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Piel L, Rajan KS, Bussotti G, Varet H, Legendre R, Proux C, Douché T, Giai-Gianetto Q, Chaze T, Cokelaer T, Vojtkova B, Gordon-Bar N, Doniger T, Cohen-Chalamish S, Rengaraj P, Besse C, Boland A, Sadlova J, Deleuze JF, Matondo M, Unger R, Volf P, Michaeli S, Pescher P, Späth GF. Experimental evolution links post-transcriptional regulation to Leishmania fitness gain. PLoS Pathog 2022; 18:e1010375. [PMID: 35294501 PMCID: PMC8959184 DOI: 10.1371/journal.ppat.1010375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/28/2022] [Accepted: 02/15/2022] [Indexed: 12/30/2022] Open
Abstract
The protozoan parasite Leishmania donovani causes fatal human visceral leishmaniasis in absence of treatment. Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy. How genome instability generates beneficial phenotypes despite potential deleterious gene dosage effects is unknown. Here we address this important open question applying experimental evolution and integrative systems approaches on parasites adapting to in vitro culture. Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth in promastigote culture (fitness gain) impairing infectivity (fitness costs). Comparative genomics, transcriptomics and proteomics analyses revealed a complex regulatory network associated with parasite fitness gain, with genome instability causing highly reproducible, gene dosage-independent and -dependent changes. Reduction of flagellar transcripts and increase in coding and non-coding RNAs implicated in ribosomal biogenesis and protein translation were not correlated to dosage changes of the corresponding genes, revealing a gene dosage-independent, post-transcriptional mechanism of regulation. In contrast, abundance of gene products implicated in post-transcriptional regulation itself correlated to corresponding gene dosage changes. Thus, RNA abundance during parasite adaptation is controled by direct and indirect gene dosage changes. We correlated differential expression of small nucleolar RNAs (snoRNAs) with changes in rRNA modification, providing first evidence that Leishmania fitness gain in culture may be controlled by post-transcriptional and epitranscriptomic regulation. Our findings propose a novel model for Leishmania fitness gain in culture, where differential regulation of mRNA stability and the generation of modified ribosomes may potentially filter deleterious from beneficial gene dosage effects and provide proteomic robustness to genetically heterogenous, adapting parasite populations. This model challenges the current, genome-centric approach to Leishmania epidemiology and identifies the Leishmania transcriptome and non-coding small RNome as potential novel sources for the discovery of biomarkers that may be associated with parasite phenotypic adaptation in clinical settings. Genome instability plays a central yet poorly understood role in human disease. Gene amplifications and deletions drive cancer development, microbial infection and therapeutic failure. The molecular mechanisms that harness the deleterious effects of genome instability to generate beneficial phenotypes in pathogenic systems are unknown. Here we study this important open question in the protozoan parasite Leishmania that causes devastating human diseases termed leishmaniases. Leishmania parasites lack transcriptional control and instead exploit genome instability to adapt to their host environment. Analyzing in vitro adaptation of hamster-derived parasites via gene copy number (genomic level) and gene expression changes (transcriptomic and proteomic levels), we show that these parasites likely exploit small nucleolar RNAs (snoRNAs) to mitigate toxic effects of genome instability by post-transcriptional regulation and the establishment of modified ribosomes. Our findings propose non-coding RNAs as potential novel biomarkers with diagnostic and prognostic value that may be linked to changes in parasite tissue tropism or drug susceptibility. This novel insight into Leishmania adaptation will be likely applicable to other fast evolving eukaryotic systems with unstable genomes, such as fungi or cancer cells.
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Affiliation(s)
- Laura Piel
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
| | - K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Giovanni Bussotti
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
| | - Hugo Varet
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Caroline Proux
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Quentin Giai-Gianetto
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Thibault Chaze
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Barbora Vojtkova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Nadav Gordon-Bar
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Praveenkumar Rengaraj
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Céline Besse
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Jovana Sadlova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Mariette Matondo
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Pascale Pescher
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- * E-mail: (PP); (GS)
| | - Gerald F. Späth
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- * E-mail: (PP); (GS)
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Teixeira DG, Monteiro GRG, Martins DRA, Fernandes MZ, Macedo-Silva V, Ansaldi M, Nascimento PRP, Kurtz MA, Streit JA, Ximenes MFFM, Pearson RD, Miles A, Blackwell JM, Wilson ME, Kitchen A, Donelson JE, Lima JPMS, Jeronimo SMB. Comparative analyses of whole genome sequences of Leishmania infantum isolates from humans and dogs in northeastern Brazil. Int J Parasitol 2017; 47:655-665. [PMID: 28606698 PMCID: PMC5641220 DOI: 10.1016/j.ijpara.2017.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 04/01/2017] [Accepted: 04/06/2017] [Indexed: 12/30/2022]
Abstract
The genomic sequences of 20 Leishmania infantum isolates collected in northeastern Brazil were compared with each other and with the available genomic sequences of 29 L. infantum/donovani isolates from Nepal and Turkey. The Brazilian isolates were obtained in the early 1990s or since 2009 from patients with visceral or non-ulcerating cutaneous leishmaniasis, asymptomatic humans, or dogs with visceral leishmaniasis. Two isolates were from the blood and bone marrow of the same visceral leishmaniasis patient. All 20 genomic sequences display 99.95% identity with each other and slightly less identity with a reference L. infantum genome from a Spanish isolate. Despite the high identity, analysis of individual differences among the 32 million base pair genomes showed sufficient variation to allow the isolates to be clustered based on the primary sequence. A major source of variation detected was in chromosome somy, with only four of the 36 chromosomes being predominantly disomic in all 49 isolates examined. In contrast, chromosome 31 was predominantly tetrasomic/pentasomic, consistent with its regions of synteny on two different disomic chromosomes of Trypanosoma brucei. In the Brazilian isolates, evidence for recombination was detected in 27 of the 36 chromosomes. Clustering analyses suggested two populations, in which two of the five older isolates from the 1990s clustered with a majority of recent isolates. Overall the analyses do not suggest individual sequence variants account for differences in clinical outcome or adaptation to different hosts. For the first known time, DNA of isolates from asymptomatic subjects were sequenced. Of interest, these displayed lower diversity than isolates from symptomatic subjects, an observation that deserves further investigation with additional isolates from asymptomatic subjects.
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Affiliation(s)
- D G Teixeira
- Department of Biochemistry, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Rio Grande do Norte, Brazil; Institute of Tropical Medicine of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - G R G Monteiro
- Institute of Tropical Medicine of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - D R A Martins
- Department of Biochemistry, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Rio Grande do Norte, Brazil; Department of Cellular Biology and Genetics, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - M Z Fernandes
- Department of Internal Medicine, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - V Macedo-Silva
- Department of Biochemistry, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Rio Grande do Norte, Brazil
| | - M Ansaldi
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - P R P Nascimento
- Department of Biochemistry, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Rio Grande do Norte, Brazil
| | - M A Kurtz
- Veterans' Affairs Medical Center, Iowa City, IA, USA
| | - J A Streit
- Veterans' Affairs Medical Center, Iowa City, IA, USA; Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - M F F M Ximenes
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - R D Pearson
- Division of Infectious Disease, Department of Internal Medicine, University of Virginia, Charlottesville, VA, USA
| | - A Miles
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - J M Blackwell
- Telethon Institute for Child Health, University of Western Australia, Perth, WA, Australia
| | - M E Wilson
- Veterans' Affairs Medical Center, Iowa City, IA, USA; Department of Internal Medicine, University of Iowa, Iowa City, IA, USA; Departments of Microbiology and Epidemiology, University of Iowa, Iowa City, IA, USA
| | - A Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA, USA
| | - J E Donelson
- Institute of Tropical Medicine of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; Department of Biochemistry, University of Iowa, Iowa City, IA, USA
| | - J P M S Lima
- Department of Biochemistry, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Rio Grande do Norte, Brazil; Institute of Tropical Medicine of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - S M B Jeronimo
- Department of Biochemistry, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, Rio Grande do Norte, Brazil; Institute of Tropical Medicine of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil; National Institute of Science and Technology of Tropical Diseases, Natal, Rio Grande do Norte, Brazil.
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