Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, Moreira RN, Pobre V, Reis FP, Saramago M, et al. The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev. 2010;34(5):883–923.
Article
CAS
Google Scholar
Esquerre T, Laguerre S, Turlan C, Carpousis AJ, Girbal L, Cocaign-Bousquet M. Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates. Nucleic Acids Res. 2014;42(4):2460–72.
Article
CAS
Google Scholar
Silva IJ, Saramago M, Dressaire C, Domingues S, Viegas SC, Arraiano CM. Importance and key events of prokaryotic RNA decay: the ultimate fate of an RNA molecule. Wiley Interdiscip Rev RNA. 2011;2(6):818–36.
Article
CAS
Google Scholar
Bechhofer DH. Messenger RNA decay and maturation in Bacillus subtilis. Prog Mol Biol Transl Sci. 2009;85:231–73.
Article
CAS
Google Scholar
Mathy N, Benard L, Pellegrini O, Daou R, Wen T, Condon C. 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell. 2007;129(4):681–92.
Article
CAS
Google Scholar
Andrade JM, Hajnsdorf E, Régnier P, Arraiano CM. The poly(a)-dependent degradation pathway of rpsO mRNA is primarily mediated by RNase R. RNA. 2009;15(2):316–26.
Article
CAS
Google Scholar
Mohanty BK, Kushner SR. Polynucleotide phosphorylase functions both as a 3′ right-arrow 5′ exonuclease and a poly(a) polymerase in Escherichia coli. Proc Natl Acad Sci U S A. 2000;97(22):11966–71.
Article
CAS
Google Scholar
Godefroy T. Kinetics of polymerization and phosphorolysis reactions of Escherichia coli polynucleotide phosphorylase. Evidence for multiple binding of polynucleotide in phosphorolysis. Eur J Biochem. 1970;14(2):222–31.
Article
CAS
Google Scholar
Grunberg-Manago M, Oritz PJ, Ochoa S. Enzymatic synthesis of nucleic acidlike polynucleotides. Science. 1955;122(3176):907–10.
Article
CAS
Google Scholar
Spickler C, Mackie A. Action of RNases II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure. J Bacteriol. 2000;182:2422–7.
Article
CAS
Google Scholar
Frazao C, McVey CE, Amblar M, Barbas A, Vonrhein C, Arraiano CM, Carrondo MA. Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex. Nature. 2006;443(7107):110–4.
Article
CAS
Google Scholar
Andrade JM, Cairrão F, Arraiano CM. RNase R affects gene expression in stationary phase: regulation of ompA. Mol Microbiol. 2006;60(1):219–28.
Article
CAS
Google Scholar
Cairrão F, Cruz A, Mori H, Arraiano CM. Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA. Mol Microbiol. 2003;50(4):1349–60.
Article
Google Scholar
Chen C, Deutscher MP. Elevation of RNase R in response to multiple stress conditions. J Biol Chem. 2005;280(41):34393–6.
Article
CAS
Google Scholar
Cheng ZF, Zuo Y, Li Z, Rudd KE, Deutscher MP. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J Biol Chem. 1998;273(23):14077–80.
Article
CAS
Google Scholar
Donovan WP, Kushner SR. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1986;83:120–4.
Article
CAS
Google Scholar
Clements MO, Eriksson S, Thompson A, Lucchini S, Hinton JC, Normark S, Rhen M. Polynucleotide phosphorylase is a global regulator of virulence and persistency in Salmonella enterica. Proc Natl Acad Sci U S A. 2002;99(13):8784–9.
Article
CAS
Google Scholar
Erova TE, Kosykh VG, Fadl AA, Sha J, Horneman AJ, Chopra AK. Cold shock exoribonuclease R (VacB) is involved in Aeromonas hydrophila pathogenesis. J Bacteriol. 2008;190(10):3467–74.
Article
CAS
Google Scholar
Haddad N, Tresse O, Rivoal K, Chevret D, Nonglaton Q, Burns CM, Prévost H, Cappelier JM. Polynucleotide phosphorylase has an impact on cell biology of Campylobacter jejuni. Front Cell Inf Microbiol. 2012;2:30. https://doi.org/10.3389/fcimb.2012.00030.
Tobe T, Sasakawa C, Okada N, Honma Y, Yoshikawa M. vacB, a novel chromosomal gene required for expression of virulence genes on the large plasmid of Shigella flexneri. J Bacteriol. 1992;174(20):6359–67.
Article
CAS
Google Scholar
Haddad N, Matos RG, Pinto T, Rannou P, Cappelier JM, Prevost H, Arraiano CM. The RNase R from Campylobacter jejuni has unique features and is involved in the first steps of infection. J Biol Chem. 2014;289(40):27814–24.
Article
CAS
Google Scholar
Andrade JM, Arraiano CM. PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins. RNA. 2008;14(3):543–51.
Article
CAS
Google Scholar
Andrade JM, Pobre V, Matos AM, Arraiano CM. The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq. RNA. 2012;18(4):844–55.
Article
CAS
Google Scholar
Andrade JM, Pobre V, Arraiano CM. Small RNA modules confer different stabilities and interact differently with multiple targets. PLoS One. 2013;8(1):e52866.
Article
CAS
Google Scholar
Liang W, Deutscher MP. Ribosomes regulate the stability and action of RNase R. J Biol Chem. 2013;288(48):34791–8.
Article
CAS
Google Scholar
Malecki M, Bárria C, Arraiano CM. Characterization of the RNase R association with ribosomes. BMC Microbiol. 2014;14:34.
Article
Google Scholar
Liang W, Malhotra A, Deutscher MP. Acetylation regulates the stability of a bacterial protein: growth stage-dependent modification of RNase R. Mol Cell. 2011;44(1):160–6.
Article
CAS
Google Scholar
Bandyra KJ, Sinha D, Syrjanen J, Luisi BF, De Lay NR. The ribonuclease polynucleotide phosphorylase can interact with small regulatory RNAs in both protective and degradative modes. RNA. 2016;22(3):360–72.
Article
CAS
Google Scholar
Bernstein JA, Lin PH, Cohen SN, Lin-Chao S. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc Natl Acad Sci U S A. 2004;101(9):2758–63.
Article
CAS
Google Scholar
Fonseca P, Moreno R, Rojo F. Genomic analysis of the role of RNase R in the turnover of Pseudomonas putida mRNAs. J Bacteriol. 2008;190(18):6258–63.
Article
CAS
Google Scholar
Liu B, Deikus G, Bree A, Durand S, Kearns DB, Bechhofer DH. Global analysis of mRNA decay intermediates in Bacillus subtilis wild-type and polynucleotide phosphorylase-deletion strains. Mol Microbiol. 2014;94(1):41–55.
Article
CAS
Google Scholar
Mohanty BK, Kushner SR. Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. Mol Microbiol. 2003;50(2):645–58.
Article
CAS
Google Scholar
Pobre V, Arraiano CM. Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli. BMC Genomics. 2015;16:72.
Article
Google Scholar
Chen H, Shiroguchi K, Ge H, Xie XS. Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. Mol Syst Biol. 2015;11(5):808 n/a.
Article
Google Scholar
Moffitt JR, Pandey S, Boettiger AN, Wang S, Zhuang X. Spatial organization shapes the turnover of a bacterial transcriptome. Elife. 2016:5. https://doi.org/10.7554/eLife.13065.
Dressaire C, Picard F, Redon E, Loubiere P, Queinnec I, Girbal L, Cocaign-Bousquet M. Role of mRNA stability during bacterial adaptation. PLoS One. 2013;8(3):e59059.
Article
CAS
Google Scholar
Nurmohamed S, Vincent HA, Titman CM, Chandran V, Pears MR, Du D, Griffin JL, Callaghan AJ, Luisi BF. Polynucleotide phosphorylase activity may be modulated by metabolites in Escherichia coli. J Biol Chem. 2011;286(16):14315–23.
Article
CAS
Google Scholar
Viegas SC, Pfeiffer V, Sittka A, Silva IJ, Vögel J, Arraiano CM. Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Res. 2007;35(22):7651–64.
Article
CAS
Google Scholar
Liu MY, Gui G, Wei B, Preston JF 3rd, Oakford L, Yuksel U, Giedroc DP, Romeo T. The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. J Biol Chem. 1997;272(28):17502–10.
Article
CAS
Google Scholar
Yakhnin AV, Baker CS, Vakulskas CA, Yakhnin H, Berezin I, Romeo T, Babitzke P. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage. Mol Microbiol. 2013;87(4):851–66.
Article
CAS
Google Scholar
Esquerre T, Bouvier M, Turlan C, Carpousis AJ, Girbal L, Cocaign-Bousquet M. The Csr system regulates genome-wide mRNA stability and transcription and thus gene expression in Escherichia coli. Sci Rep. 2016;6:25057.
Article
CAS
Google Scholar
Nouaille S, Mondeil S, Finoux AL, Moulis C, Girbal L, Cocaign-Bousquet M. The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression. Nucleic Acids Res. 2017;45(20):11711–24.
Article
CAS
Google Scholar
Bowden KE, Wiese NS, Perwez T, Mohanty BK, Kushner SR. The rph-1-encoded truncated RNase PH protein inhibits RNase P maturation of pre-tRNAs with short leader sequences in the absence of RppH. J Bacteriol. 2017;199(22). https://doi.org/10.1128/JB.00301-17.
Carpousis AJ. The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol. 2007;61:71–87.
Article
CAS
Google Scholar
De Lay N, Gottesman S. Role of polynucleotide phosphorylase in sRNA function in Escherichia coli. RNA. 2011;17(6):1172–89.
Article
CAS
Google Scholar
Saramago M, Bárria C, Dos Santos RF, Silva IJ, Pobre V, Domingues S, Andrade JM, Viegas SC, Arraiano CM. The role of RNases in the regulation of small RNAs. Curr Opin Microbiol. 2014;18:105–15.
Article
CAS
Google Scholar
Park H, Yakhnin H, Connolly M, Romeo T, Babitzke P. CsrA participates in a PNPase autoregulatory mechanism by selectively repressing translation of pnp transcripts that have been previously processed by RNase III and PNPase. J Bacteriol. 2015;197(24):3751–9.
Article
CAS
Google Scholar
Marujo PE, Hajnsdorf E, Le Derout J, Andrade R, Arraiano CM, Régnier P. RNase II removes the oligo(a) tails that destabilize the rpsO mRNA of Escherichia coli. RNA. 2000;6(8):1185–93.
Article
CAS
Google Scholar
Rustad TR, Minch KJ, Brabant W, Winkler JK, Reiss DJ, Baliga NS, Sherman DR. Global analysis of mRNA stability in Mycobacterium tuberculosis. Nucleic Acids Res. 2013;41(1):509–17.
Article
CAS
Google Scholar
Esquerre T, Moisan A, Chiapello H, Arike L, Vilu R, Gaspin C, Cocaign-Bousquet M, Girbal L. Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates. BMC Genomics. 2015;16:275.
Article
Google Scholar
Arraiano CM, Yancey SD, Kushner SR. Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12. J Bacteriol. 1988;170(10):4625–33.
Article
CAS
Google Scholar
Sambrook J, Russell D. Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2001.
Google Scholar
Gautier L, Cope L, Bolstad BM, Irizarry RA. Affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004;20(3):307–15.
Article
CAS
Google Scholar
Smyth GK, Michaud J, Scott HS. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics. 2005;21(9):2067–75.
Article
CAS
Google Scholar
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4(2):249–64.
Article
Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol. 1995;57(1):289–300.
Google Scholar
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics. 2000;16(10):944–5.
Article
CAS
Google Scholar
Edgar R, Domrachev M, Lash AE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30(1):207–10.
Article
CAS
Google Scholar