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Wong ED, Miyasato SR, Aleksander S, Karra K, Nash RS, Skrzypek MS, Weng S, Engel SR, Cherry JM. Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources. Genetics 2023; 224:iyac191. [PMID: 36607068 PMCID: PMC10158836 DOI: 10.1093/genetics/iyac191] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/16/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting the scientific research community since 1993. As technologies and research evolve, so does SGD: from updates in software architecture, to curation of novel data types, to incorporation of data from, and collaboration with, other knowledgebases. We are continuing to make steps toward providing the community with an S. cerevisiae pan-genome. Here, we describe software upgrades, a new nomenclature system for genes not found in the reference strain, and additions to gene pages. With these improvements, we aim to remain a leading resource for students, researchers, and the broader scientific community.
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Affiliation(s)
- Edith D Wong
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Stuart R Miyasato
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Suzi Aleksander
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Robert S Nash
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Marek S Skrzypek
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Shuai Weng
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Stacia R Engel
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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Aza P, Molpeceres G, de Salas F, Camarero S. Design of an improved universal signal peptide based on the α-factor mating secretion signal for enzyme production in yeast. Cell Mol Life Sci 2021; 78:3691-3707. [PMID: 33687500 PMCID: PMC8038962 DOI: 10.1007/s00018-021-03793-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 11/26/2022]
Abstract
Saccharomyces cerevisiae plays an important role in the heterologous expression of an array of proteins due to its easy manipulation, low requirements and ability for protein post-translational modifications. The implementation of the preproleader secretion signal of the α-factor mating pheromone from this yeast contributes to increase the production yields by targeting the foreign protein to the extracellular environment. The use of this signal peptide combined with enzyme-directed evolution allowed us to achieve the otherwise difficult functional expression of fungal laccases in S. cerevisiae, obtaining different evolved α-factor preproleader sequences that enhance laccase secretion. However, the design of a universal signal peptide to enhance the production of heterologous proteins in S. cerevisiae is a pending challenge. We describe here the optimisation of the α-factor preproleader to improve recombinant enzyme production in S. cerevisiae through two parallel engineering strategies: a bottom-up design over the native α-factor preproleader (αnat) and a top-down design over the fittest evolved signal peptide obtained in our lab (α9H2 leader). The goal was to analyse the effect of mutations accumulated in the signal sequence throughout iterations of directed evolution, or of other reported mutations, and their possible epistatic interactions. Both approaches agreed in the positive synergism of four mutations (Aα9D, Aα20T, Lα42S, Dα83E) contained in the final optimised leader (αOPT), which notably enhanced the secretion of several fungal oxidoreductases and hydrolases. Additionally, we suggest a guideline to further drive the heterologous production of a particular enzyme based on combinatorial saturation mutagenesis of positions 86th and 87th of the αOPT leader fused to the target protein.
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Affiliation(s)
- Pablo Aza
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Gonzalo Molpeceres
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Felipe de Salas
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.
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Repair characteristics and time-dependent effects in response to heavy-ion beam irradiation in Saccharomyces cerevisiae: a comparison with X-ray irradiation. Appl Microbiol Biotechnol 2020; 104:4043-4057. [PMID: 32144474 DOI: 10.1007/s00253-020-10464-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/07/2020] [Accepted: 02/12/2020] [Indexed: 12/14/2022]
Abstract
Heavy-ion beam (HIB) irradiation has been widely used in microbial mutation breeding. However, a global cellular response to such radiation remains mostly uncharacterised. In this study, we used transcriptomics to analyse the damage repair response in Saccharomyces cerevisiae following a semi-lethal HIB irradiation (80 Gy), which induced a significant number of DNA double-strand breaks. Our analysis of differentially expressed genes (DEGs) from 50 to 150 min post-irradiation revealed that upregulated genes were significantly enriched for gene ontology and Kyoto encyclopaedia of genes and genomes terms related to damage repair response. Based on the number of DEGs, their annotation, and their relative expression, we established that the peak of the damage repair response occurred 75 min post-irradiation. Moreover, we exploited the data from our recent study on X-ray irradiation-induced repair to compare the transcriptional patterns induced by semi-lethal HIB and X-ray irradiations. Although these two radiations have different properties, we found a significant overlap (> 50%) for the DEGs associated with five typical DNA repair pathways and, in both cases, identified homologous recombination repair (HRR) as the predominant repair pathway. Nevertheless, when we compared the relative enrichment of the five DNA repair pathways at the key time point of the repair process, we found that the relative enrichment of HRR was higher after HIB irradiation than after X-ray irradiation. Additionally, the peak stage of HRR following HIB irradiation was ahead of that following X-ray irradiation. Since mutations occur during the DNA repair process, uncovering detailed repair characteristics should further the understanding of the associated mutagenesis features.
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A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome. Mol Cell Biol 2017; 38:MCB.00302-17. [PMID: 29038160 DOI: 10.1128/mcb.00302-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/11/2017] [Indexed: 11/20/2022] Open
Abstract
To interrogate genes essential for cell growth, proliferation and survival in human cells, we carried out a genome-wide clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 screen in a B-cell lymphoma line using a custom extended-knockout (EKO) library of 278,754 single-guide RNAs (sgRNAs) that targeted 19,084 RefSeq genes, 20,852 alternatively spliced exons, and 3,872 hypothetical genes. A new statistical analysis tool called robust analytics and normalization for knockout screens (RANKS) identified 2,280 essential genes, 234 of which were unique. Individual essential genes were validated experimentally and linked to ribosome biogenesis and stress responses. Essential genes exhibited a bimodal distribution across 10 different cell lines, consistent with a continuous variation in essentiality as a function of cell type. Genes essential in more lines had more severe fitness defects and encoded the evolutionarily conserved structural cores of protein complexes, whereas genes essential in fewer lines formed context-specific modules and encoded subunits at the periphery of essential complexes. The essentiality of individual protein residues across the proteome correlated with evolutionary conservation, structural burial, modular domains, and protein interaction interfaces. Many alternatively spliced exons in essential genes were dispensable and were enriched for disordered regions. Fitness defects were observed for 44 newly evolved hypothetical reading frames. These results illuminate the contextual nature and evolution of essential gene functions in human cells.
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Hellerstedt ST, Nash RS, Weng S, Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM. Curated protein information in the Saccharomyces genome database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3066359. [PMID: 28365727 PMCID: PMC5467551 DOI: 10.1093/database/bax011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/27/2017] [Indexed: 12/21/2022]
Abstract
Due to recent advancements in the production of experimental proteomic data, the Saccharomyces genome database (SGD; www.yeastgenome.org) has been expanding our protein curation activities to make new data types available to our users. Because of broad interest in post-translational modifications (PTM) and their importance to protein function and regulation, we have recently started incorporating expertly curated PTM information on individual protein pages. Here we also present the inclusion of new abundance and protein half-life data obtained from high-throughput proteome studies. These new data types have been included with the aim to facilitate cellular biology research. Database URL: www.yeastgenome.org
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Affiliation(s)
| | - Robert S Nash
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Shuai Weng
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kelley M Paskov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Edith D Wong
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Stacia R Engel
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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Eppig JT. Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. ILAR J 2017; 58:17-41. [PMID: 28838066 PMCID: PMC5886341 DOI: 10.1093/ilar/ilx013] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 03/14/2017] [Accepted: 03/28/2017] [Indexed: 12/13/2022] Open
Abstract
The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory mouse. MGI serves a strategic role for the scientific community in facilitating biomedical, experimental, and computational studies investigating the genetics and processes of diseases and enabling the development and testing of new disease models and therapeutic interventions. This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings of MGI. MGI develops and maintains a gold-standard resource that reflects the current state of knowledge, provides semantic and contextual data integration that fosters hypothesis testing, continually develops new and improved tools for searching and analysis, and partners with the scientific community to assure research data needs are met. Here we describe one slice of MGI relating to the development of community-wide large-scale mutagenesis and phenotyping projects and introduce ways to access and use these MGI data. References and links to additional MGI aspects are provided.
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Affiliation(s)
- Janan T. Eppig
- Janan T. Eppig, PhD, is Professor Emeritus at The Jackson Laboratory in Bar Harbor, Maine
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Identification of Genes in Candida glabrata Conferring Altered Responses to Caspofungin, a Cell Wall Synthesis Inhibitor. G3-GENES GENOMES GENETICS 2016; 6:2893-907. [PMID: 27449515 PMCID: PMC5015946 DOI: 10.1534/g3.116.032490] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Candida glabrata is an important human fungal pathogen whose incidence continues to rise. Because many clinical isolates are resistant to azole drugs, the drugs of choice to treat such infections are members of the echinocandin family, although there are increasing reports of resistance to these drugs as well. In efforts to better understand the genetic changes that lead to altered responses to echinocandins, we screened a transposon-insertion library of mutants for strains to identify genes that are important for cellular responses to caspofungin, a member of this drug family. We identified 16 genes that, when disrupted, caused increased tolerance, and 48 genes that, when disrupted, caused increased sensitivity compared to the wild-type parental strain. Four of the genes identified as causing sensitivity are orthologs of Saccharomyces cerevisiae genes encoding proteins important for the cell wall integrity (CWI) pathway. In addition, several other genes are orthologs of the high affinity Ca2+ uptake system (HACS) complex genes. We analyzed disruption mutants representing all 64 genes under 33 different conditions, including the presence of cell wall disrupting agents and other drugs, a variety of salts, increased temperature, and altered pH. Further, we generated knockout mutants in different genes within the CWI pathway and the HACS complex, and found that they too exhibited phenotypes consistent with defects in cell wall construction. Our results indicate that small molecules that inhibit the CWI pathway, or that the HACS complex, may be an important means of increasing the efficacy of caspofungin.
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