1. Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen [i]Streptococcus agalactiae[/i]
- Author
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Adrien Villain, Philippe Glaser, Elisabeth Sauvage, Philippe Bouloc, Violette Da Cunha, Marie-Frédérique Lartigue, Marie-Elise Caliot, Isabelle Rosinski-Chupin, Patrick Trieu-Cuot, Odile Sismeiro, Marie-Agnès Dillies, Biologie des Bactéries pathogènes à Gram-positif, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Transcriptome et Epigénome (PF2), Institut Pasteur [Paris], Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), French National Research Agency ANR-13-PRTS-0006-04 - Labex IBEID, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, UR Infectiologie animale et Santé publique (UR IASP), Institut National de la Recherche Agronomique (INRA), Rosinski-Chupin, Isabelle, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Transcriptome et Epigénome ( PF2 ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), UR Infectiologie animale et Santé publique ( UR IASP ), Institut National de la Recherche Agronomique ( INRA ), Centre Hospitalier Régional Universitaire de Tours ( CHRU TOURS ), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), and Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Deep sequencing ,csRNAs ,Biology ,medicine.disease_cause ,Transcriptome ,03 medical and health sciences ,[ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology ,Transcription (biology) ,Antisense transcription ,Operon ,séquençage ,Genetics ,medicine ,Non coding RNAs ,Gene Regulatory Networks ,RNA, Messenger ,Gene ,030304 developmental biology ,Regulation of gene expression ,0303 health sciences ,Nucleotides ,Sequence Analysis, RNA ,030306 microbiology ,Gene Expression Profiling ,Reiterative transcription ,Microbiology and Parasitology ,High-Throughput Nucleotide Sequencing ,RNA ,Promoter ,Gene Expression Regulation, Bacterial ,mécanisme de régulation ,Microbiologie et Parasitologie ,RNA, Bacterial ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Streptococcus agalactiae ,Genes, Bacterial ,Riboswitches ,CRISPR ,streptococcus agalactiae ,Promoters ,transcription ,Research Article ,Biotechnology - Abstract
Background Streptococcus agalactiae, or Group B Streptococcus, is a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. In an effort to reconstruct the transcriptional networks involved in S. agalactiae physiology and pathogenesis, we performed an extensive and robust characterization of its transcriptome through a combination of differential RNA-sequencing in eight different growth conditions or genetic backgrounds and strand-specific RNA-sequencing. Results Our study identified 1,210 transcription start sites (TSSs) and 655 transcript ends as well as 39 riboswitches and cis-regulatory regions, 39 cis-antisense non-coding RNAs and 47 small RNAs potentially acting in trans. Among these putative regulatory RNAs, ten were differentially expressed in response to an acid stress and two riboswitches sensed directly or indirectly the pH modification. Strikingly, 15% of the TSSs identified were associated with the incorporation of pseudo-templated nucleotides, showing that reiterative transcription is a pervasive process in S. agalactiae. In particular, 40% of the TSSs upstream genes involved in nucleotide metabolism show reiterative transcription potentially regulating gene expression, as exemplified for pyrG and thyA encoding the CTP synthase and the thymidylate synthase respectively. Conclusions This comprehensive map of the transcriptome at the single nucleotide resolution led to the discovery of new regulatory mechanisms in S. agalactiae. It also provides the basis for in depth analyses of transcriptional networks in S. agalactiae and of the regulatory role of reiterative transcription following variations of intra-cellular nucleotide pools. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1583-4) contains supplementary material, which is available to authorized users.
- Published
- 2015