Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism
Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism
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DOI：
10.1093/nar/gkh830
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Beppu, T
中科院分区：
文献类型：
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作者：
Ueda, K;Yamashita, A;Beppu, T
嗜热共生杆菌是从堆肥中分离出来的一种依赖微生物共生的不可培养细菌。基于16S核糖体DNA的系统发育分析表明，该细菌属于革兰氏阳性菌群中的一个未知分类群。在这里，我们描述了嗜热链球菌3.57Mb的基因组序列。基因组由3338个蛋白质编码序列组成，其中2082个具有功能分配。尽管G+C含量很高(68.7%)，但基因组最接近于由低G+C革兰氏阳性细菌组成的门Firmicits的基因组。这为革兰氏阳性细菌群中存在一个未定义的类别提供了证据。SPO及其相关基因的存在和显微镜观察表明，嗜热链霉菌是第一个形成内孢子的高G+C生物体。嗜热链霉菌基因组的特征还包括广泛插入C组II类内含子，这些内含子与染色体复制方向相同。基因组有许多膜转运蛋白，其中一些参与了多肽和氨基酸的摄取。除了编码几种生物合成酶和碳酸氢酶的基因外，参与初级新陈代谢的基因在很大程度上被识别出来。这种微生物还具有多种呼吸系统，包括NAP硝酸还原酶，这种酶只在革兰氏阴性细菌中发现。总体而言，这些特征表明嗜热链球菌能够适应并生活在各种环境中，因此它的生长需求可能是自然环境中普遍存在的一种物质或生理条件，而不是只存在于有限的生态位中的高度特定的物质。来自嗜热链霉菌的基因组信息为微生物多样性和进化科学提供了新的见解，并为表征微生物共生的分子基础提供了一个框架。
Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium belongs to an unknown taxon in the Gram-positive bacterial cluster. Here, we describe the 3.57 Mb genome sequence of S.thermophilum. The genome consists of 3338 protein-coding sequences, out of which 2082 have functional assignments. Despite the high G + C content (68.7%), the genome is closest to that of Firmicutes, a phylum consisting of low G + C Gram-positive bacteria. This provides evidence for the presence of an undefined category in the Gram-positive bacterial group. The presence of both spo and related genes and microscopic observation indicate that S.thermophilum is the first high G + C organism that forms endospores. The S.thermophilum genome is also characterized by the widespread insertion of class C group II introns, which are oriented in the same direction as chromosomal replication. The genome has many membrane transporters, a number of which are involved in the uptake of peptides and amino acids. The genes involved in primary metabolism are largely identified, except those that code several biosynthetic enzymes and carbonic anhydrase. The organism also has a variety of respiratory systems including Nap nitrate reductase, which has been found only in Gram-negative bacteria. Overall, these features suggest that S.thermophilum is adaptable to and thus lives in various environments, such that its growth requirement could be a substance or a physiological condition that is generally available in the natural environment rather than a highly specific substance that is present only in a limited niche. The genomic information from S.thermophilum offers new insights into microbial diversity and evolutionary sciences, and provides a framework for characterizing the molecular basis underlying microbial commensalism.