Is Thermosensing Property of RNA Thermometers Unique?

• Published in: PloS one Vol. 5; no. 7; p. e11308
• Main Authors: Shah, Premal, Gilchrist, Michael A.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 02.07.2010; Public Library of Science (PLoS)
• Subjects: Bacillus subtilis; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding sites; Bioinformatics; Biophysics/RNA Structure; Biophysics/Transcription and Translation; Computational Biology/Comparative Sequence Analysis; E coli; Escherichia coli; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Evolutionary biology; Gammaproteobacteria - genetics; Gammaproteobacteria - metabolism; Gene expression; Genomes; Genomics; Heat-Shock Proteins - chemistry; Heat-Shock Proteins - metabolism; Melting; Messenger RNA; Mutation; Nucleic Acid Conformation; Nucleotide sequence; Probability; Prokaryotes; Proteobacteria; Ribonucleic acid; RNA; RNA, Bacterial - chemistry; RNA, Bacterial - metabolism; Sigma Factor - chemistry; Sigma Factor - metabolism; Software; Studies; Temperature; Thermometers; Translation (Genetics); Translation initiation; United States > US; Tennessee
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0011308

A large number of studies have been dedicated to identify the structural and sequence based features of RNA thermometers, mRNAs that regulate their translation initiation rate with temperature. It has been shown that the melting of the ribosome-binding site (RBS) plays a prominent role in this thermosensing process. However, little is known as to how widespread this melting phenomenon is as earlier studies on the subject have worked with a small sample of known RNA thermometers. We have developed a novel method of studying the melting of RNAs with temperature by computationally sampling the distribution of the RNA structures at various temperatures using the RNA folding software Vienna. In this study, we compared the thermosensing property of 100 randomly selected mRNAs and three well known thermometers--rpoH, ibpA and agsA sequences from E. coli. We also compared the rpoH sequences from 81 mesophilic proteobacteria. Although both rpoH and ibpA show a higher rate of melting at their RBS compared with the mean of non-thermometers, contrary to our expectations these higher rates are not significant. Surprisingly, we also do not find any significant differences between rpoH thermometers from other gamma-proteobacteria and E. coli non-thermometers.