A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome

Chen, Shawn; Lesnik, Elena A.; Hall, Thomas A.; Sampath, Rangarajan; Griffey, Richard H.; Ecker, David J.; Blyn, Lawrence B.

doi:10.1016/s0303-2647(02)00013-8

Cited by 201 publications

(168 citation statements)

References 23 publications

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“…A descriptor of an RNA structure is made using the program's scripting language and is then used to search primary sequence databases. It has been used successfully to predict Rev response elements in lentivirus , small RNA molecules in the Escherichia coli genome (Chen et al 2002), and tRNA genes (Tsui et al 2003). It has also been coupled with an ''evolutionary algorithm'' starting with a loose structure descriptor with no sequence constraints and successfully picked up iron response elements and signal recognition particles in a wide variety of organisms (Fogel et al 2002).…”

Section: Pattern Searchingmentioning

confidence: 99%

Searching for IRES

Baird¹,

Turcotte²,

Korneluk³

et al. 2006

RNA

276

270

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The cell has many ways to regulate the production of proteins. One mechanism is through the changes to the machinery of translation initiation. These alterations favor the translation of one subset of mRNAs over another. It was first shown that internal ribosome entry sites (IRESes) within viral RNA genomes allowed the production of viral proteins more efficiently than most of the host proteins. The RNA secondary structure of viral IRESes has sometimes been conserved between viral species even though the primary sequences differ. These structures are important for IRES function, but no similar structure conservation has yet to be shown in cellular IRES. With the advances in mathematical modeling and computational approaches to complex biological problems, is there a way to predict an IRES in a data set of unknown sequences? This review examines what is known about cellular IRES structures, as well as the data sets and tools available to examine this question. We find that the lengths, number of upstream AUGs, and %GC content of 59-UTRs of the human transcriptome have a similar distribution to those of published IRES-containing UTRs. Although the UTRs containing IRESes are on the average longer, almost half of all 59-UTRs are long enough to contain an IRES. Examination of the available RNA structure prediction software and RNA motif searching programs indicates that while these programs are useful tools to fine tune the empirically determined RNA secondary structure, the accuracy of de novo secondary structure prediction of large RNA molecules and subsequent identification of new IRES elements by computational approaches, is still not possible.

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Section: Pattern Searchingmentioning

confidence: 99%

Searching for IRES

Baird¹,

Turcotte²,

Korneluk³

et al. 2006

RNA

276

270

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“…In Escherichia coli, z100 sRNAs that typically range in size from 50 to 250 nt have been identified (Argaman et al 2001;Wassarman et al 2001;Chen et al 2002;Vogel et al 2003;Zhang et al 2003). Approximately one-third of these sRNAs have been shown to bind to the RNA chaperone Hfq (Wassarman et al 2001;Zhang et al 2003), which is homologous to the eukaryotic family of Sm splicing proteins.…”

Section: Introductionmentioning

confidence: 99%

Role of polynucleotide phosphorylase in sRNA function in Escherichia coli

Lay¹,

Gottesman²

2011

RNA

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In Escherichia coli, many small noncoding regulatory RNAs (sRNAs) post-transcriptionally regulate gene expression by basepairing to mRNAs in a process that is mediated by the RNA chaperone Hfq. Binding of the sRNA to the mRNA can lead to increased or decreased mRNA stability and/or translation. It is not known if proteins other than Hfq are necessary for this process. In order to identify additional genes required for the post-transcriptional regulation of gene expression by Hfqdependent sRNAs, we developed a novel combined genetic selection and screen for mutants defective in sRNA regulation. In our combined genetic selection and screen, we isolated hfq mutants and mutants in pnp, encoding polynucleotide phosphorylase (PNPase). We show that loss-of-function mutations in pnp result in a decreased stability of several sRNAs including RyhB, SgrS, and CyaR and also decrease both the negative and positive regulation by sRNAs. The defect in stability of CyaR and in negative and positive regulation are suppressed by deletion mutations in RNase E. Altogether, our results suggest that the lack of sRNA-mediated regulation in the absence of an active form of PNPase is due to the rapid turnover of sRNA resulting from an increase in RNase E activity and/or an increase in access of other ribonucleases to sRNAs.

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“…Renewed interest in gene expression regulation at the posttranscriptional level in prokaryotes has been sparked recently by the discovery in 2001-2002 of the existence of large numbers of small regulatory RNAs (sRNAs) 1 in Escherichia coli and other bacteria (1)(2)(3)(4). These sRNAs may regulate translation of numerous mRNAs (5) often mediated by the RNA chaperone Hfq (6).…”

mentioning

confidence: 99%

Proteome-wide Alterations in Escherichia coli Translation Rates upon Anaerobiosis

Kramer

Sprenger

Nessen

et al. 2010

Molecular & Cellular Proteomics

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Enzyme reprofiling in bacteria during adaptation from one environmental condition to another may be regulated by both transcription and translation. However, little is known about the contribution of translational regulation. Recently, we have developed a pulse labeling method using the methionine analog azidohomoalanine to determine the relative amounts of proteins synthesized by Escherichia coli in a brief time frame upon a change in environmental conditions. Here we present an extension of our analytical strategy, which entails measuring changes in total protein levels on the same time scale as new protein synthesis. This allows identification of stable and labile proteins and demonstrates that altered levels of most newly synthesized proteins are the result of a change in translation rate rather than degradation rate. With this extended strategy, average relative translation rates for 10 min immediately after a switch from aerobiosis to anaerobiosis were determined. The majority of proteins with increased synthesis rates upon an anaerobic switch are involved in glycolysis and pathways aimed at preventing glycolysis grinding to a halt by a cellular redox imbalance. Our method can be used to compare relative translation rates with relative mRNA levels at the same time. Discrepancies between these parameters may reveal genes whose expression is regulated by translation rather than by transcription. This may help unravel molecular mechanism underlying changes in translation rates, e.g. mediated by small regulatory RNAs. Molecular & Cellular Proteomics 9:2508 -2516, 2010.An integrated view of the molecular events underlying adaptation of bacteria to major environmental changes requires insight into both transcriptional and post-transcriptional regulation of gene expression. With the availability of annotated genome databases, much has been learned about global changes induced in mRNA levels and the transcription factors involved as well as about changes in steady state protein levels upon a switch in environmental conditions. However, little is known concerning genome-wide changes in protein synthesis and degradation rates and about the contributions of transcription and translation to the regulation of gene expression when bacteria adapt to major changes in the environment. An important reason for this is the fact that it is much easier, using genome-wide microarray analysis, to find candidate genes with expression levels regulated via RNA transcription or degradation than to identify candidate genes with expression levels regulated at the level of translation.Renewed interest in gene expression regulation at the posttranscriptional level in prokaryotes has been sparked recently by the discovery in 2001-2002 of the existence of large numbers of small regulatory RNAs (sRNAs) 1 in Escherichia coli and other bacteria (1-4). These sRNAs may regulate translation of numerous mRNAs (5) often mediated by the RNA chaperone Hfq (6). Although the function of many sRNAs is not yet known, several recently reviewed findings (...

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A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome

Cited by 201 publications

References 23 publications

Searching for IRES

Searching for IRES

Role of polynucleotide phosphorylase in sRNA function in Escherichia coli

Proteome-wide Alterations in Escherichia coli Translation Rates upon Anaerobiosis

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