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; Laurence Ma; Magali  Tichit; Christiane Bouchier; Patrick Van Dijck; Carol A. Munro; Christophe d'Enfert

doi:10.1093/nar/gky594

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. JulienLaurence Ma, Magali Tichit, Christiane Bouchier, Patrick Van Dijck, Carol A. Munro (Corresponding Author), Christophe d'Enfert (Corresponding Author)

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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 language	English
Pages (from-to)	6935-6949
Number of pages	14
Journal	Nucleic Acids Research
Volume	46
Issue number	14
Early online date	6 Jul 2018
DOIs	https://doi.org/10.1093/nar/gky594 https://doi.org/10.1093/nar/gky747
Publication status	Published - 21 Aug 2018

Keywords

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

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10.1093/nar/gky594Licence: CC BY
10.1093/nar/gky747Licence: CC BY

Generating genomic platforms to study Candida albicans pathogenesis
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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Corrigendum
(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.
Other version, 75.2 KBLicence: CC BY

Carol Munro
- School of Medicine, Medical Sciences & Nutrition, Medical Sciences - Personal Chair
- Institute of Medical Sciences
Person: Academic

Cite this

Legrand, M., Bachellier-Bassi, S., Lee, K. K., Chaudhari, Y., Tournu, H., Arbogast, L., Boyer, H., Chauvel, M., Cabral, V., Maufrais, C., Nesseir, A., Maslanka, I., Permal, E., Rossignol, T., Walker, L. A., Zeidler, U., Znaidi, S., Schoeters, F., Majgier, C., ... 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

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

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title = "Generating genomic platforms to study Candida albicans pathogenesis",

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{\texttrademark} 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{\texttrademark}-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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author = "M{\'e}lanie Legrand and Sophie Bachellier-Bassi and Lee, {Keunsook K.} and Yogesh Chaudhari and H{\'e}l{\`e}ne Tournu and Laurence Arbogast and H{\'e}l{\`e}ne Boyer and Murielle Chauvel and Vitor Cabral and Corinne Maufrais and Audrey Nesseir and Irena Maslanka and Emmanuelle Permal and Tristan Rossignol and Walker, {Louise A.} and Ute Zeidler and Sadri Znaidi and Floris Schoeters and Charlotte Majgier and Julien, {Renaud A.} and Laurence Ma and Magali Tichit and Christiane Bouchier and Dijck, {Patrick Van} and Munro, {Carol A.} and Christophe d'Enfert",

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{\textquoteright}s Investissement d{\textquoteright}Avenir program (Laboratoire d{\textquoteright}Excellence Integrative Biology of Emerging Infectious Diseases, ANR-10-LABX-62-IBEID).",

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T1 - Generating genomic platforms to study Candida albicans pathogenesis

AU - Legrand, Mélanie

AU - Bachellier-Bassi, Sophie

AU - Lee, Keunsook K.

AU - Chaudhari, Yogesh

AU - Tournu, Hélène

AU - Arbogast, Laurence

AU - Boyer, Hélène

AU - Chauvel, Murielle

AU - Cabral, Vitor

AU - Maufrais, Corinne

AU - Nesseir, Audrey

AU - Maslanka, Irena

AU - Permal, Emmanuelle

AU - Rossignol, Tristan

AU - Walker, Louise A.

AU - Zeidler, Ute

AU - Znaidi, Sadri

AU - Schoeters, Floris

AU - Majgier, Charlotte

AU - Julien, Renaud A.

AU - Ma, Laurence

AU - Tichit, Magali

AU - Bouchier, Christiane

AU - Dijck, Patrick Van

AU - Munro, Carol A.

AU - d'Enfert, Christophe

N1 - 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 Région 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 Génomique 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).

PY - 2018/8/21

Y1 - 2018/8/21

N2 - 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.

AB - 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.

KW - ORFeome

KW - Candida albicans

KW - Two-hybrid system

KW - Gateway recombination cloning system

KW - Database

U2 - 10.1093/nar/gky594

DO - 10.1093/nar/gky594

M3 - Article

VL - 46

SP - 6935

EP - 6949

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 14

ER -

Generating genomic platforms to study Candida albicans pathogenesis

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