Griffiths Emma, Gupta Radhey S
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8N 3Z5, Canada.
J Mol Evol. 2006 Aug;63(2):283-96. doi: 10.1007/s00239-005-0286-x. Epub 2006 Jul 7.
The chlamydiae are important human and animal pathogens which form a phylogentically distinct lineage within the Bacteria. There is evidence that some genes in these obligate intracellular parasites have undergone lateral exchange with other free-living organisms. In the present work, we describe two interesting cases of lateral gene transfer between chlamydiae and actinobacteria, which have been identified based on the shared presence of conserved inserts in two important proteins. In the enzyme serine hydroxymethyltransferase (SHMT or GlyA protein), which links amino acid and nucleotide metabolisms by generating the key intermediate for one-carbon transfer reactions, two conserved inserts of 3 and 31 amino acids (aa) are uniquely present in various chlamydiae species as well as in a subset of Actinobacteria and in the Treponema species. Similarly, in the enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), which is involved in the synthesis of cell wall peptidoglycan, a 16-aa conserved insert is specifically present in various sequenced chlamydiae and a subset of actinobacteria (i.e., Streptomyces, Actinomyces, Tropheryma, Bifidobacterium, Leifsonia, Arthrobacter, and Brevibacterium). To determine the phylogenetic depths of the GlyA and MurA inserts, the fragments of these genes from two chlamydiae-like species, Simkania negevensis and Waddlia chondrophila, were PCR amplified and sequenced. The presence of the corresponding inserts in both these species strongly indicates that these inserts are distinctive characteristics of the Chlamydiales order. In phylogenetic trees based on GlyA and MurA protein sequences, the chlamydiae species (and also the Treponema species in the case of GlyA) branched with a high affinity with various insert-containing actinobacteria within a clade of other actinobacteria. These results provide strong evidence that the shared presence of these indels in these bacteria is very likely a consequence of ancient lateral gene transfers from actinobacteria to chlamydiae. Pairwise sequence identity and the branching pattern of the GlyA homologues in the phylogenetic tree indicates that the glyA gene was initially transferred from an actinobacteria to an ancestor of the Treponema genus and from there it was acquired by the common ancestor of the Chlamydiales.
衣原体是重要的人类和动物病原体，在细菌中形成了一个系统发育上独特的谱系。有证据表明，这些专性细胞内寄生虫中的一些基因已与其他自由生活的生物体进行了横向交换。在本研究中，我们描述了衣原体与放线菌之间两个有趣的横向基因转移案例，这是基于两种重要蛋白质中保守插入序列的共同存在而确定的。在通过生成一碳转移反应的关键中间体来连接氨基酸和核苷酸代谢的丝氨酸羟甲基转移酶（SHMT或GlyA蛋白）中，3个和31个氨基酸（aa）的两个保守插入序列独特地存在于各种衣原体物种以及一部分放线菌和密螺旋体物种中。同样，在参与细胞壁肽聚糖合成的UDP-N-乙酰葡糖胺烯醇丙酮酸转移酶（MurA）中，一个16个氨基酸的保守插入序列特异性地存在于各种已测序的衣原体和一部分放线菌（即链霉菌属、放线菌属、嗜肺军团菌属、双歧杆菌属、利夫森菌属、节杆菌属和短杆菌属）中。为了确定GlyA和MurA插入序列的系统发育深度，对来自两个衣原体样物种，即内氏西曼卡菌和嗜软骨沃氏菌的这些基因片段进行了PCR扩增和测序。这两个物种中相应插入序列的存在强烈表明这些插入序列是衣原体目的独特特征。在基于GlyA和MurA蛋白序列的系统发育树中，衣原体物种（在GlyA的情况下还有密螺旋体物种）与其他放线菌分支中的各种含有插入序列的放线菌具有高度亲和力。这些结果提供了有力证据，表明这些细菌中这些插入缺失的共同存在很可能是古代从放线菌到衣原体横向基因转移的结果。GlyA同源物在系统发育树中的成对序列同一性和分支模式表明，glyA基因最初是从一种放线菌转移到密螺旋体属的一个祖先，然后从那里被衣原体的共同祖先获得。
