Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2004 May;5(5):538-43.
doi: 10.1038/sj.embor.7400126. Epub 2004 Apr 23.

The prokaryotic selenoproteome

Gregory V Kryukov  1 , Vadim N Gladyshev
Affiliations

The prokaryotic selenoproteome

Gregory V Kryukov et al. EMBO Rep. 2004 May.

Abstract

In the genetic code, the UGA codon has a dual function as it encodes selenocysteine (Sec) and serves as a stop signal. However, only the translation terminator function is used in gene annotation programs, resulting in misannotation of selenoprotein genes. Here, we applied two independent bioinformatics approaches to characterize a selenoprotein set in prokaryotic genomes. One method searched for selenoprotein genes by identifying RNA stem-loop structures, selenocysteine insertion sequence elements; the second approach identified Sec/Cys pairs in homologous sequences. These analyses identified all or almost all selenoproteins in completely sequenced bacterial and archaeal genomes and provided a view on the distribution and composition of prokaryotic selenoproteomes. In addition, lineage-specific and core selenoproteins were detected, which provided insights into the mechanisms of selenoprotein evolution. Characterization of selenoproteomes allows interpretation of other UGA codons in completed genomes of prokaryotes as terminators, addressing the UGA dual-function problem.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Alignment of SECIS elements in archaeal selenoprotein genes. SECIS elements from eight selenoprotein genes in the M. jannaschii genome and seven selenoprotein genes in the M. kandleri genome were manually aligned on the basis of their primary sequences and secondary structure features. Strictly conserved nucleotides are highlighted.
Figure 2
Figure 2
Archaeal SECIS element structures. Archaeal SECIS element consensus sequence (right structure) and the SECIS element in M. jannaschii HesB-like gene (left structure) are shown. Conserved structural features in the consensus structure are also indicated.
Figure 3
Figure 3
Amino-acid sequence alignment of archaeal and bacterial HesB-like selenoproteins and their Cys-containing homologues. U is Sec.
Figure 4
Figure 4
Identification of prokaryotic selenoproteins by searching for Sec/Cys pairs in homologous sequences (SECIS-independent method). For details of the searches, see Methods.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410 - PubMed
    1. Berry MJ, Banu L, Chen YY, Mandel SJ, Kieffer JD, Harney JW, Larsen PR (1991) Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3′ untranslated region. Nature 353: 273–276 - PubMed
    1. Böck A (2000) Biosynthesis of selenoproteins—an overview. Biofactors 11: 77–78 - PubMed
    1. Castellano S, Morozova N, Morey M, Berry MJ, Serras F, Corominas M, Guigo R (2001) In silico identification of novel selenoproteins in the Drosophila melanogaster genome. EMBO Rep 2: 697–702 - PMC - PubMed
    1. Dsouza M, Larsen N, Overbeek R (1997) Searching for patterns in genomic data. Trends Genet 13: 497–498 - PubMed

Publication types

LinkOut - more resources

  NODES
twitter 2