891

Index a adaptive laboratory evolution (ALE) acetaldehyde production, in 50, 285, 343, 384, 493, 499, Streptococcus thermophilus 534, 555, 566, 567–570, 694 574–575 adenosine triphosphate (ATP) 31, 102, acetate 472 140, 147–148, 180, 188, 191, acetate-to-acetyl-CoA process 750 194, 196, 213, 224, 284, 354, production 749 355, 362, 424, 427, 434, 477, acetoin 196, 432, 472, 492, 495, 558, 487, 495–496, 522, 524, 575–578 528–529, 532, 555, 558, 585, acetolactate synthase (ALS) 196, 354, 631, 693, 701, 704–705, 714, 697, 706 740, 742, 744–746, 748–751, acetone–butanol–ethanol (ABE) 775–777, 808–809 metabolic route 611, 613 α-ketoglutarate (αKG) production 363, butanol production 698 420, 427, 703, 736, 738, acetyl-CoA 14–15, 738 740–744, 750 cytoplasmic acetyl-CoA 713 alanine 117, 374, 416, 574 cytosolic acetyl-CoA 746, 750, 753, alanine (ALA ) 117 754 2-3 alarmones guanosine tetra- and AcidifyME model 48 penta-phosphate 471 actinomycetes CRISPR-based genome editing alcohol dehydrogenase (ADH) 283, techniques 663–665 343, 354, 356, 359–360, 363, generalized systems metabolic 432, 576–577, 583–585, 613, engineering workflow for 692–693, 695, 697–698, 672 700–702, 704 genome editing of 663 algae biomass 829 actinomycetes synthetic biology algal biomass 415 biological parts of 665, 667–669 alkaloids 367, 368, 370, 713, 775, 812, biosensors 669–670 817, 820, 824–825 full pathway refactoring 671 production, in S. cerevisiae riboswitches 670–671 710–712 activity-independent screening of target alkane biosynthetic pathway 702 molecule synthesis 492–493 alleleome 33–34 acyl carrier (ACPs) 354–356, Allelic Coupled Exchange (ACE) 370, 377, 699–702 couples 618, 703

Metabolic Engineering: Concepts and Applications, First Edition. Edited by Sang Yup Lee, Jens Nielsen, and Gregory Stephanopoulos. © 2021 WILEY-VCH GmbH. Published 2021 by WILEY-VCH GmbH. 892 Index

amino acids arabinose 408, 413–415, 420, 432, 523, aminovalerate 421–423 571–572, 495, 697 L-arginine 364 arabinoxylans 412, 415, 816 auxotrophic markers 745 L-arginine 364, 403, 405, 419 cell factory 403 aromatic amino acids 824 ectoine 425–426 bacterial production of 200–202 L-glutamate 419–420 bisynthesis, in S. cerevisiae 708 4-HIL production 427 synthesis 824 L-lysine 420–421 aromatic compounds L-pipecolic acid 426 mandelic acid 366 L-theanine 427 methyl anthranilate 366 L-threonine 364 S-styrene oxide 366, 367 trans-4-hydroxyproline 426–427 L-tyrosine 365, 366 L-valine 365 artemisinic acid production 369, 713, ω-amino acids 715 4ABA 357 Aspart 720 5AVA 357–359 Aspartate transcarbamylase (ATCase) 4-aminobutyric acid (4ABA) 357, 363 188 6-aminocaproic acid 357, 359, 363 Aspergillus niger 765, 766, 776, 785, aminovalerate 359, 421, 422, 430–431 789 5-aminovaleric acid (5AVA) 357, 359, set for plant polysaccharide 361, 362, 423 degradation 773 anaerobic reporter 631 genom-scale metabolic models anaplerosis 74, 101 770 anaplerotic glyoxylate pathway 472 glucoamylase 777 anhydrotetracycline (aTc)-inducible hyperbranching strain 786 systems 627 metabolic and regulatory functions anoxic P. putida chassis 531 771 anthocyanin 588, 709, 818–820, X-ray microcomputed tomography 834–835 (μCT) 788 antimicrobial activity (AA), of Aspergillus oryzae 766, 778 bacteriocins 557, 582 enzyme set for plant polysaccharide anti-CRISPR proteins 620 degradation 773 resistance 302, 479, Aspergillus terreus 430, 767, 779–780 615, 868–869, 878 asRNA knockdown method 625 302, 313, 317, 365–366, atmospheric pressure chemical 406, 496, 561, 581, 583, 653, ionization (APCI) 269 665–666, 673–676, 769, atom enumeration scheme 103–104 780–781, 788–789, 865 atom transition network 91, 92, 94–95, Antirrhinum majus 819 104 antiSMASH 658–660 atom transition network specification approximative rate expression 103 159–160 atom transitions 91–92, 97, 99, aquatic cyanobacteria 806 103–104 Arabidopsis thaliana 180, 356, 588, auto-scaling 275 632, 710, 806, 815 azadirachtin 817 Index 893 b bioethanol production Bacillus amyloliquefaciens strains 472, first-generation 691–694 493 second generation 694–697 Bacillus subtilis 469 bioluminescent reporters 631 B. subtilis ATCC6051a 482 biomass effluxes 102–103 B. subtilis BSK814 475 bioproducer strains 238 B. subtilis MGB469 475 bioproduction 243, 253–254, 285, 408, B. subtilis MGB874 475 415, 519, 530–531, 535, 780, CRISPR/Cas and related strains 810–811, 817, 829–830, 873 481–486 bioremediation 875 genome reduction projects challenges 859 473–476 chemical emissions and parameters Bacillus licheniformis 470 862, 867 B. licheniformis 2709 482 definition 859 isocitrate (aceB) 472 transition from 2.0 to 3.0 862 Bacillus thuringiensis cry3Bb bioremediation 3.0 862–865, 867–869 829 bioremediation 4.0 879–880 Bacillus BioBrick Box 490 bioremediation agent 521, 861, 862, Bacillus origin of replication (ori) 481 865, 870, 872, 878–879 bacitracin 486, 494, 496–497 P. putida 873 42.7 kb bacitracin synthase gene biosensors 13, 16, 383, 493, 525, 669, cluster bacABC 486 670, 865 backslopping process 566 biostimulation 861–862 bacterial 3-dehydroshikimate biosustainable industrial production 816 platforms 806–808 bacterial cellulose 379–380 biosynthetic gene clusters (BGCs) 655, bacteriocins production, in LAB 581 657 bacteriophage infections 565 cloning and heterologous expression basic helix-loop-helix (bHLH) 660–663 transcription factor 818–819 batch cultures 109, 111, 112, 356, 530 genome mining 657–660 benzylisoquinoline alkaloids (BIAs) promoter engineering 667 370, 710–712 reporter-guided mutant selection bioactive natural products 653, 804 (RGMS) 670 biosynthetic pathways 655, 667, 668 biosynthetic pathways tools and strategies for discovery of natural products 655, 657 653–655 search for 251 bioaugmentation 861–862 block elasticities 186 biochemical databases 238, 240, 244, blood proteins 721 251 B. methanolicus MGA3 482, 489 biochemical network 166, 240, bondomers 121 242–243, 249 bottromycin biosynthetic pathway biochemical search space 238, 240 667 Biochemical Systems Theory (BST) branched chain amino acids (BCAA) 173, 175 359, 365, 496, 552 biocondensates 803, 833–835 branched-chain alcohols 354 bioenergetics 213–214 BsubCyc 470 894 Index

butanediol (BDO)-isomers 577 chalcone (CHI) 369, 417, 1,4-butanediol 57, 249, 363 418, 708, 709 2,3-butanediol 472, 494, 706 chalcone synthase (CHS) 369, 417, butanol 343, 697 418, 708, 709 production of 343, 588, 611–613, chassis development 861 698–699 chassis for bioremediation 873 butyrolactam 357, 363 chassis metabolic model 246 chemical ionization (CI) 269 c Chinese Hamster Ovary (CHO) 166, cadaverine 359, 361–362, 423 188, 317–320 camalexin 833 ChIPseq 61 cannabidiolic acid synthase 837 Chlamydomonas reinhardtii 806, 830 Cannabis sativa 834, 837 acetyltransferase cannibalism 374, 471, 478 (CAT) reporter 630 capillary electrophoresis (CE) 267 chlorophyll 822, 825–826, 828, 829 capitate-stalked trichome 834, 837 chloroplast stroma-localized ferredoxin caprolactam 363, 533 (AtFedA) 825 Carbohydrate-Active enzyme database chloroplast thylakoid 809, 826 (CAZy) 773 chloroplasts 805, 806, 810, 821–830, carbon atom transitions 91–92 834–835, 837 carbon catabolite repressor 496 -less bacteria (SimCells) β-carotene production 758, 759, 820 860 carotenoids 433, 524, 713, 718, 758, cinnamic acid 367, 707, 708, 819 817, 820, 826, 828–830 circular gRNA-containing plasmids Cas- 308, 310, 312, 316, 320 311 Cas12a (Cpf1) enzyme 312, 663 cis,cis-muconate 428, 429 Cas9 nickase (Cas9n) systems 482, 620 cis-cis-muconic acid 417 Cas9-Assisted Targeting of in P. putida 533, 534 CHromosome segments (CATCH) 662 citrate production 739, 745–746 Cas9-mediated mutagenesis 564 Y. lipolytica 738 Caulobacter crescentus 379, 413, 473 citrate synthase CitZ 496 CAZyme gene expression, molecular citric acid production 765, 780, 788 mechanism of 773 in A. niger 776 13 cell type specific metabolic engineering C-labeled 77 815 Class II and Class I diterpenoid cell-free in vitro transcription systems synthases 822 865 cloning, of BGCs 661 cell-free agents 860 Clostridium cellular compartments 103, 282, 718, 5′-UTRs & Riboswitches 634 834 genetic parts 626–627 cellular constraints 137–139 promoters 627–630 cellulase Egl-237 477 reporters 630 CeluStar CL 783 enzymatic-based reporters central carbon intermediates 112 630–631 13CFLUX2 117 bioluminescent reporters 631 13 C1 glucose 106 fluorescent reporters 631–632 Index 895

FbFP-based fluorescent reporters combinatorial supertransformation of 632–633 transplastomic recipient lines FAST, HaloTag, and SNAP-tag (COSTREL) 828–829 fluorescent reporters 633 computational pathway design 238, genome editing 614–615 239, 252, 253 ClosTron system 615 computer–aided simulation 172 counter-selection markers concentration control coefficient 617–619 179–180, 185, 188 CRISPR systems 619–626 confidence intervals (CoI) 89–90, 229 transposon-based random conjugative transposons 615 mutagenesis 615–617 connectivity matrix 31 terminators 633–634 conserved metabolites 186 ClosTron systems 615 constrained optimization 26 cloud microbiology 879 COnstraint-Based Reconstruction and Clustered Regularly Interspaced Short Analysis (COBRA) method Palindromic Repeats (CRISPR) 26–28, 30, 41, 51, 62, 240 304, 308, 309, 619, 625 continuous culture 77, 83, 110–113, associated (Cas) genes 308 174 COPI vesicles 719–720 based metabolic engineering, in T. COPII cargo proteins 720 thermophilus 783 core phenylpropanoid biosynthesis mediated gene manipulation systems, 819 for filamentous actinomycetes CoReCo metabolic model 664 reconstruction algorithm technology, for C. glutamicum 770 407 Corynebacterium glutamicum 191, 13C metabolic flux analysis 76, 98, 162, 194, 403, 437, 473 404, 406, 413, 415, 420, aquatic sugars 415–416 739–740, 748 amino acids 419–427 2-C-methyl-D-erythritol-4-phosphate biopolymers 434–436 pathway 496 CRISPR technology 407 codBA system 479 genome editing approaches 406 CO2 fixation 15, 535, 783, 806, 811, hemicellulosic biomass 408, 409, 830 412 coarse grained thermodynamic industrial production 419 information 31 natural products and active coarse-grained integration of proteome ingredients 433 constraints 139–144 industrial raw materials 407–408 cobalamin () production lignin aromatics, valorization of 578, 579 416–419 coclaurine N-methyltransferase lignocellulosic sugars 408–415 (CNMT) 370 L-lysine production 404 Coleus forskohlii 823, 834 marker-free genome editing 407 combinatorial biosynthesis 662, 667, metabolome analysis 405 670 organic acids and alcohols 427 combinatorial metabolic engineering cis-cis muconate 428–429 9, 12–14 3-hydroxypropionate 430–432 896 Index

Corynebacterium glutamicum (contd.) cross–over theorem 179 glutarate production 429–430 cucurbitacin synthesis 4 itaconate 430 cumomers 121 short-chain alcohols 432 cutin 813 plasmid-based expression 406 cyanobacteria 356, 805–806, 808, 811, systems biology 404 822, 825–826, 829–831, 873 systems metabolic engineering 404 cyanogenic glucosides 817–818, 820, Cosmid/fosmid library vectors 662 824, 832–833 coumarins 817 cyanophycin 380–381 biosynthesis 706, 708, 817 cyborgization of bacterial strains 863 p-coumaroyl-CoA 707, 816 cyclodepsipeptides (CDPs) 784–785 counter-selection and markerless cytochrome P450 (CYP) enzymes 369, genome editing 478–481 701, 707–708, 710, 714, 812, counter-selection markers 616, 816, 826 617–619 cytochrome P450 2 coupling constraints 144–145, 816 147–150 cytoplasmic acetyl-CoA 713, 716 Crabtree effect 141, 142, 150 cytosolic acetyl-CoA 705, 717, 736, 14C radioisotope 80 746–747, 750, 756, 757 Cre/loxP system 315, 479, 561 availability 698, 753–754 CRISPR-BEST system 665, 666 CRISPR-Cas-technology 304, 313 d -based genome editing 314 data analysis, in metabolomics in B. subtilis and related strains multivariate statistics 278 481–486 pathway analysis 278–279 LAB genome editing 563–565 univariate statistics 277–278 CRISPR-Cas9 untargeted MS data processing and Cas12a-based genome editing 273–277 methods 663 data dependent acquisition (DDA) 272 based approach 873 data-independent acquisition (DIA) based genome editing 481, 489 272 CRISPR-dCas9 Daucus carota 818 mediated base editing 488–489 DcMYB6 818 mediated cytosine deaminase base Del/Ros1 transgenic plant 819 editing system 489 Δ9 stearoyl-CoA desaturase (D9) 746, mediated deaminase base editing 747 489 de novo triacylglycerols biosynthesis CRISPR interference (CRISPRi) 745–746 487–490, 497, 564–565, dead’ Cas9 (dCas9) 309 625–626 Debye–Hückel approximation 216, CRISPR interference and activation 221–223 (CRISPRi/a) 487, 489 deep alleleome 34 CRISPR/PmanPA-Cas9 vectors 486 2-dehydro-3-deoxy-phosphogluconate CRISPR RNAs (crRNAs) 308, 624 aldolase reaction 91–92 CRISPR/SpCas9-based genome editing dehydrogenase 92 system 490 alcohol 283, 343, 354, 356, 359–360, cross collisional section (CCS) 267 363, 432, 576–577, 583–585, Index 897

613, 692–693, 695, 697–698, double-gene knockout (DKO) 700–702, 704 predictions 34 GAP 428, 432, 748–749 double-helix model 320 lactate 196, 362, 377, 423–424, double-stranded breaks (DSBs) 302 434–435, 554, 571–573, 577, Drosophila DNA-binding Ubx 587–588 homeodomain 305 3-dehydroshikimate 428–429, 816 dSpyCas9 625 deoxyviolacein 433 dual plasmid approaches 482 desorption electrospray ionization dwarf-type mutants 814 (DESI) 269 D-xylose 695, 697 dhurrin synthesis 835 dynamic degradation of TAG’ (ddTAG) diacetyl production 574 strategy 673 diamines 360–361 dynamic mass balances 23–25, 28 1,3-diaminopropane 360 dynamic metabolons 831 cadaverine 361 putrescine 361 e diaminopimelate 92, 359, 416, 421, ecModels 140, 142, 144–145, 147, 422, 431 150–151 1,3-diaminopropane 360–361 ectoine production 425–426 dicarboxylic acids 361–362 EDEMP cycle 524–525 glutaric acid 361, 362 Ehrlich degradation pathway 354 succinic acid 362 eicosapentaenoic acid (EPA) 755–756, dihydrofolate reductase (DHFR) 760, 830 317–318 electron impact (EI) ionization 269 L-3,4-dihydroxyphenylalanine electrospray ionization (ESI) 268–269, (L-DOPA) 370 280–281 dimethylallyl diphosphate (DMAPP) Elementary Metabolite Units (EMU) 355, 367, 369, 713–716, 121 757–758, 822 Embden–Meyerhof–Parnas pathway diols 524 1,4-butanediol 363 Embryophyta 806 production 706 emodepside 785 1,3-propanediol 362–363 enantiopure L-lactic acid production “direct” omics approach 100 572 diterpenoid forskolin 834–835 endogenous chloroplast-localized diterpenoids 821, 830 NADP-malic enzyme 810 DNA double-strand break (DSB) endometabolomics 260 489 endonucleases DNA double-strand breaks (DSB) CRISPR 308–310 302–303, 305, 307–314, TALEs 306–308 317–318, 407, 489, 563–565, ZFN 304–306 619–620, 624, 626, 663–665 endoplasmic reticulum (ER) 8, 701, DNA microarray analysis 722 745–746, 750, 778, 818 DNA microarrays 405 endoplasmic reticulum-associated docosanol 702 degradation (ERAD) L-DOPA decarboxylase (DODC) 370 719 double crossover 615–619 endoxylanases 436 898 Index

energy-demanding sporulation process renewable biofuels 342 471 microbial biopolymers energy-rich adenosine triphosphate non-protein poly()s (ATP) 808 380–381 Entner–Doudoroff pathway 92, 101, PHAs 374–379 282, 283, 524 polysaccharides 379–380 environmental biocatalysts, nanomaterials (NMs) 381–383 development of 870 natural products 367–371 environmental Galenics 861, 877– recombinant protein production Environmental Galenic Science 877 371, 372 environmental microbiology 865 membrane proteins 372, 373 environmental microbiomes, protein-based materials 374 fortification of 879 therapeutic proteins 371, 373 environmental pollution 859, 865, 867, specialty chemicals 874 aromatic compounds 365–367 microbiological agents for L-amino acids 364–365 bioremediation 860 Escherichia coli K-12 MG1655 23, 36 enzymatic rate equations 25 essential genes 32, 437, 470, 473–475, enzyme abundance 155–156, 163 478, 488, 497, 499, 565, 626, enzyme bottom–up approach 186 824 ethanol production 229, 233, 284, 343, factors affecting intracellular enzyme 575, 611, 691–695, 697–698, kinetics 155–156 703–706 Michaelis–Menten formula eukaryotic microalgae 806 153–154 evolutionary engineering 341, 571, 697 enzyme mechanisms 91, 174 exometabolomics 260 enzyme prediction exopolysaccharide 379–380 for orphan and novel reactions 244–246, 251, 257 expression cassette 302, 310, 318, 479, enzyme properties 153, 155, 172, 482, 737, 741, 747, 755, 760, 180–186 769 equality constraints 107 extended Debye–Hückel limiting law ERG9 714–715, 717 221, 222 erythrose-4-phosphate (E4P) 14, 201, external constraints 138–139 428, 709 external metabolites 174 Escherichia coli (E. coli) 36, 473, 556 extra-cytoplasmic function sigma bulk chemicals factors (ECF) 493 ω-amino acids 357–359 extracellular alkaline cellulase Egl-237 diamines 360–361 477 dicarboxylic acids 361–362 extracellular fluxes 6, 78–79, 83–85, diols 362–363 91, 93, 98, 106, 111–113 hydroxy acids 359–360 extracellular reactions 78, 103 lactams 363 definition 341 f fuels production FAIMS 267 non-native biofuel producers 343 Faraday constant 223, 227 non-natural biofuels 343 β-farnesene production 713, 716 Index 899 fatty acid de novo biosynthesis 355, five-carbon containing prenyl isomers 375, 377 822 fatty acid alkyl esters (FAAEs) 355 FK506 biosynthesis 674 fatty acid ethyl esters (FAEEs) 354–356 flavonoids 817, 819 fatty acid methyl esters (FAMEs) biosynthesis 708, 818 354–356 in S. cerevisiae 709 fatty acid pathway 355–356 flavonols 418–419, 708–710, 819 feedback inhibition simulation fluorescence-activating and 205–207 absorption-shifting tag (FAST) fermentative pathway 343, 354 protein 633 ferulic acids 588, 816, 835 fluorescent reporters 631–633 filamentous actinomycetes 5-fluoro-dUMP 479 genome-scale metabolic models 5-fluorouracil (5-FU) 479 674–675 flux balance analysis (FBA) 6, 7, 162, multi-omics studies 671–674 172, 215, 251 filamentous fungi 313, 767, 784 additional constraints 27, 29 A. niger 765, 776–778 analogy to deriving enzymatic rate A. oryzae 778–779 equations 25 A. terreus 779–780 constrained optimization 26 carbon 775 dynamic mass balances 23–25 cell factories and products 766 flux-concentration duality 28 CRISPR genome editing protocols for genome-scale 25, 26 768, 769 flux-concentration duality 28 genetic and genome tool development flux connectivity theorem 184 768–769 flux constraints 107 improved substrate utilization flux control coefficient 175–180, 184, 773–775 186–191, 195–198, 201–202, industrially exploited 768 204–206, 283 macromorphology of 785–788 flux quotient 96 metabolic and regulatory models flux summation theorem 178–179, 199 770–772 flux vector 25 morphologies 767 flux–enzyme relationship 176–178 natural metabolic capacities of 765 fluxomics 50, 75, 77–79, 167, 406, 864 P. chrysogenum 780–781 FMN-based fluorescent proteins protein production 788 (FbFPs) 632 secondary metabolites from 784 FokI-cleavage domain 305 T. reesei 781–783 folate production, in LAB 579 T. thermophilus 783 forskolin 822–823, 834–835, 837 fine-tuned integration of proteome forward simulation 84–85, 98, 121, constraints 123 coupling constraints 148, 150 Fourier-transform ion cyclotron pcModels 144, 145, 147 resonance (FT-ICR) 271 ribosome assembly reaction 148 fractional labeling enrichment (FLE) TPI enzyme 146 81, 82, 106, 116 first-generation bioethanol production free amino acids 112, 115, 116, 735, 691–694 755 900 Index

free fatty acids (FFAs) 354, 355, 701, CRISPR/Cas in B. subtilis and related 735, 755 strains 481–486 free/independent fluxes 84 genome mining 581, 671, 673, fructose 6-phosphate 31, 140, 434, 675–676, 784 481, 580 for biosynthetic gene clusters fruit-specific E8 promoter 819 657–660 fumaric acid 783 genome mining tools 658, 660 functional CRISPR/Cas9-sgRNA limitations 658 complex formation 490 genome reduction projects in B. subtilis functional kinetic model 157–158, 473–477, 481 163, 165–166 genome-reduced strain MGB874 fungal biotechnology 766, 775, 476–477 788–789 genome-reduced variants, of P. putida fusafungine 785 528–529 genome-scale kinetic models 7, 156, g 168 γ-aminobutyrate (GABA) 587 genome-scale metabolic models (GEMs) GAP dehydrogenase (GapA) 428, 432, 213, 215, 674, 770 748–749 internal constraints gas chromatography (GC) 114, 266 membrane economics 139 GE-free synthetic biology 865 molecular crowding 139 GEM with enzymatic constraints using proteome constraints 139 kinetics and omics data genome scale models (GSM) 7, 23–63, (GECKO) 139–142, 144 137–151, 156, 240 gene expression knockdowns 625 genome-scale models (GEMs) 7, 23 gene expression, in lactic acid bacteria E. coli 36–42 557 developments 50–55 gene/genetically modified organisms from to the proteome (GMOs) 555, 565–566, 574, 42–49 579, 590, 829, 867, 872, 873, perspectives 56–59 877 genome-wide CRISPRi 488 gene-protein-reaction (GPR) 32–33, genome-wide transcriptome analysis 674 690 generalized mass action (GMA) Geobacillus thermodenitrificans 490 159–160 geranylgeranyl diphosphate (GGDP) genome annotation 7, 32, 36, 157, 168, 758, 822–824, 828 470, 522 geranylgeranyl pyrophosphate (GGPP) genome editing 496, 713, 714, 717–718, 758 definition of 301 geranylgeranyl pyrophosphate synthase of industrially relevant eukaryotes (GGPPS) 496 CHO 317–320 gibberellins 817, 826 filamentous fungi 313, 315–316 Gibbs free energy 214–218, 220–223, yeast 310–313 225–228, 233, 247 principles of 301–304 of pseudoisomer 222 genome editing tools global environmental problems, by counter-selection and markerless urban and industrial activities genome editing 478–481 866 Index 901 global gene expression analyses 470 gram cell dry weight (gCDW) 8, 144, global scale 6, 404, 803, 821, 838, 880 149 global Transcriptional Machinery graph-based search 243–244 Engineering (gTME) method green fluorescent protein (GFP) 318, 12, 366, 373, 492 492–493, 631–632, 667 glpX gene 495 guide RNA (gRNA) 308–309, 620, 663 glucoamylase 776–778, 786 guilt-by-association approach 771 glucose 6-phosphate (G6P) generation 31–32, 165, 180, 224, 359, 413, h 422, 431, 434–435, 495, 497, Haemophilus influenzae 23 524–525, 554, 750 “hard” constraints 138–139 glucose-6-phosphate dehydrogenase heat stress tolerance 567–569 495, 497, 554 height equivalent of a theoretical plate glucose-6-phosphate isomerase (PGI) (HETP) 264 32, 142, 162, 165, 554 heme biosynthesis 721 β-glucosidase 436–437, 530, 571, 697, hemicellulosic polysaccharides 813 774 hemoglobin 495, 721 glucosinolates 817, 820 hepatitis B surface antigen (HBsAg) L-glutamate 364, 383, 403, 405, 412, 722 hepatitis B vaccines 722 419–420, 427, 435–436, 587 high resolution mass spectrometry glutamate (GLU ) 117 1-5 270, 280 glutamate dehydrogenase RocG 476 high-resolution fluxomics 406 glutamate racemases 497 high-throughput metabolomics Glutamine Synthase (GS) 318 279–280 glutarate production 431, 741, 742 Hill coefficient 184 glutaric acid 357, 361, 362 Hill equation 159, 206 glyceraldehyde 3-phosphate (GAP) homogalacturonan 813 dehydrogenase approach 749 homogentisic acid 826 dehydrogenase-encoding gene 496 homologous recombination (HR) glycerate 809 mechanism 301, 303, 406, glycerol kinase (GlpK) 38, 495 559–560, 564, 616–620, 626, glycerol metabolism, in LAB 585 662–663, 737, 769, 807, 826, glycerol transport facilitator (GlpF) 830, 831 495 horizontal gene transfer (HGT) 861 glycine betaine 829 based, large-scale biormediation 14, 31–32, 101, 112, 140, 878 142, 145, 156, 161, 165, 188, events 868 192, 205, 224, 229, 233, 497, HR-mediated technique for genome 524–525, 553, 674, 704–705, editing 302, 304 738, 740, 743, 745, 778 human insulin 720–721 glycosylated proteins 373, 720 human papillomavirus (HPV) vaccines glyoxylate shunt 101, 360, 472, 703, 722 742, 750, 779 Hunter’s syndrome 306 Golden Rice 820 hyaluronan 379–380 Golgi apparatus 718–720, 821 hyaluronic acid (HA) production 435 Golgi-derived secretory vesicles 720 in C. glutamicum 434, 435 902 Index

hydrocortisone 717 intracellular enzyme kinetics hydrophilic interaction liquid 155–156 chromatography (HILIC) intracellular fluxes 46, 75, 77–79, 265, 276 82–84, 91, 93, 99–100, 103, hydroxy acids 107, 112, 260 3HP 360 intracellular metabolite pool size 78, 4HB 360 95, 106, 123 4-hydroxybutyric acid (4HB) inverse problem 85, 98, 121 359–360 in vitro enzyme assays 161 4-hydroxycinnamic acid (p-HCA) in vivo RBS-selector 667 707–709 ion chromatography (IC) 264, 267 3-hydroxydecanoate (3HD) 375 ion mobility 267 3-hydroxydodecanoate (3HDD) 375, ion-pairing RPLC (IP-RPLC) 265–266, 377 283 3-hydroxyhexanoate (3HHx) 375 ionization techniques 268–269, 280 4-hydroxyisoleucine (4-HIL) production irregular xylem (IRX) mutants 814 403, 427 IRX7 deficient plants 814 3-hydroxyoctanoate (3HO) 375 isobutanol production 698–699 3-hydroxypropionate (3-HP) 375, 377, isocitrate dehydrogenase Icd 496 430, 432 isoflavonoids 708, 710, 817 3-hydroxypropionic acid (3-HP) isopentenyl diphosphate 354–355, 359–360, 585, 703, 705 434, 757–758, 822 hygromycin B 315, 737, 745, 747 isopentenyl pyrophosphate (IPP) 14, 354–355, 367–369, 661, i 713–717, 757–758 iBsu1103 470 isoprenoid pathway 343, 355 iChip 654 isopropanol 263, 265, 343, 354, 613 illumina sequencing 760 isotope labeling experiment 100 iModulons 52–55, 57, 62 atom transition network specification in-depth global transcriptome 470 103–104 inactivated whole cells 860 input labeling composition INCA 117 104–106 independent component analysis (ICA) specification 51 101–103 inducible promoters 620, 627 modeling and simulation 101 inequality constraints 107 isotopic labeling 78–80, 96, 98, 115 input labeling composition 104 isotopic steady state (ISS) 77, 90, 123 input labeling design 93 approximation 115–116 in silico cell 33 isotopic tracers 4, 6, 77, 79–80, 99 in silico experimental ILE design 108 isotopic tracing 8–9 INST-13C-MFA 83, 123 isotopically labelled tracer 8 integrative analysis of omics data 166 isotopologues 97, 261, 274 intermediates, toxicity of 247 isotopomer fractions 94, 96–97, 103 internal constraints 138–139 isotopomers 91–98, 106, 114, 116 internal metabolites 174, 179, 184, 200 itaconate 428, 430, 777, 779, 780 intracellular compartments 8 A. niger 777 Index 903 k biotransformations 587–588 keto acid decarboxylase (KDC) 354, bulk chemical production 697 acetoin 575–577 2-keto-acid route 698 butanediol-isomers 577–578 α-ketoglutarate production 741–742 ethanol 575 ketones bioreduction 584–585 butanol production 588 keyicin production 673 CRISPR-Cas-technology for genome kinetic feasibility 246, 247 editing 563–565 kinetic model features and phylogeny of 552, 553 applications 166–167 552 approximative rate expression food ingredients 159–160 acetaldehyde 574–575 description 156 alanine 574 functional 157–158 diacetyl 574 mechanistic rate expressions lactic acid 572, 573 158–159 gene expression 557–559 perspectives 167–168 genetic engineering of 559–565 rate expressions 160–166 glycerol conversion 585–587 scope 156–157 heat tolerance toy example 164–165 acid tolerance 569 toy model 164–165 oxygen tolerance 570–571 yeast 165–166 host for plant metabolite production kinetome 51, 168 588 kirromycin biosynthesis 656, 657 ketones bioreduction 584–585 knowledge bases 24, 35, 57, 62, 404, metabolism of 553–555 838, 862 multistress-resistance 567 kojic acid plasmid integration by homologous A. oryzae 778, 779 recombination 559–560 k-OptForce 41 plasmid integration using phage attachment sites 560–561 l polyols production 579–580 L- and/or D-glutamic acid monomers preservative effect 551 495 recombineering based genetic L-arabinose 283, 695, 697 engineering 561–563 labeled substrate 77, 80–81, 99, 104, roles and functions 551 108, 110–113, 116 shuttle vectors 556–557 labeling enrichments 81–83, 85, starter cultures for food fermentation 90–91, 100, 103, 106, 109, 113, 565–567 115–117, 121, 123 stress tolerance lactams 357, 363 heat tolerance 567–569 lactate dehydrogenase (LDH) 196, 362, substrate utilization routes 571–572 377, 423–424, 434–435, 554, therapeutic proteins production 571–573, 577, 587–588 580–581 lactic acid 195, 572, 573, 613, 705 thermotolerance 568 lactic acid bacteria (LAB) 555 transformation of 556–557 as biocatalysts 583–589 vitamins production bacteriocins 581–583 cobalamin (vitamin B12) 579 904 Index

lactic acid bacteria (LAB) (contd.) m folate (vitamin B9 579 machine learning approaches 241, 242, riboflavin (vitamin B2) 578 249, 660 lactic acid production 569, 572, 587, maize 806, 821 705 malate synthase 472, 697, 810 Lactobacillus casei 556, 561, 563–564, malate–pyruvate–oxaloacetate cycle 568–569, 577, 580, 582, 584, approach 749 587 malic acid production 703–704 Lactobacillus reuteri 561–562, 579, A. oryzae 779 584, 586 maltose consumption 477 Lactococcus lactis 473, 556–558, 560, mandelic acid 366, 378–379 570 Manihot esculenta 832 for bulk chemicals production 576 mannitol 420–421, 579–580 as drug delivery vehicle (DDV) 580 utilization 415–416 for over-producing flavor compounds mannose 414 573 mannose phosphoenolpyruvate- dependent phosphotransferase lanthipeptides 581–582 system 481 ligD positive strains 487 mannose-specific transporter ManP lignans 817 481 lignocellulose 530, 694, 782 manPA alleles 481 lignocellulosic biofuel production 694 manual pathway design 238 limiting rate 172, 181, 183 Mariner-transposable Himar1-based lin-log modeling approach 160 systems 617 linear ion traps (LITs) 270 markerless-deletion system 619 linear plus linear homologous Markov chain Monte Carlo (MCMC) recombination (LLHR) 662 approach 89 linearized statistics 89–90 sampling 26 lipid synthesis 747, 833 mass isotopomers 97–98, 114, lipid-rich yeast 753 116–117 lipolase 313 mass spectrometry (MS) 268 lipopeptide surfactin 497 acquisition modes Lisianthius nigrescens 834–835 for targeted metabolomics liquid chromatography (LC) 114, 271–272 264–266, 669 for targeted MS 272 liquid–liquid extraction (LLE) 263 for untargeted metabolomics 272 lithium acetate method 737 features 268 lovastatin 653, 779–780 high resolution 270–271 low resolution mass spectrometry ionization techniques 268–269 269–270 low resolution 269–270 Lpd1 740 Mathieu equations 270 lycopene, in S. avermitilis 667 matrix effect 263, 268–269, 279 L-lysine 110, 357, 359, 361, 364, matrix-assisted laser desorption 403–405, 413, 415–416, ionization (MALDI) 419–423, 425–426 269–270, 280 lysophosphatidate acyltransferase max-min driving force (MDF) of (LPAAT) 204–205 pathway 282 Index 905

Maximum Likelihood Estimator (MLE) activity-independent screening of 163 target molecule synthesis maximum reaction velocity 25 492–493 mCherry-reporter cassette 319 biotechnological application ME models 42–49, 57 493–497 mechanistic rate expressions generally regarded as safe 470 158–160 minimal cell concept 472–478 medium chain length PHA (MCL-PHA) optimization, standardization, and 375, 378 modularity in gene expression meganucleases 302–304, 320 490–492 membrane bound cytochrome P450 physiological traits and circuits (P450) enzymes 812 470–472 metabolic control analysis (MCA) 6, quality presumption of safety 470 153, 171, 173, 283 tools for genome editing 478–490 aromatic amino acids, bacterial cellular metabolism and physiology production of 200–202 ‘omics’ technologies 7–9 based methods 166 FBA 6, 7 concentration control coefficient isotopic tracing 8, 9 MCA 6 179–180 MFA 6, 7 demand for product 194–195 combinatorial metabolic engineering flux control coefficient 175–176 12–14 flux summation theorem 178–179 Escherichia coli 341–384 flux–enzyme relationship 176–178 goal of 171 inhibition of competing pathways history and overview of 3 195–196 host organism selection 15 limitation of 171, 188 industrial biotechnology 17 linking control coefficients to enzyme rational metabolic engineering properties 181 10–11 alterations of enzyme activity strain development process 17, 18 188–190 substrates 15–16 block elasticities 186 synthetic biology 16 control coefficients and elasticities systems metabolic engineering 14 184–186 Metabolic Engineering: Principles and elasticity coefficient 181–184 Methodologies 3 enzyme rate equations 181–184 metabolic flux analysis (MFA) 6, 7 feedback inhibition 186–188 13C-MFA 97–99, 124–125 feedback inhibition, abolishing 13C-MFA variants 76–77 191–194 bidirectional reaction steps 95–96 top–down analysis 186 biotechnologically relevant organisms metabolic steady state 174–175 108 Universal Method 199–200 carbon atom transitions 91–93 yeast tryptophan synthesis 197–198 extracellular fluxes 111–112 yield impacts 203–205 flux constraints 107 metabolic engineering fluxomics 77–79 bioenergetics in life 213–214 from the data to the intracellular of Bacillus fluxes 82–83 906 Index

metabolic flux analysis (MFA) (contd.) and interpretation 277–279 in silico experimental ILE design engineer medium composition 285 108 experimental design 260 input labeling design 93–94 improving stress tolerance 284–285 INST-13C-MFA 83–84, 123–124 internal standards 261 introduction 73–77 pathway design by thermodynamic isotope labeling experiment analysis 281–283 100–108 reduction of side products and isotopic labeling 79–81 metabolite damage 284 isotopic steady state approximation sequences and standards 261–262 115–116 targeted and untargeted 260–261 isotopomer fractions 96–97 metabolons 825, 831–833 MetaCyc 101 isotopomers 94–95 metallo-proteome 43–45, 55 labeled substrate 112–113 meta-organismal catalysts 875 measurement specification 106–107 methotrexate (MTX) inhibits 317 metabolic and isotopic stationarity methyl anthranilate 366, 404 110–111 2-methyl-D-erythritol 4-phosphate metabolic and isotopic stationary (MEP) pathway 822 state 90–91 methylerythritol-4-phosphate (MEP) metabolomics 113–115 355 natural isotope abundance 116–117 mevalonate (MVA) pathway 354, 355, parameter fitting 84–86 822 simulation of labeling data and flux in S. cerevisiae 714 estimation 117–123 mevalonate diphosphate (MVAPP) statistical analysis 86, 89–90 758 statistical evaluation and optimal mevalonate pathway 588–589, experimental design 99–100 757–759 design 237–238 Michaelis constant 159, 181 metabolic pseudo-steady state Michaelis–Menten constant 25 approaches 76, 109 Michaelis–Menten formula 153–154 metabolic steady state (MSS) 77, enzyme kinetics 154 173–175, 182, 188, 281 formulation 159 assumption 77 Michaelis–Menten kinetics 7, 154, 164 metabolism 153 Michaelis–Menten reaction mechanism of LAB 553–555 25 metabolism 523 microalgae 803, 806, 811, 829–831 sugar 554 microbial activities, multi-scale metabolite extraction 8, 262 propagation of 869 metabolomics 8, 113, 259 microbial biocatalysts 4 analytical techniques microbial biopolymers sample preparation 262–264 non-protein poly(amino acid)s 380 separation techniques 264–267 PHAs 374–379 applications 281–285 polysaccharides 379–380 calibration curves 261 microbial consortia 874, 879 challenges 259 microbiological agents for data analysis 272–277 bioremediation 860 Index 907 microfluidics 13, 280–281, 483, 654, n 784 NADH oxidase (NOX) of Lactococcus microhomology-mediated end-joining lactis 196 (MMEJ) 301, 302, 319 NADPH-P450 oxidoreductase SbPOR2b minGenome 41 825 MiniBacillus 494 NADPH-P450 (PORs) MiniBacillus framework 475 817 minimal cell concept Nannochloropsis oceanica 806, 830 genome reduction projects in B. nanomaterials (NMs) 381–383 subtilis 473–476 nanopore sequencing technology 655 minimal genomes 472–473 nanopore sequencing, in Y. lipolytica productivity of genome-reduced genome 760 strains 477–478 nanostructure-initiator mass minimal genomes 61, 472–473, 499, spectrometry (NIMS) 280 789 natural abundance (NA) 80 missing values 85, 274 correction 116–117 mixed-integer linear program (MILP) NAtural Deep Eutectic Solvent 38, 215, 227–228 (NADES) 834–835, 837 mixed-integer nonlinear program natural isotope abundance 116–117 (MINLP) 41 natural isotope enrichments 105 monoclonal antibodies (mAbs) 371, natural products 373 alkaloids 368, 370 monoterpene indole alkaloids (MIAs) phenylpropanoids 368–370 370, 710–712 polyketides 368, 370–371 monoterpenes, in S. cerevisiae terpenoids 367–369 716 naturally labeled 12Cglucose 80 Monte Carlo based approach 163 N-containing bioactive natural products MPD pipeline 787–788 820–821 M. thermoacetica gas fermentation network data representation 242 751 network reconstruction multi-strain reconstructions 33 availability of GEMs 35 multiple reaction monitoring (MRM) basic principles 30–32 method 271 computational queries 32–33 multiplex automated genome curation 32 editing/engineering (MAGE) genomic basis 32 342, 526, 863 knowledge bases 35 multiplex genome editing 486–487 scope expansion 33–35 multivariate statistics 278 Nicotiana benthamiana 807 Mummichog algorithm 279 nicotinamide adenine dinucleotide mutagenic ssDNA recombineering phosphate (NADPH) 714, 870 808, 809 mutS mutations 569 Nisin controlled gene expression (NICE) Mycoplasma mycoides JCVI-syn3.0 system, in LAB 557, 558, 565 strain 473 nisin Z 582 mycosporine-like amino acid (MAA) nisK 557, 558 423 nisR 557, 558 908 Index

non-homologous end joining (NHEJ) organic acids production mechanism 301, 302, 313, S. cerevisiae 702 314, 318, 489, 619, 626, 663, orotate transporter (oroP) 559, 560 737, 741, 745, 747, 760 Oryza sativa 806 non-native biofuel producers oxidative pentose phosphate pathway fatty acids pathway 355–356 553, 748 fermentative pathway 343–354 oxidative TCA cycle 703, 704 isoprenoid pathway 355 OxidizeME 43, 46, 48 keto acid pathway 354–355 2-oxoglutarate 419, 476, 711 non-natural biofuels 343 oxygen tolerance 570–571 non-oxidative pentose phosphate pathway (PPP) 96, 101, 284, p 285, 495, 553, 554, 748, 750, 367, 717, 818 751, 753, 754 pangenome 41, 61, 522 non-protein poly(amino acid)s paralogous proteins 473 380–381 parameter covariance matrix 89 nonribosomal synthetases parameter fitting 84–86, 96, 98, 107, (NRPSs) 371, 496, 534, 657, 116, 121, 123, 163 667 parametric Monte Carlo bootstrap 89 R,S-norlaudanosoline 370 pathway design 238 normal-phase liquid chromatography available tools for 247–249 (NPLC) 265 practical example of 249 novel reactions 244–245, 251, 257, 583 successful applications of 249 nuclear localization signal (NLS) 306, pathway feasibility 246–247 308 pathway search 237, 242–243, 244, 249 o algorithm 244 PCR-generated sgRNA expression 487 Obiwarp method 274 P450-dependent biosynthetic pathway off-target effects 305, 307, 309, 316, 319 824, 825 oleochemicals 699 peak grouping 274 oligo-annealed promoter shuffling peak picking 273–274 (OAPS) 491 pectin matrix 813 oligosaccharides 412, 414–415, 773 penicillin 202–203, 420, 653, 769, 780, omega-3 fatty acid 818 781 4′-O-methyltransferase (4′OMT) 368, penicillin-producing fungi 313 370 Penicillium chrysogenum 767, 780 omics’ technologies 7–9 enzyme set for plant polysaccharide OPENFLUX 117 degradation 773 OptForce 38, 41 GEMs for 770 optimal experimental design (OED) production 89, 99–100, 101, 108, 109, 774 123 X-ray microcomputed tomography OptKnock 38 (μCT) 787–788 OptStrain 38 pentose fermentation rate 695 orbital trap 270 pentose phosphate pathway (PPP) 96, Orbitrap instruments 270, 271 101, 156, 229, 284, 285, 495, Index 909

524, 553, 554, 674, 695, 748, physiological effects 8, 499 750, 753, 754 L-pipecolic acid 403, 426 pentose sugars 413, 553, 695, 697 plant bioactive natural products γ-PGA biosynthesis 495 phenylpropanoids 817 pG+host system 560 synthesis and regulation of 817–818 phage-assisted continuous evolution terpenoids 817 (PACE) 13 upregulated anthocyanin synthesis phenylalanine ammonia lyase (PAL) 818–819 359, 367, 707, 708, 819, 820 plant cell wall 530, 803, 814, 816, 813 3-phenyllactic acid (PLA) 375, 378, plant metabolic engineering 803, 804, 587, 588 820, 838 phenylpropanoid biosynthesis 819 plant metabolites 588–589, 807, 822 phenylpropanoid pathway 707, 819, plant-derived taxadiene synthase 495 833 plants 803–808 phenylpropanoids 367, 368–370, plasmid copy number effect 477 706–710, 813, 817, 819 plasmid-based CRISPR/Cas9 systems phosphite oxidoreductase (PtxD) 829 482 phosphoenolpyruvate carboxykinase plastoquinols 826 gene 416, 422, 431, 496, 744 plastoquinone 809, 826, 829 phosphofructokinase (PFK1) 31, 180, pollutant-responding whole cell 188, 191, 414, 432, 497, 498, biosensors 865 554, 674, 692, 776 poly(diaminobutyric acid) 380 6-phosphofructokinase 497, 498, 674 poly(diaminopropionic acid) 380 butanol production 698 poly(glutamic acid) 380, 381 phosphoglucose isomerase (PGI) 31, poly(lactate-co-glycolate) (PLGA) 377, 32, 33, 142, 165, 692 378, 379 3-phosphoglycerate 165, 692, 809 poly(lysine) 380 phosphoglycerate mutase (PGM) 165, 692 poly(PhLA-co-3HB) production 379 phosphotransferase systems (PTS) poly-γ-glutamic acid (γ-PGA) 494, 495 201, 414, 415, 428, 522, 523, polyglutamate (PGA) 435–436, 494, 554, 555, 580 495 photorespiration 809, 810 polyglutamate synthesis 495 photosynthetic cells polyhydroxyalkanoates (PHAs) biosustainable industrial production energy and redox storage material platforms 806–808 374 plants 803–805 MCL-PHA 375, 378 solar radiation 805–806 PHA (SCL-PHA) 375 photosynthetic organisms PhaCs 378 cyanobacteria 808 PLGA 379 metabolic engineering strategies poly(3HB) 375, 377 810 poly(PhLA-co-3HB) production 379 photorespiration 809 polyketides 14, 367, 368, 370–371, ribulose-1,5-bisphosphate 809 534, 581, 713, 754, 775 Rubisco 808 polymerase chain reaction (PCR) 12, thylakoids 808 311, 478, 481, 482, 487, 527, phylloquinone 826 558, 662, 663, 736 910 Index

polysaccharides 374, 379–380, 408, biosynthesis of natural products 534 530, 773, 775, 782, 813, 814, carbon substrate range, expansion of 815, 816 529–530 pOri plasmid 560 characteristics of 521–522 practical non-identifiability 100 CRISPR/Cas–based gene editing pravastatin 781 techniques 526 precursor compound 237, 242, 243, features 529 253 genome-reduced variants 528–529 P43 reference promoter 491 glucose uptake 523 prenyl 822 glycerol metabolism 523 principal component analysis 55, 278 high-efficiency multiple genomic site pristinamycin 663, 664 engineering (HEMSE) of 526 pro-vitamin A 820 nutritional landscape 530 productivity of genome-reduced strains organic acids, production of 533 477–478 oxygen-dependent lifestyle profile likelihoods 89 engineering 530–532 proinsulin 720, 721 solvent-tolerant strains 521 promoters 627–630 substrate utilization and core promoters, in actinomycetes 667 metabolism 522–524 1,2-propanediol 428, 432, 706 synthetic biology tools for 524–528 1,3-propanediol (1,3-PDO) 360, 362, taxonomic credentials 521 363, 375, 377, 428, 430, 432, xylose catabolism, pathways for 523 519, 585, 586 Pseudomonas putida KT2440 357, 519 protein precipitation 262, 263 ptb 619, 627 protein sequence 47, 244, 246 putative BCAA permease 496 protein structures 35, 47, 50, 55, 57, putrescine 359, 360, 361, 412, 423 632, 782 pyrazines 433 protein-based biopharmaceuticals 371 pyruvate 741 proteinogenic amino acids 112, 114, -acetaldehyde-acetate-AcCoA route 115, 116, 403, 406, 419, 655, 756 657 and α-ketoglutarate production 740 proteome constraints pyruvate decarboxylase negative strain coarse-grained integration of (PDC) 704, 705 139–144 fine-tuned integration of 144–150 q proteome-constrained models quadrupoles 269–271 (pcModel) 144, 145, 147, quantum mechanical/molecular 150, 168 dynamics (QM/MD) 216 protospacer adjacent motif (PAM) quasi-steady state assumption (QSSA) sequence 308, 309, 407, 620 25, 174 Prunus dulcis 818 quenching 110, 114, 262, 281, 811, 830 Pseudomonas putida 473, 528 quorum sensing systems 876 EDEMP cycle 524 in silico analysis 522 r in silico metabolic potential 522 random mutagenesis 12, 304, 378, 419, aromatic molecules, production of 491, 532, 566, 567, 615–617, 532–534 670, 781 Index 911 rate expressions 153, 156–166, 163, reversible Michaelis–Menten equation 164, 167, 168 181, 182 rate–limiting steps 173, 365, 721 rhamnogalacturonan 813 rational metabolic engineering 9, Ribo-seq 61 10–11, 613 ribosomal binding sites (RBSs) 433, reaction directionality 214, 242 667, 668, 871 reaction prediction 237, 240–241, 242 ribosomal proteins 147, 473, 476 reaction reversibility 214 riboswitches 493, 634, 670, 865 Recombinant DNA Biotechnology III + ribozymes 316, 312 The Integration of Biological ribulose-1,5-bisphosphate 808, 809 and Engineering Science 3 carboxylase-oxygenase (Rubisco) recombinant DNA technologies 3, 862 808 recombinant proteins 371, 372, 404, rice 571, 778, 806, 809, 816, 818, 820 436, 718–723, 828, 830 RNA sequencing 48, 51, 53, 61, 405 recombinant protein production roseoflavin 578 membrane proteins 371, 372, 373 RPLC 265, 266, 268, 276, 283 protein-based materials 374 rRNAs 473 therapeutic proteins 371–373 16s rRNA-based unrooted phylogenetic recombinant RNA 437 tree, of LAB 552–553 Recombinase-Mediated Cassette s Exchange (RMCE) 319, 320 SABIO-RK13 161–162 recombineering based genetic Saccharomyces cerevisiae engineering, in LAB alkaloid compounds production 710 561–562 aromatic amino acids 708 reduced-genome variants, of P. commodity chemicals production taiwanensis VLB120 529 diols 706 RelA/SpoT homologues 471 organic acids 702–705 renewable biofuels 342 cytosolic 699 Repeat Variable Diresidues (RVDs) fatty acid synthesis 699–700 306, 307 fatty acids synthesis 699–700 reporter-guided mutant selection first-generation bioethanol (RGMS) 670 production 691–694 repression under secretion stress (RESS) flavonoids biosynthesis 710 778, 782 higher alcohol production 695–697 rep60-specific sgRNA 487 history 689 resveratrol 369, 418, 818 insulin analogue expression 721 retention time 264, 266, 272, 274, 276 mevalonate and sterol pathway (S)-reticuline derived morphine type 713–714 alkaloids 824 monoterpenes, triterpenes, and retrobiosynthesis 241–242, 243, 251 isoprenoids production retrobiosynthetic approach 115, 243 716–718 reverse catabolite repression strategy phenylpropanoids production 523 706–710 reverse-phase liquid chromatography protein secretory pathway 718–719 (RPLC) 265, 266, 268, 276, recombinant proteins production 283 718–723 912 Index

Saccharomyces cerevisiae (contd.) SigB-controlled general stress response second generation bioethanol 471 694–697 SigB-controlled regulon 471 timeline 690 sigma factor SigB 471 virus like particles in 721–723 signal-recognition particle (SRP) 718 S-adenosylmethionine (SAM) synthesis simultaneous saccharification and 356, 366, 493 fermentation (SSF) 694 Salinispora genomes 672 single cell metabolomics 280–281 SAM-dependent methyltransferase single-gene knockout (SKO) 33, 34 (AAMT1) 366 single-strain multi-step process vs. sample batches 275 consortium-based distributed sample-specific variations, correction of catalysis 874–875 275 site-directed mutagenesis 357, 582, S. cerevisiae GEM 140, 157 711 scrambling reactions 102, 104, 107 SNPeffect 41 second generation bioethanol Solanum lycopersicum 819 694–697 solar radiation 805–806, 825 second law of thermodynamics solid-phase extraction (SPE) 263, 264 213–215, 227 Sophora japonica 834 Secondary Metabolite Bioinformatics sorbitol 579, 580, 694 Portal 658 space charging 270 secondary metabolites 653, 655, 665, SpCas9-mediated dsDNA cleavage 673 490 biosynthesis 660–671 specialized metabolites 653, 804, 805 BGC cloning for heterologous spectinabilin gene cluster 671 expression 661–663 SporeWeb 470 genome mining, software for 658, SpyCas9 624, 625 659 squalene 714, 715, 717 host strain selection, for S-reticuline by an epimerase (STORR) heterologous expression 368, 370 660–661 Standard European Vector Architecture genome mining, software for 658 (SEVA) 525, 527 -related bioinformatics tools 658 statistical analysis 86–90, 122, 161, sedoheptulose-1,7-bisphosphatase 830 163–166 selected reaction monitoring (SRM) sterol pathway, in S. cerevisiae 714 271 stilbenes 418, 817 sequencing-based approaches 655 stoichiometric coefficient 25, 27, 31, sesquiterpenoid artemisinic acid 829 138, 139, 140, 143, 215, 754 sgRNA-guided Cas9 488 stoichiometric feasibility 246 shallow’ alleleome 34 stoichiometric matrix-based search shikimate p-coumaroyl 816 243 shinorine production, in C. glutamicum stoichiometric pathway evaluation 423, 424 249, 251 short chain length PHA (SCL-PHA) strain development methods 566 375 strain development process 17, 342 short-chain alcohols 432, 534, 697 strand invasion 302 Index 913

Streptococcus thermophilus 308, 555, synthetic biology-based technologies 565 for large-scale bioremediation 868–869 antibiotics producers 673 synthetic morphologies 875 biosensor 669 synthetic promotor libraries (SPL) metabolic engineering 654 557–558 species 489, 661 synthetically lethal gene pairs 32 strains 473 systems biology 11, 14, 28, 35, 36, 41, Streptomyces coelicolor 659, 660, 663, 55, 56, 63, 73, 181, 341, 404, 666, 670, 673, 675 438, 519, 520, 614, 627, 654, genome-scale metabolic models 672 674–675 systems metabolic engineering 5, 9, Streptomyces tsukubaensis 673 14, 73, 341, 342, 383, 384, genome-scale metabolic models 404–407, 420, 424, 429, 435, 674–675 671–675, 776 527, 665 streptothricin 665 t stressME model 43, 46 target compound 237, 238, 240, 241, structural non-identifiability 100 242, 243, 246, 249, 250, 251, structural systems biology 35, 55, 56 660, 663, 674, 817, 818, 831, S-styrene oxide 366, 367 861, 864, 865 suberin 813 targeted metabolomics 260–261, 262, substrate mixture 94, 104, 105 268, 272, 273, 274, 275, 276, substrate utilization routes, LAB 571 277, 278, 284, 285 subtilisin-like alkaline protease M 477 target gene egl-237 477 SubtiWiki 470 TATA-box 312 succinate dehydrogenase (Sdh) complex taxa-4,11-diene 496 360, 704, 743, 744 taxadiene 368, 369, 495, 496, 717, 830 succinate production 343, 412, 743, Taylor cone 268 744 TCA cycle 229 succinic acid 361, 362, 690, 703, 704, in cancer cells 4 743 temperature-sensitive derivative succinylase 92, 359 pE194ts 481 sugar metabolism, of lactic acid bacteria temperature-sensitive pSG5 ori 481 554 temporal control 11 supercritical fluid chromatography temporal drifts 275 (SFC) 264, 266, 267, 268 terminators 436, 612, 633, 634, 667 supervised methods, in untargeted terminators, in actinomycetes 667 metabolomics 278 terpenes 367, 712–714, 775, 812 surfactin 494, 497 terpenoid production 713, 718, 812 surfactin biosynthesis 497 terpenoids 367–369, 433, 534, 712, switchgrass 816 713, 714, 716, 717, 718, 817, synthetic biology 862 821, 822, 824, 825, 830, 837 metabolic engineering 16 Terraforming Earth’ approach 868 synthetic biology agents (SBAs) 872, terrestrial charophycean green algae 873, 874, 877 805 914 Index

tert-butyl dimethylsilyl (TBDMS) 117, time-resolved metabolomic 118 measurements 281 tetLM riboswitch 486 tocochromanols 826, 828 486, 581, 627, 653, 673 tocopherols 818, 826, 828 tetrahydro-cannabinoic acid synthase tocotrienols 826, 828 837 top–down control analysis 186, 204 L-theanine production 427 toxic pyrimidine analogue 5-fluorouracil theophylline responsive riboswitch (5-FU) 479, 618 634, 670 toxin-antitoxin systems 479, 619 therapeutic proteins 371–373, 552, toy model 142, 145. 148, 164 580–583 TP901-1 integration system has 561 thermodynamic feasibility 214, 232, trans-activating RNA (tracrRNA) 308, 237, 246–247, 251, 253, 282 309, 482 thermodynamic flux analysis (TFA) transcription factor (TF)-based 215, 227, 228, 229, 232, 247, biosensors 493 251, 252, 253 Transcription-Activator Like Effectors thermodynamic pathway evaluation (TALEs) 306 249, 251–257 Transcription-Activator Like Effector Nucleases (TALENs) 304, thermodynamics-based flux analysis 306–308, 310, 315, 318 (TFA) workflow 215 transcriptional regulatory networks characterizing feasible concentration (TRNs) 51 space 229–233 transcriptomics 8, 259, 405, 413, 470, compartment-specific ionic strength 589, 672, 673, 675, 690, 769, and pH 220–221 771, 778, 837 constraining flux space with transformation-associated metabolomics data 228–229, recombination (TAR) 662 232 trans-4-hydroxyproline (4-HYP) estimation of standard free energies production 403, 426–427 of formation 216–221 triacetic acid lactone (TAL) production free energy of formation for isomer 756–757 distributions 221–223 triacylglycerols (TAGs) 673, 735, 736, mathematical formulation 227–228 745, 747, 748, 751, 753, 754, model curation 215–216 755, 756 transformed free energies of reaction triacylglycerols production 223–227 Y. lipolytica thermostable cellulases 782 cytosolic acetyl-CoA availability thermostable ThermoCas9 490 753–754 Thermothelomyces thermophilus desaturation of fatty acyl chains 766–767, 774, 783 747–748 L-threonine 359, 364, 365, 431 lower raw substrate cost 749–753 thylakoids 808, 821, 831, 837 pathway yield through balancing thymidylate synthase 479, 581 redox cofactors 748–749 time-course simulations of dynamic push-and-pull strategy 747 processes 166 Triticum aestivum 806 time-of-flight (TOF) MS 114, 270, 271, tricarboxylic acid (TCA) cycle 156, 272, 273, 274, 405 472, 522, 703 Index 915 tricarboxylic (TCA) 4, normalization approach 275 101, 110, 124, 156, 229, 233, peak alignment and retention time 362, 407, 413, 419, 421, 426, correction 274 427, 472, 403, 406, 674, 703, peak grouping 274 704, 705, 739, 742, 743, 750, peak picking 273–274 751 preprocessing step 273 Trichoderma reesei 767, 771, 781 upper glycolysis in S. cerevisiae enzyme set for plant polysaccharide 139–140, 142 degradation 773 upregulated anthocyanin synthesis growth on cellulose 774 818–819 overexpression of hybrid uracil-phosphoribosyltransferase transcription factor in 774 (UPRTase) gene upp 479, 560 2,4,5-trimethyl-1,3-dioxolane (TMDX) uridine diphosphate-glucuronic acid 284 497, 498 triple-quadrupole (QQQ) instruments 271 v Triticum aestivum 806 valerolactam 357, 363, 534 tRNAs 147, 473, 712 L-valine 364, 365, 405, 419, 431 type I-B CRISPR systems 624 vanilla orchid 824, 834, 835 type II CRISPR system 620, 624 Vanilla planifolia 824, 834 tyrosinase (TYR) 370, 382, 383, 778 vanillin 417, 588, 835, 837 L-tyrosine 365, 366, 369, 370, 379, 419, vegetative SigA-type promoter 477 707–710 very-long-chain fatty acid tyrosine-derived cyanogenic glucoside (VLCFA)-derived chemicals dhurrin (D-glucopyranosyl- 702 oxy-(S)-p-hydroxymandelo- violacein 404, 423, 433 nitrile) 824–825 Viridiplantae 806 virus like particles (VLPs), in S. u cerevisiae 721 ubiquinone 829 vitamin E 818, 825, 826, 828 UDP-Glucose 380, 435, 498, 588, 824, 825 w UDP-glucosyltransferase mediated waste-free circular economy 867 de-toxification 824 weighted sum of squared residual (SSR) UDP-N-acetyl-glucosamine 497 86, 89, 121, 527 UDPG-glucosyltransferase SbUGT85B1 wheat 571, 806, 809 825 whole-cell biocatalysis 519, 520, 524, unfolded protein response (UPR) 719 589 univariate intervals 89 Universal Method 199, 200, 564 x unlabeled isotopomer 94 XlnR transcriptional regulator 778 unsteady FBA (uFBA) 27 xylan production 814–816 untargeted metabolomics 260–261, xylo-oligosaccharides (XOSs) 412, 268, 272–278, 284, 285 414, 415 untargeted MS data processing xylose 408 annotation 276–277 inducible PxylA 486 missing values 274 inducible promoter PxylA 488, 627 916 Index

y triacetic acid lactone (TAL) Yarrowia lipolytica 15, 285 production 756–757 applications 736 triacylglycerol production 746, β-carotene production 757–759 747–748, 750 cytosolic acetyl-CoA 753–754 de novo biosynthesis 745–746 eicosapentaenoic acid production cytosolic acetyl-CoA availability 755–756 753–754 genetic engineering tools for desaturation of fatty acyl chains 737–738 747–748 genotypic features 735 lower raw substrate cost 749–753 homologous recombination pathway yield through balancing mechanism 737 redox cofactors 748–749 lactose as carbon source 752 push-and-pull strategy 747 NHEJ mechanism 737 yeast 310–313 opportunities and challenges S. cerevisiae 689 759–760 Y. lipolytica 735 phenotypic features 735 yeast tryptophan synthesis 197–198 proteases secretion 735 y-genes 36 short-chain organic acid production yellow fluorescent protein (YFP) 632 738 citrate 738–740 z pyruvate and α-ketoglutarate Zea mays 806 740–741 zinc-finger nucleases (ZFNs) 304–306, succinate 743–745 307, 308, 310, 318, 320