The relaxing ori-ter balance of Mycoplasma genomes

Science in China, Series C: Life Sciences

Volumn 51, Issue 2, 2008, Pages 182-189

  Zheng, Xin ^a   Liu, ShuLin ^a,b  

^a PEKING UNIVERSITY HEALTH SCIENCE CENTER   (China)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

Evolution; Genome balance; Mycoplasma; ori and ter; Z curve

Indexed keywords

BACTERIAL DNA; CIRCULAR DNA;

ARTICLE; BACTERIAL GENOME; COMPARATIVE STUDY; DNA REPLICATION; DNA REPLICATION ORIGIN; GENETICS; MOLECULAR EVOLUTION; MYCOPLASMA; PHYSIOLOGY; REGULATOR GENE;

DNA REPLICATION; DNA, BACTERIAL; DNA, CIRCULAR; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; MYCOPLASMA; REPLICATION ORIGIN; TERMINATOR REGIONS (GENETICS);

BACTERIA (MICROORGANISMS); MYCOPLASMA; MYCOPLASMATALES;

EID: 38849154503     PISSN: 10069305     EISSN: 18622798     Source Type: Journal    
DOI: 10.1007/s11427-008-0017-9     Document Type: Article

References (38)

1. Hill C W, Gray J A. Effects of chromosomal inversion on cell fitness in Escherichia coli K-12. Genetics, 1988, 119(4): 771-778
2. Fleischmann R D, Adams M D, White O, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 1995, 269(5223): 496-512
3. Liu S L, Sanderson K E. Rearrangements in the genome of the bacterium Salmonella typhi. Proc Natl Acad Sci USA, 1995, 92(4): 1018-1022
4. Liu S L, Sanderson K E. Highly plastic chromosomal organization in Salmonella typhi. Proc Natl Acad Sci USA, 1996, 93(19): 10303-10308
5. Kothapalli S, Nair S, Alokam S, et al. Diversity of genome structure in Salmonella enterica serovar Typhi populations. J Bacteriol, 2005, 187(8): 2638-2650
6. Liu G R, Liu W Q, Johnston R N, et al. Genome plasticity and ori-ter rebalancing in Salmonella typhi. Mol Biol Evol, 2006, 23(2): 365-371
7. Liu S L, Sanderson K E. Genomic cleavage map of Salmonella typhi Ty2. J Bacteriol, 1995, 177(17): 5099-5107
8. Parkhill J, Dougan G, James KD, et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature, 2001, 413(6858): 848-852
9. Deng W, Liou S R, Plunkett G 3rd, et al. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol, 2003, 185(7): 2330-2337
10. McClelland M, Sanderson K E, Spieth J, et al. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature, 2001, 413(6858): 852-856
11. McClelland M, Sanderson K E, Clifton S W, et al. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet, 2004, 36(12): 1268-1274
12. Liu S L, Sanderson K E. The chromosome of Salmonella paratyphi A is inverted by recombination between rrnH and rrnG. J Bacteriol, 1995, 177(22): 6585-6592
13. Song J, Ware A, Liu S L. Wavelet to predict bacterial ori and ter: A tendency towards a physical balance. BMC Genomics, 2003, 4(1): 17
14. Woese C R, Maniloff J, Zablen L B. Phylogenetic analysis of the mycoplasmas. Proc Natl Acad Sci USA, 1980, 77(1): 494-498
15. Oshima K, Kakizawa S, Nishigawa H, et al. Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat Genet, 2004, 36(1): 27-29
16. Fraser C M, Gocayne J D, White O, et al. The minimal gene complement of Mycoplasma genitalium. Science, 1995, 270(5235): 397-403
17. Chambaud I, Heilig R, Ferris S, et al. The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res, 2001, 29(10): 2145-2153
18. Papazisi L, Gorton T S, Kutish G, et al. The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain R(low). Microbiology, 2003, 149(Pt 9): 2307-2316
19. Minion F C, Lefkowitz E J, Madsen M L, et al. The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J Bacteriol, 2004, 186(21): 7123-7133
20. Bird R E, Louarn J, Martuscelli J, et al. Origin and sequence of chromosome replication in Escherichia coli. J Mol Biol, 1972, 70(3): 549-566
21. Marians K J. Prokaryotic DNA replication. Annu Rev Biochem, 1992, 61: 673-719
22. Marczynski G T, Shapiro L. Bacterial chromosome origins of replication. Curr Opin Genet Dev, 1993, 3(5): 775-782
23. Yoshikawa H, Ogasawara N. Structure and function of DnaA and the DnaA-box in eubacteria: Evolutionary relationships of bacterial replication origins. Mol Microbiol 1991, 5(11):2589-2597.
24. Ye F, Renaudin J, Bove JM, et al. Cloning and sequencing of the replication origin (oriC) of the Spiroplasma citri chromosome and construction of autonomously replicating artificial plasmids. Curr Microbiol, 1994, 29(1): 23-29
25. Zhang C T, Zhang R. Analysis of distribution of bases in the coding sequences by a diagrammatic technique. Nucleic Acids Res, 1991, 19(22): 6313-6317
26. Zhang R, Zhang C. Z curves, an intutive tool for visualizing and analyzing the DNA sequences. J Biomol Struct Dyn, 1994, 11(4): 767-782
27. Zhang R, Zhang C. Single replication origin of the archaeon Methanosarcina mazei revealed by the Z curve method. Biophys Res Commun, 2002, 297(2): 396-400
28. Zhang R, Zhang C. Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem Biophys Res Commun, 2003, 302(4): 728-734
29. Zhang R, Zhang C. Identification of replication origins in the genome of the methanogenic archaeon, Methanocaldococcus jannaschii. Extremophiles, 2004, 8(3): 253-258
30. Kunst F, Ogasawara N, Moszer I, et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature, 1997, 390(6657): 249-256
31. Cordova CM, Lartigue C, Sirand-Pugnet P, et al. Identification of the origin of replication of the Mycoplasma pulmonis chromosome and its use in oriC replicative plasmids. J Bacteriol, 2002, 184(19): 5426-5 435
32. Vasconcelos A T, Ferreira H B, Bizarro C V, et al. Swine and poultry pathogens: The complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. J Bacteriol, 2005, 187(16): 5568-5577
33. Sasaki Y, Ishikawa J, Yamashita A, et al. The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans. Nucleic Acids Res, 2002, 30(23): 5293-5300
34. Himmelreich R, Hilbert H, Plagens H, et al. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res, 1996, 24(22): 4420-4449
35. Jaffe J D, Stange-Thomann N, Smith C, et al. The complete genome and proteome of Mycoplasma mobile. Genome Res 2004, 14(8): 1447-1461
36. Westberg J, Persson A, Holmberg A, et al. The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Res, 2004, 14(2): 221-227
37. Blattner F R, Plunkett G 3rd, Bloch CA, et al. The complete genome sequence of Escherichia coli K-12. Science, 1997, 277(5331): 1453-1474
38. Chiu C H, Tang P, Chu C, et al. The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res, 2005, 33(5): 1690-1698