Vishwanath Prashanth, Favaretto Paola, Hartman Hyman, Mohr Scott C, Smith Temple F
BioMolecular Engineering Research Center, Boston University, 36 Cummington St., Boston, MA 02215, USA.
Mol Phylogenet Evol. 2004 Dec;33(3):615-25. doi: 10.1016/j.ympev.2004.07.003.
Amino acid sequence alignments of orthologous ribosomal proteins found in Bacteria, Archaea, and Eukaryota display, relative to one another, an unusual segment or block structure, with major evolutionary implications. Within each of the prokaryotic phylodomains the sequences exhibit substantial similarity, but cross-domain alignments break up into (a) universal blocks (conserved in both phylodomains), (b) bacterial blocks (unalignable with any archaeal counterparts), and (c) archaeal blocks (unalignable with any bacterial counterparts). Sequences of those eukaryotic cytoplasmic riboproteins that have orthologs in both Bacteria and Archaea, exclusively match the archaeal block structure. The distinct blocks do not correlate consistently with any identifiable functional or structural feature including RNA and protein contacts. This phylodomain-specific block pattern also exists in a number of other proteins associated with protein synthesis, but not among enzymes of intermediary metabolism. While the universal blocks imply that modern Bacteria and Archaea (as defined by their translational machinery) clearly have had a common ancestor, the phylodomain-specific blocks imply that these two groups derive from single, phylodomain-specific types that came into existence at some point long after that common ancestor. The simplest explanation for this pattern would be a major evolutionary bottleneck, or other scenario that drastically limited the progenitors of modern prokaryotic diversity at a time considerably after the evolution of a fully functional translation apparatus. The vast range of habitats and metabolisms that prokaryotes occupy today would thus reflect divergent evolution after such a restricting event. Interestingly, phylogenetic analysis places the origin of eukaryotes at about the same time and shows a closer relationship of the eukaryotic ribosome-associated proteins to crenarchaeal rather than euryarchaeal counterparts.
在细菌、古菌和真核生物中发现的直系同源核糖体蛋白的氨基酸序列比对显示，相对于彼此，它们具有一种不寻常的片段或模块结构，具有重要的进化意义。在每个原核生物系统发育域内，序列表现出显著的相似性，但跨域比对会分解为：（a）通用模块（在两个系统发育域中都保守），（b）细菌模块（与任何古菌对应物无法比对），以及（c）古菌模块（与任何细菌对应物无法比对）。那些在细菌和古菌中都有直系同源物的真核细胞质核糖体蛋白的序列，只与古菌模块结构匹配。这些不同的模块与任何可识别的功能或结构特征（包括RNA和蛋白质接触）都没有一致的相关性。这种系统发育域特异性的模块模式也存在于许多其他与蛋白质合成相关的蛋白质中，但在中间代谢酶中不存在。虽然通用模块意味着现代细菌和古菌（由它们的翻译机制定义）显然有一个共同的祖先，但系统发育域特异性模块意味着这两组来自单一的、系统发育域特异性类型，这些类型在那个共同祖先出现后的某个时间点才出现。对此模式最简单的解释是一个主要的进化瓶颈，或者是其他在完全功能性翻译装置进化后的某个时间点极大地限制了现代原核生物多样性祖细胞数量的情况。因此，原核生物今天所占据的广泛栖息地和代谢方式将反映出在这样一个限制事件之后的趋异进化。有趣的是，系统发育分析表明真核生物的起源大约在同一时间，并且显示真核核糖体相关蛋白与泉古菌而非广古菌的对应物关系更密切。
