Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons

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Publication Type Journal Article
School or College School of Medicine
Department Human Genetics
Creator Gesteland, Raymond F.; Atkins, John F.; Baranov, Pavel V.
Other Author Vestergaard, Bente; Nyborg, Jens; Hamelryck, Thomas
Title Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons
Date 2006
Description ABSTRACT: Background: While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria, there are two RFs with overlapping specificity, RF1 recognizes UA(A/G) and RF2 recognizes U(A/G)A. The hypothesis: First, we hypothesize that orthologues of the E. coli K12 pseudogene prfH encode a third class-I RF that we designate RFH. Second, it is likely that RFH responds to signals other than conventional stop codons. Supporting evidence comes from the following facts: (i) A number of bacterial genomes contain prfH orthologues with no discernable interruptions in their ORFs. (ii) RFH shares strong sequence similarity with other class-I bacterial RFs. (iii) RFH contains a highly conserved GGQ motif associated with peptidyl hydrolysis activity (iv) residues located in the areas supposedly interacting with mRNA and the ribosomal decoding center are highly conserved in RFH, but different from other RFs. RFH lacks the functional, but non-essential domain 1. Yet, RFH-encoding genes are invariably accompanied by a highly conserved gene of unknown function, which is absent in genomes that lack a gene for RFH. The accompanying gene is always located upstream of the RFH gene and with the same orientation. The proximity of the 3' end of the former with the 5' end of the RFH gene makes it likely that their expression is co-regulated via translational coupling. In summary, RFH has the characteristics expected for a class-I RF, but likely with different specificity than RF1 and RF2. Testing the hypothesis: The most puzzling question is which signals RFH recognizes to trigger its release function. Genetic swapping of RFH mRNA recognition components with its RF1 or RF2 counterparts may reveal the nature of RFH signals. Implications of the hypothesis: The hypothesis implies a greater versatility of release-factor like activity in the ribosomal Asite than previously appreciated. A closer study of RFH may provide insight into the evolution of the genetic code and of the translational machinery responsible for termination of translation.
Type Text
Publisher BioMed Central
Journal Title Biology Direct
Volume 1
Issue 1
First Page 28
DOI 10.1186/1745-6150-1-28
citatation_issn 17456150
Subject Class-I release factors; RF1; RF2; Bacterial genomes
Subject MESH Codon, Terminator; Bacteria; Gene Expression Regulation, Bacterial
Language eng
Bibliographic Citation Baranov PV, Vestergaard B, Hamelryck T, Gesteland RF, Nyborg J, Atkins JF. 2006. Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons. Biol Direct 1:28
Rights Management (c) [Author(s)]. Creative Commons Attribution License http://creativecommons.org/licenses/by/2.0/
Format Medium application/pdf
Format Extent 701,992 Bytes
Identifier ir-main,3775
ARK ark:/87278/s696023j
Setname ir_uspace
Date Created 2012-06-13
Date Modified 2012-06-13
ID 706325
Reference URL https://collections.lib.utah.edu/ark:/87278/s696023j
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