Engineering of Microbial Biosynthetic Pathways PDF
Preview Engineering of Microbial Biosynthetic Pathways
Vijai Singh · Ajay Kumar Singh Poonam Bhargava · Madhvi Joshi Chaitanya G. Joshi Editors Engineering of Microbial Biosynthetic Pathways Engineering of Microbial Biosynthetic Pathways (cid:129) (cid:129) Vijai Singh Ajay Kumar Singh (cid:129) (cid:129) Poonam Bhargava Madhvi Joshi Chaitanya G. Joshi Editors Engineering of Microbial Biosynthetic Pathways Editors VijaiSingh AjayKumarSingh DepartmentofBiosciences,Schoolof DepartmentofFoodProcessEngineering Science SamHigginbottomUniversityofAgriculture, IndrashilUniversity TechnologyandSciences Mehsana,Gujarat,India Allahabad,UttarPradesh,India PoonamBhargava MadhviJoshi GujaratBiotechnologyResearchCenter GujaratBiotechnologyResearchCenter DepartmentofScienceandTechnology DepartmentofScienceandTechnology Gandhinagar,Gujarat,India Gandhinagar,Gujarat,India ChaitanyaG.Joshi GujaratBiotechnologyResearchCenter DepartmentofScienceandTechnology Gandhinagar,Gujarat,India ISBN978-981-15-2603-9 ISBN978-981-15-2604-6 (eBook) https://doi.org/10.1007/978-981-15-2604-6 #SpringerNatureSingaporePteLtd.2020 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionor informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbook arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsorthe editorsgiveawarranty,expressedorimplied,withrespecttothematerialcontainedhereinorforany errorsoromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictional claimsinpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSingaporePteLtd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Foreword Iamhappytowriteanintroductorymassagefor“EngineeringofMicrobialBiosyn- thetic Pathways,” a timely volume on the rapidly evolving field of metabolic engineering. The engineering of biosynthetic pathways has the potential to produce a large amount of valuable biomolecules by extension or modification of biosynthetic pathwaysinawiderangeoforganisms.Modifiedorganismshaveabilitytoproduce ahighamountofchemicals,drugs,enzymes,aminoacids,antibiotics,biofuels,and so on. The recent advances in metabolic engineering along with fermentation and bioprocess technology have widened our understanding of industrial scale produc- tion of biomolecules in an eco-friendly manner. This book covers key areas of metabolicengineeringthatwouldallowthereaderstoeasilyunderstandtheconcepts andimplementthem. This comprehensive book contains 17 chapters with several aspects of biosyn- thetic pathways from basic to advance level for laboratory scale to industrial scale production of biomolecules. It covers a number of major topics including an introduction to metabolic engineering, strain development and improvement, a biosensor for metabolite detection, metabolic engineering for the production of a wide range of industrially useful enzymes, proteins, organic acids, vitamins, antibiotics, therapeutics, chemicals, and biofuels, genome editing via CRISPR- Cas9 system, along with ethical and regulatory issues which have been presented usinganeasy-to-understandyetelaborativenarration. IampleasedtorecognizethevaluableeffortsofDr.VijaiSingh,Dr.AjayKumar Singh,Dr.PoonamBhargava,Dr.MadhviJoshi,andProf.ChaitanyaG.Joshi,who collaborativelybroughtoutanexcellentvolumethroughthesupportfromSpringer Nature. I strongly believe that this book will be really useful for the students, researchers,scientists,stakeholdersandpolicymakers,amongmanyothers. IndrashilUniversity JhilluSinghYadav Mehsana,Gujarat,India vv Preface Engineeringofmicrobialbiosyntheticpathwayshasthepotentialtoproduceabroad spectrum of biomolecules by extension or modification of native pathways of microorganisms. It has recently gained a lot of scientific and industrial attention because of its capacity to overproduce targeted molecules in a renewable and sustainable manner. The production and optimization can be easily tuned or regulated by a wide range of synthetic biology, molecular biology, and genome editing tools. Though the natural microorganisms have the potential to produce requiredbiomolecules,theproductionisnotenoughforcommercializationpurpose to fulfill the current market demands. Therefore, either assembly of biosynthetic pathwaysinheterologoushostsorredesigningtheexistingbiosyntheticpathwayin naturalorganismsisrequisite. Additionally, a pressing need has arisen to improve the quality of products for good health and management of diseases by using biomolecules that can be pro- ducedinagreenmanner.Therecentadvancesinmetabolicengineeringalongwith fermentation and bioprocess technology have widened our understanding of industrial-scale production in a simple, cost-effective, and sustainable manner. This book covers a wide range of information from basic to advanced level for laboratory-scale to industrial-scale fermentation and production. The book is focusedondifferentaspectsofmetabolicengineering,strainengineering,techniques for detection and extraction of metabolites, biosensors, fermentation methods, genetic engineering and synthetic biology toolboxes, and ethical, patents, and regulatory issues. This book also covers a wide range of topics on microbial production of vitamins, enzymes, therapeutics, antibiotics, biofuels, amino acids, andmuchmore. Thisbookbringstogetherthecontributionsofeminentscientistsworldwidewho have extensive experience in different aspects of microbial engineering and its applications.Thisbookhasbeendesignedtobenefitstudents,researchers,scientists, stakeholders,policymakers,andmanymore.Itcoversarichliterarytextofexcellent depth,clarity,andcoveragewhichallowstoeasilyunderstandandstartresearchin this area. This book is a compilation of 17 chapters written by eminent scientists from five countries including China, India, Japan, South Africa, and the United Kingdom. vii viii Preface Wehopethatthisbookwillnotonlyprovideabetterunderstandingofthedesign ofbiosyntheticpathwaysbutalsotriggerunansweredquestions.Despitethefactthat immense efforts have been invested to make this book user-friendly, we are aware that the first version always comes withbugs. This book will bean excellent basis fromwhichscientificknowledgecangrow,widen,andacceleratedesignaswellas the construction of a metabolic pathway for high production of biomolecules. We wouldbedelightedtoreceivesuggestionstoimprovethebookfurther. Mehsana,Gujarat,India VijaiSingh Allahabad,UttarPradesh,India AjayKumarSingh Gandhinagar,Gujarat,India PoonamBhargava Gandhinagar,Gujarat,India MadhviJoshi Gandhinagar,Gujarat,India ChaitanyaG.Joshi Acknowledgments VijaiSingh IamdelightedtoexpressmysinceregratitudeanddeepappreciationtoDr.J.S. Yadav,Director(Research),IndrashilUniversity,India,forextendinghisoutstand- ingsupportandmotivationtocompletethisbook.Iwouldliketoextendmythanks to all coeditors (Dr. Ajay Kumar Singh, Dr. Poonam Bhargava, Dr. Madhvi Joshi, and Prof. Chaitanya G. Joshi) of this book who gave me outstanding personal and professionalsupportaswellasinspirationtoconcludethisbook. Iamhappytoexpressmythankstoalltheauthorsfortheirexcellentcontributions tothisbook.IwouldliketothankDr.BhavikSawhney(associateeditor—Biomedi- cine) and Ms. Vaishnavi Venkatesh (production editor) from Springer for their supportandexceptionalmanagementofthisproject. Igreatlyappreciate thesupportofmystudents Mr.Nisarg GohilandMs.Gargi Bhattacharjee, whose discussion and comments helped to shape this book. I thank Dr.IndraMani,Dr.SatyaPrakash,andthosewhosenamesdonotfeatureherebut havedirectlyorindirectlycontributedtoshapingthisproject. I wish to express my gratitude to my beloved wife Pritee Singh for her endless support,patience,andinspiration.LotsofaffectionformykidsAaradhyaandAyush whomissedmeduringthisproject. I would like to warmly thank the faculty and staff of Indrashil University for providingagreatworkingenvironment. Last but not least, my sincere thanks to GOD for his supreme POWER and endowingmetolivewithjoyandvictoryintheshapeofthisbook. AjayKumarSingh Iwouldlike toexpressmyspecial thanksofgratitudetoDr.VijaiSingh forhis ableguidanceandperseveranceforcompletingthebook.Ialsothankalleditorsfor their valuable guidance, keen interest and encouragement at the various stages of completion of this book. I acknowledge with thanks the kind of patronage, loving inspiration, and timely guidance that I have received from coeditors Dr. Poonam Bhargava,Dr.MadhaviJoshi,andProf.ChaitanyaG.Joshi. I also take this opportunity to express a deep sense of gratitude to my beloved wifeDr.PunamSinghforhersupportandencouragement. ix x Acknowledgments Finally, I am fortunate that I had the kind of association and their exemplary guidanceandcarefulmonitoringthroughoutthecompletionofthebook. PoonamBhargava I express my sincere thanks to Prof Chaitanya G. Joshi (Director, GBRC, Gandhinagar) and Dr. Madhvi Joshi (Joint Director) for rendering the support for theworkcarriedoutforthebook.IwarmlythankmyfelloweditorDr.VijaiSingh whose meticulous work has resulted in the form of this book. I am thankful to Ms. Pooja Doshi, Ms. Priyanka Sharma, and Dr. Manjushree who helped in the formulationofbookchaptersandalsoputinahelpinghandasandwhenrequired. Ithankmyfamilyforthecontinuoussupportinmyworkandalsothankstothe almightyforgivingmethestrengthtocontributetothebook. MadhviJoshi I am thankful to Prof. Chaitanya G. Joshi, Director, Gujarat Biotechnology Research Center (GBRC), Govt. of Gujarat, Gandhinagar, for his support and encouragement.Iamthankfultotheco-editorsandGBRCstaffforputtingintheir effortstobringshapestothebook. Iwishtoexpressmygratitudetoallfamilymembersfortheirsupport,inspiration, andpatience.Myspecialthanksgotomykidswhomissedmeduringthisproject. ChaitanyaG.Joshi Iexpressmysincerethankstoalltheauthorsfortheirexcellentcontributionsto thisbook.Iamthankfultoallcoeditorsofthebookwhohaveworkedrelentlesslyfor thecompletionofthebook.Iamalsothankfultoallthecoeditorsfortheirsupport. I wish to thank Gujarat State Biotechnology Mission and GBRC, Gandhinagar, staffforprovidingagreatsupportiveenvironment.Onapersonallevel,mysincere thankstoallmyfamilymembers,students,andfriendsfortheirgreatsupport. Contents 1 AnIntroductiontoDesignofMicrobialStrainusingSynthetic BiologyToolboxesforProductionofBiomolecules. . . . . . . . . . . . . 1 GargiBhattacharjee,NisargGohil,andVijaiSingh 2 MicrobialStrainEngineering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 GauravSanghavi,PrabuddhaGupta,MahendrapalsinghRajput, TejasOza,UjwalTrivedi,andNitinKumarSingh 3 TechniquesforDetectionandExtractionofMetabolites. . . . . . . . . 33 PayalGupta,SonamGupta,andVikasPruthi 4 GeneticallyEncodedBiosensorsandTheirApplicationsinthe DevelopmentofMicrobialCellFactories. . . . . . . . . . . . . . . . . . . . . 53 YaokangWu,GuochengDu,JianChen,andLongLiu 5 MetabolicProductsofMixedCultureFermentation. . . . . . . . . . . . 75 SiddharthaPandey,NitinKumarSingh,TaraChandYadav, AnkurKumarBansal,ArtiThanki,ManishYadav,andJayatoNayak 6 RecentAdvancesinGeneticEngineeringToolsforMetabolic Engineering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 JerolenNaidoo,EzioFok,LichelleGrobler,ReitumetseMolaoa, ZandileNxumalo,P.Selvamani,S.Latha, andDeepakB.ThimiriGovindaRaj 7 RecentDevelopmentsinSyntheticBiologyToolbox. . . . . . . . . . . . . 111 PriyankaPatelVatsa,ManjuShri,PoonamBhargava, ChaitanyaG.Joshi,andMadhviJoshi 8 Ethical,Patent,andRegulatoryIssuesinMicrobialEngineering. . . 133 SumerSinghMeenaandAneeMohanty 9 MicrobialProductionofVitamins. . . . . . . . . . . . . . . . . . . . . . . . . . 143 IndraMani xxii
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