Comparative 3-D modeling of tmRNA

30Citations
Citations of this article
37Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

Background: Trans-translation releases stalled ribosomes from truncated mRNAs and tags defective proteins for proteolytic degradation using transfer-messenger RNA (tmRNA). This small stable RNA represents a hybrid of tRNA- and mRNA-like domains connected by a variable number of pseudoknots. Comparative sequence analysis of tmRNAs found in bacteria, plastids, and mitochondria provides considerable insights into their secondary structures. Progress toward understanding the molecular mechanism of template switching, which constitutes an essential step in trans-translation, is hampered by our limited knowledge about the three-dimensional folding of tmRNA. Results: To facilitate experimental testing of the molecular intricacies of trans-translation, which often require appropriately modified tmRNA derivatives, we developed a procedure for building three-dimensional models of tmRNA. Using comparative sequence analysis, phylogenetically-supported 2-D structures were obtained to serve as input for the program ERNA-3D. Motifs containing loops and turns were extracted from the known structures of other RNAs and used to improve the tmRNA models. Biologically feasible 3-D models for the entire tmRNA molecule could be obtained. The models were characterized by a functionally significant close proximity between the tRNA-like domain and the resume codon. Potential conformational changes which might lead to a more open structure of tmRNA upon binding to the ribosome are discussed. The method, described in detail for the tmRNAs of Escherichia coli, Bacillus anthracis, and Caulobacter crescentus, is applicable to every tmRNA. Conclusion: Improved molecular models of biological significance were obtained. These models will guide in the design of experiments and provide a better understanding of trans-translation. The comparative procedure described here for tmRNA is easily adopted for the modeling the members of other RNA families. © 2005 Burks et al; licensee BioMed Central Ltd.

References Powered by Scopus

Basic local alignment search tool

78967Citations
N/AReaders
Get full text

Gapped BLAST and PSI-BLAST: A new generation of protein database search programs

63211Citations
N/AReaders
Get full text

CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

58459Citations
N/AReaders
Get full text

Cited by Powered by Scopus

ModeRNA: A tool for comparative modeling of RNA 3D structure

225Citations
N/AReaders
Get full text

Bridging the gap in RNA structure prediction

156Citations
N/AReaders
Get full text

Rna2d3d: A program for generating, viewing, and comparing 3-dimensional models of rna

144Citations
N/AReaders
Get full text

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Cite

CITATION STYLE

APA

Burks, J., Zwieb, C., Müller, F., Wower, I., & Wower, J. (2005). Comparative 3-D modeling of tmRNA. BMC Molecular Biology, 6. https://doi.org/10.1186/1471-2199-6-14

Readers' Seniority

Tooltip

Professor / Associate Prof. 11

38%

PhD / Post grad / Masters / Doc 10

34%

Researcher 8

28%

Readers' Discipline

Tooltip

Agricultural and Biological Sciences 20

67%

Biochemistry, Genetics and Molecular Bi... 5

17%

Chemistry 3

10%

Computer Science 2

7%

Save time finding and organizing research with Mendeley

Sign up for free