Bioinformatic Prediction of an tRNASec Gene Nested inside an Elongation Factor SelB Gene in Alphaproteobacteria

In bacteria, selenocysteine (Sec) is incorporated into proteins via the recoding of a particular codon, the UGA stop codon in most cases. Sec-tRNA(Sec) 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-tRNA(Sec) under selenium deficiency or oxidative stress, the expression levels of SelB and tRNA(Sec) 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 tRNA(Sec) sequence (selC) and overlaps with the start codon of the downstream ORF. A remnant tRNA(Sec) 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 tRNA(Sec) 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.

Automated summary

The study analyzed the SelB genes of Rhizobiales species and found overlapping tRNA(Sec) sequences in some Alphaproteobacteria and Sinorhizobium meliloti SelB genes. It was hypothesized that once the tRNA(Sec) is processed, the expression of full-length SelB may be repressed. This is the first report of a nested tRNA gene within a protein ORF in bacteria.