title: The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress.
abstract: As an intracellular human pathogen, Mycobacterium tuberculosis (Mtb) is facing multiple stressful stimuli inside the macrophage and the granuloma. Understanding Mtb responses to stress is essential to identify new virulence factors and pathways that play a role in the survival of the tubercle bacillus. The main goal of this study was to map the regulatory networks of differentially expressed (DE) transcripts in Mtb upon various forms of genotoxic stress. We exposed Mtb cells to oxidative (H2O2or paraquat), nitrosative (DETA/NO), or alkylation (MNNG) stress or mitomycin C, inducing double-strand breaks in the DNA. Total RNA was isolated from treated and untreated cells and subjected to high-throughput deep sequencing. The data generated was analysed to identify DE genes encoding mRNAs, non-coding RNAs (ncRNAs), and the genes potentially targeted by ncRNAs.
  
  
  
  The most significant transcriptomic alteration with more than 700 DE genes was seen under nitrosative stress. In addition to genes that belong to the replication, recombination and repair (3R) group, mainly found under mitomycin C stress, we identified DE genes important for bacterial virulence and survival, such as genes of the type VII secretion system (T7SS) and the proline-glutamic acid/proline-proline-glutamic acid (PE/PPE) family. By predicting the structures of hypothetical proteins (HPs) encoded by DE genes, we found that some of these HPs might be involved in mycobacterial genome maintenance. We also applied a state-of-the-art method to predict potential target genes of the identified ncRNAs and found that some of these could regulate several genes that might be directly involved in the response to genotoxic stress.
  
  
  
  Our study reflects the complexity of the response of Mtb in handling genotoxic stress. In addition to genes involved in genome maintenance, other potential key players, such as the members of the T7SS and PE/PPE gene family, were identified. This plethora of responses is detected not only at the level of DE genes encoding mRNAs but also at the level of ncRNAs and their potential targets.
authors.affiliation: Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.
authors.forename: Amine
authors.initials: A
authors.lastname: Namouchi
authors.affiliation: Department of Microbiology, University of Oslo, Oslo, Norway.
authors.forename: Marta
authors.initials: M
authors.lastname: Gómez-Muñoz
authors.affiliation: Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.
authors.forename: Stephan A
authors.initials: SA
authors.lastname: Frye
authors.affiliation: Department of Informatics, University of Oslo, Oslo, Norway.|Current address: Department of Nutrition, University of Oslo, Oslo, Norway.
authors.forename: Line Victoria
authors.initials: LV
authors.lastname: Moen
authors.affiliation: Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.|Department of Informatics, University of Oslo, Oslo, Norway.
authors.forename: Torbjørn
authors.initials: T
authors.lastname: Rognes
authors.affiliation: Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.|Department of Microbiology, University of Oslo, Oslo, Norway.
authors.forename: Tone
authors.initials: T
authors.lastname: Tønjum
authors.affiliation: Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway. sbala@rr-research.no.
authors.forename: Seetha V
authors.initials: SV
authors.lastname: Balasingham
mesh_terms: D016000:Cluster Analysis; D004249:DNA Damage / Q000187:drug effects; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D006801:Humans; D006861:Hydrogen Peroxide / Q000633:toxicity; D008769:Methylnitronitrosoguanidine / Q000633:toxicity; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000235:genetics*; D059467:Transcriptome; D000069377:Type VII Secretion Systems / Q000235:genetics
chemical_list: D000069377:Type VII Secretion Systems; D008769:Methylnitronitrosoguanidine; D006861:Hydrogen Peroxide
keywords: Genotoxic stress; Mycobacterium tuberculosis; Non-coding RNA (ncRNA); RNA deep-sequencing; Transcriptomics