A comparison of the Caulobacter NA1000 and K31 genomes reveals extensive genome rearrangements and differences in metabolic potential

被引:15
作者
Ash, Kurt [1 ]
Brown, Theta [1 ]
Watford, Tynetta [1 ]
Scott, LaTia E. [1 ]
Stephens, Craig [2 ]
Ely, Bert [1 ]
机构
[1] Univ S Carolina, Dept Biol Sci, Columbia, SC 29208 USA
[2] Santa Clara Univ, Dept Biol, Santa Clara, CA 95053 USA
来源
OPEN BIOLOGY | 2014年 / 4卷 / 10期
基金
美国国家科学基金会;
关键词
Caulobacter; plasmids; genome rearrangements; gene insertions; inversions; BACTERIAL-CELL CYCLE; GENETIC CIRCUIT; CRESCENTUS; TRANSCRIPTION; PHYLOGENY; DIVERSITY; SEQUENCE;
D O I
10.1098/rsob.140128
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The genus Caulobacter is found in a variety of habitats and is known for its ability to thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 4 degrees C with a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) that code for 438 additional proteins. A comparison of the K31 and the Caulobacter crescentus NA1000 genomes revealed extensive rearrangements of gene order, suggesting that the genomes had been randomly scrambled. However, a careful analysis revealed that the distance from the origin of replication was conserved for the majority of the genes and that many of the rearrangements involved inversions that included the origin of replication. On a finer scale, numerous small indels were observed. K31 proteins involved in essential functions shared 80-95% amino acid sequence identity with their C. crescentus homologues, while other homologue pairs tended to have lower levels of identity. In addition, the K31 chromosome contains more than 1600 genes with no homologue in NA1000.
引用
收藏
页数:9
相关论文
共 27 条
  • [1] Phylogeny and polyphasic taxonomy of Caulobacter species.: Proposal of Maricaulis gen. nov with Maricaulis maris (Poindexter) comb. nov as the type species, and emended description of the genera Brevundimonas and Caulobacter
    Abraham, WR
    Strömpl, C
    Meyer, H
    Lindholst, S
    Moore, ERB
    Christ, R
    Vancanneyt, M
    Tindall, BJ
    Bennasar, A
    Smit, J
    Tesar, M
    [J]. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY, 1999, 49 : 1053 - 1073
  • [2] Comparative Genomics Reveal Extensive Transposon-Mediated Genomic Plasticity and Diversity among Potential Effector Proteins within the Genus Coxiella
    Beare, Paul A.
    Unsworth, Nathan
    Andoh, Masako
    Voth, Daniel E.
    Omsland, Anders
    Gilk, Stacey D.
    Williams, Kelly P.
    Sobral, Bruno W.
    Kupko, John J., III
    Porcella, Stephen F.
    Samuel, James E.
    Heinzen, Robert A.
    [J]. INFECTION AND IMMUNITY, 2009, 77 (02) : 642 - 656
  • [3] Regulation of the bacterial cell cycle by an integrated genetic circuit
    Biondi, Emanuele G.
    Reisinger, Sarah J.
    Skerker, Jeffrey M.
    Arif, Muhammad
    Perchuk, Barrett S.
    Ryan, Kathleen R.
    Laub, Michael T.
    [J]. NATURE, 2006, 444 (7121) : 899 - 904
  • [4] METABOLISM OF AROMATIC-COMPOUNDS BY CAULOBACTER-CRESCENTUS
    CHATTERJEE, DK
    BOURQUIN, AW
    [J]. JOURNAL OF BACTERIOLOGY, 1987, 169 (05) : 1993 - 1996
  • [5] Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes
    Couturier, E
    Rocha, EPC
    [J]. MOLECULAR MICROBIOLOGY, 2006, 59 (05) : 1506 - 1518
  • [6] progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
    Darling, Aaron E.
    Mau, Bob
    Perna, Nicole T.
    [J]. PLOS ONE, 2010, 5 (06):
  • [7] Dynamics of Genome Rearrangement in Bacterial Populations
    Darling, Aaron E.
    Miklos, Istvan
    Ragan, Mark A.
    [J]. PLOS GENETICS, 2008, 4 (07):
  • [8] Bacterial Genome Instability
    Darmon, Elise
    Leach, David R. F.
    [J]. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, 2014, 78 (01) : 1 - 39
  • [9] ELY B, 1991, METHOD ENZYMOL, V204, P372
  • [10] Correction of the Caulobacter crescentus NA1000 Genome Annotation
    Ely, Bert
    Scott, LaTia Etheredge
    [J]. PLOS ONE, 2014, 9 (03):