51
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Brunnsåker D, Kronström F, Tiukova IA, King RD. Interpreting protein abundance in Saccharomyces cerevisiae through relational learning. Bioinformatics 2024; 40:btae050. [PMID: 38273672 PMCID: PMC10868306 DOI: 10.1093/bioinformatics/btae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 01/27/2024] Open
Abstract
MOTIVATION Proteomic profiles reflect the functional readout of the physiological state of an organism. An increased understanding of what controls and defines protein abundances is of high scientific interest. Saccharomyces cerevisiae is a well-studied model organism, and there is a large amount of structured knowledge on yeast systems biology in databases such as the Saccharomyces Genome Database, and highly curated genome-scale metabolic models like Yeast8. These datasets, the result of decades of experiments, are abundant in information, and adhere to semantically meaningful ontologies. RESULTS By representing this knowledge in an expressive Datalog database we generated data descriptors using relational learning that, when combined with supervised machine learning, enables us to predict protein abundances in an explainable manner. We learnt predictive relationships between protein abundances, function and phenotype; such as α-amino acid accumulations and deviations in chronological lifespan. We further demonstrate the power of this methodology on the proteins His4 and Ilv2, connecting qualitative biological concepts to quantified abundances. AVAILABILITY AND IMPLEMENTATION All data and processing scripts are available at the following Github repository: https://github.com/DanielBrunnsaker/ProtPredict.
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Affiliation(s)
- Daniel Brunnsåker
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Filip Kronström
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Ievgeniia A Tiukova
- Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Department of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm 106 91, Sweden
| | - Ross D King
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
- The Alan Turing Institute, London NW1 2DB, United Kingdom
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52
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O'Meara MJ, Rapala JR, Nichols CB, Alexandre AC, Billmyre RB, Steenwyk JL, Alspaugh JA, O'Meara TR. CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair. PLoS Genet 2024; 20:e1011158. [PMID: 38359090 PMCID: PMC10901339 DOI: 10.1371/journal.pgen.1011158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/28/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Elucidating gene function is a major goal in biology, especially among non-model organisms. However, doing so is complicated by the fact that molecular conservation does not always mirror functional conservation, and that complex relationships among genes are responsible for encoding pathways and higher-order biological processes. Co-expression, a promising approach for predicting gene function, relies on the general principal that genes with similar expression patterns across multiple conditions will likely be involved in the same biological process. For Cryptococcus neoformans, a prevalent human fungal pathogen greatly diverged from model yeasts, approximately 60% of the predicted genes in the genome lack functional annotations. Here, we leveraged a large amount of publicly available transcriptomic data to generate a C. neoformans Co-Expression Network (CryptoCEN), successfully recapitulating known protein networks, predicting gene function, and enabling insights into the principles influencing co-expression. With 100% predictive accuracy, we used CryptoCEN to identify 13 new DNA damage response genes, underscoring the utility of guilt-by-association for determining gene function. Overall, co-expression is a powerful tool for uncovering gene function, and decreases the experimental tests needed to identify functions for currently under-annotated genes.
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Affiliation(s)
- Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jackson R Rapala
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Connie B Nichols
- Departments of Medicine and Molecular Genetics/Microbiology; and Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - A Christina Alexandre
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - R Blake Billmyre
- Departments of Pharmaceutical and Biomedical Sciences/Infectious Disease, College of Pharmacy/College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Jacob L Steenwyk
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - J Andrew Alspaugh
- Departments of Medicine and Molecular Genetics/Microbiology; and Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Teresa R O'Meara
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
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53
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Pavesic MW, Gale AN, Nickels TJ, Harrington AA, Bussey M, Cunningham KW. Calcineurin-dependent contributions to fitness in the opportunistic pathogen Candida glabrata. mSphere 2024; 9:e0055423. [PMID: 38171022 PMCID: PMC10826367 DOI: 10.1128/msphere.00554-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/19/2023] [Indexed: 01/05/2024] Open
Abstract
The protein phosphatase calcineurin is vital for the virulence of the opportunistic fungal pathogen Candida glabrata. The host-induced stresses that activate calcineurin signaling are unknown, as are the targets of calcineurin relevant to virulence. To potentially shed light on these processes, millions of transposon insertion mutants throughout the genome of C. glabrata were profiled en masse for fitness defects in the presence of FK506, a specific inhibitor of calcineurin. Eighty-seven specific gene deficiencies depended on calcineurin signaling for full viability in vitro both in wild-type and pdr1∆ null strains lacking pleiotropic drug resistance. Three genes involved in cell wall biosynthesis (FKS1, DCW1, FLC1) possess co-essential paralogs whose expression depended on calcineurin and Crz1 in response to micafungin, a clinical antifungal that interferes with cell wall biogenesis. Interestingly, 80% of the FK506-sensitive mutants were deficient in different aspects of vesicular trafficking, such as endocytosis, exocytosis, sorting, and biogenesis of secretory proteins in the endoplasmic reticulum (ER). In response to the experimental antifungal manogepix that blocks GPI-anchor biosynthesis in the ER, calcineurin signaling increased and strongly prevented cell death independent of Crz1, one of its major targets. Comparisons between manogepix, micafungin, and the ER-stressing tunicamycin reveal a correlation between the degree of calcineurin signaling and the degree of cell survival. These findings suggest that calcineurin plays major roles in mitigating stresses of vesicular trafficking. Such stresses may arise during host infection and in response to antifungal therapies.IMPORTANCECalcineurin plays critical roles in the virulence of most pathogenic fungi. This study sheds light on those roles in the opportunistic pathogen Candida glabrata using a genome-wide analysis in vitro. The findings could lead to antifungal developments that also avoid immunosuppression.
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Affiliation(s)
- Matthew W. Pavesic
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew N. Gale
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Timothy J. Nickels
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Maya Bussey
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kyle W. Cunningham
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
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54
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Campos ACS, Araújo TM, Moraes L, Corrêa dos Santos RA, Goldman GH, Riano-Pachon DM, Oliveira JVDC, Squina FM, Castro IDM, Trópia MJM, da Cunha AC, Rosse IC, Brandão RL. Selected cachaça yeast strains share a genomic profile related to traits relevant to industrial fermentation processes. Appl Environ Microbiol 2024; 90:e0175923. [PMID: 38112453 PMCID: PMC10807443 DOI: 10.1128/aem.01759-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/01/2023] [Indexed: 12/21/2023] Open
Abstract
The isolation and selection of yeast strains to improve the quality of the cachaça-Brazilian Spirit-have been studied in our research group. Our strategy considers Saccharomyces cerevisiae as the predominant species involved in sugarcane juice fermentation and the presence of different stressors (osmolarity, temperature, ethanol content, and competition with other microorganisms). It also considers producing balanced concentrations of volatile compounds (higher alcohols and acetate and/or ethyl esters), flocculation capacity, and ethanol production. Since the genetic bases behind these traits of interest are not fully established, the whole genome sequencing of 11 different Saccharomyces cerevisiae strains isolated and selected from different places was analyzed to identify the presence of a specific genetic variation common to cachaça yeast strains. We have identified 20,128 single-nucleotide variants shared by all genomes. Of these shared variants, 37 were new variants (being six missenses), and 4,451 were identified as missenses. We performed a detailed functional annotation (using enrichment analysis, protein-protein interaction network analysis, and database and in-depth literature searches) of these new and missense variants. Many genes carrying these variations were involved in the phenotypes of flocculation, tolerance to fermentative stresses, and production of volatile compounds and ethanol. These results demonstrate the existence of a genetic profile shared by the 11 strains under study that could be associated with the applied selective strategy. Thus, this study points out genes and variants that may be used as molecular markers for selecting strains well suited to the fermentation process, including genetic improvement by genome editing, ultimately producing high-quality beverages and adding value.IMPORTANCEThis work demonstrates the existence of new genetic markers related to different phenotypes used to select yeast strains and mutations in genes directly involved in producing flavoring compounds and ethanol, and others related to flocculation and stress resistance.
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Affiliation(s)
- Anna Clara Silva Campos
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
| | - Thalita Macedo Araújo
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
- Área de Ciências Biológicas, Instituto Federal de Minas Gerais, Campus Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Lauro Moraes
- Laboratório Multiusuário de Bioinformática, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Renato Augusto Corrêa dos Santos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Diego Maurício Riano-Pachon
- Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | | | | | - Ieso de Miranda Castro
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
| | - Maria José Magalhães Trópia
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
| | - Aureliano Claret da Cunha
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
- Laboratório de Engenharia de Alimentos, Departamento de Alimentos, Escola de Nutrição, Salvador, Brazil
| | - Izinara C. Rosse
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
- Laboratório Multiusuário de Bioinformática, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Rogelio Lopes Brandão
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
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55
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Chen JL, Leeder WM, Morais P, Adachi H, Yu YT. Pseudouridylation-mediated gene expression modulation. Biochem J 2024; 481:1-16. [PMID: 38174858 DOI: 10.1042/bcj20230096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
RNA-guided pseudouridylation, a widespread post-transcriptional RNA modification, has recently gained recognition for its role in cellular processes such as pre-mRNA splicing and the modulation of premature termination codon (PTC) readthrough. This review provides insights into its mechanisms, functions, and potential therapeutic applications. It examines the mechanisms governing RNA-guided pseudouridylation, emphasizing the roles of guide RNAs and pseudouridine synthases in catalyzing uridine-to-pseudouridine conversion. A key focus is the impact of RNA-guided pseudouridylation of U2 small nuclear RNA on pre-mRNA splicing, encompassing its influence on branch site recognition and spliceosome assembly. Additionally, the review discusses the emerging role of RNA-guided pseudouridylation in regulating PTC readthrough, impacting translation termination and genetic disorders. Finally, it explores the therapeutic potential of pseudouridine modifications, offering insights into potential treatments for genetic diseases and cancer and the development of mRNA vaccine.
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Affiliation(s)
- Jonathan L Chen
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, U.S.A
| | | | | | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, U.S.A
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, U.S.A
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56
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Tummler K, Klipp E. Data integration strategies for whole-cell modeling. FEMS Yeast Res 2024; 24:foae011. [PMID: 38544322 PMCID: PMC11042497 DOI: 10.1093/femsyr/foae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Data makes the world go round-and high quality data is a prerequisite for precise models, especially for whole-cell models (WCM). Data for WCM must be reusable, contain information about the exact experimental background, and should-in its entirety-cover all relevant processes in the cell. Here, we review basic requirements to data for WCM and strategies how to combine them. As a species-specific resource, we introduce the Yeast Cell Model Data Base (YCMDB) to illustrate requirements and solutions. We discuss recent standards for data as well as for computational models including the modeling process as data to be reported. We outline strategies for constructions of WCM despite their inherent complexity.
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Affiliation(s)
- Katja Tummler
- Humboldt-Universität zu Berlin, Faculty of Life Sciences, Institute of Biology, Theoretical Biophysics,, Invalidenstr. 42, 10115 Berlin, Germany
| | - Edda Klipp
- Humboldt-Universität zu Berlin, Faculty of Life Sciences, Institute of Biology, Theoretical Biophysics,, Invalidenstr. 42, 10115 Berlin, Germany
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57
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Putman TE, Schaper K, Matentzoglu N, Rubinetti V, Alquaddoomi F, Cox C, Caufield JH, Elsarboukh G, Gehrke S, Hegde H, Reese J, Braun I, Bruskiewich R, Cappelletti L, Carbon S, Caron A, Chan L, Chute C, Cortes K, De Souza V, Fontana T, Harris N, Hartley E, Hurwitz E, Jacobsen JB, Krishnamurthy M, Laraway B, McLaughlin J, McMurry J, Moxon ST, Mullen K, O’Neil S, Shefchek K, Stefancsik R, Toro S, Vasilevsky N, Walls R, Whetzel P, Osumi-Sutherland D, Smedley D, Robinson P, Mungall C, Haendel M, Munoz-Torres M. The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Nucleic Acids Res 2024; 52:D938-D949. [PMID: 38000386 PMCID: PMC10767791 DOI: 10.1093/nar/gkad1082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/21/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI's ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.
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Affiliation(s)
- Tim E Putman
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kevin Schaper
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Vincent P Rubinetti
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Faisal S Alquaddoomi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Corey Cox
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - J Harry Caufield
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Glass Elsarboukh
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sarah Gehrke
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Harshad Hegde
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Justin T Reese
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ian Braun
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | | | | | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anita R Caron
- European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katherina G Cortes
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Tommaso Fontana
- Dipartimento di Informatica, Università degli Studi di Milano Statale, Milano, Italy
| | - Nomi L Harris
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily L Hartley
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | - Eric Hurwitz
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Madan Krishnamurthy
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bryan J Laraway
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Julie A McMurry
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sierra A T Moxon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathleen R Mullen
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Shawn T O’Neil
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kent A Shefchek
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ray Stefancsik
- European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Sabrina Toro
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Ramona L Walls
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | - Patricia L Whetzel
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 6032, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Melissa A Haendel
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Monica C Munoz-Torres
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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58
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Lemieux P, Bradley D, Dubé AK, Dionne U, Landry CR. Dissection of the role of a Src homology 3 domain in the evolution of binding preference of paralogous proteins. Genetics 2024; 226:iyad175. [PMID: 37793087 PMCID: PMC10763533 DOI: 10.1093/genetics/iyad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/07/2023] [Accepted: 08/07/2023] [Indexed: 10/06/2023] Open
Abstract
Protein-protein interactions (PPIs) drive many cellular processes. Some interactions are directed by Src homology 3 (SH3) domains that bind proline-rich motifs on other proteins. The evolution of the binding specificity of SH3 domains is not completely understood, particularly following gene duplication. Paralogous genes accumulate mutations that can modify protein functions and, for SH3 domains, their binding preferences. Here, we examined how the binding of the SH3 domains of 2 paralogous yeast type I myosins, Myo3 and Myo5, evolved following duplication. We found that the paralogs have subtly different SH3-dependent interaction profiles. However, by swapping SH3 domains between the paralogs and characterizing the SH3 domains freed from their protein context, we find that very few of the differences in interactions, if any, depend on the SH3 domains themselves. We used ancestral sequence reconstruction to resurrect the preduplication SH3 domains and examined, moving back in time, how the binding preference changed. Although the most recent ancestor of the 2 domains had a very similar binding preference as the extant ones, older ancestral domains displayed a gradual loss of interaction with the modern interaction partners when inserted in the extant paralogs. Molecular docking and experimental characterization of the free ancestral domains showed that their affinity with the proline motifs is likely not the cause for this loss of binding. Taken together, our results suggest that a SH3 and its host protein could create intramolecular or allosteric interactions essential for the SH3-dependent PPIs, making domains not functionally equivalent even when they have the same binding specificity.
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Affiliation(s)
- Pascale Lemieux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec, Université Laval, Québec, QC, Canada G1R 2J6
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada M5G 1X5
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Regroupement Québécois de Recherche sur la Fonction, l’Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Centre de recherche en données massives (CRDM), Université Laval, 1065, Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biochimie, microbiologie et bio-informatique, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
- Département de biologie, Université Laval, 1045 Avenue de la Médecine, Québec, QC, Canada G1V 0A6
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59
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Pons C, van Leeuwen J. Meta-analysis of dispensable essential genes and their interactions with bypass suppressors. Life Sci Alliance 2024; 7:e202302192. [PMID: 37918966 PMCID: PMC10622647 DOI: 10.26508/lsa.202302192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023] Open
Abstract
Genes have been historically classified as essential or non-essential based on their requirement for viability. However, genomic mutations can sometimes bypass the requirement for an essential gene, challenging the binary classification of gene essentiality. Such dispensable essential genes represent a valuable model for understanding the incomplete penetrance of loss-of-function mutations often observed in natural populations. Here, we compiled data from multiple studies on essential gene dispensability in Saccharomyces cerevisiae to comprehensively characterize these genes. In analyses spanning different evolutionary timescales, dispensable essential genes exhibited distinct phylogenetic properties compared with other essential and non-essential genes. Integration of interactions with suppressor genes that can bypass the gene essentiality revealed the high functional modularity of the bypass suppression network. Furthermore, dispensable essential and bypass suppressor gene pairs reflected simultaneous changes in the mutational landscape of S. cerevisiae strains. Importantly, species in which dispensable essential genes were non-essential tended to carry bypass suppressor mutations in their genomes. Overall, our study offers a comprehensive view of dispensable essential genes and illustrates how their interactions with bypass suppressors reflect evolutionary outcomes.
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Affiliation(s)
- Carles Pons
- https://ror.org/01z1gye03 Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Jolanda van Leeuwen
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
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60
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Navarro-Quiles C, Lup SD, Muñoz-Nortes T, Candela H, Micol JL. The genetic and molecular basis of haploinsufficiency in flowering plants. TRENDS IN PLANT SCIENCE 2024; 29:72-85. [PMID: 37633803 DOI: 10.1016/j.tplants.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 08/28/2023]
Abstract
In diploid organisms, haploinsufficiency can be defined as the requirement for more than one fully functional copy of a gene. In contrast to most genes, whose loss-of-function alleles are recessive, loss-of-function alleles of haploinsufficient genes are dominant. However, forward and reverse genetic screens are biased toward obtaining recessive, loss-of-function mutations, and therefore, dominant mutations of all types are underrepresented in mutant collections. Despite this underrepresentation, haploinsufficient loci have intriguing implications for studies of genome evolution, gene dosage, stability of protein complexes, genetic redundancy, and gene expression. Here we review examples of haploinsufficiency in flowering plants and describe the underlying molecular mechanisms and evolutionary forces driving haploinsufficiency. Finally, we discuss the masking of haploinsufficiency by genetic redundancy, a widespread phenomenon among angiosperms.
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Affiliation(s)
- Carla Navarro-Quiles
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Samuel Daniel Lup
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Tamara Muñoz-Nortes
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain.
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61
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Serbus LR. A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging. Methods Mol Biol 2024; 2739:349-373. [PMID: 38006562 DOI: 10.1007/978-1-0716-3553-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.
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Affiliation(s)
- Laura Renee Serbus
- Department of Biological Sciences, Florida International University, Miami, FL, USA.
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62
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Krska T, Twaruschek K, Valente N, Mitterbauer R, Moll D, Wiesenberger G, Berthiller F, Adam G. Development of a fumonisin-sensitive Saccharomyces cerevisiae indicator strain and utilization for activity testing of candidate detoxification genes. Appl Environ Microbiol 2023; 89:e0121123. [PMID: 38054733 PMCID: PMC10746191 DOI: 10.1128/aem.01211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Fumonisins can cause diseases in animals and humans consuming Fusarium-contaminated food or feed. The search for microbes capable of fumonisin degradation, or for enzymes that can detoxify fumonisins, currently relies primarily on chemical detection methods. Our constructed fumonisin B1-sensitive yeast strain can be used to phenotypically detect detoxification activity and should be useful in screening for novel fumonisin resistance genes and to elucidate fumonisin metabolism and resistance mechanisms in fungi and plants, and thereby, in the long term, help to mitigate the threat of fumonisins in feed and food.
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Affiliation(s)
- Tamara Krska
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, FFoQSI GmbH, Tulln, Austria
| | - Krisztian Twaruschek
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety & Innovation, FFoQSI GmbH, Tulln, Austria
| | - Nina Valente
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Rudolf Mitterbauer
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Dieter Moll
- dsm-firmenich ANH Research Center Tulln, Tulln, Austria
| | - Gerlinde Wiesenberger
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
- Department of Agrobiotechnology, Institute of Bioanalytics and Agro-Metabolomics, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Franz Berthiller
- Department of Agrobiotechnology, Institute of Bioanalytics and Agro-Metabolomics, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Gerhard Adam
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
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63
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Coradini ALV, Ville CN, Krieger ZA, Roemer J, Hull C, Yang S, Lusk DT, Ehrenreich IM. Building synthetic chromosomes from natural DNA. Nat Commun 2023; 14:8337. [PMID: 38123566 PMCID: PMC10733283 DOI: 10.1038/s41467-023-44112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
De novo chromosome synthesis is costly and time-consuming, limiting its use in research and biotechnology. Building synthetic chromosomes from natural components is an unexplored alternative with many potential applications. In this paper, we report CReATiNG (Cloning, Reprogramming, and Assembling Tiled Natural Genomic DNA), a method for constructing synthetic chromosomes from natural components in yeast. CReATiNG entails cloning segments of natural chromosomes and then programmably assembling them into synthetic chromosomes that can replace the native chromosomes in cells. We use CReATiNG to synthetically recombine chromosomes between strains and species, to modify chromosome structure, and to delete many linked, non-adjacent regions totaling 39% of a chromosome. The multiplex deletion experiment reveals that CReATiNG also enables recovery from flaws in synthetic chromosome design via recombination between a synthetic chromosome and its native counterpart. CReATiNG facilitates the application of chromosome synthesis to diverse biological problems.
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Affiliation(s)
- Alessandro L V Coradini
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Christopher Ne Ville
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Zachary A Krieger
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Joshua Roemer
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Cara Hull
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Shawn Yang
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Daniel T Lusk
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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64
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Khamwachirapithak P, Guillaume-Schoepfer D, Chansongkrow P, Teichmann SA, Wigge PA, Charoensawan V. Characterizing Different Modes of Interplay Between Rap1 and H3 Using Inducible H3-depletion Yeast. J Mol Biol 2023; 435:168355. [PMID: 37935256 DOI: 10.1016/j.jmb.2023.168355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Histones and transcription factors (TFs) are two important DNA-binding proteins that interact, compete, and together regulate transcriptional processes in response to diverse internal and external stimuli. Condition-specific depletion of histones in Saccharomyces cerevisiae using a galactose-inducible H3 promoter provides a suitable framework for examining transcriptional alteration resulting from reduced nucleosome content. However, the effect on DNA binding activities of TFs is yet to be fully explored. In this work, we combine ChIP-seq of H3 with RNA-seq to elucidate the genome-scale relationships between H3 occupancy patterns and transcriptional dynamics before and after global H3 depletion. ChIP-seq of Rap1 is also conducted in the H3-depletion and control treatments, to investigate the interplay between this master regulator TF and nucleosomal H3, and to explore the impact on diverse transcriptional responses of different groups of target genes and functions. Ultimately, we propose a working model and testable hypotheses regarding the impact of global and local H3 depletion on transcriptional changes. We also demonstrate different potential modes of interaction between Rap1 and H3, which sheds light on the potential multifunctional regulatory capabilities of Rap1 and potentially other pioneer factors.
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Affiliation(s)
- Peerapat Khamwachirapithak
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Pakkanan Chansongkrow
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom; University Potsdam, Institute for Biochemistry and Biology, Molecular Biology, Karl-Liebknecht-Str, Potsdam-Golm, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany.
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand; Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom; Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Bangkok, Thailand; Integrative Computational BioScience (ICBS) center, Mahidol University, Nakhon Pathom, Thailand; School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
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65
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Mendoza B, Zheng X, Clements JC, Cotter C, Trinh CT. Potency of CRISPR-Cas Antifungals Is Enhanced by Cotargeting DNA Repair and Growth Regulatory Machinery at the Genetic Level. ACS Infect Dis 2023; 9:2494-2503. [PMID: 37955405 PMCID: PMC10714396 DOI: 10.1021/acsinfecdis.3c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023]
Abstract
The emergence of virulent, resistant, and rapidly evolving fungal pathogens poses a significant threat to public health, agriculture, and the environment. Targeting cellular processes with standard small-molecule intervention may be effective but requires long development times and is prone to antibiotic resistance. To overcome the current limitations of antibiotic development and treatment, this study harnesses CRISPR-Cas systems as antifungals by capitalizing on their adaptability, specificity, and efficiency in target design. The conventional design of CRISPR-Cas antimicrobials, based on induction of DNA double-strand breaks (DSBs), is potentially less effective in fungi due to robust eukaryotic DNA repair machinery. Here, we report a novel design principle to formulate more effective CRISPR-Cas antifungals by cotargeting essential genes with DNA repair defensive genes that remove the fungi's ability to repair the DSB sites of essential genes. By evaluating this design on the model fungus Saccharomyces cerevisiae, we demonstrated that essential and defensive gene cotargeting is more effective than either essential or defensive gene targeting alone. The top-performing CRISPR-Cas antifungals performed as effectively as the antibiotic Geneticin. A gene cotargeting interaction analysis revealed that cotargeting essential genes with RAD52 involved in homologous recombination (HR) was the most synergistic combination. Fast growth kinetics of S. cerevisiae induced resistance to CRISPR-Cas antifungals, where genetic mutations mostly occurred in defensive genes and guide RNA sequences.
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Affiliation(s)
- Brian
J. Mendoza
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Xianliang Zheng
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jared C. Clements
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Christopher Cotter
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Cong T. Trinh
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
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66
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Dolan M, St. John N, Zaidi F, Doyle F, Fasullo M. High-throughput screening of the Saccharomyces cerevisiae genome for 2-amino-3-methylimidazo [4,5-f] quinoline resistance identifies colon cancer-associated genes. G3 (BETHESDA, MD.) 2023; 13:jkad219. [PMID: 37738679 PMCID: PMC11025384 DOI: 10.1093/g3journal/jkad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 10/25/2022] [Accepted: 09/15/2023] [Indexed: 09/24/2023]
Abstract
Heterocyclic aromatic amines (HAAs) are potent carcinogenic agents found in charred meats and cigarette smoke. However, few eukaryotic resistance genes have been identified. We used Saccharomyces cerevisiae (budding yeast) to identify genes that confer resistance to 2-amino-3-methylimidazo[4,5-f] quinoline (IQ). CYP1A2 and NAT2 activate IQ to become a mutagenic nitrenium compound. Deletion libraries expressing human CYP1A2 and NAT2 or no human genes were exposed to either 400 or 800 µM IQ for 5 or 10 generations. DNA barcodes were sequenced using the Illumina HiSeq 2500 platform and statistical significance was determined for exactly matched barcodes. We identified 424 ORFs, including 337 genes of known function, in duplicate screens of the "humanized" collection for IQ resistance; resistance was further validated for a select group of 51 genes by growth curves, competitive growth, or trypan blue assays. Screens of the library not expressing human genes identified 143 ORFs conferring resistance to IQ per se. Ribosomal protein and protein modification genes were identified as IQ resistance genes in both the original and "humanized" libraries, while nitrogen metabolism, DNA repair, and growth control genes were also prominent in the "humanized" library. Protein complexes identified included the casein kinase 2 (CK2) and histone chaperone (HIR) complex. Among DNA Repair and checkpoint genes, we identified those that function in postreplication repair (RAD18, UBC13, REV7), base excision repair (NTG1), and checkpoint signaling (CHK1, PSY2). These studies underscore the role of ribosomal protein genes in conferring IQ resistance, and illuminate DNA repair pathways for conferring resistance to activated IQ.
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Affiliation(s)
- Michael Dolan
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Nick St. John
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Faizan Zaidi
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Francis Doyle
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Michael Fasullo
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
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67
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Lemière J, Chang F. Quantifying turgor pressure in budding and fission yeasts based upon osmotic properties. Mol Biol Cell 2023; 34:ar133. [PMID: 37903220 PMCID: PMC10848946 DOI: 10.1091/mbc.e23-06-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 11/01/2023] Open
Abstract
Walled cells, such as plants, fungi, and bacteria cells, possess a high internal hydrostatic pressure, termed turgor pressure, that drives volume growth and contributes to cell shape determination. Rigorous measurement of turgor pressure, however, remains challenging, and reliable quantitative measurements, even in budding yeast are still lacking. Here, we present a simple and robust experimental approach to access turgor pressure in yeasts based upon the determination of isotonic concentration using protoplasts as osmometers. We propose three methods to identify the isotonic condition - three-dimensional cell volume, cytoplasmic fluorophore intensity, and mobility of a cytGEMs nano-rheology probe - that all yield consistent values. Our results provide turgor pressure estimates of 1.0 ± 0.1 MPa for Schizosaccharomyces pombe, 0.49 ± 0.01 MPa for Schizosaccharomyces japonicus, 0.5 ± 0.1 MPa for Saccharomyces cerevisiae W303a and 0.31 ± 0.03 MPa for Saccharomyces cerevisiae BY4741. Large differences in turgor pressure and nano-rheology measurements between the Saccharomyces cerevisiae strains demonstrate how fundamental biophysical parameters can vary even among wild-type strains of the same species. These side-by-side measurements of turgor pressure in multiple yeast species provide critical values for quantitative studies on cellular mechanics and comparative evolution.
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Affiliation(s)
- Joël Lemière
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143
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68
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Wacholder A, Carvunis AR. Biological factors and statistical limitations prevent detection of most noncanonical proteins by mass spectrometry. PLoS Biol 2023; 21:e3002409. [PMID: 38048358 PMCID: PMC10721188 DOI: 10.1371/journal.pbio.3002409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 12/14/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023] Open
Abstract
Ribosome profiling experiments indicate pervasive translation of short open reading frames (ORFs) outside of annotated protein-coding genes. However, shotgun mass spectrometry (MS) experiments typically detect only a small fraction of the predicted protein products of this noncanonical translation. The rarity of detection could indicate that most predicted noncanonical proteins are rapidly degraded and not present in the cell; alternatively, it could reflect technical limitations. Here, we leveraged recent advances in ribosome profiling and MS to investigate the factors limiting detection of noncanonical proteins in yeast. We show that the low detection rate of noncanonical ORF products can largely be explained by small size and low translation levels and does not indicate that they are unstable or biologically insignificant. In particular, proteins encoded by evolutionarily young genes, including those with well-characterized biological roles, are too short and too lowly expressed to be detected by shotgun MS at current detection sensitivities. Additionally, we find that decoy biases can give misleading estimates of noncanonical protein false discovery rates, potentially leading to false detections. After accounting for these issues, we found strong evidence for 4 noncanonical proteins in MS data, which were also supported by evolution and translation data. These results illustrate the power of MS to validate unannotated genes predicted by ribosome profiling, but also its substantial limitations in finding many biologically relevant lowly expressed proteins.
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Affiliation(s)
- Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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69
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Georgiou X, Dimou S, Diallinas G, Samiotaki M. The interactome of the UapA transporter reveals putative new players in anterograde membrane cargo trafficking. Fungal Genet Biol 2023; 169:103840. [PMID: 37730157 DOI: 10.1016/j.fgb.2023.103840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
Neosynthesized plasma membrane (PM) proteins co-translationally translocate to the ER, concentrate at regions called ER-exit sites (ERes) and pack into COPII secretory vesicles which are sorted to the early-Golgi through membrane fusion. Following Golgi maturation, membrane cargoes reach the late-Golgi, from where they exit in clathrin-coated vesicles destined to the PM, directly or through endosomes. Post-Golgi membrane cargo trafficking also involves the cytoskeleton and the exocyst. The Golgi-dependent secretory pathway is thought to be responsible for the trafficking of all major membrane proteins. However, our recent findings in Aspergillus nidulans showed that several plasma membrane cargoes, such as transporters and receptors, follow a sorting route that seems to bypass Golgi functioning. To gain insight on membrane trafficking and specifically Golgi-bypass, here we used proximity dependent biotinylation (PDB) coupled with data-independent acquisition mass spectrometry (DIA-MS) for identifying transient interactors of the UapA transporter. Our assays, which included proteomes of wild-type and mutant strains affecting ER-exit or endocytosis, identified both expected and novel interactions that might be physiologically relevant to UapA trafficking. Among those, we validated, using reverse genetics and fluorescence microscopy, that COPI coatomer is essential for ER-exit and anterograde trafficking of UapA and other membrane cargoes. We also showed that ArfAArf1 GTPase activating protein (GAP) Glo3 contributes to UapA trafficking at increased temperature. This is the first report addressing the identification of transient interactions during membrane cargo biogenesis using PDB and proteomics coupled with fungal genetics. Our work provides a basis for dissecting dynamic membrane cargo trafficking via PDB assays.
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Affiliation(s)
- Xenia Georgiou
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens 15784, Greece
| | - Sofia Dimou
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens 15784, Greece
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, Athens 15784, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion 70013, Greece.
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming", Institute for Bioinnovation, Vari 16672, Greece.
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70
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Lane DM, Valentine DL, Peng X. Genomic analysis of the marine yeast Rhodotorula sphaerocarpa ETNP2018 reveals adaptation to the open ocean. BMC Genomics 2023; 24:695. [PMID: 37986036 PMCID: PMC10662464 DOI: 10.1186/s12864-023-09791-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Despite a rising interest in the diversity and ecology of fungi in marine environments, there are few published genomes of fungi isolated from the ocean. The basidiomycetous yeast (unicellular fungus) genus Rhodotorula are prevalent and abundant in the open ocean, and they have been isolated from a wide range of other environments. Many of these environments are nutrient poor, such as the Antarctica and the Atacama deserts, raising the question as to how Rhodotorula yeasts may have adapted their metabolic strategies to optimize survival under low nutrient conditions. In order to understand their adaptive strategies in the ocean, the genome of R. sphaerocarpa ETNP2018 was compared to that of fourteen representative Rhodotorula yeasts, isolated from a variety of environments. RESULTS Rhodotorula sphaerocarpa ETNP2018, a strain isolated from the oligotrophic part of the eastern tropical North Pacific (ETNP) oxygen minimum zone (OMZ), hosts the smallest of the fifteen genomes and yet the number of protein-coding genes it possesses is on par with the other strains. Its genome exhibits a distinct reduction in genes dedicated to Major Facilitator Superfamily transporters as well as biosynthetic enzymes. However, its core metabolic pathways are fully conserved. Our research indicates that the selective pressures of the ETNP OMZ favor a streamlined genome with reduced overall biosynthetic potential balanced by a stable set of core metabolisms and an expansion of mechanisms for nutrient acquisition. CONCLUSIONS In summary, this study offers insights into the adaptation of fungi to the oligotrophic ocean and provides valuable information for understanding the ecological roles of fungi in the ocean.
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Affiliation(s)
- Dylan M Lane
- School of Earth, Ocean, and Environment, University of South Carolina, Columbia, SC, USA
| | - David L Valentine
- Marine Science Institute, University of California, Santa Barbara, CA, USA
- Department of Earth Science, University of California, Santa Barbara, CA, USA
| | - Xuefeng Peng
- School of Earth, Ocean, and Environment, University of South Carolina, Columbia, SC, USA.
- Marine Science Institute, University of California, Santa Barbara, CA, USA.
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Tremblay R, Mehrjoo Y, Ahmed O, Simoneau A, McQuaid ME, Affar EB, Nislow C, Giaever G, Wurtele H. Persistent Acetylation of Histone H3 Lysine 56 Compromises the Activity of DNA Replication Origins. Mol Cell Biol 2023; 43:566-595. [PMID: 37811746 PMCID: PMC10791153 DOI: 10.1080/10985549.2023.2259739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 08/09/2023] [Indexed: 10/10/2023] Open
Abstract
In Saccharomyces cerevisiae, newly synthesized histones H3 are acetylated on lysine 56 (H3 K56ac) by the Rtt109 acetyltransferase prior to their deposition on nascent DNA behind replication forks. Two deacetylases of the sirtuin family, Hst3 and Hst4, remove H3 K56ac from chromatin after S phase. hst3Δ hst4Δ cells present constitutive H3 K56ac, which sensitizes cells to replicative stress via unclear mechanisms. A chemogenomic screen revealed that DBF4 heterozygosity sensitizes cells to NAM-induced inhibition of sirtuins. DBF4 and CDC7 encode subunits of the Dbf4-dependent kinase (DDK), which activates origins of DNA replication during S phase. We show that (i) cells harboring the dbf4-1 or cdc7-4 hypomorphic alleles are sensitized to NAM, and that (ii) the sirtuins Sir2, Hst1, Hst3, and Hst4 promote DNA replication in cdc7-4 cells. We further demonstrate that Rif1, an inhibitor of DDK-dependent activation of origins, causes DNA damage and replication defects in NAM-treated cells and hst3Δ hst4Δ mutants. cdc7-4 hst3Δ hst4Δ cells are shown to display delayed initiation of DNA replication, which is not due to intra-S checkpoint activation but requires Rtt109-dependent H3 K56ac. Our results suggest that constitutive H3 K56ac sensitizes cells to replicative stress in part by negatively influencing the activation of origins of DNA replication.
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Affiliation(s)
- Roch Tremblay
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Yosra Mehrjoo
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Oumaima Ahmed
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Antoine Simoneau
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montreal, Québec, Canada
| | - Mary E. McQuaid
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Department of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Québec, Canada
- Department of Medicine, Université de Montréal, Montreal, Québec, Canada
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72
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LaPeruta AJ, Micic J, Woolford Jr. JL. Additional principles that govern the release of pre-ribosomes from the nucleolus into the nucleoplasm in yeast. Nucleic Acids Res 2023; 51:10867-10883. [PMID: 35736211 PMCID: PMC10639060 DOI: 10.1093/nar/gkac430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 05/05/2022] [Accepted: 06/20/2022] [Indexed: 11/14/2022] Open
Abstract
During eukaryotic ribosome biogenesis, pre-ribosomes travel from the nucleolus, where assembly is initiated, to the nucleoplasm and then are exported to the cytoplasm, where assembly concludes. Although nuclear export of pre-ribosomes has been extensively investigated, the release of pre-ribosomes from the nucleolus is an understudied phenomenon. Initial data indicate that unfolded rRNA interacts in trans with nucleolar components and that, when rRNA folds due to ribosomal protein (RP) binding, the number of trans interactions drops below the threshold necessary for nucleolar retention. To validate and expand on this idea, we performed a bioinformatic analysis of the protein components of the Saccharomyces cerevisiae ribosome assembly pathway. We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs. We also analyzed cryo-EM structures of ribosome assembly intermediates to determine how nucleolar pre-ribosomes differ from post-nucleolar pre-ribosomes, specifically the capacity of RPs, RiBi factors, and rRNA components to interact in trans. We observed a significant decrease in the theoretical trans-interacting capability of pre-ribosomes between nucleolar and post-nucleolar stages of assembly due to the release of RiBi factors from particles and the folding of rRNA. Here, we provide a mechanism for the release of pre-ribosomes from the nucleolus.
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Affiliation(s)
- Amber J LaPeruta
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jelena Micic
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - John L Woolford Jr.
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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73
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Hodgens C, Flaherty DT, Pullen AM, Khan I, English NJ, Gillan L, Rojas-Pierce M, Akpa BS. Model-based inference of a plant-specific dual role for HOPS in regulating guard cell vacuole fusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.565947. [PMID: 37986942 PMCID: PMC10659295 DOI: 10.1101/2023.11.07.565947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Stomata are the pores on a leaf surface that regulate gas exchange. Each stoma consists of two guard cells whose movements regulate pore opening and thereby control CO2 fixation and water loss. Guard cell movements depend in part on the remodeling of vacuoles, which have been observed to change from a highly fragmented state to a fused morphology during stomata opening. This change in morphology requires a membrane fusion mechanism that responds rapidly to environmental signals, allowing plants to respond to diurnal and stress cues. With guard cell vacuoles being both large and responsive to external signals, stomata represent a unique system in which to delineate mechanisms of membrane fusion. Fusion of vacuole membranes is a highly conserved process in eukaryotes, with key roles played by two multi-subunit complexes: HOPS (homotypic fusion and vacuolar protein sorting) and SNARE (soluble NSF attachment protein receptor). HOPS is a vacuole tethering factor that is thought to chaperone SNAREs from apposing vacuole membranes into a fusion-competent complex capable of rearranging membranes. To resolve a counter-intuitive observation regarding the role of HOPS in regulating plant vacuole morphology, we derived a quantitative model of vacuole fusion dynamics and used it to generate testable predictions about HOPS-SNARE interactions. We derived our model by applying simulation-based inference to integrate prior knowledge about molecular interactions with limited, qualitative observations of emergent vacuole phenotypes. By constraining the model parameters to yield the emergent outcomes observed for stoma opening - as induced by two distinct chemical treatments - we predicted a dual role for HOPS and identified a stalled form of the SNARE complex that differs from phenomena reported in yeast. We predict that HOPS has contradictory actions at different points in the fusion signaling pathway, promoting the formation of SNARE complexes, but limiting their activity.
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Affiliation(s)
- Charles Hodgens
- Department of Chemical and Biomolecular Engineering, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - DT Flaherty
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Anne-Marie Pullen
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Imran Khan
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Nolan J English
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Lydia Gillan
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Marcela Rojas-Pierce
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Belinda S Akpa
- Department of Chemical and Biomolecular Engineering, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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74
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Blount BA, Lu X, Driessen MR, Jovicevic D, Sanchez MI, Ciurkot K, Zhao Y, Lauer S, McKiernan RM, Gowers GOF, Sweeney F, Fanfani V, Lobzaev E, Palacios-Flores K, Walker RS, Hesketh A, Cai J, Oliver SG, Cai Y, Stracquadanio G, Mitchell LA, Bader JS, Boeke JD, Ellis T. Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics. CELL GENOMICS 2023; 3:100418. [PMID: 38020971 PMCID: PMC10667340 DOI: 10.1016/j.xgen.2023.100418] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 07/13/2023] [Accepted: 09/08/2023] [Indexed: 12/01/2023]
Abstract
We describe construction of the synthetic yeast chromosome XI (synXI) and reveal the effects of redesign at non-coding DNA elements. The 660-kb synthetic yeast genome project (Sc2.0) chromosome was assembled from synthesized DNA fragments before CRISPR-based methods were used in a process of bug discovery, redesign, and chromosome repair, including precise compaction of 200 kb of repeat sequence. Repaired defects were related to poor centromere function and mitochondrial health and were associated with modifications to non-coding regions. As part of the Sc2.0 design, loxPsym sequences for Cre-mediated recombination are inserted between most genes. Using the GAP1 locus from chromosome XI, we show that these sites can facilitate induced extrachromosomal circular DNA (eccDNA) formation, allowing direct study of the effects and propagation of these important molecules. Construction and characterization of synXI contributes to our understanding of non-coding DNA elements, provides a useful tool for eccDNA study, and will inform future synthetic genome design.
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Affiliation(s)
- Benjamin A. Blount
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Xinyu Lu
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Maureen R.M. Driessen
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Dejana Jovicevic
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Mateo I. Sanchez
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Klaudia Ciurkot
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Stephanie Lauer
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Robert M. McKiernan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Glen-Oliver F. Gowers
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Fiachra Sweeney
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Viola Fanfani
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Evgenii Lobzaev
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- School of Informatics, The University of Edinburgh, Edinburgh, UK
| | - Kim Palacios-Flores
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, México
| | - Roy S.K. Walker
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh, UK
| | - Andy Hesketh
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jitong Cai
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Yizhi Cai
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | - Leslie A. Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
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75
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Jakobson CM, Aguilar-Rodríguez J, Jarosz DF. Hsp90 shapes adaptation by controlling the fitness consequences of regulatory variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564848. [PMID: 37961536 PMCID: PMC10634948 DOI: 10.1101/2023.10.30.564848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The essential stress-responsive chaperone Hsp90 impacts development and adaptation from microbes to humans. Yet despite evidence of its role in evolution, pathogenesis, and oncogenic transformation, the molecular mechanisms by which Hsp90 alters the consequences of mutations remain vigorously debated. Here we exploit the power of nucleotide-resolution genetic mapping in Saccharomyces cerevisiae to uncover more than 1,000 natural variant-to-phenotype associations governed by this molecular chaperone. Strikingly, Hsp90 more frequently modified the phenotypic effects of cis-regulatory variation than variants that altered protein sequence. Moreover, these interactions made the largest contribution to Hsp90-dependent heredity. Nearly all interacting variants-both regulatory and protein-coding-fell within clients of Hsp90 or targets of its direct binding partners. Hsp90 activity affected mutations in evolutionarily young genes, segmental deletions, and heterozygotes, highlighting its influence on variation central to evolutionary novelty. Reconciling the diverse epistatic effects of this chaperone, synthetic transcriptional regulation and reconstructions of natural alleles by genome editing revealed a central role for Hsp90 in regulating the fundamental relationship between activity and phenotype. Our findings establish that non-coding variation is a core driver of Hsp90's influence on heredity, offering a mechanistic explanation for the chaperone's strong effects on evolution and development across species.
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Affiliation(s)
- Christopher M. Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally
| | - José Aguilar-Rodríguez
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- These authors contributed equally
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
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76
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Klugherz I, Basch M, Ng N, Zhu Z, Wagener N, Wagener J. Only One of Three Bcs1 Homologs in Aspergillus fumigatus Confers Respiratory Growth. J Fungi (Basel) 2023; 9:1074. [PMID: 37998879 PMCID: PMC10672213 DOI: 10.3390/jof9111074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
The mitochondrial translocase Bcs1 is required for the correct assembly of complex III of the mitochondrial respiratory chain. Because of its importance, Bcs1 was recently proposed as a target for antifungal agents. The function of this AAA (ATPase Associated with diverse cellular Activities) protein has been extensively characterized in Saccharomyces cerevisiae. This yeast as well as previously studied mammals each encode only one homolog. In contrast, the pathogenic mold Aspergillus fumigatus encodes three putative Bcs1 homologs, none of which have been characterized to date. To study the role of these three homologs in A. fumigatus, conditional and deletion mutants of the respective genes AFUA_3G13000 (bcs1A), AFUA_4G01260 (bcs1B), and AFUA_2G14760 (bcs1C) were generated. A deletion or downregulation of bcs1A resulted in drastically reduced growth and sporulation rates and in a significantly altered susceptibility to azole antifungals. In contrast, mutants lacking Bcs1B or Bcs1C did not show any phenotypes differing from the wild type. Salicylhydroxamic acid-an inhibitor of the alternative oxidase that allows the respiratory chain to bypass complex III in some species-caused a complete growth arrest of the bcs1A deletion mutant. In a Galleria mellonella infection model, the deletion of bcs1A resulted in significantly decreased virulence. Only Bcs1A was able to partially complement a deletion of BCS1 in S. cerevisiae. The subcellular localization of Bcs1B and Bcs1C outside of mitochondria suggests that these Bcs1 homologs exert cellular functions different from that of Bcs1. Our data demonstrate that Bcs1A is the sole Bcs1 ortholog in A. fumigatus.
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Affiliation(s)
- Isabel Klugherz
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, Ludwig-Maximilians-Universität München, 80336 Munich, Germany; (I.K.)
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Marion Basch
- Zell- und Entwicklungsbiologie, Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152 Munich, Germany
| | - Natanya Ng
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, The University of Dublin, St James’s Hospital Campus, D08 RX0X Dublin, Ireland
| | - Zhaojun Zhu
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, Ludwig-Maximilians-Universität München, 80336 Munich, Germany; (I.K.)
| | - Nikola Wagener
- Zell- und Entwicklungsbiologie, Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152 Munich, Germany
| | - Johannes Wagener
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, Ludwig-Maximilians-Universität München, 80336 Munich, Germany; (I.K.)
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, The University of Dublin, St James’s Hospital Campus, D08 RX0X Dublin, Ireland
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77
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Yella VR, Vanaja A. Computational analysis on the dissemination of non-B DNA structural motifs in promoter regions of 1180 cellular genomes. Biochimie 2023; 214:101-111. [PMID: 37311475 DOI: 10.1016/j.biochi.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/05/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
The promoter regions of gene regulation are under evolutionary constraints and earlier studies uncovered that they are characterized by enrichment of functional non-B DNA structural signatures like curved DNA, cruciform DNA, G-quadruplex, triple-helical DNA, slipped DNA structures, and Z-DNA. However, these studies are restricted to a few model organisms, single non-B DNA motif types, or whole genomic sequences, and their comparative accumulation in promoter regions of different domains of life has not been reported comprehensively. In this study, for the first time, we investigated the preponderance of non-B DNA-prone motifs in promoter regions in 1180 genomes belonging to 28 taxonomic groups using the non-B DNA Motif Search Tool (nBMST). The trends suggest that they are predominant in promoters compared to the upstream and downstream regions of all three domains of life and variably linked to taxonomic groups. Cruciform DNA motif is the most abundant form of non-B DNA, spanning from archaea to lower eukaryotes. Curved DNA motifs are prominent in host-associated bacteria, and suppressed in mammals. Triplex-DNA and slipped DNA structure repeats are discretely dispersed in all lineages. G-quadruplex motifs are significantly enriched in mammals. We also observed that the unique enrichment of non-B DNA in promoters is strongly linked to genome GC, size, evolutionary time divergence, and ecological adaptations. Overall, our work systematically reports the unique non-B DNA structural landscape of cellular organisms from the perspective of the cis-regulatory code of genomes.
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Affiliation(s)
- Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India.
| | - Akkinepally Vanaja
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India; KL College of Pharmacy, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India
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78
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Záhonová K, Füssy Z, Stairs CW, Leger MM, Tachezy J, Čepička I, Roger AJ, Hampl V. Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans. Microb Genom 2023; 9. [PMID: 37994879 DOI: 10.1099/mgen.0.001143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles (MROs) adapted to function anaerobically. We compared in silico reconstructed MRO proteomes of eight species (six genera) and found that the common ancestor of Archamoebae possessed very few typical components of the protein translocation machinery, electron transport chain and tricarboxylic acid cycle. On the other hand, it contained a sulphate activation pathway and bacterial iron-sulphur (Fe-S) assembly system of MIS-type. The metabolic capacity of the MROs, however, varies markedly within this clade. The glycine cleavage system is widely conserved among Archamoebae, except in Entamoeba, probably owing to its role in catabolic function or one-carbon metabolism. MRO-based pyruvate metabolism was dispensed within subgroups Entamoebidae and Rhizomastixidae, whereas sulphate activation could have been lost in isolated cases of Rhizomastix libera, Mastigamoeba abducta and Endolimax sp. The MIS (Fe-S) assembly system was duplicated in the common ancestor of Mastigamoebidae and Pelomyxidae, and one of the copies took over Fe-S assembly in their MRO. In Entamoebidae and Rhizomastixidae, we hypothesize that Fe-S cluster assembly in both compartments may be facilitated by dual localization of the single system. We could not find evidence for changes in metabolic functions of the MRO in response to changes in habitat; it appears that such environmental drivers do not strongly affect MRO reduction in this group of eukaryotes.
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Affiliation(s)
- Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Courtney W Stairs
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Microbiology Research Group, Department of Biology, Lund University, Lund, Sweden
| | - Michelle M Leger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
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79
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Wacholder A, Carvunis AR. Biological Factors and Statistical Limitations Prevent Detection of Most Noncanonical Proteins by Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.09.531963. [PMID: 36945638 PMCID: PMC10028962 DOI: 10.1101/2023.03.09.531963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Ribosome profiling experiments indicate pervasive translation of short open reading frames (ORFs) outside of annotated protein-coding genes. However, shotgun mass spectrometry experiments typically detect only a small fraction of the predicted protein products of this noncanonical translation. The rarity of detection could indicate that most predicted noncanonical proteins are rapidly degraded and not present in the cell; alternatively, it could reflect technical limitations. Here we leveraged recent advances in ribosome profiling and mass spectrometry to investigate the factors limiting detection of noncanonical proteins in yeast. We show that the low detection rate of noncanonical ORF products can largely be explained by small size and low translation levels and does not indicate that they are unstable or biologically insignificant. In particular, proteins encoded by evolutionarily young genes, including those with well-characterized biological roles, are too short and too lowly-expressed to be detected by shotgun mass spectrometry at current detection sensitivities. Additionally, we find that decoy biases can give misleading estimates of noncanonical protein false discovery rates, potentially leading to false detections. After accounting for these issues, we found strong evidence for four noncanonical proteins in mass spectrometry data, which were also supported by evolution and translation data. These results illustrate the power of mass spectrometry to validate unannotated genes predicted by ribosome profiling, but also its substantial limitations in finding many biologically relevant lowly-expressed proteins.
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80
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Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. MICROBIOME RESEARCH REPORTS 2023; 3:2. [PMID: 38455081 PMCID: PMC10917621 DOI: 10.20517/mrr.2023.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 03/09/2024]
Abstract
Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.
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Affiliation(s)
| | | | | | - Duccio Cavalieri
- Correspondence to: Prof. Duccio Cavalieri, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy. E-mail:
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81
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Sterrett MC, Cureton LA, Cohen LN, van Hoof A, Khoshnevis S, Fasken MB, Corbett AH, Ghalei H. Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562946. [PMID: 37904946 PMCID: PMC10614903 DOI: 10.1101/2023.10.18.562946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The RNA exosome is an evolutionarily conserved exoribonuclease complex that consists of a 3-subunit cap, a 6-subunit barrel-shaped core, and a catalytic base subunit. Missense mutations in genes encoding structural subunits of the RNA exosome cause a growing family of diseases with diverse pathologies, collectively termed RNA exosomopathies. The disease symptoms vary and can manifest as neurological defects or developmental disorders. The diversity of the RNA exosomopathy pathologies suggests that the different missense mutations in structural genes result in distinct in vivo consequences. To investigate these functional consequences and distinguish whether they are unique to each RNA exosomopathy mutation, we generated a collection of in vivo models using budding yeast by introducing pathogenic missense mutations in orthologous S. cerevisiae genes. We then performed a comparative RNA-seq analysis to assess broad transcriptomic changes in each mutant model. Three of the mutant models rrp4-G226D, rrp40-W195R and rrp46-L191H, which model mutations in the genes encoding structural subunits of the RNA exosome, EXOSC2, EXOSC3 and EXOSC5 showed the largest transcriptomic differences. Further analyses revealed shared increased transcripts enriched in translation or ribosomal RNA modification/processing pathways across the three mutant models. Studies of the impact of the mutations on translation revealed shared defects in ribosome biogenesis but distinct impacts on translation. Collectively, our results provide the first comparative analysis of several RNA exosomopathy mutant models and suggest that different RNA exosomopathy mutations result in in vivo consequences that are both unique and shared across each variant, providing more insight into the biology underlying each distinct pathology.
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Affiliation(s)
- Maria C. Sterrett
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
| | - Lauryn A. Cureton
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Lauren N. Cohen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Sohail Khoshnevis
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Milo B. Fasken
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | | | - Homa Ghalei
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
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82
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Farley FW, McCully RR, Maslo PB, Yu L, Sheff MA, Sadeghi H, Elion EA. Effects of HSP70 chaperones Ssa1 and Ssa2 on Ste5 scaffold and the mating mitogen-activated protein kinase (MAPK) pathway in Saccharomyces cerevisiae. PLoS One 2023; 18:e0289339. [PMID: 37851593 PMCID: PMC10584130 DOI: 10.1371/journal.pone.0289339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 07/17/2023] [Indexed: 10/20/2023] Open
Abstract
Ste5 is a prototype of scaffold proteins that regulate activation of mitogen-activated protein kinase (MAPK) cascades in all eukaryotes. Ste5 associates with many proteins including Gβγ (Ste4), Ste11 MAPKKK, Ste7 MAPKK, Fus3 and Kss1 MAPKs, Bem1, Cdc24. Here we show that Ste5 also associates with heat shock protein 70 chaperone (Hsp70) Ssa1 and that Ssa1 and its ortholog Ssa2 are together important for Ste5 function and efficient mating responses. The majority of purified overexpressed Ste5 associates with Ssa1. Loss of Ssa1 and Ssa2 has deleterious effects on Ste5 abundance, integrity, and localization particularly when Ste5 is expressed at native levels. The status of Ssa1 and Ssa2 influences Ste5 electrophoresis mobility and formation of high molecular weight species thought to be phosphorylated, ubiquitinylated and aggregated and lower molecular weight fragments. A Ste5 VWA domain mutant with greater propensity to form punctate foci has reduced predicted propensity to bind Ssa1 near the mutation sites and forms more punctate foci when Ssa1 Is overexpressed, supporting a dynamic protein quality control relationship between Ste5 and Ssa1. Loss of Ssa1 and Ssa2 reduces activation of Fus3 and Kss1 MAPKs and FUS1 gene expression and impairs mating shmoo morphogenesis. Surprisingly, ssa1, ssa2, ssa3 and ssa4 single, double and triple mutants can still mate, suggesting compensatory mechanisms exist for folding. Additional analysis suggests Ssa1 is the major Hsp70 chaperone for the mating and invasive growth pathways and reveals several Hsp70-Hsp90 chaperone-network proteins required for mating morphogenesis.
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Affiliation(s)
- Francis W. Farley
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Ryan R. McCully
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Paul B. Maslo
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Lu Yu
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Mark A. Sheff
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Homayoun Sadeghi
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
| | - Elaine A. Elion
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, United States of America
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83
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Postaru M, Tucaliuc A, Cascaval D, Galaction AI. Cellular Stress Impact on Yeast Activity in Biotechnological Processes-A Short Overview. Microorganisms 2023; 11:2522. [PMID: 37894181 PMCID: PMC10609598 DOI: 10.3390/microorganisms11102522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/28/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
The importance of Saccharomyces cerevisiae yeast cells is known worldwide, as they are the most used microorganisms in biotechnology for bioethanol and biofuel production. Also, they are analyzed and studied for their similar internal biochemical processes to human cells, for a better understanding of cell aging and response to cell stressors. The special ability of S. cerevisiae cells to develop in both aerobic and anaerobic conditions makes this microorganism a viable model to study the transformations and the way in which cellular metabolism is directed to face the stress conditions due to environmental changes. Thus, this review will emphasize the effects of oxidative, ethanol, and osmotic stress and also the physiological and genetic response of stress mitigation in yeast cells.
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Affiliation(s)
- Madalina Postaru
- Department of Biomedical Science, Faculty of Medical Bioengineering, “Grigore T. Popa” University of Medicine and Pharmacy of Iasi, M. Kogălniceanu 9-13, 700454 Iasi, Romania;
| | - Alexandra Tucaliuc
- Department of Organic, Biochemical and Food, “Cristofor Simionescu” Faculty of Chemical, Engineering and Environmental Protection, Engineering, “Gheorghe Asachi” Technical University of Iasi, D. Mangeron 73, 700050 Iasi, Romania; (A.T.); (D.C.)
| | - Dan Cascaval
- Department of Organic, Biochemical and Food, “Cristofor Simionescu” Faculty of Chemical, Engineering and Environmental Protection, Engineering, “Gheorghe Asachi” Technical University of Iasi, D. Mangeron 73, 700050 Iasi, Romania; (A.T.); (D.C.)
| | - Anca-Irina Galaction
- Department of Biomedical Science, Faculty of Medical Bioengineering, “Grigore T. Popa” University of Medicine and Pharmacy of Iasi, M. Kogălniceanu 9-13, 700454 Iasi, Romania;
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84
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Sharp NP, Smith DR, Driscoll G, Sun K, Vickerman CM, Martin SCT. Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast. Genome Biol Evol 2023; 15:evad179. [PMID: 37847861 PMCID: PMC10581546 DOI: 10.1093/gbe/evad179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
The ribosomal DNA array in Saccharomyces cerevisiae consists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that unselected mutations elsewhere in the genome can disrupt copy number maintenance. In consequence, copy number generally declines gradually, consistent with a previously proposed model of rDNA maintenance where a downward mutational bias is normally compensated by mechanisms that increase copy number when it is low. This pattern holds across ploidy levels and strains in the standard lab environment but differs under some stressful conditions. We identify several alleles, gene categories, and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself are distinct from the rest of the genome and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.
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Affiliation(s)
- Nathaniel P Sharp
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Denise R Smith
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gregory Driscoll
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kexin Sun
- Present address: Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Sterling C T Martin
- Present address: Department of Biology, Washington University, St. Louis, Missouri, USA
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85
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Lemière J, Chang F. Quantifying turgor pressure in budding and fission yeasts based upon osmotic properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544129. [PMID: 37333400 PMCID: PMC10274794 DOI: 10.1101/2023.06.07.544129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Walled cells, such as plants, fungi, and bacteria cells, possess a high internal hydrostatic pressure, termed turgor pressure, that drives volume growth and contributes to cell shape determination. Rigorous measurement of turgor pressure, however, remains challenging, and reliable quantitative measurements, even in budding yeast are still lacking. Here, we present a simple and robust experimental approach to access turgor pressure in yeasts based upon the determination of isotonic concentration using protoplasts as osmometers. We propose three methods to identify the isotonic condition - 3D cell volume, cytoplasmic fluorophore intensity, and mobility of a cytGEMs nano-rheology probe - that all yield consistent values. Our results provide turgor pressure estimates of 1.0 ± 0.1 MPa for S. pombe, 0.49 ± 0.01 MPa for S. japonicus, 0.5 ± 0.1 MPa for S. cerevisiae W303a and 0.31 ± 0.03 MPa for S. cerevisiae BY4741. Large differences in turgor pressure and nano-rheology measurements between the S. cerevisiae strains demonstrate how fundamental biophysical parameters can vary even among wildtype strains of the same species. These side-by-side measurements of turgor pressure in multiple yeast species provide critical values for quantitative studies on cellular mechanics and comparative evolution.
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Affiliation(s)
- Joël Lemière
- Department of Cell and Tissue Biology, University of San Francisco, CA, USA
| | - Fred Chang
- Department of Cell and Tissue Biology, University of San Francisco, CA, USA
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86
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Dixon TA, Walker RSK, Pretorius IS. Visioning synthetic futures for yeast research within the context of current global techno-political trends. Yeast 2023; 40:443-456. [PMID: 37653687 DOI: 10.1002/yea.3897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
Yeast research is entering into a new period of scholarship, with new scientific tools, new questions to ask and new issues to consider. The politics of emerging and critical technology can no longer be separated from the pursuit of basic science in fields, such as synthetic biology and engineering biology. Given the intensifying race for technological leadership, yeast research is likely to attract significant investment from government, and that it offers huge opportunities to the curious minded from a basic research standpoint. This article provides an overview of new directions in yeast research with a focus on Saccharomyces cerevisiae, and places these trends in their geopolitical context. At the highest level, yeast research is situated within the ongoing convergence of the life sciences with the information sciences. This convergent effect is most strongly pronounced in areas of AI-enabled tools for the life sciences, and the creation of synthetic genomes, minimal genomes, pan-genomes, neochromosomes and metagenomes using computer-assisted design tools and methodologies. Synthetic yeast futures encompass basic and applied science questions that will be of intense interest to government and nongovernment funding sources. It is essential for the yeast research community to map and understand the context of their research to ensure their collaborations turn global challenges into research opportunities.
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Affiliation(s)
- Thomas A Dixon
- School of Social Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Roy S K Walker
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
| | - Isak S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
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87
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Garge RK, Geck RC, Armstrong JO, Dunn B, Boutz DR, Battenhouse A, Leutert M, Dang V, Jiang P, Kwiatkowski D, Peiser T, McElroy H, Marcotte EM, Dunham MJ. Systematic Profiling of Ale Yeast Protein Dynamics across Fermentation and Repitching. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558736. [PMID: 37790497 PMCID: PMC10543003 DOI: 10.1101/2023.09.21.558736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Studying the genetic and molecular characteristics of brewing yeast strains is crucial for understanding their domestication history and adaptations accumulated over time in fermentation environments, and for guiding optimizations to the brewing process itself. Saccharomyces cerevisiae (brewing yeast) is amongst the most profiled organisms on the planet, yet the temporal molecular changes that underlie industrial fermentation and beer brewing remain understudied. Here, we characterized the genomic makeup of a Saccharomyces cerevisiae ale yeast widely used in the production of Hefeweizen beers, and applied shotgun mass spectrometry to systematically measure the proteomic changes throughout two fermentation cycles which were separated by 14 rounds of serial repitching. The resulting brewing yeast proteomics resource includes 64,740 protein abundance measurements. We found that this strain possesses typical genetic characteristics of Saccharomyces cerevisiae ale strains and displayed progressive shifts in molecular processes during fermentation based on protein abundance changes. We observed protein abundance differences between early fermentation batches compared to those separated by 14 rounds of serial repitching. The observed abundance differences occurred mainly in proteins involved in the metabolism of ergosterol and isobutyraldehyde. Our systematic profiling serves as a starting point for deeper characterization of how the yeast proteome changes during commercial fermentations and additionally serves as a resource to guide fermentation protocols, strain handling, and engineering practices in commercial brewing and fermentation environments. Finally, we created a web interface (https://brewing-yeast-proteomics.ccbb.utexas.edu/) to serve as a valuable resource for yeast geneticists, brewers, and biochemists to provide insights into the global trends underlying commercial beer production.
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Affiliation(s)
- Riddhiman K. Garge
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Renee C. Geck
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Joseph O. Armstrong
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Barbara Dunn
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Daniel R. Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Houston Methodist Research Institute, Houston, Texas, USA
| | - Anna Battenhouse
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Vy Dang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Pengyao Jiang
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | | | | | - Edward M. Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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88
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Alidou-D'Anjou I, Patel A, Sleiman S, Dragon F. Human SHQ1 variants R335C and A426V lead to severe ribosome biogenesis defects when expressed in yeast. Front Genet 2023; 14:1240416. [PMID: 37818102 PMCID: PMC10560722 DOI: 10.3389/fgene.2023.1240416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/17/2023] [Indexed: 10/12/2023] Open
Abstract
SHQ1 is an essential chaperone that binds the pseudouridine synthase dyskerin in the cytoplasm and escorts the enzyme to the nucleus, where dyskerin is assembled into small nucleolar RNPs (snoRNPs) of the H/ACA class. These particles carry out pseudouridine formation in ribosomal RNAs (rRNAs) and participate in maturation of rRNA precursors (pre-rRNAs). Variants of human SHQ1 have been linked to neurodevelopmental deficiencies; here we focused on two compound heterozygous mutations identified in a child showing a severe neurological disorder comprising cerebellar degeneration. To investigate the molecular defects caused by mutations R335C and A426V we used a conditional yeast strain that can be depleted of the endogenous Shq1 protein while constitutively expressing human SHQ1 (wild-type or variants). Although wild-type SHQ1 complemented the Shq1-depleted strain, cells expressing variant R335C could not support growth, and cells expressing variant A426V were temperature-sensitive. When shifted to restrictive conditions, yeast cells progressively lost H/ACA snoRNAs and accumulated unprocessed pre-rRNAs, which led to reduced production of ribosomes. Levels of Cbf5 (yeast homologue of dyskerin) were decreased in yeast cells expressing SHQ1 variants under restrictive conditions. Immunoprecipitation experiments revealed that interaction of Cbf5 with SHQ1 variants was weakened but not abolished, and yeast two-hybrid assays showed that mutation R335C is more deleterious than mutation A426V. Our data provide additional evidence for the critical role of SHQ1 in chaperoning the pseudouridine synthase dyskerin, and how its inadequate function has detrimental consequences on the production of H/ACA snoRNPs and ribosomes.
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Affiliation(s)
- Ismaël Alidou-D'Anjou
- Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Départment des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Aniket Patel
- Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Départment des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Sophie Sleiman
- Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Départment des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - François Dragon
- Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Départment des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
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89
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Lupo O, Kumar DK, Livne R, Chappleboim M, Levy I, Barkai N. The architecture of binding cooperativity between densely bound transcription factors. Cell Syst 2023; 14:732-745.e5. [PMID: 37527656 DOI: 10.1016/j.cels.2023.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/23/2023] [Accepted: 06/27/2023] [Indexed: 08/03/2023]
Abstract
The binding of transcription factors (TFs) along genomes is restricted to a subset of sites containing their preferred motifs. TF-binding specificity is often attributed to the co-binding of interacting TFs; however, apart from specific examples, this model remains untested. Here, we define dependencies among budding yeast TFs that localize to overlapping promoters by profiling the genome-wide consequences of co-depleting multiple TFs. We describe unidirectional interactions, revealing Msn2 as a central factor allowing TF binding at its target promoters. By contrast, no case of mutual cooperation was observed. Particularly, Msn2 retained binding at its preferred promoters upon co-depletion of fourteen similarly bound TFs. Overall, the consequences of TF co-depletions were moderate, limited to a subset of promoters, and failed to explain the role of regions outside the DNA-binding domain in directing TF-binding preferences. Our results call for re-evaluating the role of cooperative interactions in directing TF-binding preferences.
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Affiliation(s)
- Offir Lupo
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Divya Krishna Kumar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Livne
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Chappleboim
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idan Levy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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90
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Garcia-Pardo J, Badaczewska-Dawid AE, Pintado-Grima C, Iglesias V, Kuriata A, Kmiecik S, Ventura S. A3DyDB: exploring structural aggregation propensities in the yeast proteome. Microb Cell Fact 2023; 22:186. [PMID: 37716955 PMCID: PMC10504709 DOI: 10.1186/s12934-023-02182-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND The budding yeast Saccharomyces cerevisiae (S. cerevisiae) is a well-established model system for studying protein aggregation due to the conservation of essential cellular structures and pathways found across eukaryotes. However, limited structural knowledge of its proteome has prevented a deeper understanding of yeast functionalities, interactions, and aggregation. RESULTS In this study, we introduce the A3D yeast database (A3DyDB), which offers an extensive catalog of aggregation propensity predictions for the S. cerevisiae proteome. We used Aggrescan 3D (A3D) and the newly released protein models from AlphaFold2 (AF2) to compute the structure-based aggregation predictions for 6039 yeast proteins. The A3D algorithm exploits the information from 3D protein structures to calculate their intrinsic aggregation propensities. To facilitate simple and intuitive data analysis, A3DyDB provides a user-friendly interface for querying, browsing, and visualizing information on aggregation predictions from yeast protein structures. The A3DyDB also allows for the evaluation of the influence of natural or engineered mutations on protein stability and solubility. The A3DyDB is freely available at http://biocomp.chem.uw.edu.pl/A3D2/yeast . CONCLUSION The A3DyDB addresses a gap in yeast resources by facilitating the exploration of correlations between structural aggregation propensity and diverse protein properties at the proteome level. We anticipate that this comprehensive database will become a standard tool in the modeling of protein aggregation and its implications in budding yeast.
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Affiliation(s)
- Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | | | - Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Aleksander Kuriata
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain.
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91
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Davis J, Meyer T, Smolnig M, Smethurst DG, Neuhaus L, Heyden J, Broeskamp F, Edrich ES, Knittelfelder O, Kolb D, Haar TVD, Gourlay CW, Rockenfeller P. A dynamic actin cytoskeleton is required to prevent constitutive VDAC-dependent MAPK signalling and aberrant lipid homeostasis. iScience 2023; 26:107539. [PMID: 37636069 PMCID: PMC10450525 DOI: 10.1016/j.isci.2023.107539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/14/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Abstract
The dynamic nature of the actin cytoskeleton is required to coordinate many cellular processes, and a loss of its plasticity has been linked to accelerated cell aging and attenuation of adaptive response mechanisms. Cofilin is an actin-binding protein that controls actin dynamics and has been linked to mitochondrial signaling pathways that control drug resistance and cell death. Here we show that cofilin-driven chronic depolarization of the actin cytoskeleton activates cell wall integrity mitogen-activated protein kinase (MAPK) signalling and disrupts lipid homeostasis in a voltage-dependent anion channel (VDAC)-dependent manner. Expression of the cof1-5 mutation, which reduces the dynamic nature of actin, triggers loss of cell wall integrity, vacuole fragmentation, disruption of lipid homeostasis, lipid droplet (LD) accumulation, and the promotion of cell death. The integrity of the actin cytoskeleton is therefore essential to maintain the fidelity of MAPK signaling, lipid homeostasis, and cell health in S. cerevisiae.
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Affiliation(s)
- Jack Davis
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Thorsten Meyer
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Martin Smolnig
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | | | - Lisa Neuhaus
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Jonas Heyden
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | - Filomena Broeskamp
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
| | | | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Dagmar Kolb
- Medical University of Graz, Core Facility Ultrastructure Analysis, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Campbell W. Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Patrick Rockenfeller
- Chair of Biochemistry and Molecular Medicine, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke (UW/H), Stockumer Str. 10, 58453 Witten, Germany
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92
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Jonas F, Vidavski M, Benuck E, Barkai N, Yaakov G. Nucleosome retention by histone chaperones and remodelers occludes pervasive DNA-protein binding. Nucleic Acids Res 2023; 51:8496-8513. [PMID: 37493599 PMCID: PMC10484674 DOI: 10.1093/nar/gkad615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023] Open
Abstract
DNA packaging within chromatin depends on histone chaperones and remodelers that form and position nucleosomes. Cells express multiple such chromatin regulators with overlapping in-vitro activities. Defining specific in-vivo activities requires monitoring histone dynamics during regulator depletion, which has been technically challenging. We have recently generated histone-exchange sensors in Saccharomyces cerevisiae, which we now use to define the contributions of 15 regulators to histone dynamics genome-wide. While replication-independent exchange in unperturbed cells maps to promoters, regulator depletions primarily affected gene bodies. Depletion of Spt6, Spt16 or Chd1 sharply increased nucleosome replacement sequentially at the beginning, middle or end of highly expressed gene bodies. They further triggered re-localization of chaperones to affected gene body regions, which compensated for nucleosome loss during transcription complex passage, but concurred with extensive TF binding in gene bodies. We provide a unified quantitative screen highlighting regulator roles in retaining nucleosome binding during transcription and preserving genomic packaging.
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Matan Vidavski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eli Benuck
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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93
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Hasenjäger S, Bologna A, Essen LO, Spadaccini R, Taxis C. C-terminal sequence stability profiling in Saccharomyces cerevisiae reveals protective protein quality control pathways. J Biol Chem 2023; 299:105166. [PMID: 37595870 PMCID: PMC10493509 DOI: 10.1016/j.jbc.2023.105166] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/22/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
Protein quality control (PQC) mechanisms are essential for degradation of misfolded or dysfunctional proteins. An essential part of protein homeostasis is recognition of defective proteins by PQC components and their elimination by the ubiquitin-proteasome system, often concentrating on protein termini as indicators of protein integrity. Changes in amino acid composition of C-terminal ends arise through protein disintegration, alternative splicing, or during the translation step of protein synthesis from premature termination or translational stop-codon read-through. We characterized reporter protein stability using light-controlled exposure of the random C-terminal peptide collection (CtPC) in budding yeast revealing stabilizing and destabilizing features of amino acids at positions -5 to -1 of the C terminus. The (de)stabilization properties of CtPC-degrons depend on amino acid identity, position, as well as composition of the C-terminal sequence and are transferable. Evolutionary pressure toward stable proteins in yeast is evidenced by amino acid residues under-represented in cytosolic and nuclear proteins at corresponding C-terminal positions, but over-represented in unstable CtPC-degrons, and vice versa. Furthermore, analysis of translational stop-codon read-through peptides suggested that such extended proteins have destabilizing C termini. PQC pathways targeting CtPC-degrons involved the ubiquitin-protein ligase Doa10 and the cullin-RING E3 ligase SCFDas1 (Skp1-Cullin-F-box protein). Overall, our data suggest a proteome protection mechanism that targets proteins with unnatural C termini by recognizing a surprisingly large number of C-terminal sequence variants.
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Affiliation(s)
- Sophia Hasenjäger
- Department of Biology/Genetics, Philipps-University Marburg, Marburg, Germany
| | - Andrea Bologna
- Department of Science and Technology, Universita' Degli Studi Del Sannio, Benevento, Italy
| | - Lars-Oliver Essen
- Department of Chemistry/Biochemistry, Philipps-University Marburg, Marburg, Germany
| | - Roberta Spadaccini
- Department of Science and Technology, Universita' Degli Studi Del Sannio, Benevento, Italy; Department of Chemistry/Biochemistry, Philipps-University Marburg, Marburg, Germany
| | - Christof Taxis
- Department of Medicine, Health and Medical University, Erfurt, Germany.
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94
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Petti S, Reddy G, Desai MM. Inferring sparse structure in genotype-phenotype maps. Genetics 2023; 225:iyad127. [PMID: 37437111 PMCID: PMC10471201 DOI: 10.1093/genetics/iyad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 05/24/2023] [Accepted: 06/21/2023] [Indexed: 07/14/2023] Open
Abstract
Correlation among multiple phenotypes across related individuals may reflect some pattern of shared genetic architecture: individual genetic loci affect multiple phenotypes (an effect known as pleiotropy), creating observable relationships between phenotypes. A natural hypothesis is that pleiotropic effects reflect a relatively small set of common "core" cellular processes: each genetic locus affects one or a few core processes, and these core processes in turn determine the observed phenotypes. Here, we propose a method to infer such structure in genotype-phenotype data. Our approach, sparse structure discovery (SSD) is based on a penalized matrix decomposition designed to identify latent structure that is low-dimensional (many fewer core processes than phenotypes and genetic loci), locus-sparse (each locus affects few core processes), and/or phenotype-sparse (each phenotype is influenced by few core processes). Our use of sparsity as a guide in the matrix decomposition is motivated by the results of a novel empirical test indicating evidence of sparse structure in several recent genotype-phenotype datasets. First, we use synthetic data to show that our SSD approach can accurately recover core processes if each genetic locus affects few core processes or if each phenotype is affected by few core processes. Next, we apply the method to three datasets spanning adaptive mutations in yeast, genotoxin robustness assay in human cell lines, and genetic loci identified from a yeast cross, and evaluate the biological plausibility of the core process identified. More generally, we propose sparsity as a guiding prior for resolving latent structure in empirical genotype-phenotype maps.
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Affiliation(s)
- Samantha Petti
- NSF-Simons Center for the Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gautam Reddy
- NSF-Simons Center for the Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
- Physics & Informatics Laboratories, NTT Research, Inc., Sunnyvale, CA 94085, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology and Department of Physics, Harvard University, Cambridge, MA 02138, USA
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95
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Hammond N, Snider J, Stagljar I, Mitchell K, Lagutin K, Jessulat M, Babu M, Teesdale-Spittle PH, Sheridan JP, Sturley SL, Munkacsi AB. Identification and characterization of protein interactions with the major Niemann-Pick type C disease protein in yeast reveals pathways of therapeutic potential. Genetics 2023; 225:iyad129. [PMID: 37440478 PMCID: PMC10471228 DOI: 10.1093/genetics/iyad129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/12/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Niemann-Pick type C (NP-C) disease is a rare lysosomal storage disease caused by mutations in NPC1 (95% cases) or NPC2 (5% cases). These proteins function together in cholesterol egress from the lysosome, whereby upon mutation, cholesterol and other lipids accumulate causing major pathologies. However, it is not fully understood how cholesterol is transported from NPC1 residing at the lysosomal membrane to the endoplasmic reticulum (ER) and plasma membrane. The yeast ortholog of NPC1, Niemann-Pick type C-related protein-1 (Ncr1), functions similarly to NPC1; when transfected into a mammalian cell lacking NPC1, Ncr1 rescues the diagnostic hallmarks of cholesterol and sphingolipid accumulation. Here, we aimed to identify and characterize protein-protein interactions (PPIs) with the yeast Ncr1 protein. A genome-wide split-ubiquitin membrane yeast two-hybrid (MYTH) protein interaction screen identified 11 ER membrane-localized, full-length proteins interacting with Ncr1 at the lysosomal/vacuolar membrane. These highlight the importance of ER-vacuole membrane interface and include PPIs with the Cyb5/Cbr1 electron transfer system, the ceramide synthase complex, and the Sec61/Sbh1 protein translocation complex. These PPIs were not detected in a sterol auxotrophy condition and thus depend on normal sterol metabolism. To provide biological context for the Ncr1-Cyb5 PPI, a yeast strain lacking this PPI (via gene deletions) exhibited altered levels of sterols and sphingolipids including increased levels of glucosylceramide that mimic NP-C disease. Overall, the results herein provide new physical and genetic interaction models to further use the yeast model of NP-C disease to better understand human NP-C disease.
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Affiliation(s)
- Natalie Hammond
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Mediterranean Institute for Life Sciences, Meštrovićevo Šetalište 45, HR-21000 Split, Croatia
| | | | | | - Matthew Jessulat
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Paul H Teesdale-Spittle
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeffrey P Sheridan
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Stephen L Sturley
- Department of Biology, Barnard College-Columbia University, New York, NY 10027, USA
| | - Andrew B Munkacsi
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
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96
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Bakti F, Stupperich H, Schmitt K, Valerius O, Köhler AM, Meister C, Strohdiek A, Harting R, Sasse C, Heimel K, Neumann P, Ficner R, Braus GH. Fungal COP9 signalosome assembly requires connection of two trimeric intermediates for integration of intrinsic deneddylase. Proc Natl Acad Sci U S A 2023; 120:e2305049120. [PMID: 37603767 PMCID: PMC10477865 DOI: 10.1073/pnas.2305049120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023] Open
Abstract
The conserved eight-subunit COP9 signalosome (CSN) is required for multicellular fungal development. The CSN deneddylase cooperates with the Cand1 exchange factor to control replacements of E3 ubiquitin cullin RING ligase receptors, providing specificity to eukaryotic protein degradation. Aspergillus nidulans CSN assembles through a heptameric pre-CSN, which is activated by integration of the catalytic CsnE deneddylase. Combined genetic and biochemical approaches provided the assembly choreography within a eukaryotic cell for native fungal CSN. Interactomes of functional GFP-Csn subunit fusions in pre-CSN deficient fungal strains were compared by affinity purifications and mass spectrometry. Two distinct heterotrimeric CSN subcomplexes were identified as pre-CSN assembly intermediates. CsnA-C-H and CsnD-F-G form independently of CsnB, which connects the heterotrimers to a heptamer and enables subsequent integration of CsnE to form the enzymatically active CSN complex. Surveillance mechanisms control accurate Csn subunit amounts and correct cellular localization for sequential assembly since deprivation of Csn subunits changes the abundance and location of remaining Csn subunits.
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Affiliation(s)
- Fruzsina Bakti
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Helena Stupperich
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Anna M. Köhler
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Cindy Meister
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Anja Strohdiek
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Rebekka Harting
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Christoph Sasse
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Kai Heimel
- Department of Microbial Cell Biology, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
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97
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Hegazy YA, Cloutier SC, Utturkar SM, Das S, Tran E. The genomic region of the 3' untranslated region (3'UTR) of PHO84, rather than the antisense RNA, promotes gene repression. Nucleic Acids Res 2023; 51:7900-7913. [PMID: 37462073 PMCID: PMC10450162 DOI: 10.1093/nar/gkad579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/20/2023] [Accepted: 07/14/2023] [Indexed: 08/26/2023] Open
Abstract
PHO84 is a budding yeast gene reported to be negatively regulated by its cognate antisense transcripts both in cis and in trans. In this study, we performed Transient-transcriptome sequencing (TT-seq) to investigate the correlation of sense/antisense pairs in a dbp2Δ strain and found over 700 sense/antisense pairs, including PHO84, to be positively correlated, contrasting the prevailing model. To define what mechanism regulates the PHO84 gene and how this regulation could have been originally attributed to repression by the antisense transcript, we conducted a series of molecular biology and genetics experiments. We now report that the 3' untranslated region (3'UTR) of PHO84 plays a repressive role in sense expression, an activity not linked to the antisense transcripts. Moreover, we provide results of a genetic screen for 3'UTR-dependent repression of PHO84 and show that the vast majority of identified factors are linked to negative regulation. Finally, we show that the PHO84 promoter and terminator form gene loops which correlate with transcriptional repression, and that the RNA-binding protein, Tho1, increases this looping and the 3'UTR-dependent repression. Our results negate the current model for antisense non-coding transcripts of PHO84 and suggest that many of these transcripts are byproducts of open chromatin.
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Affiliation(s)
- Youssef A Hegazy
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN 47907-2063, USA
| | - Sara C Cloutier
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN 47907-2063, USA
| | - Sagar M Utturkar
- Purdue University Institute for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street West Lafayette, IN 47907-2064, USA
| | - Subhadeep Das
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN 47907-2063, USA
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN 47907-2063, USA
- Purdue University Institute for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street West Lafayette, IN 47907-2064, USA
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98
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Franco-Losilla M, Nordzieke S, Feldmann I, Limón MC, Avalos J. HmbC, a Protein of the HMG Family, Participates in the Regulation of Carotenoid Biosynthesis in Fusarium fujikuroi. Genes (Basel) 2023; 14:1661. [PMID: 37628712 PMCID: PMC10454146 DOI: 10.3390/genes14081661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
In the fungus Fusarium fujikuroi, carotenoid production is up-regulated by light and down-regulated by the CarS RING finger protein, which modulates the mRNA levels of carotenoid pathway genes (car genes). To identify new potential regulators of car genes, we used a biotin-mediated pull-down procedure to detect proteins capable of binding to their promoters. We focused our attention on one of the proteins found in the screening, belonging to the High-Mobility Group (HMG) family that was named HmbC. The deletion of the hmbC gene resulted in increased carotenoid production due to higher mRNA levels of car biosynthetic genes. In addition, the deletion resulted in reduced carS mRNA levels, which could also explain the partial deregulation of the carotenoid pathway. The mutants exhibited other phenotypic traits, such as alterations in development under certain stress conditions, or reduced sensitivity to cell wall degrading enzymes, revealed by less efficient protoplast formation, indicating that HmbC is also involved in other cellular processes. In conclusion, we identified a protein of the HMG family that participates in the regulation of carotenoid biosynthesis. This is probably achieved through an epigenetic mechanism related to chromatin structure, as is frequent in this class of proteins.
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Affiliation(s)
- Marta Franco-Losilla
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (M.F.-L.); (J.A.)
| | - Steffen Nordzieke
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (M.F.-L.); (J.A.)
| | - Ingo Feldmann
- Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V., 44227 Dortmund, Germany;
| | - M. Carmen Limón
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (M.F.-L.); (J.A.)
| | - Javier Avalos
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (M.F.-L.); (J.A.)
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99
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O’Meara MJ, Rapala JR, Nichols CB, Alexandre C, Billmyre RB, Steenwyk JL, Alspaugh JA, O’Meara TR. CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553567. [PMID: 37645941 PMCID: PMC10462067 DOI: 10.1101/2023.08.17.553567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Elucidating gene function is a major goal in biology, especially among non-model organisms. However, doing so is complicated by the fact that molecular conservation does not always mirror functional conservation, and that complex relationships among genes are responsible for encoding pathways and higher-order biological processes. Co-expression, a promising approach for predicting gene function, relies on the general principal that genes with similar expression patterns across multiple conditions will likely be involved in the same biological process. For Cryptococcus neoformans, a prevalent human fungal pathogen greatly diverged from model yeasts, approximately 60% of the predicted genes in the genome lack functional annotations. Here, we leveraged a large amount of publicly available transcriptomic data to generate a C. neoformans Co-Expression Network (CryptoCEN), successfully recapitulating known protein networks, predicting gene function, and enabling insights into the principles influencing co-expression. With 100% predictive accuracy, we used CryptoCEN to identify 13 new DNA damage response genes, underscoring the utility of guilt-by-association for determining gene function. Overall, co-expression is a powerful tool for uncovering gene function, and decreases the experimental tests needed to identify functions for currently under-annotated genes.
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Affiliation(s)
- Matthew J. O’Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jackson R. Rapala
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Connie B. Nichols
- Departments of Medicine and Molecular Genetics/Microbiology; and Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christina Alexandre
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - R. Blake Billmyre
- Departments of Pharmaceutical and Biomedical Sciences/Infectious Disease, College of Pharmacy/College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - J. Andrew Alspaugh
- Departments of Medicine and Molecular Genetics/Microbiology; and Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Teresa R. O’Meara
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
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100
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Sterrett MC, Farchi D, Strassler SE, Boise LH, Fasken MB, Corbett AH. In vivo characterization of the critical interaction between the RNA exosome and the essential RNA helicase Mtr4 in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2023; 13:jkad049. [PMID: 36861343 PMCID: PMC10411580 DOI: 10.1093/g3journal/jkad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 03/03/2023]
Abstract
The RNA exosome is a conserved molecular machine that processes/degrades numerous coding and non-coding RNAs. The 10-subunit complex is composed of three S1/KH cap subunits (human EXOSC2/3/1; yeast Rrp4/40/Csl4), a lower ring of six PH-like subunits (human EXOSC4/7/8/9/5/6; yeast Rrp41/42/43/45/46/Mtr3), and a singular 3'-5' exo/endonuclease DIS3/Rrp44. Recently, several disease-linked missense mutations have been identified in structural cap and core RNA exosome genes. In this study, we characterize a rare multiple myeloma patient missense mutation that was identified in the cap subunit gene EXOSC2. This missense mutation results in a single amino acid substitution, p.Met40Thr, in a highly conserved domain of EXOSC2. Structural studies suggest that this Met40 residue makes direct contact with the essential RNA helicase, MTR4, and may help stabilize the critical interaction between the RNA exosome complex and this cofactor. To assess this interaction in vivo, we utilized the Saccharomyces cerevisiae system and modeled the EXOSC2 patient mutation into the orthologous yeast gene RRP4, generating the variant rrp4-M68T. The rrp4-M68T cells show accumulation of certain RNA exosome target RNAs and show sensitivity to drugs that impact RNA processing. We also identified robust negative genetic interactions between rrp4-M68T and specific mtr4 mutants. A complementary biochemical approach revealed that Rrp4 M68T shows decreased interaction with Mtr4, consistent with these genetic results. This study suggests that the EXOSC2 mutation identified in a multiple myeloma patient impacts the function of the RNA exosome and provides functional insight into a critical interface between the RNA exosome and Mtr4.
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Affiliation(s)
- Maria C Sterrett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Daniela Farchi
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Sarah E Strassler
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, School of Medicine, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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