Data from: Horizontal gene transfer and genome evolution in Methanosarcina

Background: Genomes of Methanosarcina spp. are among the largest archaeal genomes. One suggested reason for that is massive horizontal gene transfer (HGT) from bacteria. Genes of bacterial origin may be involved in the central metabolism and solute transport, in particular sugar synthesis, sulfur metabolism, phosphate metabolism, DNA repair, transport of small molecules etc. Horizontally transferred (HT) genes are considered to play the key role in the ability of Methanosarcina spp. to inhabit diverse environments. At the moment, genomes of three Methanosarcina spp. have been sequenced, and while these genomes vary in length and number of protein-coding genes, they all have been shown to accumulate HT genes. However, previous estimates had been made when fewer archaeal genomes were known. Moreover, several Methanosarcinaceae genomes from other genera have been sequenced recently. Here, we revise the census of genes of bacterial origin in Methanosarcinaceae. Results: About 5 % of Methanosarcina genes have been shown to be horizontally transferred from various bacterial groups to the last common ancestor either of Methanosarcinaceae, or Methanosarcina, or later in the evolution. Simulation of the composition of the NCBI protein non-redundant database for different years demonstrates that the estimates of the HGT rate have decreased drastically since 2002, the year of publication of the first Methanosarcina genome. The phylogenetic distribution of HT gene donors is non-uniform. Most HT genes were transferred from Firmicutes and Proteobacteria, while no HGT events from Actinobacteria to the common ancestor of Methanosarcinaceae were found. About 50 % of HT genes are involved in metabolism. Horizontal transfer of transcription factors is not common, while 46 % of horizontally transferred genes have demonstrated differential expression in a variety of conditions. HGT of complete operons is relatively infrequent and half of HT genes do not belong to operons. Conclusions: While genes of bacterial origin are still more frequent in Methanosarcinaceae than in other Archaea, most HGT events described earlier as Methanosarcina-specific seem to have occurred before the divergence of Methanosarcinaceae. Genes horizontally transferred from bacteria to archaea neither tend to be transferred with their regulators, nor in long operons.背景：甲烷八叠球菌属（Methanosarcina spp.）的基因组是目前已知最大的古菌（Archaea）基因组之一。有研究推测，其基因组规模庞大的原因之一是发生了大量来自细菌的水平基因转移（Horizontal Gene Transfer, HGT）。这类源自细菌的基因可参与核心代谢与溶质转运过程，具体涵盖糖合成、硫代谢、磷代谢、DNA修复以及小分子转运等多个方面。水平转移基因（Horizontally Transferred, HT）被认为在甲烷八叠球菌属适应多样生境的能力中发挥关键作用。截至目前，已有3株甲烷八叠球菌属的基因组完成测序。尽管这些基因组的长度与蛋白编码基因数量存在差异，但所有测序结果均证实它们均积累了大量水平转移基因（HT）。然而，此前的相关评估是在已知古菌基因组数量较少的背景下完成的。此外，近期已有多个隶属于其他属的甲烷八叠球菌科（Methanosarcinaceae）基因组完成测序。本研究针对甲烷八叠球菌科中源自细菌的基因进行了重新统计与分析。 研究结果显示，约5%的甲烷八叠球菌属基因是从不同细菌类群水平转移而来，其转移对象分别为甲烷八叠球菌科的最近共同祖先、甲烷八叠球菌属的最近共同祖先，或是在演化后期发生的转移事件。对不同年份的美国国家生物技术信息中心（National Center for Biotechnology Information, NCBI）非冗余蛋白质数据库的组成进行模拟分析后发现，自2002年（首个甲烷八叠球菌属基因组发表年份）起，水平基因转移（HGT）频率的评估结果已大幅下降。水平转移基因供体的系统发育分布并不均匀：多数水平转移基因（HT）来源于厚壁菌门（Firmicutes）与变形菌门（Proteobacteria），而未发现从放线菌门（Actinobacteria）向甲烷八叠球菌科最近共同祖先发生的水平基因转移事件。约50%的水平转移基因（HT）参与代谢过程。转录因子（Transcription Factors）的水平转移并不常见，但46%的水平转移基因在多种环境条件下均表现出差异表达。完整操纵子（Operons）的水平基因转移事件相对少见，且半数水平转移基因（HT）并不隶属于操纵子结构。 结论：尽管甲烷八叠球菌科中源自细菌的基因占比仍高于其他古菌类群，但此前被认为是甲烷八叠球菌属特有的多数水平基因转移（HGT）事件，实际上似乎发生在甲烷八叠球菌科物种分化之前。从细菌水平转移至古菌的基因，既不会倾向于与其调控因子一同发生转移，也极少出现在长操纵子结构中。