Advertisement

Evolution of Multipartite Genomes in Prokaryotes

  • Madhusudan Choudhary
  • Hyuk Cho
  • Anish Bavishi
  • Cheramie Trahan
  • Bat-Erdene Myagmarjav
Chapter

Abstract

Recent findings have shed light on the interplay and roles of multipartite genome structure in relation to bacterial survival and specialization. The majority of bacteria with two chromosomes are members of the Proteobacteria group and recent evidence suggests that the primary (CI) and the accessory chromosomes (CII) are essential and ancient partners of these complex prokaryotic genomes. However, accessory chromosomes have evolved more rapidly to provide increased metabolic plasticity as the CI encodes more essential proteins necessary for cell survival. The flexibility and the high divergence of CII may allow increased adaptability to specialized environments in which the possession of a single chromosome may not fully permit. Models and hypotheses pertaining to the formation of accessory chromosomes and the roles of different inherent genomic factors integral to the evolution of the accessory chromosomes in bacteria such as evolutionary constraints, horizontal gene transfer, partitioning of genes representing different COGs, gene regulation mechanisms, and replication mechanisms are discussed in this chapter.

Keywords

Horizontal Gene Transfer Codon Usage Bias Horizontal Gene Transfer Event Multiple Chromosome Brucella Melitensis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This work was supported by the Enhancement Grant for Research (EGR) from Sam Houston State University to Madhusudan Choudhary.

References

  1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402PubMedCrossRefGoogle Scholar
  2. Balsiger S, Ragaz C, Baron C, Narberhaus F (2004) Replicon-specific regulation of small heat shock genes in Agrobacterium tumefaciens. J Bacteriol 186(20):6824–6829PubMedCrossRefGoogle Scholar
  3. Bavishi A, Abhishek A, Lin L, Choudhary M (2010a) Complex prokaryotic genome structure: rapid evolution of chromosome II. Genome 53(9):675–687PubMedCrossRefGoogle Scholar
  4. Bavishi A, Lin L, Schroeder K, Peters A, Cho H, Choudhary M (2010b) The prevalence of gene duplications and their ancient origin in Rhodobacter sphaeroides 2.4.1. BMC Microbiol 10:331PubMedCrossRefGoogle Scholar
  5. Bendich AJ, Drlica K (2000) Prokaryotic and eukaryotic chromosomes: what’s the difference? BioEssays: News Rev Mol Cell Dev Biol 22(5):481–486CrossRefGoogle Scholar
  6. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277(5331):1453–1462PubMedCrossRefGoogle Scholar
  7. Choudhary M, Fu YX, Mackenzie C, Kaplan S (2004) DNA sequence duplication in Rhodobacter sphaeroides 2.4.1: evidence of an ancient partnership between chromosomes I and II. J Bacteriol 186(7):2019–2027PubMedCrossRefGoogle Scholar
  8. Choudhary M, Mackenzie C, Nereng K, Sodergren E, Weinstock GM, Kaplan S (1997) Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1: chromosome II is a true chromosome. Microbiology 143(10):3085–3099PubMedCrossRefGoogle Scholar
  9. Choudhary M, Mackenzie C, Nereng KS, Sodergren E, Weinstock GM, Kaplan S (1994) Multiple chromosomes in bacteria: structure and function of chromosome II of Rhodobacter sphaeroides 2.4.1. J Bacteriol 176(24):7694–7702PubMedGoogle Scholar
  10. Choudhary M, Zanhua X, Fu YX, Kaplan S (2007) Genome analyses of three strains of Rhodobacter sphaeroides: evidence of rapid evolution of chromosome II. J Bacteriol 189(5):1914–1921PubMedCrossRefGoogle Scholar
  11. Cooper VS, Vohr SH, Wrocklage SC, Hatcher PJ (2010) Why genes evolve faster on secondary chromosomes in bacteria. PLoS Comput Biol 6(4):e1000732PubMedCrossRefGoogle Scholar
  12. Darling AC, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14(7):1394–1403PubMedCrossRefGoogle Scholar
  13. Dryden SC, Kaplan S (1990) Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides. Nucleic Acids Res 18(24):7267–7277PubMedCrossRefGoogle Scholar
  14. Duigou S, Knudsen KG, Skovgaard O, Egan ES, Lobner-Olesen A, Waldor MK (2006) Independent control of replication initiation of the two Vibrio cholerae chromosomes by DnaA and RctB. J Bacteriol 188(17):6419–6424PubMedCrossRefGoogle Scholar
  15. Egan ES, Fogel MA, Waldor MK (2005) Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol Microbiol 56(5):1129–1138PubMedCrossRefGoogle Scholar
  16. Guo X, Flores M, Mavingui P, Fuentes SI, Hernandez G, Davila G, Palacios R (2003) Natural genomic design in Sinorhizobium meliloti: novel genomic architectures. Genome Res 13(8):1810–1817PubMedGoogle Scholar
  17. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM (2000) DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406(6795):477–483PubMedCrossRefGoogle Scholar
  18. Itaya M, Tanaka T (1997) Experimental surgery to create subgenomes of Bacillus subtilis 168. Proc Nat Acad Sci U S A 94(10):5378–5382CrossRefGoogle Scholar
  19. Carins J (1963) The bacterial chromosome and its manner of replication as seen by autoradiography. J Mol Biol 6(3):208–213Google Scholar
  20. Jumas-Bilak E, Michaux-Charachon S, Bourg G, Ramuz M, Allardet-Servent A (1998) Unconventional genomic organization in the alpha subgroup of the Proteobacteria. J Bacteriol 180(10):2749–2755PubMedGoogle Scholar
  21. Karlin S, Barnett MJ, Campbell AM, Fisher RF, Mrazek J (2003) Predicting gene expression levels from codon biases in alpha-proteobacterial genomes. Proc Nat Acad Sci U S A 100(12):7313–7318CrossRefGoogle Scholar
  22. Kuhn HW (1955) The Hungarian method for the assignment problem. Nav Res Logist Q 2(1–2):83–97CrossRefGoogle Scholar
  23. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Danchin A et al (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390(6657):249–256PubMedCrossRefGoogle Scholar
  24. Langille MG, Brinkman FS (2009) IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25(5):664–665PubMedCrossRefGoogle Scholar
  25. Mackenzie C, Choudhary M, Larimer FW, Predki PF, Stilwagen S, Armitage JP, Barber RD, Donohue TJ, Hosler JP, Newman JE, Shapleigh JP, Sockett RE, Zeilstra-Ryalls J, Kaplan S (2001) The home stretch, a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1. Photosynth Res 70(1):19–41PubMedCrossRefGoogle Scholar
  26. Mackenzie C, Kaplan S, Choudhary M (2004) Multiple chromosomes: intracellular mechanism for generating sequence diversity. In: Miller RV, Day MJ (eds) Microbial evolution: gene establishment, survival, and exchange. ASM Press, Washington, DC, pp 82–101Google Scholar
  27. Neidle EL, Kaplan S (1993) Expression of the Rhodobacter sphaeroides hemA and hemT genes, encoding two 5-aminolevulinic acid synthase isozymes. J Bacteriol 175(8):2292–2303PubMedGoogle Scholar
  28. Nereng KS, Kaplan S (1999) Genomic complexity among strains of the facultative photoheterotrophic bacterium Rhodobacter sphaeroides. J Bacteriol 181(5):1684–1688PubMedGoogle Scholar
  29. Novichkov PS, Wolf YI, Dubchak I, Koonin EV (2009) Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol 191(1):65–73PubMedCrossRefGoogle Scholar
  30. Park K, Han E, Paulsson J, Chattoraj DK (2001) Origin pairing (‘handcuffing’) as a mode of negative control of P1 plasmid copy number. EMBO J 20(24):7323–7332PubMedCrossRefGoogle Scholar
  31. Rasmussen T, Jensen RB, Skovgaard O (2007) The two chromosomes of Vibrio cholerae are initiated at different time points in the cell cycle. EMBO J 26(13):3124–3131PubMedCrossRefGoogle Scholar
  32. Smith CL, Econome JG, Schutt A, Klco S, Cantor CR (1987) A physical map of the Escherichia coli K12 genome. Science 236(4807):1448–1453PubMedCrossRefGoogle Scholar
  33. Suwanto A, Kaplan S (1989a) Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: genome size, fragment identification, and gene localization. J Bacteriol 171(11):5840–5849PubMedGoogle Scholar
  34. Suwanto A, Kaplan S (1989b) Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes. J Bacteriol 171(11):5850–5859PubMedGoogle Scholar
  35. Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22(18):2196–2203PubMedCrossRefGoogle Scholar
  36. Wake RG (1973) Circularity of the Bacillus subtilis chromosome and further studies on its bidirectional replication. J Mol Biol 77(4):569–575PubMedCrossRefGoogle Scholar
  37. Xu Q, Dziejman M, Mekalanos JJ (2003) Determination of the transcriptome of Vibrio cholerae during intraintestinal growth and midexponential phase in vitro. Proc Natl Acad Sci U S A 100(3):1286–1291PubMedCrossRefGoogle Scholar
  38. Zhou Y, Landweber LF (2007) BLASTO: a tool for searching orthologous groups. Nucleic Acids Res 35(Web Server issue): W678–W682Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Madhusudan Choudhary
    • 1
  • Hyuk Cho
    • 2
  • Anish Bavishi
    • 1
  • Cheramie Trahan
    • 1
  • Bat-Erdene Myagmarjav
    • 1
  1. 1.Department of Biological SciencesSam Houston State UniversityHuntsvilleUSA
  2. 2.Department of Computer ScienceSam Houston State UniversityHuntsvilleUSA

Personalised recommendations