Abstract
In bacteria, selenocysteine (Sec) is incorporated into proteins via the recoding of a particular codon, the UGA stop codon in most cases. Sec-tRNASec is delivered to the ribosome by the Sec-dedicated elongation factor SelB that also recognizes a Sec-insertion sequence element following the codon on the mRNA. Since the excess of SelB may lead to sequestration of Sec-tRNASec under selenium deficiency or oxidative stress, the expression levels of SelB and tRNASec should be regulated. In this bioinformatic study, I analyzed the Rhizobiales SelB species because they were annotated to have a non-canonical C-terminal extension. I found that the open reading frame (ORF) of diverse Alphaproteobacteria selB genes includes an entire tRNASec sequence (selC) and overlaps with the start codon of the downstream ORF. A remnant tRNASec sequence was found in the Sinorhizobium meliloti selB genes whose products have a shorter C-terminal extension. Similar overlapping traits were found in Gammaproteobacteria and Nitrospirae. I hypothesized that once the tRNASec moiety is folded and processed, the expression of the full-length SelB may be repressed. This is the first report on a nested tRNA gene inside a protein ORF in bacteria.
Highlights
Selenocysteine is the 21st amino acid used in diverse bacteria, archaea, and eukaryotes for expressing selenoproteins [1]
SelB binds to a Sec-tRNASec and a Sec-insertion sequence (SECIS) element on mRNA to mediate Sec-insertion [3]
To the best of my knowledge, this is the first report of an entire tRNA sequence nested in the protein coding region of mRNA in bacteria, while tRNA-like structures of varying sizes and shapes have been found in the coding regions or untranslated regions of mRNAs in diverse organisms and viruses [21,22,23]
Summary
Selenocysteine is the 21st amino acid used in diverse bacteria, archaea, and eukaryotes for expressing selenoproteins [1]. Unlike most of the canonical amino acids, Sec is synthesized on tRNASec molecules and delivered to a growing polypeptide in the ribosome by the dedicated elongation factor SelB. SelB binds to a Sec-tRNASec and a Sec-insertion sequence (SECIS) element on mRNA to mediate Sec-insertion (see Figure 1A) [3]. Sec-utilizing bacteria, the UGA stop codon directly followed by a SECIS element is recoded in a competition with release factor 2 [5], while some bacteria use the UAG stop codon or the UGC/UGU cysteine codons together with anticodon variants of tRNASec [6]. A careful analysis of these Rhizobiales SelB sequences was performed to reveal the possible reason
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