Han Xiang Y, Sizer Kurt C, Thompson Erika J, Kabanja Juma, Li Jun, Hu Peter, Gómez-Valero Laura, Silva Francisco J
Department of Laboratory Medicine, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA.
J Bacteriol. 2009 Oct;191(19):6067-74. doi: 10.1128/JB.00762-09. Epub 2009 Jul 24.
Mycobacterium lepromatosis is a newly discovered leprosy-causing organism. Preliminary phylogenetic analysis of its 16S rRNA gene and a few other gene segments revealed significant divergence from Mycobacterium leprae, a well-known cause of leprosy, that justifies the status of M. lepromatosis as a new species. In this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). Overall, the level of matching of these sequences with M. leprae sequences was 90.9%, which substantiated the species-level difference; the levels of matching for the 16S rRNA genes and 14 protein-encoding genes were 98.0% and 93.1%, respectively, but the level of matching for five pseudogenes was only 79.1%. Five conserved protein-encoding genes were selected to construct phylogenetic trees and to calculate the numbers of synonymous substitutions (dS values) and nonsynonymous substitutions (dN values) in the two species. Robust phylogenetic trees constructed using concatenated alignment of these genes placed M. lepromatosis and M. leprae in a tight cluster with long terminal branches, implying that the divergence occurred long ago. The dS and dN values were also much higher than those for other closest pairs of mycobacteria. The dS values were 14 to 28% of the dS values for M. leprae and Mycobacterium tuberculosis, a more divergent pair of species. These results thus indicate that M. lepromatosis and M. leprae diverged approximately 10 million years ago. The M. lepromatosis pseudogenes analyzed that were also pseudogenes in M. leprae showed nearly neutral evolution, and their relative ages were similar to those of M. leprae pseudogenes, suggesting that they were pseudogenes before divergence. Taken together, the results described above indicate that M. lepromatosis and M. leprae diverged from a common ancestor after the massive gene inactivation event described previously for M. leprae.
瘤型麻风分枝杆菌是一种新发现的致麻风病病原体。对其16S rRNA基因和其他一些基因片段进行的初步系统发育分析显示，它与著名的麻风病病原体麻风分枝杆菌存在显著差异，这证明瘤型麻风分枝杆菌作为一个新物种的地位是合理的。在本研究中，我们分析了20个基因和假基因（共22814个核苷酸）的序列。总体而言，这些序列与麻风分枝杆菌序列的匹配水平为90.9%，这证实了物种水平的差异；16S rRNA基因和14个蛋白质编码基因的匹配水平分别为98.0%和93.1%，但5个假基因的匹配水平仅为79.1%。选择了5个保守的蛋白质编码基因来构建系统发育树，并计算这两个物种中的同义替换数（dS值）和非同义替换数（dN值）。使用这些基因的串联比对构建的稳健系统发育树将瘤型麻风分枝杆菌和麻风分枝杆菌置于一个具有长末端分支的紧密聚类中，这意味着分歧发生在很久以前。dS和dN值也远高于其他最接近的分枝杆菌对。dS值是麻风分枝杆菌和结核分枝杆菌（一对差异更大的物种）dS值的14%至28%。因此，这些结果表明瘤型麻风分枝杆菌和麻风分枝杆菌大约在1000万年前发生了分歧。分析的瘤型麻风分枝杆菌假基因在麻风分枝杆菌中也是假基因，显示出近乎中性的进化，并且它们的相对年龄与麻风分枝杆菌假基因相似，表明它们在分歧之前就是假基因。综上所述，上述结果表明，瘤型麻风分枝杆菌和麻风分枝杆菌是在先前描述的麻风分枝杆菌大规模基因失活事件之后从一个共同祖先分化而来的。
