The tmRNA website

Hudson, Corey M.; Williams, Kelly P.

doi:10.1093/nar/gku1109

Title: The tmRNA website

Abstract

We report that the transfer-messenger RNA (tmRNA) and its partner protein SmpB act together in resolving problems arising when translating bacterial ribosomes reach the end of mRNA with no stop codon. Their genes have been found in nearly all bacterial genomes and in some organelles. The tmRNA Website serves tmRNA sequences, alignments and feature annotations, and has recently moved to http: //bioinformatics.sandia.gov/tmrna/. New features include software used to find the sequences, an update raising the number of unique tmRNA sequences from 492 to 1716, and a database of SmpB sequences which are served along with the tmRNA sequence from the same organism.

Authors:

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

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

Publication Date:: Wed Nov 05 00:00:00 EST 2014

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

Sponsoring Org.:: USDOE National Nuclear Security Administration (NNSA)

OSTI Identifier:: 1183117

Report Number(s):: SAND2014-17264J
Journal ID: ISSN 0305-1048; 537177

Grant/Contract Number:: AC04-94AL85000

Resource Type:: Accepted Manuscript

Journal Name:: Nucleic Acids Research

Additional Journal Information:: Journal Volume: 43; Journal Issue: D1; Journal ID: ISSN 0305-1048

Publisher:: Oxford University Press

Country of Publication:: United States

Language:: English

Subject:: 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Hudson, Corey M., and Williams, Kelly P. The tmRNA website.  United States: N. p., 2014. 
Web.  doi:10.1093/nar/gku1109.

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                    Hudson, Corey M., & Williams, Kelly P. The tmRNA website.  United States.  https://doi.org/10.1093/nar/gku1109

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                    Hudson, Corey M., and Williams, Kelly P. Wed .  
"The tmRNA website".  United States.  https://doi.org/10.1093/nar/gku1109.  https://www.osti.gov/servlets/purl/1183117.

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@article{osti_1183117,

  title        = {The tmRNA website},

  author       = {Hudson, Corey M. and Williams, Kelly P.},

  abstractNote = {We report that the transfer-messenger RNA (tmRNA) and its partner protein SmpB act together in resolving problems arising when translating bacterial ribosomes reach the end of mRNA with no stop codon. Their genes have been found in nearly all bacterial genomes and in some organelles. The tmRNA Website serves tmRNA sequences, alignments and feature annotations, and has recently moved to http: //bioinformatics.sandia.gov/tmrna/. New features include software used to find the sequences, an update raising the number of unique tmRNA sequences from 492 to 1716, and a database of SmpB sequences which are served along with the tmRNA sequence from the same organism.},

  doi          = {10.1093/nar/gku1109},

  journal      = {Nucleic Acids Research},

  number       = D1,

  volume       = 43,

  place        = {United States},

  year         = {Wed Nov 05 00:00:00 EST 2014},

  month        = {Wed Nov 05 00:00:00 EST 2014}

}

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https://doi.org/10.1093/nar/gku1109

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Works referenced in this record:

Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA
journal, February 1996

Keiler, K. C.; Waller, P. R. H.; Sauer, R. T.
Science, Vol. 271, Issue 5251
DOI: 10.1126/science.271.5251.990

Protein factors associated with the SsrA*SmpB tagging and ribosome rescue complex
journal, February 2001

Karzai, A. W.; Sauer, R. T.
Proceedings of the National Academy of Sciences, Vol. 98, Issue 6
DOI: 10.1073/pnas.051628298

Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA
journal, May 2007

Bessho, Y.; Shibata, R.; Sekine, S. -i.
Proceedings of the National Academy of Sciences, Vol. 104, Issue 20
DOI: 10.1073/pnas.0700402104

Decoding in the Absence of a Codon by tmRNA and SmpB in the Ribosome
journal, March 2012

Neubauer, C.; Gillet, R.; Kelley, A. C.
Science, Vol. 335, Issue 6074
DOI: 10.1126/science.1217039

Ends of the line for tmRNA-SmpB
journal, August 2014

Hudson, Corey M.; Lau, Britney Y.; Williams, Kelly P.
Frontiers in Microbiology, Vol. 5
DOI: 10.3389/fmicb.2014.00421

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997

Lowe, Todd M.; Eddy, Sean R.
Nucleic Acids Research, Vol. 25, Issue 5
DOI: 10.1093/nar/25.5.0955

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
journal, January 2004

Laslett, Dean; Canback, Bjorn
Nucleic Acids Research, Vol. 32, Issue 1, p. 11-16
DOI: 10.1093/nar/gkh152

RefSeq microbial genomes database: new representation and annotation strategy
journal, December 2013

Tatusova, Tatiana; Ciufo, Stacy; Fedorov, Boris
Nucleic Acids Research, Vol. 42, Issue D1
DOI: 10.1093/nar/gkt1274

tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter
journal, July 2000

Keiler, K. C.; Shapiro, L.; Williams, K. P.
Proceedings of the National Academy of Sciences, Vol. 97, Issue 14
DOI: 10.1073/pnas.97.14.7778

RNAcentral: A vision for an international database of RNA sequences
journal, September 2011

Bateman, A.; Agrawal, S.; Birney, E.
RNA, Vol. 17, Issue 11
DOI: 10.1261/rna.2750811

The International Nucleotide Sequence Database Collaboration
journal, November 2012

Nakamura, Y.; Cochrane, G.; Karsch-Mizrachi, I.
Nucleic Acids Research, Vol. 41, Issue D1
DOI: 10.1093/nar/gks1084

Pfam: the protein families database
journal, November 2013

Finn, Robert D.; Bateman, Alex; Clements, Jody
Nucleic Acids Research, Vol. 42, Issue D1
DOI: 10.1093/nar/gkt1223

CDD: conserved domains and protein three-dimensional structure
journal, November 2012

Marchler-Bauer, Aron; Zheng, Chanjuan; Chitsaz, Farideh
Nucleic Acids Research, Vol. 41, Issue D1
DOI: 10.1093/nar/gks1243

Interactive metagenomic visualization in a Web browser
journal, September 2011

Ondov, Brian D.; Bergman, Nicholas H.; Phillippy, Adam M.
BMC Bioinformatics, Vol. 12, Issue 1
DOI: 10.1186/1471-2105-12-385

The tmRDB and SRPDB resources
journal, January 2006

Andersen, E. S.
Nucleic Acids Research, Vol. 34, Issue 90001
DOI: 10.1093/nar/gkj142

Rfam 11.0: 10 years of RNA families
journal, November 2012

Burge, Sarah W.; Daub, Jennifer; Eberhardt, Ruth
Nucleic Acids Research, Vol. 41, Issue D1
DOI: 10.1093/nar/gks1005