Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective

Abstract

Selenium (Se) is an important trace element that mainly occurs in the form of selenocysteine in selected proteins. In prokaryotes, Se is also required for the synthesis of selenouridine and Se-containing cofactor. A large number of selenoprotein families have been identified in diverse prokaryotic organisms, most of which are thought to be involved in various redox reactions. In the last decade or two, computational prediction of selenoprotein genes and comparative genomics of Se metabolic pathways and selenoproteomes have arisen, providing new insights into the metabolism and function of Se and their evolutionary trends in bacteria and archaea. This review aims to offer an overview of recent advances in bioinformatics analysis of Se utilization in prokaryotes. We describe current computational strategies for the identification of selenoprotein genes and generate the most comprehensive list of prokaryotic selenoproteins reported to date. Furthermore, we highlight the latest research progress in comparative genomics and metagenomics of Se utilization in prokaryotes, which demonstrates the divergent and dynamic evolutionary patterns of different Se metabolic pathways, selenoprotein families, and selenoproteomes in sequenced organisms and environmental samples. Overall, bioinformatics analyses of Se utilization, function, and evolution may contribute to a systematic understanding of how this micronutrient is used in nature.

The Selenoproteome as a Dynamic Response Mechanism to Oxidative Stress in Hydrogenotrophic Methanogenic Communities

“…Although selenoproteins have been identified across all domains of life, the utilization of selenocysteine has been documented in only a limited fraction of methanogens. 34,37 Recently, it has also been associated with the Asgardarchaeota superphylum. 38−40 Considering the benefits of selenocysteine, it is surprising that selenium utilization is not more widespread.…”

“…The SECIS element, which can identify selenoproteins, varies across domains and can be located in both up-and downstream locations in archaea. 37 As a result of its infrequent occurrence, selenocysteine is absent in homology scoring matrices, which hampers the annotation of newly identified selenopeptides. Similar to phosphorylations, standard proteomic analysis often underestimates the abundance of modifications.…”

“…In eukaryotes, selenoproteins, such as thioredoxin reductase and glutathione peroxidase, play a role in oxidative stress management . Selenocysteine has also been detected in relation to methanogenesis, where it is present in various hydrogenases. , In comparison to its cysteine counterpart, selenocysteine confers different properties, such as a lower p K a and redox potential but also increased nucleophilicity and enhanced enzymatic turnover. , Despite its advantages in methanogenesis, selenium utilization has only been identified in a limited number of class I archaeal genera (Methanococcus, Methanocaldococcus, and Methanopyus) and the Lokiarcheaota phylum, which is not yet linked to a ROS-mitigating class. However, the recoding of stop codons in the Asgardarchaeota superphylum suggests a potentially broader distribution in this domain. − …”

Modification of Some Structural and Functional Parameters of Living Culture of Arthrospira platensis as the Result of Selenium Nanoparticle Biosynthesis

“…At the same time, there is evidence that prokaryotic organisms can produce SeNPs intracellularly, this being an active process involving the specific enzymes selenate reductase and selenite reductase. Selenite can be also reduced to elemental Se in a non-enzymatic way with the participation of glutathione (GSH) or enzymatically using nonspecific enzymes, such as respiratory and/or detoxifying enzymes, for example, periplasmic nitrite reductase and sulfite reductase [ 37 ].…”

Effect of inoculation with arbuscular mycorrhizal fungi on the energy metabolism of selenite‐rich amaranth

“…The synthesis of CoQ can be enhanced by Se, which shows a positive correlation with the CoQ content [19]. Se safeguards tissues against oxidative harm as a constituent of glutathione peroxidase [20]. Hence, the capacity to produce reduced CoQ was preserved, and the oxidative breakdown of CoQ was averted.…”