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 N2-fixing cyanobacteria 422, 423 biocontaminants 256, 258 Cyanobacteria Biotechnology, First Edition. Edited by Paul Hudson. © 2021 WILEY-VCH GmbH. Published 2021 by WILEY-VCH GmbH. 532 Index 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