Comparative genomics of green sulfur bacteria

被引：8

作者：

Davenport, Colin ^{[2
]}

Ussery, David W. ^{[3
]}

Tuemmler, Burkhard ^{[1
,2
]}

机构：

[1] Hannover Med Sch, Klin Forschergrp, OE 6710, D-30625 Hannover, Germany

[2] Hannover Med Sch, Klin Forschergrp, Klin Padiatr Pneumol & Neonatol, OE 6711, D-30625 Hannover, Germany

[3] Tech Univ Denmark, Ctr Biol Sequence Anal, DK-2800 Lyngby, Denmark

来源：

PHOTOSYNTHESIS RESEARCH | 2010年 / 104卷 / 2-3期

关键词：

Comparative genomics; Chlorobaculum; Chlorobium; Genome atlas; Oligonucleotide usage; MATTHEWS-OLSON PROTEIN; 16S RIBOSOMAL-RNA; CHLOROBIUM-TEPIDUM; EVOLUTIONARY IMPLICATIONS; MICROBIAL GENOMES; ARCHAEAL GENOMES; USAGE PATTERNS; GENE-SEQUENCES; HOT-SPRINGS; PROKARYOTES;

D O I：

10.1007/s11120-009-9515-2

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Eleven completely sequenced Chlorobi genomes were compared in oligonucleotide usage, gene contents, and synteny. The green sulfur bacteria (GSB) are equipped with a core genome that sustains their anoxygenic phototrophic lifestyle by photosynthesis, sulfur oxidation, and CO2 fixation. Whole-genome gene family and single gene sequence comparisons yielded similar phylogenetic trees of the sequenced chromosomes indicating a concerted vertical evolution of large gene sets. Chromosomal synteny of genes is not preserved in the phylum Chlorobi. The accessory genome is characterized by anomalous oligonucleotide usage and endows the strains with individual features for transport, secretion, cell wall, extracellular constituents, and a few elements of the biosynthetic apparatus. Giant genes are a peculiar feature of the genera Chlorobium and Prosthecochloris. The predicted proteins have a huge molecular weight of 10(6), and are probably instrumental for the bacteria to generate their own intimate (micro)environment.

引用

页码：137 / 152

页数：16

共 50 条

[1] Phylogeny of green sulfur bacteria on the basis of gene sequences of 16S rRNA and of the Fenna-Matthews-Olson protein [J].

Alexander, B ;

Andersen, JH ;

Cox, RP ;

Imhoff, JF .

ARCHIVES OF MICROBIOLOGY, 2002, 178 (02) :131-140

[2] Sequence analysis by additive scales:: DNA structure for sequences and repeats of all lengths [J].

Baldi, P ;

Baisnée, PF .

BIOINFORMATICS, 2000, 16 (10) :865-889

[3] Comparative genomic structure of prokaryotes [J].

Bentley, SD ;

Parkhill, J .

ANNUAL REVIEW OF GENETICS, 2004, 38 :771-792

[4] GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses [J].

Besemer, J ;

Borodovsky, M .

NUCLEIC ACIDS RESEARCH, 2005, 33 :W451-W454

[5] Investigations of oligonucleotide usage variance within and between prokaryotes [J].

Bohlin, Jon ;

Skjerve, Eystein ;

Ussery, David W. .

PLOS COMPUTATIONAL BIOLOGY, 2008, 4 (04)

[6] Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes [J].

Bohlin, Jon ;

Skjerve, Eystein ;

Ussery, David W. .

BMC GENOMICS, 2008, 9 (1)

[7] Prokaryotic photosynthesis and phototrophy illuminated [J].

Bryant, Donald A. ;

Frigaard, Niels-Ulrik .

TRENDS IN MICROBIOLOGY, 2006, 14 (11) :488-496

[8] Transcription regulation and environmental adaptation in bacteria [J].

Cases, I ;

de Lorenzo, V ;

Ouzounis, CA .

TRENDS IN MICROBIOLOGY, 2003, 11 (06) :248-253

[9] ANOXYGENIC MICROBIAL MATS OF HOT-SPRINGS - THERMOPHILIC CHLOROBIUM SP [J].

CASTENHOLZ, RW ;

BAULD, J ;

JORGENSON, BB .

FEMS MICROBIOLOGY ECOLOGY, 1990, 74 (04) :325-336

[10] A genomic region required for phototrophic thiosulfate oxidation in the green sulfur bacterium Chlorobium tepidum (syn. Chlorobaculum tepidum) [J].

Chan, Leong-Keat ;

Weber, Timothy S. ;

Morgan-Kiss, Rachael M. ;

Hanson, Thomas E. .

MICROBIOLOGY-SGM, 2008, 154 :818-829

← 1 2 3 4 5 →