RNA Sequencing Identifies New RNase III Cleavage Sites in
            <i>Escherichia coli</i>
            and Reveals Increased Regulation of mRNA

Gordon, Gina C.; Cameron, Jeffrey C.; Pfleger, Brian F.

doi:10.1128/mbio.00128-17

Cited by 53 publications

(59 citation statements)

References 71 publications

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“…Bacteria use transcript degradation extensively as a strategy for gene regulation [27][28][29][30][31][32][37][38][39]. Degradation helps to tightly couple transcription and translation, such that protein abundances closely match those of transcripts and bacteria can more quickly respond to changes in their environment.…”

Section: Discussionmentioning

confidence: 99%

“…Degradation helps to tightly couple transcription and translation, such that protein abundances closely match those of transcripts and bacteria can more quickly respond to changes in their environment. In many cases, however, specific transcript properties drive differential degradation patterns [30]. In E. coli operons, for example, secondary structure creates patterns of differential degradation within single polycistronic transcripts [39].…”

Section: Discussionmentioning

confidence: 99%

“…Pinetree employs a directional model of transcript degradation modeled after observations from E. coli [27][28][29]. In E. coli, degradation occurs either from the 5'-end of a newly-synthesized transcript or from the 5'-end of a transcript recently cleaved by an RNase III ribnuclease [30]. A combination of endo-and exonucleases degrade transcripts, but the net effect is that transcript degradation is directional-the 5' end of a transcript has a shorter lifespan than the 3' end [31].…”

Section: Degradation Can Produce Gene Expression Patterns Similar To mentioning

confidence: 99%

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Transcript degradation and codon usage regulate gene expression in a lytic phage

Jack

Boutz

Paff

et al. 2019

Preprint

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Many viral genomes are small, containing only single-or double-digit numbers of genes and relatively few regulatory elements. Yet viruses successfully execute complex regulatory programs as they take over their host cells. Here, we propose that some viruses regulate gene expression via a carefully balanced interplay between transcription, translation, and transcript degradation. As our model system, we employ bacteriophage T7, whose genome of approximately 60 genes is well annotated and for which there is a long history of computational models of gene regulation. We expand upon prior modeling work by implementing a stochastic gene expression simulator that tracks individual transcripts, polymerases, ribosomes, and RNases participating in the transcription, translation, and transcript-degradation processes occurring during a T7 infection. By combining this detailed mechanistic modeling of a phage infection with high throughput gene expression measurements of several strains of bacteriophage T7, evolved and engineered, we can show that both the dynamic interplay between transcription and transcript degradation, and between these two processes and translation, appear to be critical components of T7 gene regulation. Our results point to a generic gene regulation strategy that may have evolved in many other viruses. Further, our results suggest that detailed mechanistic modeling may uncover the biological mechanisms at work in both evolved and engineered virus variants.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Degradation Can Produce Gene Expression Patterns Similar To mentioning

confidence: 99%

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Transcript degradation and codon usage regulate gene expression in a lytic phage

Jack

Boutz

Paff

et al. 2019

Preprint

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“…However, besides RNase E, there are a significant number of other endonucleases that initiate the decay of mRNAs as minor players. For example, RNase III, which will be discussed in more detail later in the context of rRNA processing, has been shown to affect the steady-state levels of up to 10% of the mRNAs in exponentially growing cells of E. coli resulting in either destabilization or stabilization of the transcripts (24, 25). RNase P, which is a ribozyme that contains an RNA catalytic subunit (26), specifically cleaves a small number of polycistronic mRNAs in intercistronic regions (27).…”

Section: General Messenger Rna Decaymentioning

confidence: 99%

Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria

Mohanty¹,

Kushner

2018

Microbiol Spectr

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Gene expression in Gram-negative bacteria is regulated at many levels, including transcription initiation, RNA processing, RNA/RNA interactions, mRNA decay, and translational controls involving enzymes that alter translational efficiency. In this chapter we discuss the various enzymes that control transcription, translation and RNA stability through RNA processing and degradation. RNA processing is essential to generate functional RNAs, while degradation helps control the steady-state level of each individual transcript. For example, all the pre-tRNAs are transcribed with extra nucleotides at both their 5′ and 3′ termini, which are subsequently processed to produce mature tRNAs that can be aminoacylated. Similarly, rRNAs that are transcribed as part of a 30S polycistronic transcript, are matured to individual 16S, 23S and 5S rRNAs. Decay of mRNAs plays a key role in gene regulation through controlling the steady-state level of each transcript, which is essential for maintaining appropriate protein levels. In addition, degradation of both translated and non-translated RNAs recycles nucleotides to facilitate new RNA synthesis. To carry out all these reactions Gram-negative bacteria employ a large number of endonucleases, exonucleases, RNA helicases, and poly(A) polymerase as well as proteins that regulate the catalytic activity of particular ribonucleases. Under certain stress conditions an additional group of specialized endonucleases facilitate the cell’s ability to adapt and survive. Many of the enzymes, such as RNase E, RNase III, polynucleotide phosphorylase, RNase R, and poly(A) polymerase I participate in multiple RNA processing and decay pathways.

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“…asRNA and RNase III regulate 12 gene expression of plasmids and toxins. The E. coli ColE1 plasmid replication origin encodes 13 two non-coding RNAs -RNA II, which serves as a DNA replication primer, and RNA I, which 14 is shorter and fully complementary to the 5´ portion of RNA II (7)(8)(9)(10). RNA I inhibits plasmid 15 replication by binding to the RNA II plasmid replication primer.…”

mentioning

confidence: 99%

Tombusvirusp19 captures RNase III-cleaved double-stranded RNAs formed by overlapping sense and antisense transcripts inE. coli

Huang

Deighan

Jin³

et al. 2019

Preprint

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1Antisense transcription is widespread in bacteria. By base pairing with overlapping sense 2 RNAs, antisense RNAs (asRNA) can form long double-stranded RNAs (dsRNA), which are 3 cleaved by RNase III, a dsRNA endoribonuclease. Ectopic expression of plant tombusvirus 4 p19 in E. coli stabilizes ~21 bp dsRNA RNase III decay intermediates, which enabled us to 5 characterize otherwise highly unstable asRNA by deep sequencing of p19-captured dsRNA 6 and total RNA. dsRNA formed at most bacterial genes in the bacterial chromosome and in a 7 plasmid. The most abundant dsRNA clusters were mostly formed by divergent transcription of 8 sense and antisense transcripts overlapping at their 5'-ends. The most abundant clusters 9 included small RNAs, such as ryeA/ryeB, 4 toxin-antitoxin genes, and 3 tRNAs, and some 10 longer coding genes, including rsd and cspD. The sense and antisense transcripts in abundant 11 dsRNA clusters were more plentiful and had longer half-lives in RNase III mutant strains, 12suggesting that formation of dsRNAs promoted RNA decay at these loci. However, widespread 13 changes in protein levels did not occur in RNase III mutant bacteria. Nonetheless, some 14 proteins involved in antioxidant responses and glycolysis changed reproducibly. dsRNAs 15 accumulated in bacterial cells lacking RNase III, increasing in stationary phase, and correlated 16 with increased cell death in RNase III mutant bacteria in late stationary phase. The 17 physiological importance of widespread antisense transcription in bacteria remains unclear but 18 it may become important during environmental stress. Ectopic expression of p19 is a sensitive 19 method for identifying antisense transcripts and RNase III cleavage sites in bacteria.

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RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA

Cited by 53 publications

References 71 publications

Transcript degradation and codon usage regulate gene expression in a lytic phage

Transcript degradation and codon usage regulate gene expression in a lytic phage

Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria

Tombusvirusp19 captures RNase III-cleaved double-stranded RNAs formed by overlapping sense and antisense transcripts inE. coli

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