Generating genomic platforms to study Candida albicans pathogenesis

Mélanie Legrand, Sophie Bachellier-Bassi, Keunsook K. Lee, Yogesh Chaudhari, Hélène Tournu, Laurence Arbogast, Hélène Boyer, Murielle Chauvel, Vitor Cabral, Corinne Maufrais, Audrey Nesseir, Irena Maslanka, Emmanuelle Permal, Tristan Rossignol, Louise A. Walker, Ute Zeidler, Sadri Znaidi, Floris Schoeters, Charlotte Majgier, Renaud A. Julien & 6 others Laurence Ma, Magali Tichit, Christiane Bouchier, Patrick Van Dijck, Carol A. Munro, Christophe d'Enfert

Research output: Contribution to journal › Article

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Abstract

The advent of the genomic era has made elucidating gene function on a large scale a pressing challenge. ORFeome collections, whereby almost all ORFs of a given species are cloned and can be subsequently leveraged in multiple functional genomic approaches, represent valuable resources towards this endeavor. Here we provide novel, genome-scale tools for the study of
Candida albicans, a commensal yeast that is also responsible for frequent superficial and disseminated infections in humans. We have generated an ORFeome collection composed of 5,099 ORFs cloned in a Gateway™ donor vector, representing 83% of the currently annotated coding sequences of C. albicans. Sequencing data of the cloned ORFs are available in the CandidaOrfDB database at http://candidaorfeome.eu. We also engineered 49 expression vectors with a choice of promoters, tags, and selection markers and demonstrated their applicability to the study of target ORFs transferred from the
C. albicans ORFeome. In addition, the use of the ORFeome in the detection of protein-protein interaction was demonstrated. Mating-compatible strains as well as Gateway™-compatible two-hybrid vectors were engineered, validated and used in a proof of concept experiment. These unique and valuable resources should greatly facilitate future functional studies in C. albicans and the elucidation of mechanisms that underlie its pathogenicity.
Original languageEnglish
Pages (from-to)6935-6949
Number of pages14
JournalNucleic Acids Research
Volume46
Issue number14
Early online date6 Jul 2018
DOIs
Publication statusPublished - 21 Aug 2018

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Candida albicans
Open Reading Frames
Virulence
Proteins
Yeasts
Genome
Databases
Infection
Genes

Keywords

  • ORFeome
  • Candida albicans
  • Two-hybrid system
  • Gateway recombination cloning system
  • Database

Cite this

Legrand, M., Bachellier-Bassi, S., Lee, K. K., Chaudhari, Y., Tournu, H., Arbogast, L., ... d'Enfert, C. (2018). Generating genomic platforms to study Candida albicans pathogenesis. Nucleic Acids Research, 46(14), 6935-6949. https://doi.org/10.1093/nar/gky594, https://doi.org/10.1093/nar/gky747

Generating genomic platforms to study Candida albicans pathogenesis. / Legrand, Mélanie; Bachellier-Bassi, Sophie; Lee, Keunsook K.; Chaudhari, Yogesh; Tournu, Hélène; Arbogast, Laurence; Boyer, Hélène; Chauvel, Murielle ; Cabral, Vitor ; Maufrais, Corinne; Nesseir, Audrey; Maslanka, Irena; Permal, Emmanuelle; Rossignol, Tristan; Walker, Louise A.; Zeidler, Ute; Znaidi, Sadri; Schoeters, Floris; Majgier, Charlotte; Julien, Renaud A.; Ma, Laurence; Tichit, Magali ; Bouchier, Christiane; Dijck, Patrick Van; Munro, Carol A. (Corresponding Author); d'Enfert, Christophe (Corresponding Author).

In: Nucleic Acids Research, Vol. 46, No. 14, 21.08.2018, p. 6935-6949.

Research output: Contribution to journal › Article

Legrand, M, Bachellier-Bassi, S, Lee, KK, Chaudhari, Y, Tournu, H, Arbogast, L, Boyer, H, Chauvel, M, Cabral, V, Maufrais, C, Nesseir, A, Maslanka, I, Permal, E, Rossignol, T, Walker, LA, Zeidler, U, Znaidi, S, Schoeters, F, Majgier, C, Julien, RA, Ma, L, Tichit, M, Bouchier, C, Dijck, PV, Munro, CA & d'Enfert, C 2018, 'Generating genomic platforms to study Candida albicans pathogenesis', Nucleic Acids Research, vol. 46, no. 14, pp. 6935-6949. https://doi.org/10.1093/nar/gky594, https://doi.org/10.1093/nar/gky747
Legrand M, Bachellier-Bassi S, Lee KK, Chaudhari Y, Tournu H, Arbogast L et al. Generating genomic platforms to study Candida albicans pathogenesis. Nucleic Acids Research. 2018 Aug 21;46(14):6935-6949. https://doi.org/10.1093/nar/gky594, https://doi.org/10.1093/nar/gky747
Legrand, Mélanie ; Bachellier-Bassi, Sophie ; Lee, Keunsook K. ; Chaudhari, Yogesh ; Tournu, Hélène ; Arbogast, Laurence ; Boyer, Hélène ; Chauvel, Murielle ; Cabral, Vitor ; Maufrais, Corinne ; Nesseir, Audrey ; Maslanka, Irena ; Permal, Emmanuelle ; Rossignol, Tristan ; Walker, Louise A. ; Zeidler, Ute ; Znaidi, Sadri ; Schoeters, Floris ; Majgier, Charlotte ; Julien, Renaud A. ; Ma, Laurence ; Tichit, Magali ; Bouchier, Christiane ; Dijck, Patrick Van ; Munro, Carol A. ; d'Enfert, Christophe. / Generating genomic platforms to study Candida albicans pathogenesis. In: Nucleic Acids Research. 2018 ; Vol. 46, No. 14. pp. 6935-6949.
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abstract = "The advent of the genomic era has made elucidating gene function on a large scale a pressing challenge. ORFeome collections, whereby almost all ORFs of a given species are cloned and can be subsequently leveraged in multiple functional genomic approaches, represent valuable resources towards this endeavor. Here we provide novel, genome-scale tools for the study ofCandida albicans, a commensal yeast that is also responsible for frequent superficial and disseminated infections in humans. We have generated an ORFeome collection composed of 5,099 ORFs cloned in a Gateway™ donor vector, representing 83{\%} of the currently annotated coding sequences of C. albicans. Sequencing data of the cloned ORFs are available in the CandidaOrfDB database at http://candidaorfeome.eu. We also engineered 49 expression vectors with a choice of promoters, tags, and selection markers and demonstrated their applicability to the study of target ORFs transferred from the C. albicans ORFeome. In addition, the use of the ORFeome in the detection of protein-protein interaction was demonstrated. Mating-compatible strains as well as Gateway™-compatible two-hybrid vectors were engineered, validated and used in a proof of concept experiment. These unique and valuable resources should greatly facilitate future functional studies in C. albicans and the elucidation of mechanisms that underlie its pathogenicity.",
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note = "This work has been supported by a Biomedical Resources grant from the Wellcome Trust (The Candida albicans ORFeome project, 088858/Z/09/Z to CAM and CD), the European Commission (FINSysB, PITN-GA-2008-214004 to CD), the Agence Nationale de la Recherche (KANJI, ANR-08-MIE-033-01 to CD; CANDICOL, ANR-10-01 to CD) and the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office for funding (IAP P7/28 to PVD). CAM would like to acknowledge support from a Medical Research Council New Investigator Award (G0400284) and the MRC Centre for Medical Mycology and the University of Aberdeen (MR/M026663/1). VC was the recipient of a PhD fellowship in the framework of the FINSysB consortium (PITN-A-2008-214004). AN was the recipient of a PhD fellowship from the DIM-MalInf R{\'e}gion Ile-de-France. EP was the recipient of a post-doctoral fellowship in the framework of the C. albicans ORFeome project (WT088858MA). TR was the recipient of a postdoctoral fellowship in the framework of the NPARI consortium (LSHE-CT-2006-037692). UZ was the recipient of a postdoctoral fellowship in the framework of Programme Fungi from Institut Carnot-Pasteur Maladies Infectieuses. SZ was the recipient from post-doctoral fellowships in the framework of the FINSysB (PITN-GA-2008-214004) and KANJI (ANR-08-MIE-033-01) consortia. HT was the recipient of a KU Leuven CREA grant (2011-2013). High throughput sequencing has been performed on the Genomics Platform, member of France G{\'e}nomique consortium (ANR10-INBS-09-08). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We acknowledge support from the French Government’s Investissement d’Avenir program (Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases, ANR-10-LABX-62-IBEID).",
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AU - Arbogast, Laurence

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    (C) The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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