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Phylogenomics provides new insights into gains and losses of selenoproteins among Archaeplastida

By Hongping Liang, Tong Wei, Yan Xu, Linzhou Li, Sunil Kumar Sahu, Hongli Wang, Haoyuan Li, Xian Fu, Gengyun Zhang, Michael Melkonian, Xin Liu, Sibo Wang, Huan Liu

Posted 01 Jul 2019
bioRxiv DOI: 10.1101/674895 (published DOI: 10.3390/ijms20123020)

Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the BV clade (Bangiophyceae-Florideophyceae) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria. * Sec : Selenocysteine Se : Selenium SECIS : Selenocysteine Insertion Sequence PSTK : O-phosphoseryl-transfer tRNASec kinase SecS : Sec synthase SPS : selenophosphate synthetase 2 SBP2 : SECIS-binding protein 2 eEFSec : Sec-specific elongation factor CTAB : Cetyl trimethylammonium bromide

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