Current Developments in Biotechnology and Bioengineering. Functional Genomics and Metabolic Engineering PDF
Preview Current Developments in Biotechnology and Bioengineering. Functional Genomics and Metabolic Engineering
Current Developments in Biotechnology and Bioengineering Functional Genomics and Metabolic Engineering Edited by Paramasamy Gunasekaran, Santosh Noronha, Ashok Pandey AMSTERDAM l BOSTON lHEIDELBERG lLONDON lNEWYORK lOXFORD PARIS l SANDIEGO lSANFRANCISCOlSINGAPORE lSYDNEYl TOKYO Elsevier Radarweg29, POBox211,1000 AEAmsterdam,Netherlands TheBoulevard,LangfordLane,Kidlington, OxfordOX51GB,United Kingdom 50HampshireStreet,5thFloor,Cambridge, MA02139,United States Copyright©2017 ElsevierB.V. Allrights reserved. Nopartofthispublication maybereproducedortransmittedinanyform orbyany means, electronicormechanical,including photocopying,recording,oranyinformation storage andretrievalsystem,without permissioninwritingfromthepublisher.Detailsonhowto seekpermission,furtherinformation aboutthePublisher’s permissions policiesandour arrangements withorganizations suchastheCopyrightClearance CenterandtheCopyright LicensingAgency,canbefoundatourwebsite:www.elsevier.com/permissions. 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LibraryofCongress Cataloging-in-Publication Data Acatalog recordforthisbook isavailablefromtheLibraryofCongress BritishLibraryCataloguing-in-Publication Data Acataloguerecord forthis bookisavailablefromtheBritishLibrary ISBN:978-0-444-63667-6 ForinformationonallElsevierpublications visitourwebsiteathttps://www.elsevier.com/ Publisher:JohnFedor AcquisitionEditor:Kostas Marinakis EditorialProjectManager:Anneka Hess ProductionProjectManager: MohanapriyanRajendran Designer:GregHarris TypesetbyTNQBooksandJournals List of Contributors P.K. Agarwal Gennova BioPharmaceuticals, Pune, Maharasthra, India B. Ashokkumar Madurai Kamaraj University, Madurai, Tamil Nadu, India A. Badri Indian Institute of Technology Madras, Chennai, Tamil Nadu, India D.Choudhury IndianInstituteofTechnologyBombay,Mumbai,Maharasthra,India A. Dasgupta Madurai Kamaraj University, Madurai, Tamil Nadu, India K. Gandhimathi Madurai Kamaraj University, Madurai, Tamil Nadu, India P. Gunasekaran Madurai Kamaraj University, Madurai, Tamil Nadu, India A.H. Iyer Indian Institute of Technology-Kanpur, Kanpur, Uttar Pradesh, India Kirti Jain Indian Institute of Technology Bombay, Mumbai, Maharashtra, India Kunal Jain Sardar Patel University, Vallabh Vidyanagar, Gujarat, India M. Jaya PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, India J. Johnson Sardar Patel University, Vallabh Vidyanagar, Gujarat, India K. Krishnan Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India D. Madamwar Sardar Patel University, Vallabh Vidyanagar, Gujarat, India S. Majumdar Indian Institute of Technology-Kanpur, Kanpur, Uttar Pradesh, India D. Mehta University of Delhi South Campus, New Delhi, India S.B. Noronha IIT Bombay, Mumbai, Maharasthra, India M.K. Prajapat IndianInstituteofTechnologyBombay,Mumbai,Maharashtra,India J. Rajendhran Madurai Kamaraj University, Madurai, Tamil Nadu, India xi xii List of Contributors T. Rajesh The University of New South Wales, Sydney, NSW, Australia K. Raman Indian Institute of Technology Madras, Chennai, Tamil Nadu, India S. Ramasamy Madurai Kamaraj University, Madurai, Tamil Nadu, India J. Ranjani Madurai Kamaraj University, Madurai, Tamil Nadu, India S. Saini Indian Institute of Technology Bombay, Mumbai, Maharashtra, India M. Saravanan IndianInstituteofTechnology-Kanpur,Kanpur,UttarPradesh,India K. Satpute IIT Bombay, Mumbai, Maharasthra, India T. Satyanarayana University of Delhi South Campus, New Delhi, India P. Singh Indian Institute of Technology-Kanpur, Kanpur, Uttar Pradesh, India A. Sivakumar Madurai Kamaraj University, Madurai, Tamil Nadu, India A. Srinivasan Indian Institute of Technology Madras, Chennai, Tamil Nadu, India G.A. Swaminathan Embio Limited, Mumbai, Maharasthra, India T. Udhayabanu Madurai Kamaraj University, Madurai, Tamil Nadu, India V. Uppada Guru Ghasidas University, Bilaspur, Chattisgarh, India P. Varalakshmi Madurai Kamaraj University, Madurai, Tamil Nadu, India G. Velmurugan Madurai Kamaraj University, Madurai, Tamil Nadu, India J.C. Yacob Madurai Kamaraj University, Madurai, Tamil Nadu, India About the Editors P. Gunasekaran Professor P. Gunasekaran is a senior professor of Microbiology in India. He has 33years of teaching and research experience in microbiology, biotechnology, and genomics and is currently guiding eight Ph.D. students at MKU. He has published 150 research articles in national andinternationaljournalswithacumulativeimpactfactor of250,andhisresearcharticleshavebeencited1923time in various journal articles with an h-index of 23 and i10 index of 50. In addition, he has contributed 28 book chapters to books published by leading publishers. Professor Gunasekaran has presented his research findings at more than 200 national and inter- national conferences and serves as the editor of three international journals: Applied Biotechnology and Biotechnology (USA), Journal of Microbiology and Biotechnology (SouthKorea),andIndianJournalofMicrobiology(India).Inaddition,hehasservedasa guesteditorofspecialissuesinleadingIndianjournalssuch asCurrent Science, Journal of Scientific Research, Indian Journal of Biotechnology, and Indian Journal of Experimental Biology. He has received several medals, awards, and honors in India and abroad for his immense research contributions. Major recognitions include an Outstanding Service Award from the International Board of the American Society for Microbiologyd2011. Santosh Noronha Dr. Santosh Noronha is a biochemical engineerby training whohasevolvedmultidisciplinaryinterests.Hehasfocused onunderstandingvariousmetabolicandregulatoryaspects of microbial systems, toward rationally manipulating their productivity for the production of therapeutics. He is an assistant professor in the Department of Chemical Engineering, Indian Institute of Technology, Mumbai, India. xiii xiv About the Editors Ashok Pandey ProfessorAshokPandeyisEminentScientistattheCenterof Innovative and Applied Bioprocessing, Mohali (a national institute under the Department of Biotechnology, Ministry of Science and Technology, Government of India), and former chief scientist and head of the Biotechnology DivisionattheCSIR’sNationalInstituteforInterdisciplinary Science and Technology at Trivandrum. He is an adjunct professor at Mar Athanasios College for Advanced Studies Thiruvalla,Kerala,andatKalasalingamUniversity,Krishnan Koil, Tamil Nadu. His major research interests are in the areas of microbial, enzyme, and bioprocess technology, which span various programs, including biomass to fuels and chemicals, probiotics and nutraceuticals, industrial enzymes, solid-state fermentation, etc. He has more than 1100 publications and communications, which include 16 patents,50+books,125bookchapters,and425originalandreviewpapers,withanhindex of 75 and more than 23,500 citations (Google Scholar). He has transferred several tech- nologiestoindustriesandhasbeenanindustrialconsultantforaboutadozenprojectsfor Indian and international industries. Professor Pandey is the recipient of many national and international awards and fellowships, which include Elected Member of the European Academy of Sciences and Arts, Germany; Fellow of the International Society for Energy, Environment and Sustainability; Fellow of the National Academy of Science (India); Fellow of the Biotech Research Society, India; Fellow of the International Organization of Biotechnology and Bioengineering;FellowoftheAssociationofMicrobiologistsofIndia;honorarydoctorate degree from the Universite´ Blaise Pascal, France; Thomson Scientific India Citation Laureate Award, United States; Lupin Visiting Fellowship; Visiting Professor at the Universite´ Blaise Pascal, France, the Federal University of Parana, Brazil, and the E´cole Polytechnique Fe´de´rale de Lausanne, Switzerland; Best Scientific Work Achievement Award, Government of Cuba; UNESCO Professor; Raman Research Fellowship Award, CSIR;GBF,Germany,andCNRS,Francefellowships;YoungScientistAward;andothers. He was chairman of the International Society of Food, Agriculture and Environment, Finland (Food & Health) during 2003e04. He is the Founder President of the Biotech Research Society, India (www.brsi.in); International Coordinator of the International Forum on Industrial Bioprocesses, France (www.ifibiop.org); chairman of the InternationalSocietyforEnergy,Environment&Sustainability(www.isees.org);andvice president of the All India Biotech Association (www.aibaonline.com). Professor Pandey About the Editors xv iseditor-in-chiefofBioresourceTechnology,HonoraryExecutiveAdvisoroftheJournalof Water Sustainability and Journal of Energy and Environmental Sustainability, subject editoroftheProceedingsoftheNationalAcademyofSciences(India),andeditorialboard member of several international and Indian journals, and also a member of several national and international committees. Preface ThisisthesecondvolumeinaseriesbeingbroughtoutbyElsevieronCurrentDevelopments inBiotechnologyandBioengineering(Editor-in-Chief:AshokPandey),anditcoversadvances intheareasoffunctionalgenomicsandmetabolicengineering.Itseekstoaddressandsurvey frontier research issues that have an impact on our understanding of cellular and genetic regulation,withtheultimateintentofunderstandingandimplementingrationalstrain-level interventions that result in improved industrial bioprocesses. Students looking to enter into this endeavor will find substantially detailed material that helps them come up to speed; moreexperiencedpractitionersinthefieldwillfindthistobeaconvenientreferencesource. In this context, this book seeks to bridge the gap between introductory textbooks at one extreme and original research articles at the other. Thereare12chapterspresentedinthisvolume,intwosections;abriefoverviewofthese contributionsisprovided below.Thefirstsection providessurveysofworkin thedomainof functional genomics. In the first contribution, Majumdar et al. survey aspects of functional epigenetics,includingitsinvolvementinseveraldiseases,andsuggestapproachestowardthe characterization of epigenetic changes on a genome. This sets up the intriguing possibility of the manipulation of the epigenome itself. The second chapter by Johnson et al. surveys advancesmadeinthedomainoffunctionalmetagenomics.Inadditiontomassivelyparallel sequencing of metagenomes, the customization of other omics technologies now offers the potential for identification of individual traits of interest. Mehta and Satyanarayana provide an overview of the application of functional geno- micstowardprovidingadetailedunderstandingoftheevolution,physiology,andadaptation of extremophilic bacteria. Udhayabanu and others provide, in the next chapter, a review of the functional genomics of the transport of riboflavin, an essential micronutrient. A description of how riboflavin transporter malfunction arises and the resultant clinical indications is also provided. Velmurugan and others next survey the biology of microRNAs (miRNAs); these small single-stranded RNA molecules play a significant role in regulation by facilitating post- translationalsilencing.Thispromisestobeavaluableapproachforthedevelopmentoflow- cost diagnostics, as well as for therapeutic intervention in human disease conditions. In the next contribution, Ranjani and coworkers look into the application of functional genomics techniques for elucidation of pathogenesis mechanisms and in particular the nature of hostepathogen interactions. The set of known pathogen genomes is limited; transcriptome andproteomeanalysesprovideleadsrelevanttotheinferenceofrelevantsignalingpathways. The applicability of transposon mutagenesis approaches toward the identification of hoste pathogen interactions and genes associated with infection is also discussed. In the final contributioninthissection,RajeshandJayadiscussadvancesinnext-generationsequencing technologies. The second section covers aspects of computational approaches to metabolic engi- neering and of a few case studies reviewing experimental efforts recently described in the field. Badri and coworkers start this section with a review of in silico approaches that have been deployed; these methods attempt to predict targets for rational strain development by xvii xviii Preface combiningnetwork-basedinformationwithkineticandthermodynamicconstraints.Jainand others next elaborate further on constraint-based model development and identify applica- tionsofsuchapproachesinstudiesonmetabolism,evolution,anddrugdiscovery.Inthenext chapter,Uppadaetal.surveyvariousapproachestowardensuringtheavailabilityofcofactors in synthetic engineering efforts: efficient regeneration of cofactors is critical for cyclic and continuous use of enzymes, particularly when the metabolic engineering effort is directed toward the synthesis of metabolites themselves as products, or in biotransformations. Cofactor optimization concepts and examples of their successful implementation are also discussed. Choudhury and Saini next review aspects of sugar co-utilization in microor- ganisms. This issue is of immense importance given the need to efficiently utilize all sugars present in hydrolyzed lignocellulosic biomass toward ensuring the cost-effectiveness of schemes being developed for the production of biofuels and other platform chemicals. The major efforts are oriented toward deregulating the extensive carbon catabolite repression mechanisms that industrially preferred hosts have evolved. A specific challenge remains the co-utilizationofarabinoseandxylose,bothpentoses,withglucose.Inthefinalcontribution, Uppada and coworkers describe efforts that have been taken toward the engineering of efficient synthesis pathways for the production of ephedrine alkaloids in Saccharomyces cerevisiae. This process, for the synthesis of what is a chiral intermediate, is one of the few whole-cell biotransformations undertaken at very large scales commercially. They describe attempts to manipulate yeast metabolism and the associated product and by-product for- mation reactions using strain, enzyme, and cofactor engineering. The successful completion of this volume has been made possible by the timely cooperationofthecontributorstothisvolume.Wethankthemfortheirefforts.Wehopethat readers will enjoy going through the chapters and find them useful. We thank Dr. Kostas Marinakis, Book Acquisition Editor; Ms. Anneka Hess; and the entire production team at Elsevier for their help and support in bringing out this volume. Without their commitment, efficiency, and dedicated work, this volume could not have ever been accomplished. Editors Paramasamy Gunasekaran Santosh Noronha Ashok Pandey 1 Functional Epigenomics S. Majumdar, P. Singh, A.H. Iyer, M. Saravanan* INDIAN INSTITUTE OF TECHNOLOGY-KANPUR, KANPUR, UTTAR PRADESH, INDIA 1.1 Introduction Diversity driven by inheritance and evolution is the essence of life. For decades re- searchers have attempted to comprehend these aspects for a holistic understanding of livingorganisms.Intheyear1859,therevolutionarytheoryofevolutionthroughnatural selection by Charles Darwin changed the whole paradigm of the field [1]. The theory essentially comprised three components: variation, inheritance, and competition for survival. Darwin defined inheritance as the transfer of adaptations (both wanted and unwanted) from one generation to the next. Ever since, innumerable efforts were focused on understanding how these adaptations are transferred across generations. A crucial turning point was the year 1953, when Watson and Crick revealed the double helical structure of DNA and clearly showed that this molecule is solely responsible for the inheritance of genetic traits [2]. Another remarkable discovery was in the year 1961, when Marshall Nirenberg deciphered the genetic code [3]. It could successfully explain one of the fundamental aspects of Darwinian theory, which is variation. The genetic code is based on five nucleotides, A, C, G, T, and U, which combine to generate 64 codons (triplets), which in turn code for 20 different amino acids. The variations prev- alentinapopulationwereattributedtochangesinthesecodons,whichwouldthencode for a different amino acid and reflect on the properties of the final protein being built. Overall, the above studies established the flow of genetic information within an organ- ism from DNA to RNA to protein. It was difficult, however, to believe that the immense diversity of life could be attributed to something so simple. The field of epigenetics addedanother dimension to our view of the DNA world. Epigenetics refers to variations in the activity of a gene without altering its nucleotide sequence. The term “epigenetics” was coined in the year 1942 by Conrad Hal Waddington [4]. He proposed that development is an epigenetic process wherein a phenotype not only is a manifestation of genetic processes but also dependsonenvironmentalinteractions.Eversince,extensiveefforthasbeenfocusedon refiningtheconceptofepigenetics,whichrevealedthatepigeneticmodificationsinvolve chemical alterations of chromatin affecting gene expression. *CorrespondingAuthor. CurrentDevelopmentsinBiotechnologyandBioengineering:FunctionalGenomicsandMetabolicEngineering http://dx.doi.org/10.1016/B978-0-444-63667-6.00001-8 3 Copyright©2017ElsevierB.V.Allrightsreserved.
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