A. J. Carpousis, B. F. Luisi, and K. J. Mcdowall, Endonucleolytic initiation of mRNA decay in Escherichia coli, Prog. Mol. Biol. Transl. Sci, vol.85, pp.91-135, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00368990

S. Durand and C. Condon, RNases and helicases in Gram-positive bacteria, Microbiol. Spectr, vol.6, pp.37-53, 2018.

B. K. Mohanty and S. R. Kushner, Regulation of mRNA decay in bacteria, Annu. Rev. Microbiol, vol.70, pp.25-44, 2016.

U. Mäder, L. Zig, J. Kretschmer, G. Homuth, and H. Putzer, mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale, Mol. Microbiol, vol.70, pp.183-196, 2008.

J. V. Bugrysheva and J. R. Scott, The ribonucleases J1 and J2 are essential for growth and have independent roles in mRNA decay in Streptococcus pyogenes, Mol. Microbiol, vol.75, pp.731-743, 2010.

N. Mathy, 5'-to-3' exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5' stability of mRNA, Cell, vol.129, pp.681-692, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00159472

M. P. Deutscher, Twenty years of bacterial RNases and RNA processing: how we've matured, RNA, vol.21, pp.597-600, 2015.

Y. Chao, In vivo cleavage map illuminates the central role of RNase E in coding and non-coding RNA pathways, Mol. Cell, vol.65, pp.39-51, 2017.

K. Shahbabian, A. Jamalli, L. Zig, and H. Putzer, RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis, EMBO J, vol.28, pp.3523-3533, 2009.

V. Khemici, J. Prados, P. Linder, and P. Redder, Decay-initiating endoribonucleolytic cleavage by RNase Y is kept under tight control via sequence preference and sub-cellular localisation, PLoS Genet, vol.11, p.1005577, 2015.

L. Broglia, RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B, RNA Biol, vol.15, pp.1336-1347, 2018.

G. Marincola and C. Wolz, Downstream element determines RNase Y cleavage of the saePQRS operon in Staphylococcus aureus, Nucleic Acids Res, vol.45, pp.5980-5994, 2017.

J. M. Andrade, V. Pobre, I. J. Silva, S. Domingues, and C. M. Arraiano, The role of 3'-5' exoribonucleases in RNA degradation, Prog. Mol. Biol. Transl. Sci, vol.85, pp.187-229, 2009.

C. Chen and M. P. Deutscher, RNase R is a highly unstable protein regulated by growth phase and stress, RNA, vol.16, pp.667-672, 2010.

W. P. Donovan and S. R. Kushner, Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12, Proc. Natl Acad. Sci. USA, vol.83, pp.120-124, 1986.

I. A. Oussenko, T. Abe, H. Ujiie, A. Muto, and D. H. Bechhofer, Participation of 3'-to-5' exoribonucleases in the turnover of Bacillus subtilis mRNA, J. Bacteriol, vol.187, pp.2758-2767, 2005.

A. Lécrivain, In vivo 3?-to-5? exoribonuclease targetomes of Streptococcus pyogenes, Proc. Natl Acad. Sci. USA, vol.115, pp.11814-11819, 2018.

A. Deloughery, J. Lalanne, R. Losick, and G. Li, Maturation of polycistronic mRNAs by the endoribonuclease RNase Y and its associated Y-complex in Bacillus subtilis, Proc. Natl Acad. Sci. USA, vol.115, pp.5585-5594, 2018.

A. Le-rhun, Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes, Nucleic Acids Res, vol.45, pp.2329-2340, 2017.

J. Casinhas, R. G. Matos, N. Haddad, and C. M. Arraiano, Biochemical characterization of Campylobacter jejuni PNPase, an exoribonuclease important for bacterial pathogenicity, Biochimie, vol.147, pp.70-79, 2018.

C. Spickler and G. A. Mackie, Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure, J. Bacteriol, vol.182, pp.2422-2427, 2000.

Z. Li and M. P. Deutscher, Maturation pathways for E. coli tRNA precursors: a random multienzyme process in vivo, Cell, vol.86, pp.503-512, 1996.

R. S. Mclaren, S. F. Newbury, G. S. Dance, H. C. Causton, and C. F. Higgins, mRNA degradation by processive 3'-5' exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo, J. Mol. Biol, vol.221, pp.81-95, 1991.

B. Liu, D. B. Kearns, and D. H. Bechhofer, Expression of multiple Bacillus subtilis genes is controlled by decay of slrA mRNA from Rho-dependent 3' ends, Nucleic Acids Res, vol.44, pp.3364-3372, 2016.

H. Liao, M. Liu, and X. Guo, The special existences: nanoRNA and nanoRNase, Microbiol. Res, vol.207, pp.134-139, 2018.

T. A. Cameron, L. M. Matz, D. Sinha, and N. R. De-lay, Polynucleotide phosphorylase promotes the stability and function of Hfq-binding sRNAs by degrading target mRNA-derived fragments, Nucleic Acids Res, vol.46, pp.8821-8837, 2019.

B. C. Jester, P. Romby, and E. Lioliou, When ribonucleases come into play in pathogens: a survey of gram-positive bacteria, Int. J. Microbiol, vol.2012, p.592196, 2012.

Z. Chen, A. Itzek, H. Malke, J. J. Ferretti, and J. Kreth, Multiple roles of RNase Y in Streptococcus pyogenes mRNA processing and degradation, J. Bacteriol, vol.195, pp.2585-2594, 2013.

E. Salvo, S. Alabi, B. Liu, A. Schlessinger, and D. H. Bechhofer, Interaction of Bacillus subtilis Polynucleotide phosphorylase and RNase Y: structural mapping and effect on mRNA turnover, J. Biol. Chem, vol.291, pp.6655-6663, 2016.

S. Laalami, L. Zig, and H. Putzer, Initiation of mRNA decay in bacteria, Cell. Mol. Life Sci, vol.71, pp.1799-1828, 2014.

G. Deikus and D. H. Bechhofer, Initiation of decay of Bacillus subtilis trp leader RNA, J. Biol. Chem, vol.282, pp.20238-20244, 2007.

P. Bruscella, K. Shahbabian, S. Laalami, and H. Putzer, RNase Y is responsible for uncoupling the expression of translation factor IF3 from that of the ribosomal proteins L35 and L20 in Bacillus subtilis, Mol. Microbiol, vol.81, pp.1526-1541, 2011.

J. T. Robinson, Integrative genomics viewer, Nat. Biotechnol, vol.29, pp.24-26, 2011.

H. Thorvaldsdóttir, J. T. Robinson, and J. P. Mesirov, Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration, Brief. Bioinforma, vol.14, pp.178-192, 2013.

Y. Liao, G. K. Smyth, and W. Shi, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, vol.30, pp.923-930, 2014.

M. D. Robinson, D. J. Mccarthy, and G. K. Smyth, edgeR: a bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, pp.139-140, 2010.

D. J. Mccarthy, Y. Chen, and G. K. Smyth, Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation, Nucleic Acids Res, vol.40, pp.4288-4297, 2012.

R. Lorenz, ViennaRNA Package 2.0, Algorithms Mol. Biol, vol.6, p.26, 2011.

G. E. Crooks, G. Hon, J. Chandonia, and S. E. Brenner, WebLogo: a sequence logo generator, Genome Res, vol.14, pp.1188-1190, 2004.

A. Le-rhun, Y. Y. Beer, J. Reimegård, K. Chylinski, and E. Charpentier, RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes, RNA Biol, vol.13, pp.177-195, 2016.