All Title Author
Keywords Abstract

Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex

DOI: 10.1371/journal.pcbi.1004723

Full-Text   Cite this paper   Add to My Lib


Escherichia coli and Salmonella enterica are models for many experiments in molecular biology including chemotaxis, and most of the results obtained with one organism have been generalized to another. While most components of the chemotaxis pathway are strongly conserved between the two species, Salmonella genomes contain some chemoreceptors and an additional protein, CheV, that are not found in E. coli. The role of CheV was examined in distantly related species Bacillus subtilis and Helicobacter pylori, but its role in bacterial chemotaxis is still not well understood. We tested a hypothesis that in enterobacteria CheV functions as an additional adaptor linking the CheA kinase to certain types of chemoreceptors that cannot be effectively accommodated by the universal adaptor CheW. Phylogenetic profiling, genomic context and comparative protein sequence analyses suggested that CheV interacts with specific domains of CheA and chemoreceptors from an orthologous group exemplified by the Salmonella McpC protein. Structural consideration of the conservation patterns suggests that CheV and CheW share the same binding spot on the chemoreceptor structure, but have some affinity bias towards chemoreceptors from different orthologous groups. Finally, published experimental results and data newly obtained via comparative genomics support the idea that CheV functions as a “phosphate sink” possibly to off-set the over-stimulation of the kinase by certain types of chemoreceptors. Overall, our results strongly suggest that CheV is an additional adaptor for accommodating specific chemoreceptors within the chemotaxis signaling complex.


[1]  Wadhams GH, Armitage JP. Making sense of it all: Bacterial chemotaxis. Nat Rev Mol Cell Bio. 2004;5: 1024–1037. doi: 10.1038/nrm1524
[2]  Hazelbauer GL, Falke JJ, Parkinson JS. Bacterial chemoreceptors: high-performance signaling in networked arrays. Trends Biochem Sci. 2008;33: 9–19. doi: 10.1016/j.tibs.2007.09.014. pmid:18165013
[3]  Briegel A, Ortega DR, Tocheva EI, Wuichet K, Li Z, Chen S, et al. Universal architecture of bacterial chemoreceptor arrays. Proc Natl Acad Sci USA. 2009;106: 17181–17186. doi: 10.1073/pnas.0905181106. pmid:19805102
[4]  Briegel A, Li X, Bilwes AM, Hughes KT, Jensen GJ, Crane BR. Bacterial chemoreceptor arrays are hexagonally packed trimers of receptor dimers networked by rings of kinase and coupling proteins. Proc Natl Acad Sci USA. 2012;109: 3766–3771. doi: 10.1073/pnas.1115719109. pmid:22355139
[5]  Shimizu TS, Le Novere N, Levin MD, Beavil AJ, Sutton BJ, Bray D. Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis. Nat Cell Biol. 2000;2: 792–796. pmid:11056533 doi: 10.1038/35041030
[6]  Hazelbauer GL, Lai WC. Bacterial chemoreceptors: providing enhanced features to two-component signaling. Curr Opin Microbiol. 2010;13: 124–132. doi: 10.1016/j.mib.2009.12.014. pmid:20122866
[7]  Springer MS, Goy MF, Adler J. Sensory transduction in Escherichia coli: two complementary pathways of information processing that involve methylated proteins. Proc Natl Acad Sci USA. 1977;74: 3312–3316. pmid:333433 doi: 10.1073/pnas.74.8.3312
[8]  Hazelbauer GL. The binding of maltose to 'virgin' maltose-binding protein is biphasic. Eur J Biochem. 1975;60: 445–449. pmid:1107043 doi: 10.1111/j.1432-1033.1975.tb21022.x
[9]  Tso WW, Adler J. Negative chemotaxis in Escherichia coli. J Bacteriol. 1974;118: 560–576. pmid:4597449
[10]  Hegde M, Englert DL, Schrock S, Cohn WB, Vogt C, Wood TK, et al. Chemotaxis to the quorum-sensing signal AI-2 requires the Tsr chemoreceptor and the periplasmic LsrB AI-2-binding protein. J Bacteriol. 2011;193: 768–773. doi: 10.1128/JB.01196-10. pmid:21097621
[11]  Rebbapragada A, Johnson MS, Harding GP, Zuccarelli AJ, Fletcher HM, Zhulin IB, et al. The Aer protein and the serine chemoreceptor Tsr independently sense intracellular energy levels and transduce oxygen, redox, and energy signals for Escherichia coli behavior. Proc Natl Acad Sci U S A. 1997;94: 10541–10546. pmid:9380671 doi: 10.1073/pnas.94.20.10541
[12]  Greer-Phillips SE, Alexandre G, Taylor BL, Zhulin IB. Aer and Tsr guide Escherichia coli in spatial gradients of oxidizable substrates. Microbiology. 2003;149: 2661–2667. pmid:12949190 doi: 10.1099/mic.0.26304-0
[13]  Harayama S, Palva ET, Hazelbauer GL. Transposon-insertion mutants of Escherichia coli K12 defective in a component common to galactose and ribose chemotaxis. Mol Gen Genet. 1979;171: 193–203. pmid:375029 doi: 10.1007/bf00270005
[14]  Manson MD, Blank V, Brade G, Higgins CF. Peptide chemotaxis in E. coli involves the Tap signal transducer and the dipeptide permease. Nature. 1986;321: 253–256. pmid:3520334 doi: 10.1038/321253a0
[15]  Liu X, Parales RE. Chemotaxis of Escherichia coli to pyrimidines: a new role for the signal transducer tap. J Bacteriol. 2008;190: 972–979. pmid:18065551 doi: 10.1128/jb.01590-07
[16]  Bibikov SI, Biran R, Rudd KE, Parkinson JS. A signal transducer for aerotaxis in Escherichia coli. J Bacteriol. 1997;179: 4075–4079. pmid:9190831
[17]  Wuichet K, Alexander RP, Zhulin IB. Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis. Methods Enzymol. 2007;422:1–31. pmid:17628132 doi: 10.1016/s0076-6879(06)22001-9
[18]  Stock JB, Surette MG. Chemotaxis. In: Neidhardt FC, Curtiss RI, Ingraham JL, Lin ECC, Low KB, Magasanik B, et al., editors. Escherichia coli and Salmonella: cellular and molecular biology. 2nd ed. Washington, D.C.: American Society of Microbiology Press; 1996.
[19]  DeFranco AL, Parkinson JS, Koshland DE Jr. Functional homology of chemotaxis genes in Escherichia coli and Salmonella typhimurium. J Bacteriol. 1979;139: 107–14. pmid:378950
[20]  Karatan E, Saulmon MM, Bunn MW, Ordal GW. Phosphorylation of the response regulator CheV is required for adaptation to attractants during Bacillus subtilis chemotaxis. J Biol Chem. 2001;276: 43618–43626. pmid:11553614 doi: 10.1074/jbc.m104955200
[21]  Walukiewicz HE, Tohidifar P, Ordal GW, Rao CV. Interactions among the three adaptation systems of Bacillus subtilis chemotaxis as revealed by an in vitro receptor-kinase assay. Mol Microbiol. 2014;93: 1104–1118. doi: 10.1111/mmi.12721. pmid:25039821
[22]  Alexander RP, Lowenthal AC, Harshey RM, Ottemann KM. CheV: CheW-like coupling proteins at the core of the chemotaxis signaling network. Trends Microbiol. 2010;18: 494–503. doi: 10.1016/j.tim.2010.07.004. pmid:20832320
[23]  Wuichet K, Zhulin IB. Origins and diversification of a complex signal transduction system in prokaryotes. Sci Signal. 2010;3: ra50. doi: 10.1126/scisignal.2000724. pmid:20587806
[24]  Boukhvalova MS, Dahlquist FW, Stewart RC. CheW binding interactions with CheA and Tar. Importance for chemotaxis signaling in Escherichia coli. J Biol Chem. 2002;277: 22251–22259. pmid:11923283 doi: 10.1074/jbc.m110908200
[25]  Wang Q, Mariconda S, Suzuki A, McClelland M, Harshey RM. Uncovering a large set of genes that affect surface motility in Salmonella enterica serovar Typhimurium. J Bacteriol. 2006;188: 7981–7984. pmid:16980469 doi: 10.1128/jb.00852-06
[26]  Lowenthal AC, Simon C, Fair AS, Mehmood K, Terry K, Anastasia S, et al. A fixed-time diffusion analysis method determines that the three cheV genes of Helicobacter pylori differentially affect motility. Microbiology. 2009;155: 1181–1191. doi: 10.1099/mic.0.021857-0. pmid:19332820
[27]  Bilwes AM, Alex LA, Crane BR, Simon MI. Structure of CheA, a signal-transducing histidine kinase. Cell. 1999;96: 131–141. pmid:9989504 doi: 10.1016/s0092-8674(00)80966-6
[28]  Reebye V, Frilling A, Hajitou A, Nicholls JP, Habib NA, Mintz PJ. A perspective on non-catalytic Src homology (SH) adaptor signalling proteins. Cell Signal. 2012;24: 388–392. doi: 10.1016/j.cellsig.2011.10.003. pmid:22024281
[29]  Yamamoto K, Imae Y. Cloning and characterization of the Salmonella typhimurium-specific chemoreceptor Tcp for taxis to citrate and from phenol. Proc Natl Acad Sci U S A. 1993;90: 217–221. pmid:8419927 doi: 10.1073/pnas.90.1.217
[30]  Lazova MD, Butler MT, Shimizu TS, Harshey RM. Salmonella chemoreceptors McpB and McpC mediate a repellent response to L-cystine: a potential mechanism to avoid oxidative conditions. Mol Microbiol. 2012;84: 697–711. doi: 10.1111/j.1365-2958.2012.08051.x. pmid:22486902
[31]  Russo AF, Koshland DE Jr,. Identification of the tip-encoded receptor in bacterial sensing. J Bacteriol. 1986;165: 276–282. pmid:3001027
[32]  Frye J, Karlinsey JE, Felise HR, Marzolf B, Dowidar N, McClelland M, et al. Identification of new flagellar genes of Salmonella enterica serovar Typhimurium. J Bacteriol. 2006;188: 2233–2243. pmid:16513753 doi: 10.1128/jb.188.6.2233-2243.2006
[33]  Ulrich LE, Zhulin IB. The MiST2 database: a comprehensive genomics resource on microbial signal transduction. Nucleic Acids Res. 2010;38: D401–D407. doi: 10.1093/nar/gkp940. pmid:19900966
[34]  Hartley-Tassell LE, Shewell LK, Day CJ, Wilson JC, Sandhu R, Ketley JM, et al. Identification and characterization of the aspartate chemosensory receptor of Campylobacter jejuni. Mol Microbiol. 2010;75: 710–730. doi: 10.1111/j.1365-2958.2009.07010.x. pmid:20025667
[35]  Mo G, Zhou H, Kawamura T, Dahlquist FW. Solution structure of a complex of the histidine autokinase CheA with its substrate CheY. Biochemistry. 2012;51: 3786–3798. doi: 10.1021/bi300147m. pmid:22494339
[36]  Briegel A, Wong ML, Hodges HL, Oikonomou CM, Piasta KN, Harris MJ, et al. New insights into bacterial chemoreceptor array structure and assembly from electron cryotomography. Biochemistry. 2014;53: 1575–1585. doi: 10.1021/bi5000614. pmid:24580139
[37]  Briegel A, Ladinsky MS, Okonomou C, Jones CW, Harris MJ, Fowler DJ, et al. Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotacitc signaling. eLife. 2014;3: e02151. doi: 10.7554/eLife.02151. pmid:24668172
[38]  Alexandre G, Zhulin IB. Different evolutionary constraints on chemotaxis proteins CheW and CheY revealed by heterologous expression studies and protein sequence analysis. J Bacteriol. 2003;185: 544–552. pmid:12511501 doi: 10.1128/jb.185.2.544-552.2003
[39]  Ortega DR, Mo G, Lee K, Zhou H, Baudry J, Dahlquist FW, et al. Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein. PLoS Comp Biol. 2013;9: e1003337. doi: 10.1371/journal.pcbi.1003337
[40]  Ferrada E, Wagner A. Protein robustness promotes evolutionary innovations on large evolutionary time-scales. Proc Biol Sci. 2008;275: 15951–602. doi: 10.1098/rspb.2007.1617
[41]  Tokuriki N, Tawfik DS. Protein dynamism and evolvability. Science. 2009;324: 203–207. doi: 10.1126/science.1169375. pmid:19359577
[42]  Alexander RP, Zhulin IB. Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors. Proc Natl Acad Sci USA. 2007;104: 2885–2890. pmid:17299051 doi: 10.1073/pnas.0609359104
[43]  Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997;278: 631–637. pmid:9381173 doi: 10.1126/science.278.5338.631
[44]  Borziak K, Fleetwood AD, Zhulin IB. Chemoreceptor gene loss and acquisition via horizontal gene transfer in Escherichia coli. J Bacteriol. 2013;195: 3596–3602. doi: 10.1128/JB.00421-13. pmid:23749975
[45]  Iwama T, Ito Y, Aoki H, Sakamoto H, Yamagata S, Kawai K, et al. Differential recognition of citrate and a metal-citrate complex by the bacterial chemoreceptor Tcp. J Biol Chem. 2006;281: 17727–17735. pmid:16636062 doi: 10.1074/jbc.m601038200
[46]  Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A. 1999;96: 4285–4288. pmid:10200254 doi: 10.1073/pnas.96.8.4285
[47]  Huynen M, Snel B, Lathe W 3rd, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 2000;10: 1204–1210. pmid:10958638 doi: 10.1101/gr.10.8.1204
[48]  Kroger C, Colgan A, Srikumar S, Handler K, Sivasankaran SK, Hammarlof DL, et al. An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium. Cell Host Microbe. 2013;14: 683–695. doi: 10.1016/j.chom.2013.11.010. pmid:24331466
[49]  Li X, Fleetwood AD, Bayas C, Bilwes AM, Ortega DR, Falke JJ, et al. The 3.2 A resolution structure of a receptor:CheA:CheW signaling complex defines overlapping binding sites and key residue interactions within bacterial chemosensory arrays. Biochemistry. 2013;52: 3852–3865. doi: 10.1021/bi400383e. pmid:23668907
[50]  Vu A, Wang X, Zhou H, Dahlquist FW. The receptor-CheW binding interface in bacterial chemotaxis. J Mol Biol. 2012;415: 7597–67. doi: 10.1016/j.jmb.2011.11.043
[51]  Pedetta A, Parkinson JS, Studdert CA. Signalling-dependent interactions between the kinase-coupling protein CheW and chemoreceptors in living cells. Mol Microbiol. 2014;93:1144–55. doi: 10.1111/mmi.12727. pmid:25060668
[52]  Trammell MA, Falke JJ. Identification of a site critical for kinase regulation on the central processing unit (CPU) helix of the aspartate receptor. Biochemistry. 1999;38: 329–336. pmid:9890914 doi: 10.1021/bi981964u
[53]  Ortega DR, Yang C, Ames P, Baudry J, Parkinson JS, Zhulin IB. A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors. Nat Commun. 2013;4: 2881. doi: 10.1038/ncomms3881. pmid:24335957
[54]  Coleman MD, Bass RB, Mehan RS, Falke JJ. Conserved glycine residues in the cytoplasmic domain of the aspartate receptor play essential roles in kinase coupling and on-off switching. Biochemistry. 2005;44: 7687–7695. pmid:15909983 doi: 10.1021/bi0501479
[55]  Vaknin A, Berg HC. Direct evidence for coupling between bacterial chemoreceptors. J Mol Biol. 2008;382: 573–577. doi: 10.1016/j.jmb.2008.07.026. pmid:18657546
[56]  Kim KK, Yokota H, Kim SH. Four-helical-bundle structure of the cytoplasmic domain of a serine chemotaxis receptor. Nature. 1999;400: 787–792. pmid:10466731
[57]  Li Y, Hu Y, Fu W, Xia B, Jin C. Solution structure of the bacterial chemotaxis adaptor protein CheW from Escherichia coli. Biochem Biophys Res Commun. 2007;360: 863–867. pmid:17631272 doi: 10.1016/j.bbrc.2007.06.146
[58]  Underbakke ES, Zhu Y, Kiessling LL. Protein footprinting in a complex milieu: identifying the interaction surfaces of the chemotaxis adaptor protein CheW. J Mol Biol. 2011;409: 483–495. doi: 10.1016/j.jmb.2011.03.040. pmid:21463637
[59]  Ames P, Studdert CA, Reiser RH, Parkinson JS. Collaborative signaling by mixed chemoreceptor teams in Escherichia coli. Proc Natl Acad Sci USA. 2002;99: 7060–7065. pmid:11983857 doi: 10.1073/pnas.092071899
[60]  Sourjik V, Schmitt R. Phosphotransfer between CheA, CheY1, and CheY2 in the chemotaxis signal transduction chain of Rhizobium meliloti. Biochemistry. 1998;37: 2327–35. pmid:9485379 doi: 10.1021/bi972330a
[61]  Pittman MS, Goodwin M, Kelly DJ. Chemotaxis in the human gastric pathogen Helicobacter pylori: different roles for CheW and the three CheV paralogues, and evidence for CheV2 phosphorylation. Microbiology. 2001;147: 2493–2504. pmid:11535789 doi: 10.1099/00221287-147-9-2493
[62]  Wisniewski-Dye F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, et al. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet. 2011;7: e1002430. doi: 10.1371/journal.pgen.1002430. pmid:22216014
[63]  Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7: e1002195. doi: 10.1371/journal.pcbi.1002195. pmid:22039361
[64]  Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14: 755–763. pmid:9918945 doi: 10.1093/bioinformatics/14.9.755
[65]  Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008;9: 286–298. doi: 10.1093/bib/bbn013. pmid:18372315
[66]  Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52: 696–704. pmid:14530136 doi: 10.1080/10635150390235520
[67]  Wickham H. ggplot2: elegant graphics for data analysis: Springer New York; 2009.
[68]  Hagberg AA, Schult DA, Swart PJ, editors. Exploring Network Structure, Dynamics, and Function using NetworkX. Proceedings of the 7th Python in Science Conference; 2008; Pasadena, CA USA.
[69]  Oliphant TE. Python for scientific computing. Comput Sci Eng. 2007;9:10–20. doi: 10.1109/mcse.2007.58
[70]  Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14: 1188–1190. pmid:15173120 doi: 10.1101/gr.849004
[71]  Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215: 403–410. pmid:2231712 doi: 10.1016/s0022-2836(05)80360-2


comments powered by Disqus