title: Comparative genomics reveals new evolutionary and ecological patterns of selenium utilization in bacteria.
abstract: Selenium (Se) is an important micronutrient for many organisms, which is required for the biosynthesis of selenocysteine, selenouridine and Se-containing cofactor. Several key genes involved in different Se utilization traits have been characterized; however, systematic studies on the evolution and ecological niches of Se utilization are very limited. Here, we analyzed more than 5200 sequenced organisms to examine the occurrence patterns of all Se traits in bacteria. A global species map of all Se utilization pathways has been generated, which demonstrates the most detailed understanding of Se utilization in bacteria so far. In addition, the selenophosphate synthetase gene, which is used to define the overall Se utilization, was also detected in some organisms that do not have any of the known Se traits, implying the presence of a novel Se form in this domain. Phylogenetic analyses of components of different Se utilization traits revealed new horizontal gene transfer events for each of them. Moreover, by characterizing the selenoproteomes of all organisms, we found a new selenoprotein-rich phylum and additional selenoprotein-rich species. Finally, the relationship between ecological environments and Se utilization was investigated and further verified by metagenomic analysis of environmental samples, which indicates new macroevolutionary trends of each Se utilization trait in bacteria. Our data provide insights into the general features of Se utilization in bacteria and should be useful for a further understanding of the evolutionary dynamics of Se utilization in nature.
authors.affiliation: Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China.
authors.forename: Ting
authors.identifier: 0000-0001-9597-9239
authors.initials: T
authors.lastname: Peng
authors.affiliation: Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China.
authors.forename: Jie
authors.initials: J
authors.lastname: Lin
authors.affiliation: Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China.
authors.forename: Yin-Zhen
authors.initials: YZ
authors.lastname: Xu
authors.affiliation: Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PR China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics; D005075:Biological Evolution; D004463:Ecology; D022761:Gene Transfer, Horizontal; D023281:Genomics; D010770:Phosphotransferases / Q000235:genetics; D010802:Phylogeny; D012643:Selenium / Q000378:metabolism*; D051140:Selenoproteins / Q000235:genetics; D014131:Trace Elements / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D051140:Selenoproteins; D014131:Trace Elements; D010770:Phosphotransferases; C062762:selenophosphate synthetase; D012643:Selenium