The algal selenoproteomes

Liang Jiang,Lin Zheng,Jiazuan Ni,Lianchang Chen,Yan Zhang,Qiong Liu,Gaopeng Li,Yiqian Lu,Maona Zhang

doi:10.1186/s12864-020-07101-z

Liang Jiang, Lin Zheng + Show 7 more

Open Access

https://doi.org/10.1186/s12864-020-07101-z

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Journal: BMC Genomics	Publication Date: Oct 7, 2020
Citations: 8	License type: open-access

Affiliation: Shenzhen Bay Laboratory, Shenzhen University

Abstract

BackgroundSelenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA codon encoding Sec but also the SECIS element in mRNA and the conservation of the Sec-flanking region. These unique features have led to the development of a series of bioinformatics methods to predict and research selenoprotein genes. There have been some studies and reports on the evolution and distribution of selenoprotein genes in prokaryotes and multicellular eukaryotes, but the systematic analysis of single-cell eukaryotes, especially algae, has been very limited.ResultsIn this study, we predicted selenoprotein genes in 137 species of algae by using a program we previously developed. More than 1000 selenoprotein genes were obtained. A database website was built to record these algae selenoprotein genes (www.selenoprotein.com). These genes belong to 42 selenoprotein families, including three novel selenoprotein gene families.ConclusionsThis study reveals the primordial state of the eukaryotic selenoproteome. It is an important clue to explore the significance of selenium for primordial eukaryotes and to determine the complete evolutionary spectrum of selenoproteins in all life forms.

Highlights

Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo
In recent years, based on the critical features detected in Sec insertion sequence (SECIS) elements and the conservation between selenoproteins and their cysteine (Cys)-containing homologs, several bioinformatics algorithms have been successfully developed for the prediction of selenoprotein genes in eukaryotic genomes [11,12,13,14,15]
Composition and distribution of the algal selenoproteome We predicted more than 1000 selenoprotein genes from genomic (36 organisms) and/or transcriptomic datasets of 137 algal species

Summary

Introduction

Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include the TGA codon encoding Sec and the SECIS element in mRNA and the conservation of the Sec-flanking region. These unique features have led to the development of a series of bioinformatics methods to predict and research selenoprotein genes. Identification of full sets of selenoproteins in organisms (called selenoproteomes) is key for understanding the biological roles of Se. In recent years, based on the critical features detected in SECIS elements and the conservation between selenoproteins and their cysteine (Cys)-containing homologs, several bioinformatics algorithms have been successfully developed for the prediction of selenoprotein genes in eukaryotic genomes [11,12,13,14,15].

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