Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project

Abstract

Selenium is an important trace element that occurs in proteins in the form of selenocysteine (Sec) and in tRNAs in the form of selenouridine. Recent large-scale metagenomics projects provide an opportunity for understanding global trends in trace element utilization. Herein, we characterized the selenoproteome of the microbial marine community derived from the Global Ocean Sampling (GOS) expedition. More than 3,600 selenoprotein gene sequences belonging to 58 protein families were detected, including sequences representing 7 newly identified selenoprotein families, such as homologs of ferredoxin–thioredoxin reductase and serine protease. In addition, a new eukaryotic selenoprotein family, thiol reductase GILT, was identified. Most GOS selenoprotein families originated from Cys-containing thiol oxidoreductases. In both Pacific and Atlantic microbial communities, SelW-like and SelD were the most widespread selenoproteins. Geographic location had little influence on Sec utilization as measured by selenoprotein variety and the number of selenoprotein genes detected; however, both higher temperature and marine (as opposed to freshwater and other aquatic) environment were associated with increased use of this amino acid. Selenoproteins were also detected with preference for either environment. We identified novel fusion forms of several selenoproteins that highlight redox activities of these proteins. Almost half of Cys-containing SelDs were fused with NADH dehydrogenase, whereas such SelD forms were rare in terrestrial organisms. The selenouridine utilization trait was also analyzed and showed an independent evolutionary relationship with Sec utilization. Overall, our study provides insights into global trends in microbial selenium utilization in marine environments.

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

“…Two ORFs encoding ABC-type periplasmic solute-binding proteins seemed to be specific to open ocean-dwelling Pelagibacter, and were highly expressed. One ORF encodes a selenium-binding protein, which may contribute to the synthesis of selenoproteins (Zhang and Gladyshev, 2008). The other ORF encodes an extracellular solute-binding protein family 1, which is associated with the uptake of malto-oligosaccharides, multiple sugars, alpha-glycerol phosphate and iron (Tam and Saier, 1993).…”

Comparative selenoproteome analysis reveals a reduced utilization of selenium in parasitic platyhelminthes

“…Based on the specific selenocysteine insertion and selenoprotein biosynthesis mechanisms (such as UGA codon, SECIS element, etc. ), as well as the conservation of the sequence that flanks selenocysteine in different homologs of selenoproteins, several bioinformatics algorithms, such as SECISearch and SelGenAmic, have been developed to identify new selenoproteins in a variety of organisms including human (Castellano et al 2001;Jiang et al 2010;Jiang et al 2012;Kryukov et al 2003;Kryukov et al 1999;Mariotti et al 2013;Zhang & Gladyshev 2008;Zhang et al 2006). Many of these newly predicted selenoproteins have been experimentally verified, implying that these computational approaches are highly efficient for selenoprotein identification.…”

“…Several bioinformatics tools have been developed to identify the whole set of selenoproteins (or selenoproteome) that one organism may have (Kryukov et al 2003;Hatfield, Gladyshev,2002). These programs have successfully identified many new selenoproteins in bacteria, algae, insects, nematodes, and a variety of both invertebrates and vertebrates, implying that selenium plays an important role in all the three kingdoms of life (Castellano et al 2001;Kryukov & Gladyshev 2000;Lobanov et al 2006a;Lobanov et al 2006b;Mariotti et al 2013;Mariotti et al 2012;Novoselov et al 2002;Zhang et al 2005;Zhang & Gladyshev 2008;Zhang et al 2006). It is obvious that investigation of the selenoproteomes of various organisms is helpful for understanding evolutionary dynamics of selenium utilization as well as its relationship with different living conditions and lifestyles.…”

GenGIS: A geospatial information system for genomic data

“…The initial publication ) analyzed 44 metagenome samples (0.1-0.8 mm fraction) collected from 41 sites, including Sargasso Sea sites examined previously by Venter et al (2004). Data from these locations have been analyzed to reveal an immense set of novel proteins and breadth of taxonomic and functional diversity in different habitats Yutin et al 2007;Zhang and Gladyshev 2008;Sharma et al 2009). …”