Advances in Cyanobacterial Biology PDF
Preview Advances in Cyanobacterial Biology
Advances in Cyanobacterial Biology Advances in Cyanobacterial Biology Edited by Prashant Kumar Singh Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Centre, Rishon LeZion, Israel Ajay Kumar Department of Post-harvest Science, Agricultural Research Organization, The Volcani Centre, Rishon LeZion, Israel Vipin Kumar Singh Department of Botany, Institute of Sciences, Banaras Hindu University, Varanasi, India Alok Kumar Shrivastava Department of Botany, Mahatma Gandhi Central University, Motihari, India AcademicPressisanimprintofElsevier 125LondonWall,LondonEC2Y5AS,UnitedKingdom 525BStreet,Suite1650,SanDiego,CA92101,UnitedStates 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom Copyright©2020ElsevierInc.Allrightsreserved. Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans,electronicormechanical,including photocopying,recording,oranyinformationstorageandretrievalsystem,withoutpermissioninwritingfromthepublisher. Detailsonhowtoseekpermission,furtherinformationaboutthePublisher’spermissionspoliciesandourarrangementswith organizationssuchastheCopyrightClearanceCenterandtheCopyrightLicensingAgency,canbefoundatourwebsite: www.elsevier.com/permissions. ThisbookandtheindividualcontributionscontainedinitareprotectedundercopyrightbythePublisher(otherthanasmaybe notedherein). Notices Knowledgeandbestpracticeinthisfieldareconstantlychanging.Asnewresearchandexperiencebroadenourunderstanding, changesinresearchmethods,professionalpractices,ormedicaltreatmentmaybecomenecessary. Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgeinevaluatingandusinganyinformation, methods,compounds,orexperimentsdescribedherein.Inusingsuchinformationormethodstheyshouldbemindfuloftheir ownsafetyandthesafetyofothers,includingpartiesforwhomtheyhaveaprofessionalresponsibility. Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,oreditors,assumeanyliabilityforanyinjury and/ordamagetopersonsorpropertyasamatterofproductsliability,negligenceorotherwise,orfromanyuseoroperationof anymethods,products,instructions,orideascontainedinthematerialherein. BritishLibraryCataloguing-in-PublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress ISBN:978-0-12-819311-2 ForInformationonallAcademicPresspublications visitourwebsiteathttps://www.elsevier.com/books-and-journals Publisher:CharlotteCockle AcquisitionsEditor:NancyMaragioglio EditorialProjectManager:ReddingMorse ProductionProjectManager:PremKumarKaliamoorthi CoverDesigner:ChristianBilbow TypesetbyMPSLimited,Chennai,India Contents Listofcontributors xiii 2.3 Selectivemolecularmarkersfor cyanobacterialdiversity 23 1. Cyanobacterial imprints in diversity 2.3.1 16SribosomalRNAgeneasa and phylogeny 1 phylogeneticmarkergene 24 2.3.2 rpoBasanalternativephylogenetic SwatiMishra markergene 24 1.1 Introduction 1 2.3.3 nifHasanalternativephylogenetic 1.2 Biodiversityofcyanobacteria 1 markergene 24 1.3 Morphologicaldiversity(cid:1)basedclassification 2 2.4 Polyphasiccharacterizationforthe 1.4 Habitatheterogeneity(cid:1)based cyanobacterialdiversityandrecent classification 3 developments 25 2.5 Conclusionandfutureprospects 27 1.5 Taxonomyofcyanobacteria 3 Acknowledgments 27 1.5.1 Differenttaxonomicapproaches 3 References 27 1.5.2 Currenttaxonomicstatus 4 1.5.3 Comparisonofdifferenttaxonomic approaches 5 3. Cyanobacteria in tropical and 1.6 Phylogeneticanalysis 5 subtropical marine environments: 1.6.1 16SrRNAgeneasaphylogenetic bloom formation and ecological role 35 marker 6 KolcharM.Rajaneesh,RavidasKrishnaNaik, 1.6.2 Variousotherphylogeneticmarkers 6 RajdeepRoyandPriyaM.D’Costa 1.6.3 Acomparisonbetweenpolyphasicand differentphylogeneticapproaches 7 3.1 Introduction 35 1.6.4 Phylogeneticanalysisofheterocyte- 3.2 Cyanobacterialdistributionaroundthe formingcyanobacteria 8 Indianwaters 36 1.7 Cyanobacterialsystematics:current 3.2.1 ProchlorococcusandSynechococcus 36 challengesandfutureprojections 8 3.2.2 Trichodesmium 38 1.8 Recentdevelopmentsincyanobacterial 3.3 Cyanobacterialdiazotrophs 38 phylogenetictaxonomy 8 3.4 Interactionsbetweenheterotrophicbacteria 1.9 Conclusion 9 andcyanobacteria 39 Acknowledgments 11 3.4.1 The“phycosphere”ofcyanobacteria: References 11 interactionswithprokaryotes 39 Furtherreading 15 3.4.2 Unicellular,free-livingcyanobacteria 39 3.4.3 Filamentous,nonheterocyst-forming 2. Cyanobacterial diversity: molecular cyanobacteria 40 insights under multifarious 3.4.4 Filamentous,heterocyst-forming environmental conditions 17 cyanobacteria 40 3.4.5 Unicellularsymbioticcyanobacteria 41 NidhiKumariandLalChandRai 3.4.6 Cyanobacteria(cid:1)heterotrophicbacteria 2.1 Introduction 17 interactions:biotechnological 2.2 Molecularmethodstoexaminecyanobacterial potential 41 diversity 18 3.5 Conclusion 42 2.2.1 PCR-basedDNAprofilingmethods 19 Acknowledgments 42 2.2.2 PCR-independent/genome-basedDNA References 42 profilingmethods 22 Furtherreading 46 v vi Contents 4 Database resources for cyanobacterial 5.6 Approachestoenhancepigment research 47 production 66 5.6.1 Geneticengineeringapproach 66 AnilKumarandPraffullaKumarArya 5.6.2 Systembiologyapproach 66 4.1 Introduction 47 5.7 Conclusion 67 4.2 Databaseresourcesforcyanobacterial Acknowledgments 67 research 47 References 67 4.2.1 CyanobacterialKnowledgeBase 47 Furtherreading 72 4.2.2 CyanoBase 49 4.2.3 CYORF 49 6 Cyanobacterial membrane biology 4.2.4 cTFbase 49 under environmental stresses with 4.2.5 CyanoPhyChe 49 particular reference to photosynthesis 4.2.6 CyanoClust 50 and photomorphogenesis 73 4.2.7 CyanoEXpress 50 SoniaSen 4.2.8 CyanoLyase 50 4.2.9 Cyanorak 50 6.1 Introduction 73 4.2.10 Cyanosite 50 6.2 Membraneorganizationincyanobacteria 74 4.2.11 CyanoDB 51 6.3 Cyanobacterialmembraneresponseto 4.2.12 SynechoNET 51 environmentalstresses 75 4.2.13 ProPortal 51 6.3.1 Temperaturestress 75 4.2.14 RegCyanoDB 51 6.3.2 Saltstress 76 4.2.15 Cyanobacterialproteinstructure 6.3.3 Drought 77 informationresourceforC1 6.3.4 UV-Bstress 77 metabolism 51 6.3.5 Impactsoflightoncyanobacteria 78 4.2.16 Cyanotype 52 6.4 Conclusionandfutureprospects 79 4.2.17 TAU-MACCultureCollection 52 Acknowledgments 79 4.2.18 CyanoCOG 52 References 80 4.2.19 CyanOmics 52 Furtherreading 84 4.3 Summary 52 Acknowledgment 53 7 Iron homeostasis of cyanobacteria: References 53 advancements in siderophores and Furtherreading 54 metal transporters 85 5 Cyanobacterial pigments and their LeonardS.Fresenborg,JuliaGraf,Hannah fluorescence characteristics: Scha¨tzleandEnricoSchleiff applications in research and industry 55 7.1 Introduction 85 7.1.1 Themetalrequirementof MadanKumarMandal,Ng.KunjaraniChanuand cyanobacteria 85 NehaChaurasia 7.1.2 Theevolutionofmetaluptake 5.1 Introduction 55 systems 89 5.2 Chlorophylls 56 7.2 Siderophore-dependentirontransportin 5.2.1 Physiochemicalcharacterizationsof cyanobacteria 90 cyanobacterialchlorophylls 56 7.2.1 Fe(III)formsoctahedralcomplexes 5.2.2 Industrialapplicationofchlorophylls 58 withsuitableligands 91 5.3 Carotenoids 58 7.2.2 TonB-dependenttransportsystemsfor 5.3.1 Physiochemicalcharacterization 58 iron(cid:1)siderophorecomplexuptake 91 5.3.2 Industrialapplications 60 7.2.3 Thecyanobacterialsiderophores 95 5.4 Phycobiliproteins 60 7.2.4 ThecycleofFe-schizokinenuptake 99 5.4.1 Physiochemicalcharacterization 60 7.2.5 Hemeuptakeincyanobacteria 100 5.4.2 Industrialapplications 62 7.3 ReductiveIronUptake 100 5.5 Scytonemin 64 7.4 Currentviewonironuptakeby 5.5.1 Physiochemicalcharacterizations 64 siderophore-producingcyanobacteria 101 5.5.2 Industrialapplicationsofscytonemin 65 7.5 Uptakeofmetalsotherthaniron 101 Contents vii 7.5.1 Afunctionofsiderophoresin 9 Cyanobacterial genome editing generalmetalsequestration 101 toolboxes: recent advancement and 7.5.2 Manganeseuptakebycyanobacteria 102 future projections for basic and 7.5.3 Thezincandcoppertransportacross synthetic biology researches 129 membranes 102 7.5.4 Theuptakeofnickelandcobaltby SandeepKumarSingh,AlokKumarShrivastava, cyanobacteria 103 AjayKumar,VipinKumarSingh,DeepankerYadav, 7.6 Theregulationofmetaltransport 103 ArpanModi,WenjingWang,AvinashSingh, 7.6.1 Two-componentmetalsensor ToolikaSingh,VijiSittherandPrashantKumar systems 104 Singh 7.6.2 Thecentralfur-mediatedregulation 105 Abbreviations 129 7.6.3 Regulationofmetalhomeostasisby 9.1Introduction 129 smallRNAs 106 9.2Recentadvancesincyanobacterial 7.6.4 Thelinkbetweenmetal-dependent andabioticcondition(cid:1)dependent toolboxes 131 9.2.1 Promoters 131 regulation 108 9.2.2 Riboswitches 134 7.6.5 TonB-dependenttransporter-based 9.2.3 Engineeringofribosome-binding regulation:anundiscovered site 135 principleincyanobacteriatodate 108 9.2.4 CRISPR/Cassystem 136 7.6.6 Thedifferentlayersofmetalquota 9.2.5 SmallregulatoryRNAsasa regulation 108 toolbox 137 7.7 Futureperspective 109 9.2.6 Genome-scalemodeling Acknowledgment 110 approaches 139 References 110 9.2.7 Othergenetictoolsfor cyanobacteria 140 8 Molecular chaperones in protein 9.2.8 Roleofhigh-throughputscreening folding and stress management in systemsforgenetictool cyanobacteria 119 development 140 9.2.9 Transcriptionalregulatorsand AroniChatterjee,KeshavRajarshi,HiyaGhosh, self-cleavableriboswitch MrityunjayKSingh,OmPrakashRoyand development 140 ShashikantRay 9.2.10 Progressandoptimizationofnew 8.1 Introduction 119 genomeeditingtoolsbasedonthe 8.2 Cyanobacteriaandabioticstress 119 nativeCRISPR/Cassystems 141 8.3 Chaperones:whatarethey? 120 9.2.11 mRNAenhancersadvancement 141 8.4 Roleofmolecularchaperonesinprotein 9.2.12 User-friendlygenomemodelingtool foldingandaggregation 121 development 141 8.5 Molecularchaperonesandcellularstress 121 9.3Large-scaletoolboxesapplicationfor 8.6 Molecularchaperonesincyanobacteria 122 cyanobacterialcultivation 141 8.6.1 Theheat-shockresponsesystem 122 9.3.1 Forgeneexpressionanalysisthe 8.6.2 Smallheat-shockproteins 123 nativeplasmidsorneutralsites 142 8.6.3 hsp100(clpB)family 123 9.3.2 Controlledexpressionof 8.6.4 hsp70/hsp40/hsp25family 123 cyanobacterialgenes:searchforideal 8.6.5 hsp90family 123 induciblemodule 142 8.6.6 hsp60/hsp10family 124 9.3.3 Developingandextendingtoolboxes 8.7 Regulationofexpressionpatternof forsyntheticorindustrialbiology 142 chaperonesunderenvironmentsof 9.4Conclusion 142 stress 124 Acknowledgments 142 8.8 Understandingthebasicsofchaperone References 143 functioning 124 Furtherreading 149 8.9 Conclusion 125 8.10 Futureprospects 126 References 126 viii Contents 10 Impact of pesticides applications on the 12.1 Introduction 173 growth and function of 12.2 Processofextractionofbioactive cyanobacteria 151 compoundsfromalgae 174 12.3 Primaryscreeningforbioactive VipinKumarSingh,SandeepKumarSingh, compoundsfromalgae:screening PrashantKumarSingh,HariomVerma, assays 174 K.D.Pandey,P.K.SinghandAjayKumar 12.4 Antibacterialapplicationsofalgaeand cyanobacteria 175 10.1 Introduction 151 12.5 Antifungalapplicationsofalgaeand 10.2 Nitrogenfixersincultivatedrice cyanobacteria 178 environment 152 12.6 Antiprotozoalapplicationsofalgaeand 10.3 Factorsinfluencingthecyanobacterial cyanobacteria 179 occurrenceandtheprocessofnitrogen 12.7 Antioxidantapplicationsofalgaeand fixation 153 cyanobacteria 179 10.4 Distributionandactionpatternof 12.8 Pigments 179 pesticides 153 12.9 Lipids 180 10.5 Impactofpesticidesonthenontarget 12.10 Polysaccharides 180 cyanobacteria 154 12.11 Antioxidantcomponentspossessing 10.5.1 Effectofinsecticideson antiinflammatoryactivity 180 cyanobacteria 154 12.12 Anticancerapplicationsofalgaeand 10.5.2 Effectofherbicideson cyanobacteria 181 cyanobacteria 157 12.13 Antiviralapplicationsofalgaeand 10.6 Futureperspective 158 cyanobacteria 183 References 158 12.14 Anticoagulantapplicationsofalgaeand Furtherreading 162 cyanobacteria 183 12.15 Immunosuppressiveapplicationsof 11 Cyanoomics: an advancement in the algaeandcyanobacteria 183 fields cyanobacterial omics biology 12.16 Clinicaltrialstatusofalgaeand with special reference to proteomics cyanobacteria 184 and transcriptomics 163 12.17 Conclusion 185 SavitaSingh Acknowledgement 186 References 186 11.1 Introduction 163 11.2 Insightstocyanobacterialomicsandits 13 Cyanobacterial stress-responsive perspectives 164 small RNAs (sRNAs): players of stress 11.3 Functionalgenomics:atranscriptomic and developmental responses 195 andproteomicperspective 165 11.3.1 Developmentsinthefieldof TusharRanjan,MayankKumar,BishunDeoPrasad, cyanobacterialtranscriptome 165 RaviRanjanKumar,AwadheshKumarPal, 11.3.2 Developmentsinthefieldof Md.AnsarandBirenderSingh cyanobacterialproteomics 165 13.1 Introduction 195 11.3.3 Interactomeandmetabolic 13.2 Mechanismandfunctionsof profiling 166 cyanobacterialsRNAs 196 11.4 Bioinformatictools:thesupportsystem 167 13.3 sRNAstakepartindifferentstress- 11.5 Conclusionandprospects 168 responsepathways 197 Acknowledgments 168 13.3.1 Responsetolightandoxidative References 168 stress 197 Furtherreading 171 13.3.2 Responsetoironstress 199 13.3.3 Responsetolightandcarbon- 12 Algae and cyanobacteria as a source limitedstress 199 of novel bioactive compounds for 13.3.4 Responseto1-butanolstress 200 biomedical applications 173 13.3.5 Responsetohighsaltandcalcium SudarshanKini,MithoorDivyashree,MadhuK limitation 200 ManiandBangeraSheshappaMamatha 13.3.6 Responsetophosphorous limitation 201 Contents ix 13.3.7 Responsetonitrogenstarvation stress 201 15.7Mycosporine-likeaminoacidsas 13.3.8 sRNAscontrollingphotosynthetic multipurposesecondarymetabolites 227 functions 201 15.7.1 Stabilityofmycosporine-like 13.4 RoleofcyanobacterialsRNAsingrowth aminoacids 227 anddevelopment 201 15.7.2 Mycosporine-likeaminoacids 13.5 Conclusion 202 asanitrogensource 227 Acknowledgment 202 15.7.3 Mycosporine-likeaminoacidsas Conflictofinterest 202 antioxidants 227 References 202 15.8Applicationofmycosporine-likeamino acids 228 14 Physiological aspects of cyanobacterial 15.9Conclusionandprospects 228 nitrogen fixation and its applications Acknowledgments 228 in modern sciences 205 Conflictofinterest 228 References 229 RakeshSilSarmaandPravinPrakash Furtherreading 232 14.1 Introduction 205 14.2 Cyanobacteriaandnutrientmetabolism 16 Heterocyst and akinete differentiation inplants 206 in cyanobacteria: a view toward 14.3 Heterocystandnitrogenfixationin cyanobacterial symbiosis 235 cyanobacteria 206 PratikaSingh,AzmiKhanandAmritaSrivastava 14.4 Roleofnitrogenaseanditsregulationin cyanobacteria 207 16.1 Introductionofcyanobacteria:acloser 14.5 Hydrogenaseenzymesanditsregulation look 235 incyanobacterialsystems 208 16.2 Structuralvariantsofvegetativecells 236 14.6 Cyanobacteriaandsustainable 16.2.1 Heterocyst 236 agriculture 209 16.2.2 Genesrequiredforheterocyst 14.7 Cyanobacteriaanditsindustrial differentiation 236 applications 210 16.2.3 Heterocystspacing 237 14.8 Conclusionandprospect 211 16.3 Akinete 238 Acknowledgment 212 16.3.1 Factorsaffectingakinete References 212 differentiation 238 Furtherreading 217 16.3.2 Genesrequiredforakinete differentiation 240 15 Ultraviolet-screening compound 16.3.3 Akinetegermination 240 mycosporine-like amino acids in 16.4 Cellularlevelfunctionaldiversityin cyanobacteria: biosynthesis, cyanobacteria 241 functions, and applications 219 16.4.1 Heterocystmetabolism 241 16.4.2 Roleofakinetesasstressadaptor 242 DeepakK.Singh,JainendraPathak,AbhaPandey, 16.5 Cyanobacterialsymbiosis 242 VidyaSingh,HaseenAhmed,Rajneesh,Deepak 16.6 Conclusion 243 KumarandRajeshwarP.Sinha Acknowledgment 243 Abbreviations 219 References 243 Furtherreading 248 15.1Introduction 219 15.2Distributionofmycosporine-likeamino 17 Cyanobacterial peroxiredoxins and acidsamongcyanobacteria 220 their role in cyanobacterial stress 15.3Chemicalstructureofmycosporine-like aminoacids 221 biology 249 15.4Geneticsandbiosyntheticpathwaysof AlokKumarShrivastava,PrashantKumarSingh,Viji mycosporine-likeaminoacids 221 Sitther,ShilpiSinghandSonamSrivastava 15.5Stabilityofmycosporine-likeaminoacids undervariousenvironmentalstresses 225 17.1 Introduction 249 17.2 EvolutionofPrxs 251 15.6Potentialsofmycosporine-likeamino 17.3 ClassificationofPrxs 252 acidsasphotoprotectant 226 x Contents 17.4 Universalcharacteristicofthe 19 Cyanobacteria: as a promising peroxiredoxincatalyticcycle 254 candidate for heavy-metals 17.5 MechanismofPrxs’action 255 removal 291 17.5.1 Catalysisreactionoftheperoxide reduction:theenzymatic DnyaneshwarK.Kulal,PrakashC.Loni,Criss reactionatthecysteineresidue 256 Dcosta,SurajitSomeandPramodK.Kalambate 17.5.2 TherepairingproteinsofPrx 256 19.1 Introduction 291 17.5.3 Thehyperoxidationofenzyme 19.2 Effectofheavy-metalpollutionon peroxiredoxin 256 surfaceandgroundwaterquality 294 17.6 Peroxiredoxinandcyanobacteria 257 19.3 Bioremediationapproachesfor 17.6.1 1-Cysperoxiredoxin 260 inorganicpollutants 294 17.6.2 2-Cysperoxiredoxin 260 19.4 Cyanobacteriuminbioremediation 295 17.6.3 TypeIIperoxiredoxin 260 19.4.1 Coprecipitation 295 17.6.4 PeroxiredoxinQ 261 19.4.2 Cloud-pointextraction 295 17.7 Peroxidaseactivityofperoxiredoxins 261 19.4.3 Ionexchange 296 17.8 Cyanobacteriaandalkyl 19.4.4 Solid-phaseextraction 296 hydroperoxides 262 19.5 Cyanobacteriaforsorption 296 17.9 Conclusion 263 19.6 Futureperspectives 297 Acknowledgments 264 Acknowledgment 297 References 264 References 297 Furtherreading 268 20 Dynamics of harmful cyanobacterial 18 Cyanobacteria as a biofuel source: blooms and their toxins: advances and applications 269 environmental and human health VijiSitther,BehnamTabatabai,SomayehGharaie perspectives and management Fathabad,SamsonGichuki,HuanChenand strategies 301 AnithaChristyS.Arumanayagam AnjaliSinghandPiyooshKumarBabele 18.1 Introduction 269 20.1 Introduction 301 18.2 Cyanobacteriaasabiofuelsource 269 20.1.1 Cyano-Hbs:featuresand 18.2.1 Biofuelmarketandfuelquality 269 dynamics 302 18.2.2 Typesofcyanobacteria-derived 20.2 Environmentalfactorsdriving biofuels 270 Cyano-Hbsgrowthandexpansion 303 18.2.3 Majorstepsofcyanobacteria-to- 20.2.1 Nutrientavailabilityand fuelprocess 270 eutrophication 303 18.3 Othercyanobacteria-basedapplications 274 20.2.2 RisingCO andtemperature 304 18.3.1 Coproducts 274 2 20.2.3 Stratificationandradiations 304 18.3.2 Nutraceuticals 274 20.3 Cyanotoxinsandhumanhealth 18.3.3 Pharmaceuticals 275 concerns 305 18.3.4 Cosmeticsanddyes 276 20.4 Cyanotoxin:structural,molecular 18.4 Advancesforimprovingcommercial biologyandtheirmodeofaction 305 viabilityofcyanobacteria-basedbiofuels 276 20.4.1 Hepatotoxins 305 18.4.1 Energyproductivity 276 20.4.2 Neurotoxins 308 18.4.2 Designoptimization 278 20.4.3 Dermotoxins 309 18.5 Challengesinscale-up 281 20.5 Methodsofcyanotoxinsdetection 310 18.5.1 Cultivationandharvesting 281 20.6 Managementstrategies:bloom 18.5.2 Marketchallenges 282 preventionandcyanotoxinstreatment 310 18.6 Conclusionandfutureprospects 282 20.7 Conclusion 312 Acknowledgments 282 Acknowledgment 313 References 282 References 313 Furtherreading 289
The list of books you might like
