Ends of the line for tmRNA-SmpB

Hudson, Corey M.; Lau, Britney Y.; Williams, Kelly P.

doi:10.3389/fmicb.2014.00421

Title: Ends of the line for tmRNA-SmpB

Journal Article · Wed Aug 13 00:00:00 EDT 2014 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2014.00421· OSTI ID:1137319

Hudson, Corey M. ^[1]; Lau, Britney Y. ^[1]; Williams, Kelly P. ^[1]

Sandia National Lab. (SNL-CA), Livermore, CA (United States). Department of Systems Biology

Genes for the RNA tmRNA and protein SmpB, partners in the trans-translation process that rescues stalled ribosomes, have previously been found in all bacteria and some organelles. We validate recent identification of tmRNA homologs in oomycete mitochondria by finding partner genes from oomycete nuclei that target SmpB to the mitochondrion. Exhaustive search now identifies a small number of complete, often highly derived, bacterial genomes that appear to lack a functional copy of one or the other partner gene (but not both). Three groups with reduced genomes have lost the central loop of SmpB, which is thought to improve alanylation and EF-Tu activation: Carsonella, Hodgkinia and the hemplasmas (hemotropic Mycoplasma). Carsonella has also lost the SmpB C-terminal tail, thought to stimulate the decoding center of the ribosome. Carsonella moreover exhibits gene overlap such that tmRNA maturation should produce a non-stop smpB mRNA, and one isolate exhibits complete degradation of the tmRNA gene yet its smpB shows no evidence for relaxed selective constraint. After loss of the SmpB central loop in the hemoplasmas, a subclade apparently lost tmRNA. At least some of the tmRNA/SmpB-deficient strains appear to further lack the ArfA and ArfB backup systems for ribosome rescue. The most frequent neighbors of smpB are the tmRNA gene, a ratA/rnfH unit, and the gene for RNaseR, a known physical and functional partner of tmRNA-SmpB. The tmRNA Website has moved and been updated, adding an SmpB sequence database (http://bioinformatics.sandia.gov/tmrna).

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Research Organization:: Sandia National Lab. (SNL-CA), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: AC04-94AL85000

OSTI ID:: 1137319

Report Number(s):: SAND2014-4976J; 523896

Journal Information:: Frontiers in Microbiology, Vol. 5; Related Information: Proposed for publication in Frontiers in Microbiology.; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 26 works

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Title: Ends of the line for tmRNA-SmpB

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