Comparative structural bioinformatics analysis of Bacillus amyloliquefaciens chemotaxis proteins within Bacillus subtilis group

Applied Microbiology and Biotechnology

Volumn 92, Issue 5, 2011, Pages 997-1008

  Yssel, Anna ^a   Reva, Oleg ^b   Tastan Bishop, Ozlem ^a  

^a RHODES UNIVERSITY   (South Africa)

^b UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

Chemotaxis receptor; Homology modeling; Positive selection; Purifying selection

Indexed keywords

ACTIVE SITE; AMINO ACID SUBSTITUTION; BACILLUS AMYLOLIQUEFACIENS; BACILLUS SUBTILIS; BACTERIAL CHEMOTAXIS; CHEMICAL ENVIRONMENT; CHEMOTAXIS RECEPTOR; FAVORABLE CONDITIONS; HOMOLOGY MODELING; HOMOLOGY MODELS; HOST PLANTS; MOLECULAR MECHANISM; PLANT COLONIZATION; POSITIVE SELECTION; PROCESS OF EVOLUTION; PURIFYING SELECTION; SOIL ORGANISMS; SPATIAL EVOLUTION; STRUCTURAL BIOINFORMATICS;

AMINO ACIDS; BACILLI; BACTERIOLOGY; BIOINFORMATICS; CHEMICAL ANALYSIS; PROTEINS;

BIOCHEMISTRY;

AMINO ACID; BACTERIAL PROTEIN;

AMINO ACID; BACTERIUM; BIOINFORMATICS; BIOPESTICIDE; CHEMOTAXIS; COLONIZATION; COMPARATIVE STUDY; HOMOLOGY; HOST PLANT; PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; BACILLUS AMYLOLIQUEFACIENS; BACILLUS SUBTILIS; BACTERIAL SURVIVAL; CHEMOTAXIS; COMPARATIVE STUDY; CONTROLLED STUDY; GENETIC CONSERVATION; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; PLANT DEVELOPMENT; SEQUENCE ANALYSIS; SOIL ORGANISM; STRUCTURAL BIOINFORMATICS;

AMINO ACID SEQUENCE; BACILLUS; BACILLUS SUBTILIS; BACTERIAL PROTEINS; BIOLOGICAL EVOLUTION; CHEMOTAXIS; COMPUTATIONAL BIOLOGY; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT;

BACILLUS AMYLOLIQUEFACIENS; BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS);

EID: 82355175268     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-011-3582-y     Document Type: Article

References (58)

1. SF Altschul W Gish W Miller EW Myers DJ Lipman 1990 Basic local alignment search tool J Mol Biol 215 403 410 1:CAS:528:DyaK3MXitVGmsA%3D%3D
2. Borriss R, Chen X, Rueckert C, Blom J, Becker A, Baumgarth B, Fan B, Pukall R, Schumann P, Spröer C, Junge H, Vater J, Pühler A, Klenk HP (2010) Relationship of Bacillus amyloliquefaciens clades associated with strains DSM7T and FZB42: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on their discriminating complete genome sequences. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.023267-0
3. A Buchan B Crombie GM Alexandre 2010 Temporal dynamics and genetic diversity of chemotactic-competent microbial populations in the rhizosphere Environ Microbiol 12 12 3171 3184 10.1111/j.1462-2920.2010.02290.x 1:CAS:528:DC%2BC3MXltlejug%3D%3D
4. MW Bunn GW Ordal 2003 Transmembrane organization of the Bacillus subtilis chemoreceptor McpB deduced by cysteine disulfide crosslinking J Mol Biol 331 941 949 10.1016/S0022-2836(03)00834-9 1:CAS:528:DC%2BD3sXlvFGnsrs%3D (Pubitemid 36945446)
5. X Chao TJ Muff S Park S Zhang AM Pollard GW Ordal AM Bilwes BR Crane 2006 A receptor-modifying deamidase in complex with a signaling phosphatase reveals reciprocal regulation Cell 124 561 571 10.1016/j.cell.2005.11.046 1:CAS:528:DC%2BD28Xhslaqs7k%3D (Pubitemid 43199441)
6. XH Chen A Koumoutsi R Scholz A Eisenreich K Schneider I Heinemeyer B Morgenstern B Voss WR Hess O Reva H Junge B Voigt PR Jungblut J Vater R Süssmuth H Liesegang A Strittmatter G Gottschalk R Borriss 2007 Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42 Nat Biotech 25 1007 1014 10.1038/nbt1325 1:CAS:528:DC%2BD2sXhtVWksLvL (Pubitemid 47517636)
7. XH Chen A Koumoutsi R Scholz K Schneider J Vater R Süssmuth J Piel R Borriss 2009 Genome analysis of Bacillus amyloliquefaciens FZB42 reveals its potential for biocontrol of plant pathogens J Biotechnol 140 27 37 10.1016/j.jbiotec.2008.10.011 1:CAS:528:DC%2BD1MXjtFOjtLg%3D
8. DK Choudhary BN Johri 2009 Interactions of Bacillus spp. and plants-with special reference to induced Microbiol Res 164 5 493 513 10.1016/j.micres.2008. 08.007 1:CAS:528:DC%2BD1MXhsVOlsrbF
9. J Chun KS Bae 2000 Phylogenetic analysis of Bacillus subtilis and related taxa based on partial gyrA gene sequences Antonie van Leeuwenhoek 78 123 127 10.1023/A:1026555830014 1:CAS:528:DC%2BD3MXpvVartQ%3D%3D (Pubitemid 32046754)
10. S Djordjevic AM Stock 1997 Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine Structure 5 545 558 10.1016/S0969-2126(97)00210-4 1:CAS:528:DyaK2sXjt1SjtL0%3D (Pubitemid 27191230)
11. S Djordjevic PN Goudreau Q Xu AM Stock AH West 1998 Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain Proc Natl Acad Sci USA 95 1381 1386 10.1073/pnas.95.4.1381 1:CAS:528:DyaK1cXht1WqsLs%3D (Pubitemid 28103400)
12. A Doron-Faigenboim T Pupko 2007 A combined empirical and mechanistic codon model Mol Biol Evol 24 388 397 10.1093/molbev/msl175 1:CAS:528: DC%2BD2sXhslyisLc%3D (Pubitemid 46204372)
13. A Doron-Faigenboim A Stern I Mayrose E Bacharach T Pupko 2005 Selecton: a server for detecting evolutionary forces at a single amino-acid site Bioinformatics 21 2101 2103 10.1093/bioinformatics/bti259 1:CAS:528: DC%2BD2MXjsl2ns7s%3D (Pubitemid 40668056)
14. R Edgar 2004 MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 5 113 10.1186/1471-2105-5-113 (Pubitemid 40195393)
15. D Eisenberg R Lüthy JU Bowie 1997 VERIFY3D: assessment of protein models with three-dimensional profiles Methods Enzymol 277 396 404 10.1016/S0076-6879(97)77022-8 1:CAS:528:DyaK2sXntFamurY%3D (Pubitemid 27390932)
16. JJ Falke GL Hazelbauer 2001 Transmembrane signaling in bacterial chemoreceptors Trends Biochem Sci 26 257 265 10.1016/S0968-0004(00)01770-9 1:CAS:528:DC%2BD3MXisF2ntL0%3D (Pubitemid 32289244)
17. J Felsenstein GA Churchill 1996 A Hidden Markov Model approach to variation among sites in rate of evolution Mol Biol Evol 13 93 104 1:CAS:528:DyaK28XhtVylur0%3D (Pubitemid 26012458)
18. D Fritze 2004 Taxonomy of the genus Bacillus and related genera: the aerobic endospore-forming bacteria Phytopathology 94 1245 1248 10.1094/PHYTO.2004.94.11.1245 (Pubitemid 39448203)
19. LF Garrity GW Ordal 1995 Chemotaxis in Bacillus subtilis: how bacteria monitor environmental signals Pharmacol Ther 68 87 104 10.1016/0163-7258(95) 00027-5 1:CAS:528:DyaK2MXpsVOru7c%3D
20. LF Garrity SL Schiel R Merrill J Reizer MH Saier Jr GW Ordal 1998 Unique regulation of carbohydrate chemotaxis in Bacillus subtilis by the phosphoenolpyruvate-dependent phosphotransferase system and the methyl-accepting chemotaxis protein McpC J Bacteriol 180 4475 4480 1:CAS:528:DyaK1cXlvVCmu70%3D (Pubitemid 28405571)
21. DJ Goldman GW Ordal 1984 In vitro methylation and demethylation of methyl-accepting chemotaxis proteins in Bacillus subtilis Biochemistry 23 2600 2606 10.1021/bi00307a010 1:CAS:528:DyaL2cXitVGis7w%3D
22. TA Hall 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symp Ser 41 95 98 1:CAS:528:DC%2BD3cXhtVyjs7Y%3D
23. R Hamer P Chen J Armitage G Reinert C Deane 2010 Deciphering chemotaxis pathways using cross species comparisons BMC Systems Biology 4 3 10.1186/1752-0509-4-3
24. C Hernández-Sánchez A Mansilla F de Pablo R Zardoya 2008 Evolution of the insulin receptor family and receptor isoform expression in vertebrates Mol Biol Evol 25 1043 1053 10.1093/molbev/msn036
25. JR Kirby TB Niewold S Maloy GW Ordal 2000 CheB is required for behavioural responses to negative stimuli during chemotaxis in Bacillus subtilis Mol Microbiol 35 44 57 10.1046/j.1365-2958.2000.01676.x 1:CAS:528: DC%2BD3cXot1Shug%3D%3D (Pubitemid 30032269)
26. JR Kirby CJ Kristich M Saulmon MA Zimmer L Garrity IB Zhulin G Ordal 2001 CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis Mol Microbiol 42 573 585 10.1046/j.1365-2958.2001.02581.x 1:CAS:528:DC%2BD3MXos1Kgsb4%3D (Pubitemid 33064471)
27. CJ Kristich GW Ordal 2002 Bacillus subtilis CheD is a chemoreceptor modification enzyme required for chemotaxis J Biol Chem 277 25356 25362 10.1074/jbc.M201334200 1:CAS:528:DC%2BD38XlsVWhsrg%3D (Pubitemid 34951846)
28. CJ Kristich GW Ordal 2004 Analysis of chimeric chemoreceptors in Bacillus subtilis reveals a role for CheD in the function of the McpC HAMP domain J Bacteriol 186 5950 5955 10.1128/JB.186.17.5950-5955.2004 1:CAS:528: DC%2BD2cXntlCmurs%3D (Pubitemid 39128670)
29. CJ Kristich GD Glekas GW Ordal 2003 The conserved cytoplasmic module of the transmembrane chemoreceptor McpC mediates carbohydrate chemotaxis in Bacillus subtilis Mol Microbiol 47 1353 1366 10.1046/j.1365-2958.2003.03375.x 1:CAS:528:DC%2BD3sXitFWrt7k%3D (Pubitemid 36307857)
30. A Lupas J Stock 1989 Phosphorylation of an N-terminal regulatory domain activates the CheB methylesterase in bacterial chemotaxis J Biol Chem 264 17337 17342 1:CAS:528:DyaK3cXkt1Sq (Pubitemid 19255565)
31. R Lux VRN Munasinghe F Castellano JW Lengeler JET Corrie S Khan 1999 Elucidation of a PTS-carbohydrate chemotactic signal pathway in Escherichia coli using a time-resolved behavioral assay Mol Biol Cell 10 1133 1146 1:CAS:528:DyaK1MXisVGksLg%3D (Pubitemid 29193736)
32. MD Manson JP Armitage JA Hoch RM Macnab 1998 Bacterial locomotion and signal transduction J Bacteriol 180 1009 1022 1:CAS:528:DyaK1cXhsFyjtbc%3D (Pubitemid 28119456)
33. SL Mowbray MOJ Sandgren 1998 Chemotaxis receptors: a progress report on structure and function J Struct Biol 124 257 275 10.1006/jsbi.1998.4043 1:CAS:528:DyaK1MXhtlKlsrk%3D (Pubitemid 29143065)
34. TJ Muff GW Ordal 2007 The CheC phosphatase regulates chemotactic adaptation through CheD J Biol Chem 282 34120 34128 10.1074/jbc.M706432200 1:CAS:528:DC%2BD2sXhtlSltr3I (Pubitemid 350159481)
35. S Park X Chao G Gonzalez-Bonet BD Beel AM Bilwes BR Crane 2004 Structure and function of an unusual family of protein phosphatases: the bacterial chemotaxis proteins CheC and CheX Mol Cell 16 563 574 1:CAS:528: DC%2BD2cXhtVKht7rE (Pubitemid 39531879)
36. S Park BD Beel MI Simon AM Bilwes BR Crane 2004 In different organisms, the mode of interaction between two signaling proteins is not necessarily conserved Proc Natl Acad Sci USA 101 11646 11651 10.1073/pnas.0401038101 1:CAS:528:DC%2BD2cXntVekurs%3D (Pubitemid 39095350)
37. S Park PP Borbat G Gonzalez-Bonet J Bhatnagar AM Pollard JH Freed AM Bilwes BR Crane 2006 Reconstruction of the chemotaxis receptor-kinase assembly Nat Struct Mol Biol 13 400 407 10.1038/nsmb1085 1:CAS:528:DC%2BD28XltFWlsrw%3D (Pubitemid 43881579)
38. M Pawlowski M Gajda R Matlak J Bujnicki 2008 MetaMQAP: a meta-server for the quality assessment of protein models BMC Bioinformatics 9 403 10.1186/1471-2105-9-403
39. Y Pazy MA Motaleb MT Guarnieri NW Charon R Zhao RE Silversmith 2010 Identical phosphatase mechanisms achieved through distinct modes of binding phosphoprotein substrate Proc Natl Acad Sci USA 107 1924 1929 10.1073/pnas.0911185107 1:CAS:528:DC%2BC3cXhvFSns7k%3D
40. J Pei B Kim NV Grishin 2008 PROMALS3D: a tool for multiple protein sequence and structure alignments Nucl Acids Res 36 2295 2300 10.1093/nar/gkn072 1:CAS:528:DC%2BD1cXkvFGgtrs%3D (Pubitemid 351567002)
41. CV Rao JR Kirby AP Arkin 2004 Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis PLoS Biol 2 e49 10.1371/journal.pbio.0020049 (Pubitemid 39234562)
42. CV Rao GD Glekas GW Ordal 2008 The three adaptation systems of Bacillus subtilis chemotaxis Trends Microbiol 16 480 487 10.1016/j.tim.2008.07.003 1:CAS:528:DC%2BD1cXht1SmsrzO
43. ON Reva C Dixelius J Meijer FG Priest 2004 Taxonomic characterization and plant colonizing abilities of some bacteria related to Bacillus amyloliquefaciens and Bacillus subtilis FEMS Microbiol Ecol 48 249 259 10.1016/j.femsec.2004.02.003 1:CAS:528:DC%2BD2cXjs1aqtbs%3D (Pubitemid 38553968)
44. MM Rosario KL Fredrick GW Ordal JD Helmann 1994 Chemotaxis in Bacillus subtilis requires either of two functionally redundant CheW homologs J Bacteriol 176 2736 2739 1:CAS:528:DyaK2cXjtFyqurk%3D (Pubitemid 24139056)
45. MML Rosario JR Kirby DA Bochar GW Ordal 1995 Chemotactic methylation and behavior in Bacillus subtilis: role of two unique proteins, CheC and CheD Biochemistry 34 3823 3831 10.1021/bi00011a040 1:CAS:528:DyaK2MXktFegurg%3D
46. A Sali TL Blundell 1993 Comparative protein modelling by satisfaction of spatial restraints J Mol Biol 234 779 815 10.1006/jmbi.1993.1626 1:CAS:528:DyaK2cXnt1ylug%3D%3D (Pubitemid 24007801)
47. MM Saulmon E Karatan GW Ordal 2004 Effect of loss of CheC and other adaptational proteins on chemotactic behaviour in Bacillus subtilis Microbiology 150 581 589 10.1099/mic.0.26463-0 1:CAS:528:DC%2BD2cXis1eisbo%3D (Pubitemid 38386667)
48. M Shen A Sali 2006 Statistical potential for assessment and prediction of protein structures Protein Sci 15 2507 2524 10.1110/ps.062416606 1:CAS:528:DC%2BD28XhtFygsrfO (Pubitemid 44771688)
49. J Soding A Biegert AN Lupas 2005 The HHpred interactive server for protein homology detection and structure prediction Nucl Acids Res 33 W244 W248 10.1093/nar/gki408 (Pubitemid 44529917)
50. Tastan Bishop O, Kroon M (2011) Study of protein complexes via homology modeling, applied to cysteine proteases and their protein inhibitors. J Mol Model. doi: 10.1007/s00894-011-0990-y
51. KC Usher AFA De La Cruz FW Dahlquist S James Remington RV Swanson MI Simon 1998 Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability Protein Sci 7 403 412 10.1002/pro.5560070221 1:CAS:528:DyaK1cXhtFGhsL4%3D (Pubitemid 28092862)
52. A Van de Broek M Lambrecht J Vanderleyden 1998 Bacterial chemotactic motility is important for the initiation of wheat root colonization by Azospirillum brasilense Microbiology 144 2599 2606 10.1099/00221287-144-9-2599 (Pubitemid 28457170)
53. B Wallner A Elofsson 2003 Can correct protein models be identified? Protein Sci 12 1073 1086 10.1110/ps.0236803 1:CAS:528:DC%2BD3sXjtl2jtLk%3D (Pubitemid 36505441)
54. J Yao C Allen 2006 Chemotaxis is required for virulence and competitive fitness of the bacterial wilt pathogen Ralstonia solanacearum J Bacteriol 188 3697 3708 10.1128/JB.188.10.3697-3708.2006 1:CAS:528:DC%2BD28XkslClu7k%3D (Pubitemid 43726232)
55. W Yao L Shi D Liang 2007 Crystal structure of scaffolding protein CheW from Thermoanaerobacter tengcongensis Biochem Biophys Res Commun 361 1027 1032 10.1016/j.bbrc.2007.07.130 (Pubitemid 47259042)
56. W Zhang GN Phillips 2003 Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry Structure 11 1097 1110 10.1016/S0969-2126(03)00169-2 1:CAS:528:DC%2BD3sXntVKitb0%3D (Pubitemid 37103071)
57. MA Zimmer J Tiu MA Collins GW Ordal 2000 Selective methylation changes on the Bacillus subtilis chemotaxis receptor McpB promote adaptation J Biol Chem 275 24264 24272 10.1074/jbc.M004001200 1:CAS:528:DC%2BD3cXlslyqtbc%3D (Pubitemid 30626514)
58. MA Zimmer H Szurmant MM Saulmon MA Collins JS Bant GW Ordal 2002 The role of heterologous receptors in McpB-mediated signalling in Bacillus subtilis chemotaxis Mol Microbiol 45 555 568 10.1046/j.1365-2958.2002.03035.x 1:CAS:528:DC%2BD38XmtVehsLc%3D (Pubitemid 34779844)