Proteomic identification of tmRNA substrates

Hong, Sue; Lessner, Faith H.; Mahen, Elisabeth; Keiler, Kenneth C.

doi:10.1073/pnas.0707671104

Cited by 27 publications

(32 citation statements)

References 56 publications

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“…Although not essential in E. coli , SsrA activity is essential for bacterial growth under adverse conditions because of its function in trans translation (Hong et al ., 2007). We previously indicated that SsrA may be under the control of Hha, and both are involved in the activation of prophage and cell lysis (García-Contreras et al ., 2008).…”

Section: Resultsmentioning

confidence: 99%

Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms

2009

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Earlier, we discovered that the global regulator, Hha, is related to cell death in biofilms and regulates cryptic prophage genes. Here, we show that Hha induces excision of prophages, CP4-57 and DLP12, by inducing excision genes and by reducing SsrA synthesis. SsrA is a tmRNA that is important for rescuing stalled ribosomes, contains an attachment site for CP4-57 and is shown here to be required for CP4-57 excision. These prophages impact biofilm development, as the deletion of 35 genes individually of prophages, CP4-57 and DLP12, increase biofilm formation up to 17-fold, and five genes decrease biofilm formation up to sixfold. In addition, CP4-57 excises during early biofilm development but not in planktonic cells, whereas DLP12 excision was detected at all the developmental stages for both biofilm and planktonic cells. CP4-57 excision leads to a chromosome region devoid of prophage and to the formation of a phage circle (which is lost). These results were corroborated by a whole-transcriptome analysis that showed that complete loss of CP4-57 activated the expression of the flg, flh and fli motility operons and repressed expression of key enzymes in the tricarboxylic acid cycle and of enzymes for lactate utilization. Prophage excision also results in the expression of cell lysis genes that reduce cell viability (for example, alpA, intA and intD). Hence, defective prophages are involved in host physiology through Hha and in biofilm formation by generating a diversified population with specialized functions in terms of motility and nutrient metabolism.

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Section: Resultsmentioning

confidence: 99%

Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms

2009

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“…41 Using epistasis experiments, we tested this model with respect to SsrA-tagged proteins, the largest known group of ClpXP substrates. 35 When we eliminated all SsrAtagged substrates from Caulobacter, RcdA was still required for rapid cell-cycle-dependent degradation of CtrA. Therefore, RcdA does not accelerate CtrA proteolysis in vivo by eliminating competition from SsrA-tagged substrates.…”

Section: Discussionmentioning

confidence: 95%

“…33,34 In Caulobacter cells containing an altered ssrA RNA, which prevented degradation of the tagged substrates, at least 73 different SsrA-tagged proteins were identified by mass spectrometry. 35 In addition, the presence of an SsrA-tagged protein and the adaptor SspB can inhibit the degradation of CtrA by ClpXP in vitro. 22 Thus, the ability of ClpXP to degrade SsrA-tagged proteins could influence CtrA degradation in vivo.…”

Section: Rcda Does Not Stimulate Ctra Proteolysis By Blocking the Degmentioning

confidence: 99%

Mutations that Alter RcdA Surface Residues Decouple Protein Localization and CtrA Proteolysis in Caulobacter crescentus

Taylor

Wilbur

Smith

et al. 2009

Journal of Molecular Biology

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“…However, rather than rescuing protein synthesis, there are data from many reports suggesting that tmRNA may alter gene expression by targeting specific substrates for tagging and proteolysis. For instance, in the alphaproteobacterium Caulobacter crescentus, many proteins were found to be normally tagged by tmRNA, some of which included genes involved in regulating cell division (18). As the deletion of tmRNA causes cell cycle defects (24), the function of this tagging may be to alter the half-life of these proteins.…”

Section: Discussionmentioning

confidence: 99%

Significant Bias against the ACA Triplet in the tmRNA Sequence of Escherichia coli K-12

et al. 2009

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The toxin MazF in Escherichia coli cleaves single-stranded RNAs specifically at ACA sequences. MazF overexpression virtually eliminates all cellular mRNAs to completely block protein synthesis. However, protein synthesis can continue on an mRNA that is devoid of ACA triplets. The finding that ribosomal RNAs remain intact in the face of complete translation arrest suggested a purpose for such preservation. We therefore examined the sequences of all transcribed RNAs to determine if there was any statistically significant bias against ACA. While ACA motifs are absent from tmRNA, 4.5S RNA, and seven of the eight 5S rRNAs, statistical analysis revealed that only for tmRNA was the absence nonrandom. The introduction of single-strand ACAs makes tmRNA highly susceptible to MazF cleavage. Furthermore, analysis of tmRNA sequences from 442 bacteria showed that the discrimination against ACA in tmRNAs was seen mostly in enterobacteria. We propose that the unusual bias against ACA in tmRNA may have coevolved with the acquisition of MazF.

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Proteomic identification of tmRNA substrates

Cited by 27 publications

References 56 publications

Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms

Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms

Mutations that Alter RcdA Surface Residues Decouple Protein Localization and CtrA Proteolysis in Caulobacter crescentus

Significant Bias against the ACA Triplet in the tmRNA Sequence of Escherichia coli K-12

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