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Engel SR, Wong ED, Nash RS, Aleksander S, Alexander M, Douglass E, Karra K, Miyasato SR, Simison M, Skrzypek MS, Weng S, Cherry JM. New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. Genetics 2022; 220:iyab224. [PMID: 34897464 PMCID: PMC9209811 DOI: 10.1093/genetics/iyab224] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/11/2021] [Indexed: 02/03/2023] Open
Abstract
Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.
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Affiliation(s)
- Stacia R Engel
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Edith D Wong
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Robert S Nash
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Suzi Aleksander
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Micheal Alexander
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Eric Douglass
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Stuart R Miyasato
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Matt Simison
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Marek S Skrzypek
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Shuai Weng
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
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Novačić A, Vučenović I, Primig M, Stuparević I. Non-coding RNAs as cell wall regulators in Saccharomyces cerevisiae. Crit Rev Microbiol 2020; 46:15-25. [PMID: 31994960 DOI: 10.1080/1040841x.2020.1715340] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The cell wall of Saccharomyces cerevisiae is an extracellular organelle crucial for preserving its cellular integrity and detecting environmental cues. The cell wall is composed of mannoproteins attached to a polysaccharide network and is continuously remodelled as cells undergo cell division, mating, gametogenesis or adapt to stressors. This makes yeast an excellent model to study the regulation of genes important for cell wall formation and maintenance. Given that certain yeast strains are pathogenic, a better understanding of their life cycle is of clinical relevance. This is why transcriptional regulatory mechanisms governing genes involved in cell wall biogenesis or maintenance have been the focus of numerous studies. However, little is known about the roles of long non-coding RNAs (lncRNAs), a class of transcripts that are thought to possess little or no protein coding potential, in controlling the expression of cell wall-related genes. This review outlines currently known mechanisms of lncRNA-mediated regulation of gene expression in S. cerevisiae and describes examples of lncRNA-regulated genes encoding cell wall proteins. We suggest that the association of currently annotated lncRNAs with the coding sequences and/or promoters of cell wall-related genes highlights a potential role for lncRNAs as important regulators of the yeast cell wall structure.
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Affiliation(s)
- Ana Novačić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Ivan Vučenović
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, Rennes, France
| | - Igor Stuparević
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
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Genome-wide C-SWAT library for high-throughput yeast genome tagging. Nat Methods 2018; 15:598-600. [DOI: 10.1038/s41592-018-0045-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/04/2018] [Indexed: 11/08/2022]
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Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:4950591. [PMID: 29765496 PMCID: PMC5889882 DOI: 10.1155/2018/4950591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/07/2018] [Indexed: 02/02/2023]
Abstract
We summarize current knowledge regarding regulatory functions of long noncoding RNAs (lncRNAs) in yeast, with emphasis on lncRNAs identified recently in yeast colonies and biofilms. Potential regulatory functions of these lncRNAs in differentiated cells of domesticated colonies adapted to plentiful conditions versus yeast colony biofilms are discussed. We show that specific cell types differ in their complements of lncRNA, that this complement changes over time in differentiating upper cells, and that these lncRNAs target diverse functional categories of genes in different cell subpopulations and specific colony types.
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