The epidemiology of severe Streptococcus pyogenes associated disease in Europe, Euro Surveill Bull Eur Sur Mal Transm Eur Commun Dis Bull, vol.10, pp.179-84, 2005. ,
The serotypes of Streptococcus pyogenes present in Britain during 1980-1990 and their association with disease, J Med Microbiol, vol.39, pp.165-78, 1993. ,
Evolutionary pathway to increased virulence and epidemic group a Streptococcus disease derived from 3,615 genome sequences, Proc Natl Acad Sci U S A, vol.111, pp.1768-76, 2014. ,
Evolutionary origin and emergence of a highly successful clone of serotype M1 group a Streptococcus involved multiple horizontal gene transfer events, J Infect Dis, vol.192, pp.771-82, 2005. ,
A molecular trigger for intercontinental epidemics of group a Streptococcus, J Clin Invest, vol.125, pp.3545-59, 2015. ,
Natural variation in the promoter of the gene encoding the Mga regulator alters host-pathogen interactions in group a Streptococcus carrier strains, Infect Immun, vol.81, pp.4128-4166, 2013. ,
Natural disruption of two regulatory networks in serotype M3 group a Streptococcus isolates contributes to the virulence factor profile of this hypervirulent serotype, Infect Immun, vol.82, pp.1744-54, 2014. ,
Transcriptome remodeling contributes to epidemic disease caused by the human pathogen Streptococcus pyogenes, mBio, vol.7, pp.403-419, 2016. ,
Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations, Proc Natl Acad Sci U S A, vol.108, pp.5039-5083, 2011. ,
Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae, BMC Genomics, vol.16, p.419, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01169621
The Streptococcus suis transcriptional landscape reveals adaptation mechanisms in pig blood and cerebrospinal fluid, RNA N Y N, vol.20, pp.882-98, 2014. ,
Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39, Nucleic Acids Res, 2018. ,
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III, Nature, vol.471, pp.602-609, 2011. ,
RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes, RNA Biol, vol.13, pp.177-95, 2016. ,
High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs, PLoS One, vol.3, p.3197, 2008. ,
sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes, Nucleic Acids Res, vol.33, pp.4096-105, 2005. ,
Identification of novel growth phase-and media-dependent small noncoding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays, BMC Genomics, vol.13, p.550, 2012. ,
A genome-wide analysis of small regulatory RNAs in the human pathogen group a Streptococcus, PLoS One, vol.4, p.7668, 2009. ,
Non-coding RNA detection methods combined to improve usability, reproducibility and precision, BMC Bioinformatics, vol.11, p.491, 2010. ,
Novel regulatory small RNAs in Streptococcus pyogenes, PLoS One, vol.8, p.64021, 2013. ,
Group a streptococcal growth phase-associated virulence factor regulation by a novel operon (Fas) with homologies to two-component-type regulators requires a small RNA molecule, Mol Microbiol, vol.39, pp.392-406, 2001. ,
Synthesis of group a streptococcal virulence factors is controlled by a regulatory RNA molecule, Mol Microbiol, vol.53, pp.1515-1542, 2004. ,
The regulatory small RNA MarS supports virulence of Streptococcus pyogenes, Sci Rep, vol.7, p.12241, 2017. ,
RivR and the small RNA RivX: the missing links between the CovR regulatory cascade and the Mga regulon, Mol Microbiol, vol.66, pp.1506-1528, 2007. ,
Riboswitch discovery by combining RNA-seq and genome-wide identification of transcriptional start sites, Methods Enzymol, vol.549, pp.3-27, 2014. ,
Mg(2+) signalling defines the group a streptococcal CsrRS (CovRS) regulon, Mol Microbiol, vol.65, pp.671-83, 2007. ,
Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA, Nucleic Acids Res, vol.23, pp.2351-60, 1995. ,
Expression of the secondary sigma factor sigmaX in Streptococcus pyogenes is restricted at two levels, J Bacteriol, vol.185, pp.4291-4298, 2003. ,
Compilation and analysis of Escherichia coli promoter DNA sequences, Nucleic Acids Res, vol.11, pp.2237-55, 1983. ,
Attenuation control of pyrG expression in Bacillus subtilis is mediated by CTP-sensitive reiterative transcription, Proc Natl Acad Sci U S A, vol.101, pp.10943-10951, 2004. ,
Prediction of transcriptional terminators in Bacillus subtilis and related species, PLoS Comput Biol, vol.1, p.25, 2005. ,
ARNold: a web tool for the prediction of rho-independent transcription terminators, RNA Biol, vol.8, pp.11-14, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00590438
Rapid, accurate, computational discovery of rho-independent transcription terminators illuminates their relationship to DNA uptake, Genome Biol, vol.8, p.22, 2007. ,
Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes, Nucleic Acids Res, vol.45, pp.2329-2369, 2017. ,
PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader, EMBO J, vol.20, pp.6845-55, 2001. ,
The Holliday junction resolvase RecU is required for chromosome segregation and DNA damage repair in Staphylococcus aureus, BMC Microbiol, vol.13, p.18, 2013. ,
A novel adaptation of aldolase regulates virulence in Streptococcus pyogenes, EMBO J, vol.25, pp.5414-5436, 2006. ,
Mga is sufficient to activate transcription in vitro of sof-sfbX and other Mga-regulated virulence genes in the group a Streptococcus, J Bacteriol, vol.188, pp.2038-2085, 2006. ,
Defining the Mga regulon: comparative transcriptome analysis reveals both direct and indirect regulation by Mga in the group a streptococcus, Mol Microbiol, vol.62, pp.491-508, 2006. ,
RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B, RNA Biol, vol.15, pp.1336-1383, 2018. ,
Interference of a speB 5? untranslated region partial deletion with mRNA degradation in Streptococcus pyogenes, Mol Oral Microbiol, vol.32, pp.390-403, 2017. ,
Rfam 11.0: 10 years of RNA families, Nucleic Acids Res, pp.226-258, 2013. ,
RNA structures regulating ribosomal protein biosynthesis in bacilli, RNA Biol, vol.10, pp.1180-1184, 2013. ,
Dunin-Horkawicz S. S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA, RNA N Y N, vol.19, pp.1341-1348, 2013. ,
A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes, PLoS Comput Biol, vol.3, p.126, 2007. ,
Identification of the nature of reading frame transitions observed in prokaryotic genomes, Nucleic Acids Res, vol.41, pp.6514-6544, 2013. ,
Release factor 2 frameshifting sites in different bacteria, EMBO Rep, vol.3, pp.373-380, 2002. ,
Translational regulation of the L11 ribosomal protein operon of Escherichia coli: mutations that define the target site for repression by L1, Nucleic Acids Res, vol.15, pp.3085-96, 1987. ,
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs, RNA N Y N, vol.18, pp.900-914, 2012. ,
Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs, Nucleic Acids Res, vol.32, pp.3354-63, 2004. ,
Modulation of ribosomal recruitment to 5?-terminal start codons by translation initiation factors IF2 and IF3, FEBS Lett, vol.495, pp.167-71, 2001. ,
Temperature-dependent translation of leaderless and canonical mRNAs in Escherichia coli, FEMS Microbiol Lett, vol.211, pp.161-168, 2002. ,
Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli, Cell, vol.147, pp.147-57, 2011. ,
Conservation of transcription start sites within genes across a bacterial genus, mBio, vol.5, pp.1398-1412, 2014. ,
Mauve: multiple alignment of conserved genomic sequence with rearrangements, Genome Res, vol.14, pp.1394-403, 2004. ,
CovS/ CovR of group B streptococcus: a two-component global regulatory system involved in virulence, Mol Microbiol, vol.54, pp.1250-68, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00019892
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet J, vol.17, pp.10-12, 2011. ,
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, p.25, 2009. ,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinforma Oxf Engl, vol.26, pp.139-179, 2010. ,
Controlling the false discovery rate: a practical and powerful approach to multiple testing, J R Stat Soc Ser B Methodol, vol.57, pp.289-300, 1995. ,
Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration, Brief Bioinform, vol.14, pp.178-92, 2013. ,
Phylogenomics and the dynamic genome evolution of the genus Streptococcus, Genome Biol Evol, vol.6, pp.741-53, 2014. ,
MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets, Mol Biol Evol, vol.33, pp.1870-1874, 2016. ,
Leaderless secreted peptide signaling molecule alters global gene expression and increases virulence of a human bacterial pathogen, Proc Natl Acad Sci, 2017. ,