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）的基因组属于已知规模最大的古菌（Archaea）基因组之一。有假说指出，其成因之一是该类群发生了大量来自细菌的水平基因转移（horizontal gene transfer, HGT）。细菌来源的基因可参与中央代谢与溶质转运过程，具体涵盖糖合成、硫代谢、磷酸代谢、DNA修复以及小分子转运等诸多方面。一般认为，水平转移（horizontally transferred, HT）基因在甲烷八叠球菌属适应多样化环境的能力中扮演关键角色。目前已有3株甲烷八叠球菌属菌株的基因组完成测序，尽管这些基因组的长度与蛋白质编码基因数量存在差异，但均被证实积累了大量HT基因。不过，此前的相关估算均是在已知古菌基因组数量较少的背景下完成的。此外，近年来已有多个隶属于其他属的甲烷八叠球菌科（Methanosarcinaceae）基因组被测序。本研究重新统计了甲烷八叠球菌科中细菌来源基因的分布情况。
结果：约5%的甲烷八叠球菌属基因被证实是从各类细菌类群水平转移而来，相关转移事件要么发生在甲烷八叠球菌科的最近共同祖先阶段，要么发生在甲烷八叠球菌属自身的演化历程中，或是在后续的演化过程中发生。针对不同年份的NCBI蛋白质非冗余数据库（NCBI Protein non-redundant database）开展模拟分析后发现，自2002年（首个甲烷八叠球菌属基因组发表年份）起，HGT发生率的估算值已出现大幅下降。HT基因供体的系统发育分布并不均匀：多数HT基因来自厚壁菌门（Firmicutes）与变形菌门（Proteobacteria），而未发现放线菌门（Actinobacteria）向甲烷八叠球菌科共同祖先发生HGT事件的相关证据。约50%的HT基因参与代谢过程。转录因子的水平转移并不常见，而46%的HT基因在多种环境条件下呈现出差异表达特征。完整操纵子的水平转移相对少见，且半数HT基因并不隶属于操纵子结构。
结论：尽管甲烷八叠球菌科中的细菌来源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HGT事件，实际上似乎发生在甲烷八叠球菌科类群发生趋异演化之前。从细菌向古菌水平转移的基因，既不会倾向于与其调控因子一同完成转移，也极少发生在长操纵子结构中。