Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (92K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Gueneau de Novoa, P.
Right arrow Articles by Williams, K. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Gueneau de Novoa, P.
Right arrow Articles by Williams, K. P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2004, Vol. 32, Database issue D104-D108
© 2004 Oxford University Press

The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts

Pulcherie Gueneau de Novoa and Kelly P. Williams*,1

Centro de Biofisica y Bioquimica, Instituto Venezolano de Investigaciones Cientificas, Altos de Pipe, MI, Venezuela and 1 Department of Biology, Indiana University, Bloomington, IN 47405, USA

*To whom correspondence should be addressed at 1001 E. Third Street, Bloomington, IN 47405, USA. Tel: +1 812 856 5697; Fax: +1 812 855 6705; Email: kellwill{at}indiana.edu
+AY313266–AY313270, AF169625, AF169626 and AF550350–AF550357

tmRNA combines tRNA- and mRNA-like properties and ameliorates problems arising from stalled ribosomes. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA website (http://www.indiana.edu/~tmrna), a collection of sequences, alignments, secondary structures and other information. Because many of these sequences are not in GenBank, a BLAST server has been added; another new feature is an abbreviated alignment for the tRNA-like domain only. Many tmRNA sequences from plastids have been added, five found in public sequence data and another 10 generated by direct sequencing; detection in early-branching members of the green plastid lineage brings coverage to all three primary plastid lineages. The new sequences include the shortest known tmRNA sequence. While bacterial tmRNAs usually have a lone pseudoknot upstream of the mRNA segment and a string of three or four pseudoknots downstream, plastid tmRNAs collectively show loss of pseudoknots at both postions. The pseudoknot-string region is also too short to contain the usual pseudoknot number in another new entry, the tmRNA sequence from a bacterial endosymbiont of insect cells, Tremblaya princeps. Pseudoknots may optimize tmRNA function in free-living bacteria, yet become dispensible when the endosymbiotic lifestyle relaxes selective pressure for fast growth.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
J. H. Russell and K. C. Keiler
Subcellular localization of a bacterial regulatory RNA
PNAS, September 22, 2009; 106(38): 16405 - 16409.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
I. K. Wower, C. Zwieb, and J. Wower
Escherichia coli tmRNA lacking pseudoknot 1 tags truncated proteins in vivo and in vitro
RNA, January 1, 2009; 15(1): 128 - 137.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Kurita, R. Sasaki, A. Muto, and H. Himeno
Interaction of SmpB with ribosome from directed hydroxyl radical probing
Nucleic Acids Res., December 18, 2007; 35(21): 7248 - 7255.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
T. Konno, D. Kurita, K. Takada, A. Muto, and H. Himeno
A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation
RNA, October 1, 2007; 13(10): 1723 - 1731.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
Y. Bessho, R. Shibata, S.-i. Sekine, K. Murayama, K. Higashijima, C. Hori-Takemoto, M. Shirouzu, S. Kuramitsu, and S. Yokoyama
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA
PNAS, May 15, 2007; 104(20): 8293 - 8298.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
K. Takada, C. Takemoto, M. Kawazoe, T. Konno, K. Hanawa-Suetsugu, S. Lee, M. Shirouzu, S. Yokoyama, A. Muto, and H. Himeno
In vitro trans-translation of Thermus thermophilus: Ribosomal protein S1 is not required for the early stage of trans-translation
RNA, April 1, 2007; 13(4): 503 - 510.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
R. Gillet, S. Kaur, W. Li, M. Hallier, B. Felden, and J. Frank
Scaffolding as an Organizing Principle in Trans-translation: THE ROLES OF SMALL PROTEIN B AND RIBOSOMAL PROTEIN S1
J. Biol. Chem., March 2, 2007; 282(9): 6356 - 6363.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
F. H. Lessner, B. J. Venters, and K. C. Keiler
Proteolytic Adaptor for Transfer-Messenger RNA-Tagged Proteins from {alpha}-Proteobacteria
J. Bacteriol., January 1, 2007; 189(1): 272 - 275.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
C. I. Montero, D. L. Lewis, M. R. Johnson, S. B. Conners, E. A. Nance, J. D. Nichols, and R. M. Kelly
Colocation of Genes Encoding a tRNA-mRNA Hybrid and a Putative Signaling Peptide on Complementary Strands in the Genome of the Hyperthermophilic Bacterium Thermotoga maritima.
J. Bacteriol., October 1, 2006; 188(19): 6802 - 6807.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
D. R. Tanner, J. D. Dewey, M. R. Miller, and A. R. Buskirk
Genetic Analysis of the Structure and Function of Transfer Messenger RNA Pseudoknot 1
J. Biol. Chem., April 14, 2006; 281(15): 10561 - 10566.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. D. Prickett, M. Page, A. E. Douglas, and G. H. Thomas
BuchneraBASE: a post-genomic resource for Buchnera sp. APS
Bioinformatics, March 1, 2006; 22(5): 641 - 642.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H.-Y. Ou, L.-L. Chen, J. Lonnen, R. R. Chaudhuri, A. B. Thani, R. Smith, N. J. Garton, J. Hinton, M. Pallen, M. R. Barer, et al.
A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria
Nucleic Acids Res., January 9, 2006; 34(1): e3 - e3.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Nonin-Lecomte, B. Felden, and F. Dardel
NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation.
Nucleic Acids Res., January 1, 2006; 34(6): 1847 - 1853.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. S. Andersen, M. A. Rosenblad, N. Larsen, J. C. Westergaard, J. Burks, I. K. Wower, J. Wower, J. Gorodkin, T. Samuelsson, and C. Zwieb
The tmRDB and SRPDB resources
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D163 - D168.
[Abstract] [Full Text] [PDF]

Home page
 J BiochemHome page
N. Nameki, T. Someya, S. Okano, R. Suemasa, M. Kimoto, K. Hanawa-Suetsugu, T. Terada, M. Shirouzu, I. Hirao, H. Takaku, et al.
Interaction Analysis between tmRNA and SmpB from Thermus thermophilus
J. Biochem., December 1, 2005; 138(6): 729 - 739.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Asano, D. Kurita, K. Takada, T. Konno, A. Muto, and H. Himeno
Competition between trans-translation and termination or elongation of translation
Nucleic Acids Res., October 4, 2005; 33(17): 5544 - 5552.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
I. K. WOWER, C. ZWIEB, and J. WOWER
Transfer-messenger RNA unfolds as it transits the ribosome
RNA, May 1, 2005; 11(5): 668 - 673.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Metzinger, M. Hallier, and B. Felden
Independent binding sites of small protein B onto transfer-messenger RNA during trans-translation
Nucleic Acids Res., April 28, 2005; 33(8): 2384 - 2394.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
Y. Jacob, S. M. Sharkady, K. Bhardwaj, A. Sanda, and K. P. Williams
Function of the SmpB Tail in Transfer-messenger RNA Translation Revealed by a Nucleus-encoded Form
J. Biol. Chem., February 18, 2005; 280(7): 5503 - 5509.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
M. A. Rosenblad and T. Samuelsson
Identification of Chloroplast Signal Recognition Particle RNA Genes
Plant Cell Physiol., November 15, 2004; 45(11): 1633 - 1639.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. M. Sharkady and K. P. Williams
A third lineage with two-piece tmRNA
Nucleic Acids Res., August 23, 2004; 32(15): 4531 - 4538.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Konno, T. Takahashi, D. Kurita, A. Muto, and H. Himeno
A minimum structure of aminoglycosides that causes an initiation shift of trans-translation
Nucleic Acids Res., August 4, 2004; 32(14): 4119 - 4126.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
M. J. TRIMBLE, A. MINNICUS, and K. P. WILLIAMS
tRNA slippage at the tmRNA resume codon
RNA, May 1, 2004; 10(5): 805 - 812.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
Y. JACOB, E. SEIF, P.-O. PAQUET, and B. F. LANG
Loss of the mRNA-like region in mitochondrial tmRNAs of jakobids
RNA, April 1, 2004; 10(4): 605 - 614.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Laslett and B. Canback
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
Nucleic Acids Res., January 2, 2004; 32(1): 11 - 16.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.