Prediction of transcription terminators in bacterial genomes 1 1Edited by F. E. Cohen

Ermolaeva, Maria D.; Khalak, Hanif; White, Owen; Smith, Hamilton O.; Salzberg, Steven L.

doi:10.1006/jmbi.2000.3836

Cited by 227 publications

(202 citation statements)

References 21 publications

(24 reference statements)

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“…Since this polar effect on gene expression is mediated through an effect on transcription, it closely resembles the process of polarity in bacteria. However, the mechanism responsible for polarity in archaea is unclear since homologues of the bacterial termination factor, Rho, are not evident in the genome of S. solfataricus or other archaea (Santangelo & Reeve, 2006), and bacterial terminators are largely absent (Ermolaeva et al, 2000;Unniraman et al, 2002). While cotranscription can be inferred by detection of transcribed intergenic sequences using RT-PCR, in the case of mer an internal promoter had been proposed that could bypass a requirement for coupled gene expression (Schelert et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus

et al. 2013

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Crenarchaeota include extremely thermoacidophilic organisms that thrive in geothermal environments dominated by sulfidic ores and heavy metals such as mercury. Mercuric ion, Hg(II), inactivates transcription in the crenarchaeote Sulfolobus solfataricus and simultaneously derepresses transcription of a resistance operon, merHAI, through interaction with the MerR transcription factor. While mercuric reductase (MerA) is required for metal resistance, the role of MerH, an adjacent small and predicted product of an ORF, has not been explored. Inactivation of MerH either by nonsense mutation or by in-frame deletion diminished Hg(II) resistance of mutant cells. Promoter mapping studies indicated that Hg(II) sensitivity of the merH nonsense mutant arose through transcriptional polarity, and its metal resistance was restored partially by single copy merH complementation. Since MerH was not required in vitro for MerA-catalysed Hg(II) reduction, MerH may play an alternative role in metal resistance. Inductively coupled plasma-mass spectrometry analysis of the MerH deletion strain following metal challenge indicated that there was prolonged retention of intracellular Hg(II). Finally, a reduced rate of mer operon induction in the merH deletion mutant suggested that the requirement for MerH could result from metal trafficking to the MerR transcription factor.

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Section: Discussionmentioning

confidence: 99%

Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus

et al. 2013

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“…The predictive algorithm first identified the intergenic regions in the genome of the L. pneumophila Philadelphia-1 genome, and then searched them for Rho-independent terminators. To this end, we used the search module for the Rho-independent terminator developed by us previously based on their sequence and structure properties (18), as well as two other search strategies, RNAMotif (29) and TransTerm (30), implemented in the sRNAPredict2 algorithm (17). The sequence upstream of the terminator was then checked for conservation against the whole-genome sequences of 590 bacterial strains available at the time of the analysis, including the other three sequenced strains of L. pneumophila: Paris, Lens, and Corby.…”

Section: Methodsmentioning

confidence: 99%

Legionella pneumophila 6S RNA optimizes intracellular multiplication

Faucher

Friedlander²,

Livny³

et al. 2010

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

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Legionella pneumophila is a Gram-negative opportunistic human pathogen that infects and multiplies in a broad range of phagocytic protozoan and mammalian phagocytes. Based on the observation that small regulatory RNAs (sRNAs) play an important role in controlling virulence-related genes in several pathogenic bacteria, we attempted to identify sRNAs expressed by L. pneumophila. We used computational prediction followed by experimental verification to identify and characterize sRNAs encoded in the L. pneumophila genome. A 50-mer probe microarray was constructed to test the expression of predicted sRNAs in bacteria grown under a variety of conditions. This strategy successfully identified 22 expressed RNAs, out of which 6 were confirmed by northern blot and RACE. One of the identified sRNAs is highly expressed in postexponential phase, and computational prediction of its secondary structure reveals a striking similarity to the structure of 6S RNA, a widely distributed prokaryotic sRNA, known to regulate the activity of σ 70 -containing RNA polymerase. A 70-mer probe microarray was used to identify genes affected by L. pneumophila 6S RNA in stationary phase. The 6S RNA positively regulates expression of genes encoding type IVB secretion system effectors, stress response genes such as groES and recA, as well as many genes involved in acquisition of nutrients and genes with unknown or hypothetical functions. Deletion of 6S RNA significantly reduced L. pneumophila intracellular multiplication in both protist and mammalian host cells, but had no detectable effect on growth in rich media.Legionella pneumophila genome | microarray | sRNA | sRNA prediction | competition assay

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“…Upstream and downstream UTR boundaries for 5Ј UTRs were read from the genomic annotation accompanying the GenBank genomic sequence (32, 38); the downstream end of 3Ј UTRs was predicted by using the TRANSTERM program by Ermolaeva et al (39) to locate probable rho-independent transcription-terminating sequences. Overall, 2,193 5Ј UTRs and 688 3Ј UTRs were predicted.…”

Section: Global Analysis Of Mrna Half-life In Cells Growing At Differmentioning

confidence: 99%

Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays

Bernstein

Khodursky

Lin

et al. 2002

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

767

711

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Much of the information available about factors that affect mRNA decay in Escherichia coli, and by inference in other bacteria, has been gleaned from study of less than 25 of the Ϸ4,300 predicted E. coli messages. To investigate these factors more broadly, we examined the half-lives and steady-state abundance of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. An rRNA-based strategy for normalization of microarray data was developed to permit quantitation of mRNA decay after transcriptional arrest by rifampicin. We found that globally, mRNA half-lives were similar in nutrient-rich media and defined media in which the generation time was approximately tripled. A wide range of stabilities was observed for individual mRNAs of E. coli, although Ϸ80% of all mRNAs had half-lives between 3 and 8 min. Genes having biologically related metabolic functions were commonly observed to have similar stabilities. Whereas the half-lives of a limited number of mRNAs correlated positively with their abundance, we found that overall, increased mRNA stability is not predictive of increased abundance. Neither the density of putative sites of cleavage by RNase E, which is believed to initiate mRNA decay in E. coli, nor the free energy of folding of 5 or 3 untranslated region sequences was predictive of mRNA half-life. Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability.RNA degradation ͉ RNA half-life ͉ transcript abundance T he rate of mRNA degradation plays a central role in the metabolism of nucleic acids in both prokaryotic and eukaryotic cells (for reviews see refs. 1-5). mRNA decay has been studied in a range of organisms, and much has been learned about the substrate features and ribonucleolytic enzymes that influence mRNA stability. In the case of Escherichia coli, experimenters have demonstrated that extensive variation exists in the rate of decay of individual mRNAs and that specific features of the mRNA sequence as well as transcript secondary structure can be important determinants of such variation (1, 3). Additionally, although the half-lives of some RNAs depend on the physiological state of the cell, as influenced by genetic and environmental factors, the half-lives of other RNAs seem to be independent of cell physiology (6, 7).Much of the information available about RNA decay has been derived from study of RNAs encoded by a very limited number of genes. In fact, we can find published reports of RNA half-life for less than 25 of the 4,288 predicted ORFs in the E. coli genome. Current models of mRNA decay are based on this relatively limited experimental sampling of message turnover. To gain a broader understanding of the fate of mRNAs in E. coli we adapted DNA microarray methodology to measure the decay of each chromosomally encoded mRNA simultaneously.DNA microarrays containing sequences derived ...

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Prediction of transcription terminators in bacterial genomes 1 1Edited by F. E. Cohen

Cited by 227 publications

References 21 publications

Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus

Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus

Legionella pneumophila 6S RNA optimizes intracellular multiplication

Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays

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