scholarly journals RNase III-Independent Autogenous Regulation of Escherichia coli Polynucleotide Phosphorylase via Translational Repression

2015 ◽  
Vol 197 (11) ◽  
pp. 1931-1938 ◽  
Author(s):  
Thomas Carzaniga ◽  
Gianni Dehò ◽  
Federica Briani
Keyword(s):  
Escherichia Coli ◽  
Posttranscriptional Regulation ◽  
Mrna Degradation ◽  
Translational Repression ◽  
Rnase E ◽  
Polynucleotide Phosphorylase ◽  
Rnase Iii ◽  
Primary Transcript ◽  
Content Type ◽  
Autogenous Regulation

ABSTRACTThe complex posttranscriptional regulation mechanism of theEscherichia colipnpgene, which encodes the phosphorolytic exoribonuclease polynucleotide phosphorylase (PNPase), involves two endoribonucleases, namely, RNase III and RNase E, and PNPase itself, which thus autoregulates its own expression. The models proposed forpnpautoregulation posit that the target of PNPase is a maturepnpmRNA previously processed at its 5′ end by RNase III, rather than the primarypnptranscript (RNase III-dependent models), and that PNPase activity eventually leads topnpmRNA degradation by RNase E. However, some published data suggest thatpnpexpression may also be regulated through a PNPase-dependent, RNase III-independent mechanism. To address this issue, we constructed isogenic Δpnp rnc+and ΔpnpΔrncstrains with a chromosomalpnp-lacZtranslational fusion and measured β-galactosidase activity in the absence and presence of PNPase expressed by a plasmid. Our results show that PNPase also regulates its own expression via a reversible RNase III-independent pathway acting upstream from the RNase III-dependent branch. This pathway requires the PNPase RNA binding domains KH and S1 but not its phosphorolytic activity. We suggest that the RNase III-independent autoregulation of PNPase occurs at the level of translational repression, possibly by competition forpnpprimary transcript between PNPase and the ribosomal protein S1.IMPORTANCEInEscherichia coli, polynucleotide phosphorylase (PNPase, encoded bypnp) posttranscriptionally regulates its own expression. The two models proposed so far posit a two-step mechanism in which RNase III, by cutting the leader region of thepnpprimary transcript, creates the substrate for PNPase regulatory activity, eventually leading topnpmRNA degradation by RNase E. In this work, we provide evidence supporting an additional pathway for PNPase autogenous regulation in which PNPase acts as a translational repressor independently of RNase III cleavage. Our data make a new contribution to the understanding of the regulatory mechanism ofpnpmRNA, a process long since considered a paradigmatic example of posttranscriptional regulation at the level of mRNA stability.

scholarly journals Autogenous Regulation of Escherichia coli Polynucleotide Phosphorylase Expression Revisited

2009 ◽  
Vol 191 (6) ◽  
pp. 1738-1748 ◽  
Author(s):  
Thomas Carzaniga ◽  
Federica Briani ◽  
Sandro Zangrossi ◽  
Giuseppe Merlino ◽  
Paolo Marchi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Current Model ◽  
Dependent Manner ◽  
Rnase E ◽  
Polynucleotide Phosphorylase ◽  
Rnase Iii ◽  
Independent Manner ◽  
Stem Loop ◽  
Autogenous Regulation ◽  
Additional Support

ABSTRACT The Escherichia coli polynucleotide phosphorylase (PNPase; encoded by pnp), a phosphorolytic exoribonuclease, posttranscriptionally regulates its own expression at the level of mRNA stability and translation. Its primary transcript is very efficiently processed by RNase III, an endonuclease that makes a staggered double-strand cleavage about in the middle of a long stem-loop in the 5′-untranslated region. The processed pnp mRNA is then rapidly degraded in a PNPase-dependent manner. Two non-mutually exclusive models have been proposed to explain PNPase autogenous regulation. The earlier one suggested that PNPase impedes translation of the RNase III-processed pnp mRNA, thus exposing the transcript to degradative pathways. More recently, this has been replaced by the current model, which maintains that PNPase would simply degrade the promoter proximal small RNA generated by the RNase III endonucleolytic cleavage, thus destroying the double-stranded structure at the 5′ end that otherwise stabilizes the pnp mRNA. In our opinion, however, the first model was not completely ruled out. Moreover, the RNA decay pathway acting upon the pnp mRNA after disruption of the 5′ double-stranded structure remained to be determined. Here we provide additional support to the current model and show that the RNase III-processed pnp mRNA devoid of the double-stranded structure at its 5′ end is not translatable and is degraded by RNase E in a PNPase-independent manner. Thus, the role of PNPase in autoregulation is simply to remove, in concert with RNase III, the 5′ fragment of the cleaved structure that both allows translation and prevents the RNase E-mediated PNPase-independent degradation of the pnp transcript.

scholarly journals Decreased Expression of Stable RNA Can Alleviate the Lethality Associated with RNase E Deficiency in Escherichia coli

2017 ◽  
Vol 199 (8) ◽  
Author(s):  
P. Himabindu ◽  
K. Anupama
Keyword(s):  
Escherichia Coli ◽  
Mrna Degradation ◽  
Gram Negative Bacteria ◽  
Rrna Processing ◽  
Rnase E ◽  
Rnase R ◽  
Content Type ◽  
E Coli ◽  
Rrna Species ◽  
Rna Levels

ABSTRACT The endoribonuclease RNase E participates in mRNA degradation, rRNA processing, and tRNA maturation in Escherichia coli, but the precise reasons for its essentiality are unclear and much debated. The enzyme is most active on RNA substrates with a 5′-terminal monophosphate, which is sensed by a domain in the enzyme that includes residue R169; E. coli also possesses a 5′-pyrophosphohydrolase, RppH, that catalyzes conversion of 5′-terminal triphosphate to 5′-terminal monophosphate on RNAs. Although the C-terminal half (CTH), beyond residue approximately 500, of RNase E is dispensable for viability, deletion of the CTH is lethal when combined with an R169Q mutation or with deletion of rppH. In this work, we show that both these lethalities can be rescued in derivatives in which four or five of the seven rrn operons in the genome have been deleted. We hypothesize that the reduced stable RNA levels under these conditions minimize the need of RNase E to process them, thereby allowing for its diversion for mRNA degradation. In support of this hypothesis, we have found that other conditions that are known to reduce stable RNA levels also suppress one or both lethalities: (i) alterations in relA and spoT, which are expected to lead to increased basal ppGpp levels; (ii) stringent rpoB mutations, which mimic high intracellular ppGpp levels; and (iii) overexpression of DksA. Lethality suppression by these perturbations was RNase R dependent. Our work therefore suggests that its actions on the various substrates (mRNA, rRNA, and tRNA) jointly contribute to the essentiality of RNase E in E. coli. IMPORTANCE The endoribonuclease RNase E is essential for viability in many Gram-negative bacteria, including Escherichia coli. Different explanations have been offered for its essentiality, including its roles in global mRNA degradation or in the processing of several tRNA and rRNA species. Our work suggests that, rather than its role in the processing of any one particular substrate, its distributed functions on all the different substrates (mRNA, rRNA, and tRNA) are responsible for the essentiality of RNase E in E. coli.

Subunit Composition of Ribosome in the yqgF Mutant Is Deficient in pre-16S rRNA Processing of Escherichia coli

2018 ◽  
Vol 28 (4) ◽  
pp. 179-182
Author(s):  
Tatsuaki  Kurata ◽  
Shinobu Nakanishi ◽  
Masayuki Hashimoto ◽  
Masato Taoka ◽  
Toshiaki Isobe ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
Active Form ◽  
Rrna Processing ◽  
Rnase E ◽  
Rnase Iii ◽  
Primary Transcript ◽  
E Coli ◽  
Copy Numbers ◽  
Inactive Form

<i>Escherichia coli</i> 16S, 23S, and 5S ribosomal RNAs (rRNAs) are transcribed as a single primary transcript, which is subsequently processed into mature rRNAs by several RNases. Three RNases (RNase III, RNase E, and RNase G) were reported to function in processing the 5′-leader of precursor 16S rRNA (pre-16S rRNA). Previously, we showed that a novel essential YqgF is involved in that processing. Here we investigated the ribosome subunits of the <i>yqgF</i><sup>ts</sup> mutant by LC-MS/MS. The mutant ribosome had decreased copy numbers of ribosome protein S1, suggesting that the <i>yqgF</i> gene enables incorporation of ribosomal protein S1 into ribosome by processing of the 5′-end of pre-16S rRNA. The ribosome protein S1 is essential for translation in <i>E. coli</i>; therefore, our results suggest that YqgF converts the inactive form of newly synthesized ribosome into the active form at the final step of ribosome assembly.

scholarly journals Global Analysis of Posttranscriptional Regulation by GlmY and GlmZ in Enterohemorrhagic Escherichia coli O157:H7

2015 ◽  
Vol 83 (4) ◽  
pp. 1286-1295 ◽  
Author(s):  
Charley C. Gruber ◽  
Vanessa Sperandio
Keyword(s):  
Escherichia Coli ◽  
Rna Sequencing ◽  
Posttranscriptional Regulation ◽  
Global Analysis ◽  
Acid Resistance ◽  
Enterohemorrhagic Escherichia Coli ◽  
Global Changes ◽  
Content Type ◽  
Enterocyte Effacement ◽  
K 12

EnterohemorrhagicEscherichia coli(EHEC) is a significant human pathogen and is the cause of bloody diarrhea and hemolytic-uremic syndrome. The virulence repertoire of EHEC includes the genes within the locus of enterocyte effacement (LEE) that are largely organized in five operons,LEE1toLEE5, which encode a type III secretion system, several effectors, chaperones, and regulatory proteins. In addition, EHEC also encodes several non-LEE-encoded effectors and fimbrial operons. The virulence genes of this pathogen are under a large amount of posttranscriptional regulation. The small RNAs (sRNAs) GlmY and GlmZ activate the translation of glucosamine synthase (GlmS) inE. coliK-12, and in EHEC they destabilize the 3′ fragments of theLEE4andLEE5operons and promote translation of the non-LEE-encoded effector EspFu. We investigated the global changes of EHEC gene expression governed by GlmY and GlmZ using RNA sequencing and gene arrays. This study extends the known effects of GlmY and GlmZ regulation to show that they promote expression of the curli adhesin, repress the expression of tryptophan metabolism genes, and promote the expression of acid resistance genes and the non-LEE-encoded effector NleA. In addition, seven novel EHEC-specific sRNAs were identified using RNA sequencing, and three of them—sRNA56, sRNA103, and sRNA350—were shown to regulate urease, fimbria, and the LEE, respectively. These findings expand the knowledge of posttranscriptional regulation in EHEC.

RNase E, the Major Player in mRNA Degradation, Is Down-Regulated in Escherichia coli during a Transient Growth Retardation (Diauxic Lag)

1998 ◽  
Vol 379 (1) ◽  
Author(s):  
Tamara Barlow ◽  
Mehmet Berkmen ◽  
Dimitris Georgeliis ◽  
Lourdes Bayr ◽  
Staffan Arvidson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Retardation ◽  
Mrna Degradation ◽  
Transient Growth ◽  
Rnase E ◽  
Major Player ◽  
Diauxic Lag

scholarly journals The Virulence of Salmonella enterica Serovar Typhimurium in the Insect Model Galleria mellonella Is Impaired by Mutations in RNase E and RNase III

2013 ◽  
Vol 79 (19) ◽  
pp. 6124-6133 ◽  
Author(s):  
Sandra C. Viegas ◽  
Dalila Mil-Homens ◽  
Arsénio M. Fialho ◽  
Cecília M. Arraiano
Keyword(s):  
Salmonella Enterica ◽  
Defense Mechanisms ◽  
Galleria Mellonella ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Virulence Gene ◽  
Rnase E ◽  
Rnase Iii ◽  
Content Type ◽  
Protein Levels ◽  
Serovar Typhimurium

ABSTRACTSalmonella entericaserovar Typhimurium is a Gram-negative bacterium able to invade and replicate inside eukaryotic cells. To cope with the host defense mechanisms, the bacterium has to rapidly remodel its transcriptional status. Regulatory RNAs and ribonucleases are the factors that ultimately control the fate of mRNAs and final protein levels in the cell. There is growing evidence of the direct involvement of these factors in bacterial pathogenicity. In this report, we validate the use of aGalleria mellonelamodel inS. Typhimurium pathogenicity studies through the parallel analysis of a mutant with a mutation inhfq, a well-establishedSalmonellavirulence gene. The results obtained with this mutant are similar to the ones reported in a mouse model. Through the use of this insect model, we demonstrate a role for the main endoribonucleases RNase E and RNase III inSalmonellavirulence. These ribonuclease mutants show an attenuated virulence phenotype, impairment in motility, and reduced proliferation inside the host. Interestingly, the two mutants trigger a distinct immune response in the host, and the two mutations seem to have an impact on distinct bacterial functions.

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