Codon and amino acid usage in two major human pathogens of genus Bartonella -: Optimization between replicational-transcriptional selection, translational control and cost minimization

被引:28
作者
Das, Sabyasachi [1 ]
Paul, Sandip [1 ]
Chatterjee, Sanjib [1 ]
Dutta, Chitra [1 ]
机构
[1] Indian Inst Chem Biol, Bioinformat Ctr, Kolkata 700032, India
关键词
synonymous codon usage; relative amino acid usage; correspondence analysis; strand asymmetry; gene expression;
D O I
10.1093/dnares/12.2.91
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Intra-genomic variation in synonymous codon and amino acid usage in two human pathogens Bartonella, henselae and B. quintana has been carried out through multivariate analysis. Asymmetric mutational bias, coupled with replicational-transcriptional selection, has been identified as the prime selection force behind synonymous codon selection - a characteristic of the genus Bartonella, not exhibited by any other alpha-proteobacterial genome. Distinct codon usage patterns and low synonymous divergence values between orthologous sequences of highly expressed genes from the two Bartonella species indicate that there exists a residual intra-strand synonymous codon bias in the highly expressed genes, possibly operating at the level of translation. In the case of amino acid usage, the mean hydropathy level and aromaticity are the major sources of variation, both having nearly equal impact, while strand-specific mutational pressure and gene expressivity strongly influence the inter-strand variations. In both species under study, the highly expressed gene products tend not to contain heavy and/or aromatic residues, following the cost-minimization hypothesis in spite of their intracellular lifestyle. The codon and amino acid usage in these two human pathogens are, therefore, consequences of a complex balance between replicational-transcriptional selection, translational control, protein hydropathy and cost minimization.
引用
收藏
页码:91 / 102
页数:12
相关论文
共 40 条
  • [1] The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae
    Alsmark, CM
    Frank, AC
    Karlberg, EO
    Legault, BA
    Ardell, DH
    Canbäck, B
    Eriksson, AS
    Näslund, AK
    Handley, SA
    Huvet, M
    La Scola, B
    Holmberg, M
    Andersson, SGE
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (26) : 9716 - 9721
  • [2] Genomic rearrangements during evolution of the obligate intracellular parasite Rickettsia prowazekii as inferred from an analysis of 52015 bp nucleotide sequence
    Andersson, JO
    Andersson, SGE
    [J]. MICROBIOLOGY-SGM, 1997, 143 : 2783 - 2795
  • [3] The genome sequence of Rickettsia prowazekii and the origin of mitochondria
    Andersson, SGE
    Zomorodipour, A
    Andersson, JO
    Sicheritz-Pontén, T
    Alsmark, UCM
    Podowski, RM
    Näslund, AK
    Eriksson, AS
    Winkler, HH
    Kurland, CG
    [J]. NATURE, 1998, 396 (6707) : 133 - 140
  • [4] Evolutionary forces in shaping the codon and amino acid usages in Blochmannia floridanus
    Banerjee, T
    Basak, S
    Gupta, SK
    Ghosh, TC
    [J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2004, 22 (01) : 13 - 23
  • [5] Sequential strand exchange by XerC and XerD during site-specific recombination at dif
    Blakely, GW
    Davidson, AO
    Sherratt, DJ
    [J]. JOURNAL OF BIOLOGICAL CHEMISTRY, 2000, 275 (14) : 9930 - 9936
  • [6] Computational inference of scenarios for α-proteobacterial genome evolution
    Boussau, B
    Karlberg, EO
    Frank, AC
    Legault, BA
    Andersson, SGE
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (26) : 9722 - 9727
  • [7] Conserved gene cluster at replication origins of the α-proteobacteria Caulobacter crescentus and Rickettsia prowazekii
    Brassinga, AKC
    Siam, R
    Marczynski, GT
    [J]. JOURNAL OF BACTERIOLOGY, 2001, 183 (05) : 1824 - 1829
  • [8] Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021
    Capela, D
    Barloy-Hubler, F
    Gouzy, J
    Bothe, G
    Ampe, F
    Batut, J
    Boistard, P
    Becker, A
    Boutry, M
    Cadieu, E
    Dréano, S
    Gloux, S
    Godrie, T
    Goffeau, A
    Kahn, D
    Kiss, E
    Lelaure, V
    Masuy, D
    Pohl, T
    Portetelle, D
    Pühler, A
    Purnelle, B
    Ramsperger, U
    Renard, C
    Thébault, P
    Vandenbol, M
    Weidner, S
    Galibert, F
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (17) : 9877 - 9882
  • [9] Gene expression, amino acid conservation, and hydrophobicity are the main factors shaping codon preferences in Mycobacterium tuberculosis and Mycobacterium leprae
    de Miranda, AB
    Alvarez-Valin, F
    Jabbari, K
    Degrave, WM
    Bernardi, G
    [J]. JOURNAL OF MOLECULAR EVOLUTION, 2000, 50 (01) : 45 - 55
  • [10] Strand asymmetries in DNA evolution
    Francino, MP
    Ochman, H
    [J]. TRENDS IN GENETICS, 1997, 13 (06) : 240 - 245