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Kachroo AH, Vandeloo M, Greco BM, Abdullah M. Humanized yeast to model human biology, disease and evolution. Dis Model Mech 2022; 15:275614. [PMID: 35661208 PMCID: PMC9194483 DOI: 10.1242/dmm.049309] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
For decades, budding yeast, a single-cellular eukaryote, has provided remarkable insights into human biology. Yeast and humans share several thousand genes despite morphological and cellular differences and over a billion years of separate evolution. These genes encode critical cellular processes, the failure of which in humans results in disease. Although recent developments in genome engineering of mammalian cells permit genetic assays in human cell lines, there is still a need to develop biological reagents to study human disease variants in a high-throughput manner. Many protein-coding human genes can successfully substitute for their yeast equivalents and sustain yeast growth, thus opening up doors for developing direct assays of human gene function in a tractable system referred to as 'humanized yeast'. Humanized yeast permits the discovery of new human biology by measuring human protein activity in a simplified organismal context. This Review summarizes recent developments showing how humanized yeast can directly assay human gene function and explore variant effects at scale. Thus, by extending the 'awesome power of yeast genetics' to study human biology, humanizing yeast reinforces the high relevance of evolutionarily distant model organisms to explore human gene evolution, function and disease.
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Vyas A, Freitas AV, Ralston ZA, Tang Z. Fission Yeast Schizosaccharomyces pombe: A Unicellular "Micromammal" Model Organism. Curr Protoc 2021; 1:e151. [PMID: 34101381 PMCID: PMC8193909 DOI: 10.1002/cpz1.151] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The fission yeast Schizosaccharomyces pombe is a rod-shaped unicellular eukaryote, well known for its contributions as a model organism for our understanding of regulation and conservation of the eukaryotic cell cycle. As a yeast divergent from the budding yeast Saccharomyces cerevisiae, S. pombe shares more common features with humans including gene structures, chromatin dynamics, and the prevalence of introns, as well as the control of gene expression through pre-mRNA splicing, epigenetic gene silencing, and RNAi pathways. With the advent of new methodologies for research, S. pombe has become an increasingly used model to investigate various molecular and cellular processes over the last 50 years. Also, S. pombe serves as an excellent system for undergraduate students to obtain hands-on research experience. Versatile experimental approaches are amenable using the fission yeast system due to its relative ease of maintenance, its inherent cellular properties, its power in classic and molecular genetics, and its feasibility in genomics and proteomics analyses. This article provides an overview of S. pombe's rise as a valuable model organism and presents examples to highlight the significance of S. pombe as a unicellular "micromammal" in investigating biological questions. We especially focus on the advantages of and the advancements in using fission yeast for studying biological processes that are characteristic of metazoans to decipher the underlining molecular mechanisms fundamental to all eukaryotes. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- Aditi Vyas
- W.M. Keck Science Department, The Claremont Colleges, Claremont, CA 91711, USA
| | - Anna V. Freitas
- W.M. Keck Science Department, The Claremont Colleges, Claremont, CA 91711, USA
| | - Zachary A. Ralston
- W.M. Keck Science Department, The Claremont Colleges, Claremont, CA 91711, USA
| | - Zhaohua Tang
- W.M. Keck Science Department, The Claremont Colleges, Claremont, CA 91711, USA
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3
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Suehiro Y, Yoshina S, Motohashi T, Iwata S, Dejima K, Mitani S. Efficient collection of a large number of mutations by mutagenesis of DNA damage response defective animals. Sci Rep 2021; 11:7630. [PMID: 33828169 PMCID: PMC8027614 DOI: 10.1038/s41598-021-87226-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/24/2021] [Indexed: 02/01/2023] Open
Abstract
With the development of massive parallel sequencing technology, it has become easier to establish new model organisms that are ideally suited to the specific biological phenomena of interest. Considering the history of research using classical model organisms, we believe that the efficient construction and sharing of gene mutation libraries will facilitate the progress of studies using these new model organisms. Using C. elegans, we applied the TMP/UV mutagenesis method to animals lacking function in the DNA damage response genes atm-1 and xpc-1. This method produces genetic mutations three times more efficiently than mutagenesis of wild-type animals. Furthermore, we confirmed that the use of next-generation sequencing and the elimination of false positives through machine learning could automate the process of mutation identification with an accuracy of over 95%. Eventually, we sequenced the whole genomes of 488 strains and isolated 981 novel mutations generated by the present method; these strains have been made available to anyone who wants to use them. Since the targeted DNA damage response genes are well conserved and the mutagens used in this study are also effective in a variety of species, we believe that our method is generally applicable to a wide range of animal species.
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Affiliation(s)
- Yuji Suehiro
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Sawako Yoshina
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Tomoko Motohashi
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Satoru Iwata
- Chubu University Center for Education in Laboratory Animal Research, Kasugai, Aichi, Japan
| | - Katsufumi Dejima
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan.
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Shinjuku, Tokyo, Japan.
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4
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Kastamonuluoğlu S, Büyükgüzel K, Büyükgüzel E. The Use of Dietary Antifungal Agent Terbinafine in Artificial Diet and Its Effects on Some Biological and Biochemical Parameters of the Model Organism Galleria mellonella (Lepidoptera: Pyralidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:1110-1117. [PMID: 32173755 DOI: 10.1093/jee/toaa039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Indexed: 06/10/2023]
Abstract
Diet quality widely affects the survival, development, fecundity, longevity, and hatchability of insects. We used the greater wax moth Galleria mellonella (Linnaeus) to determine the effects of the antifungal, antibiotic terbinafine on some of its' biological parameters. The effects of terbinafine on malondialdehyde (MDA) and protein carbonyl (PCO) contents and the activity of the detoxification enzyme, glutathione S-transferase (GST), in the midgut of seventh-instar larvae of G. mellonella were also investigated. The insects were reared on an artificial diet containing terbinafine at concentrations of 0.001, 0.01, 0.1, and 1 g. The survival rates at all development stages of G. mellonella were significantly decreased at all terbinafine concentrations. The females from a control diet produced 82.9 ± 18.1 eggs; however, this number was significantly reduced to 51.4 ± 9.6 in females given a 0.1 g terbinafine diet. The highest concentration of terbinafine (1 g) completely inhibited egg laying. Terbinafine significantly increased MDA content and GST activity in the midgut tissue of seventh-instar larvae in a dose-dependent manner. Relative to controls, these low dietary concentrations of terbinafine significantly increased midgut PCO content; a 0.1 g terbinafine concentration raised PCO content from 155.19 ± 21.8 to 737.17 ± 36.4 nmol/mg protein. This study shows concentration-dependent effects on the biological traits of the greater wax moth G. mellonella, including the oxidative status and detoxification capacity of the midgut. Low terbinafine concentrations may be possible for use as an antifungal agent in insect-rearing diets.
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Affiliation(s)
- Suzan Kastamonuluoğlu
- Zonguldak Bülent Ecevit University, Science and Art Faculty, Moleculer Biology and Genetics Department, Zonguldak, Turkey
| | - Kemal Büyükgüzel
- Zonguldak Bülent Ecevit University, Science and Art Faculty, Biology Department, Zonguldak, Turkey
| | - Ender Büyükgüzel
- Zonguldak Bülent Ecevit University, Science and Art Faculty, Moleculer Biology and Genetics Department, Zonguldak, Turkey
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5
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Vilches-Moure JG. Embryonic Chicken ( Gallus gallus domesticus) as a Model of Cardiac Biology and Development. Comp Med 2019; 69:184-203. [PMID: 31182184 PMCID: PMC6591676 DOI: 10.30802/aalas-cm-18-000061] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/06/2018] [Accepted: 11/29/2018] [Indexed: 12/13/2022]
Abstract
Cardiovascular disease remains one of the top contributors to morbidity and mortality in the United States. Increasing evidence suggests that many processes, pathways, and programs observed during development and organogenesis are recapitulated in adults in the face of disease. Therefore, a heightened understanding of cardiac development and organogenesis will help increase our understanding of developmental defects and cardiovascular diseases in adults. Chicks have long served as a model system in which to study developmental problems. Detailed descriptions of morphogenesis, low cost, accessibility, ease of manipulation, and the optimization of genetic engineering techniques have made chicks a robust model for studying development and make it a powerful platform for cardiovascular research. This review summarizes the cardiac developmental milestones of embryonic chickens, practical considerations when working with chicken embryos, and techniques available for use in chicks (including tissue chimeras, genetic manipulations, and live imaging). In addition, this article highlights examples that accentuate the utility of the embryonic chicken as model system in which to study cardiac development, particularly epicardial development, and that underscore the importance of how studying development informs our understanding of disease.
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Affiliation(s)
- José G Vilches-Moure
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California,
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Lau BYC, Othman A, Ramli US. Application of Proteomics Technologies in Oil Palm Research. Protein J 2018; 37:473-499. [DOI: 10.1007/s10930-018-9802-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C. Model organism data evolving in support of translational medicine. Lab Anim (NY) 2018; 47:277-289. [PMID: 30224793 PMCID: PMC6322546 DOI: 10.1038/s41684-018-0150-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
Abstract
Model organism databases (MODs) have been collecting and integrating biomedical research data for 30 years and were designed to meet specific needs of each model organism research community. The contributions of model organism research to understanding biological systems would be hard to overstate. Modern molecular biology methods and cost reductions in nucleotide sequencing have opened avenues for direct application of model organism research to elucidating mechanisms of human diseases. Thus, the mandate for model organism research and databases has now grown to include facilitating use of these data in translational applications. Challenges in meeting this opportunity include the distribution of research data across many databases and websites, a lack of data format standards for some data types, and sustainability of scale and cost for genomic database resources like MODs. The issues of widely distributed data and application of data standards are some of the challenges addressed by FAIR (Findable, Accessible, Interoperable, and Re-usable) data principles. The Alliance of Genome Resources is now moving to address these challenges by bringing together expertly curated research data from fly, mouse, rat, worm, yeast, zebrafish, and the Gene Ontology consortium. Centralized multi-species data access, integration, and format standardization will lower the data utilization barrier in comparative genomics and translational applications and will provide a framework in which sustainable scale and cost can be addressed. This article presents a brief historical perspective on how the Alliance model organisms are complementary and how they have already contributed to understanding the etiology of human diseases. In addition, we discuss four challenges for using data from MODs in translational applications and how the Alliance is working to address them, in part by applying FAIR data principles. Ultimately, combined data from these animal models are more powerful than the sum of the parts.
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Affiliation(s)
- Douglas G Howe
- The Institute of Neuroscience, University of Oregon, Eugene, OR, USA.
| | | | - Yvonne M Bradford
- The Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Stacia R Engel
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | | | | | - Ranjana Kishore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stanley J F Laulederkind
- Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI, USA
| | - Suzanna E Lewis
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sierra A T Moxon
- The Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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8
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Alberts B, Hyman T, Pickett CL, Tilghman S, Varmus H. Improving support for young biomedical scientists. Science 2018; 360:716-718. [PMID: 29773737 DOI: 10.1126/science.aar8405] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Bruce Alberts
- University of California, San Francisco, San Francisco, CA, USA.
| | - Tony Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Christopher L Pickett
- American Association for the Advancement of Science, Washington, DC, USA.,Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Shirley Tilghman
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Harold Varmus
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
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9
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de Abreu MS, Friend AJ, Amstislavskaya TG, Kalueff AV. Commentary: Establishing zebrafish as a model to study the anxiolytic effects of scopolamine. Front Pharmacol 2018; 9:293. [PMID: 29667652 PMCID: PMC5891632 DOI: 10.3389/fphar.2018.00293] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/14/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Murilo S de Abreu
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil.,Postgraduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, Brazil.,Neuroscience Program, School of Science and Engineering, Tulane University, New Orleans, LA, United States
| | - Ashton J Friend
- Neuroscience Program, School of Science and Engineering, Tulane University, New Orleans, LA, United States.,The International Zebrafish Neuroscience Research Consortium, Slidell, LA, United States
| | | | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China.,Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.,Institute of Experimental Medicine, Almazov National Medical Research Center, St. Petersburg, Russia.,Ural Federal University, Ekaterinburg, Russia.,Russian National Granov's Research Center for Radiology and Surgical Technologies, Pesochny, Russia.,Laboratory of Translational Biopsychiatry, Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia.,ZENEREI Research Center, Slidell, LA, United States
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10
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Drubin DG, Hyman AA. Stem cells: the new "model organism". Mol Biol Cell 2017; 28:1409-1411. [PMID: 28559439 PMCID: PMC5449140 DOI: 10.1091/mbc.e17-03-0183] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/04/2017] [Indexed: 01/15/2023] Open
Abstract
Human tissue culture cells have long been a staple of molecular and cell biology research. However, although these cells are derived from humans, they have often lost considerable aspects of natural physiological function. Here we argue that combined advances in genome editing, stem cell production, and organoid derivation from stem cells represent a revolution in cell biology. These advances have important ramifications for the study of basic cell biology mechanisms, as well as for the ways in which discoveries in mechanisms are translated into understanding of disease.
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Affiliation(s)
- David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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11
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Rabe F, Bosch J, Stirnberg A, Guse T, Bauer L, Seitner D, Rabanal FA, Czedik-Eysenberg A, Uhse S, Bindics J, Genenncher B, Navarrete F, Kellner R, Ekker H, Kumlehn J, Vogel JP, Gordon SP, Marcel TC, Münsterkötter M, Walter MC, Sieber CMK, Mannhaupt G, Güldener U, Kahmann R, Djamei A. A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem. eLife 2016; 5:e20522. [PMID: 27835569 PMCID: PMC5106213 DOI: 10.7554/elife.20522] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/12/2016] [Indexed: 11/18/2022] Open
Abstract
Due to their economic relevance, the study of plant pathogen interactions is of importance. However, elucidating these interactions and their underlying molecular mechanisms remains challenging since both host and pathogen need to be fully genetically accessible organisms. Here we present milestones in the establishment of a new biotrophic model pathosystem: Ustilago bromivora and Brachypodium sp. We provide a complete toolset, including an annotated fungal genome and methods for genetic manipulation of the fungus and its host plant. This toolset will enable researchers to easily study biotrophic interactions at the molecular level on both the pathogen and the host side. Moreover, our research on the fungal life cycle revealed a mating type bias phenomenon. U. bromivora harbors a haplo-lethal allele that is linked to one mating type region. As a result, the identified mating type bias strongly promotes inbreeding, which we consider to be a potential speciation driver.
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Affiliation(s)
- Franziska Rabe
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jason Bosch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Alexandra Stirnberg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Tilo Guse
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Lisa Bauer
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Denise Seitner
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Fernando A Rabanal
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | | | - Simon Uhse
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Janos Bindics
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Bianca Genenncher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Fernando Navarrete
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Ronny Kellner
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Heinz Ekker
- Vienna Biocenter Core Facilities GmbH, Vienna, Austria
| | - Jochen Kumlehn
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
| | - John P Vogel
- DOE Joint Genome Institute, California, United States
| | - Sean P Gordon
- DOE Joint Genome Institute, California, United States
| | - Thierry C Marcel
- INRA UMR BIOGER, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mathias C Walter
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Christian MK Sieber
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Gertrud Mannhaupt
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ulrich Güldener
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Armin Djamei
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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12
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Amberg DC, Burke DJ. Classical Genetics with Saccharomyces cerevisiae. Cold Spring Harb Protoc 2016; 2016:2016/5/pdb.top077628. [PMID: 27140921 DOI: 10.1101/pdb.top077628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The budding yeast Saccharomyces cerevisiae is an outstanding experimental model organism that has been exploited since the early part of the twentieth century for studies in biochemistry and genetics. It has been the premiere experimental system for modern functional genomics and continues to make important contributions to many areas of biology. Here we discuss its many virtues as an organism for classical genetic research.
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Affiliation(s)
- David C Amberg
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Daniel J Burke
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908-0733
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13
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Sun S, Yang F, Tan G, Costanzo M, Oughtred R, Hirschman J, Theesfeld CL, Bansal P, Sahni N, Yi S, Yu A, Tyagi T, Tie C, Hill DE, Vidal M, Andrews BJ, Boone C, Dolinski K, Roth FP. An extended set of yeast-based functional assays accurately identifies human disease mutations. Genome Res 2016; 26:670-80. [PMID: 26975778 PMCID: PMC4864455 DOI: 10.1101/gr.192526.115] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 03/08/2016] [Indexed: 12/19/2022]
Abstract
We can now routinely identify coding variants within individual human genomes. A pressing challenge is to determine which variants disrupt the function of disease-associated genes. Both experimental and computational methods exist to predict pathogenicity of human genetic variation. However, a systematic performance comparison between them has been lacking. Therefore, we developed and exploited a panel of 26 yeast-based functional complementation assays to measure the impact of 179 variants (101 disease- and 78 non-disease-associated variants) from 22 human disease genes. Using the resulting reference standard, we show that experimental functional assays in a 1-billion-year diverged model organism can identify pathogenic alleles with significantly higher precision and specificity than current computational methods.
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Affiliation(s)
- Song Sun
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Fan Yang
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Guihong Tan
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Rose Oughtred
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Jodi Hirschman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Chandra L Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Pritpal Bansal
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Nidhi Sahni
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Song Yi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Analyn Yu
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Tanya Tyagi
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Cathy Tie
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Brenda J Andrews
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Kara Dolinski
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1Z8, Canada
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14
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Abstract
Regulation of the cell-division cycle is fundamental for the growth, development, and reproduction of all species of life. In the past several decades, a conserved theme of cell cycle regulation has emerged from research in diverse model organisms. A comparison of distinct features of several diverse model organisms commonly used in cell cycle studies highlights their suitability for various experimental approaches, and recaptures their contributions to our current understanding of the eukaryotic cell cycle. A historic perspective presents a recollection of the breakthrough upon unfolding the universal principles of cell cycle control by scientists working with diverse model organisms, thereby appreciating the discovery pathways in this field. A comprehensive understanding is necessary to address current challenging questions about cell cycle control. Advances in genomics, proteomics, quantitative methodologies, and approaches of systems biology are redefining the traditional concept of what constitutes a model organism and have established a new era for development of novel, and refinement of the established model organisms. Researchers working in the field are no longer separated by their favorite model organisms; they have become more integrated into a larger community for gaining greater insights into how a cell divides and cycles. The new technologies provide a broad evolutionary spectrum of the cell-division cycle and allow informative comparisons among different species at a level that has never been possible, exerting unimaginable impact on our comprehensive understanding of cell cycle regulation.
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Affiliation(s)
- Zhaohua Tang
- W.M. Keck Science Center, The Claremont Colleges, 925 North Mills Avenue, Claremont, CA, 91711, USA,
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15
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An Updated Collection of Sequence Barcoded Temperature-Sensitive Alleles of Yeast Essential Genes. G3-GENES GENOMES GENETICS 2015; 5:1879-87. [PMID: 26175450 PMCID: PMC4555224 DOI: 10.1534/g3.115.019174] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Systematic analyses of essential gene function using mutant collections in Saccharomyces cerevisiae have been conducted using collections of heterozygous diploids, promoter shut-off alleles, through alleles with destabilized mRNA, destabilized protein, or bearing mutations that lead to a temperature-sensitive (ts) phenotype. We previously described a method for construction of barcoded ts alleles in a systematic fashion. Here we report the completion of this collection of alleles covering 600 essential yeast genes. This resource covers a larger gene repertoire than previous collections and provides a complementary set of strains suitable for single gene and genomic analyses. We use deep sequencing to characterize the amino acid changes leading to the ts phenotype in half of the alleles. We also use high-throughput approaches to describe the relative ts behavior of the alleles. Finally, we demonstrate the experimental usefulness of the collection in a high-content, functional genomic screen for ts alleles that increase spontaneous P-body formation. By increasing the number of alleles and improving the annotation, this ts collection will serve as a community resource for probing new aspects of biology for essential yeast genes.
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16
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Abstract
In this commentary, Philip Hieter and Kym Boycott discuss the importance of model organisms for understanding pathogenesis of rare human genetic diseases, and highlight the work of Brooks et al., "Dysfunction of 60S ribosomal protein L10 (RPL10) disrupts neurodevelopment and causes X-linked microcephaly in humans," published in this issue of GENETICS.
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