Table Of ContentCurrent 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
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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
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