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Giraud-Gatineau A, Ayachit G, Nieves C, Dagbo KC, Bourhy K, Pulido F, Huete SG, Benaroudj N, Picardeau M, Veyrier FJ. Inter-species Transcriptomic Analysis Reveals a Constitutive Adaptation Against Oxidative Stress for the Highly Virulent Leptospira Species. Mol Biol Evol 2024; 41:msae066. [PMID: 38573174 PMCID: PMC11021026 DOI: 10.1093/molbev/msae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
Transcriptomic analyses across large scales of evolutionary distance have great potential to shed light on regulatory evolution but are complicated by difficulties in establishing orthology and limited availability of accessible software. We introduce here a method and a graphical user interface wrapper, called Annotator-RNAtor, for performing interspecies transcriptomic analysis and studying intragenus evolution. The pipeline uses third-party software to infer homologous genes in various species and highlight differences in the expression of the core-genes. To illustrate the methodology and demonstrate its usefulness, we focus on the emergence of the highly virulent Leptospira subclade known as P1+, which includes the causative agents of leptospirosis. Here, we expand on the genomic study through the comparison of transcriptomes between species from P1+ and their related P1- counterparts (low-virulent pathogens). In doing so, we shed light on differentially expressed pathways and focused on describing a specific example of adaptation based on a differential expression of PerRA-controlled genes. We showed that P1+ species exhibit higher expression of the katE gene, a well-known virulence determinant in pathogenic Leptospira species correlated with greater tolerance to peroxide. Switching PerRA alleles between P1+ and P1- species demonstrated that the lower repression of katE and greater tolerance to peroxide in P1+ species was solely controlled by PerRA and partly caused by a PerRA amino-acid permutation. Overall, these results demonstrate the strategic fit of the methodology and its ability to decipher adaptive transcriptomic changes, not observable by comparative genome analysis, that may have been implicated in the emergence of these pathogens.
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Affiliation(s)
- Alexandre Giraud-Gatineau
- Microbiology Department, Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
| | - Garima Ayachit
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Cecilia Nieves
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Kouessi C Dagbo
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Konogan Bourhy
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Francisco Pulido
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
| | - Samuel G Huete
- Microbiology Department, Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
| | - Nadia Benaroudj
- Microbiology Department, Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
| | - Mathieu Picardeau
- Microbiology Department, Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
| | - Frédéric J Veyrier
- INRS-Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec H7V 1B7, Canada
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