation mechanisms 207 hydrogen bond mutants 186 spectral properties 199, 200–209 in vitro assembly Stark spectroscopy 208 intermediates 192 static disorder 206 RC-LH1 complex 192 structural variability 202 LH1-only mutant 161 light-harvesting 1 complex 10, 45–46, 136, 156, 160–162, modifi ed carotenoids 929 182–184, 186–188, 206–208, 214, 223, 226–227, 232, native membrane environment 916 235–239, 243–244, 254, 257, 269, 511, 523, 841, 846, Ni-bacteriochlorophyll a 928 871, 873, 915, 916, 942–944 NMR studies 156, 188 β polypeptide 188 Phaeospirillum molischianum 191 16-fold LH1 ring 163 polypeptides 156 2-D crystals of carotenoidless complex 160 quinone exchange 157–159, 161, 165–167 2-D crystals of Rhodospirillum rubrum complex quinone passage 523 closed ring 160 reassociation with reaction center 192 cryo-EM projection map 160 reconstitution 181–198, 916, 925 structure of complex 160 carotenoids 929-934 absorption spectra 925 red-shift 45 assembly 924–935 reversible dissociation 182 assembly intermediates 933 bacteriochlorophyll analogs 184 B780 930 bacteriochlorophyll ligand 184 B820 930 cofactor requirements 184 B870 930 dissociation constant 184 association constants 186 metal requirements 184 atomic force microscopy ring variety of structures 161 binding 163 B820 subunits 926 gaps 166 bacteriochlorophyll exchange 928 role of carotenoids 929 bacteriochlorophyll coordination state 930 Rhodospirillum rubrum blue-shift 45 2-D crystals 160 building blocks 175 self-organized on mica 873 C-terminal region 187 sequence alignment 185 C-terminal side 871 singlet-singlet annihilation spectroscopy 188 CD spectra 188, 925, 927 steric requirements for BChl binding 187 chemically-synthesized β polypeptide 186 subunits 926 circular dichroism 206 supramolecular structure 873 cofactor interactions 188 Thermochromatium tepidum 10 core antenna 915 unit size 928 effect of carotenoids on assembly 930 wavelength shift 188 ellipiticity 207 light-harvesting 2 complex 45–46, 110, 136, 143, 145–147, elliptical conformations 163 149, 165, 185, 188, 189, 191, 202, 207, 208, 214–227, elliptical ring 166 232, 235–239, 244–247, 254, 255, 257, 258, 267–269, energy transfer 226–227 279, 511, 513, 783, 801, 803, 841, 882–889, 915, 918, energy trapping 243–244 920, 921, 942, 944, 946, 948 EPR 188 α polypeptide 188 excitonic coupling 188 β polypeptide 188, 202 fi rst purifi cation 160 absorption 921, 923 fl exibility 160 assembly 923 fl uorescence polarization 188 assembly factor 174 formation 930 B800 band 279, 882–885 fractionation into oligomers 160 B800 molecule fundamental B820 subunit 183 acetyl carbonyl 203 fundamental subunit 183 B850 band 279, 885–889 histindine ligand mutants 185 B850 BChl hydrogen-bonding 161 coupling strength 205 effect on B820 161 excitonic interactions 205 effect on fl exibility 161 pure excition model 205 Index 995

BChl-B850 915 lipid-defi cient genetic mutants 120 BChl molecule lipid bilayer 854, 855 distorted conformation 205 lipid biosynthesis 119, 120–132 binding sites 920 lipid glycosyltransferase 126 circular dichroism 923 lipidic cubic phases 140 CD signal 921 crystallization 140 conformational substates 207 lipid profi les 120 conservative CD signal 206 lipids 193 crystal structure 202 lipid tubules 262 densely packed hexagonal arrays 267 lipophilic four-helix bundle 906 domains 260 liposomes 257 energy transfer 216–226 liquid state conception 519 fl uorescence excitation 923 local dielectric constant 204 spectra 882 Loktanella 19 fl uorescence excitation spectra 207 Loktanella vestfoldensis SKA53 790, 792 low-light Rhodopseudomonas palustris 203, 948 Lon protease 850 model 920–921, 922 lotic 51 mutants lacking 168, 171 LOV. See light, oxygen or voltage (LOV) Phaeospirillum molischianum 166, 189 LOV domain 731, 811, 813–816, 822–823 polypeptides 783 low-light conditions 143–153, 149, 150, 945, 948

Qy electronic transitions 205 low-light growth 148 resonance Raman spectroscopy 922 low-light intensities 150 Rhodobacter capsulatus 205 low-light light-harvesting 2 complex 255, 261, 945, 948, 949 Rhodobacter sphaeroides 203, 205 low aeration conditions 58 B850 BChl 204 lower energy transition site-directed mutagenesis 204 tuning position 205 α polypeptide 204 lower eukaryotes 410 β polypeptide 205 low light 255 Rhodopseudomonas acidophila 203 low oxygen 785–788 Rhodopseudomonas molischianum 165 low potential chain 453 sequence alignment 185 lycopene 98, 103–104, 108–110, 112, 113, 141, 218, 219, 225, size heterogeneity 255, 948 929, 931, 934 spectral heterogeneity 255 all trans 103 spectral properties 922 lycopene cyclase 113 stability 922 lyso-ornithine beta-hydroxy acyltransferase 121 structure of Rhodopseudomonas acidophila complex 185 lyso-ornithine lipid 130 light-harvesting 3 complex 150, 214 LysR 789 light-harvesting 4 complex 150, 801, 803 LysR-type transcriptional regulators (LTTRs) 565 light-harvesting assembly effective Hamiltonian 279 M light-induced cyclic electron fl ow 43, 511 light-induced oxygen uptake 543 M2 infl uenza proton channel 906 light-induced respiration 543 macro-movement 431, 441, 444 light-input domain 812 macrocycle 58, 438, 899 light-protection 898 distortion 899 light-responding antirepressor magnesium chelatase 58, 66, 67, 69, 70, 90, 717, 787 AppA 718 magnesium ion 139 light control 783 magnesium protoporphyrin IX 67, 68, 71 light intensity 98, 945, 948 magnesium protoporphyrin IX monomethyl ester 68, 794 light oxygen voltage (LOV) 731 magnesium protoporphyrin IX monomethyl ester oxidative light regulation 717–718 cyclase 42, 67, 71 lignin 578, 581 origin of oxo-group 71 lignin monomer 577 magnetic fi elds 357 linear dichroism (LD) 168, 169, 172, 258, 261, 286 magnetic resonance 389, 393–396 linear electron-phonon coupling 884 magnetic resonance spectroscopy 954 linear electron pathway 510 Major Facilitator Superfamily 148 linear plasmids 45 MALDI-TOF 167 linear tetrapyrrole 800, 827 malonyl-CoA:ACP-trasnacylase 122 lipid 935 manganese 349 function 130–131 oxidation 312 membrane 914 manganous protoporphyrin IX 71 996 Index

Marcus equation 364 membrane sheets 855 Marcus theory 345, 355, 363–367, 382 membrane tubules 258 Marichromatium 10 menahydroquinone oxidase 418 Marichromatium purpuratum 109, 515 menaquinol oxidation 548 marine environments 47 menaquinone 394, 511, 530 marker rescue techniques 66 mercaptomalate 601 MarR family 589 mercaptopyridine 862 massive transfer 694 meromictic lakes 40, 51 mass spectrometry 417 mer operon 663 master equation 280 MerP protein 663 Mastigocladus laminosus 468 Mer system 675 matrix ENDOR 959, 962 Mesorhizobium loti MAFF303099 794 maturation mesoscopic conditions 826 cytochrome c 408 metabolic channeling 530 maturation process 407, 408 metabolic engineering 854 McMurdo Dry Valleys, Antarctica 4, 11 metabolic versatility 696–701 MCP chemoreceptors 647 metal 656–682 mechanoenzymes 70 bacterial interactions 666–675 membrane 495 resistance 658 anchor/linker domain 843 genes 659–661 cytoplasmic side 137, 164 toxicity 657–658 eutectic phase behavior 260 metal-binding sites 63 incorporation of foreign protein 842 metal clusters 444 intracytoplasmic membrane (ICM) 136, 147 metalloid 656–682 LH2 protomer 138 bacterial interactions 666–675 lipid-rich areas 266 metallothionein 665, 668, 678 N-terminal anchor 412 in SmtA 665 native 942, 949 metallotolerance 52 n side 426 methanogenesis 7 organization 949 methionine synthase 83 periplasmic side 164 methoxy-hydroxylycopene glucoside 112 p side 426, 436 methoxylycopenal 108 reconstituted 943 methoxyneurosporene 107 remodeling 120 methoxyneurosporene dehydrogenase 107 ring size 137 methyl accepting chemotaxis proteins (MCPs) 647, 649, 651 topology 146, 158 methylamine dehydrogenase 853 translocation 410 methylation 674 vesicles 946 methylcobalamin 82 membrane-bound cytochrome cy 542–543 Methylibium petroleiphilum PM1 26 membrane-bound nitrate reductase 552 methylmalonyl CoA mutase 83 membrane assembly factors 269 Methylobacterium 19, 20, 113 membrane associated complexes 120 Methylobacterium extorquens 32, 102, 113 membrane bilayer 172 Methylobacterium extorquens AM1 790, 792 dilution 257 Methylobacterium radiotolerans 113 membrane curvature 170, 172 Methylobacterium rhodinum 110, 113 membrane development 262 methyltransferase 82, 84, 87, 89 membrane domains mevalonate pathway 103 PufX 172–174 Mg. See also magnesium membrane fragments 261 binding motif 791 membrane growth coordination 139, 140, 144, 184–188, 898 early stages 172 Mg-chelatase 90, 717, 787 membrane lipid biosynthesis 119, 120–132 Mg-protoporphyrin IX monomethylester 794 membrane lipids 899, 914 Mg-protoporphyrin monomethyl ester cyclase 42 membrane organization 170 Mg 3,8-divinylphaeoporphyrin a5 68 membrane phospholipids 267 mica substrate 861, 864–865 membrane potential 266, 517 mica supports 259 membrane protein 840, 841, 845, 846, 847–849, 854, 855, 924 mica surface 864, 947 folding 914 micelle 146, 157 monotopic 411 mixed micelles 183 membrane proteome microaerophilic photosynthesis 46 Escherichia coli 851 microarray 781, 783, 784, 786, 787 Index 997 microarray expression 696 CXXCH heme binding 409 microbial mats 8 HemN-type 794 microfl uidizer 846 leucine zipper-like 414 microscopic examination 8 limitation 417 mid-point potential 520 Mg-binding 791

QA 39, 46 tetratricopeptide repeat (TPR)-like 414 Mims-type pulsed 1H ENDOR 959 tryptophan-rich WWD 411, 414 mine drainage systems 41 Zn-binding 791 minimal medium 844 mucidin 455 mitochondria 409, 410, 416–418, 420, 476 multi-domain proteins 831 human 409 multi-subunit complex 852, 853 yeast 409 multidrug effl ux pumps 702 mitochondrial Complex IV 408 multiphasic kinetics 361–362 mitochondrial inner membrane 264 multiple chromosome-like replicons 694 mitochondrial respiratory chain 264 multiple domain motifs 701 mitochondrial supercomplex 526, 527 mutagenesis 338, 915, 916 Mn 419 mutant Mn/Fe superoxide dismutase 674 carotenoid 107

MOA-stilbene 455, 462 DLL mutant 347, 339 MOA-type inhibitor 435 fnrL 721 mobile cytochromes 515–517 G1c 218, 222, 930 mobile loop 504 holocyt c production 408 models LH2– mutant M21 168, 263 monomeric core complexes 165 mutant lacking B800 BChl 206 model sequence 923 protochlorophyllide-reduction 854 modifi ed Q cycle mechanism 426 PrrC 418 modifi ed Redfi eld theory 237, 242, 244, 245 PUC705BA 866 modularity 284, 285 R26 165, 303, 383, 386 modular organized Chl protein 901–904 R-26 302, 304, 339 modular organized proteins 896 R26.1 218–220, 223, 225, 387, 667, 668, 924 molecular-dynamics (MD) 358 R-26.1 299, 304 simulations 265, 358, 364, 370, 397 suppression 413 with quantum chemistry 282 reaction center-light-harvesting 1 complexes 164 molecular assembly 869–873 strain sym-1 308 molecular chaperone 69 strain QAQA 309 molecular devices 862 strain DLL 307 molecular orbital 342 strain A6D1 310 molecular voltmeter 483 mutants molybdenum 610, 761 carotenoidless mutants 193

transport 768 cytochrome bc1 molybdoenzymes 611 Rhodobacter 428–430 molydopterin cofactor 611 deletion mutants 839-860 monoglycosyldiacylglycerol glycosyltransferase 121 strain DD13 307 monomer bacteriochlorophylls 338, 341 strain DD13/G1 307 monomeric/dimeric complex comparison 169 lacking LH2 complex 168, 171 monomeric core complexes lipid-defi cient genetic 120 models 165 PUF∆LMX21 844, 846 monomeric RC-LH1-helix W core complex 171 Rhodobacter monooxygenase 84 cytochrome bc1 428–430 monotopic membrane protein 411 Rhodobacter sphaeroides Monte-Carlo simulations 172, 265 reaction center-light-harvesting 1 complexes 164 MopA 768 mutations 359, 360, 363 mopA-modABCD 765 myxothiazol 435, 442, 455, 521 MopB 768 motif N 4F-4S cluster binding 417 apoCyt c heme binding 413 N-dimethyundecylamine-N-oxide 146 ATB binding 411 2-n-heptyl-4-hydroxyquinoline-N-oxide (HQNO) 445 CFCF 417 n-octyl β-D-glucopyranoside (β-OG) 182, 925 conserved copper-binding 417, 420 N-terminal 6xHis-Tag 69 conserved metal binding 417 N-terminal amino acid 581 998 Index

α N-terminal domain of LH1 175 cd1 type 635 N-terminal membrane anchor 412 nitrite reduction 632 N-terminal signal sequence 843 nitrogenase 74, 582, 745, 760 N-terminal Strep-tag 74 alternative 769 N´-Dimethyldodecylamine N-oxide (LDAO) 869 post-translational control 767–768

N2O 780 nitrogen availability 789 NAD 746 nitrogen cycle 624 NADH 495, 501, 571 nitrogen fi xation 7, 624, 637, 707, 760–772 NADH: ubiquinone oxidoreductase 745 genes 762 NADH dehydrogenase (NDH-1) 538–539 regulation 760–772 NADH dehydrogenase (NDH-2) 539 regulatory cascade control 763 Nadi reagents 408 Rhodobacter capsulatus 762–768 NADP 495, 501, 746 Rhodobacter sphaeroides 770 NADPH 88, 500, 571 Rhodopseudomonas palustris 771 NADPH:protochlorophyllide oxidoreductase 73, 854 Rhodospirillum rubrum 771 nanodevices 861 nitrogen oxide reduction 624–639 nanodissection 259 Nitrosomonas 415 nanoscale apparatus 862 Nitrosospira 415 naphthoquinone 382 nitrous oxide reductase 626 native membrane 941, 942, 949 NNR orthologs 634 native membrane environment 923 nnrS 630 NDH-1. See NADH dehydrogenase (NDH-1) nnrU 630 NDH-2. See NADH dehydrogenase (NDH-2) Nobel prizes 276 negatively stained thin sections 171 non-phosphorous lipid 120 negative stain analysis 168 non-photosynthetic bacteria 109 electron microscopy 168 non-photosynthetic carotenoids 113 network non-sulfur bacteria 111 hydrogen bonds 175 nonameric rings 944 Neurospora crassa 813, 828 nonphosphorylated neurosporene 98, 103–105, 107–110, 112, 216, 218, 219, 221, RegA 715 222, 225, 227, 854, 931, 934 nonsulfur purple photosynthetic bacteria 563–575 neutral semiquinone 820 carbon dioxide metabolism neutron diffraction 145 regulation 564–575 Ni-bacteriochlorophyll. See Ni-bacteriopheophorbide normal spirilloxanthin pathway 104–106, 110 Ni-bacteriochlorophyll a 303, 928 Nos 636 Ni-bacteriopheophorbide 902, 907 NosR 634 Nicotiana tabacum 64 nostoxanthin 113 NifA 744, 753, 766–767 NQNO 468 post-translational control 766–767 n side 426 nifA2 765 NtrC 748, 752, 764 NifA regulon 766–767 NtrC regulon 765–766 NifD 74 Ntr systems 764 NiFe active site 750 nuclear magnetic resonance (NMR) 155–157, 183, 389, 391, nif genes 760 478, 529, 731, 904, 905, 925, 955 NifH 74 2-D 584 nifHDK 761 protein maquette 904 NifK 74 nuclear motion 345 NifL 766 nuclear quadrupole 396 nirS 635 nuclear quadrupole coupling 393 NirT family 548 nucleic acid probing studies 11 nitrate 670, 780, 781 nucleophilic attack 815 nitrate assimilation 624, 636–638 nucleotide-binding sites 477 nitrate reductase 548, 611, 625, 637, 670 nuo operon 539 nitrate reduction 623–639 nutritional status 43 nitrate respiration 630 nitric oxide reductase 625–627 O nitric oxide toxicity 627 nitrite 632 O-acetyl-l-serine 613 nitrite oxide reductase 626 O-acetyl-l-serine-(thiol)-lyase 613 nitrite reductase 625, 635, 637, 670 1-O-acylglycerol 3-phosphate 2-O-acyltransferase 121 Index 999

O-acetylhomoserine 613 oxygen-dependent CPO 64

O2 750, 752–753 oxygen-independent CPO 64

O2 regulation 752–753 oxygenase 578, 579

O2 sensor 753 oxygen concentration 98 obligately aerobic anoxygenic phototrophs 32 oxygen control 777, 778, 781–784, 787, 789 Oceanicola 440 oxygenic light-harvesting apparatus 276 okenone 98, 109, 110, 216, 218 oxygenic photosynthesis 380 okenone pathway 97, 99, 101, 108, 110, 112 oxygen tension 707, 780–789, 844 oligomycin sensitivity conferring protein (OSCP) 477 oligonucleotide 716 P oligonucleotide affi nity trapping 716 oligotrophic ocean 50 π-conjugated thiol 868 olsA 121 π-π interactions 190 olsB 121 bacteriochlorophyll 190 one-exciton coherence 243 π-π stacking 915, 931, 934 + – optical absorption maxima 431 P 700A1 968 + – optical mapping 694 P 865QA 965 + – optical spectra 339–340 P QA 297, 299, 304, 305, 343, 347, 382, 386, 387, 393, 396, optical spectroscopy 877–891, 954 398, 954, 956, 967, 969 + – optimality 285 P QA formation orf1148 784 dielectric response 967 + – Orf162b 174 P QB state 304, 345, 347, 386, 388, 396, 954, 956, 963 orf162b 174 P+ reduction 515–517 orf1696 174 P+ reduction orf214 174 kinetics 515–517 orf428 148 p-aminosalicylic acid 70 organic acids 40 p-coumaric acid 823 organic carbon 50 P-type ATPases 661 organic solvent extraction 193 P680 343 organosulfur compounds 596 P700 343 organyl polysulfanes 608 Painter reaction 670, 671 organylsulfanes 607 pair correlation function 945 orientational selectivity 961 palandromic sequence 717 ornithine 2-N-acyltransferase 121 Pantoea ananatis 103 ornithine lipid 119, 120, 129–130, 527 Pantoea stewartii 110 orthogonal synthesis 896, 900, 901 PAPS reductase 613 orthologs 693, 696 ParA chromosome partitioning protein 649 oscillations 362 Paracoccus 38 oscillator strength 207 Paracoccus denitrifi cans 264, 418, 479, 612, 695 OSCP. See oligomycin sensitivity conferring protein (OSCP) Paracoccus pantotrophus 602 osmotic pressure 657 Paracoccus versutus 602 osmotic stress 702 Paracraurococcus 34, 113 outer membrane protein 608 paralogs 696, 699 output domains 813, 817, 828, 831 paramagnetic metal clusters 444 oxidase parameter insensitivity 285 partial denitrifi cation 629, 631, 638 aa3-type Cyt c oxidase 408 heme-copper 416 partial denitrifi er 626, 631 HemF-type coproporphyrinogen III 794 PAS-fold 823 HemN-type coproporphyrinogen III 794 PAS domain 717, 728, 735, 750 menahydroquinone 418 PAS motif 572, 717 ubihydroquinone 416 PAS superfamily 753 oxidation/reduction midpoint potential 341 pathogenicity 701 oxidation/reduction midpoint potentials 340–342 pathway oxidative cyclase 72 asymmetrical ζ-carotene 104 oxidative damage 38, 545 bacteriochlorophyll 147 oxidative protein folding 412 carotenal 97, 108, 109, 112 oxidative stress 417 carotenoid biosynthesis 101 oxo-group carotenoid pathways 99 origin 71 DOXP 103 2-oxoglutarate 764 DsbA-DsbB 412 mevalonate 103 oxygen 777–791, 794. See also O2 1000 Index

normal spirilloxanthin 104–106 phonon-induced relaxation 206 okenone 97, 99, 101, 108, 110, 112 phosphate-limited growth 120 periplasmic apoCyt c thioreduction 412 phosphate defi ciency 120 quinol oxidase 554 phosphate exchange 70 R.g.-keto 97, 108 phosphatidate 124 Sec-dependent 412 phosphatidic acid 123 spheroidene 97, 107–108 phosphatidylcholine 120, 125 spirilloxanthin 97, 99, 101, 104–106, 110, 112 10-phosphatidylcholine 160 tetrapyrrole 778 phosphatidylcholine synthase 121 unusual spirilloxanthin 106 phosphatidyl cytidyltransferase 121 ζ-carotene 104 phosphatidylethanolamine 120, 124 pbr operon 662 phosphatidylethanolamine N-methyltransferase 121 PCR 44, 606, 842, 851, 852 phosphatidylglycerol 120, 124 quantitative 47, 48 phosphatidylglycerol 3-phosphate 125 real-time 47 phosphatidylglycerol 3-phosphate phosphatase 121 pcs 121 phosphatidylglycerol 3-phosphate synthase 121, 125 pea 854 phosphatidylserine decarboxylase 121, 124 Pelodictyon 746 phosphatidylserine synthase 121, 125 pentaheme c-type cytochrome 547 phosphatidyl Tris 120 pentaheme protein 548 phosphoadenosine phosphosulfate 613 Per Arnt Sim (PAS) 728 3´-phosphoadenosine-5´-phosphosulfate (PAPS) 610, 613 domain 728 3´-phosphoadenosine-5´-phosphosulfate reductase 610 motifs 717 phosphoenolpyruvate 571 perchlorate reductase 550 phosphoenolpyruvate carboxylase 41 percolation 528 2-phosphoglycerate 571 peripheral antenna 917 3-phosphoglycerate 571 peripheral light-harvesting antenna complex. See light-harvest- phosphoglycerolipid 123–126 ing 2 complex 2-phosphoglycolate 571 peripheral substituents 903 phospholipid 119, 146, 173, 183 periplasm 413, 521, 606 phosphorescence 357 periplasmic apoCyt c thioreduction pathway 412 phosphoribulokinase 566, 569 periplasmic heme ligation 410 phosphorylated regulators 830 periplasmic ICM surface 259 phosphorylation 715, 806 periplasmic nitrate reductase 552 RegA 715 periplasmic space 413, 843 phosphorylation site 715, 806 pernicious anemia 81 phosphotransfer 802 peroxiredoxin 418 photo-conversion 800, 804, 805 persulfi de sulfur 608 photoactive carotenoids 38 perthiol 609 photoactive yellow protein (PYP) 652, 735, 811, 823

PGC. See photosynthesis gene cluster photoautotrophic CO2 fi xation 40 pgpA 121 photoautotrophy 40, 50 pgsA 121 primary producer 2 Phaeospirillum fulvum 6, 110, 112, 579 photocurrent generators 862 Phaeospirillum molischianum 136, 137, 148, 166, 183, 185, photocurrent responses 862 189, 191, 255, 259, 942, 945–946; See also Rhodo- photocycle 814, 823 spirillum molischianum bacteriophytochrome 829 light-harvesting 1 complex 191 BLUF 818 light-harvesting 2 complex 137–150, 165, 166, 182–191, light, oxygen or voltage (LOV) 814 202, 214, 218, 222, 225, 235, 242, 255, 259, 260, 278, photoactive yellow protein 823, 826 282, 283, 878–880, 884, 885, 946–948 photocycle reaction 733 photosynthetic apparatus 259, 260, 945, 946 photoheterotrophic growth 6, 564, 596 reaction center-light-harvesting 1 complex 163, 259, 260, photoheterotrophy 6–7 945, 946 photoinduced electron transfer pH buffer 484 –20 °C 521 pH dependence 826, 348 photolithoautotrophic growth 564, 596 phenol 578, 579, 581 photomorphogenesis regulators 728 phenylacetate 579, 581, 588, 589 photon-echo 239 pheophytin a 356 photon capture 136 pheophytinization 42 photooxidation 517 phoB region 673 photooxidative damage 71 phonon 235 photooxidative stress 736 Index 1001 photophosphorylation 2, 702 phytoene dehydrogenase 717 photoprotection 41, 97, 111, 348 phytoene desaturase 105 photoreceptor 728–735 phytoene synthase 103, 717 photoreceptor families 812 phytol 74, 164, 300 photoreceptor proteins 811–832 phytyl-pyrophosphate 74 photoreversibility 828 phytyl chains 946 photosynthesis gene cluster 20, 44, 65, 148, 699 pigment 139–142, 144, 146 photosynthetic apparatus 44–47, 844, 942–951 pigment-pigment interactions 934 supramolecular assembly 942–951 pigment-protein complex 44 photosynthetic CO2 fi xation 48 pigment-protein sites 916 photosynthetic complexes pigment exchange 359 biogenesis 175 pigment substitution 360 photosynthetic culture 842, 848 pigment synthesis photosynthetic electron donor 4, 597 regulation 42–44 photosynthetic electron fl ux 50 pigment tuning photosynthetic electron transport 735 light-harvesting complex 935 photosynthetic membranes 162 Pisum sativum 854 photosynthetic methylotrophs 32 pKa 439, 445 photosynthetic pigment synthesis plant carotenoids 113 regulatory factor 43 plasmid photosynthetic rhizobia 32 broad host-range 842 photosynthetic unit (PSU) 146–147, 172, 257–263, 275–290, pBLM2 40 862 pBBR1 842 atomic level structural model 287 pRK404 842, 843 chromatophore model 287 plasticity 295–314 cordon sanitaire 285 reaction center 295–314 energy transfer 889–891 platform vectors 843, 844, 845 organization 257–267 pleomorphism 34 stoichiometry 286 plsB 121 supramolecular organization 286, 288 plsC 121 Photosystem I 267, 276, 343, 380, 915, 916, 918, 919, 968 pmf. See proton motive force (pmf) high resolution structures 917 pmtA 121 P700 343 point-dipole calculation 393 structure 916 Poisson-Boltzmann equation 358 Photosystem II 265, 267, 343, 349, 380, 384, 916, 918, 919 Poisson distribution 520 high resolution structures 917 polarized absorption 477 P680 343 polar lipids 119 structure 916 polonium 675 phototaxis 652, 735 polyene 924 phototoxicity 38, 41, 849 polyene chain 919 phototransfer 649 carotenoid 919 phototrophic alphaproteobacteria 597 polyhistidine tag 842 phototropin 731–732, 811 polyhydroxyalcanoic acid 602 phycobilisome 384 polymeric sulfur 607, 608 cyanobacteria 384 polyol ABC transporter 670 phycocyanobilin 804, 829 polysulfi de reductase 549, 552, 612 Phyllobacteriaceae 35 polysulfi des 596, 600, 601, 606, 607 phylogenetic analysis 719–721 porphobilinogen 60, 783, 784, 791 CrtJ/PpsR 719, 720 porphobilinogen deaminase 63 purple bacteria 4 porphobilinogen synthase 62, 783, 791. See also δ-aminolevu- phylogenetic surveys 47 linic acid dehydratase phylogenetic tree 456 porphyrin 58, 164, 277, 288, 409, 896, 897, 899, 900 transhydrogenase 498–500 porphyrin binding site 69 phylogeny 17, 21, 22 porphyrinogen 58 physical constraints of evolution 284–286 Porphyrobacter 40, 113 physiology Porphyrobacter meromictius 34 purple bacteria 4–7 Porphyrobacter neustonensis 34 phytochrome 267, 799, 800–807, 811, 827, 828 post-translational control phytochromobilin 804, 827 nitrogenase 767–768 phytoene 103–104, 107, 108 PpaA 785, 791 15-cis form 103 ppaA 785, 789 all trans form 103 PpsR 708, 716–720, 729, 784–787, 791, 795, 819 1002 Index

PpsR/CrtJ binding site 784, 785, 795 protomer 139, 144, 147 PpsR/CrtJ core consensus sequence 795 proton-motive force 495 PpsR2 807 protonation 815 Bradyrhizhobium 719 protonation changes 826 Rubriviax gelatinosus 719 proton electrochemical potential difference 510, 517 precorrin-2 86 proton environment 962 precorrin-3A 86 proton motive force (pmf) 425, 452, 476 precorrin-4 87 proton permeability 484 precorrin-5 87 proton transfer 830 precorrin-6A 87 proton translocation 426, 476–488 precorrin-8 89 ATP synthase 476–488 primary donor 340, 382 transhydrogenase 501 primary electron donor 356 protoporphyrin IX 58, 60, 66, 778, 787, 794 primary producer protoporphyrin IX-Fe 436

CO2 fi xation 2 protoporphyrin IX binding photoautotrophy 2 BchH 70 primary productivity 48 protoporphyrinogen 64 Prochlorococcus 47 protoporphyrinogen IX 60, 785–787, 794 populations 47 protoporphyrinogen IX oxidase 60, 65 product inhibition 522 Prr 782 progressive deletion 165 PrrA 715, 754, 782, 783, 784, 785, 786, 789, 795 C-terminus of LH1 α 165 PrrA/B histidine kinase system 651 projection map 160, 169 PrrA/PrrB 541. See also RegA/RegB Propionibacterium acnes KPA171202 778 PrrA/RegA binding sites 783, 795 Propionibacterium freudenreichii subsp. shermanii CIP103027 PrrA binding sites 783 778 PrrB 652, 782, 785, 789, 790 Propionibacterium shermanii 778 PrrB/PrrA 633, 735, 754, 770 propionic acid side chain 897 two-component system 735, 736 Propionigenium modestum 479 PrrC 418 protease thermolysin 446 PS I. See Photosystem I protein-Chl/BChl assembly 896 PS II. See Photosystem II protein-chlorophyll interactions 897–899 psd 121 protein-pigment interactions 905 pseudoazurin 627 protein-protein interactions 190, 426 Pseudomonas 669, 702 protein-quinone conformation 383 Pseudomonas aeruginosa 63, 658, 701, 828 protein conformational changes 954–973 Pseudomonas denitrifi cans 83 protein dynamics 337, 338, 345, 346 Pseudomonas fl uorescens 696, 699 protein maquette 904–905 Pseudomonas putida 816 crystal structure 904 Pseudomonas radiora 113 design 896 Pseudomonas syringae 665 NMR 904 pss 121 protein packing 903 PSU. See photosynthetic unit protein purifi cation 849, 855 PtdCho synthase 125 Proteobacteria 32, 98 PtdEtn N-methyltransferase 125 α 409 puc 841 α-2 34 puc multigene cluster 147 α-3 34 puc operon 46, 92, 147, 149, 782, 842 α-4 34 puc promoter 844, 845, 848 β 409 PUC705-BA 844, 846, 866 δ 409 pucA 842 ε 409 pucB 842 γ 409 pucBAC operon 150 proteoliposomes 870 pucBACDE 147 proteomic analysis 589 pucBA gene 149 proteomics 269 multiple copies 149–150 proteorhodopsin 812 PucC 147, 148 Proteus mirabilis 851 pucC 148, 174 protochlorophyllide 68, 73 pucC gene 801 protochlorophyllide-reduction 854 puf 841 protochlorophyllide reductase 67, 72, 73, 74 puf operon 92, 268, 732 Index 1003 puf promotor 844–848, 854 pump-probe 238, 239 pufA 842 pure exciton model 205 pufB 842 purple bacteria pufBA 45 evolution 17–28 pufC 45 extremophilic 9 pufL 842 habitat 7–9, 149 pufL gene 40 overview 2–12 pufLM 44, 47, 51 phylogenetic analysis 4 pufM 11, 40, 45, 842 physiology 4–7 nucleic acid probing studies 11 purple nonsulfur bacteria 4–6, 9, 10, 37, 42, 577–591, PufQ 268 596–600 pufQBALMX operon 256 purple sulfur bacteria 4, 5 PufX 45, 167, 191–192, 201, 207, 256–258, 263, 265, 269, laboratory culture 4 278, 525, 530, 942, 946, 947 pyridoxal phosphate 778 dimerization of core complex 172 pyridoxal phosphate-dependent 778 excitation sharing 172–174 pyridoxal phosphate cofactor 61 location 169 membrane domains 172–174 Q NMR structure 167 quinone sequestration 172–174 Q-cycle 426, 455–456, 460–469, 510, 511, 517, 518 PufX-minus strain 164 framework 455–456 Rhodobacter sphaeroides 164 Q-fl ip 822 – PufX mutant Q/QH2 binding site 430, 433–435

quinone traffi c 522–524 QA 46, 517 pufX gene 45 midpoint potential 46

PufX polypeptide 157–160, 513 QA 384, 385, 392, 398 assembly into core complex 159 methoxy groups 384 – association with LH1 α 159 QA 522

BChl binding 191 QB 385, 387, 395, 396, 397, 517, 522 in vitro 159 distal 388, 396, 956 C-terminal processing 191 methoxy groups 388 chemical synthesis 159, 191 proximal 387, 388, 396 – core segment 191 QB binding sites 961 functional role 192 QB site 256, 258, 265 glycine-rich region 159 QH2:Cyt c oxidoreductase activity 672 homodimerization 160 QH2 oxidation 430 inhibition of LH1 formation in vitro 191 Qi 512. See also quinone reduction site labeling with fl uorescence 191 Qi site 433, 434, 435, 436 location within dimer complex 191–192 cytochrome bc1 467–468 membrane topology 158 qmo genes 611 N-terminal region 169 Qo 512. See also quinol oxidation site deletion of residues 169 Qo site 430, 435, 442, 460–467 PufX mutants 191 distal niche 462 purifi cation 159, 191 molecular mechanism 460–467 quinol/quinone exchange 158 proximal niche 455, 462 role in core complex dimerization 160, 191 Qp 454 solution structure 158, 159, 160 quantitative polymerase chain reaction 49 alternative solution structure 159 quantum chemical calculations 205, 815 C-terminus 159 quantum chemistry glycine-rich sequence 159 molecular dynamics 282 intersection with LH1 α 159 quantum coherence 278 N-terminal region 159 quantum effi ciency 276, 862 transmembrane region 159 quantum mechanics 276, 502 suppressor mutants 158 description of photosynthesis 276 TOXCAT analysis 160 quantum theory puh 841 fi nite temperature 282 puhA gene 175, 268 quantum yield 193, 280, 360 puhB 174 quenching of LH1 emission 928, 929 pulse-fi eld gel electrophoresis 694 quinol 254, 257 pulsed EPR 955 quinol/quinone exchange 157, 158, 947 pump-dump-probe 227 quinol oxidase 717 1004 Index

quinol oxidase (Qo) 454. See also proton motive force (pmf) random collision model 520, 526 quinol oxidase pathway 46, 554 random matrix theory 282 quinol oxidation site 452 rare codons 850 quinone 173, 254, 257, 264, 379–399, 510, 518–519, 523, 754 rate-zone centrifugation 267 methoxy 385, 388, 389 RB. See Rieske/Cytochrome b complex (RB) pool 529, 554 RB operons 458 primary 380 RC. See reaction center (RC) proximal 397 RC-H subunit reconstitution 382 6-Histidine tag 170 redox signal 754 RC-LH1-PufX. See reaction center-light-harvesting 1-PufX secondary 380 complex quinone/quinol 258 RC-LH1-PufX core dimer quinone/quinol diffusion 949 3-D reconstruction 170 quinone/quinol exchange 947 RC-LH1 core structures 267 quinone/quinol gate 948 re-isomerization 827 quinone/quinol passage 944 reaction center (RC) 44–45, 193–195, 232, 254, 263, 264, quinone binding 712 295–314, 323, 337–349, 355–370, 380, 452, 509–530, quinone binding pockets 46 699, 703, 841, 942 quinone binding sites 942 A-branch 301 hydrogen bonding 389 B-branch 301, 306 quinone confi nement 528–529 bacteriochlorin exclusion 301 Rhodobacter sphaeroides 522 bacteriochlorin replacement 302 quinone diffusion 263, 289 bacteriochlorophyll quinone exchange 161 histidine ligand 344 quinone exclusion 301 replacement 305 quinone passage water ligand 344 light-harvesting 1 complex 523 BPhe replacement 306 quinone pool 46, 170, 395, 426, 517 charge separation 356–370

Em 554 chimeric RCs 298 redox poise 554 current-voltage curves 867 quinone reactions 518–519 cytochrome subunit 298 quinone reduction site 452 directed modifi cation 338–349 quinone replacement 303 DLL mutant 339, 347 quinone sequestration electron donor 514–515 PufX 172–174 electron transfer quinone traffi c B-branch 348 PufX– mutant 522–524 new reactions 348 quorum sensing 702 pH dependence 348

Qy absorption band 136, exponential dependence on distance 345

Qy absorption band shift 46 Fe removal 305

Qy electronic transitions 205, 232 Fe replacement 304, 305

Qy transition 203, 204, 208 heterodimer 137, 305, 310, 338

Qy transition dipoles 145 heterodimer mutant 340 H-polypeptide 297, 298 + – R inactive P QB 957, 958, 962 in vitro reconstituion 193 R26 165, 303, 383, 386 LM complex 297 R-26 302, 304, 339 orientation 168 R26.1 218–220, 223, 225, 387, 667, 668, 924, plasticity 295–314 R-26.1 299, 304 QB site 168, 173, 256, 258 R-26 RC 299 distal position 956 radiationless excitation transfer 276 – proximal vs. distal shift of QB 962 radical-pair 356 quinone radical-pair recombination 815 exclusion 301 radical pair intermediates 357–359 methoxy 385, 388, 389 + – radical pair state P QA 956 replacement 303 radical S-adenosylmethionine superfamily 794 proximal quinone 397 Ralstonia eutropha 566, 744–757, 749, 750, 752 R-26 299, 302, 304 Ralstonia metallidurans 658, 662 R-26.1 299, 304 Raman spectroscopy 46, 166, 175, 184, 185, 203, 204, 221, RC-H subunit 224, 227, 362, 389, 390, 394, 396, 733, 804, 819, 821, 6-Histidine tag 170 922–924 Index 1005

reconsititution 193–195 redox-active cysteine 713, 714 Rhodobacter sphaeroides 323, 324–333 redox-box 714 solvent extraction of subunit 193 redox-regulation 707 special pair 39, 46, 163, 166, 168, 169, 238, 243, 280, 301, redox active tyrosine 349 356, 381, 514, 550, 866, 871, 956, redox balancing 630, 631 specifi c assembly factor 174 redox cofactors 853, 856 transmembrane helices 164 redox mid point potentials 431 type I 380 redox poise 46 type II 380, 385 redox pool 631 zinc substituted 305, 396 redox potential 175 β mutation 347 redox processes 657 reaction center-light-harvesting 1-PufX complex 147, redox reaction 495 166–174, 201, 254, 261, 263, 269, 278 redox regulation 717–718, 753–754 dimeric complexes 168–174 redox sensing 652, 713–714 helical arrays 168 redox signal 712, 714, 754 Rhodobacter veldkampii 166–168 quinone 754 reaction center-light-harvesting 1-W complex reduction of geranylgeraniol to phytol 74 Rhodopseudomonas palustris 166 reductive dehalogenases 82 reaction center-light-harvesting 1 complex 136, 155–175, refolding process 864 162–166, 201, 255, 257–259, 268, 512, 523, 807, 862, RegA 567, 707, 708, 712–717, 753, 754, 783, 786, 789, 795 863, 870, 935, 942, 949 binding site 715 AFM and EM model 165 homologs 709–711 Blastochloris viridis 162 nonphosphorylated 715 deletion of C-terminus of LH1α 165 phosphorylation 715 hexagonal packing 162, 165, 168, 171 response regulator 714–725 monomeric complexes 162–166 regA 783, 785, 787, 790 AFM topographs 162 RegA/RegB 541, 651. See also PrrA/PrrB cryo-EM 162 RegAB/PrrAB 563, 564, 567 electron microscopy 162 RegB 652, 707, 708, 712–716 hexagonal packing 162 autophosphorylation 713 Phaeospirillum molischianum 163 homologs 709–711 Rhodobacter sphaeroides regB 567, 708, 712, 715 mutants 164 RegB/PrrB/RegS-RegA/Prra/RegR 743 Rhodopseudomonas palustris 261 RegB/RegA 633, 708, 708–716, 735, 744, 754, 770 Rhodospirillum photometricum 165 two component system 735, 736 Rhodospirillum rubrum 163 RegR 715 role of carotenoid in assembly 193 consensus sequence 716 structures 267 RegS-RegR 754 reaction center H 260, 268 regulation reaction center proteins 21 gene expression 707–722 reaction center QB site 157 nitrogen fi xation 760–772 reaction mechanism 60 pigment synthesis 42–44 reactive oxygen species (ROS) 666, 668 synthesis 707 production 674 regulation by Fnr 721–722 reassociation 864 regulatory factor recA 850 photosynthetic pigment synthesis 43 recognition sequence regulatory proteins 762 CrtJ 717 relaxation 233, 235, 239, 241, 246, 361, 363, 365 reconstituted membranes 943 remodeling membranes 120 reconstitution 382 renewable energy 771 cofactor 924 reorganization energy 233, 343, 347, 348, 358, 359, 364, 382 experiments 186 rescue-mutagenesis 922 reaction center 193–195 resistance-nodulation-cell division (RND) 658 rectifi cation 862, 868 respiration 149, 510, 526, 707, 713, 745 red-shift 45, 188, 193, 200, 203–205, 208, 235–247, 729, 733, respiratory arsenate reductase 552 818, 820–823, 825, 827, 879, 921–923, 926–934 respiratory chain 264, 510, 526, 527 red-shifted signaling state 820 respiratory membrane 262 Redfi eld theory 281 respiratory uncouplers 417 modifi ed Redfi eld theory 237, 242, 244, 245 response regulator 751 redox RegA 714–725 cellular 708 response regulators 572, 819 1006 Index restriction/modifi cation system 850 563–569, 572, 573, 597, 598, 603, 614, 626, 635, 637, reverse electron transfer 380 638, 643, 647–651, 667, 668, 671, 672, 674–676, 692, Complex I 512 708, 728, 732, 735, 736, 745, 747–749, 754, 761, 770, Rheinheimera 601 777, 780–789, 791, 794, 804, 813, 817, 819, 824, 828, Rhizobacteria 694 841–847, 849, 850, 851, 853, 854, 855, 878, 920, Rhizobales 598 925–927, 942, 947, 955, 956, 960, 964, 969 rhizobia 35 AppA 652, 718, 732-736, 785, 817-821, 831 Rhizobiales 442, 597 bacteriochlorophyll biosynthesis genes 57-79 Rhizobium 100, 113, 549, 693, 702 carbon dioxide metabolism 563-576 Rhizobium leguminosarum 716, 744, 753 chemotaxis 647–651 Rhizobium leguminosarum bv viciae 3841 479 Chromosome 1 122, 150, 691–706 Rhizobium meliloti 700 cobalamin biosynthetic genes 84 rhodanese 605 core dimers 168–171

Rhodobaca 11 cytochrome bc1 455

Rhodobaca bogoriensis 3, 108, 599 cytochrome c2 323, 324–333

Rhodobacter 3, 11, 34, 666, 669, 841, 850–856 cytochrome c2:reaction center complex 323–333 cell-free expression system 852 electron transfer pathways 382

cytochrome bc1 G1c mutant 218, 222, 930 mutants 428–430 gene regulation expression system 842 oxygen 707–725 Rhodobacteraceae 23, 380, 603, 614 light 727–741 Rhodobacterales 112, 597, 598, 614 tetrapyrrole biosynthesis 777–798 Rhodobacterales bacterium 627 genome 86, 417, 538, 539, 542, 626, 627, 633, 646, 649, Rhodobacter azotoformans 597, 598 652, 676, 691–706, 712, 731, 780, 786, 790, 791, 813, Rhodobacter blasticus 168–171, 256, 261, 513, 598, 668, 819, 828, 850, 920, 946–947 heterologous gene expression 839-860 core dimers 168–171 hydrogenase 743-757 dimeric core complex 170 inclusion bodies 847 Rhodobacter capsulatus 3, 6, 7, 9, 19, 40, 58, 61, 65, 71, 72, light-harvesting 2 complex 135–153, 156, 161, 165, 166, 102, 103, 107, 112, 175, 191, 205, 267, 338–353, 356, 172, 173, 186, 187, 203, 204, 206, 214, 218, 220, 222, 360, 384, 397, 408, 417, 426, 427, 437, 440, 479, 512, 223, 225–257, 260, 262, 279, 513, 524, 528, 632, 667, 513, 515, 521, 527, 538–542, 554, 563–565, 567, 569, 699, 841, 842, 854, 913-924, 947 570, 572, 597, 598, 606, 627, 629, 633, 634, 635, 637, lipid biosynthesis 119–134 666–668, 670, 672–674, 700, 708, 735, 744–757, mutant See Mutant/mutants 760–768, 777, 780, 782–791, 794, 795, 824, 843, 845, N-terminal signal sequence 843 847, 851, 853, 854, 942 nitrate reduction 623-642 cobalamin biosynthetic genes 84 nitrogen fi xation 770 cytochrome biogenesis 407–423 PrrB/PrrA 708, 735, 754

cytochrome bc1 complex 425–450 PrrA/PrrB 541

cytochrome cy 845 PufX-minus strain 164 gene regulation PufX polypeptide oxygen 707–725 solution structure 169 light 727–741 quinone confi nement 522 hydrogenase 743–757 reaction center 295–321, 337–353, 379–405 nitrogen fi xation 762–768 R26 165, 303, 383, 386 Q sites 434 R-26 302, 304, 339, 520 RegB/RegA 754 R26.1 218-220, 223, 225, 387, 667, 668, 924, strain A6D1 310 R-26.1 299, 304

strain DLL 307 R-26 RC 299

strain QAQA 309 strain DD13 307 strain sym-1 308 strain DD13/G1 307 supramolecular organization 519–522 supramolecular organization 253–273, 275–294, 519–522, U43 strain 307 947 Rhodobacter capsulatus SB1003 780, 782–792, 794, 795 Rhodobacter sphaeroides 2.4.1 539, 780–792, 795 Rhodobacter capsulatus strain PAS100 783 Rhodobacter sphaeroides ATCC17025 790, 792 Rhodobacter sphaeroides 3, 7, 9, 19, 21, 22, 58, 61–65, 71, Rhodobacter sphaeroides ATCC17029 792 102, 103, 107, 108, 112, 137, 144, 145, 157, 159, 160, Rhodobacter sphaeroides f. sp. denitrifi cans 671 164, 168–171, 183, 184, 191, 201, 205, 215, 217–226, Rhodobacter sphaeroides RS630 780 239, 254, 256, 257, 260, 264, 267, 268, 277, 278, 286, Rhodobacter sphaeroides wild type strain NCIB8253 785 296, 323, 338–353, 356–358, 360, 365, 368, 380, 381, Rhodobacter sulfi dophilus 3 383–385, 388, 397, 408, 426, 427, 437, 455, 479, 512, Rhodobacter veldkampii 166–168, 270, 513, 597, 598 513, 515–517, 521, 527, 538–543, 545, 546, 550, 554, dimerization motifs 168 Index 1007

PufX-PufX transmembrane association 168 supramolecular organization 253-273, 948-950 PufX N-terminus 167 Rhodopseudomonas palustris BisA53 676, 790, 792 purifi cation 167 Rhodopseudomonas palustris BisB18 676, 790, 792 reaction center-light-harvesting 1-PufX complex 166–168 Rhodopseudomonas palustris BisB5 676, 790, 792 structure 167 Rhodopseudomonas palustris CGA009 479, 676, 790, 793 Rhodobium 10 Rhodopseudomonas palustris HaA2 676, 790, 793 Rhodobium marinum 149, 597, 598, 930 Rhodopseudomonas palustris strain 2.1.6 150 Rhodobium orientis 597, 598 Rhodopseudomonas viridis See Blastochloris viridis 183, 201, Rhodoblastus acidophilus 11, 98, 108, 109, 112, 514, 579, 792 239, 380 Rhodoblastus sphagricola 112 rhodopsin 596, 730–731 Rhodocista centenaria 10, 728, 736 sensory 730–731 Rhodocista centenum 824 rhodoquinone 383, 392, 511, 530 Rhodocyclales 599 Rhodospira trueperi 106, 597, 598 Rhodocyclus 543 Rhodospirillaceae 603, 614 Rhodocyclus gelatinosus 183, 745 Rhodospirillales 597, 598 Rhodocyclus purpureus 34, 579, 599 Rhodospirillum 543, 669 Rhodocyclus tenuis 9, 98, 515, 599, 668, 674 Rhodospirillum centenum 10, 19, 643, 645, 728, 800, 828 Rhodoferax 543 Rhodospirillum fulvum 579 Rhodoferax antarcticus 3, 11, 599 Rhodospirillum molischianum 165, 214, 218, 219, 221, 222, Rhodoferax fermentans 515, 543, 599 225, 235, 242, 278, 512, 878, 930. See also Phaeo- Rhodoferax ferrireducens 23, 414, 606, 614, 676 spirillum molischianum Rhodoferax ferrireducens T118 23, 26 light-harvesting 2 complex 137–150, 165, 166, 182–191, Rhodomicrobium 666 202, 214, 218, 218, 222, 225, 235, 242, 255, 259, 260, Rhodomicrobium vannielii 104, 112, 579, 597, 598 278, 282, 283, 878–880, 884, 885, 946–948 Rhodopila globiformis 11, 104, 108, 597, 598, 612 Rhodospirillum palustris 863 rhodopin 110, 141, 929, 930, 931 Rhodospirillum photometricum 9, 137, 165, 255, 256, 259, rhodopin glucoside 142, 148, 215, 217, 220, 221 265, 266, 942, 944, 945 rhodopinal 108 AFM data 165 rhodopinal glucoside 108–110, 148 reaction center-light-harvesting 1 complexes 165 rhodopinol 108, 110 Rhodospirillum rubrum 3, 7, 19, 20, 58, 87, 102, 103, 106, Rhodoplanes elegans 597, 598 156, 160, 164, 182, 184, 189, 192, 201, 215, 223, 226, Rhodoplanes roseus 597, 598 239, 254, 256, 258, 259, 265, 384, 440, 441, 512, 517, Rhodopseudomonas acidophila 11, 46, 135–151, 185, 201, 521, 539, 597, 598, 603, 614, 651, 667, 668, 674, 679, 202, 204, 214, 215, 217–223, 225, 235, 241, 254, 277, 692, 743, 746, 752, 761, 771, 789, 863, 899, 925, 926, 278, 579, 878, 942 927, 942 crystal structure 202 carotenoidless mutants 926 light-harvesting 2 complex 46, 110, 135–153, 165, 185, 186, containing wild-type carotenoids 160 201–205, 214–225, 235, 236, 241, 245, 254, 255, 277, CooLH hydrogenase 746 278, 878, 882, 883, 886, 923, 942, 948 LH1 core complex 254 Rhodopseudomonas acidophila strain 10050 135–151 nitrogen fi xation 771 Rhodopseudomonas acidophila strain 7050 137, 143, 148 puhA gene 175 Rhodopseudomonas cryptolactis 10, 148 reaction center-light-harvesting 1 complexes 163 Rhodopseudomonas julia 597, 598 reconstitution of LH1 complex 181-198, 924-935 Rhodopseudomonas marina 160, 183 Rhodospirillum rubrum ATCC 11170 479, 676, 789–791, 793, Rhodopseudomonas molischianum 202, 256, 266 794 crystal structure 202 Rhodospirillum rubrum S1 930 Rhodopseudomonas palustris 3, 7, 9, 19, 64, 102, 103, 145, Rhodospirillum rubrum strain G9 304 166, 201, 254, 255, 257, 261, 265–267, 29, 513, 539, Rhodothalassium 10 542, 546, 563–565, 572–574, 578–581, 583–591, 597, Rhodothalassium salexigens 824 598, 603, 614, 626–630, 634, 637, 638, 646, 651, 676, Rhodovibrio 10 679, 692, 719, 728, 743, 745–749, 751, 752, 754, 761, Rhodovibrio sodomensis 10 771, 799–807, 819, 824, 828, 829, 945, 948–949 Rhodovulum 10, 34 bacteriophytochromes 799–809 Rhodovulum adriaticum 598, 612 degradation of aromatic compounds 577–594 Rhodovulum euryhalinum 598, 612 genome 149, 150, 268, 578, 586, 590, 628, 629, 634, 636, Rhodovulum iodosum 598, 612 651, 692, 693, 695, 696, 699–702, 828 Rhodovulum marinum 598 monomeric RC-LH1-helix W core complex 171 Rhodovulum PS88 668 nitrogen fi xation 771 Rhodovulum robiginosum 598, 612 reaction center-light-harvesting 1 core complex 261 Rhodovulum strictum 598 reaction center-light-harvesting 1-W complex 166 Rhodovulum sulfi dophilum 58, 102, 137, 515, 547, 550, 598, RegS-RegR 754 607, 616 1008 Index

Rhodovulum sulfi dophilum W4 790 Roseospira 10 Rhodovulum sulfi dophilus 202 Roseospira mediosalina 597, 598 Rhodovulum sulphidophilum 71 Roseospirillum parvum 597, 598 ribofl avin 816 Roseotales depolymerans 599 ribose-5-phosphate 571 Roseovarius 34, 440, 614 ribosomal protein 418 Roseovarius mucosus 34 ribosomal subunit 418 Roseovarius nubinhibens 599, 603 ribosome binding site 842 Roseovarius sp. 19 ribulose-1 41 Roseovarius sp. 217 603, 627, 790, 791, 793 ribulose 1,5-bisphosphate (RuBP) 570, 571, 572 rosette-forming species 34 ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) rotary catalysis

19, 20, 25, 27, 564, 566, 569, 570, 572–574 FOF1-ATP synthase 476–478 Rickettsia 440, 694 rotary ion translocation 481 Rickettsia bellii 436 rotational power spectrum 163 Rickettsia prowazekii 694 rotor 477, 644 Rieske/Cytochrome b complex (RB) 452–460, 469 Rubisco. See ribulose 1,5-bisphosphate carboxylase/oxygenase catalysis 455–456 (Rubisco) evolution 456–458 rubredoxin-like metal binding fold 439 operons 458 Rubrimonas 34 structure 453–455 Rubritepida 34 Rieske FeS protein 263 Rubrivivax gelatinosa 745 Rieske iron-sulfur center 452 Rubrivivax gelatinosus 9, 19, 24, 40, 58, 72, 102, 103, 108, Rieske protein 427, 942 137, 147, 149, 258, 298, 414, 435, 514, 518, 599, 603, Riftia pachyptila 611 614, 679, 719, 722, 795, 813, 819, 943 rivers 51 AFM 943 RNA polymerase 754, 765 fnrL null mutant 722 RNA secondary structure 843 PpsR2 719 RND. See resistance-nodulation-cell division (RND) Rubrivivax gelatinosus PM1 676 RND protein 658 Rubrivivax gelatinosus S1 and IL144 790 Rnf 745 Ruegeria gallaciensis 38 robustness graceful degradation 285 S parameter insensitivity 285 σ σ robustness and optimality 285 28. See fl agellar-specifi c sigma factor ( 28) σ rodopinal glucoside 144 54 644, 645, 646, 650, 748, 749 σ roller coaster pattern 514 54-RNA polymerase 749, 753 σ Roseateles depolymerans 40 70 748 σ Roseibacterium 34 70 RNA polymerase 749, 753 Roseibium 34 σ factor. See sigma factor Roseicyclus 34, 40 S* state 222–224 Roseicyclus mahoneyensis 34 energy transfer 222–224 Roseifl exus castenholzii DSM13941 676 S-adenosyl-L-methionine (SAM) 71, 81, 83, 86, 107, 674, 794 Roseifl exus sp. RS-1 676 S-adenosyl-L-methionine:magnesium protoporphyrin IX-O- Roseinatronobacter 34 methyltransferase 71 Roseinatronobacter thiooxidans 599 S-adenosyl-L-methionine uroporphyrinogen III methyltrans- Roseisalinus 34 ferase 86 Roseisalinus antarcticus 34 16S rDNA sequence 33 Roseivivax 34 analysis 33, 34 Roseoateles 113 16S rRNA 19, 21, 22, 23 Roseobacter 34, 40, 113, 554, 651, 695 23S rRNA sequence analysis 35 Roseobacter clade 34, 40, 48 S1 state 219–222 Roseobacter denitrifi cans 19, 22, 71, 102, 104, 107, 108, 112, energy transfer 219–222 113, 170, 299, 514, 515, 546, 547, 599, 603, 627, 629, S2 state 216–219 634, 635, 636, 637, 813 energy transfer 216–219 Roseobacter denitrifi cans OCh114 790, 791, 793 Saccharomyces cerevisiae 479, 612, 615, 694 Roseobacter denitrifi cans Ohc114 676 Salinibacter ruber 824 Roseobacter gallaciensis 38 Salmonella typhimurium 612 Roseobacter sp. 58 salt bridge 815, 822 Roseobacter sp. MED193 603 salt fl ats 51 Roseococcus 34 SAM. See S-adenosyl-L-methionine (SAM) Roseococcus thiosulfatophilus 110, 113, 201, 204, 599 SAM O-methyltransferase 67 Index 1009

Sandaracinobacter 34, 40 SgpB 608 Sandarakinorhabdus 34 SgpC 608 SAR11 37 sgp genes 608 sat 614 Sgp proteins 608 SAXS. See small angle X-ray scattering Shemin pathway 59, 778, 780 scanning permutagenesis 922 Shewanella 664 scanning probe analysis 863 shielding helices 902, 903 scanning tunneling microscopy 863 short-circuit reactions 460 Schiff’s base 61, 62 sigma-E 736 Schizosaccharomyces pombe 418 sigma factor 700, 701 Sco1 418, 419 sigma factor RpoN 766 SCRP. See spin-correlated radical pair (SCRP) signal generation 812 SDS-PAGE. See SDS-polyacrylamide gel electrophoresis signaling 747–754 (SDS-PAGE) signaling state 819–822, 825, 830–831 SDS-polyacrylamide gel electrophoresis (SDS-PAGE) 193, signal transduction 43 846 signal transduction chain 812 Sec-dependent pathway 412 signal transduction systems 43 Sec61 protein-conducting channel 269 Silicibacter pomeroyi DSS-3 479 SecA 269 simulations 355 SecDF 269 single-molecule spectroscopy 166, 207, 237, 877–879, 883, secondary electrochromic markers 954 885, 891 secondary quinone 380, 395 single light-harvesting complex 244 second order electron transfer 332–333 single molecule imaging 950 second order rate constant 325, 327–332, 516, single particle EM analysis 70, 170 second order reaction 325, single photosynthetic unit Sec translocon 269 energy transfer 889–891 SecY 269 singlet-singlet annihilation 183, 188, 257, 258, 262 SecYEG 436 singlet-triplet annihilation 183 selective deuteration 961 singlet-triplet quenching 257 selenate 669, 671 singlet oxygen 38, 736–737 selenate reductase 547, 548, 550 Sinorhizobium meliloti 91, 629, 781 selenate reduction 550 siroheme 82, 86, 637, selenate respiration 550 siroheme-[Fe4S4] 613 selenite 669, 671 sirohydrochlorin ferrochelatase 86 selenium 669–671 site-directed mutagenesis 204, 439 selenium oxyanions 671 small angle X-ray scattering 805 selenocysteine 670 SodA 673 selenomethionine 670, 844, 851 soda lakes 11 self-assembled monolayer (SAM) 862, 863, 865 SodB 673 self-assembly 904 sodium dodecyl sulfate 846 selfi sh operon theory 21 soil 51 semi-aerobic 107, 785–788, 845, 848, 849, 853 sojourn expansion 281 semi-aerobic conditions 107 sojourn time 282 semi-automated purifi cation 849 Solibacter usitatus 458 semiquinone (SQ) 391, 392, 394, 395, 460, 820 solid state conception 519

O2-sensitive 460 solid state NMR 391 semiquinone anion 396, 467 solid support 861 SenC 419 solubilization 855 sensing fi xed nitrogen 763–766 soluble periplasmic Cyt c2 45 sensor kinase RegB 712 solution structure 482 sequence alignment AppA BLUF domain 818 ATP synthase 479 LH1α polypeptide 157–158 hydrogenase 744, 748 LH1β polypeptide 157–158 ALA synthase 791 phot1 LOV2 813 light-harvesting polypeptides 145, 185, 917, 921 PufX 158, 169, 270 PucC 148 RegA 716 Cyt b 431, 455 solvation mechanisms 207 sequential electron transfer 963 SorAB 611 serine/threonine kinase domain 731 sorAB 603, 611 sewage 9 sox genes 599, 602 SgpA 608 Sox proteins 606 1010 Index

Sox system 602–606, 612, 616 steric hindrance 203 SoxB 602, 606 stigmatellin 389, 435, 442, 454, 462, 521 SoxCD 602, 605 stochastic Liouville equation 369 soxCD 603 stoichiometric excess 518 SoxE 606 stoichiometric ratio Q:RC 523 soxEF 603 stoichiometry 944 SoxF 606 photosynthetic unit 286 SoxR 602 stratifi ed lakes 32 SoxS 602 blooms 7–8 SoxV 602 Streptomyces hygroscopicus 852 SoxXA 602, 605 Streptomyces nodosus subsp. asukaensis 778 soxXABYZ 603 structural genomics 847, 856 SoxYZ 602, 605 structural genomics initiative 848 Spb 736 structural stabilization 915 special pair 39, 46, 163, 166, 168, 169, 238, 243, 280, 301, structural variability 255–257 356, 381, 514, 550, 866, 871, 956, structural water 310 specifi city 360–361 sucrose density gradient centrifugation 855, 856 spectral density 233 sulfate 598, 610–612, 615 spectral diffusion 885 sulfate-reducers 591 spectral hole-burning 361 sulfate assimilation 612–615 spectral overlap 148, 280 sulfate permease 612, 615 spectral universality theorems 283. See also thermal disorder sulfate reducing bacteria 609 spherical vesicles 845 sulfate reductase 670 spheroidene 97, 108, 110, 215, 218, 220–222, 225, 227, 929, sulfate transport 612, 613 931 sulfate transporter and antisigma factor antagonist domain spheroidene monooxygenase 107 (STAS) 813, 816; See also fl avin mononucleotide spheroidene pathway 107–108, 110 (FMN) spheroidenone 41, 107, 110, 216, 222, 226 sulfate transporters 616 spheroplast 66, 855 sulfate uptake 612 Sphingomonadales 113 sulfi de 596, 598, 600, 602 spin-correlated radical pair (SCRP) 963, 968 sulfi de:cytochrome c oxidoreductase 606 electron-nuclear double resonance (ENDOR) 965, 966 sulfi de:quinone oxidoreductase (SQR) 602, 606–607 + – P 700A1 968 sulfi de oxidation 4, 602, 606, 607 Spinacia oleracea 479 sulfi de springs 32 spin boson 368 sulfi te 598, 602, 616 spirilloxanthin 41, 97, 104, 108, 220, 223, 226, 927, 929, 931, oxidation 610–612 933 sulfi te:cytochrome c oxidoreductase 599, 853 biosynthesis 104, 104–108 sulfi te dehydrogenase 610, 611 spirilloxanthin pathway 99, 101, 104–106, 110, 112 sulfi te oxidase 611 Spirulina platensis 479 sulfi te oxidation 610–612 sqd genes 120 sulfi te reductase 602, 605, 607, 609, 615, 616, 670 sqdA 121 sulfolipid 613 sqdB 121 Sulfolobus acidocaldarius 459 sqdC 121 sulfoquinovosyldiacylglycerol 119, 120, 127 sqdD 121 sulfoquinovosyl transferase 128 sqr 603 sulfur 596–616. See also elemental sulfur stabilization energy 190 elemental 596–597

Staleya 34 S7 rings 607

Staleya guttiformis 34 S8 rings 607 standing crop 50 sulfur chain 608 Staphylococcus aureus 661 sulfur compounds 596–616 Stappia marina 34 sulfur cycle 40 Starkeya novella 611, 853 sulfur dehydrogenase 602, 605 Stark spectroscopy 208, 344 sulfur globule proteins 608 STAS domain. See sulfate transporter and antisigma factor sulfur globules 605–609 antagonist domain (STAS) sulfur metabolism 40, 596–616 static disorder 206, 207, 238, 246 Sulfurospirillum 669 stator 477, 644 sulfur oxidation 596, 596–602, 602–612, 616 steady-state spectra 236–237 pathways 602–612 stereo-selectivity sulfur speciation 608 heme sulfurtransferase 605, 606 attachment 413 Index 1011 supercomplex 263, 512, 520, 521, 524–526, 530 tetrathionate hydrolase 599 dimer 525 tetratricopeptide repeat (TPR)-like motif 414 mitochondrial 526, 527 Thalassobacter 34 model 524–526 Thauera 669 superexchange 348, 356 Thauera aromatica 581, 583, 584, 591 superoperon 44, 65, 770 thermal disorder 277, 282–284 superoxide production 673 fi nite temperature quantum theory 282 superradiance 237, 244 thermal springs 39, 51 suppressor mutants 158 Thermochromatium tepidum 3, 6, 8, 10, 12, 19, 356, 380, 384, supramolecular architecture 288, 943, 945 514, 728, 730, 824 supramolecular arrangement 525-527, 891 light-harvesting 1 complex 10 supramolecular assembly 527, 942–951 reaction center structure 387 photosynthetic apparatus 942–951 thermophilic purple bacteria 10 supramolecular complexes 182, 195 Thermosynechococcus elongatus 817, 820 supramolecular organization 254, 257, 258, 267, 268, 278, T110078 820 286, 517, 519–522 Thermotoga maritima 805 photosynthetic unit 286, 288 thermotolerance 149 Rhodobacter capsulatus 519–522 Thermus thermophilus 539 Rhodobacter sphaeroides 519–522 thio-oxidoreduction 407, 410 supramolecular structure 873 Thioalkalicoccus limnaeus 106 Surf1 418 Thioalkalispira 600 assembly protein 545 Thioalkalivibrio 600 surface helix Thiobacillus acidophilus 599 cd1 436 Thiobacillus denitrifi cans 611 cd2 436 Thiobacillus ferrooxidans 566 swimming 644–646 Thiocapsa marina 112 Synechocystis 66, 71, 72, 734, 800, 804, 817, 819, 820, 827, Thiocapsa pfennigii 106 830 Thiocapsa roseopersicina 3, 6, 8, 102, 601, 613, 615, 667, synteny 629 720, 745–749, 751, 753 synthetic chlorophyll protein Thiocapsa roseopersicina BBS 790 screening 901 Thiocapsa roseopersicina strain BBS1 793 solid support synthesis 901 Thiococcus pfennigii 108 synthetic phospholipid 160 Thiocystis 8 Thiocystis gelatinosa 109 T Thiocystis violacea 6, 108 Thiocystis violascens 108 tac promoter 854 thioether bond 408, 410 taxonomic-phylogenetic tangles 37–38 Thiofl avicoccus mobilis 106 tehAB gene pair 665 Thiohalocapsa 10 tellurate 671 thiol:disulfi de oxidoreductase 418, 555, 673 tellurite 671 thiol modifying reagents 71 transport 673 thiol modulation 477 tellurium 671–673 Thiopedia 8 tellurium oxyanions 671 thioredoxin 613 Te resistance determinants 673 thioredoxin reductase 669 tetracycline 842, 844, 849 thioredoxin TrxA 413 tetraheme 258 Thiorhodococcus drewsii 600 tetraheme cytochrome 515, 942, 943 Thiorhodospira 600, 601 tetraheme reaction center subunit 514 Thiorhodospira sibirica 600, 601 7,8,17,18-tetrahydroporphyrin 897. See also chlorin Thiorhodovibrio sibirica 600 tetrahydrospirilloxanthin 106, 108, 110, 112 Thiospirillum 8 3,4,3´,4´ tetrahydrospirilloxanthin 106 Thiospirillum jenense 601 Tetrahymena thermophila 851 thiosulfate 596, 597, 600, 602, 612, 616 tetramethylbenzoquinone 390 thiosulfate:cytochrome c oxidoreductase 599 tetrapyrrole ring thiosulfate dehydrogenase 612 bacteriochlorophyll 42 thiosulfate oxidation 602, 605 tetrapyrrole 82, 339, 700, 778–795, 804 thiouridine biosynthesis 609 tetrapyrrole biosynthesis pathway 777–795 thylakoid membranes 267 regulation 777, 778–795 time-resolved fl uorescence 814 tetrapyrrole planes 431 time-resolved high-frequency ENDOR 963 tetrathionate 597, 599, 612 delay after laser fl ash (DAF) 964 1012 Index time–dependent infrared epifl uorescence microscopy 49 trimethylamine-N-oxide (TMAO) 41, 546 time resolved EPR 955 3-triol 146 Tll0078 818, 820 triplet bacteriochlorophyll 38 TMAO-reductase 547 triplet formation 223 TMAO/Trimethylamine couple 547 triplet state 357 Tmp system 675 Tris 120 toluene 577, 578, 581 trithionate hydrolase 599 topographs 159–164, 256–265, 863–868, 943–950 Triton X-100 162, 182, 298, 869, 926, 928, 929 TorC 548 tRNAglutamate 778 torque 475 trophic pyramid 50 torsional spring constant 485 tryptophan-rich WWD motif 411, 414 torsion angles 144 tryptophan fl uorescence quenching 69 trans-cis isomerization 825 tubular membranes 171, 172, 256, 260, 263, 844 trans-sulfuration 613 tuning position transcription control 747–754 energy transition 205 transcription-translation system 175, 269 tunneling matrix element 361 transcriptional anti-repressor 819 tunneling pathway 326, 327 transcriptional regulation 701–702, 777, 787, 795 twin arginine translocation system 439 transcriptional regulator 800 specifi c signal sequence 439 transcriptional regulator ArcA 754 two-component regulatory protein PrrA 782 transcriptional reporter 747 two-component regulatory system 748–750 transcription factors 707 two-component response regulators 715 transcription terminators 842 two-component signal transduction system 754 transcriptomic analysis 589 two-component system 800 transfer rates two-dimensional electronic spectroscopy 227 cluster-to-cluster 288 two-dimensional nuclear magnetic resonance spectroscopy transhydrogenase 495–506 584 conformational changes 505 two-photon absorption 221 crystal structure 496 two-photon excitation 220 evolution 497 type 1 histidine kinase 805 function 500–501 type II fatty acid synthase 122 hydride transfer 501–503 Type I reaction center 380 mobile loop 504 Type II reaction center 380, 384, 385 phylogenetic tree 498–500 tyrosyl radical 312, 349 polypeptide composition 497 proton translocation 501 U species distribution 496–498 X-ray structure 496, 501 ubihydroquinone:cytochrome c oxidoreductase 425–447 transient absorption 217, 238, 239 ubihydroquinone oxidase 416 transient absorption spectroscopy 804 ubiquinone 44, 193, 258, 338, 383, 385, 387, 389, 392, 394, transition dipoles 206 397, 712, 713, 714, 754 bacteriochlorophyll 168 ubiquinone-binding site 714 transketolase (cbbTII) 566 ubiquinone-ubiquinol exchange See quinone/quinol 256 translocation 407, 409, 410, 412, 414 ubiquinone diffusion 265 transmembrane electro-chemical potential difference 232 ubiquinone pool 712, 713, 714 transmembrane helix 137, 164, 201–202, 412, 513, 916, 918, UDP-sulfoquinovose sulfoquinovosyltransferase 121 922 UDP-sulfoquinovose synthase 121 model 916, 921 UHDBT. See 5-undecyl-6-hydroxy-4,7-dioxobenzothiazole prediction 918 (UHDBT) reaction center 164 ultrafast relaxation 206 transmembrane segments 187 5-undecyl-6-hydroxy-4,7-dioxobenzothiazole (UHDBT) 445 transmembrane voltage 484 unitary proton conductance 482–484 transmembrane α-helices 914 unusual spirilloxanthin pathway 106, 110 transporter upper pigmented band 147, 268 copper 420 uptake hydrogenase hupSLC genes 753 transposon mutagenesis 65, 781 ureDABCEFG 765 transposons 702 uroporphyrinogen III 60, 63, 81, 86, 778, 784, 794 tree of life 19, 456, 457, 459 uroporphyrinogen III decarboxylase 60, 64 tributyltin chloride 478 bovine 64 tricarboxylic acid cycle 83 human 64 triheme reaction center subunits 515 Index 1013 uroporphryinogen III synthase 60, 63 X-ray crystallography 146, 202, 204, 286, 381, 383, 398, 941, crystal structure 64 955 Ustilago maydis 817 X-ray crystal structure 397, 954, 961 X-ray diffraction 963 V X-ray diffraction spectroscopy 954 X-ray structure 383, 390, 391, 805 van der Waals interactions 140 Blastochloris viridis 383, 386 vectorial charge separation 446 Rhodobacter sphaeroides 385, 386 vertebrates 410 Thermochromatium tepidum 387 vestibule for quinones 174 Xanthobacter fl avus 566 vibrational coherence 239, 240 xanthophyll 103 vibrational modes 355, 367–368, 370 xanthopsin 811, 823–827 vibrational relaxation 227, 362, 370 xenobiotic lipid 120 vibrational spectroscopy 389 vibrational wavepackets 355, 362–363 Y Vibrio 702 vinyl-2 408 YcgF 820 vinyl-4 408 yeast 409, 526 3-vinyl bacteriochlorophyllide a 68, 74 yeast extract 6 3-vinyl bacteriochlorophyllide a hydroxylase 67 yfp 649 8-vinyl reductase 67, 72, 73 YidC 269 virulence 820 vise region 441 Z vitamin B12 57, 72, 81–92, 791 biosynthetic pathway 65 ζ-carotene 104 vnfHDK 761 ζ-carotene pathway 104 zeaxanthin diglucoside 110 W zero-phonon 235, 236, 361, 362 zero-phonon line (ZPL) 884 W-helix 166, 167, 169, 172, 513, 530, 948, 949 zinc 393, 396 Walker A and B motifs 411, 748, 749 Zn 419 waste lagoon 9 binding motif 791 water-soluble Chl protein 898, 899 Zn-bacteriochlorophyll. See Zn-bacteriopheophorbide water-soluble heme-binding protein maquettes 900 Zn-bacteriochlorophyll a 112 water-soluble protein maquettes 905 Zn-bacteriopheophorbide 902, 905 White Collar 1 813 Zn-BChl 42, 45, 794 Wolinella 669 Zn-BChl a 303, 873 Wolinella succinogenes 612 Zn-dependent enzymes 791 Zn-substitution 305 X X-ray absorption near-edge structure (XANES) 608