Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland.
Mol Biol Evol. 2011 Nov;28(11):3183-93. doi: 10.1093/molbev/msr154. Epub 2011 Jun 14.
Microorganisms occupy a myriad of ecological niches that show an astonishing diversity. The molecular mechanisms underlying microbes' ecological diversity remain a fundamental conundrum in evolutionary biology. Evidence points to that the secretion of a particular set of proteins mediates microbes' interaction with the environment. Several systems are involved in this secretion, including the Sec secretion system and the Tat pathway. Shifts in the functions of proteins from the secretion systems may condition the set of secreted proteins and can, therefore, mediate adaptations to new ecological niches. In this manuscript, we have investigated processes of functional divergence (FD)-a term used here to refer to the emergence of novel functions by the modification of ancestral ones-of Tat pathway proteins using a large set of microbes with different lifestyles. The application of a novel approach to identify FD allowed us to distinguish molecular changes in the three Tat proteins among different groups of archaea and bacteria. We found these changes as well as the composition of secreted proteins to be correlated with differences in microbe's lifestyles. We identified major signatures of FD in halophilic and thermophilic archaea as well as in pathogenic bacteria. The location of amino acids affected by FD in functionally important domains of Tat proteins made it possible to find the link between the molecular changes in Tat, the set of secreted proteins and the environmental features of the microbes. We present evidence that links specific molecular changes in secretion mediating proteins of microbes to their ecological adaptations.
微生物栖息于生态位的千差万别中，表现出令人惊讶的多样性。微生物生态多样性的分子机制仍然是进化生物学中的一个基本难题。有证据表明，一组特定蛋白质的分泌介导了微生物与环境的相互作用。几个系统参与了这种分泌，包括 Sec 分泌系统和 Tat 途径。分泌系统中蛋白质功能的转变可能会调节分泌蛋白的集合，从而介导对新生态位的适应。在本手稿中，我们使用具有不同生活方式的大量微生物，研究了 Tat 途径蛋白的功能分化（FD）过程——这里使用该术语来表示通过修饰祖先蛋白而产生新功能。应用一种新方法来识别 FD，使我们能够区分不同古菌和细菌群体中三种 Tat 蛋白的分子变化。我们发现这些变化以及分泌蛋白的组成与微生物生活方式的差异相关。我们在嗜盐菌和嗜热古菌以及致病菌中鉴定出 FD 的主要特征。FD 影响 Tat 蛋白功能重要域中氨基酸的位置，使得我们能够找到 Tat 中的分子变化、分泌介导蛋白的集合以及微生物环境特征之间的联系。我们提出的证据表明，将微生物中特定的分泌介导蛋白的分子变化与它们的生态适应联系起来。
