Extending the reach of homology by using successive computational filters to find yeast pheromone genes.
Yarrowia
gene annotation
pheromones
small peptides
yeast mating
Journal
Current biology : CB
ISSN: 1879-0445
Titre abrégé: Curr Biol
Pays: England
ID NLM: 9107782
Informations de publication
Date de publication:
09 10 2023
09 10 2023
Historique:
received:
13
12
2022
revised:
04
07
2023
accepted:
14
08
2023
pmc-release:
09
10
2024
medline:
12
10
2023
pubmed:
13
9
2023
entrez:
12
9
2023
Statut:
ppublish
Résumé
The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in a small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are shorter than 100 amino acids long, and contain a proteolytic-processing motif upstream of the potential mature pheromone sequence and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 Saccharomycotina genomes, we identified strong candidate pheromone genes in 241 genomes, covering 13 clades that are each separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology among small pheromone genes. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.
Identifiants
pubmed: 37699395
pii: S0960-9822(23)01118-1
doi: 10.1016/j.cub.2023.08.039
pmc: PMC10592104
mid: NIHMS1927275
pii:
doi:
Substances chimiques
Pheromones
0
Peptides
0
Mating Factor
61194-02-3
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
4098-4110.e3Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM043987
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM120996
Pays : United States
Organisme : NIGMS NIH HHS
ID : R37 GM043987
Pays : United States
Informations de copyright
Copyright © 2023 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no competing interests.
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