RNase II levels change according to the growth conditions: characterization of <i>gmr</i>, a new <i>Escherichia coli</i> gene involved in the modulation of RNase II

Cairrão, Fátima; Chora, Ângelo Ferreira; Zilhão, Rita; Carpousis, Agamemnon J.; Arraiano, Cecília M.

doi:10.1046/j.1365-2958.2001.02342.x

Cited by 56 publications

(68 citation statements)

References 63 publications

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“…Although a number of other unstable bacterial proteins have been identified, most proteins are stable during the exponential phase (Gottesman 2003;Jenal and Hengge-Aronis 2003;Ehrmann and Clausen 2004), and this high degree of instability of RNase R has not been observed previously for RNases. Interestingly, the related protein RNase II also is somewhat unstable (half-life z50 min), and its instability is affected by the gene gmr (Cairrão et al 2001). Our data also show that RNase R becomes stabilized under a variety of physiological conditions that lead to slower growth.…”

Section: Effect Of Proteases On Rnase R Stabilitymentioning

confidence: 57%

RNase R is a highly unstable protein regulated by growth phase and stress

Chen¹,

Deutscher²

2010

RNA

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RNase R is an important exoribonuclease that participates in the degradation of structured RNAs in Escherichia coli. In earlier work, it was shown that RNase R levels increase dramatically under certain stress conditions, particularly during cold shock and stationary phase. However, the regulatory processes that lead to this elevation are not well understood. We show here that the increase in RNase R in stationary phase is unaffected by the global regulators, RpoS and (p)ppGpp, and that it occurs despite a major reduction in rnr message. Rather, we find that RNase R is a highly unstable protein in exponential phase, with a half-life of~10 min, and that the protein is stabilized in stationary phase, leading to its relative increase. RNase R is also stabilized during cold shock and by growth in minimal medium, two other conditions that lead to its elevation. These data demonstrate that RNase R is subject to regulation by a novel, posttranslational mechanism that may have important implications for our complete understanding of RNA metabolism.

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Section: Effect Of Proteases On Rnase R Stabilitymentioning

confidence: 57%

RNase R is a highly unstable protein regulated by growth phase and stress

Chen¹,

Deutscher²

2010

RNA

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“…The pFCT6.1 plasmid (Cairrão et al 2001) was used for expression of E. coli histidine-tagged RNase II protein. This plasmid contains the rnb gene cloned into pET-15b vector (Novagen) under the control of f10 promoter, allowing the expression of the (His) 6 -tagged RNase II fusion protein.…”

Section: Construction Of Plasmids Expressing Rnase R Pnpase and Hybmentioning

confidence: 99%

“…Its activity is sequence independent but sensitive to secondary structures, and poly(A) is the preferred substrate for this enzyme (Gupta et al 1977;McLaren et al 1991;Coburn and Mackie 1996;Marujo et al 2000). RNase II expression is differentially regulated at the transcriptional and posttranscriptional levels (Zilhão et al 1993(Zilhão et al , 1996a, and the protein can be regulated by the environmental conditions (Cairrão et al 2001).…”

Section: Introductionmentioning

confidence: 99%

The role of the S1 domain in exoribonucleolytic activity: Substrate specificity and multimerization

Amblar

Barbas²,

Gómez‐Puertas³

et al. 2007

RNA

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RNase II is a 39-59 exoribonuclease that processively hydrolyzes single-stranded RNA generating 59 mononucleotides. This enzyme contains a catalytic core that is surrounded by three RNA-binding domains. At its C terminus, there is a typical S1 domain that has been shown to be critical for RNA binding. The S1 domain is also present in the other major 39-59 exoribonucleases from Escherichia coli: RNase R and polynucleotide phosphorylase (PNPase). In this report, we examined the involvement of the S1 domain in the different abilities of these three enzymes to overcome RNA secondary structures during degradation. Hybrid proteins were constructed by replacing the S1 domain of RNase II for the S1 from RNase R and PNPase, and their exonucleolytic activity and RNA-binding ability were examined. The results revealed that both the S1 domains of RNase R and PNPase are able to partially reverse the drop of RNA-binding ability and exonucleolytic activity resulting from removal of the S1 domain of RNase II. Moreover, the S1 domains investigated are not equivalent. Furthermore, we demonstrate that S1 is neither responsible for the ability to overcome secondary structures during RNA degradation, nor is it related to the size of the final product generated by each enzyme. In addition, we show that the S1 domain from PNPase is able to induce the trimerization of the RNaseII-PNP hybrid protein, indicating that this domain can have a role in the biogenesis of multimers.

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“…Conversely, in the absence of PNPase, RNase II levels increase (116). In addition, there appears to be a specific protein, called Gmr, that regulates RNase II levels (12).…”

Section: Regulation Of Mrna Decaymentioning

confidence: 99%

mRNA Decay inEscherichia coliComes of Age

2002

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When Apirion first proposed that mRNA decay in Escherichia coli involves a series of endo-and exonucleolytic events (2), the general working assumption was that the turnover of transcripts is a simple salvage pathway that is necessary for recycling of ribonucleotides. Although experimental data at that time indicated that mRNAs are rapidly degraded (11,40) and that decay of individual transcripts is independent of length (9), the number and specificities of the enzymes that actually carry out transcript degradation were still open questions. Twenty-nine years and many experiments later, a much different picture has emerged. Not only is the pathway of mRNA decay far more complex than originally envisioned, but it apparently also plays an integral role in regulating the expression of many genes. While many important features of this system remain to be elucidated, this prospective attempts to convey the current state of knowledge. In addition, it focuses primarily on those areas where there are disagreements regarding important features of the mRNA decay process. INITIATION OF mRNA DECAYOf all of the aspects associated with mRNA decay in E. coli, the question of how the process is initiated has sparked the most controversy. Not only have there been conflicting views regarding which enzyme(s) is responsible for the initial endonucleolytic cleavage events, but there have also been disagreements regarding the importance of certain multiprotein complexes. E. coli is known to contain at least five endoribonucleases: RNases III, E, G, and I/M.RNase III was first discovered as a protein that cleaves double-stranded RNA (94). In vivo, RNase III specifically degrades stem-loop structures, particularly those in intercistronic regions (34, 88). It plays a major role in processing of the 30S rRNA precursor (34). The enzyme has been shown to indirectly affect the half-lives of a limited number of transcripts (7,36,88), primarily by eliminating a stem-loop structure, usually upstream of the translation start site. However, deletion of the RNase III structural gene (rnc) does not lead to any significant change in the degradation of total pulse-labeled RNA or specific transcripts (5). Thus, it is probably not a major player in mRNA decay.In 1979, Ono and Kuwano (84) isolated a temperaturesensitive mutation, called ams-1 (for altered mRNA stability), that led to a slowing in the decay of total pulse-labeled RNA.Independently, Ghora and Apirion (37) identified RNase E on the basis of its role in the processing of 9S rRNA into a 5S form. More than a decade later, several laboratories showed that the ams-1 and rne-3071 mutations are alleles of the same gene, now called rne (6,68,77,105).In addition to being required for the maturation of 9S rRNA, RNase E has also been shown to be involved in the processing of the 5Ј end of 16S rRNA (54, 111), the maturation of the RNA subunit of RNase P (63), the degradation of the antisense inhibitor (RNA I) of plasmid colE1 DNA replication (107), and the processing of tRNAs (53, 85, 92). As such, i...

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RNase II levels change according to the growth conditions: characterization of gmr, a new Escherichia coli gene involved in the modulation of RNase II

Cited by 56 publications

References 63 publications

RNase R is a highly unstable protein regulated by growth phase and stress

RNase R is a highly unstable protein regulated by growth phase and stress

The role of the S1 domain in exoribonucleolytic activity: Substrate specificity and multimerization

mRNA Decay inEscherichia coliComes of Age

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