Synthetic Biology: Volume 1

374 Pages·11.78 MB·English

Synthetic Biology
Volume 1
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A Specialist Periodical Report
Synthetic Biology
Volume 1
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5- A Review of Recent Literature
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73 Editors
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84 Maxim Ryadnov, National Physical Laboratory, Teddington, UK
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78 Luc Brunsveld, Eindhoven University of Technology,
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9/ The Netherlands
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1 Hiroaki Suga, University of Tokyo, Japan
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d Authors
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or Nasir Bashiruddin, University of Tokyo, Japan
sc. Ralph P.G. Bosmans, Eindhoven University of Technology,
bs.r The Netherlands
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p:// Melanie Brasch, University of Twente, The Netherlands
htt Luc Brunsveld, Eindhoven University of Technology,
on The Netherlands
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1 Cristiano Chiarabelli, University of Roma Tre, Rome, Italy
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e Jeroen J.L.M. Cornelissen, University of Twente,
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Ju The Netherlands
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. n 0 Paul A. Dalby, University College London, UK
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d Aleksandra Filipovska, The University of Western Australia,
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sh Australia
ubli Yuki Goto, University of Tokyo, Japan
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Emily M. Harcourt, Stanford University, CA, USA
Christopher John Hipolito, University of Tokyo, Japan
Koki Kamiya, The University of Tokyo, Japan
Takayuki Katoh, University of Tokyo, Japan
Melissa S.T. Koay, University of Twente, The Netherlands
Eric T. Kool, Stanford University, CA, USA
Alexander Kros, Leiden University, The Netherlands
Pier Luigi Luisi, University of Roma Tre, Rome, Italy
Hana Robson Marsden, Leiden University, The Netherlands
Maarten Merkx, Eindhoven University of Technology,
The Netherlands
Birger Lindberg Møller, University of Copenhagen, Denmark
Toshihisa Osakia, The University of Tokyo, Japan
Oliver Rackham, The University of Western Australia,
Australia
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Maxim Ryadnov, National Physical Laboratory, Teddington, UK
Pasquale Stano, University of Roma Tre, Rome, Italy
Hiroaki Suga, University of Tokyo, Japan
Shoji Takeuchi, The University of Tokyo, Japan
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sc. ISBN: 978-1-84973-683-1
s.r
b DOI: 10.1039/9781849737845
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on A catalogue record for this book is available from the British Library
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e 2 & The Royal Society of Chemistry 2014
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. n 0 All rights reserved
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sh Apart from any fair dealing for the purpose of research or private study for
ubli non-commercialpurposes,orcriticismorreview,aspermittedundertheterms
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of the UK Copyright, Designs and Patents Act, 1988 and the Copyright and
Related Rights Regulations 2003, this publication may not be reproduced,
stored or transmitted, in any form or by any means, without the prior
permission in writing of The Royal Society of Chemistry, or in the case of
reprographic reproduction only in accordance with the terms of the licences
issuedbytheCopyrightLicensingAgencyintheUK,orinaccordancewiththe
terms of the licences issued by the appropriate Reproduction Rights
Organization outside the UK. Enquiries concerning reproduction outside the
terms stated here should be sent to The Royal Society of Chemistry at the
address printed on this page.
Published by The Royal Society of Chemistry,
Thomas Graham House, Science Park, Milton Road,
Cambridge CB4 0WF, UK
Registered Charity Number 207890
For further information see our web site at www.rsc.org
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Preface
DOI: 10.1039/9781849737845-FP007
WiththisvolumeRSClaunchesanewseriesofannualreportsaimingto
keepabreastofcurrentandemergingdevelopmentsinsyntheticbiology.
Synthetic biology is a new area of interdisciplinary research which com-
7 binesscienceandengineeringinordertodesignandbuildnovelbiology.
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P0 Therefore,thedefinitionofsyntheticbiologyhasbeengenerallyaccepted
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5- as the engineering of biology: the synthesis of complex, biologically
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78 based(orinspired)systems,whichdisplayfunctionsthatmaynotexistin
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97 nature. This engineering perspective may be applied at all levels of
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18 biological hierarchy from individual molecules to cells, tissues and
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97 organisms.Aswithanymulti-disciplinaryfield,thereisasubstantialand
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3 rapidly growing body of literature concerning synthetic biology, with
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0. several specialist journals now available. However, finding the best
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oi: informationoridentifyingthehottesttopicsinthisburgeoningfieldcan
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g | be time-consuming. In this vein, this series presents critical and
or comprehensive reviews of the recent literature in themed chapters pre-
c.
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s.r pared by invited authors from around the globe. Each volume strives to
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u highlightthemostrecentfindingsanddevelopmentsinspecificresearch
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p:// areas andreviewesliterature predominantly publishedoverthe last two-
n htt threeyears.Routinerevisionsofmoretraditionalconceptsinthelightof
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4 emerging discoveries, and vice versa, constitute an integral part of each
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20 chapter, which makes this series unique and different from other
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n publications and allows keeping pace with the progress without losing
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2 touch with foundations.
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. n This first volume starts with an ‘‘initiation’’ into the new field by
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ed discussing‘‘expandedDNA’’orxDNA anda‘‘newgeneticsystem’’inthe
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blis light of engineering artificial genes (Harcourt and Kool). The discussion
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P particularly stresses upon synthetic and structural aspects of designer
DNA bases and base pairs, genetic sets and their biologically relevant
activities, culminating with a critical overview of xDNA replication for
future studies in synthetic biology. A subsequent focus, logically and
synthetically,ismadeinthefollowingchapter(BosmansandBrunsveld),
which describes post-translational modifications of proteins and their
impact on the regulation of complex cellular networks. The chapter
extends the notion of a biological toolbox to protein and peptide con-
structionandaddressestheimportanceofdesigneraminoacidsenabled
by semi-synthetic and chemical approaches. The argumentation for the
intrinsic role of proteins as indispensible synthetic blocks is further
developed with a principal emphasises made on functional integration
of proteins with biology and engineered biological systems (Dalby). A
stronger focus here is made on directed evolution strategies, their com-
parison and relevance to the creation of de novo metabolic pathways as
wellasnovelanimoacids,DNAandRNA.There-useandre-purposingof
biological function mediated by RNA editing is then described from the
perspective of genetic circuits, genome regulaton, protein recognition
SyntheticBiology,2014,1,vii–ix | vii
(cid:2)c TheRoyalSocietyofChemistry2014
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and complex assemblies, with an intimate connection made to the
re-engineering of the genetic code (Filipovska and Rackham). The next
chapterfollowsthetrendandcomprehensivelyreviewessyntheticbiology
of the code (Suga, Hipolito, Goto, Katoh, Bashiruddin), which starting
from non-standard aminoacyl-tRNAs and sense codon re-assigments
covers methodological developments for the re-programming of the
geneticcode toenablethe synthesis of complex bioactive peptides, both
natural and synthetic. Three subsequent chapters take a step up in the
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00 hierarchical origin of synthetic biology and address the challenge of
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F exploitable strategies for modular protein design. Firstly, pros and cons
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84 in the development of protein sensors and switches are outlined in
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73 terms of inter-relationships between design modularity and functional
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84 integration exemplified by minimalistic protein architectures (Merkx).
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78 This is followed by de novo extracellular approaches devised to instruct
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9/ cell biology using synthetic cell-supporting matrices. Specific highlights
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1 includemodulardesignprincipleslearnedfromthefunctionalfeedback
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oi:1 between matrix ‘‘niches’’ and cellular development (Ryadnov). The
d discussion continues with how the reproducible and discrete nano-
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or structured morphologies of protein assemblies including viral, bacterial
sc. and non-viral encapsulators and protein cages define fundamental
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b biological functions and hence applications, ranging from intracellular
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p:// delivery and trafficking to catalysis (Brasch, Cornelissen, Koay).
htt Engineering functional interfaces which go beyond specialist biomole-
on cular classes, be these nucleic acids or proteins, bring the complexity of
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1 synthetic biology a further step up (Marsden and Kros). Important
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e interfacialelementsofnativemachinery,membranes,arereviewedasan
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J enablingtoolforthebottom-upsynthesisoflifethefeasiblityofwhichis
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. n 0 probed through functional biomimicry, compartmentalisation, repli-
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d cationandtransport.Providingsyntheticmembranesneatlyleadstothe
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sh concept of a synthetic cell and first of all to methods and technologies
ubli thatcanmakeitpossible.Lipid-basedmicrofluidicdevicesarediscussed
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as a promising means to deliver cell-like characteristics ranging from
cytosolic encapsulation and controlled membrane permeability for cell-
free protein expression and regulation to high-throughput generation of
model and customised artificial cells (Osaki, Kamiya, Takeuchi). How
such and other functionalities can be constructed is discussed in the
pen-ultimate chapter along the lines of chemical synthetic biology with
major efforts given to the synthesis of chemical structures that are
alternativetothoseexistinginNature(Chiarabelli,Stano,Luisi).Examples
under discussion include ‘‘never-born’’ biopolymers such as peptide
nucleic acids (PNA), de novo RNA and proteins and minimal autopoietic
cells (capable of self-production) that are constructed from liposomes
incorporatingsyntheticgenomestosupportsimplebiochemicalnetworks
mimicking metabolic pathways. Finally, an application overview of re-
engineerednaturallyoccuringmetabolicpathwaystorationallycontrolthe
channeling of metabolic fluxes towards specific targets concludes this
volume (Møller). Light-driven synthesis and the construction of supra-
molecularmetabolonsarepresentedasaradicalstepchangetodisruptive
innovation which is already beginning toproduce high-valueproducts.
viii | SyntheticBiology,2014,1,vii–ix
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Each chapter is structured around current trends in the reviewed
research area that are compared with more established approaches
whereverpossible,andtheauthors’outlookoffutureperspectives,either
asa separate section orincorporatedinthetext. Allchaptersarewritten
by leading researchers in their subject areas to enable a worldwide
information source of broad appeal to researchers in academia and
industry.
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SyntheticBiology,2014,1,vii–ix | ix
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