1
|
McGee RS, Kinsler G, Petrov D, Tikhonov M. Improving the Accuracy of Bulk Fitness Assays by Correcting Barcode Processing Biases. Mol Biol Evol 2024; 41:msae152. [PMID: 39041198 PMCID: PMC11316221 DOI: 10.1093/molbev/msae152] [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: 11/02/2023] [Revised: 06/28/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024] Open
Abstract
Measuring the fitnesses of genetic variants is a fundamental objective in evolutionary biology. A standard approach for measuring microbial fitnesses in bulk involves labeling a library of genetic variants with unique sequence barcodes, competing the labeled strains in batch culture, and using deep sequencing to track changes in the barcode abundances over time. However, idiosyncratic properties of barcodes can induce nonuniform amplification or uneven sequencing coverage that causes some barcodes to be over- or under-represented in samples. This systematic bias can result in erroneous read count trajectories and misestimates of fitness. Here, we develop a computational method, named REBAR (Removing the Effects of Bias through Analysis of Residuals), for inferring the effects of barcode processing bias by leveraging the structure of systematic deviations in the data. We illustrate this approach by applying it to two independent data sets, and demonstrate that this method estimates and corrects for bias more accurately than standard proxies, such as GC-based corrections. REBAR mitigates bias and improves fitness estimates in high-throughput assays without introducing additional complexity to the experimental protocols, with potential applications in a range of experimental evolution and mutation screening contexts.
Collapse
Affiliation(s)
| | - Grant Kinsler
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Dmitri Petrov
- Department of Biology, Stanford University, Palo Alto, CA, USA
| | - Mikhail Tikhonov
- Department of Physics, Washington University, St. Louis, MO, USA
| |
Collapse
|
2
|
van Rhijn N, Zhao C, Al-Furaiji N, Storer ISR, Valero C, Gago S, Chown H, Baldin C, Grant RF, Bin Shuraym H, Ivanova L, Kniemeyer O, Krüger T, Bignell E, Goldman GH, Amich J, Delneri D, Bowyer P, Brakhage AA, Haas H, Bromley MJ. Functional analysis of the Aspergillus fumigatus kinome identifies a druggable DYRK kinase that regulates septal plugging. Nat Commun 2024; 15:4984. [PMID: 38862481 PMCID: PMC11166925 DOI: 10.1038/s41467-024-48592-8] [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: 05/31/2023] [Accepted: 05/03/2024] [Indexed: 06/13/2024] Open
Abstract
More than 10 million people suffer from lung diseases caused by the pathogenic fungus Aspergillus fumigatus. Azole antifungals represent first-line therapeutics for most of these infections but resistance is rising, therefore the identification of antifungal targets whose inhibition synergises with the azoles could improve therapeutic outcomes. Here, we generate a library of 111 genetically barcoded null mutants of Aspergillus fumigatus in genes encoding protein kinases, and show that loss of function of kinase YakA results in hypersensitivity to the azoles and reduced pathogenicity. YakA is an orthologue of Candida albicans Yak1, a TOR signalling pathway kinase involved in modulation of stress responsive transcriptional regulators. We show that YakA has been repurposed in A. fumigatus to regulate blocking of the septal pore upon exposure to stress. Loss of YakA function reduces the ability of A. fumigatus to penetrate solid media and to grow in mouse lung tissue. We also show that 1-ethoxycarbonyl-beta-carboline (1-ECBC), a compound previously shown to inhibit C. albicans Yak1, prevents stress-mediated septal spore blocking and synergises with the azoles to inhibit A. fumigatus growth.
Collapse
Affiliation(s)
- Norman van Rhijn
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Can Zhao
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Narjes Al-Furaiji
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Department of Pharmacology, College of Medicine, University of Kerbala, Kerbala, Iraq
| | - Isabelle S R Storer
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Clara Valero
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sara Gago
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Harry Chown
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Clara Baldin
- Division of Molecular Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Rachael-Fortune Grant
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Hajer Bin Shuraym
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, 11481, Riyadh, Saudi Arabia
| | - Lia Ivanova
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Elaine Bignell
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- MRC Centre for Medical Mycology, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Jorge Amich
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Mycology Reference Laboratory (Laboratorio de Referencia e Investigación en Micología [LRIM]), National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Daniela Delneri
- Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Bowyer
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Axel A Brakhage
- Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Hubertus Haas
- Division of Molecular Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Michael J Bromley
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| |
Collapse
|
3
|
Qiu C, Arora P, Malik I, Laperuta AJ, Pavlovic EM, Ugochukwu S, Naik M, Kaplan CD. Thiolutin has complex effects in vivo but is a direct inhibitor of RNA polymerase II in vitro. Nucleic Acids Res 2024; 52:2546-2564. [PMID: 38214235 PMCID: PMC10954460 DOI: 10.1093/nar/gkad1258] [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: 02/28/2023] [Revised: 12/18/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024] Open
Abstract
Thiolutin is a natural product transcription inhibitor with an unresolved mode of action. Thiolutin and the related dithiolopyrrolone holomycin chelate Zn2+ and previous studies have concluded that RNA Polymerase II (Pol II) inhibition in vivo is indirect. Here, we present chemicogenetic and biochemical approaches to investigate thiolutin's mode of action in Saccharomyces cerevisiae. We identify mutants that alter sensitivity to thiolutin. We provide genetic evidence that thiolutin causes oxidation of thioredoxins in vivo and that thiolutin both induces oxidative stress and interacts functionally with multiple metals including Mn2+ and Cu2+, and not just Zn2+. Finally, we show direct inhibition of RNA polymerase II (Pol II) transcription initiation by thiolutin in vitro in support of classical studies that thiolutin can directly inhibit transcription in vitro. Inhibition requires both Mn2+ and appropriate reduction of thiolutin as excess DTT abrogates its effects. Pause prone, defective elongation can be observed in vitro if inhibition is bypassed. Thiolutin effects on Pol II occupancy in vivo are widespread but major effects are consistent with prior observations for Tor pathway inhibition and stress induction, suggesting that thiolutin use in vivo should be restricted to studies on its modes of action and not as an experimental tool.
Collapse
Affiliation(s)
- Chenxi Qiu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Payal Arora
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Indranil Malik
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | | | | | | | - Mandar Naik
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| |
Collapse
|
4
|
Smith JR, Martini A, Gibney PA. Utilizing functional genomics in Saccharomyces cerevisiae to characterize food preservative compounds: A pilot study. J Food Sci 2024; 89:1196-1210. [PMID: 38224173 DOI: 10.1111/1750-3841.16906] [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: 08/21/2023] [Revised: 11/17/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
Chemical preservatives are ubiquitously used to suppress the growth of or kill microorganisms across numerous industries, including the food industry. Utilizing yeast functional genomic techniques, genes and their functions can be observed at a genomic scale to elucidate how environmental stressors (e.g., chemical preservatives) impact microbial survival. These types of chemical genomics approaches can reveal genetic mutations that result in preservative resistance or sensitivity, assist in identification of preservative mechanism of action, and can be used to compare different preservatives for rational design of preservative mixtures. In this proof-of-concept study, we performed deletion and high-copy genetic expression screens to identify mutants that confer drug resistance to sodium benzoate, potassium sorbate, rosemary extract, and Natamax. By observing overlapping mutant genes between genetic screens, we were able to identify functional overlap between chemical preservatives and begin to explain mechanisms of action for these compounds.
Collapse
Affiliation(s)
- Jeremy R Smith
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Austin Martini
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Patrick A Gibney
- Department of Food Science, Cornell University, Ithaca, New York, USA
| |
Collapse
|
5
|
Tripathi S, Voogdt CGP, Bassler SO, Anderson M, Huang PH, Sakenova N, Capraz T, Jain S, Koumoutsi A, Bravo AM, Trotter V, Zimmerman M, Sonnenburg JL, Buie C, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction. Cell Rep 2024; 43:113517. [PMID: 38142397 DOI: 10.1016/j.celrep.2023.113517] [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: 07/27/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
Randomly barcoded transposon mutant libraries are powerful tools for studying gene function and organization, assessing gene essentiality and pathways, discovering potential therapeutic targets, and understanding the physiology of gut bacteria and their interactions with the host. However, construction of high-quality libraries with uniform representation can be challenging. In this review, we survey various strategies for barcoded library construction, including transposition systems, methods of transposon delivery, optimal library size, and transconjugant selection schemes. We discuss the advantages and limitations of each approach, as well as factors to consider when selecting a strategy. In addition, we highlight experimental and computational advances in arraying condensed libraries from mutant pools. We focus on examples of successful library construction in gut bacteria and their application to gene function studies and drug discovery. Given the need for understanding gene function and organization in gut bacteria, we provide a comprehensive guide for researchers to construct randomly barcoded transposon mutant libraries.
Collapse
Affiliation(s)
- Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Mary Anderson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Po-Hsun Huang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nazgul Sakenova
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tümay Capraz
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Valentine Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael Zimmerman
- Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Justin L Sonnenburg
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
6
|
Gaikani HK, Stolar M, Kriti D, Nislow C, Giaever G. From beer to breadboards: yeast as a force for biological innovation. Genome Biol 2024; 25:10. [PMID: 38178179 PMCID: PMC10768129 DOI: 10.1186/s13059-023-03156-9] [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: 02/14/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
Collapse
Affiliation(s)
- Hamid Kian Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Monika Stolar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
May DA, Taha F, Child MA, Ewald SE. How colonization bottlenecks, tissue niches, and transmission strategies shape protozoan infections. Trends Parasitol 2023; 39:1074-1086. [PMID: 37839913 DOI: 10.1016/j.pt.2023.09.017] [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: 08/28/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
Protozoan pathogens such as Plasmodium spp., Leishmania spp., Toxoplasma gondii, and Trypanosoma spp. are often associated with high-mortality, acute and chronic diseases of global health concern. For transmission and immune evasion, protozoans have evolved diverse strategies to interact with a range of host tissue environments. These interactions are linked to disease pathology, yet our understanding of the association between parasite colonization and host homeostatic disruption is limited. Recently developed techniques for cellular barcoding have the potential to uncover the biology regulating parasite transmission, dissemination, and the stability of infection. Understanding bottlenecks to infection and the in vivo tissue niches that facilitate chronic infection and spread has the potential to reveal new aspects of parasite biology.
Collapse
Affiliation(s)
- Dana A May
- Department of Microbiology, Immunology, and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Fatima Taha
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Matthew A Child
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | - Sarah E Ewald
- Department of Microbiology, Immunology, and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
| |
Collapse
|
9
|
Limdi A, Baym M. Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs. J Mol Evol 2023; 91:325-333. [PMID: 37160452 DOI: 10.1007/s00239-023-10110-7] [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: 08/19/2022] [Accepted: 04/06/2023] [Indexed: 05/11/2023]
Abstract
Pooled sequencing-based fitness assays are a powerful and widely used approach to quantifying fitness of thousands of genetic variants in parallel. Despite the throughput of such assays, they are prone to biases in fitness estimates, and errors in measurements are typically larger for deleterious fitness effects, relative to neutral effects. In practice, designing pooled fitness assays involves tradeoffs between the number of timepoints, the sequencing depth, and other parameters to gain as much information as possible within a feasible experiment. Here, we combined simulations and reanalysis of an existing experimental dataset to explore how assay parameters impact measurements of near-neutral and deleterious fitness effects using a standard fitness estimator. We found that sequencing multiple timepoints at relatively modest depth improved estimates of near-neutral fitness effects, but systematically biased measurements of deleterious effects. We showed that a fixed total number of reads, deeper sequencing at fewer timepoints improved resolution of deleterious fitness effects. Our results highlight a tradeoff between measurement of deleterious and near-neutral effect sizes for a fixed amount of data and suggest that fitness assay design should be tuned for fitness effects that are relevant to the specific biological question.
Collapse
Affiliation(s)
- Anurag Limdi
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
10
|
Li F, Tarkington J, Sherlock G. Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays. J Mol Evol 2023; 91:334-344. [PMID: 36877292 PMCID: PMC10276102 DOI: 10.1007/s00239-023-10098-0] [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: 10/26/2022] [Accepted: 02/02/2023] [Indexed: 03/07/2023]
Abstract
The fitness of a genotype is defined as its lifetime reproductive success, with fitness itself being a composite trait likely dependent on many underlying phenotypes. Measuring fitness is important for understanding how alteration of different cellular components affects a cell's ability to reproduce. Here, we describe an improved approach, implemented in Python, for estimating fitness in high throughput via pooled competition assays.
Collapse
Affiliation(s)
- Fangfei Li
- Department of Genetics, Stanford University, Stanford, USA
| | | | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, USA.
| |
Collapse
|
11
|
Johnson MS, Venkataram S, Kryazhimskiy S. Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes. J Mol Evol 2023; 91:263-280. [PMID: 36651964 PMCID: PMC10276077 DOI: 10.1007/s00239-022-10083-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023]
Abstract
Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.
Collapse
Affiliation(s)
- Milo S Johnson
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Sandeep Venkataram
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
12
|
van Rhijn N, Zhao C, Al-Furaji N, Storer I, Valero C, Gago S, Chown H, Baldin C, Fortune-Grant R, Shuraym HB, Ivanova L, Kniemeyer O, Krüger T, Bignell E, Goldman G, Amich J, Delneri D, Bowyer P, Brakhage A, Haas H, Bromley M. Functional analysis of the Aspergillus fumigatus kinome reveals a DYRK kinase involved in septal plugging is a novel antifungal drug target. RESEARCH SQUARE 2023:rs.3.rs-2960526. [PMID: 37398159 PMCID: PMC10312919 DOI: 10.21203/rs.3.rs-2960526/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
More than 10 million people suffer from lung diseases caused by the pathogenic fungus Aspergillus fumigatus. The azole class of antifungals represent first line therapeutics for most of these infections however resistance is rising. Identification of novel antifungal targets that, when inhibited, synergise with the azoles will aid the development of agents that can improve therapeutic outcomes and supress the emergence of resistance. As part of the A. fumigatus genome-wide knockout program (COFUN), we have completed the generation of a library that consists of 120 genetically barcoded null mutants in genes that encode the protein kinase cohort of A. fumigatus. We have employed a competitive fitness profiling approach (Bar-Seq), to identify targets which when deleted result in hypersensitivity to the azoles and fitness defects in a murine host. The most promising candidate from our screen is a previously uncharacterised DYRK kinase orthologous to Yak1 of Candida albicans, a TOR signalling pathway kinase involved in modulation of stress responsive transcriptional regulators. Here we show that the orthologue YakA has been repurposed in A. fumigatus to regulate blocking of the septal pore upon exposure to stress via phosphorylation of the Woronin body tethering protein Lah. Loss of YakA function reduces the ability of A. fumigatus to penetrate solid media and impacts growth in murine lung tissue. We also show that 1-ethoxycarbonyl-beta-carboline (1-ECBC), a compound previously shown to inhibit Yak1 in C. albicans prevents stress mediated septal spore blocking and synergises with the azoles to inhibit A. fumigatus growth.
Collapse
Affiliation(s)
| | - Can Zhao
- Manchester Fungal Infection Group
| | | | | | | | | | | | | | | | | | - Lia Ivanova
- Leibniz Institute for Natural Product Research and Infection Biology
| | - Olaf Kniemeyer
- Leibniz Institute for Natural Product Research and Infection Biology
| | - Thomas Krüger
- Leibniz Institute for Natural Product Research and Infection Biology
| | | | - Gustavo Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Bloco Q, Universidade de São Paulo
| | | | | | | | - Axel Brakhage
- Leibniz Institute for Natural Product Research and Infection Biology - University of Jena
| | - Hubertus Haas
- Institute of Molecular Biology/Biocenter, Innsbruck Medical University
| | | |
Collapse
|
13
|
Trotter VV, Shatsky M, Price MN, Juba TR, Zane GM, De León KB, Majumder ELW, Gui Q, Ali R, Wetmore KM, Kuehl JV, Arkin AP, Wall JD, Deutschbauer AM, Chandonia JM, Butland GP. Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough. Front Microbiol 2023; 14:1095191. [PMID: 37065130 PMCID: PMC10102598 DOI: 10.3389/fmicb.2023.1095191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.
Collapse
Affiliation(s)
- Valentine V. Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maxim Shatsky
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Morgan N. Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Thomas R. Juba
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Kara B. De León
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Erica L.-W. Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Rida Ali
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kelly M. Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jennifer V. Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Gareth P. Butland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| |
Collapse
|
14
|
Chauvel M, Bachellier-Bassi S, Guérout AM, Lee KK, Maufrais C, Permal E, Da Fonseca JP, Znaidi S, Mazel D, Munro CA, d'Enfert C, Legrand M. High-throughput functional profiling of the human fungal pathogen Candida albicans genome. Res Microbiol 2023; 174:104025. [PMID: 36587858 DOI: 10.1016/j.resmic.2022.104025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
Candida albicans is a major fungal pathogen of humans. Although its genome has been sequenced more than two decades ago, there are still over 4300 uncharacterized C. albicans genes. We previously generated an ORFeome as well as a collection of destination vectors to facilitate overexpression of C. albicans ORFs. Here, we report the construction of ∼2500 overexpression mutants and their evaluation by in vitro spotting on rich medium and in a liquid pool experiment in rich medium, allowing the identification of genes whose overexpression has a fitness cost. The candidates were further validated at the individual strain level. This new resource allows large-scale screens in different growth conditions to be performed routinely. Altogether, based on the concept of identifying functionally related genes by cluster analysis, the availability of this overexpression mutant collection will facilitate the characterization of gene functions in C. albicans.
Collapse
Affiliation(s)
- Murielle Chauvel
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
| | - Sophie Bachellier-Bassi
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
| | - Anne-Marie Guérout
- Institut Pasteur, Université Paris Cité, UMR3525 CNRS, Unité Plasticité du Génome Bactérien, F-75015 Paris, France.
| | - Keunsook K Lee
- Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK; NGeneBio, 307 Daerung Post-tower 1, 288 Digital-ro, Guro-gu, Seoul 08390, Republic of Korea.
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France; Institut Pasteur, Université Paris Cité, Hub de Bioinformatique, F-75015 Paris, France.
| | - Emmanuelle Permal
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France; Institut Pasteur, Université Paris Cité, UMR3525 CNRS, Unité Plasticité du Génome Bactérien, F-75015 Paris, France; Institut Pasteur, Université Paris Cité, Hub de Bioinformatique, F-75015 Paris, France.
| | - Juliana Pipoli Da Fonseca
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques (C2RT), F-75015 Paris, France.
| | - Sadri Znaidi
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France; Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis-Belvédère, Tunisia.
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, UMR3525 CNRS, Unité Plasticité du Génome Bactérien, F-75015 Paris, France.
| | - Carol A Munro
- Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK.
| | - Christophe d'Enfert
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
| | - Melanie Legrand
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
| |
Collapse
|
15
|
Kijima Y, Evans-Yamamoto D, Toyoshima H, Yachie N. A universal sequencing read interpreter. SCIENCE ADVANCES 2023; 9:eadd2793. [PMID: 36598975 PMCID: PMC9812397 DOI: 10.1126/sciadv.add2793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Massively parallel DNA sequencing has led to the rapid growth of highly multiplexed experiments in biology. These experiments produce unique sequencing results that require specific analysis pipelines to decode highly structured reads. However, no versatile framework that interprets sequencing reads to extract their encoded information for downstream biological analysis has been developed. Here, we report INTERSTELLAR (interpretation, scalable transformation, and emulation of large-scale sequencing reads) that decodes data values encoded in theoretically any type of sequencing read and translates them into sequencing reads of another structure of choice. We demonstrated that INTERSTELLAR successfully extracted information from a range of short- and long-read sequencing reads and translated those of single-cell (sc)RNA-seq, scATAC-seq, and spatial transcriptomics to be analyzed by different software tools that have been developed for conceptually the same types of experiments. INTERSTELLAR will greatly facilitate the development of sequencing-based experiments and sharing of data analysis pipelines.
Collapse
Affiliation(s)
- Yusuke Kijima
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Daniel Evans-Yamamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan
| | - Hiromi Toyoshima
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Nozomu Yachie
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
- Twitter: @yachielab
| |
Collapse
|
16
|
Li Y, Molyneaux N, Zhang H, Zhou G, Kerr C, Adams MD, Berkner KL, Runge KW. A multiplexed, three-dimensional pooling and next-generation sequencing strategy for creating barcoded mutant arrays: construction of a Schizosaccharomyces pombe transposon insertion library. Nucleic Acids Res 2022; 50:e102. [PMID: 35766443 PMCID: PMC9508820 DOI: 10.1093/nar/gkac546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/02/2022] [Accepted: 06/12/2022] [Indexed: 11/14/2022] Open
Abstract
Arrayed libraries of defined mutants have been used to elucidate gene function in the post-genomic era. Yeast haploid gene deletion libraries have pioneered this effort, but are costly to construct, do not reveal phenotypes that may occur with partial gene function and lack essential genes required for growth. We therefore devised an efficient method to construct a library of barcoded insertion mutants with a wider range of phenotypes that can be generalized to other organisms or collections of DNA samples. We developed a novel but simple three-dimensional pooling and multiplexed sequencing approach that leveraged sequence information to reduce the number of required sequencing reactions by orders of magnitude, and were able to identify the barcode sequences and DNA insertion sites of 4391 Schizosaccharomyces pombe insertion mutations with only 40 sequencing preparations. The insertion mutations are in the genes and untranslated regions of nonessential, essential and noncoding RNA genes, and produced a wider range of phenotypes compared to the cognate deletion mutants, including novel phenotypes. This mutant library represents both a proof of principle for an efficient method to produce novel mutant libraries and a valuable resource for the S. pombe research community.
Collapse
Affiliation(s)
- Yanhui Li
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
- Department of Genetics and Genomic Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Neil Molyneaux
- Department of Genetics and Genomic Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Haitao Zhang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
| | - Gang Zhou
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
| | - Carly Kerr
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
| | - Mark D Adams
- Department of Genetics and Genomic Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kathleen L Berkner
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
| | - Kurt W Runge
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
- Department of Genetics and Genomic Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland, OH 44195, USA
| |
Collapse
|
17
|
Wincott CJ, Sritharan G, Benns HJ, May D, Gilabert-Carbajo C, Bunyan M, Fairweather AR, Alves E, Andrew I, Game L, Frickel EM, Tiengwe C, Ewald SE, Child MA. Cellular barcoding of protozoan pathogens reveals the within-host population dynamics of Toxoplasma gondii host colonization. CELL REPORTS METHODS 2022; 2:100274. [PMID: 36046624 PMCID: PMC9421581 DOI: 10.1016/j.crmeth.2022.100274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/20/2022] [Accepted: 07/22/2022] [Indexed: 02/09/2023]
Abstract
Cellular barcoding techniques are powerful tools to understand microbial pathogenesis. However, barcoding strategies have not been broadly applied to protozoan parasites, which have unique genomic structures and virulence strategies compared with viral and bacterial pathogens. Here, we present a CRISPR-based method to barcode protozoa, which we successfully apply to Toxoplasma gondii and Trypanosoma brucei. Using libraries of barcoded T. gondii, we evaluate shifts in the population structure from acute to chronic infection of mice. Contrary to expectation, most barcodes were present in the brain one month post-intraperitoneal infection in both inbred CBA/J and outbred Swiss mice. Although parasite cyst number and barcode diversity declined over time, barcodes representing a minor fraction of the inoculum could become a dominant population in the brain by three months post-infection. These data establish a cellular barcoding approach for protozoa and evidence that the blood-brain barrier is not a major bottleneck to colonization by T. gondii.
Collapse
Affiliation(s)
- Ceire J. Wincott
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Gayathri Sritharan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Department of Biological Sciences, Birkbeck, University of London, Mallet Street, Bloomsbury, London WC1E 7HX, UK
| | - Henry J. Benns
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Department of Chemistry, Imperial College London, White City Campus, London W12 0BZ, UK
| | - Dana May
- Department of Microbiology, Immunology and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Carla Gilabert-Carbajo
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Monique Bunyan
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1BF, UK
| | - Aisling R. Fairweather
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Eduardo Alves
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Ivan Andrew
- UKRI London Institute of Medical Sciences Genomics Laboratory, Shepherd’s Bush, London W12 0NN, UK
| | - Laurence Game
- UKRI London Institute of Medical Sciences Genomics Laboratory, Shepherd’s Bush, London W12 0NN, UK
| | - Eva-Maria Frickel
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1BF, UK
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Calvin Tiengwe
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Sarah E. Ewald
- Department of Microbiology, Immunology and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Matthew A. Child
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| |
Collapse
|
18
|
Ngubo M, Reid JL, Patterton H. Distinct structural groups of histone H3 and H4 residues have divergent effects on chronological lifespan in Saccharomyces cerevisiae. PLoS One 2022; 17:e0268760. [PMID: 35622816 PMCID: PMC9140238 DOI: 10.1371/journal.pone.0268760] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
We have performed a comprehensive analysis of the involvement of histone H3 and H4 residues in the regulation of chronological lifespan in yeast and identify four structural groups in the nucleosome that influence lifespan. We also identify residues where substitution with an epigenetic mimic extends lifespan, providing evidence that a simple epigenetic switch, without possible additional background modifications, causes longevity. Residues where substitution result in the most pronounced lifespan extension are all on the exposed face of the nucleosome, with the exception of H3E50, which is present on the lateral surface, between two DNA gyres. Other residues that have a more modest effect on lifespan extension are concentrated at the extremities of the H3-H4 dimer, suggesting a role in stabilizing the dimer in its nucleosome frame. Residues that reduce lifespan are buried in the histone handshake motif, suggesting that these mutations destabilize the octamer structure. All residues exposed on the nucleosome disk face and that cause lifespan extension are known to interact with Sir3. We find that substitution of H4K16 and H4H18 cause Sir3 to redistribute from telomeres and silent mating loci to secondary positions, often enriched for Rap1, Abf1 or Reb1 binding sites, whereas H3E50 does not. The redistribution of Sir3 in the genome can be reproduced by an equilibrium model based on primary and secondary binding sites with different affinities for Sir3. The redistributed Sir3 cause transcriptional repression at most of the new loci, including of genes where null mutants were previously shown to extend chronological lifespan. The transcriptomic profiles of H4K16 and H4H18 mutant strains are very similar, and compatible with a DNA replication stress response. This is distinct from the transcriptomic profile of H3E50, which matches strong induction of oxidative phosphorylation. We propose that the different groups of residues are involved in binding to heterochromatin proteins, in destabilizing the association of the nucleosome DNA, disrupting binding of the H3-H4 dimer in the nucleosome, or disrupting the structural stability of the octamer, each category impacting on chronological lifespan by a different mechanism.
Collapse
Affiliation(s)
- Mzwanele Ngubo
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Jessica Laura Reid
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Hugh–George Patterton
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
- * E-mail:
| |
Collapse
|
19
|
Vanderwaeren L, Dok R, Voordeckers K, Vandemaele L, Verstrepen KJ, Nuyts S. An Integrated Approach Reveals DNA Damage and Proteotoxic Stress as Main Effects of Proton Radiation in S. cerevisiae. Int J Mol Sci 2022; 23:ijms23105493. [PMID: 35628303 PMCID: PMC9145671 DOI: 10.3390/ijms23105493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023] Open
Abstract
Proton radiotherapy (PRT) has the potential to reduce the normal tissue toxicity associated with conventional photon-based radiotherapy (X-ray therapy, XRT) because the active dose can be more directly targeted to a tumor. Although this dosimetric advantage of PRT is well known, the molecular mechanisms affected by PRT remain largely elusive. Here, we combined the molecular toolbox of the eukaryotic model Saccharomyces cerevisiae with a systems biology approach to investigate the physiological effects of PRT compared to XRT. Our data show that the DNA damage response and protein stress response are the major molecular mechanisms activated after both PRT and XRT. However, RNA-Seq revealed that PRT treatment evoked a stronger activation of genes involved in the response to proteotoxic stress, highlighting the molecular differences between PRT and XRT. Moreover, inhibition of the proteasome resulted in decreased survival in combination with PRT compared to XRT, not only further confirming that protons induced a stronger proteotoxic stress response, but also hinting at the potential of using proteasome inhibitors in combination with proton radiotherapy in clinical settings.
Collapse
Affiliation(s)
- Laura Vanderwaeren
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Rüveyda Dok
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
| | - Karin Voordeckers
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Laura Vandemaele
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium;
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
- Correspondence: (K.J.V.); (S.N.); Tel.: +32-(0)16-75-1393 (K.J.V.); +32-1634-7600 (S.N.); Fax: +32-1634-7623 (S.N.)
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; (L.V.); (R.D.); (L.V.)
- Department of Radiation Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium
- Correspondence: (K.J.V.); (S.N.); Tel.: +32-(0)16-75-1393 (K.J.V.); +32-1634-7600 (S.N.); Fax: +32-1634-7623 (S.N.)
| |
Collapse
|
20
|
Nguyen Ba AN, Lawrence KR, Rego-Costa A, Gopalakrishnan S, Temko D, Michor F, Desai MM. Barcoded Bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast. eLife 2022; 11:73983. [PMID: 35147078 PMCID: PMC8979589 DOI: 10.7554/elife.73983] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/11/2022] [Indexed: 11/25/2022] Open
Abstract
Mapping the genetic basis of complex traits is critical to uncovering the biological mechanisms that underlie disease and other phenotypes. Genome-wide association studies (GWAS) in humans and quantitative trait locus (QTL) mapping in model organisms can now explain much of the observed heritability in many traits, allowing us to predict phenotype from genotype. However, constraints on power due to statistical confounders in large GWAS and smaller sample sizes in QTL studies still limit our ability to resolve numerous small-effect variants, map them to causal genes, identify pleiotropic effects across multiple traits, and infer non-additive interactions between loci (epistasis). Here, we introduce barcoded bulk quantitative trait locus (BB-QTL) mapping, which allows us to construct, genotype, and phenotype 100,000 offspring of a budding yeast cross, two orders of magnitude larger than the previous state of the art. We use this panel to map the genetic basis of eighteen complex traits, finding that the genetic architecture of these traits involves hundreds of small-effect loci densely spaced throughout the genome, many with widespread pleiotropic effects across multiple traits. Epistasis plays a central role, with thousands of interactions that provide insight into genetic networks. By dramatically increasing sample size, BB-QTL mapping demonstrates the potential of natural variants in high-powered QTL studies to reveal the highly polygenic, pleiotropic, and epistatic architecture of complex traits.
Collapse
Affiliation(s)
- Alex N Nguyen Ba
- Department of Organismic and Evolutionary Biology, Harvard University
| | | | - Artur Rego-Costa
- Department of Organismic and Evolutionary Biology, Harvard University
| | | | | | | | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University
| |
Collapse
|
21
|
Kramme C, Plesa AM, Wang HH, Wolf B, Smela MP, Guo X, Kohman RE, Chatterjee P, Church GM. MegaGate: A toxin-less gateway molecular cloning tool. STAR Protoc 2021; 2:100907. [PMID: 34746865 PMCID: PMC8551244 DOI: 10.1016/j.xpro.2021.100907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Gateway cloning employs the use of the ccdb toxin and has low colony numbers, making it difficult to apply at scale to clone libraries of cDNA vectors. In this protocol, we describe MegaGate, a toxin-less Gateway technology capable of robust cDNA library cloning that is efficient, cheap, and scalable. MegaGate eliminates the ccdb toxin used in Gateway recombinase cloning and instead utilizes meganuclease-mediated digestion to eliminate background vectors during cloning and is 99.8% efficient with high colony numbers. For complete details on the use and execution of this protocol, please refer to Kramme et al. (2021).
Collapse
Affiliation(s)
- Christian Kramme
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Alexandru M. Plesa
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Helen H. Wang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Bennett Wolf
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Merrick Pierson Smela
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Xiaoge Guo
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Richie E. Kohman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Pranam Chatterjee
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| |
Collapse
|
22
|
Kramme C, Plesa AM, Wang HH, Wolf B, Smela MP, Guo X, Kohman RE, Chatterjee P, Church GM. An integrated pipeline for mammalian genetic screening. CELL REPORTS METHODS 2021; 1:100082. [PMID: 35474898 PMCID: PMC9017118 DOI: 10.1016/j.crmeth.2021.100082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
With the recent advancements in genome editing, next-generation sequencing (NGS), and scalable cloning techniques, scientists can now conduct genetic screens at unprecedented levels of scale and precision. With such a multitude of technologies, there is a need for a simple yet comprehensive pipeline to enable systematic mammalian genetic screening. In this study, we develop unique algorithms for target identification and a toxin-less Gateway cloning tool, termed MegaGate, for library cloning which, when combined with existing genetic perturbation methods and NGS-coupled readouts, enable versatile engineering of relevant mammalian cell lines. Our integrated pipeline for sequencing-based target ascertainment and modular perturbation screening (STAMPScreen) can thus be utilized for a host of cell state engineering applications.
Collapse
Affiliation(s)
- Christian Kramme
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Alexandru M. Plesa
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Helen H. Wang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Bennett Wolf
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Merrick Pierson Smela
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Xiaoge Guo
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Richie E. Kohman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Pranam Chatterjee
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
23
|
Decourty L, Malabat C, Frachon E, Jacquier A, Saveanu C. Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast. Nucleic Acids Res 2021; 49:8535-8555. [PMID: 34358317 PMCID: PMC8421204 DOI: 10.1093/nar/gkab680] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 11/15/2022] Open
Abstract
Gene deletion and gene expression alteration can lead to growth defects that are amplified or reduced when a second mutation is present in the same cells. We performed 154 genetic interaction mapping (GIM) screens with query mutants related with RNA metabolism and estimated the growth rates of about 700 000 double mutant Saccharomyces cerevisiae strains. The tested targets included the gene deletion collection and 900 strains in which essential genes were affected by mRNA destabilization (DAmP). To analyze the results, we developed RECAP, a strategy that validates genetic interaction profiles by comparison with gene co-citation frequency, and identified links between 1471 genes and 117 biological processes. In addition to these large-scale results, we validated both enhancement and suppression of slow growth measured for specific RNA-related pathways. Thus, negative genetic interactions identified a role for the OCA inositol polyphosphate hydrolase complex in mRNA translation initiation. By analysis of suppressors, we found that Puf4, a Pumilio family RNA binding protein, inhibits ribosomal protein Rpl9 function, by acting on a conserved UGUAcauUA motif located downstream the stop codon of the RPL9B mRNA. Altogether, the results and their analysis should represent a useful resource for discovery of gene function in yeast.
Collapse
Affiliation(s)
- Laurence Decourty
- Unité de Génétique des Interactions Macromoléculaires, Département Génomes et Génétique, Institut Pasteur, 75015 Paris, France.,UMR3525, Centre national de la recherche scientifique (CNRS), 75015 Paris, France
| | - Christophe Malabat
- Hub Bioinformatique et Biostatistique, Département de Biologie Computationnelle, Institut Pasteur, 75015 Paris, France
| | - Emmanuel Frachon
- Plate-forme Technologique Biomatériaux et Microfluidique, Centre des ressources et recherches technologiques, Institut Pasteur, 75015 Paris, France
| | - Alain Jacquier
- Unité de Génétique des Interactions Macromoléculaires, Département Génomes et Génétique, Institut Pasteur, 75015 Paris, France.,UMR3525, Centre national de la recherche scientifique (CNRS), 75015 Paris, France
| | - Cosmin Saveanu
- Unité de Génétique des Interactions Macromoléculaires, Département Génomes et Génétique, Institut Pasteur, 75015 Paris, France.,UMR3525, Centre national de la recherche scientifique (CNRS), 75015 Paris, France
| |
Collapse
|
24
|
Ogbede JU, Giaever G, Nislow C. A genome-wide portrait of pervasive drug contaminants. Sci Rep 2021; 11:12487. [PMID: 34127714 PMCID: PMC8203678 DOI: 10.1038/s41598-021-91792-1] [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: 01/26/2021] [Accepted: 05/25/2021] [Indexed: 11/08/2022] Open
Abstract
Using a validated yeast chemogenomic platform, we characterized the genome-wide effects of several pharmaceutical contaminants, including three N-nitrosamines (NDMA, NDEA and NMBA), two related compounds (DMF and 4NQO) and several of their metabolites. A collection of 4800 non-essential homozygous diploid yeast deletion strains were screened in parallel and the strain abundance was quantified by barcode sequencing. These data were used to rank deletion strains representing genes required for resistance to the compounds to delineate affected cellular pathways and to visualize the global cellular effects of these toxins in an easy-to-use searchable database. Our analysis of the N-nitrosamine screens uncovered genes (via their corresponding homozygous deletion mutants) involved in several evolutionarily conserved pathways, including: arginine biosynthesis, mitochondrial genome integrity, vacuolar protein sorting and DNA damage repair. To investigate why NDMA, NDEA and DMF caused fitness defects in strains lacking genes of the arginine pathway, we tested several N-nitrosamine metabolites (methylamine, ethylamine and formamide), and found they also affected arginine pathway mutants. Notably, each of these metabolites has the potential to produce ammonium ions during their biotransformation. We directly tested the role of ammonium ions in N-nitrosamine toxicity by treatment with ammonium sulfate and we found that ammonium sulfate also caused a growth defect in arginine pathway deletion strains. Formaldehyde, a metabolite produced from NDMA, methylamine and formamide, and which is known to cross-link free amines, perturbed deletion strains involved in chromatin remodeling and DNA repair pathways. Finally, co-administration of N-nitrosamines with ascorbic or ferulic acid did not relieve N-nitrosamine toxicity. In conclusion, we used parallel deletion mutant analysis to characterize the genes and pathways affected by exposure to N-nitrosamines and related compounds, and provide the data in an accessible, queryable database.
Collapse
Affiliation(s)
- Joseph Uche Ogbede
- Genome Science & Technology Graduate Program, University of British Columbia, Vancouver, Canada
| | - Guri Giaever
- Faculty of Pharmaceutical Science, University of British Columbia, Vancouver, Canada
| | - Corey Nislow
- Genome Science & Technology Graduate Program, University of British Columbia, Vancouver, Canada.
- Faculty of Pharmaceutical Science, University of British Columbia, Vancouver, Canada.
| |
Collapse
|
25
|
Arita Y, Kim G, Li Z, Friesen H, Turco G, Wang RY, Climie D, Usaj M, Hotz M, Stoops EH, Baryshnikova A, Boone C, Botstein D, Andrews BJ, McIsaac RS. A genome-scale yeast library with inducible expression of individual genes. Mol Syst Biol 2021; 17:e10207. [PMID: 34096681 PMCID: PMC8182650 DOI: 10.15252/msb.202110207] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 11/09/2022] Open
Abstract
The ability to switch a gene from off to on and monitor dynamic changes provides a powerful approach for probing gene function and elucidating causal regulatory relationships. Here, we developed and characterized YETI (Yeast Estradiol strains with Titratable Induction), a collection in which > 5,600 yeast genes are engineered for transcriptional inducibility with single-gene precision at their native loci and without plasmids. Each strain contains SGA screening markers and a unique barcode, enabling high-throughput genetics. We characterized YETI using growth phenotyping and BAR-seq screens, and we used a YETI allele to identify the regulon of Rof1, showing that it acts to repress transcription. We observed that strains with inducible essential genes that have low native expression can often grow without inducer. Analysis of data from eukaryotic and prokaryotic systems shows that native expression is a variable that can bias promoter-perturbing screens, including CRISPRi. We engineered a second expression system, Z3 EB42, that gives lower expression than Z3 EV, a feature enabling conditional activation and repression of lowly expressed essential genes that grow without inducer in the YETI library.
Collapse
Affiliation(s)
- Yuko Arita
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
- RIKEN Centre for Sustainable Resource ScienceWakoSaitamaJapan
| | - Griffin Kim
- Calico Life Sciences LLCSouth San FranciscoCAUSA
| | - Zhijian Li
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Helena Friesen
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Gina Turco
- Calico Life Sciences LLCSouth San FranciscoCAUSA
| | | | - Dale Climie
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Matej Usaj
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
| | - Manuel Hotz
- Calico Life Sciences LLCSouth San FranciscoCAUSA
| | | | | | - Charles Boone
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
- RIKEN Centre for Sustainable Resource ScienceWakoSaitamaJapan
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | | | - Brenda J Andrews
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | | |
Collapse
|
26
|
Helsen J, Voordeckers K, Vanderwaeren L, Santermans T, Tsontaki M, Verstrepen KJ, Jelier R. Gene Loss Predictably Drives Evolutionary Adaptation. Mol Biol Evol 2021; 37:2989-3002. [PMID: 32658971 PMCID: PMC7530610 DOI: 10.1093/molbev/msaa172] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Loss of gene function is common throughout evolution, even though it often leads to reduced fitness. In this study, we systematically evaluated how an organism adapts after deleting genes that are important for growth under oxidative stress. By evolving, sequencing, and phenotyping over 200 yeast lineages, we found that gene loss can enhance an organism’s capacity to evolve and adapt. Although gene loss often led to an immediate decrease in fitness, many mutants rapidly acquired suppressor mutations that restored fitness. Depending on the strain’s genotype, some ultimately even attained higher fitness levels than similarly adapted wild-type cells. Further, cells with deletions in different modules of the genetic network followed distinct and predictable mutational trajectories. Finally, losing highly connected genes increased evolvability by facilitating the emergence of a more diverse array of phenotypes after adaptation. Together, our findings show that loss of specific parts of a genetic network can facilitate adaptation by opening alternative evolutionary paths.
Collapse
Affiliation(s)
- Jana Helsen
- Laboratory of Predictive Genetics and Multicellular Systems, CMPG, KU Leuven, Leuven, Belgium.,Laboratory of Genetics and Genomics, CMPG, KU Leuven, Leuven, Belgium.,Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Karin Voordeckers
- Laboratory of Genetics and Genomics, CMPG, KU Leuven, Leuven, Belgium.,Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Laura Vanderwaeren
- Laboratory of Predictive Genetics and Multicellular Systems, CMPG, KU Leuven, Leuven, Belgium.,Laboratory of Genetics and Genomics, CMPG, KU Leuven, Leuven, Belgium.,Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Toon Santermans
- Laboratory of Predictive Genetics and Multicellular Systems, CMPG, KU Leuven, Leuven, Belgium
| | - Maria Tsontaki
- Laboratory of Genetics and Genomics, CMPG, KU Leuven, Leuven, Belgium.,Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Kevin J Verstrepen
- Laboratory of Genetics and Genomics, CMPG, KU Leuven, Leuven, Belgium.,Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Rob Jelier
- Laboratory of Predictive Genetics and Multicellular Systems, CMPG, KU Leuven, Leuven, Belgium
| |
Collapse
|
27
|
Lalanne J, Parker DJ, Li G. Spurious regulatory connections dictate the expression-fitness landscape of translation factors. Mol Syst Biol 2021; 17:e10302. [PMID: 33900014 PMCID: PMC8073009 DOI: 10.15252/msb.202110302] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022] Open
Abstract
During steady-state cell growth, individual enzymatic fluxes can be directly inferred from growth rate by mass conservation, but the inverse problem remains unsolved. Perturbing the flux and expression of a single enzyme could have pleiotropic effects that may or may not dominate the impact on cell fitness. Here, we quantitatively dissect the molecular and global responses to varied expression of translation termination factors (peptide release factors, RFs) in the bacterium Bacillus subtilis. While endogenous RF expression maximizes proliferation, deviations in expression lead to unexpected distal regulatory responses that dictate fitness reduction. Molecularly, RF depletion causes expression imbalance at specific operons, which activates master regulators and detrimentally overrides the transcriptome. Through these spurious connections, RF abundances are thus entrenched by focal points within the regulatory network, in one case located at a single stop codon. Such regulatory entrenchment suggests that predictive bottom-up models of expression-fitness landscapes will require near-exhaustive characterization of parts.
Collapse
Affiliation(s)
- Jean‐Benoît Lalanne
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
- Present address:
Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Darren J Parker
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Present address:
Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Gene‐Wei Li
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
| |
Collapse
|
28
|
Yu R, Cao X, Sun L, Zhu JY, Wasko BM, Liu W, Crutcher E, Liu H, Jo MC, Qin L, Kaeberlein M, Han Z, Dang W. Inactivating histone deacetylase HDA promotes longevity by mobilizing trehalose metabolism. Nat Commun 2021; 12:1981. [PMID: 33790287 PMCID: PMC8012573 DOI: 10.1038/s41467-021-22257-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023] Open
Abstract
Histone acetylations are important epigenetic markers for transcriptional activation in response to metabolic changes and various stresses. Using the high-throughput SEquencing-Based Yeast replicative Lifespan screen method and the yeast knockout collection, we demonstrate that the HDA complex, a class-II histone deacetylase (HDAC), regulates aging through its target of acetylated H3K18 at storage carbohydrate genes. We find that, in addition to longer lifespan, disruption of HDA results in resistance to DNA damage and osmotic stresses. We show that these effects are due to increased promoter H3K18 acetylation and transcriptional activation in the trehalose metabolic pathway in the absence of HDA. Furthermore, we determine that the longevity effect of HDA is independent of the Cyc8-Tup1 repressor complex known to interact with HDA and coordinate transcriptional repression. Silencing the HDA homologs in C. elegans and Drosophila increases their lifespan and delays aging-associated physical declines in adult flies. Hence, we demonstrate that this HDAC controls an evolutionarily conserved longevity pathway.
Collapse
Affiliation(s)
- Ruofan Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Xiaohua Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Luyang Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Jun-Yi Zhu
- Center for Precision Disease Modeling, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA, USA
- University of Houston, Clear Lake, TX, USA
| | - Wei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Emeline Crutcher
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Haiying Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | | | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Zhe Han
- Center for Precision Disease Modeling, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Weiwei Dang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
29
|
Identification of Genetic Modifiers of TDP-43: Inflammatory Activation of Astrocytes for Neuroinflammation. Cells 2021; 10:cells10030676. [PMID: 33803845 PMCID: PMC8003223 DOI: 10.3390/cells10030676] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Transactive response DNA-binding protein 43 (TDP-43) is a ubiquitously expressed DNA/RNA-binding protein linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). TDP-43 has been implicated in numerous aspects of the mRNA life cycle, as well as in cell toxicity and neuroinflammation. In this study, we used the toxicity of the TDP-43 expression in Saccharomyces cerevisiae as an assay to identify TDP-43 genetic interactions. Specifically, we transformed human TDP-43 cDNAs of wild-type or disease-associated mutants (M337V and Q331K) en masse into 4653 homozygous diploid yeast deletion mutants and then used next-generation sequencing readouts of growth to identify yeast toxicity modifiers. Genetic interaction analysis provided a global view of TDP-43 pathways, some of which are known to be involved in cellular metabolic processes. Selected putative loci with the potential of genetic interactions with TDP-43 were assessed for associations with neurotoxicity and inflammatory activation of astrocytes. The pharmacological inhibition of succinate dehydrogenase flavoprotein subunit A (SDHA) and voltage-dependent anion-selective channel 3 (VDAC3) suppressed TDP-43-induced expression of proinflammatory cytokines in astrocytes, indicating the critical roles played by SDHA and VDAC3 in TDP-43 pathways during inflammatory activation of astrocytes and neuroinflammation. Thus, the findings of our TDP-43 genetic interaction screen provide a global landscape of TDP-43 pathways and may help improve our understanding of the roles of glia and neuroinflammation in ALS and FTD pathogenesis.
Collapse
|
30
|
Garza NM, Griffin AT, Zulkifli M, Qiu C, Kaplan CD, Gohil VM. A genome-wide copper-sensitized screen identifies novel regulators of mitochondrial cytochrome c oxidase activity. J Biol Chem 2021; 296:100485. [PMID: 33662401 PMCID: PMC8027276 DOI: 10.1016/j.jbc.2021.100485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 11/30/2022] Open
Abstract
Copper is essential for the activity and stability of cytochrome c oxidase (CcO), the terminal enzyme of the mitochondrial respiratory chain. Loss-of-function mutations in genes required for copper transport to CcO result in fatal human disorders. Despite the fundamental importance of copper in mitochondrial and organismal physiology, systematic identification of genes that regulate mitochondrial copper homeostasis is lacking. To discover these genes, we performed a genome-wide screen using a library of DNA-barcoded yeast deletion mutants grown in copper-supplemented media. Our screen recovered a number of genes known to be involved in cellular copper homeostasis as well as genes previously not linked to mitochondrial copper biology. These newly identified genes include the subunits of the adaptor protein 3 complex (AP-3) and components of the cellular pH-sensing pathway Rim20 and Rim21, both of which are known to affect vacuolar function. We find that AP-3 and Rim mutants exhibit decreased vacuolar acidity, which in turn perturbs mitochondrial copper homeostasis and CcO function. CcO activity of these mutants could be rescued by either restoring vacuolar pH or supplementing growth media with additional copper. Consistent with these genetic data, pharmacological inhibition of the vacuolar proton pump leads to decreased mitochondrial copper content and a concomitant decrease in CcO abundance and activity. Taken together, our study uncovered novel genetic regulators of mitochondrial copper homeostasis and provided a mechanism by which vacuolar pH impacts mitochondrial respiration through copper homeostasis.
Collapse
Affiliation(s)
- Natalie M Garza
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Aaron T Griffin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Mohammad Zulkifli
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Chenxi Qiu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Craig D Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Vishal M Gohil
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.
| |
Collapse
|
31
|
Amer B, Baidoo EEK. Omics-Driven Biotechnology for Industrial Applications. Front Bioeng Biotechnol 2021; 9:613307. [PMID: 33708762 PMCID: PMC7940536 DOI: 10.3389/fbioe.2021.613307] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.
Collapse
Affiliation(s)
- Bashar Amer
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Edward E. K. Baidoo
- Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- U.S. Department of Energy, Agile BioFoundry, Emeryville, CA, United States
| |
Collapse
|
32
|
Park YK, Yoon BH, Park SJ, Kim BK, Kim SY. BaSDAS: a web-based pooled CRISPR-Cas9 knockout screening data analysis system. Genomics Inform 2021; 18:e46. [PMID: 33412762 PMCID: PMC7808871 DOI: 10.5808/gi.2020.18.4.e46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/24/2020] [Indexed: 11/20/2022] Open
Abstract
We developed the BaSDAS (Barcode-Seq Data Analysis System), a GUI-based pooled knockout screening data analysis system, to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information.
Collapse
Affiliation(s)
| | - Byoung-Ha Yoon
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Seung-Jin Park
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34113, Korea
| | | | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34113, Korea
| |
Collapse
|
33
|
Multiplexed Competition in a Synthetic Squid Light Organ Microbiome Using Barcode-Tagged Gene Deletions. mSystems 2020; 5:5/6/e00846-20. [PMID: 33323415 PMCID: PMC7771539 DOI: 10.1128/msystems.00846-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Beneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Beneficial symbioses between microbes and their eukaryotic hosts are ubiquitous and have widespread impacts on host health and development. The binary symbiosis between the bioluminescent bacterium Vibrio fischeri and its squid host Euprymna scolopes serves as a model system to study molecular mechanisms at the microbe-animal interface. To identify colonization factors in this system, our lab previously conducted a global transposon insertion sequencing (INSeq) screen and identified over 300 putative novel squid colonization factors in V. fischeri. To pursue mechanistic studies on these candidate genes, we present an approach to quickly generate barcode-tagged gene deletions and perform high-throughput squid competition experiments with detection of the proportion of each strain in the mixture by barcode sequencing (BarSeq). Our deletion approach improves on previous techniques based on splicing by overlap extension PCR (SOE-PCR) and tfoX-based natural transformation by incorporating a randomized barcode that results in unique DNA sequences within each deletion scar. Amplicon sequencing of the pool of barcoded strains before and after colonization faithfully reports on known colonization factors and provides increased sensitivity over colony counting methods. BarSeq enables rapid and sensitive characterization of the molecular factors involved in establishing the Vibrio-squid symbiosis and provides a valuable tool to interrogate the molecular dialogue at microbe-animal host interfaces. IMPORTANCE Beneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Model symbioses are therefore invaluable for studying the mechanisms of beneficial microbe-host interactions. Here, we present a combined barcode-tagged deletion and BarSeq approach to interrogate the molecular dialogue that ensures specific and reproducible colonization of the Hawaiian bobtail squid by Vibrio fischeri. The ability to precisely manipulate the bacterial genome, combined with multiplex colonization assays, will accelerate the use of this valuable model system for mechanistic studies of how environmental microbes—both beneficial and pathogenic—colonize specific animal hosts.
Collapse
|
34
|
Kim JH, Seo Y, Jo M, Jeon H, Kim YS, Kim EJ, Seo D, Lee WH, Kim SR, Yachie N, Zhong Q, Vidal M, Roth FP, Suk K. Interrogation of kinase genetic interactions provides a global view of PAK1-mediated signal transduction pathways. J Biol Chem 2020; 295:16906-16919. [PMID: 33060198 PMCID: PMC7863907 DOI: 10.1074/jbc.ra120.014831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 09/23/2020] [Indexed: 12/29/2022] Open
Abstract
Kinases are critical components of intracellular signaling pathways and have been extensively investigated with regard to their roles in cancer. p21-activated kinase-1 (PAK1) is a serine/threonine kinase that has been previously implicated in numerous biological processes, such as cell migration, cell cycle progression, cell motility, invasion, and angiogenesis, in glioma and other cancers. However, the signaling network linked to PAK1 is not fully defined. We previously reported a large-scale yeast genetic interaction screen using toxicity as a readout to identify candidate PAK1 genetic interactions. En masse transformation of the PAK1 gene into 4,653 homozygous diploid Saccharomyces cerevisiae yeast deletion mutants identified ∼400 candidates that suppressed yeast toxicity. Here we selected 19 candidate PAK1 genetic interactions that had human orthologs and were expressed in glioma for further examination in mammalian cells, brain slice cultures, and orthotopic glioma models. RNAi and pharmacological inhibition of potential PAK1 interactors confirmed that DPP4, KIF11, mTOR, PKM2, SGPP1, TTK, and YWHAE regulate PAK1-induced cell migration and revealed the importance of genes related to the mitotic spindle, proteolysis, autophagy, and metabolism in PAK1-mediated glioma cell migration, drug resistance, and proliferation. AKT1 was further identified as a downstream mediator of the PAK1-TTK genetic interaction. Taken together, these data provide a global view of PAK1-mediated signal transduction pathways and point to potential new drug targets for glioma therapy.
Collapse
Affiliation(s)
- Jae-Hong Kim
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Yeojin Seo
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Myungjin Jo
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Hyejin Jeon
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Young-Seop Kim
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Eun-Jung Kim
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Donggun Seo
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Won-Ha Lee
- School of Life Sciences, Brain Korea 21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Sang Ryong Kim
- School of Life Sciences, Brain Korea 21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Nozomu Yachie
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Quan Zhong
- Department of Biological Sciences, Wright State University, Dayton, Ohio, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kyoungho Suk
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, South Korea.
| |
Collapse
|
35
|
PhenoMIP: High-Throughput Phenotyping of Diverse Caenorhabditis elegans Populations via Molecular Inversion Probes. G3-GENES GENOMES GENETICS 2020; 10:3977-3990. [PMID: 32868407 PMCID: PMC7642933 DOI: 10.1534/g3.120.401656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Whether generated within a lab setting or isolated from the wild, variant alleles continue to be an important resource for decoding gene function in model organisms such as Caenorhabditis elegans. With advances in massively parallel sequencing, multiple whole-genome sequenced (WGS) strain collections are now available to the research community. The Million Mutation Project (MMP) for instance, analyzed 2007 N2-derived, mutagenized strains. Individually, each strain averages ∼400 single nucleotide variants amounting to ∼80 protein-coding variants. The effects of these variants, however, remain largely uncharacterized and querying the breadth of these strains for phenotypic changes requires a method amenable to rapid and sensitive high-throughput analysis. Here we present a pooled competitive fitness approach to quantitatively phenotype subpopulations of sequenced collections via molecular inversion probes (PhenoMIP). We phenotyped the relative fitness of 217 mutant strains on multiple food sources and classified these into five categories. We also demonstrate on a subset of these strains, that their fitness defects can be genetically mapped. Overall, our results suggest that approximately 80% of MMP mutant strains may have a decreased fitness relative to the lab reference, N2. The costs of generating this form of analysis through WGS methods would be prohibitive while PhenoMIP analysis in this manner is accomplished at less than one-tenth of projected WGS costs. We propose methods for applying PhenoMIP to a broad range of population selection experiments in a cost-efficient manner that would be useful to the community at large.
Collapse
|
36
|
Fenster JA, Eckert CA. High-Throughput Functional Genomics for Energy Production. Curr Opin Biotechnol 2020; 67:7-14. [PMID: 33152605 DOI: 10.1016/j.copbio.2020.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Functional genomics remains a foundational field for establishing genotype-phenotype relationships that enable strain engineering. High-throughput (HTP) methods accelerate the Design-Build-Test-Learn cycle that currently drives synthetic biology towards a forward engineering future. Trackable mutagenesis techniques including transposon insertion sequencing and CRISPR-Cas-mediated genome editing allow for rapid fitness profiling of a collection, or library, of mutants to discover beneficial mutations. Due to the relative speed of these experiments compared to adaptive evolution experiments, iterative rounds of mutagenesis can be implemented for next-generation metabolic engineering efforts to design complex production and tolerance phenotypes. Additionally, the expansion of these mutagenesis techniques to novel bacteria are opening up industrial microbes that show promise for establishing a bio-based economy.
Collapse
Affiliation(s)
- Jacob A Fenster
- Chemical and Biological Engineering, University of Colorado, Boulder CO, United States; Renewable and Sustainable Energy Institute, University of Colorado, Boulder CO, United States
| | - Carrie A Eckert
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder CO, United States; National Renewable Energy Laboratory, Golden CO, United States.
| |
Collapse
|
37
|
Burge RJ, Damianou A, Wilkinson AJ, Rodenko B, Mottram JC. Leishmania differentiation requires ubiquitin conjugation mediated by a UBC2-UEV1 E2 complex. PLoS Pathog 2020; 16:e1008784. [PMID: 33108402 PMCID: PMC7647121 DOI: 10.1371/journal.ppat.1008784] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/06/2020] [Accepted: 09/10/2020] [Indexed: 12/27/2022] Open
Abstract
Post-translational modifications such as ubiquitination are important for orchestrating the cellular transformations that occur as the Leishmania parasite differentiates between its main morphological forms, the promastigote and amastigote. 2 E1 ubiquitin-activating (E1), 13 E2 ubiquitin-conjugating (E2), 79 E3 ubiquitin ligase (E3) and 20 deubiquitinating cysteine peptidase (DUB) genes can be identified in the Leishmania mexicana genome but, currently, little is known about the role of E1, E2 and E3 enzymes in this parasite. Bar-seq analysis of 23 E1, E2 and HECT/RBR E3 null mutants generated in promastigotes using CRISPR-Cas9 revealed numerous loss-of-fitness phenotypes in promastigote to amastigote differentiation and mammalian infection. The E2s UBC1/CDC34, UBC2 and UEV1 and the HECT E3 ligase HECT2 are required for the successful transformation from promastigote to amastigote and UBA1b, UBC9, UBC14, HECT7 and HECT11 are required for normal proliferation during mouse infection. Of all ubiquitination enzyme null mutants examined in the screen, Δubc2 and Δuev1 exhibited the most extreme loss-of-fitness during differentiation. Null mutants could not be generated for the E1 UBA1a or the E2s UBC3, UBC7, UBC12 and UBC13, suggesting these genes are essential in promastigotes. X-ray crystal structure analysis of UBC2 and UEV1, orthologues of human UBE2N and UBE2V1/UBE2V2 respectively, reveal a heterodimer with a highly conserved structure and interface. Furthermore, recombinant L. mexicana UBA1a can load ubiquitin onto UBC2, allowing UBC2-UEV1 to form K63-linked di-ubiquitin chains in vitro. Notably, UBC2 can cooperate in vitro with human E3s RNF8 and BIRC2 to form non-K63-linked polyubiquitin chains, showing that UBC2 can facilitate ubiquitination independent of UEV1, but association of UBC2 with UEV1 inhibits this ability. Our study demonstrates the dual essentiality of UBC2 and UEV1 in the differentiation and intracellular survival of L. mexicana and shows that the interaction between these two proteins is crucial for regulation of their ubiquitination activity and function. The post-translational modification of proteins is key for allowing Leishmania parasites to transition between the different life cycle stages that exist in its insect vector and mammalian host. In particular, components of the ubiquitin system are important for the transformation of Leishmania from its insect (promastigote) to mammalian (amastigote) stage and normal infection in mice. However, little is known about the role of the enzymes that generate ubiquitin modifications in Leishmania. Here we characterise 28 enzymes of the ubiquitination pathway and show that many are required for life cycle progression or mouse infection by this parasite. Two proteins, UBC2 and UEV1, were selected for further study based on their importance in the promastigote to amastigote transition. We demonstrate that UBC2 and UEV1 form a heterodimer capable of carrying out ubiquitination and that the structural basis for this activity is conserved between Leishmania, Saccharomyces cerevisiae and humans. We also show that the interaction of UBC2 with UEV1 alters the nature of the ubiquitination activity performed by UBC2. Overall, we demonstrate the important role that ubiquitination enzymes play in the life cycle and infection process of Leishmania and explore the biochemistry underlying UBC2 and UEV1 function.
Collapse
Affiliation(s)
- Rebecca J. Burge
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | - Andreas Damianou
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Anthony J. Wilkinson
- York Biomedical Research Institute and York Structural Biology Laboratory, Department of Chemistry, University of York, United Kingdom
| | - Boris Rodenko
- UbiQ Bio BV, Amsterdam Science Park, the Netherlands
| | - Jeremy C. Mottram
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
- * E-mail:
| |
Collapse
|
38
|
Fasanello VJ, Liu P, Botero CA, Fay JC. High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae. PeerJ 2020; 8:e10118. [PMID: 33088623 PMCID: PMC7571412 DOI: 10.7717/peerj.10118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/16/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Experimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system in Saccharomyces cerevisiae that utilizes genetic barcoding to overcome this challenge. RESULTS We first confirm that barcode insertions do not alter fitness and that barcode sequencing can be used to efficiently detect fitness differences via pooled competition-based fitness assays. Next, we examine the effects of ploidy, chemical stress, and population bottleneck size on the evolutionary dynamics and fitness gains (adaptation) in a total of 76 experimentally evolving, asexual populations by conducting 1,216 fitness assays and analyzing 532 longitudinal-evolutionary samples collected from the evolving populations. In our analysis of these data we describe the strengths of this experimental evolution system and explore sources of error in our measurements of fitness and evolutionary dynamics. CONCLUSIONS Our experimental treatments generated distinct fitness effects and evolutionary dynamics, respectively quantified via multiplexed fitness assays and barcode lineage tracking. These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.
Collapse
Affiliation(s)
- Vincent J. Fasanello
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Ping Liu
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Carlos A. Botero
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Justin C. Fay
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, United States of America
- Department of Biology, University of Rochester, Rochester, NY, United States of America
| |
Collapse
|
39
|
Fletcher E, Baetz K. Multi-Faceted Systems Biology Approaches Present a Cellular Landscape of Phenolic Compound Inhibition in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2020; 8:539902. [PMID: 33154962 PMCID: PMC7591714 DOI: 10.3389/fbioe.2020.539902] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/02/2020] [Indexed: 01/18/2023] Open
Abstract
Synthetic biology has played a major role in engineering microbial cell factories to convert plant biomass (lignocellulose) to fuels and bioproducts by fermentation. However, the final product yield is limited by inhibition of microbial growth and fermentation by toxic phenolic compounds generated during lignocellulosic pre-treatment and hydrolysis. Advances in the development of systems biology technologies (genomics, transcriptomics, proteomics, metabolomics) have rapidly resulted in large datasets which are necessary to obtain a holistic understanding of complex biological processes underlying phenolic compound toxicity. Here, we review and compare different systems biology tools that have been utilized to identify molecular mechanisms that modulate phenolic compound toxicity in Saccharomyces cerevisiae. By focusing on and comparing functional genomics and transcriptomics approaches we identify common mechanisms potentially underlying phenolic toxicity. Additionally, we discuss possible ways by which integration of data obtained across multiple unbiased approaches can result in new avenues to develop yeast strains with a significant improvement in tolerance to phenolic fermentation inhibitors.
Collapse
Affiliation(s)
- Eugene Fletcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
40
|
Mutalik VK, Adler BA, Rishi HS, Piya D, Zhong C, Koskella B, Kutter EM, Calendar R, Novichkov PS, Price MN, Deutschbauer AM, Arkin AP. High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biol 2020; 18:e3000877. [PMID: 33048924 PMCID: PMC7553319 DOI: 10.1371/journal.pbio.3000877] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage-specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.
Collapse
Affiliation(s)
- Vivek K. Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
| | - Benjamin A. Adler
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Harneet S. Rishi
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Denish Piya
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Crystal Zhong
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Britt Koskella
- Department of Integrative Biology, University of California – Berkeley, Berkeley, California, United States of America
| | | | - Richard Calendar
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Pavel S. Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Morgan N. Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
| |
Collapse
|
41
|
Tack DS, Romantseva EF, Tonner PD, Pressman A, Rammohan J, Strychalski EA. Measurements drive progress in directed evolution for precise engineering of biological systems. CURRENT OPINION IN SYSTEMS BIOLOGY 2020; 23:32-37. [PMID: 34611570 PMCID: PMC8489032 DOI: 10.1016/j.coisb.2020.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Precise engineering of biological systems requires quantitative, high-throughput measurements, exemplified by progress in directed evolution. New approaches allow high-throughput measurements of phenotypes and their corresponding genotypes. When integrated into directed evolution, these quantitative approaches enable the precise engineering of biological function. At the same time, the increasingly routine availability of large, high-quality data sets supports the integration of machine learning with directed evolution. Together, these advances herald striking capabilities for engineering biology.
Collapse
Affiliation(s)
- Drew S Tack
- National Institute of Standards and Technology, Gaithersburg, MD, 20898, USA
| | | | - Peter D Tonner
- National Institute of Standards and Technology, Gaithersburg, MD, 20898, USA
| | - Abe Pressman
- National Institute of Standards and Technology, Gaithersburg, MD, 20898, USA
| | - Jayan Rammohan
- National Institute of Standards and Technology, Gaithersburg, MD, 20898, USA
| | | |
Collapse
|
42
|
Jung KW, Lee KT, Bahn YS. A Signature-Tagged Mutagenesis (STM)-based murine-infectivity assay for Cryptococcus neoformans. J Microbiol 2020; 58:823-831. [PMID: 32989639 DOI: 10.1007/s12275-020-0341-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/12/2020] [Indexed: 11/26/2022]
Abstract
Signature-tagged mutagenesis (STM) is a high-throughput genetic technique that can be used to investigate the function of genes by constructing a large number of mutant strains with unique DNA identification tags, pooling them, and screening them for a particular phenotypic trait. STM was first designed for the identification of genes that contribute to the virulence or infectivity of a pathogen in its host. Recently, this method has also been applied for the identification of mutants with specific phenotypes, such as antifungal drug resistance and proliferation. In the present study, we describe an STM method for the identification of genes contributing to the infectivity of Cryptococcus neoformans using a mutant library, in which each strain was tagged with a unique DNA sequence.
Collapse
Affiliation(s)
- Kwang-Woo Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup o56212, Republic of Korea
| | - Kyung-Tae Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
| |
Collapse
|
43
|
Wehrs M, Thompson MG, Banerjee D, Prahl JP, Morella NM, Barcelos CA, Moon J, Costello Z, Keasling JD, Shih PM, Tanjore D, Mukhopadhyay A. Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation. Microb Cell Fact 2020; 19:167. [PMID: 32811554 PMCID: PMC7437010 DOI: 10.1186/s12934-020-01423-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background Despite the latest advancements in metabolic engineering for genome editing and characterization of host performance, the successful development of robust cell factories used for industrial bioprocesses and accurate prediction of the behavior of microbial systems, especially when shifting from laboratory-scale to industrial conditions, remains challenging. To increase the probability of success of a scale-up process, data obtained from thoroughly performed studies mirroring cellular responses to typical large-scale stimuli may be used to derive crucial information to better understand potential implications of large-scale cultivation on strain performance. This study assesses the feasibility to employ a barcoded yeast deletion library to assess genome-wide strain fitness across a simulated industrial fermentation regime and aims to understand the genetic basis of changes in strain physiology during industrial fermentation, and the corresponding roles these genes play in strain performance. Results We find that mutant population diversity is maintained through multiple seed trains, enabling large scale fermentation selective pressures to act upon the community. We identify specific deletion mutants that were enriched in all processes tested in this study, independent of the cultivation conditions, which include MCK1, RIM11, MRK1, and YGK3 that all encode homologues of mammalian glycogen synthase kinase 3 (GSK-3). Ecological analysis of beta diversity between all samples revealed significant population divergence over time and showed feed specific consequences of population structure. Further, we show that significant changes in the population diversity during fed-batch cultivations reflect the presence of significant stresses. Our observations indicate that, for this yeast deletion collection, the selection of the feeding scheme which affects the accumulation of the fermentative by-product ethanol impacts the diversity of the mutant pool to a higher degree as compared to the pH of the culture broth. The mutants that were lost during the time of most extreme population selection suggest that specific biological processes may be required to cope with these specific stresses. Conclusions Our results demonstrate the feasibility of Bar-seq to assess fermentation associated stresses in yeast populations under industrial conditions and to understand critical stages of a scale-up process where variability emerges, and selection pressure gets imposed. Overall our work highlights a promising avenue to identify genetic loci and biological stress responses required for fitness under industrial conditions.
Collapse
Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Mitchell G Thompson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Deepanwita Banerjee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Norma M Morella
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Carolina A Barcelos
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jadie Moon
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Zak Costello
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Energy Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK 2970, Horsholm, Denmark.,Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Patrick M Shih
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Biology, University of California-Davis, Davis, CA, 95616, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA. .,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| |
Collapse
|
44
|
Ong WK, Courtney DK, Pan S, Andrade RB, Kiley PJ, Pfleger BF, Reed JL. Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4. PLoS Comput Biol 2020; 16:e1008137. [PMID: 32804944 PMCID: PMC7451989 DOI: 10.1371/journal.pcbi.1008137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/27/2020] [Accepted: 07/09/2020] [Indexed: 11/18/2022] Open
Abstract
Genome-scale metabolic models have been utilized extensively in the study and engineering of the organisms they describe. Here we present the analysis of a published dataset from pooled transposon mutant fitness experiments as an approach for improving the accuracy and gene-reaction associations of a metabolic model for Zymomonas mobilis ZM4, an industrially relevant ethanologenic organism with extremely high glycolytic flux and low biomass yield. Gene essentiality predictions made by the draft model were compared to data from individual pooled mutant experiments to identify areas of the model requiring deeper validation. Subsequent experiments showed that some of the discrepancies between the model and dataset were caused by polar effects, mis-mapped barcodes, or mutants carrying both wild-type and transposon disrupted gene copies-highlighting potential limitations inherent to data from individual mutants in these high-throughput datasets. Therefore, we analyzed correlations in fitness scores across all 492 experiments in the dataset in the context of functionally related metabolic reaction modules identified within the model via flux coupling analysis. These correlations were used to identify candidate genes for a reaction in histidine biosynthesis lacking an annotated gene and highlight metabolic modules with poorly correlated gene fitness scores. Additional genes for reactions involved in biotin, ubiquinone, and pyridoxine biosynthesis in Z. mobilis were identified and confirmed using mutant complementation experiments. These discovered genes, were incorporated into the final model, iZM4_478, which contains 747 metabolic and transport reactions (of which 612 have gene-protein-reaction associations), 478 genes, and 616 unique metabolites, making it one of the most complete models of Z. mobilis ZM4 to date. The methods of analysis that we applied here with the Z. mobilis transposon mutant dataset, could easily be utilized to improve future genome-scale metabolic reconstructions for organisms where these, or similar, high-throughput datasets are available.
Collapse
Affiliation(s)
- Wai Kit Ong
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison – Madison, Madison, Wisconsin, United States of America
| | - Dylan K. Courtney
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison – Madison, Madison, Wisconsin, United States of America
| | - Shu Pan
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison – Madison, Madison, Wisconsin, United States of America
| | - Ramon Bonela Andrade
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Patricia J. Kiley
- DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison – Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison – Madison, Madison, Wisconsin, United States of America
| | - Jennifer L. Reed
- Department of Chemical and Biological Engineering, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, Univ. of Wisconsin-Madison – Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
45
|
Beneke T, Gluenz E. Bar-seq strategies for the LeishGEdit toolbox. Mol Biochem Parasitol 2020; 239:111295. [PMID: 32659298 DOI: 10.1016/j.molbiopara.2020.111295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 11/24/2022]
Abstract
The number of fully sequenced genomes increases steadily but the function of many genes remains unstudied. To accelerate dissection of gene function in Leishmania spp. and other kinetoplastids we previously developed a streamlined pipeline for CRISPR-Cas9 gene editing, which we termed LeishGEdit. To facilitate high-throughput mutant screens we have adapted this pipeline by barcoding mutants with unique 17-nucleotide barcodes, allowing loss-of-function screens in mixed populations. Here we present primer design and analysis tools that facilitate these bar-seq strategies. We have developed a standalone easy-to-use pipeline to design CRISPR primers suitable for the LeishGEdit toolbox for any given genome and have generated a list of 14,995 barcodes. Barcodes and oligo sequences are now accessible through our website www.leishgedit.net allowing researchers to pursue bar-seq experiments in all currently available TriTrypDB genomes (release 41). This will streamline CRISPR bar-seq assays in kinetoplastids, enabling pooled mutant screens across the community.
Collapse
Affiliation(s)
- Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
| | - Eva Gluenz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK; The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 120 University Place, Glasgow G12 8TA, UK
| |
Collapse
|
46
|
Cain AK, Barquist L, Goodman AL, Paulsen IT, Parkhill J, van Opijnen T. A decade of advances in transposon-insertion sequencing. Nat Rev Genet 2020; 21:526-540. [PMID: 32533119 PMCID: PMC7291929 DOI: 10.1038/s41576-020-0244-x] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2020] [Indexed: 01/12/2023]
Abstract
It has been 10 years since the introduction of modern transposon-insertion sequencing (TIS) methods, which combine genome-wide transposon mutagenesis with high-throughput sequencing to estimate the fitness contribution or essentiality of each genetic component in a bacterial genome. Four TIS variations were published in 2009: transposon sequencing (Tn-Seq), transposon-directed insertion site sequencing (TraDIS), insertion sequencing (INSeq) and high-throughput insertion tracking by deep sequencing (HITS). TIS has since become an important tool for molecular microbiologists, being one of the few genome-wide techniques that directly links phenotype to genotype and ultimately can assign gene function. In this Review, we discuss the recent applications of TIS to answer overarching biological questions. We explore emerging and multidisciplinary methods that build on TIS, with an eye towards future applications. In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.
Collapse
Affiliation(s)
- Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Andrew L Goodman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | |
Collapse
|
47
|
Damianou A, Burge RJ, Catta-Preta CMC, Geoghegan V, Nievas YR, Newling K, Brown E, Burchmore R, Rodenko B, Mottram JC. Essential roles for deubiquitination in Leishmania life cycle progression. PLoS Pathog 2020; 16:e1008455. [PMID: 32544189 PMCID: PMC7319358 DOI: 10.1371/journal.ppat.1008455] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/26/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
The parasitic protozoan Leishmania requires proteasomal, autophagic and lysosomal proteolytic pathways to enact the extensive cellular remodelling that occurs during its life cycle. The proteasome is essential for parasite proliferation, yet little is known about the requirement for ubiquitination/deubiquitination processes in growth and differentiation. Activity-based protein profiling of L. mexicana C12, C19 and C65 deubiquitinating cysteine peptidases (DUBs) revealed DUB activity remains relatively constant during differentiation of procyclic promastigote to amastigote. However, when life cycle phenotyping (bar-seq) was performed on a pool including 15 barcoded DUB null mutants created in promastigotes using CRISPR-Cas9, significant loss of fitness was observed during differentiation and intracellular infection. DUBs 4, 7, and 13 are required for successful transformation from metacyclic promastigote to amastigote and DUBs 3, 5, 6, 8, 10, 11 and 14 are required for normal amastigote proliferation in mice. DUBs 1, 2, 12 and 16 are essential for promastigote viability and the essential role of DUB2 in establishing infection was demonstrated using DiCre inducible gene deletion in vitro and in vivo. DUB2 is found in the nucleus and interacts with nuclear proteins associated with transcription/chromatin dynamics, mRNA splicing and mRNA capping. DUB2 has broad linkage specificity, cleaving all the di-ubiquitin chains except for Lys27 and Met1. Our study demonstrates the crucial role that DUBs play in differentiation and intracellular survival of Leishmania and that amastigotes are exquisitely sensitive to disruption of ubiquitination homeostasis.
Collapse
Affiliation(s)
- Andreas Damianou
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rebecca J. Burge
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | | | - Vincent Geoghegan
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | - Y. Romina Nievas
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | - Katherine Newling
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | - Elaine Brown
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | - Richard Burchmore
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Boris Rodenko
- UbiQ Bio BV, Amsterdam Science Park, The Netherlands
| | - Jeremy C. Mottram
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| |
Collapse
|
48
|
Kim JH, Seo Y, Jo M, Jeon H, Lee WH, Yachie N, Zhong Q, Vidal M, Roth FP, Suk K. Yeast-Based Genetic Interaction Analysis of Human Kinome. Cells 2020; 9:cells9051156. [PMID: 32392905 PMCID: PMC7291280 DOI: 10.3390/cells9051156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 12/17/2022] Open
Abstract
Kinases are critical intracellular signaling proteins. To better understand kinase-mediated signal transduction, a large-scale human-yeast genetic interaction screen was performed. Among 597 human kinase genes tested, 28 displayed strong toxicity in yeast when overexpressed. En masse transformation of these toxic kinase genes into 4653 homozygous diploid yeast deletion mutants followed by barcode sequencing identified yeast toxicity modifiers and thus their human orthologs. Subsequent network analyses and functional grouping revealed that the 28 kinases and their 676 interaction partners (corresponding to a total of 969 genetic interactions) are enriched in cell death and survival (34%), small-molecule biochemistry (18%) and molecular transport (11%), among others. In the subnetwork analyses, a few kinases were commonly associated with glioma, cell migration and cell death/survival. Our analysis enabled the creation of a first draft of the kinase genetic interactome network and identified multiple drug targets for inflammatory diseases and cancer, in which deregulated kinase signaling plays a pathogenic role.
Collapse
Affiliation(s)
- Jae-Hong Kim
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (J.-H.K.); (Y.S.); (M.J.); (H.J.)
| | - Yeojin Seo
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (J.-H.K.); (Y.S.); (M.J.); (H.J.)
| | - Myungjin Jo
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (J.-H.K.); (Y.S.); (M.J.); (H.J.)
| | - Hyejin Jeon
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (J.-H.K.); (Y.S.); (M.J.); (H.J.)
| | - Won-Ha Lee
- School of Life Sciences, Brain Korea 21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Korea;
| | - Nozomu Yachie
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (N.Y.); (F.P.R.)
| | - Quan Zhong
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA;
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA;
| | - Frederick P. Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (N.Y.); (F.P.R.)
| | - Kyoungho Suk
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (J.-H.K.); (Y.S.); (M.J.); (H.J.)
- Correspondence:
| |
Collapse
|
49
|
Sun S, Baryshnikova A, Brandt N, Gresham D. Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states. Mol Syst Biol 2020; 16:e9167. [PMID: 32449603 PMCID: PMC7247079 DOI: 10.15252/msb.20199167] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 03/18/2020] [Accepted: 03/31/2020] [Indexed: 01/13/2023] Open
Abstract
Cell growth and quiescence in eukaryotic cells is controlled by an evolutionarily conserved network of signaling pathways. Signal transduction networks operate to modulate a wide range of cellular processes and physiological properties when cells exit proliferative growth and initiate a quiescent state. How signaling networks function to respond to diverse signals that result in cell cycle exit and establishment of a quiescent state is poorly understood. Here, we studied the function of signaling pathways in quiescent cells using global genetic interaction mapping in the model eukaryotic cell, Saccharomyces cerevisiae (budding yeast). We performed pooled analysis of genotypes using molecular barcode sequencing (Bar-seq) to test the role of ~4,000 gene deletion mutants and ~12,000 pairwise interactions between all non-essential genes and the protein kinase genes TOR1, RIM15, and PHO85 in three different nutrient-restricted conditions in both proliferative and quiescent cells. We detect up to 10-fold more genetic interactions in quiescent cells than proliferative cells. We find that both individual gene effects and genetic interaction profiles vary depending on the specific pro-quiescence signal. The master regulator of quiescence, RIM15, shows distinct genetic interaction profiles in response to different starvation signals. However, vacuole-related functions show consistent genetic interactions with RIM15 in response to different starvation signals, suggesting that RIM15 integrates diverse signals to maintain protein homeostasis in quiescent cells. Our study expands genome-wide genetic interaction profiling to additional conditions, and phenotypes, and highlights the conditional dependence of epistasis.
Collapse
Affiliation(s)
- Siyu Sun
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNYUSA
- Department of BiologyNew York UniversityNew YorkNYUSA
| | | | - Nathan Brandt
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNYUSA
- Department of BiologyNew York UniversityNew YorkNYUSA
| | - David Gresham
- Center for Genomics and Systems BiologyNew York UniversityNew YorkNYUSA
- Department of BiologyNew York UniversityNew YorkNYUSA
| |
Collapse
|
50
|
Competition experiments in a soil microcosm reveal the impact of genetic and biotic factors on natural yeast populations. ISME JOURNAL 2020; 14:1410-1421. [PMID: 32080356 DOI: 10.1038/s41396-020-0612-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023]
Abstract
The ability to measure microbial fitness directly in natural conditions and in interaction with other microbes is a challenge that needs to be overcome if we want to gain a better understanding of microbial fitness determinants in nature. Here we investigate the influence of the natural microbial community on the relative fitness of the North American populations SpB, SpC and SpC* of the wild yeast Saccharomyces paradoxus using DNA barcodes and a soil microcosm derived from soil associated with oak trees. We find that variation in fitness among these genetically distinct groups is influenced by the microbial community. Altering the microbial community load and diversity with an irradiation treatment significantly diminishes the magnitude of fitness differences among populations. Our findings suggest that microbial interactions could affect the evolution of yeast lineages in nature by modulating variation in fitness.
Collapse
|