Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber.
Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber.
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DOI：
10.1186/1471-2164-10-570
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发表时间：
2009-12-01
期刊：
影响因子：
4.4
通讯作者：
Rodriguez-Valera F
中科院分区：
文献类型：
--
作者：
Pasić L;Rodriguez-Mueller B;Martin-Cuadrado AB;Mira A;Rohwer F;Rodriguez-Valera F
饱和卤水是低多样性的极端环境。红色盐杆菌是唯一大量栖息在这种环境中的细菌。为了确定该微生物在自然种群中的遗传多样性程度，将标准菌株DSM 13855的基因组序列与从顶峰盐场结晶器中回收的元基因组片段进行了比较，并利用454DNA测序技术获得了该菌的基因组片段。这种分析揭示了后基因组岛的存在，即种群中不同谱系之间的高度可变区域。测序后的分离物的三个区域在后基因组中几乎不存在，因此在共生的红色葡萄球菌细胞中似乎存在差异。这些后基因组岛显示了广泛的基因组破坏的证据，非典型的低GC含量，低编码密度，大量的假基因和短的假设蛋白质。对海岛基因含量的详细分析表明，元基因组海岛1中的基因编码细胞表面多糖。后基因组岛2的菌株特异性基因参与了细胞壁多糖成分的生物合成。最后，后基因组岛3含有丰富的DNA相关酶。红色沙门氏菌基因组可变区的基因组组织与海洋微生物基因组岛的研究显示出许多趋同，主要涉及可变的细胞表面特征。在没有捕食压力的环境中，细胞膜水平的这种变化可能反映了细菌逃避噬菌体捕食的全球策略。
Saturated brines are extreme environments of low diversity. Salinibacter ruber is the only bacterium that inhabits this environment in significant numbers. In order to establish the extent of genetic diversity in natural populations of this microbe, the genomic sequence of reference strain DSM 13855 was compared to metagenomic fragments recovered from climax saltern crystallizers and obtained with 454 sequencing technology. This kind of analysis reveals the presence of metagenomic islands, i.e. highly variable regions among the different lineages in the population. Three regions of the sequenced isolate were scarcely represented in the metagenome thus appearing to vary among co-occurring S. ruber cells. These metagenomic islands showed evidence of extensive genomic corruption with atypically low GC content, low coding density, high numbers of pseudogenes and short hypothetical proteins. A detailed analysis of island gene content showed that the genes in metagenomic island 1 code for cell surface polysaccharides. The strain-specific genes of metagenomic island 2 were found to be involved in biosynthesis of cell wall polysaccharide components. Finally, metagenomic island 3 was rich in DNA related enzymes. The genomic organisation of S. ruber variable genomic regions showed a number of convergences with genomic islands of marine microbes studied, being largely involved in variable cell surface traits. This variation at the level of cell envelopes in an environment devoid of grazing pressure probably reflects a global strategy of bacteria to escape phage predation.
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影响因子：
2.6
作者：
Defives, C;Werquin, M;Hornez, JP
通讯作者：
Hornez, JP
影响因子：
5.6
作者：
Nekrasov, Serge V.;Agafonova, Olga V.;Belogurov, Anatol A.
通讯作者：
Belogurov, Anatol A.
影响因子：
4.5
作者：
Kettler GC;Martiny AC;Huang K;Zucker J;Coleman ML;Rodrigue S;Chen F;Lapidus A;Ferriera S;Johnson J;Steglich C;Church GM;Richardson P;Chisholm SW
通讯作者：
Chisholm SW
影响因子：
10.7
作者：
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通讯作者：
Andersson, SGE
影响因子：
5.1
作者：
Bolhuis, H;Poele, EMT;Rodriguez-Valera, F
通讯作者：
Rodriguez-Valera, F