Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts.

Carbon / metabolism Genome, Fungal Nitrogen / metabolism Metabolic Networks and Pathways / genetics Ascomycota / genetics

Journal

Science (New York, N.Y.)
ISSN: 1095-9203
Titre abrégé: Science
Pays: United States
ID NLM: 0404511

Informations de publication

Date de publication:
26 Apr 2024
Historique:
medline: 25 4 2024
pubmed: 25 4 2024
entrez: 25 4 2024
Statut: ppublish

Résumé

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.

Identifiants

DOI: 10.1126/science.adj4503 PMID: 38662846
pubmed: 38662846
doi: 10.1126/science.adj4503
doi:

Substances chimiques

Carbon 7440-44-0
Nitrogen N762921K75

Types de publication

Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

eadj4503

Auteurs

Dana A Opulente (DA)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.
Biology Department, Villanova University, Villanova, PA 19085, USA.
ORCID: 0000-0003-3224-7510

Abigail Leavitt LaBella (AL)

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.
North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, USA.
ORCID: 0000-0003-0068-6703

Marie-Claire Harrison (MC)

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.
ORCID: 0000-0002-3013-9906

John F Wolters (JF)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.
ORCID: 0000-0002-5477-4250

Chao Liu (C)

College of Agriculture and Biotechnology and Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou 310058, China.
ORCID: 0000-0002-4252-4019

Yonglin Li (Y)

Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China.
ORCID: 0009-0008-2774-9106

Jacek Kominek (J)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.
LifeMine Therapeutics, Inc., Cambridge, MA 02140, USA.
ORCID: 0000-0002-1916-0122

Jacob L Steenwyk (JL)

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.
Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
ORCID: 0000-0002-8436-595X

Hayley R Stoneman (HR)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.
University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.

Jenna VanDenAvond (J)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.
ORCID: 0009-0007-1229-1617

Caroline R Miller (CR)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.
ORCID: 0009-0000-7177-4618

Quinn K Langdon (QK)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
ORCID: 0000-0002-2141-3571

Margarida Silva (M)

UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.

Carla Gonçalves (C)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.
UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.

Emily J Ubbelohde (EJ)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.
ORCID: 0000-0003-3672-429X

Yuanning Li (Y)

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China.
Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China.
ORCID: 0000-0002-2206-5804

Kelly V Buh (KV)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.

Martin Jarzyna (M)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
Graduate Program in Neuroscience and Department of Biology, Washington University School of Medicine, St. Louis, MO 63130, USA.
ORCID: 0000-0002-2485-6589

Max A B Haase (MAB)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.
Vilcek Institute of Graduate Biomedical Sciences and Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.
Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.
ORCID: 0000-0002-8962-0446

Carlos A Rosa (CA)

Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.
ORCID: 0000-0002-0056-9075

Neža ČCadež (N)

Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
ORCID: 0000-0002-4987-0539

Diego Libkind (D)

Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina.
ORCID: 0000-0001-9687-6186

Jeremy H DeVirgilio (JH)

Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA.
ORCID: 0009-0004-8147-364X

Amanda Beth Hulfachor (AB)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.
ORCID: 0009-0009-7387-3287

Cletus P Kurtzman (CP)

Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA.

José Paulo Sampaio (JP)

UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.

Paula Gonçalves (P)

UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.

Xiaofan Zhou (X)

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China.
ORCID: 0000-0002-2879-6317

Xing-Xing Shen (XX)

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
College of Agriculture and Biotechnology and Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou 310058, China.
ORCID: 0000-0001-5765-1419

Marizeth Groenewald (M)

Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, Netherlands.
ORCID: 0000-0003-0835-5925

Antonis Rokas (A)

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.
ORCID: 0000-0002-7248-6551

Chris Todd Hittinger (CT)

Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.
ORCID: 0000-0001-5088-7461

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Classifications MeSH

questionsmedicales.fr › Produits chimiques inorganiques › Éléments › Carbone › Genomic factors shape carbon and nitrogen...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome fongique › Genomic factors shape carbon and nitrogen...
questionsmedicales.fr › Produits chimiques inorganiques › Gaz › Azote › Genomic factors shape carbon and nitrogen...
questionsmedicales.fr › Métabolisme › Voies et réseaux métaboliques › Genomic factors shape carbon and nitrogen...
questionsmedicales.fr › Eucaryotes › Champignons › Ascomycota › Genomic factors shape carbon and nitrogen...