Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Bohlin, Jon ^a   Snipen, Lars ^a   Cloeckaert, Axel ^b   Lagesen, Karin ^c   Ussery, David ^d   Kristoffersen, Anja B ^c,e   Godfroid, Jacques ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b UR1282   (France)

^c UNIVERSITY OF OSLO   (Norway)

^d TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^e NORWEGIAN VETERINARY INSTITUTE   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIUM; CLASSIFICATION; FREQUENCY ANALYSIS; GENETIC ANALYSIS; GENETIC MARKER; GENOMICS; HOMOGENEITY; MARKOV CHAIN; MUTATION; PHENOTYPE; PHYLOGENY; PROTEIN; PROTEOMICS; SPECIES DIVERSITY; TAXONOMY;

AGROBACTERIUM; BACTERIA (MICROORGANISMS); BRUCELLA; OCHROBACTRUM; RHIZOBIUM;

BACTERIAL DNA; PROTEOME;

ARTICLE; BACTERIAL GENOME; BIOLOGICAL MODEL; BRUCELLA; CLASSIFICATION; COMPARATIVE GENOMIC HYBRIDIZATION; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; METHODOLOGY; PHYLOGENY; PROBABILITY; PROTEOMICS;

BRUCELLA; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, BACTERIAL; GENOME, BACTERIAL; MARKOV CHAINS; MODELS, GENETIC; PHYLOGENY; PROTEOME; PROTEOMICS; SEQUENCE ANALYSIS, DNA;

EID: 77955478549     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-249     Document Type: Article

References (52)

1. Current understanding of the genetic diversity of Brucella, an expanding genus of zoonotic pathogens. AM Whatmore, Infect Genet Evol 2009 9 6 1168 84 10.1016/j.meegid.2009.07.001 19628055
2. Brucella, a Monospecific Genus as Shown by Deoxyribonucleic Acid Hybridization. J Verger F Grimont PAD Grimont M Grayon, Int J Syst Bacteriol 1985 35 3 292 295 10.1099/00207713-35-3-292
3. International Committee on Systematics of Prokaryotes; Subcommittee on the taxonomy of Brucella: Minutes of the meeting, 17 September 2003, Pamplona, Spain. B Osterman I Moriyon, Int J Syst Evol Microbiol 2006 56 5 1173 1175 10.1099/ijs.0.64349-0
4. Brucella ceti sp. nov. and Brucella pinnipedialis sp. nov. for Brucella strains with cetaceans and seals as their preferred hosts. G Foster BS Osterman J Godfroid I Jacques A Cloeckaert, Int J Syst Evol Microbiol 2007 57 Pt 11 2688 2693 10.1099/ijs.0.65269-0 17978241
5. Brucella microti sp. nov., isolated from the common vole Microtus arvalis. HC Scholz Z Hubalek I Sedlacek G Vergnaud H Tomaso S Al Dahouk F Melzer P Kampfer H Neubauer A Cloeckaert M Maquart MS Zygmunt AM Whatmore E Falsen P Bahn C Gollner M Pfeffer B Huber HJ Busse K Nockler, Int J Syst Evol Microbiol 2008 58 Pt 2 375 382 10.1099/ijs.0.65356-0 18218934
6. Brucella inopinata sp. nov., isolated from a breast implant infection. HC Scholz K Nockler C Gollner P Bahn G Vergnaud H Tomaso S Al-Dahouk P Kampfer A Cloeckaert M Maquart MS Zygmunt AM Whatmore M Pfeffer B Huber HJ Busse BK De, Int J Syst Evol Microbiol 2010 60 Pt 4 801 8 10.1099/ijs.0.011148-0 19661515
7. The genome sequence of the facultative intracellular pathogen Brucella melitensis. VG DelVecchio V Kapatral RJ Redkar G Patra C Mujer T Los N Ivanova I Anderson A Bhattacharyya A Lykidis G Reznik L Jablonski N Larsen M D'Souza A Bernal M Mazur E Goltsman E Selkov PH Elzer S Hagius D O'Callaghan JJ Letesson R Haselkorn N Kyrpides R Overbeek, Proc Natl Acad Sci USA 2002 99 1 443 448 10.1073/pnas.221575398 11756688
8. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. IT Paulsen R Seshadri KE Nelson JA Eisen JF Heidelberg TD Read RJ Dodson L Umayam LM Brinkac MJ Beanan SC Daugherty RT Deboy AS Durkin JF Kolonay R Madupu WC Nelson B Ayodeji M Kraul J Shetty J Malek SE Van Aken S Riedmuller H Tettelin SR Gill O White SL Salzberg DL Hoover LE Lindler SM Halling SM Boyle CM Fraser, Proc Natl Acad Sci USA 2002 99 20 13148 13153 10.1073/pnas.192319099 12271122
9. Brucella evolution and taxonomy. E Moreno A Cloeckaert I Moriyon, Vet Microbiol 2002 90 1-4 209 227 10.1016/S0378-1135(02)00210-9 12414145
10. Whole-genome-based phylogeny and divergence of the genus Brucella. JT Foster SM Beckstrom-Sternberg T Pearson JS Beckstrom-Sternberg PS Chain FF Roberto J Hnath T Brettin P Keim, J Bacteriol 2009 191 8 2864 2870 10.1128/JB.01581-08 19201792
11. Towards a prokaryotic genomic taxonomy. T Coenye D Gevers PY Van de P Vandamme J Swings, FEMS Microbiol Rev 2005 29 2 147 167 10.1016/j.femsre.2004. 11.004 15808739
12. Examination of genome homogeneity in prokaryotes using genomic signatures. J Bohlin E Skjerve, PLoS One 2009 4 12 8113 10.1371/journal.pone. 0008113 19956556
13. An environmental signature for 323 microbial genomes based on codon adaptation indices. H Willenbrock C Friis AS Juncker DW Ussery, Genome Biol 2006 7 12 114 10.1186/gb-2006-7-12-r114 17156429
14. Prodigal: prokaryotic gene recognition and translation initiation site identification. D Hyatt GL Chen PF Locascio ML Land FW Larimer LJ Hauser, BMC Bioinformatics 2010 11 1 119 10.1186/1471-2105-11-119 20211023
15. The Genus Burkholderia: Analysis of 56 Genomic Sequences. DW Ussery K Kiil K Lagesen T Sicheritz-Ponten J Bohlin TM Wassenaar, Genome Dyn 2009 6 140 157 full-text 19696499
16. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome". H Tettelin V Masignani MJ Cieslewicz C Donati D Medini NL Ward SV Angiuoli J Crabtree AL Jones AS Durkin RT Deboy TM Davidsen M Mora M Scarselli IMY Ros JD Peterson CR Hauser JP Sundaram WC Nelson R Madupu LM Brinkac RJ Dodson MJ Rosovitz SA Sullivan SC Daugherty DH Haft J Selengut ML Gwinn LW Zhou N Zafar H Khouri D Radune G Dimitrov K Watkins KJB O'Connor S Smith TR Utterback O White CE Rubens G Grandi LC Madoff DL Kasper JL Telford MR Wessels R Rappuoli CM Fraser, 2005 102 39 13950 13955 16172379
17. Microbial comparative pan-genomics using binomial mixture models. L Snipen T Almoy DW Ussery, BMC Genomics 2009 10 385 10.1186/1471-2164-10-385 19691844
18. Genetic diversity and phylogenetic relationships of bacteria belonging to the Ochrobactrum-Brucella group by recA and 16S rRNA gene-based comparative sequence analysis. HC Scholz S Al Dahouk H Tomaso H Neubauer A Witte M Schloter P Kampfer E Falsen M Pfeffer M Engel, Syst Appl Microbiol 2008 31 1 1 16 10.1016/j.syapm.2007.10.004 18222618
19. Codon usage between genomes is constrained by genome-wide mutational processes. SL Chen W Lee AK Hottes L Shapiro HH McAdams, Proc Natl Acad Sci USA 2004 101 10 3480 3485 10.1073/pnas.0307827100 14990797
20. Genome degradation in Brucella ovis corresponds with narrowing of its host range and tissue tropism. RM Tsolis R Seshadri RL Santos FJ Sangari JM Lobo MF de Jong Q Ren G Myers LM Brinkac WC Nelson RT Deboy S Angiuoli H Khouri G Dimitrov JR Robinson S Mulligan RL Walker PE Elzer KA Hassan IT Paulsen, PLoS One 2009 4 5 5519 10.1371/journal.pone.0005519 19436743
21. Characteristics of a Brucella species from a bottlenose dolphin (Tursiops truncatus). DR Ewalt JB Payeur BM Martin DR Cummins WG Miller, J Vet Diagn Invest 1994 6 4 448 452 7858024
22. Characterisation of the genetic diversity of Brucella by multilocus sequencing. AM Whatmore LL Perrett AP MacMillan, BMC Microbiol 2007 7 34 10.1186/1471-2180-7-34 17448232
23. Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. H Willenbrock PF Hallin TM Wassenaar DW Ussery, Genome Biol 2007 8 12 267 10.1186/gb-2007-8-12-r267 18088402
24. Comparative whole-genome hybridization reveals genomic islands in Brucella species. G Rajashekara JD Glasner DA Glover GA Splitter, J Bacteriol 2004 186 15 5040 5051 10.1128/JB.186.15.5040-5051.2004 15262941
25. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. AR Wattam KP Williams EE Snyder NF Almeida Jr M Shukla AW Dickerman OR Crasta R Kenyon J Lu JM Shallom H Yoo TA Ficht RM Tsolis C Munk R Tapia CS Han JC Detter D Bruce TS Brettin BW Sobral SM Boyle JC Setubal, J Bacteriol 2009 191 11 3569 3579 10.1128/JB.01767-08 19346311
26. Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering. J Bohlin E Skjerve DW Ussery, BMC Genomics 2009 10 487 10.1186/1471-2164-10-487 19845945
27. Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. CH Kuo H Ochman, Biol Direct 2009 4 35 10.1186/1745-6150-4-35 19788732
28. Dinucleotide relative abundance extremes: a genomic signature. S Karlin C Burge, Trends Genet 1995 11 7 283 290 10.1016/S0168-9525(00)89076-9 7482779
29. Application of tetranucleotide frequencies for the assignment of genomic fragments. H Teeling A Meyerdierks M Bauer R Amann FO Glockner, Environ Microbiol 2004 6 9 938 947 10.1111/j.1462-2920.2004.00624.x 15305919
30. Microbial minimalism: genome reduction in bacterial pathogens. NA Moran, Cell 2002 108 5 583 586 10.1016/S0092-8674(02)00665-7 11893328
31. Base composition bias might result from competition for metabolic resources. EP Rocha A Danchin, Trends Genet 2002 18 6 291 294 10.1016/S0168-9525(02)02690-2 12044357
32. Origin of replication in circular prokaryotic chromosomes. P Worning LJ Jensen PF Hallin HH Staerfeldt DW Ussery, Environ Microbiol 2006 8 2 353 361 10.1111/j.1462-2920.2005.00917.x 16423021
33. GC content and genome length in Chargaff compliant genomes. D Mitchell, Biochem Biophys Res Commun 2007 353 0006-291; 1 207 210 10.1016/j.bbrc.2006.12. 008 17173863
34. Genomic GC level, optimal growth temperature, and genome size in prokaryotes. H Musto H Naya A Zavala H Romero F varez-Valin G Bernardi, Biochem Biophys Res Commun 2006 347 0006-291; 1 1 3 10.1016/j.bbrc.2006.06.054 16815305
35. Investigations of oligonucleotide usage variance within and between prokaryotes. J Bohlin E Skjerve DW Ussery, PLoS Comput Biol 2008 4 4 1000057 10.1371/journal.pcbi.1000057 18421372
36. Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction. L Gomez-Valero EP Rocha A Latorre FJ Silva, Genome Res 2007 17 8 1178 1185 10.1101/gr.6360207 17623808
37. Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. H Toh BL Weiss SA Perkin A Yamashita K Oshima M Hattori S Aksoy, Genome Res 2006 16 2 149 156 10.1101/gr.4106106 16365377
38. Accelerated evolution associated with genome reduction in a free-living prokaryote. A Dufresne L Garczarek F Partensky, Genome Biol 2005 6 2 14 10.1186/gb-2005-6-2-r14 15693943
39. Environments shape the nucleotide composition of genomes. KU Foerstner MC von SD Hooper P Bork, EMBO Rep 2005 6 1469-221; 12 1208 1213 10.1038/sj.embor.7400538 16200051
40. Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages. LL Chen CT Zhang, Biochem Biophys Res Commun 2003 306 0006-291; 1 310 317 10.1016/S0006-291X(03)00973-2 12788106
41. Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. PS Novichkov MV Omelchenko MS Gelfand AA Mironov YI Wolf EV Koonin, J Bacteriol 2004 186 19 6575 6585 10.1128/JB.186.19.6575-6585.2004 15375139
42. PATRIC: the VBI PathoSystems Resource Integration Center. EE Snyder N Kampanya J Lu EK Nordberg HR Karur M Shukla J Soneja Y Tian T Xue H Yoo F Zhang C Dharmanolla NV Dongre JJ Gillespie J Hamelius M Hance KI Huntington D Jukneliene J Koziski L Mackasmiel SP Mane V Nguyen A Purkayastha J Shallom G Yu Y Guo J Gabbard D Hix AF Azad SC Baker SM Boyle Y Khudyakov XJ Meng C Rupprecht J Vinje OR Crasta MJ Czar A Dickerman JD Eckart R Kenyon R Will JC Setubal BW Sobral, Nucleic Acids Res 2007 35 Database 401 6 10.1093/nar/gkl858 17142235
43. Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. ON Reva B Tummler, BMC Bioinformatics 2004 5 90 10.1186/1471-2105-5-90 15239845
44. Evolutionary implications of microbial genome tetranucleotide frequency biases. DT Pride RJ Meinersmann TM Wassenaar MJ Blaser, Genome Res 2003 13 2 145 158 10.1101/gr.335003 12566393
45. R: A language and environment for statistical computing. R Development Core Team, http://www.R-project.org
46. Statistical significance of sequence patterns in proteins. S Karlin, Curr Opin Struct Biol 1995 5 0959-440; 3 360 371 10.1016/0959-440X(95)80098-0 7583634
47. Compositional biases of bacterial genomes and evolutionary implications. S Karlin J Mrazek AM Campbell, J Bacteriol 1997 179 12 3899 3913 9190805
48. The reach of the genome signature in prokaryotes. MW van Passel EE Kuramae AC Luyf A Bart T Boekhout, BMC Evol Biol 2006 6 84 10.1186/1471-2148-6- 84 17040564
49. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 3 403 410 2231712
50. Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. NL Hiller B Janto JS Hogg R Boissy S Yu E Powell R Keefe NE Ehrlich K Shen J Hayes K Barbadora W Klimke D Dernovoy T Tatusova J Parkhill SD Bentley JC Post GD Ehrlich FZ Hu, J Bacteriol 2007 189 22 8186 8195 10.1128/JB.00690-07 17675389
51. Evolution of proteomes: fundamental signatures and global trends in amino acid compositions. F Tekaia E Yeramian, BMC Genomics 2006 7 307 10.1186/1471-2164-7-307 17147802
52. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. EV Koonin YI Wolf, 2008 36 21 6688 6719 18948295