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The Promise of Evolutionary Systems Biology Lessons From Bacterial Chemo Tax Is

The Promise of Evolutionary Systems Biology Lessons From Bacterial Chemo Tax Is

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(128), pe23. [DOI: 10.1126/scisignal.3128pe23]
3
Science Signaling 
Orkun S. Soyer (29 June 2010)
ChemotaxisThe Promise of Evolutionary Systems Biology: Lessons from Bacterial
This information is current as of 7 July 2010.The following resources related to this article are available online at http://stke.sciencemag.org.
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Obtain information about reproducing this article:Association for the Advancement of Science; all rights reserved.for the Advancement of Science, 1200 New York Avenue, NW, Washington, DC 20005. Copyright 2008 by the American(ISSN 1937-9145) is published weekly, except the last week in December, by the American Association
Science Signaling 
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Systems biology increasingly delivers adetailed understanding of structure and dynamics in specific biological networksin model organisms. Such accumulationof knowledge raises an important ques-tion in the field: Can we employ under-standing from specific cases to decipher “design principles” applicable to all bio-logical systems? Providing an affirma-tive answer to this question is one of thekey prospects of systems biology, and atthe same time one of its biggest chal-lenges. Evolutionary approaches could  be crucial in surmounting it. Because bi-ological systems are the product of evo-lution, their common features will be theresult of evolutionary processes. In other words, the principles we seek are notthose of an engineer but those of evolu-tion. Deciphering these principles is pos-sible only through an understanding of how evolutionary processes, both adap-tive and neutral, can shape biologicalnetworks. With this understanding, weshould be able to track the origins of complex biological systems and predicttheir dynamics and structure on the basisof the life-style, environment, or genomesequence of their bearer.Wuichet and Zhulin (
1
) provide aglimpse of this promise of evolutionarysystems biology. By analyzing the genomesof all sequenced bacteria to identify homo-logs of genes associated with chemotaxis,the authors characterize the chemotaxissignaling networks in these organisms. Al-though this phylogenetic approach is com-monly used in comparative genomics, their study stands out because it focuses on aspecific and functionally well-defined sys-tem: the chemotaxis network. This network is well characterized in several model or-ganisms including
 Escherichia coli
(
2
,
3
), but we still cannot claim to have achieved afull understanding of bacterial chemotaxis, because response dynamics and network structure show clear differences betweenthese model organisms and others (
4
,
5
).The analysis by Wuichet and Zhulin pro-vides a broad view by predicting the wiringdiagram of the chemotaxis networks asfound in most present-day bacteria. The re-sults show that although the network struc-ture found in
 E. coli
is evident as a maintheme, there are substantial deviationsfrom it in other species. In total, the au-thors identify 18 different classes of chemotaxis systems, which differ in pro-tein constituents and their interactions and in the presence or absence of multiple pathways controlling motility. The latter finding is in line with another study (
) and highlights the potential role of signal inte-gration for proper chemotaxis in manymotile bacteria.The chemotaxis network as seen in
 E.coli
comprises seven proteins that interactin a specific way and produce dynamicalfeatures such as high sensitivity (
,
8
) and  precise adaptation (
9
,
10
). These featuresseem essential for proper chemotaxis be-havior, making it difficult to imagine howthis relatively complex signaling network and its dynamical features could haveevolved and through which intermediarysteps. In addition, all chemotaxis systemsstudied to date contain dedicated receptorswith methyl-accepting domains and a spe-cific histidine kinase (CheA), which has adomain structure different from that of theclass I kinases (
11
). This suggests that thechemotaxis system has evolved throughspontaneous innovation of these pro-teins—a rather unlikely prospect given our understanding of evolution. In their study,Wuichet and Zhulin shed light on this puz-zling picture and the evolutionary origin of chemotaxis systems. By extending their comparative genomic analysis to geneneighborhoods and by using purpose-builtdatabases for detecting homology, theyfind two sets of previously unknown pro-teins. One set, termed MAC (methyl-accepting coiled-coil) proteins, containsmethylation sites as well as domains withmethyltransferase and methylesterasefunctionality. These functions are per-formed by specific proteins, CheR and CheB, in the
 E. coli
network. The second set of previously unknown proteins com- prises histidine kinases that combine do-main architectures from both class I kinasesand CheA. In particular, these kinaseshave N-terminal sensory domains, as inclass I kinases, but their phosphorylationdomain is more similar to that found inCheA. Taken together, these discoveriesallow us to link seemingly complex net-works in present-day bacteria to simpleand potentially minimal ancestral systemscomprising few signaling proteins.The analysis of Wuichet and Zhulinopens up a new and exciting research av-enue. The diverse network structuresshould be analyzed in terms of responsedynamics and chemotaxis behavior, be-cause even small changes in the structureof signaling networks can result in substan-tial changes in response dynamics (
12
 – 
14
),which would then alter cellular behavior. Inthe context of chemotaxis, we can expectthat changes in response dynamics would lead to different chemotaxis strategies, po-tentially beneficial under a particular envi-
The Promise of EvolutionarySystems Biology: Lessons fromBacterial Chemotaxis
PERSPECTIVE
Systems Biology Program, School of Engi-neering, Computing and Mathematics, Uni-versity of Exeter, Exeter EX4 4QF, UK. E-mail,o.s.soyer@exeter.ac.uk 
Orkun S. Soyer
Published 29 June 2010;Volume 3 Issue 128 pe23
Bacterial chemotaxis and the signaling networks underlying it provide us with amodel system for studying the molecular basis of behavior and informationprocessing. Although chemotaxis is well characterized at both the phenotypeand genotype levels in the model organism
Escherichia coli 
, it is not yet possi-ble to predict chemotaxis behavior in diverse bacteria on the basis of their envi-ronment or genome sequence. Moreover, we still cannot propose a plausibleevolutionary trajectory from minimal systems to present-day chemotaxis net-works. The analysis of all sequenced bacterial genomes provides a predictionof their chemotaxis networks and reveals substantial structural diversity. Addi-tionally, it uncovers a set of previously unknown proteins that could be the“missing” link between complex present-day chemotaxis networks and simpler,ancestral systems composed of a few proteins. Further evaluation of thesefindings with experimental and modeling studies will allow us to distill evolu-tionary design principles in chemotaxis signaling networks.
EVOLUTION
www.
SCIENCESIGNALING
.org29June 2010Vol 3 Issue 128 pe23
1
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ronmental condition or mecha-nism of motility (Fig. 1). Link-ing structural changes at the protein and network levels to re-sponse dynamics and physiolo-gy requires a combined effort of modeling and experimentation.Modeling studies based on thework of Wuichet and Zhulinwill lead to the generation of hypotheses regarding responsedynamics in chemotaxis and will guide experimental work inspecies beyond the typical mod-el organisms. The value of suchguidance is clear, consideringthat the detailed knowledge of chemotaxis networks in theseorganisms took many decadesto accumulate.To date, research in evolu-tionary systems biology em- ploys two main approaches. Onthe one hand are comparativegenomics approaches such asthat used by Wuichet and Zhulin. These provide insightsinto differences among organ-isms at the genetic level, whichwe can then try to interpret atthe network level as changes inconnectivity. When applied inthe context of gene regulatorynetworks (
15
,
16 
), comparativegenomics played an importantrole in achieving a global under-standing of how the evolution of these systems links to changesin development (
17 
). On theother hand, a more bottom-upapproach aims to directly ex- plore the evolution of biologicalsystems in silico. By allowingmodels derived from first prin-ciples to “evolve” in the computer (
18
 – 
24
)or by exploring the space of possible mod-els (
12
,
25
,
26 
), these studies allow us toidentify evolutionary processes and envi-ronmental conditions that can lead to spe-cific functional and structural features in biological networks. The two approachesare complementary; the former can help toidentify the common genetic innovationsselected for by evolution, whereas the latter can help to discern the links between plau-sible selective pressures at the organismlevel and the resulting effects on responsedynamics and structure at the network lev-el. Combining these two approaches so thatevolutionary simulations incorporate datafrom genomic and experimental studies[for example, using an experimentally veri-fied network as a starting point for an evo-lutionary simulation (
27 
)] will be an excit-ing avenue for future research.Evolution drives change in all biologi-cal systems. Those changes that are neutralor adaptive under the conditions experi-enced by the organism might persist in the population, leading to diversity (
4
,
28
) and complexity (
29
) at the network level that isnot present in similar human-made sys-tems. If there are any design principlesthat provide a unifying pattern underneathsuch complexity and diversity, decipheringthem requires a firm understanding of theeffects of evolutionary processes at thenetwork level.
References and Notes
1.K.Wuichet, I.B.Zhulin, Origins and diversificationof a complex signal transduction system inprokaryotes.
Sci.Signal.
3
, ra50 (2010).2.H.C.Berg, D.A.Brown, Chemotaxis in
Escherichia coli 
analyzed by three-dimensionaltracking.
Antibiot.Chemother.
19
, 55–78 (1974).3.D.Bray, M.D.Levin, K.Lipkow, The chemotacticbehavior of computer-based surrogate bacteria.
Curr.Biol.
17
, 12–19 (2007).4.R.Schmitt, Sinorhizobial chemotaxis:A departurefrom the enterobacterial paradigm.
Microbiology 
148
, 627–631 (2002).5.S.L.Porter, G.H.Wadhams, J.P.Armitage,Rhodobacter sphaeroides:Complexity in chemo-tactic signalling.
Trends Microbiol.
16
, 251–260(2008).6.R.Hamer, P.Y.Chen, J.P.Armitage, G.Reinert,C.M.Deane, Deciphering chemotaxis pathwaysusing cross species comparisons.
BMC Syst.Biol.
4
, 3 (2010).7.P.Cluzel, M.Surette, S.Leibler, An ultrasensitive
PERSPECTIVE
FluctuatingattractantsourcesSingle-fagellatedbacteriaStationaryattractantsources
 Time
    T   u   m    b    l    i   n   g    R   a   t   e    T   u   m    b    l    i   n   g    R   a   t   e    T   u   m    b    l    i   n   g    R   a   t   e
(+) Attractant (-) Time(+) Attractant (-) Time(+) Attractant (-)
Motility machineryReceptor complexCheBCheACheYCheRCheZ
Fig.1.
A cartoon representation of sample chemotaxis networks and their dynamics in bacteria living un-der different conditions and possessing different motility machinery.All motile bacteria possess a signal-ing network to regulate their motility behavior and to achieve chemotaxis.This network is composed of sixregulatory proteins in the model organism
Escherichia coli 
:a receptor complex for sensing chemoattrac-tants, two proteins (CheR and CheB) that regulate receptor activity, a histidine kinase (CheA), a responseregulator (CheY), and its phosphatase (CheZ) that acts on the response regulator.Genomic analyseshave revealed that chemotaxis networks show substantial diversity, in terms of both structure and proteincontent, across the bacterial kingdom.This diversity is a result of evolution;depending on their life-style,environment, and motility machinery, bacteria have evolved different signaling networks to achieve re-sponse dynamics and chemotaxis behavior suitable for those conditions (note that the tree shown is rep-resentative and does not reflect phylogeny of any particular species).The differences in response dynam-ics are depicted in the cartoon by the response of the network to addition and subtraction (indicated bydown and up arrows, respectively) of a chemoattractant to the media.
www.
SCIENCESIGNALING
.org29June 2010Vol 3 Issue 128 pe23
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