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Literature summary for 3.1.13.1 extracted from

  • Pobre, V.; Arraiano, C.
    Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli (2015), BMC Genomics, 16, 72-83 .
    View publication on PubMedView publication on EuropePMC
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Protein Variants

Protein Variants Comment Organism
additional information construction of deletion mutant DELTArnb. Comparison of the mutant transcriptome with the wild-type, to determine the global effects of the deletion of the exoribonucleases in exponential phase, reveals that the deletion of RNase II significantly affects 187 transcripts. Many of the transcripts are actually down-regulated in the exoribonuclease mutants when compared to the wild-type control. The exoribonuclease also affects some stable RNAs. The RNase II mutant is shown to produce more biofilm than the wild-type control. Differential expression analysis of the transcriptome of exoribonucleases mutants and phenotypes, overview. For example, nirB (Nitrite reductase [NAD(P)H] large subunit) is down-regulated in DELTArnb with a fold-change of 0.36 while in the DELTArnr mutant nirB is up-regulated with a fold-change of 9.11 Escherichia coli
additional information construction of deletion mutant DELTArnb. Comparison of the mutant transcriptome with the wild-type, to determine the global effects of the deletion of the exoribonucleases in exponential phase, reveals that the deletion of RNase R significantly affects 202 transcripts. Many of the transcripts are actually down-regulated in the exoribonuclease mutants when compared to the wild-type control. The exoribonuclease also affects some stable RNAs. The RNase R mutant is shown to produce more biofilm than the wild-type control. Differential expression analysis of the transcriptome of exoribonucleases mutants and phenotypes, overview Escherichia coli

General Stability

General Stability Organism
RNase R is a highly unstable protein in exponentially growing cells, but is stabilized in stationary phase and other stress conditions. Most of the RNase R in exponential phase has been shown to be linked with ribosomal proteins Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
additional information Escherichia coli RNase II is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction, is sensitive to secondary structures, it is also known to stall before it reaches a double-stranded region. Although RNase II degrading activity is sequence-independent, its favourite substrate is poly(A) tails. RNase II rapidly degrades poly (A) tails, but it halts if it finds secondary structures such as the Rho-independent terminators. The degradation of polyadenylated stretches by RNase II can paradoxically protect some RNAs because the other exoribonucleases (PNPase and RNase R) need a short poly(A) tail as a toehold in order to degrade secondary structures ?
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 ?
additional information Escherichia coli RNase R is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction. RNase R can easily degrade highly structured RNAs, but requires a single stranded region in order to be able to bind to the substrates. It was shown to be a key enzyme involved in the degradation of polyadenylated RNA ?
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 ?

Organism

Organism UniProt Comment Textmining
Escherichia coli P21499
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Escherichia coli P30850
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Source Tissue

Source Tissue Comment Organism Textmining
additional information RNase R is a highly unstable protein in exponentially growing cells, but is stabilized in stationary phase and other stress conditions. Most of the RNase R in exponential phase has been shown to be linked with ribosomal proteins Escherichia coli
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Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information RNase II is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction, is sensitive to secondary structures, it is also known to stall before it reaches a double-stranded region. Although RNase II degrading activity is sequence-independent, its favourite substrate is poly(A) tails. RNase II rapidly degrades poly (A) tails, but it halts if it finds secondary structures such as the Rho-independent terminators. The degradation of polyadenylated stretches by RNase II can paradoxically protect some RNAs because the other exoribonucleases (PNPase and RNase R) need a short poly(A) tail as a toehold in order to degrade secondary structures Escherichia coli ?
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 ?
additional information RNase R is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction. RNase R can easily degrade highly structured RNAs, but requires a single stranded region in order to be able to bind to the substrates. It was shown to be a key enzyme involved in the degradation of polyadenylated RNA Escherichia coli ?
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 ?

Synonyms

Synonyms Comment Organism
RNase II
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 Escherichia coli
RNase R
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 Escherichia coli
Rnb
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 Escherichia coli
RNR
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 Escherichia coli

Expression

Organism Comment Expression
Escherichia coli the activity of RNase R is modulated according to the growth conditions of the cell and is induced under several stress conditions up

General Information

General Information Comment Organism
evolution RNase II is another 3'-5' hydrolytic exoribonuclease from the RNase II family of exoribonucleases Escherichia coli
evolution RNase R is another 3'-5' hydrolytic exoribonuclease from the RNase II family of exoribonucleases Escherichia coli
malfunction RNase R mutants form more biofilms than wild-type cells Escherichia coli
metabolism the enzyme is involved in cell motility and biofilm formation Escherichia coli
additional information transcriptomic analysis Escherichia coli
physiological function the RNA steady-state levels in the cell are a balance between synthesis and degradation rates. Although transcription is important, RNA processing and turnover are also key factors in the regulation of gene expression. In Escherichia coli there are three main exoribonucleases (RNase II, RNase R and PNPase) involved in RNA degradation. RNase II, RNase R and PNPase significantly impair the motility of the cells Escherichia coli
physiological function the RNA steady-state levels in the cell are a balance between synthesis and degradation rates. Although transcription is important, RNA processing and turnover are also key factors in the regulation of gene expression. In Escherichia coli there are three main exoribonucleases (RNase II, RNase R and PNPase) involved in RNA degradation. RNase R is a critical enzyme involved in RNA and protein quality control, namely in the degradation of defective tRNAs and rRNAs and is involved in RNA degradation during trans-translation. RNase R is involved in virulence, it affects virulence by altering the motility of the pathogens. RNase II, RNase R and PNPase significantly impair the motility of the cells Escherichia coli