The tmRNA ribosome-rescue system

Janssen, Brian D.; Hayes, Christopher S.

doi:10.1016/b978-0-12-386497-0.00005-0

Cited by 129 publications

(138 citation statements)

References 202 publications

(315 reference statements)

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“…The ssrA gene specifies the SsrA RNA, which together with the SmpB protein is involved in rescuing stalled ribosomes. SsrA RNA functions both as a tRNA and as an mRNA molecule; SsrA RNA function results in the synthesis of an Ssr polypeptide fusion that is destined for degradation and the liberation of the stalled ribosome (385,386). Two temperature-sensitive mutants were isolated in an ⌬ssrA genetic background.…”

Section: E Coli and S Entericamentioning

confidence: 99%

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Hove‐Jensen

Andersen

Kilstrup

et al. 2017

Microbiol Mol Biol Rev

169

187

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SUMMARY Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.

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Section: E Coli and S Entericamentioning

confidence: 99%

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Hove‐Jensen

Andersen

Kilstrup

et al. 2017

Microbiol Mol Biol Rev

169

187

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“…vious studies have established that the SmpB protein is a requisite factor in the tmRNA-mediated ribosome rescue system (7,9,10). SmpB binds specifically and with high affinity to the tRNA-like domain of tmRNA and is necessary for the recruitment and stable association of the SmpB-tmRNA complex with stalled ribosomes (15,30).…”

Section: Smpb Glycine 132 Is Important For Trans-translation-pre-mentioning

confidence: 99%

Active and Accurate trans-Translation Requires Distinct Determinants in the C-terminal Tail of SmpB Protein and the mRNA-like Domain of Transfer Messenger RNA (tmRNA)*

Camenares

Dulebohn²,

Svetlanov

et al. 2013

Journal of Biological Chemistry

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“…Classical ncRNAs, for example, are the widely known tRNAs and rRNAs that play a role in translation, or the tmRNA that plays a role in the rescue of stalled ribosomes (Janssen and Hayes 2012). During recent years it has become evident that the ncRNA world is substantially wider and includes other types of molecules.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions

Peer

Margalit

2014

RNA

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Most bacterial small RNAs (sRNAs) are post-transcriptional regulators of gene expression, exerting their regulatory function by base-pairing with their target mRNAs. While it has become evident that sRNAs play central regulatory roles in the cell, little is known about their evolution and the evolution of their regulatory interactions. Here we used the prokaryotic phylogenetic tree to reconstruct the evolutionary history of Escherichia coli sRNAs and their binding sites on target mRNAs. We discovered that sRNAs currently present in E. coli mainly accumulated inside the Enterobacteriales order, succeeding the appearance of other types of noncoding RNAs and concurrently with the evolution of a variant of the Hfq protein exhibiting a longer C-terminal region. Our analysis of the evolutionary ages of sRNA-mRNA interactions revealed that while all sRNAs were evolutionarily older than most of their known binding sites on mRNA targets, for quite a few sRNAs there was at least one binding site that coappeared with or preceded them. It is conceivable that the establishment of these first interactions forced selective pressure on the sRNAs, after which additional targets were acquired by fitting a binding site to the active region of the sRNA. This conjecture is supported by the appearance of many binding sites on target mRNAs only after the sRNA gain, despite the prior presence of the target gene in ancestral genomes. Our results suggest a selective mechanism that maintained the sRNAs across the phylogenetic tree, and shed light on the evolution of E. coli post-transcriptional regulatory network.

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The tmRNA ribosome-rescue system

Cited by 129 publications

References 202 publications

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Active and Accurate trans-Translation Requires Distinct Determinants in the C-terminal Tail of SmpB Protein and the mRNA-like Domain of Transfer Messenger RNA (tmRNA)*

Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions

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