Arenas Nelson E, Salazar Luz M, Soto Carlos Y, Vizcaíno Carolina, Patarroyo Manuel E, Patarroyo Manuel A, Gómez Arley
Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 45 No. 26-85 Bogotá, DC. Colombia.
BMC Struct Biol. 2011 Mar 28;11:16. doi: 10.1186/1472-6807-11-16.
The TlyA protein has a controversial function as a virulence factor in Mycobacterium tuberculosis (M. tuberculosis). At present, its dual activity as hemolysin and RNA methyltransferase in M. tuberculosis has been indirectly proposed based on in vitro results. There is no evidence however for TlyA relevance in the survival of tubercle bacilli inside host cells or whether both activities are functionally linked. A thorough analysis of structure prediction for this mycobacterial protein in this study shows the need for reevaluating TlyA's function in virulence.
Bioinformatics analysis of TlyA identified a ribosomal protein binding domain (S4 domain), located between residues 5 and 68 as well as an FtsJ-like methyltranferase domain encompassing residues 62 and 247, all of which have been previously described in translation machinery-associated proteins. Subcellular localization prediction showed that TlyA lacks a signal peptide and its hydrophobicity profile showed no evidence of transmembrane helices. These findings suggested that it may not be attached to the membrane, which is consistent with a cytoplasmic localization. Three-dimensional modeling of TlyA showed a consensus structure, having a common core formed by a six-stranded β-sheet between two α-helix layers, which is consistent with an RNA methyltransferase structure. Phylogenetic analyses showed high conservation of the tlyA gene among Mycobacterium species. Additionally, the nucleotide substitution rates suggested purifying selection during tlyA gene evolution and the absence of a common ancestor between TlyA proteins and bacterial pore-forming proteins.
Altogether, our manual in silico curation suggested that TlyA is involved in ribosomal biogenesis and that there is a functional annotation error regarding this protein family in several microbial and plant genomes, including the M. tuberculosis genome.
TlyA蛋白作为结核分枝杆菌（M. tuberculosis）的一种毒力因子，其功能存在争议。目前，基于体外实验结果间接推测其在结核分枝杆菌中具有溶血素和RNA甲基转移酶的双重活性。然而，尚无证据表明TlyA与宿主细胞内结核杆菌的存活相关，也没有证据表明这两种活性在功能上存在联系。本研究对这种分枝杆菌蛋白进行的结构预测深入分析表明，有必要重新评估TlyA在毒力方面的功能。
对TlyA的生物信息学分析确定了一个核糖体蛋白结合结构域（S4结构域），位于第5至68位氨基酸之间，以及一个包含第62至247位氨基酸的FtsJ样甲基转移酶结构域，所有这些结构域先前都在与翻译机制相关的蛋白质中有所描述。亚细胞定位预测显示TlyA缺乏信号肽，其疏水性图谱也未显示跨膜螺旋的证据。这些发现表明它可能不附着于细胞膜，这与细胞质定位一致。TlyA的三维建模显示出一种共有结构，由两个α螺旋层之间的六链β折叠形成一个共同核心，这与RNA甲基转移酶结构一致。系统发育分析表明tlyA基因在分枝杆菌属物种中具有高度保守性。此外，核苷酸替换率表明在tlyA基因进化过程中存在纯化选择，并且TlyA蛋白与细菌成孔蛋白之间不存在共同祖先。
总之，我们的计算机人工筛选表明，TlyA参与核糖体生物合成，并且在包括结核分枝杆菌基因组在内的几个微生物和植物基因组中，关于这个蛋白家族存在功能注释错误。
