The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens
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DOI：
10.1073/pnas.032671499
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发表时间：
2002-04-02
影响因子：
11.1
通讯作者：
Kozyavkin, SA
中科院分区：
文献类型：
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作者：
Slesarev, AI;Mezhevaya, KV;Kozyavkin, SA
我们用全基因组直接测序法测定了康德勒甲烷甲藻富含GC的基因组的1,694,969-nT全序列。这种方法是基于基因组DNA与Kandleri拓扑异构酶V的ThermoFidelase版本的去连接和由2‘-修饰的寡核苷酸(Fimers)指导的循环测序。测序冗余度(3.3倍)足以组装基因组，每40kb不到一个错误。利用序列数据库搜索和编码潜力预测相结合的方法，鉴定了1,692个蛋白质编码基因和39个结构RNA基因。Kandleri蛋白显示出异常高的负电荷氨基酸含量，这可能是对细胞内高盐度的一种适应。此前对16S RNA的系统发育分析表明，Kandleri属于一个非常深的分支，靠近古树的根。然而，基因组比较表明，在使用核糖体蛋白质串联比对构建的树和基于基因含量的树中，康德勒分枝杆菌始终与其他古细菌产甲烷菌聚在一起。康德勒分枝杆菌与简氏甲烷球菌和热自养甲烷杆菌共享一组与产甲烷有关的基因，部分还与其操纵子组织相同。这些发现表明，古产甲烷菌是单系生物。康德勒分枝杆菌的一个显著特征是缺乏参与信号传递和基因表达调控的蛋白质。此外，与其他古生菌相比，康德勒分枝杆菌通过横向转移获得的基因似乎更少。这些特征可能反映了这种生物的极端栖息地。
We have determined the complete 1,694,969-nt sequence of the GC-rich genome of Methanopyrus kandleri by using a whole direct genome sequencing approach. This approach is based on unlinking of genomic DNA with the ThermoFidelase version of M. kandleri topoisomerase V and cycle sequencing directed by 2'-modified oligonucleotides (Fimers). Sequencing redundancy (3.3x) was sufficient to assemble the genome with less than one error per 40 kb. Using a combination of sequence database searches and coding potential prediction, 1,692 protein-coding genes and 39 genes for structural RNAs were identified. M. kandleri proteins show an unusually high content of negatively charged amino acids, which might be an adaptation to the high intracellular salinity. Previous phylogenetic analysis of 16S RNA suggested that M. kandleri belonged to a very deep branch, close to the root of the archaeal tree. However, genome comparisons indicate that, in both trees constructed using concatenated alignments of ribosomal proteins and trees based on gene content, M. kandleri consistently groups with other archaeal methanogens. M. kandleri shares the set of genes implicated in methanogenesis and, in part, its operon organization with Methanococcus jannaschii and Methanother-mobacter thermoautotrophicum. These findings indicate that archaeal methanogens are monophyletic. A distinctive feature of M. kandleri is the paucity of proteins involved in signaling and regulation of gene expression. Also, M. kandleri appears to have fewer genes acquired via lateral transfer than other archaea. These features might reflect the extreme habitat of this organism.