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 Laboratories (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, Journal Name: Frontiers in Microbiology Vol. 5; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Protein structure prediction on the Web: a case study using the Phyre server Kelley, Lawrence A.; Sternberg, Michael J. E. Nature Protocols, Vol. 4, Issue 3 https://doi.org/10.1038/nprot.2009.2	journal	February 2009
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Functional SmpB-Ribosome Interactions Require tmRNA Sundermeier, Thomas R.; Karzai, A. Wali Journal of Biological Chemistry, Vol. 282, Issue 48 https://doi.org/10.1074/jbc.M707256200	journal	October 2007
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Function of the SmpB Tail in Transfer-messenger RNA Translation Revealed by a Nucleus-encoded Form Jacob, Yannick; Sharkady, Stephen M.; Bhardwaj, Kanchan Journal of Biological Chemistry, Vol. 280, Issue 7 https://doi.org/10.1074/jbc.m409277200	journal	December 2004
Functional SmpB-Ribosome Interactions Require tmRNA Sundermeier, Thomas R.; Karzai, A. Wali Journal of Biological Chemistry, Vol. 282, Issue 48 https://doi.org/10.1074/jbc.m707256200	journal	October 2007
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Rfam: annotating non-coding RNAs in complete genomes Griffiths-Jones, S. Nucleic Acids Research, Vol. 33, Issue Database issue https://doi.org/10.1093/nar/gki081	journal	December 2004
The tmRDB and SRPDB resources Andersen, E. S. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj142	journal	January 2006
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Rfam 11.0: 10 years of RNA families Burge, Sarah W.; Daub, Jennifer; Eberhardt, Ruth Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1005	journal	November 2012
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis Castresana, J. Molecular Biology and Evolution, Vol. 17, Issue 4 https://doi.org/10.1093/oxfordjournals.molbev.a026334	journal	April 2000
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Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways: Ribosome rescue by E. coli YaeJ Chadani, Yuhei; Ono, Katsuhiko; Kutsukake, Kazuhiro Molecular Microbiology, Vol. 80, Issue 3 https://doi.org/10.1111/j.1365-2958.2011.07607.x	journal	March 2011
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ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-tRNA hydrolysis in Escherichia coli : ArfA-RF2 pathway of ribosome rescue Chadani, Yuhei; Ito, Koreaki; Kutsukake, Kazuhiro Molecular Microbiology, Vol. 86, Issue 1 https://doi.org/10.1111/j.1365-2958.2012.08190.x	journal	August 2012
A Small Microbial Genome: The End of a Long Symbiotic Relationship? Perez-Brocal, V.; Gil, R.; Ramos, S. Science, Vol. 314, Issue 5797 https://doi.org/10.1126/science.1130441	journal	October 2006
Decoding in the Absence of a Codon by tmRNA and SmpB in the Ribosome Neubauer, C.; Gillet, R.; Kelley, A. C. Science, Vol. 335, Issue 6074 https://doi.org/10.1126/science.1217039	journal	March 2012
An unusual mechanism for EF-Tu activation during tmRNA-mediated ribosome rescue Miller, M. R.; Buskirk, A. R. RNA, Vol. 20, Issue 2 https://doi.org/10.1261/rna.042226.113	journal	December 2013
RNAcentral: A vision for an international database of RNA sequences Bateman, A.; Agrawal, S.; Birney, E. RNA, Vol. 17, Issue 11 https://doi.org/10.1261/rna.2750811	journal	September 2011
Comparative Genomics and Phylogenomics of Hemotrophic Mycoplasmas Guimaraes, Ana M. S.; Santos, Andrea P.; do Nascimento, Naíla C. PLoS ONE, Vol. 9, Issue 3 https://doi.org/10.1371/journal.pone.0091445	journal	March 2014
Non-stop mRNA decay: a special attribute of trans-translation mediated ribosome rescue Venkataraman, Krithika; Guja, Kip E.; Garcia-Diaz, Miguel Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00093	journal	March 2014
A second eukaryotic group with mitochondrion-encoded tmRNA: In silico identification and experimental confirmation Hafez, Mohamed; Burger, Gertraud; Steinberg, Sergey V. RNA Biology, Vol. 10, Issue 7 https://doi.org/10.4161/rna.25376	journal	July 2013
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SmpB as the handyman of tmRNA during trans-translation Felden, Brice; Gillet, Reynald RNA Biology, Vol. 8, Issue 3 https://doi.org/10.4161/rna.8.3.15387	journal	May 2011

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Title: Ends of the line for tmRNA-SmpB

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