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Title: Ends of the line for tmRNA-SmpB

Abstract

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 neighborsmore » 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).« less

Authors:
 [1];  [1];  [1]
  1. Sandia National Lab. (SNL-CA), Livermore, CA (United States). Department of Systems Biology
Publication Date:
Research Org.:
Sandia National Lab. (SNL-CA), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1137319
Report Number(s):
SAND2014-4976J
Journal ID: ISSN 1664-302X; 523896
Grant/Contract Number:
AC04-94AL85000
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 5; Related Information: Proposed for publication in Frontiers in Microbiology.; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; tmRNA; SmpB; trans-translation; Carsonella; Mycoplasma

Citation Formats

Hudson, Corey M., Lau, Britney Y., and Williams, Kelly P. Ends of the line for tmRNA-SmpB. United States: N. p., 2014. Web. doi:10.3389/fmicb.2014.00421.
Hudson, Corey M., Lau, Britney Y., & Williams, Kelly P. Ends of the line for tmRNA-SmpB. United States. doi:10.3389/fmicb.2014.00421.
Hudson, Corey M., Lau, Britney Y., and Williams, Kelly P. Wed . "Ends of the line for tmRNA-SmpB". United States. doi:10.3389/fmicb.2014.00421. https://www.osti.gov/servlets/purl/1137319.
@article{osti_1137319,
title = {Ends of the line for tmRNA-SmpB},
author = {Hudson, Corey M. and Lau, Britney Y. and Williams, Kelly P.},
abstractNote = {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).},
doi = {10.3389/fmicb.2014.00421},
journal = {Frontiers in Microbiology},
number = ,
volume = 5,
place = {United States},
year = {Wed Aug 13 00:00:00 EDT 2014},
month = {Wed Aug 13 00:00:00 EDT 2014}
}

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Cited by: 13works
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