Acetoacetyl-Coa Synthase 220 Acetone 222 Acetone-Butanol-Ethanol

531

Index

a amphibolic reactions 94 acetoacetyl-CoA synthase 220 Anabaena 129 acetone 222 Anabaena PCC7120 211, 245, 246 acetone-butanol-ethanol (ABE) anabolic metabolism 172 fermentation 220 anoxygenic photosynthesis 66, 74, 76 acetyl-CoA 220 anoxyphotobacteria 73 biosynthesis 228 antisense RNA (asRNA) sequence 143 acetyl-CoA carboxylase (ACC) 20, 332 aquaporine-like channels 7 activation energy 409 arresting biomass formation 249 active ATP-binding cassette (ABC) 5 ATP driving force 220, 221 acyl-ACP synthetase (AAS) 335 ATP production, LET vs. CET 37 acyl-carrier protein (ACP) 333 autotrophic fluxome 101 acyl-hormoneserine lactone (AHL) autotrophic strains 493 synthase 145 acyltransferases (ATs) 333 b AdhII activity 240 Bacillus subtilis 217 Agmenellum quadruplicatum strain PR-6 bacterial glycerate pathway 19 457 bacterial micro-compartments 8 alcohol/aldehyde dehydrogenase (AdhE2) balancing photosynthesis, and nitrogen 217 fixation 412 alcohol dehydrogenase, type II 238, 240 β-barrel assembly machinery (BAM) 375 algae-bacteria aggregates 493 batch photobioreactor 448 alkaline pocket 7 beta-carboxysomes 9 alkane biosynthetic enzymes 354 beta-cyanobacteria 9 alk(a/e)ne biosynthesis 353–354 bicarbonate 5 alpha-carboxysomes (Cso-type) 9 affinity 5 alpha cyanobacteria 9 bicarbonate-based integrated carbon alternative respiratory terminal oxidase capture system (BICCS) 256 (ARTO) 40 bicarbonate/Na+ symport 5 alternative terminal oxidase (ARTO) 44 bicarbonate pore protein(s) 5 amino acids, N2-fixing cyanobacteria bicarbonate transporter (BiCA) 5 423, 425 biocatalysis 491 ammonia 422 biochemical photorespiratory cycle 17

bioelectrochemistry 493 Ci assimilation 10 biofertilizer 424 Ci-uptake proteins/mechanisms 5, biofilm cultivations, advantages and 6 disadvantages 488 engineering 16 biofilm investigation methods 495, 496 photorespiration 17, 18 chemical composition 495 definition of 4 process parameters 496 carbon fixation activity enhancement structure and architecture 495, 496 345 biofuel(s) 50 carbon-fixing synthetic photorespiratory biofuel direct production 420 pathway 19 biofuel production 331, 334 carbon flow engineering accumulation of storage lipids 336, deletion of competitive pathways 346, 337 347 biolfilms 479 modification 345, 346

biological N2-fixation (BNF) 411 carbon-free fuel 422 biological PHA production 508 carbonic anhydrases (CA) 4 biomass associated products (BAP) 491 carbon-neutral processes 65 biomass formation 492 carbon starvation 174 biomass objective function (BOF) 96 carboxysomes 8, 9 biomass productivity 513 carotenoids 41 biomass propagation 445 Cas gene 129 BioNitrogen Economy 409 Cas genome 129, 309 bio-photovoltaic cells (BPVs) 493 CD8+ T cells 390 bio-photovoltaic devices (BPVs) 44 cell dry mass (CDW) 318 biophysical CCM 4 cell immobilization 511 biorefinery process 237, 238 cell lysis induction 349, 350 bioremediation process 491 CellNetAnalyzer 96 bioremediation/wastewater treatment cell permeabilization 370 493 cellulosic ethanol 237 blue-green algae 508 central carbon metabolism of 2,3-butanediol (2,3-BD) 187 cyanobacteria production 222 amphibolic reactions 94 n-butanol pathway 130 glycolytic pathways 91, 93 photorespiratory pathway 94 c TCA cycle 94 Calvin–Benson–Bassham cycle (CBB chemical composition, biofilm cycle) 3, 67, 100, 187, 225, 270 investigation methods 495 Calvin cycle 43, 91, 98 chemoautotrophic microorganisms 65 Calvin cycle enzymes 465–466 chemo-catalytic’ approach 65 overexpression of 248 chemoheterotrophs 507 carbohydrate consumption 178 chlorophyll a (Chl a) molecules 176 carbon and light uptake proteins 467 chlorosis 107 carbon assimilation 13 chromosomal expression 127

carbon-carbon bonds 65 Ci assimilation carbon-concentrating mechanism (CCM) carbon assimilation 13 cyanobacteria carbon metabolism 10 carboxysome and RubisCO 8 CmpR transcription factor 11, 12 Index 533

cyAbrB2 transcription factor 11–13 Ci-uptake proteins/mechanisms 5, formate assimilation (FA) 20 6 metabolic changes and regulation 14 engineering 16 NdhR transcription factor 11, 12 photorespiration 17, 18 RcaE-based sensing mechanism 13 definition 3 redox regulation 15 electron transport 34 RubisCO and carboxysome protein cyanobacteria cell factories expression 11 to adapt for selective environmental circadian rhythm 451, 452 stresses 256, 258 Citramalyl-CoA 226 capacity in 251, 253 13C-labeled bicarbonate 101 cyanobacteria classification 443 Claisen condensation 220 cyanobacteria growth model 13C-metabolic flux analysis (13C-MFA) Synechococcus elongatus PCC 11801 96 456 cmp operon 5 Synechococcus elongatus UTEX 2973 CmpR transcription factor 11, 12 455, 456 COBRA 96 Synechococcus sp. PCC 7002 457, 458 cofactor optimization Synechococcus sp. PCC 11901 456, 457 NADH-specific enzymes 217–218 cyanobacteria growth rate 442, 445 NADPH-dependent enzymes 218–219 Calvin cycle enzymes 465–466 recruitment of NADPH enzymes carbon and light uptake proteins 467 215–217 carbon storage 455 Com proteins 125 cell morphology 453 concentrating mechanism (CCM) proteins circadian rhythm 451, 452 255 engineering for fast growth 465–467 conjugation efficiency 125 genome size 453–454 constitutive promoter 136 light intensity and quality 448, 449 constructing synthetic pathways vs. light usage 458 226 metabolic flux analysis 463–465 controlling translation mixotrophic growth 451 riboswitches (cis-acting) 142 nutrient supplementation 454–455 small RNAs (trans-acting) 143 overview 446, 448 conventional heterotrophic microbes PEP carboxylase 466–467 212 photoautotrophy 451 conventional sugar-based bioproductions saltwater tolerance 454 211 Synechococcus elongatus UTEX 2973 CRISPR 129, 229, 309 460–463 CRISPR-interference (CRISPRi) 139, cyanobacterial alcohol productions 223, 229, 249, 356 215 crotonyl-CoA carboxylase 226 cyanobacterial biofilms crRNAs 140 biofilm investigation methods Cupriavidus necator 305 495–496 cyAbrB2 transcription factor 11–13 biology and applications 478–482 cyanobacteria enable continuous production 498 CCM enable high cell densities (HCD) carboxysome and RubisCO 8 497–498 Ci assimilation 10 mass and light transfer 496–497 534 Index

cyanobacterial biofilms (contd.) diazotrophic cyanobacteria 412, 417 microscale systems for (photo-)biofilm in agriculture 425, 428 cultivation 487–489 economic and environmental natural and microbial mats 483–484 considerations of 417, 420 oxygen accumulation 488–491 filamentous heterocystous photo-biotechnology 484–487 cyanobacteria 412 photosynthetic applications 493–494 filamentous non-heterocystous resource management 491–493 cyanobacteria 412 cyanobacterial NDH1-like complex 7 symbiotic cyanobacteria 412 cyanobacteria response unicellular cyanobacteria 412 endogenous synthesized ethanol 255, diazotrophic filamentous cyanobacteria 256 415 exogenous added ethanol 254, 255 dimeric cytochrome 36 cyanobacterium 71 dimethylallyl diphosphate (DMAPP) cyanophycin 313 109 biology 311, 315 dinitrogenase reductase 415 CGP metabolism 314, 315 direct cell contact 44

degrading enzymes 314, 316 direct CO2 conversion 211 metabolism regulation 317, 318 direct conversion 65

N2-fixing cyanobacteria 423 dissolved inorganic carbon (DIC) 486 overproduction and potential industrial diurnal oscillations 106 applications 318 double-stranded DNA (dsDNA) 123 synthetase 315, 316 dynamic control 153 cyanophycin granule peptide (CGP) 311 cyclic diguanosine-5′-monophosphate e (c-di-GMP) 480 electrogenic electron transfers 68 cyclic electron transfer 68 electron transport cyclic electron transport (CET) 35, 37, bioenergetic membrane 105 cyclic electron transport 35–37 Cyd/COX/Flv3 mutants 43 linear electron transport 34–35 cytochrome bd-quinol oxidase (Cyd) 40 challenges 51

cytochrome c6 (cyt c6)36 electron flux cytochrome-c oxidase complex (COX) 40 ferredoxin (Fdx) 46 cytochrome P450s (P450s) 50, 191 plastoquinone pool 45

cytochromes cM (originally cytM) 51 photoprotective electron sinks carbon fixation 43 d extracellular electron export 42, 44 dark fermentative bacteria 508 flavodiiron (Flv) proteins 42 dCasprotein 140 hydrogenase complex (HOX) 41 decarboxylation 228 photorespiratory pathway 43 degradation tag 134 terminal oxidases 41 D260E mutation 462 respiratory 38, 39 dendritic cells 390 spatial organisation 47 1-deoxy-D-xylulose 5-phosphate (DXP) synthetic biology applications 111 BPV devices 49 diacylglycerol acyltransferase (DAGAT) hydrogen production 50 337 industrial compounds 50 Index 535

photosynthetic energy conversion f 49 FA biosynthesis 334 electron transport chain (ETC) 174, FAEE synthesis 154 251 Farbstreifensandwad 73 electroporation of DNA 125 FA synthase (FAS) 332, 335 Elementary Metabolite Unit (EMU) 97 overexpression of 339 Embden-Meyerhof-Parnas (EMP) fatty acid alkyl esters (FAAEs) 331, 356, pathway 91 357 enable high cell densities (HCD) 497, fatty acid biosynthesis 332, 335 498 carbon fixation activity enhancement endogenous competing pathways 222 345 engineering cofactor supply 249, 250 carbon flow engineering 345 Entner-Doudoroff (ED) pathway 91 deletion of competitive pathways enzyme perturbation 100, 101 346–347 episomal plasmid expression 125 modification 346 Escherichia coli 130 cell lysis induction 349–350 ethanol 224, 238 enhancement 339–345 ethanol production FFAs Anabaena PCC7120 245–246 production 350–351 arresting biomass formation 249 recovery 350 blocking pathways 248–249 secretion enhancement 348–349 capacity in cyanobacterial cell factories toxicity 347–348 251–253 fatty acid degradation and turnover 335 engineering cofactor supply 249–250 fatty acid ethyl esters (FAEEs) 356 non-conventional cyanobacteria species fatty acid(s), membrane-embedded 246 systems 381, 382 overexpression of Calvin cycle enzymes fatty acid methyl esters (FAMEs) 356 248 fatty acid(s) (FAs)-secreting strains 332 in silico simulation 250–251 fatty acyl-CoA reductase (FAR) 355 Synechococcus PCC6803 243–244 fatty alcohols 355 Synechococcus PCC7002 245 production enhancement 355, Synechococcus PCC7942 243–244 356 ethanol synthesis fermentable substrate 420, 422 Pdc-AdhII pathway 240–241 fermentation effluent 508 PdcZM-Slr1192 pathway 241–242 ferredoxin (Fdx) 36, 46 pyruvate decarboxylase 238–240 ferredoxin-NADP+ reductase (FNR) 37 type II alcohol dehydrogenase ferricyanide assays 44 238–240 fixed carbon 107, 173 ethylene-forming enzyme (EFE) 108, flavodiiron (Flv) proteins 42 423 flavodoxin (Fld) 36 ethylmalonyl-CoA 226 FluxAnalyzer 96 eukaryotic algae biomass 237 flux balance analysis (FBA) 95, 250 explosive outer membrane vesicles flux control coefficient 242 (EOMVs) 388 fluxomic analysis 99 extracellular electron export 42, 44 FNR protein 144 extracellular polymeric substances (EPS) food ethanol 237 377, 379, 477, 478 formate dehydrogenase (FDH) 20 536 Index

free fatty acids (FFAs) glycogen granule formation 417 from ACP 333 glycogen metabolism 248 in cyanobacteria 338, 339 glycolate dehydrogenase(s) (GDH) 17 E. coli 337, 338 glycolate oxidase (GOX) 17 recovery 350 2-glycolate production 44 secretion enhancement 348, 349 glycolytic pathways 92 toxicity 347, 348 glyoxylate 19 Fremyella diplosiphon 13 glyoxylate assimilation pathway 228 fructose/sedoheptulose bisphosphatase glyoxylate shunt 94 (FBP/SBPase) 100 gram-negative bacteria 372, 382, 386, 391, 508 g gram-positive bacterium 376 galactitol transport and catabolism (GatY) green cell factories 16

383 guanidine, N2-fixing cyanobacteria 423 γ-aminobutyric acid (GABA) shunt 94 GAP dehydrogenase I (GAPDH I) 106 h GAPDH 15 Haber–Bosch process 409, 410, 417, gaseous/aqueous extraction 224 420 genetic instability 252 hemiterpenes 272 genome-scale metabolic network heterologous hydrogenase 50 reconstructions (GENREs) heterotrophic fluxome 105 curation and refinement 96 heterotrophs 219 draft network, reconstruction of 95 hexadecameric RubisCO molecules 9 mathematical model conversion 96 hexokinases (HXKs) 179

model evaluation and validation 96 high CO2-requiring (HCR) phenotype 8 genome scale modeling (GSM) 464 Hill-function dependence of transcription genome scale reconstruction 95 rate 132 Geobacter sulfurreducens 45 homoalcoholic fermentation 240 global energy conversion 66 homologous recombination 128 Gloeothece system 146 hosphoenolpyruvate (PEP) 228 glucose 332, 451 human activity 66 glucose-facilitated diffusion (GLF) protein hybrid gluconeogenesis-pentose 379 phosphate (hGPP) pathway glucose/fructose toxicity 193 107 glucose-6-phosphate dehydrogenase hydrocarbon production (G6PDH) 250 alkane biosynthetic enzymes 354 glutamate:glyoxylate aminotransferase alk(a/e)ne biosynthesis 353, 354 (GGT) 17 in cyanobacteria 351, 353 glutathione peroxidase 41 hydrogenase complex (HOX) 41 glyceraldehyde 3-phosphate (GAP) 91 hydrogen gas 50 glyceraldehyde 3-phosphate 4-hydroxybutyrate cycles 226 dehydrogenases 14 3-hydroxybutyrate (3HB) production glycerate 2-kinase (GK) 19 220 glycerate 3-kinase (GLYK) 17, 19 3-hydroxybutyryl-CoA dehydrogenase glycerol 331 (Hbd) 215 glycine decarboxylase (GDC) 17 3-hydroxypropionate (3-HP) cycle 19, glycogen chains 422 226 Index 537 hydroxypyruvate reductase (HPR) 17 lipopolysaccharides (LPSs) 373 hypoxia-inducible factor (HIF1α ) activity liquid/liquid extraction 225 181 logic gates and timing circuits 148, 149 LuxR-LuxI system 145 i indirect biophotolysis process 516 m inner membrane (IM) 373 malonyl-CoA 220, 332 inorganic wastes 511 malyl-CoA-glycerate pathway (MCG insulator sequence 141 pathway) 20, 228 intestinal fatty acid binding protein mass isotopomer distribution vector (IFABP) 376 (MDV) 96 intracellular NADPH concentration 218 mats lithification 484 IPP isomerase (IDI) 110 membrane-embedded systems isobutanol 188, 189 alcohols 382–384 isobutyraldehyde 224 extracellular polymeric substances isopentenyl diphosphate (IPP) 109 377–379 isoprene 189 fatty acids 381–382 isoprenoid pathway proteins 373–376 IPP and DMAPP 110–111 soluble sugars and organic acids KFP 111 379–381 isotope labeling 451 terpenes 384–386 isotopically non-stationary metabolic flux membrane vesicle-mediated secretion analysis (INST-MFA) 463 cyanobacterial 388–389 novel biotechnological tools 389–391 j structure and biogenesis 386–388 Jacobian matrix 100 MenG 45 metabolic control analysis 242 k metabolic engineering 238 2-keto-3-deoxy-6-phosphogluconate carbon conserving photorespiration (KDPG) 91 225, 227, 228 α-ketoglutarate 46 cofactor optimization kill switch 154 NADH pool kinetic flux profiling (KFP) 111 transhydrogenase 218 NADH-specific enzymes 215 l NADPH-dependent enzymes 217 lactate 217 recruitment of NADPH enzymes lactate dehydrogenase (LDH) 217 215, 216

Lactobacillus bulgaricus 218 CO2 reutilization and mitigation 229 LED-driven photobioreactor 82 design principles 212, 213 light-driven formate production system enhanced carbon fixation 225, 227, 20 228 light fluctuations 449 enhancing precursor supply 288, 289 light harvesting complex (LHC) 467 increasing supply of terpene 285, 286 limonene 189, 190 MEP pathway 286, 287 linear electron transfer 68–70 MVA pathway 287, 288 linear electron transport (LET) 34, 35, of N2-fixing cyanobacteria 420, 422, 37 428 538 Index

metabolic engineering (contd.) multicellular cyanobacteria 312 optimizing production growth multi-omics data 229 conditions 289, 291 multiple antibiotic resistance (MarC) polyhydroxybutryate 308, 310 383 product capture and harvesting 291, 292 n selective environmental stresses 256, N-acetylglutamate kinase (NAGK) 317 258 natural transformation 128 in silico simulation 250 NDH1-4 (NDH1-MS) complexes 7 terpene synthases 277, 285 Ndh1-MS complex 7 thermodynamic driving force NdhR transcription factor 11, 12

ATP driving force 220, 221 N2-fixing cyanobacteria carbon flux 222 amino acids and proteins 423, 425 product removal unblocks 223 ammonia 422, 423 metabolic flux analysis (MFA) 463–465 balancing photosynthesis 412 autotrophic fluxome 101 biofuel direct production 420 biomanufacturing purposes continuous-light versus dark-light isoprenoid pathway 109 cycles impacts 416, 417 13C-MFA 96 cyanophycin 423 diurnal metabolite oscillations 106 ecological range 411, 412 FBA 95 energetic demands 412, 416 genome scale reconstruction 95 fermentable substrate 420, 422 heterotrophic fluxome 105 guanidine 423 kinetic constraints 100 nicotinamide adenine dinucleotide nitrogen deprivation 107 (NADH) 239 photoheterotrophic growth 105 nicotinamide adenine dinucleotide photomixotrophic fluxes 104 phosphate (NADPH) 239 thermodynamics analysis 99, NifDK 415 100 nitrate transporter-less mutant 349 metal uptake regulons in cyanobacteria nitrogenase 412 139 complex 415 method of minimization of metabolic enzyme 409 adjustment (MOMA) 250 oxygen-sensitivity 427 5,10-methylene-THF 20 protection 415 methylerythritol 2,4-cyclodiphosphate nitrogen deprivation 107 (MEcPP) 111 nitrogen-fertilizer production 417 methylerythritol phosphate (MEP) N-octanoyl-homoserine lactone 146 pathway 109, 110, 270 non-conventional cyanobacteria species engineering 286, 287 246 mevalonate (MVA) pathway 109 non-diazotrophic algae 417 implementation 287, 288 non-diazotrophic cyanobacteria 314 Michaelis-Menten Kinetics 99 non-oxygenic’ photosynthesis 66 microalgae 331, 494 non-photochemical quenching (NPQ) microbial fuel cells (MFCs) 493 175 microgradients 479 non-stable carboxylation product 3 microreactors 490 Nostoc (Anabaena) sp. PCC7120 mixed-trophies biofilms 494 heterocysts 20 Index 539 o 2PG-phosphatase (PGLP) 17 omics-level analysis 254 phenazines 44 OM proteins (OMPs) 375 phosphite 258 open-loop regulation 154 phosphoenolpyruvate carboxylase (PEPC) organic wastes 508, 511 20 oriV (RK2) origin 126 phosphofructokinase 17 orthogonal transcription systems 151 6-phosphogluconate dehydrogenase outer-inner membrane vesicles (OIMVs) (6PGDH) 250 388 phosphoglucose isomerase reaction 106 outer membrane (OM) 373 3-phosphoglycerate (3PGA) 3, 44 outer membrane protein (OMP) 381 phosphoglycerate mutase (PGM) 14, 19 outer membrane vesicles (OMVs) 386 2-phosphoglycolate (2PG) 3 β-oxidation pathway 335 phosphoketolase 222 oxidative pentose phosphate (OPP) pathway 91 pathway 91, 103 photoautotroph(s) 219, 507 oxidoreductases 217 cyanobacteria 101 2-oxoglutarate (2OG) 12 growth 455, 487 2-oxoglutarate decarboxylase (OGDC) microorganisms 65, 486 shunt 94 photo-biological hydrogen production oxygen accumulation 488 506, 508 oxygenase reaction 5 photobioreactor 65, 79, 410, 505, 509, oxygenic photogranule (OPG) 494 534 oxygenic photosynthesis 67 photo-biotechnology 484, 487 molecular basis and efficiency of photodamage 175 anoxygenic-and retinal-based photofermentation 485, 507, 515 phototrophy 71 photoheterotrophic fluxome 105 chlorophyll molecule 68 photoheterotrophs 507 cyclic electron transfer 68 photoinhibition 509 electron transfer 68 photomixotrophic fluxes 104 inherent free energy losses 70 photoprotection 175 light absorption 67 photoprotective electron sinks linear electron transfer 68–70 carbon fixation 43 protein complexes 67 extracellular electron export 42, 44 PAR 74–79 flavodiiron (Flv) proteins 42 photobioreactor HOX 41 LED 81 photorespiratory pathway 43 transparency of 79 terminal oxidases 41 solar radiation 72 photoprotective mechanisms 191 oxygen-insensitive 19 photorespiration 4, 464, 496 oxyphototrophic organisms 66 cyanobacterial 17 engineer 19 p 3-HP cycle 19 Pdc-AdhII pathway 240, 241 photorespiratory pathway 94 PdcZM-Slr1192 pathway 241, 242 photosynthesis PEP carboxylase (PPC) 466–467 applications 493, 494 periplasmic bicarbonate-binding protein biofilms 494 5 complex 34 540 Index

photosynthesis (contd.) polyploid 127 energy conversion 49 P450 oxidoreductase (POR) 50 microorganisms 506, 508, 509, 513, product capture and harvesting 291, 518 292 organisms 175 product export, substrate uptake and parameters via 370 fluorimetry/spectroscopy 175 prokaryotic algae biomass 237 production 505 protease tag 134 water splitting 491 protein engineering 372 photosynthetically active radiation (PAR) proteomics 288 74–79, 486 proteo-or bacterial rhodopsin 76

photosynthetic H2 production 507 proteorhodopsin molecules 77 photosynthetic microbial cell factories proton motive force (PMF) 66 (PMCFs) 484 prototyping 242 photosystem I (PSI) 36 pSYSA 127 photosystem II (PSII) 34, 75 pulse-amplitude modulated fluorometry phototrophic biofilms 496 175 phototrophic cultivation 487 purple non-sulfur bacteria (PNSB) 505, photovoltaic cells 65 507 phycobilisome 34, 71 purple photo-fermentative bacteria 508 phylloquinol (vitamin K1) biosynthesis pyruvate decarboxylase 238, 240 44 pyruvate:Fdx reductase (PFOR) 46 picoplanktonic cyanobacteria 8, 9 pyruvate kinase (PK) 463 PII-paralog SbtB 13, 14 plant-type asparaginase 316 q plastid terminal oxidase (PTOX) 40, 175 quinones 44 plastocyanin (Pc) 36 quorum sensing (QS) 147, 480 plastoquinol (PQH2) 36 quorum sensing circuits 146 plastoquinone (PQ) 36 polyhydroxyalkanoate production 508, r 509 random-design approaches 372 polyhydroxyalkanoates (PHA) 211 rational-design approaches 372 poly-hydroxyalkanoic acids (PHA) 336 reactive oxygen species (ROSs) 41 polyhydroxybutryate (PHB) 301, 509 recombinant protein secretion 376 biodegradability 306 regulatory on/off minimization (ROOM) cyanobacteria metabolism 302, 304 250 downstream processing 308 repeats-in-toxin (RTX) 376 industrial production of 305, 306 respiratory complexes 34 limitations and potential 310, 311 respiratory electron transport 38, 39 metabolic engineering 308, 310 retinal-based photosynthesis 66, 67, 71, physical properties 305, 306 73, 76, 79 plastic application 306 retinal-based phototrophy 71 production process 307, 308 retinal photosynthesis 76 reactor types 306, 307 rhamnose inducer 132, 136 synthesis 249 ribosome binding site (RBS) 133 transcription factor 309 riboswitches (cis-acting) 130, 142 poly-3-hydroxybutyrate (PHB) 223 ribulose 1,5-bisphosphate (RuBP) 3 Index 541 ribulose-1,5-bisphosphate carboxylase/ state transition 174 oxygenase (RubisCO) 3, 8, 9, structure-guided transporter 372 171, 226, 228 subcellular localization 179 RNA-IN 143 succinate dehydrogenase (SDH) 39 RNA-OUT 143 succinic semialdehyde (SSA) 94 RNA polymerase from T7 bacteriophage succinic semialdehyde dehydrogenase (T7-RNAP) 151 94 RNA polymerase (RNAP) molecules 130 sucrose 178, 183 Rossmann fold 217 sucrose non-fermenting-1 (SNF1) 180 R121Q and K134E 462 sucrose-non-fermenting-related kinases RSF1010 origin 126 (SnRKs) 179, 180 RuBisCO (RBC) pathway 101 sugar-sensing circuits 137 sulfate-reducing bacteria (SRBs) 484 s sunlight-driven conversion of C2 65 sacB gene 126 superoxide dismutase 41 Saccharomyces cerevisiae 219, 331 swapping cofactor 217 secretion (Sec) pathway 48, 373, 375 Synechococcus elongatus, 127 sedoheptulose 1,7-bisphosphate stepwise conversion of 462 phosphatase 4, 17 Synechococcus elongatus PCC 7942 211 serine/alanine:glyoxylate Synechococcus elongatus PCC 11801 456 aminotransferase (SGT) 17 Synechococcus elongatus 2973 strains serine hydroxymethyltransferase (SHMT) 460, 460 17 Synechococcus elongatus 7942 strains shuttle plasmid 124 460, 460 Signal Recognition Particle (SRP) pathway Synechococcus elongatus UTEX 2973 48 211, 455, 456, 460, 462 sink effects 190 Synechococcus PCC6803 243, 244 small RNAs (sRNA) 143, 480 Synechococcus PCC7942 243, 244 sodium-dependent bicarbonate Synechococcus sp. PCC 7002 211, 245, transporter SbtA 5 457, 458 sodium dodecyl sulphate (SDS) 382 Synechococcus sp. PCC 11901 456, soluble microbial products (SMPs) 491 457 soluble sugars, and organic acids 379, Synechocystis 7 381 cells 14 source/sink pmgA mutant 458–460 carbon starvation 174 SbtB (slr1513) 13 definition of 172 Synechocystis PCC 6803 101–103, 106, metabolites 175 211 in photosynthetic microbes 191 synthetic biology 238 plant growth chromosomal expression 127 HXKs 179 definition 123 SnRK1 180 episomal plasmid expression 125 sucrose and signaling carbohydrates exotic signals for controlling expression 178 cell density or growth phase 145 TOR kinase 181 engineering regulators 147 in plants 173, 174 light color 144 source tissues 172 oxygen 144 542 Index

synthetic biology (contd.) terpene formation 272, 274 gene expression in cyanobacteria tetrahydrofolate (THF) 20 constitutive promoter 136 Thermosynechococcus elongatus 7 controlling translation 141 thin layer chromatography (TLC) 336 CRISPR interference 139 thioredoxin (TRX) 15 regulated promoters 137, 138 thylakoid lumen 34 transcription and translation 130, thylakoid membrane 7, 34 135, 136 titration assays 241 logic gates and timing circuits 148, α-tocopherol (Vitamin E) 45 149 tocopherols 41 orthogonal transcription systems 151 transcriptomics 288 reviews 123, 124 transhydrogenase 218 solutions for cell separation and transporter protein 372 product recovery 154 trehalose-6-phosphate (T6P) 178 solutions to increase stability 152, 153 triacylglycerols (TAGs) 331 transformation 123 tricarboxylic acid (TCA) cycle 94 triosephosphate isomerase 4, 17 t tube-shaped membranous structures target of rapamycin (TOR) kinase 179 (TSMSs) 388 2,3-butanediol (2,3-BD) 187 tubular photobioreactors 487 definition of 181 tubular undulating row PBRs (TURPs) ethylene 187 516 glucose-modulated master regulators turn-over number (TON) 478 182 twin-arginine (Tat) pathway 374, 375 glycerol 188 Twin-Arginine Translocation (Tat) isobutanol 188, 189 pathways 48 isoprene 189 Type-I FAS 333 limonene 189, 190 Type-II FAS 333 mechanisms of 181 type I secretion system (T1SS) 376 photosynthetic microbes 182, 186 type II secretion system (T2SS) 375 P450s 191 sucrose 183 u terminal oxidases 41 uncoupling PHB synthesis 310 terpene(s) 51 unicellular photosynthetic cells 453 formation 272, 274 up-conversion process 80 membrane-embedded systems 384, utilization associated products (UAPs) 386 491 physiological roles of 274, 275 terpene synthases w increasing supply of 285, 286 wasteful process 17 metabolic engineering 277, 285 terpenoid(s) y and industrial applications 267, 270 Y252C mutation 461 physiological roles 274, 275 YqhD 215 production 275, 277 terpenoid biosynthesis z MEP pathway 270 Zymomonas mobilis 215