Structure and function of 10Sa RNA: Trans-translation system

Muto, Akira; Sato, Manami; Tadaki, Toshimasa; Fukushima, Masaaki; Ushida, Chisato; Himeno, Hyouta

doi:10.1016/s0300-9084(97)86721-1

Cited by 48 publications

(28 citation statements)

References 33 publications

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“…The rates in stationary phase cells were obtained by the chloramphenicol chase procedure. The error reported is the standard deviation of two independent experiments ( ϭ ͌(1/N)⌺(x i Ϫ x) 2 , where x i is an individual value, and x is the mean of N determinations). The results for the three lon mutants are from single experiments.…”

Section: ϫK⅐tmentioning

confidence: 99%

“…When protein translation does not proceed to completion or terminate properly, one alternative mechanism used to disassemble ribosomal complexes and to degrade defective or incomplete polypeptides employs the trans-translation system (2,3), the centerpiece of which is the transfer mRNA (tmRNA) (also known as 10 S RNA or SsrA RNA), the product of the ssrA or sipB gene (4,5). tmRNA is a small, stable RNA containing an alanyl-tRNA domain and an mRNA domain encoding an open reading frame of 10 amino acids followed by a stop codon (6).…”

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confidence: 99%

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Turnover of Endogenous SsrA-tagged Proteins Mediated by ATP-dependent Proteases in Escherichia coli

Lies

Maurizi

2008

Journal of Biological Chemistry

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Formation and degradation of SsrA-tagged proteins enable ribosome recycling and elimination of defective products of incomplete translation. We produced an antibody against the SsrA peptide and used it to measure the amounts of SsrA-tagged proteins in Escherichia coli cells without interfering with tagging or altering the context of the tag added at the ends of nascent polypeptides. SsrA-tagged proteins were present in very small amounts unless a component of the ClpXP protease was missing. From the levels of tagged proteins in cells in which degradation is essentially blocked, we calculate that >1 in 200 translation products receives an SsrA tag. ClpXP is responsible for >90% of the degradation of SsrA-tagged proteins. The degradation rate in wild type cells is >1.4 min ؊1 and decreases to ϳ0.10 min ؊1 in a clpX mutant. The rate of degradation by ClpXP is decreased ϳ3-fold in mutants lacking the adaptor SspB, whereas degradation by ClpAP is increased 3-5-fold. However, ClpAP degrades SsrA-tagged proteins slowly even in the absence of SspB, possibly because of interference from ClpA-specific substrates. Lon protease degrades SsrA-tagged proteins at a rate of ϳ0.05 min ؊1 in the presence or absence of SspB. We conclude that ClpXP, together with SspB, is uniquely adapted for degradation of SsrA-tagged proteins and is responsible for the major part of their degradation in vivo.

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Section: ϫK⅐tmentioning

confidence: 99%

mentioning

confidence: 99%

Turnover of Endogenous SsrA-tagged Proteins Mediated by ATP-dependent Proteases in Escherichia coli

Lies

Maurizi

2008

Journal of Biological Chemistry

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“…The 5'-and 3'-ends fold to form a tRNA-like domain with sequence and structural similarity to tRNA Ala [80][81][82][83][84]. The tRNA-like domain of tmRNA possesses an amino acid acceptor stem, a TΦC arm and a D-loop, but lacks an anticodon arm.…”

Section: Tmrna and Smpbmentioning

confidence: 99%

Quality control of bacterial mRNA decoding and decay

Richards

Sundermeier

Svetlanov

et al. 2008

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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Studies in eukaryotes and prokaryotes have revealed that gene expression is not only controlled through altering the rate of transcription but also through varying rates of translation and mRNA decay. Indeed, the expression level of a protein is strongly affected by the steady state level of its mRNA. RNA decay can, along with transcription, play an important role in regulating gene expression by fine-tuning the steady state level of a given transcript and affecting its subsequent decoding during translation. Alterations in mRNA stability can in turn have dramatic effects on cell physiology and as a consequence the fitness and survival of the organism. Recent evidence suggests that mRNA decay can be regulated in response to environmental cues in order to enable the organism to adapt to its changing surroundings. Bacteria have evolved unique post transcriptional control mechanisms to enact such adaptive responses through: 1) general mRNA decay, 2) differential mRNA degradation using small non-coding RNAs (sRNAs), and 3) selective mRNA degradation using the tmRNA quality control system. Here, we review our current understanding of these molecular mechanisms, gleaned primarily from studies of the model gram negative organism E. coli, that regulate the stability and degradation of normal and defective transcripts.

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“…5). Homologs of both rne and ssrA have been detected in a variety of Gram-negative and Gram-positive bacterial species (48)(49)(50). The role of RNase E in ssrA RNA processing also may help ensure that the endonucleolytic cleavages generated in mRNA molecules by RNase E or other RNases do not adversely affect later steps in mRNA decay (Fig.…”

Section: Blockage Of Proteolysis Of Truncated Peptides Associated Witmentioning

confidence: 99%

RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity

Lin‐Chao

Wei

Lin

1999

Proc. Natl. Acad. Sci. U.S.A.

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During recent studies of ribonucleolytic ''degradosome'' complexes of Escherichia coli, we found that degradosomes contain certain RNAs as well as RNase E and other protein components. One of these RNAs is ssrA (for small stable RNA) RNA (also known as tm RNA or 10Sa RNA), which functions as both a tRNA and mRNA to tag the C-terminal ends of truncated proteins with a short peptide and target them for degradation. Here, we show that mature 363-nt ssrA RNA is generated by RNase E cleavage at the CCA-3 terminus of a 457-nt ssrA RNA precursor and that interference with this cleavage in vivo leads to accumulation of the precursor and blockage of SsrA-mediated proteolysis. These results demonstrate that RNase E is required to produce mature ssrA RNA and for normal ssrA RNA peptide-tagging activity. Our findings indicate that RNase E, an enzyme already known to have a central role in RNA processing and decay in E. coli, also has the previously unsuspected ability to affect protein degradation through its role in maturation of the 3 end of ssrA RNA. R ibonuclease E (RNase E), which is essential for cell growth and was initially characterized as the enzyme that processes 9S RNA to yield a 5S product, p5S RNA (1), has been shown to control the rate-limiting step in the degradation of a variety of Escherichia coli mRNAs (for reviews, see refs. 2-5), and a small regulatory RNA, RNAI-an antisense repressor of the replication primer of ColE1-type plasmids (6 -8). Temperaturesensitive mutants of RNase E have been isolated (9-12) and mapped to its enzymatic active domain (13), which is located at the N-terminal half of the polypeptide (14, 15). Inactivation of RNase E activity in these mutants by culture at nonpermissive temperature prolongs the decay of bulk mRNA (11,12).Recently, an RNase E-containing multicomponent ribonucleolytic complex termed the ''RNA degradosome'' has been isolated and characterized by two distinct approaches (16, 17), both of which show that degradosomes contain the protein components RNase E, PNPase, RhlB RNA helicase, and enolase. In addition to these proteins, the degradosome was found to contain the chaperonins DnaK (16, 18) and GroEL (16), polyphosphate kinase (18), mRNA, and certain structural RNA species (16,19), including RNAI, fragmented rRNAs, 9S RNA, and 10Sa͞ssrA RNA [a small stable RNA encoded by the ssrA gene (20)(21)(22)]. Most of these RNAs are known to be substrates for RNase E (19,[23][24][25][26].Nascent polypeptides translated in E. coli from truncated mRNAs lacking stop codons commonly receive a short carboxylterminal peptide tag (27, 28), synthesized in trans (28,29), that targets the resulting fusion polypeptide for rapid degradation (28). Except for the first alanine, the amino acid sequence of this tag (AANDENYALAA) is encoded by 10Sa͞ssrA RNA (20)(21)(22), also known as tmRNA because of its dual tRNA-like and mRNA-like activities (22,(28)(29)(30). Mature 363-nt ssrA RNA, which has its 3Ј and 5Ј ends paired in a tRNA-like structure, is charged with an alanine residue (22, 30), ...

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Structure and function of 10Sa RNA: Trans-translation system

Cited by 48 publications

References 33 publications

Turnover of Endogenous SsrA-tagged Proteins Mediated by ATP-dependent Proteases in Escherichia coli

Turnover of Endogenous SsrA-tagged Proteins Mediated by ATP-dependent Proteases in Escherichia coli

Quality control of bacterial mRNA decoding and decay

RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity

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