Kobayashi Takeshi, Nonaka Lisa, Maruyama Fumito, Suzuki Satoru
Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime, Japan.
J Mol Evol. 2007 Sep;65(3):228-35. doi: 10.1007/s00239-007-9006-z. Epub 2007 Aug 4.
The ribosomal protection proteins (RPPs) mediate the resistance to tetracycline (TC) in Gram-positive and Gram-negative bacteria. The RPPs display sequence similarity to translation elongation factors, EF-G/EF-2 and EF-Tu/EF-1alpha. To determine the evolutionary origin of the RPPs, we constructed a composite phylogenetic tree of the RPPs, EF-G/EF-2 and EF-Tu/EF-1alpha. This tree includes two universal trees for the EF-G/EF-2 and EF-Tu/EF-1alpha, which form clusters corresponding to the respective two groups of proteins from three superkingdoms. The cluster of RPPs was placed at a point between the EF-G/EF-2 and EF-Tu/EF-1alpha clusters. The branch length (substitutions/site) between the node for the RPP cluster and the primary divergence of the RPPs was statistically shorter than that between the node for this cluster and the primary divergence in the EF-G/EF-2 cluster. This indicates that the RPPs derived through duplication and divergence of the ancient GTPase before the divergence of the three superkingdoms. Furthermore, this suggests the RPPs' extant function occurred before the streptomycetes that include the TC-producing strains. Therefore, the RPPs evolved independent of the presence of TCs and serve a function other than antibiotic resistance. The RPPs may provide ribosomal protection against other chemical substances in the environment.
核糖体保护蛋白（RPPs）介导革兰氏阳性菌和革兰氏阴性菌对四环素（TC）的耐药性。RPPs与翻译延伸因子EF-G/EF-2和EF-Tu/EF-1α在序列上具有相似性。为了确定RPPs的进化起源，我们构建了RPPs、EF-G/EF-2和EF-Tu/EF-1α的复合系统发育树。该树包括EF-G/EF-2和EF-Tu/EF-1α的两个通用树，它们形成了与来自三个超界的各自两组蛋白质相对应的簇。RPPs的簇位于EF-G/EF-2和EF-Tu/EF-1α簇之间的一个点上。RPP簇节点与RPPs主要分歧点之间的分支长度（替换/位点）在统计学上短于该簇节点与EF-G/EF-2簇主要分歧点之间的分支长度。这表明RPPs是在三个超界分歧之前通过古老GTPase的复制和分歧而产生的。此外，这表明RPPs现存的功能在包括产生TC的菌株的链霉菌之前就已出现。因此，RPPs的进化独立于TC的存在，并且具有抗生素耐药性以外的功能。RPPs可能为核糖体提供针对环境中其他化学物质的保护。
