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Goold HD, Moseley JL, Lauersen KJ. The synthetic future of algal genomes. Cell Genom 2024; 4:100505. [PMID: 38395701 PMCID: PMC10943592 DOI: 10.1016/j.xgen.2024.100505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/18/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Algae are diverse organisms with significant biotechnological potential for resource circularity. Taking inspiration from fermentative microbes, engineering algal genomes holds promise to broadly expand their application ranges. Advances in genome sequencing with improvements in DNA synthesis and delivery techniques are enabling customized molecular tool development to confer advanced traits to algae. Efforts to redesign and rebuild entire genomes to create fit-for-purpose organisms currently being explored in heterotrophic prokaryotes and eukaryotic microbes could also be applied to photosynthetic algae. Future algal genome engineering will enhance yields of native products and permit the expression of complex biochemical pathways to produce novel metabolites from sustainable inputs. We present a historical perspective on advances in engineering algae, discuss the requisite genetic traits to enable algal genome optimization, take inspiration from whole-genome engineering efforts in other microbes for algal systems, and present candidate algal species in the context of these engineering goals.
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Affiliation(s)
- Hugh D Goold
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia; ARC Center of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia; School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jeffrey L Moseley
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Phycoil Biotechnology International, Inc., Fremont, CA 94538, USA
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
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2
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Hannon-Hatfield JA, Chen J, Bergman CM, Garfinkel DJ. Evolution of a Restriction Factor by Domestication of a Yeast Retrotransposon. Mol Biol Evol 2024; 41:msae050. [PMID: 38442736 PMCID: PMC10951436 DOI: 10.1093/molbev/msae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024] Open
Abstract
Transposable elements drive genome evolution in all branches of life. Transposable element insertions are often deleterious to their hosts and necessitate evolution of control mechanisms to limit their spread. The long terminal repeat retrotransposon Ty1 prime (Ty1'), a subfamily of the Ty1 family, is present in many Saccharomyces cerevisiae strains, but little is known about what controls its copy number. Here, we provide evidence that a novel gene from an exapted Ty1' sequence, domesticated restriction of Ty1' relic 2 (DRT2), encodes a restriction factor that inhibits Ty1' movement. DRT2 arose through domestication of a Ty1' GAG gene and contains the C-terminal domain of capsid, which in the related Ty1 canonical subfamily functions as a self-encoded restriction factor. Bioinformatic analysis reveals the widespread nature of DRT2, its evolutionary history, and pronounced structural variation at the Ty1' relic 2 locus. Ty1' retromobility analyses demonstrate DRT2 restriction factor functionality, and northern blot and RNA-seq analysis indicate that DRT2 is transcribed in multiple strains. Velocity cosedimentation profiles indicate an association between Drt2 and Ty1' virus-like particles or assembly complexes. Chimeric Ty1' elements containing DRT2 retain retromobility, suggesting an ancestral role of productive Gag C-terminal domain of capsid functionality is present in the sequence. Unlike Ty1 canonical, Ty1' retromobility increases with copy number, suggesting that C-terminal domain of capsid-based restriction is not limited to the Ty1 canonical subfamily self-encoded restriction factor and drove the endogenization of DRT2. The discovery of an exapted Ty1' restriction factor provides insight into the evolution of the Ty1 family, evolutionary hot-spots, and host-transposable element interactions.
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Affiliation(s)
- J Adam Hannon-Hatfield
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Casey M Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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3
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Lewis AG, Carmichael L, Wang RY, Gibney PA. Characterizing a panel of amino acid auxotrophs under auxotrophic starvation conditions. Yeast 2024; 41:5-18. [PMID: 37997284 DOI: 10.1002/yea.3910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Auxotrophic strains starving for their cognate nutrient, termed auxotrophic starvation, are characterized by a shorter lifespan, higher glucose wasting phenotype, and inability to accomplish cell cycle arrest when compared to a "natural starvation," where a cell is starving for natural environmental growth-limiting nutrients such as phosphate. Since evidence of this physiological response is limited to only a subset of auxotrophs, we evaluated a panel of auxotrophic mutants to determine whether these responses are characteristic of a broader range of amino acid auxotrophs. Based on the starvation survival kinetics, the panel of strains was grouped into three categories-short-lived strains, strains with survival similar to a prototrophic wild type strain, and long-lived strains. Among the short-lived strains, we observed that the tyrosine, asparagine, threonine, and aspartic acid auxotrophs rapidly decline in viability, with all strains unable to arrest cell cycle progression. The three basic amino acid auxotrophs had a survival similar to a prototrophic strain starving in minimal media. The leucine, tryptophan, methionine, and cysteine auxotrophs displayed the longest lifespan. We also demonstrate how the phenomenon of glucose wasting is limited to only a subset of the tested auxotrophs, namely the asparagine, leucine, and lysine auxotrophs. Furthermore, we observed pleiotropic phenotypes associated with a subgroup of auxotrophs, highlighting the importance of considering unintended phenotypic effects when using auxotrophic strains especially in chronological aging experiments.
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Affiliation(s)
- Alisha G Lewis
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Laurin Carmichael
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Rebecca Y Wang
- Calico Life Sciences LLC, South San Francisco, California, USA
| | - Patrick A Gibney
- Department of Food Science, Cornell University, Ithaca, New York, USA
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4
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Chung WH. Signification and Application of Mutator and Antimutator Phenotype-Induced Genetic Variations in Evolutionary Adaptation and Cancer Therapeutics. J Microbiol 2023; 61:1013-1024. [PMID: 38100001 DOI: 10.1007/s12275-023-00091-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 01/11/2024]
Abstract
Mutations present a dichotomy in their implications for cellular processes. They primarily arise from DNA replication errors or damage repair processes induced by environmental challenges. Cumulative mutations underlie genetic variations and drive evolution, yet also contribute to degenerative diseases such as cancer and aging. The mutator phenotype elucidates the heightened mutation rates observed in malignant tumors. Evolutionary adaptation, analogous to bacterial and eukaryotic systems, manifests through mutator phenotypes during changing environmental conditions, highlighting the delicate balance between advantageous mutations and their potentially detrimental consequences. Leveraging the genetic tractability of Saccharomyces cerevisiae offers unique insights into mutator phenotypes and genome instability akin to human cancers. Innovative reporter assays in yeast model organisms enable the detection of diverse genome alterations, aiding a comprehensive analysis of mutator phenotypes. Despite significant advancements, our understanding of the intricate mechanisms governing spontaneous mutation rates and preserving genetic integrity remains incomplete. This review outlines various cellular pathways affecting mutation rates and explores the role of mutator genes and mutation-derived phenotypes, particularly prevalent in malignant tumor cells. An in-depth comprehension of mutator and antimutator activities in yeast and higher eukaryotes holds promise for effective cancer control strategies.
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Affiliation(s)
- Woo-Hyun Chung
- College of Pharmacy, Duksung Women's University, Seoul, 01369, Republic of Korea.
- Innovative Drug Center, Duksung Women's University, Seoul, 01369, Republic of Korea.
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5
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Stepchenkova EI, Zadorsky SP, Shumega AR, Aksenova AY. Practical Approaches for the Yeast Saccharomyces cerevisiae Genome Modification. Int J Mol Sci 2023; 24:11960. [PMID: 37569333 PMCID: PMC10419131 DOI: 10.3390/ijms241511960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
The yeast S. cerevisiae is a unique genetic object for which a wide range of relatively simple, inexpensive, and non-time-consuming methods have been developed that allow the performing of a wide variety of genome modifications. Among the latter, one can mention point mutations, disruptions and deletions of particular genes and regions of chromosomes, insertion of cassettes for the expression of heterologous genes, targeted chromosomal rearrangements such as translocations and inversions, directed changes in the karyotype (loss or duplication of particular chromosomes, changes in the level of ploidy), mating-type changes, etc. Classical yeast genome manipulations have been advanced with CRISPR/Cas9 technology in recent years that allow for the generation of multiple simultaneous changes in the yeast genome. In this review we discuss practical applications of both the classical yeast genome modification methods as well as CRISPR/Cas9 technology. In addition, we review methods for ploidy changes, including aneuploid generation, methods for mating type switching and directed DSB. Combined with a description of useful selective markers and transformation techniques, this work represents a nearly complete guide to yeast genome modification.
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Affiliation(s)
- Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Sergey P. Zadorsky
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Andrey R. Shumega
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.I.S.); (S.P.Z.); (A.R.S.)
| | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
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6
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Favilla LD, Herman TS, Goersch CDS, de Andrade RV, Felipe MSS, Bocca AL, Fernandes L. Expanding the Toolbox for Functional Genomics in Fonsecaea pedrosoi: The Use of Split-Marker and Biolistic Transformation for Inactivation of Tryptophan Synthase ( trpB) Gene. J Fungi (Basel) 2023; 9:jof9020224. [PMID: 36836338 PMCID: PMC9963410 DOI: 10.3390/jof9020224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Chromoblastomycosis (CBM) is a disease caused by several dematiaceous fungi from different genera, and Fonsecaea is the most common which has been clinically isolated. Genetic transformation methods have recently been described; however, molecular tools for the functional study of genes have been scarcely reported for those fungi. In this work, we demonstrated that gene deletion and generation of the null mutant by homologous recombination are achievable for Fonsecaea pedrosoi by the use of two approaches: use of double-joint PCR for cassette construction, followed by delivery of the split-marker by biolistic transformation. Through in silico analyses, we identified that F. pedrosoi presents the complete enzymatic apparatus required for tryptophan (trp) biosynthesis. The gene encoding a tryptophan synthase trpB -which converts chorismate to trp-was disrupted. The ΔtrpB auxotrophic mutant can grow with external trp supply, but germination, viability of conidia, and radial growth are defective compared to the wild-type and reconstituted strains. The use of 5-FAA for selection of trp- phenotypes and for counter-selection of strains carrying the trp gene was also demonstrated. The molecular tools for the functional study of genes, allied to the genetic information from genomic databases, significantly boost our understanding of the biology and pathogenicity of CBM causative agents.
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Affiliation(s)
- Luísa Dan Favilla
- Laboratory of Applied Immunology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Molecular Biology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
| | - Tatiana Sobianski Herman
- Laboratory of Applied Immunology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Molecular Patology, Faculty of Medicine, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
| | - Camila da Silva Goersch
- Laboratory of Applied Immunology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Microbial Biology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
| | - Rosangela Vieira de Andrade
- Graduate Program of Genomic Sciences and Biotechnology, Catholic University of Brasilia, Campus Asa Norte, Asa Norte, Federal District, Taguatinga 70790-160, Brazil
| | - Maria Sueli Soares Felipe
- Graduate Program of Genomic Sciences and Biotechnology, Catholic University of Brasilia, Campus Asa Norte, Asa Norte, Federal District, Taguatinga 70790-160, Brazil
| | - Anamélia Lorenzetti Bocca
- Laboratory of Applied Immunology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Molecular Biology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Molecular Patology, Faculty of Medicine, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
| | - Larissa Fernandes
- Laboratory of Applied Immunology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Microbial Biology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Centro Metropolitano, Faculty of Ceilândia, Campus UnB Ceilândia, University of Brasília, Ceilândia Sul, Federal District, Brasilia 72220-275, Brazil
- Correspondence:
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Meyer RE, Sartin A, Gish M, Harsha J, Wilkie E, Haworth D, LaVictoire R, Alberola I, Chuong HH, Gorbsky GJ, Dawson DS. Polyploid yeast are dependent on elevated levels of Mps1 for successful chromosome segregation. bioRxiv 2023:2023.01.09.523325. [PMID: 36712123 PMCID: PMC9882063 DOI: 10.1101/2023.01.09.523325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tumor cell lines with elevated chromosome numbers frequently have correlated elevations of Mps1 expression and these tumors are more dependent on Mps1 activity for their survival than control cell lines. Mps1 is a conserved kinase involved in controlling aspects of chromosome segregation in mitosis and meiosis. The mechanistic explanation for the Mps1-addiction of aneuploid cells is unknown. To address this question, we explored Mps1-dependence in yeast cells with increased sets of chromosomes. These experiments revealed that in yeast, increasing ploidy leads to delays and failures in orienting chromosomes on the mitotic spindle. Yeast cells with elevated numbers of chromosomes proved vulnerable to reductions of Mps1 activity. Cells with reduced Mps1 activity exhibit an extended prometaphase with longer spindles and delays in orienting the chromosomes. One known role of Mps1 is in recruiting Bub1 to the kinetochore in meiosis. We found that the Mps1-addiction of polyploid yeast cells is due in part to its role in Bub1 recruitment. Together, the experiments presented here demonstrate that increased ploidy renders cells more dependent on Mps1 for orienting chromosomes on the spindle. The phenomenon described here may be relevant in understanding why hyper-diploid cancer cells exhibit elevated reliance on Mps1 expression for successful chromosome segregation.
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Affiliation(s)
- Régis E Meyer
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Ashlea Sartin
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Madeline Gish
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Jillian Harsha
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Emily Wilkie
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Dawson Haworth
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Rebecca LaVictoire
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Isabel Alberola
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Hoa H Chuong
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Gary J Gorbsky
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Dean S Dawson
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
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Pérez D, Denat M, Pérez-Través L, Heras JM, Guillamón JM, Ferreira V, Querol A. Generation of intra- and interspecific Saccharomyces hybrids with improved oenological and aromatic properties. Microb Biotechnol 2022; 15:2266-2280. [PMID: 35485391 PMCID: PMC9328737 DOI: 10.1111/1751-7915.14068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 12/03/2022] Open
Abstract
Non‐wine yeasts could enhance the aroma and organoleptic profile of wines. However, compared to wine strains, they have specific intolerances to winemaking conditions. To solve this problem, we generated intra‐ and interspecific hybrids using a non‐GMO technique (rare‐mating) in which non‐wine strains of S. uvarum, S. kudriavzevii and S. cerevisiae species were crossed with a wine S. cerevisiae yeast. The hybrid that inherited the wine yeast mitochondrial showed better fermentation capacities, whereas hybrids carrying the non‐wine strain mitotype reduced ethanol levels and increased glycerol, 2,3‐butanediol and organic acid production. Moreover, all the hybrids produced several fruity and floral aromas compared to the wine yeast: β‐phenylethyl acetate, isobutyl acetate, γ‐octalactone, ethyl cinnamate in both varietal wines. Sc × Sk crosses produced three‐ to sixfold higher polyfunctional mercaptans, 4‐mercapto‐4‐methylpentan‐2‐one (4MMP) and 3‐mercaptohexanol (3MH). We proposed that the exceptional 3MH release observed in an S. cerevisiae × S. kudriavzevii hybrid was due to the cleavage of the non‐volatile glutathione precursor (Glt‐3MH) to detoxify the cell from the presence of methylglyoxal, a compound related to the high glycerol yield reached by this hybrid. In conclusion, hybrid generation allows us to obtain aromatically improved yeasts concerning their wine parent. In addition, they reduced ethanol and increased organic acids yields, which counteracts climate change effect on grapes.
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Affiliation(s)
- Dolores Pérez
- Lallemand Bio S.L., Barcelona, 08028, Spain.,Estación Experimental Agropecuaria Mendoza (EEA), Instituto Nacional de Tecnología Agropecuaria (INTA), Luján de Cuyo, Mendoza, 5507, Argentina.,Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA-CSIC), Valencia, 46980, Spain
| | - Marie Denat
- Laboratorio de Análisis del Aroma y Enología (LAAE), Departamento de Química Analítica, Universidad de Zaragoza, c/Pedro Cerbuna 12, Zaragoza, 50009, Spain
| | - Laura Pérez-Través
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA-CSIC), Valencia, 46980, Spain
| | | | - José Manuel Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA-CSIC), Valencia, 46980, Spain
| | - Vicente Ferreira
- Laboratorio de Análisis del Aroma y Enología (LAAE), Departamento de Química Analítica, Universidad de Zaragoza, c/Pedro Cerbuna 12, Zaragoza, 50009, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA-CSIC), Valencia, 46980, Spain
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9
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Siewers V. An Overview on Selection Marker Genes for Transformation of Saccharomyces cerevisiae. Methods Mol Biol 2022; 2513:1-13. [PMID: 35781196 DOI: 10.1007/978-1-0716-2399-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
For genetic manipulation of yeast, numerous selection marker genes have been employed. These include prototrophic markers, markers conferring drug resistance, autoselection markers, and counterselectable markers. This chapter describes the different classes of selection markers and provides a number of examples for different applications.
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Affiliation(s)
- Verena Siewers
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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10
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Moon HY, Sim GH, Kim HJ, Kim K, Kang HA. Assessment of Cre-lox and CRISPR-Cas9 as tools for recycling of multiple-integrated selection markers in Saccharomyces cerevisiae. J Microbiol 2022; 60:18-30. [PMID: 34964942 DOI: 10.1007/s12275-022-1580-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Abstract
We evaluated the Cre-lox and CRISPR-Cas9 systems as marker-recycling tools in Saccharomyces cerevisiae recombinants containing multiple-integrated expression cassettes. As an initial trial, we constructed rDNA-nontranscribed spacer- or Ty4-based multiple integration vectors containing the URA3 marker flanked by the loxP sequence. Integrants harboring multiple copies of tHMG1 and NNV-CP expression cassettes were obtained and subsequently transformed with the Cre plasmid. However, the simultaneous pop-out of the expression cassettes along with the URA3 marker hampered the use of Cre-lox as a marker-recycling tool in multiple integrants. As an alternative, we constructed a set of CRISPR-Cas9-gRNA vectors containing gRNA targeted to auxotrophic marker genes. Transformation of multiple integrants of tHMG1 and NNV-CP cassettes by the Cas9-gRNA vector in the presence of the URA3 (stop) donor DNA fragments generated the Ura- transformants retaining multiple copies of the expression cassettes. CRISPR-Cas9-based inactivation led to the recycling of the other markers, HIS3, LEU2, and TRP1, without loss of expression cassettes in the recombinants containing multiple copies of tHMG1, NNV-CP, and SfBGL1 cassettes, respectively. Reuse of the same selection marker in marker-inactivated S. cerevisiae was validated by multiple integrations of the TrEGL2 cassette into the S. cerevisiae strain expressing SfBGL1. These results demonstrate that introducing stop codons into selection marker genes using the CRISPR-Cas9 system with donor DNA fragments is an efficient strategy for markerrecycling in multiple integrants. In particular, the continual reuse of auxotrophic markers would facilitate the construction of a yeast cell factory containing multiple copies of expression cassettes without antibiotic resistance genes.
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Affiliation(s)
- Hye Yun Moon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Gyu Hun Sim
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyeon Jin Kim
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Keunpil Kim
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyun Ah Kang
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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11
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Tsuboi Y, Sakuma T, Yamamoto T, Horiuchi H, Takahashi F, Igarashi K, Hagihara H, Takimura Y. OUP accepted manuscript. FEMS Microbiol Lett 2022; 369:6524178. [PMID: 35137045 PMCID: PMC8863565 DOI: 10.1093/femsle/fnac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/11/2021] [Accepted: 02/04/2022] [Indexed: 12/02/2022] Open
Abstract
The Mucorales fungal genus Rhizopus is used for the industrial production of organic acids, enzymes and fermented foods. The metabolic engineering efficiency of Rhizopus could be improved using gene manipulation; however, exogenous DNA rarely integrates into the host genome. Consequently, a genetic tool for Mucorales fungi needs to be developed. Recently, programmable nucleases that generate DNA double-strand breaks (DSBs) at specific genomic loci have been used for genome editing in various organisms. In this study, we examined gene disruption in Rhizopus oryzae using transcription activator-like effector nucleases (TALENs), with and without exonuclease overexpression. TALENs with an overexpressing exonuclease induced DSBs, followed by target site deletions. Although DSBs are repaired mainly by nonhomologous end joining in most organisms, our results suggested that in R. oryzae microhomology-mediated end joining was the major DSB repair system. Our gene manipulation method using TALENs coupled with exonuclease overexpression contributes to basic scientific knowledge and the metabolic engineering of Rhizopus.
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Affiliation(s)
- Yuichi Tsuboi
- Corresponding author: Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan. Tel: +81-70-3297-1291; Fax: +81-73-426-5027; E-mail:
| | | | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Fumikazu Takahashi
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
| | - Kazuaki Igarashi
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
| | - Hiroshi Hagihara
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
| | - Yasushi Takimura
- Biological Science Laboratories, KAO Corporation, 1334 Minato, Wakayama, Wakayama 640-8580, Japan
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12
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Lin CL, García-Caro RDLC, Zhang P, Carlin S, Gottlieb A, Petersen MA, Vrhovsek U, Bond U. Packing a punch: understanding how flavours are produced in lager fermentations. FEMS Yeast Res 2021; 21:6316108. [PMID: 34227660 PMCID: PMC8310685 DOI: 10.1093/femsyr/foab040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/02/2021] [Indexed: 11/14/2022] Open
Abstract
Beer is one of the most popular beverages in the world and it has an irreplaceable place in culture. Although invented later than ale, lager beers dominate the current market. Many factors relating to the appearance (colour, clarity and foam stability) and sensory characters (flavour, taste and aroma) of beer, and other psychological determinants affect consumers' perception of the product and defines its drinkability. This review takes a wholistic approach to scrutinise flavour generation in the brewing process, focusing particularly on the contribution of the raw ingredients and the yeasts to the final flavour profiles of lager beers. In addition, we examine current developments to improve lager beer flavour profiles for the modern consumers.
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Affiliation(s)
- Claire Lin Lin
- Brewing 345, Novozymes A/S, Biologiensvej 2, 2800 Kongens, Lyngby, Denmark.,Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | | | - Penghan Zhang
- Metabolomic Unit, Food Quality and Nutrition Department, Research and Innovation Centre, Edmund Mach Foundation, Via E.Mach 1, 38010 S.Michele all'Adige, Italy
| | - Silvia Carlin
- Metabolomic Unit, Food Quality and Nutrition Department, Research and Innovation Centre, Edmund Mach Foundation, Via E.Mach 1, 38010 S.Michele all'Adige, Italy
| | - Andrea Gottlieb
- Brewing 345, Novozymes A/S, Biologiensvej 2, 2800 Kongens, Lyngby, Denmark
| | - Mikael Agerlin Petersen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Urska Vrhovsek
- Metabolomic Unit, Food Quality and Nutrition Department, Research and Innovation Centre, Edmund Mach Foundation, Via E.Mach 1, 38010 S.Michele all'Adige, Italy
| | - Ursula Bond
- School of Genetics and Microbiology, The Moyne Institute, Trinity College Dublin, Dublin 2, Ireland
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13
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Niño-Padilla EI, Velazquez C, Garibay-Escobar A. Mycobacterial biofilms as players in human infections: a review. Biofouling 2021; 37:410-432. [PMID: 34024206 DOI: 10.1080/08927014.2021.1925886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/18/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
The role of biofilms in pathogenicity and treatment strategies is often neglected in mycobacterial infections. In recent years, the emergence of nontuberculous mycobacterial infections has necessitated the development of novel prophylactic strategies and elucidation of the mechanisms underlying the establishment of chronic infections. More importantly, the question arises whether members of the Mycobacterium tuberculosis complex can form biofilms and contribute to latent tuberculosis and drug resistance because of the long-lasting and recalcitrant nature of its infections. This review discusses some of the molecular mechanisms by which biofilms could play a role in infection or pathological events in humans.
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Affiliation(s)
| | - Carlos Velazquez
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Adriana Garibay-Escobar
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
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14
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Tominaga M, Nozaki K, Umeno D, Ishii J, Kondo A. Robust and flexible platform for directed evolution of yeast genetic switches. Nat Commun 2021; 12:1846. [PMID: 33758180 PMCID: PMC7988172 DOI: 10.1038/s41467-021-22134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/26/2021] [Indexed: 01/31/2023] Open
Abstract
A wide repertoire of genetic switches has accelerated prokaryotic synthetic biology, while eukaryotic synthetic biology has lagged in the model organism Saccharomyces cerevisiae. Eukaryotic genetic switches are larger and more complex than prokaryotic ones, complicating the rational design and evolution of them. Here, we present a robust workflow for the creation and evolution of yeast genetic switches. The selector system was designed so that both ON- and OFF-state selection of genetic switches is completed solely by liquid handling, and it enabled parallel screen/selection of different motifs with different selection conditions. Because selection threshold of both ON- and OFF-state selection can be flexibly tuned, the desired selection conditions can be rapidly pinned down for individual directed evolution experiments without a prior knowledge either on the library population. The system's utility was demonstrated using 20 independent directed evolution experiments, yielding genetic switches with elevated inducer sensitivities, inverted switching behaviours, sensory functions, and improved signal-to-noise ratio (>100-fold induction). The resulting yeast genetic switches were readily integrated, in a plug-and-play manner, into an AND-gated carotenoid biosynthesis pathway.
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Affiliation(s)
- Masahiro Tominaga
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kenta Nozaki
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Daisuke Umeno
- grid.136304.30000 0004 0370 1101Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, Chiba, Japan
| | - Jun Ishii
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan ,grid.31432.370000 0001 1092 3077Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan ,grid.31432.370000 0001 1092 3077Engineering Biology Research Center, Kobe University, Kobe, Japan ,grid.31432.370000 0001 1092 3077Department of Chemical Science and Engineering, Faculty of Engineering, Kobe University, Kobe, Japan ,grid.7597.c0000000094465255Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
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15
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Kuivanen J, Kannisto M, Mojzita D, Rischer H, Toivari M, Jäntti J. Engineering of Saccharomyces cerevisiae for anthranilate and methyl anthranilate production. Microb Cell Fact 2021; 20:34. [PMID: 33536025 PMCID: PMC7860014 DOI: 10.1186/s12934-021-01532-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/27/2021] [Indexed: 11/10/2022] Open
Abstract
Background Anthranilate is a platform chemical used by the industry in the synthesis of a broad range of high-value products, such as dyes, perfumes and pharmaceutical compounds. Currently anthranilate is produced via chemical synthesis from non-renewable resources. Biological synthesis would allow the use of renewable carbon sources and avoid accumulation of toxic by-products. Microorganisms produce anthranilate as an intermediate in the tryptophan biosynthetic pathway. Several prokaryotic microorganisms have been engineered to overproduce anthranilate but attempts to engineer eukaryotic microorganisms for anthranilate production are scarce. Results We subjected Saccharomyces cerevisiae, a widely used eukaryotic production host organism, to metabolic engineering for anthranilate production. A single gene knockout was sufficient to trigger anthranilate accumulation both in minimal and SCD media and the titer could be further improved by subsequent genomic alterations. The effects of the modifications on anthranilate production depended heavily on the growth medium used. By growing an engineered strain in SCD medium an anthranilate titer of 567.9 mg l−1 was obtained, which is the highest reported with an eukaryotic microorganism. Furthermore, the anthranilate biosynthetic pathway was extended by expression of anthranilic acid methyltransferase 1 from Medicago truncatula. When cultivated in YPD medium, this pathway extension enabled production of the grape flavor compound methyl anthranilate in S. cerevisiae at 414 mg l−1. Conclusions In this study we have engineered metabolism of S. cerevisiae for improved anthranilate production. The resulting strains may serve as a basis for development of efficient production host organisms for anthranilate-derived compounds. In order to demonstrate suitability of the engineered S. cerevisiae strains for production of such compounds, we successfully extended the anthranilate biosynthesis pathway to synthesis of methyl anthranilate.
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Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland.,eniferBio Oy, Espoo, Finland
| | - Matti Kannisto
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland.
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Heiko Rischer
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
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16
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Turgeon Z, Sierocinski T, Brimacombe CA, Jin Y, Goldhawke B, Swanson JM, Husnik JI, Dahabieh MS. Industrially Applicable De Novo Lager Yeast Hybrids with a Unique Genomic Architecture: Creation and Characterization. Appl Environ Microbiol 2021; 87:e02434-20. [PMID: 33188002 DOI: 10.1128/AEM.02434-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/07/2020] [Indexed: 12/30/2022] Open
Abstract
All lager beer is produced using two related lager yeast types: group I and group II, which are highly similar, resulting in a lack of strain diversity for lager beer production. To date, approaches for generating new lager yeasts have generated strains possessing undesirable brewing characteristics which render them commercially inviable. Lager beer is produced by Saccharomyces pastorianus, which is a natural allopolyploid hybrid between Saccharomyces cerevisiae and Saccharomyces eubayanus. Lager strains are classified into two major groups based largely on genomic composition: group I and group II. Group I strains are allotriploid, whereas group II strains are allotetraploid. A lack of phenotypic diversity in commercial lager strains has led to substantial interest in the reconstitution of de novo allotetraploid lager strains by hybridization of S. cerevisiae and S. eubayanus strains. Such strategies rely on the hybridization of wild S. eubayanus isolates, which carry unacceptable traits for commercial lager beer such as phenolic off flavors and incomplete utilization of carbohydrates. Using an alternative breeding strategy, we have created de novo lager hybrids containing the domesticated S. eubayanus subgenome from an industrial S. pastorianus strain by hybridizing diploid meiotic segregants of this strain to a variety of S. cerevisiae ale strains. Five de novo hybrids were isolated which had fermentation characteristics similar to those of prototypical commercial lager strains but with unique phenotypic variation due to the contributions of the S. cerevisiae parents. Genomic analysis of these de novo lager hybrids identified novel allotetraploid genomes carrying three copies of the S. cerevisiae genome and one copy of the S. eubayanus genome. Most importantly, these hybrids do not possess the negative traits which result from breeding wild S. eubayanus. The de novo lager strains produced using industrial S. pastorianus in this study are immediately suitable for industrial lager beer production. IMPORTANCE All lager beer is produced using two related lager yeast types: group I and group II, which are highly similar, resulting in a lack of strain diversity for lager beer production. To date, approaches for generating new lager yeasts have generated strains possessing undesirable brewing characteristics which render them commercially inviable. We have used an alternative approach that circumvents this issue and created new lager strains that are directly suitable for lager beer production. These novel lager strains also possess a unique genomic architecture, which may lead to a better understanding of industrial yeast hybrids. We propose that strains created using our approach be classified as a third group of lager strains (group III). We anticipate that these novel lager strains will be of great industrial relevance and that this technique will be applicable to the creation of additional novel lager strains that will help broaden the diversity in commercial lager beer strains.
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17
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Álvarez-Fernández MA, Carafa I, Vrhovsek U, Arapitsas P. Modulating Wine Aromatic Amino Acid Catabolites by Using Torulaspora delbrueckii in Sequentially Inoculated Fermentations or Saccharomyces cerevisiae Alone. Microorganisms 2020; 8:E1349. [PMID: 32899614 DOI: 10.3390/microorganisms8091349] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022] Open
Abstract
Yeasts are the key microorganisms that transform grape juice into wine, and nitrogen is an essential nutrient able to affect yeast cell growth, fermentation kinetics and wine quality. In this work, we focused on the intra- and extracellular metabolomic changes of three aromatic amino acids (tryptophan, tyrosine, and phenylalanine) during alcoholic fermentation of two grape musts by two Saccharomyces cerevisiae strains and the sequential inoculation of Torulaspora delbrueckii with Saccharomyces cerevisiae. An UPLC-MS/MS method was used to monitor 33 metabolites, and 26 of them were detected in the extracellular samples and 8 were detected in the intracellular ones. The results indicate that the most intensive metabolomic changes occurred during the logarithm cellular growth phase and that pure S. cerevisiae fermentations produced higher amounts of N-acetyl derivatives of tryptophan and tyrosine and the off-odour molecule 2-aminoacetophenone. The sequentially inoculated fermentations showed a slower evolution and a higher production of metabolites linked to the well-known plant hormone indole acetic acid (auxin). Finally, the production of sulfonated tryptophol during must fermentation was confirmed, which also may explain the bitter taste of wines produced by Torulaspora delbrueckii co-fermentations, while sulfonated indole carboxylic acid was detected for the first time in such an experimental design.
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18
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Shimoi H, Kawamura N, Yamada M. Cloning of the SPO11 gene that complements a meiotic recombination defect in sake yeast. J Biosci Bioeng 2020; 130:367-373. [PMID: 32646632 DOI: 10.1016/j.jbiosc.2020.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 02/04/2023]
Abstract
Cross hybridization breeding of sake yeasts is hampered by difficulty in acquisition of haploid cells through sporulation. We previously demonstrated that typical sake yeast strains were defective in meiotic chromosome recombination, which caused poor sporulation and loss of spore viability. In this study, we screened a single copy plasmid genomic DNA library of the laboratory Saccharomyces cerevisiae GRF88 for genes that might complement the meiotic recombination defect of UTCAH-3, a strain derived from the sake yeast Kyokai no. 7 (K7). We identified the SPO11 gene of the laboratory strain (ScSPO11), encoding a meiosis-specific endonuclease that catalyzes DNA double-strand breaks required for meiotic recombination, as a gene that restored meiotic recombination and spore viability of UTCAH-3. K7SPO11 could not restore sporulation efficiency and spore viability of UTCAH-3 and a laboratory strain BY4743 spo11Δ/spo11Δ, indicating that K7SPO11 is not functional. Sequence analysis of the SPO11 genes of various Kyokai sake yeasts (K1, and K3-K10) revealed that the K7 group of sake yeasts (K6, K7, K9, and K10) had a mutual missense mutation (C73T) in addition to other three common mutations present in all Kyokai yeasts tested. ScSPO11C73T created through in vitro mutagenesis could not restore spore viability of BY4743 spo11Δ/spo11Δ. On the other hand, K8SPO11, which have the three common mutations except for C73T could restore spore viability of BY4743 spo11Δ/spo11Δ. These results suggest that C73T might be a causative mutation of recombination defect in K7SPO11. Moreover, we found that the introduction of ScRIM15 restored sporulation efficiency but not spore viability.
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Affiliation(s)
- Hitoshi Shimoi
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; Brewing Society of Japan, 2-6-30, Takinogawa, Kita-ku, Tokyo 114-0023, Japan.
| | - Natsuki Kawamura
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Miwa Yamada
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
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19
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Hoban K, Lux SY, Poprawski J, Zhang Y, Shepherdson J, Castiñeira PG, Pesari S, Yao T, Prosser DC, Norris C, Wendland B. ESCRT-dependent protein sorting is required for the viability of yeast clathrin-mediated endocytosis mutants. Traffic 2020; 21:430-450. [PMID: 32255230 DOI: 10.1111/tra.12731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/11/2022]
Abstract
Endocytosis regulates many processes, including signaling pathways, nutrient uptake, and protein turnover. During clathrin-mediated endocytosis (CME), adaptors bind to cytoplasmic regions of transmembrane cargo proteins, and many endocytic adaptors are also directly involved in the recruitment of clathrin. This clathrin-associated sorting protein family includes the yeast epsins, Ent1/2, and AP180/PICALM homologs, Yap1801/2. Mutant strains lacking these four adaptors, but expressing an epsin N-terminal homology (ENTH) domain necessary for viability (4Δ+ENTH), exhibit endocytic defects, such as cargo accumulation at the plasma membrane (PM). This CME-deficient strain provides a sensitized background ideal for revealing cellular components that interact with clathrin adaptors. We performed a mutagenic screen to identify alleles that are lethal in 4Δ+ENTH cells using a colony-sectoring reporter assay. After isolating candidate synthetic lethal genes by complementation, we confirmed that mutations in VPS4 led to inviability of a 4Δ+ENTH strain. Vps4 mediates the final step of endosomal sorting complex required for transport (ESCRT)-dependent trafficking, and we found that multiple ESCRTs are also essential in 4Δ+ENTH cells, including Snf7, Snf8 and Vps36. Deletion of VPS4 from an end3Δ strain, another CME mutant, similarly resulted in inviability, and upregulation of a clathrin-independent endocytosis pathway rescued 4Δ+ENTH vps4Δ cells. Loss of Vps4 from an otherwise wild-type background caused multiple cargoes to accumulate at the PM because of an increase in Rcy1-dependent recycling of internalized protein to the cell surface. Additionally, vps4Δ rcy1Δ mutants exhibited deleterious growth phenotypes. Together, our findings reveal previously unappreciated effects of disrupted ESCRT-dependent trafficking on endocytic recycling and the PM.
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Affiliation(s)
- Kyle Hoban
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Samantha Y Lux
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Joanna Poprawski
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yorke Zhang
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - James Shepherdson
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pedro G Castiñeira
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sanjana Pesari
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Tony Yao
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Derek C Prosser
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Carolyn Norris
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Beverly Wendland
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
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20
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Carvill GL, Helbig KL, Myers CT, Scala M, Huether R, Lewis S, Kruer TN, Guida BS, Bakhtiari S, Sebe J, Tang S, Stickney H, Oktay SU, Bhandiwad AA, Ramsey K, Narayanan V, Feyma T, Rohena LO, Accogli A, Severino M, Hollingsworth G, Gill D, Depienne C, Nava C, Sadleir LG, Caruso PA, Lin AE, Jansen FE, Koeleman B, Brilstra E, Willemsen MH, Kleefstra T, Sa J, Mathieu ML, Perrin L, Lesca G, Striano P, Casari G, Scheffer IE, Raible D, Sattlegger E, Capra V, Padilla-Lopez S, Mefford HC, Kruer MC. Damaging de novo missense variants in EEF1A2 lead to a developmental and degenerative epileptic-dyskinetic encephalopathy. Hum Mutat 2020; 41:1263-1279. [PMID: 32196822 DOI: 10.1002/humu.24015] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/14/2020] [Accepted: 03/13/2020] [Indexed: 11/08/2022]
Abstract
Heterozygous de novo variants in the eukaryotic elongation factor EEF1A2 have previously been described in association with intellectual disability and epilepsy but never functionally validated. Here we report 14 new individuals with heterozygous EEF1A2 variants. We functionally validate multiple variants as protein-damaging using heterologous expression and complementation analysis. Our findings allow us to confirm multiple variants as pathogenic and broaden the phenotypic spectrum to include dystonia/choreoathetosis, and in some cases a degenerative course with cerebral and cerebellar atrophy. Pathogenic variants appear to act via a haploinsufficiency mechanism, disrupting both the protein synthesis and integrated stress response functions of EEF1A2. Our studies provide evidence that EEF1A2 is highly intolerant to variation and that de novo pathogenic variants lead to an epileptic-dyskinetic encephalopathy with both neurodevelopmental and neurodegenerative features. Developmental features may be driven by impaired synaptic protein synthesis during early brain development while progressive symptoms may be linked to an impaired ability to handle cytotoxic stressors.
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Affiliation(s)
- Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University, Chicago, Illinois
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, Seattle, Washington
| | - Marcello Scala
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Robert Huether
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Sara Lewis
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Tyler N Kruer
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Brandon S Guida
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Joy Sebe
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Heather Stickney
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Sehribani Ulusoy Oktay
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Ashwin A Bhandiwad
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Timothy Feyma
- Department of Neurology, Gillette Children's Specialty Healthcare, St. Paul, Minnesota
| | - Luis O Rohena
- Department of Pediatrics, Division of Genetics, San Antonio Military Medical Center, San Antonio, Texas.,Department of Pediatrics, Long School of Medicine, University of Texas, San Antonio, Texas
| | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy.,Medical Genetics Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Mariasavina Severino
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy
| | - Georgina Hollingsworth
- Departments of Medicine and Paediatrics, University of Melbourne and Austin Health Royal Children's Hospital, Melbourne, Australia
| | - Deepak Gill
- Ty Nelson Department of Neurology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Christel Depienne
- INSERM UMR 975, Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, Paris, France
| | - Caroline Nava
- INSERM UMR 975, Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, Paris, France
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington South, New Zealand
| | - Paul A Caruso
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Angela E Lin
- Medical Genetics, Department of Pediatrics, MassGeneral Hospital for Children, Harvard Medical School, Boston, Massachusetts
| | - Floor E Jansen
- Department of Pediatric Neurology, University Medical Center, Utrecht, The Netherlands
| | - Bobby Koeleman
- Department of Pediatric Neurology, University Medical Center, Utrecht, The Netherlands
| | - Eva Brilstra
- Department of Genetics, Utrecht University, Utrecht, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joaquim Sa
- Serviço de Genética Médica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Marie-Laure Mathieu
- Neuropaediatrics Department, Femme Mère Enfant Hospital, Lyon, France.,Claude Bernard Lyon 1 University, Lyon, France
| | - Laurine Perrin
- Department of Paediatric Physical Medicine and Rehabilitation, CHU Saint-Etienne, Hôpital Bellevue, Saint-Étienne, France
| | - Gaetan Lesca
- CRNL Inserm U1028-CNRS UMR5292-Claude Bernard University Lyon 1, Lyon, France.,Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Pasquale Striano
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Giorgio Casari
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Ingrid E Scheffer
- Departments of Medicine and Paediatrics, University of Melbourne and Austin Health Royal Children's Hospital, Melbourne, Australia
| | - David Raible
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Evelyn Sattlegger
- School of Natural & Computational Sciences, Massey University, Auckland, New Zealand
| | - Valeria Capra
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy
| | - Sergio Padilla-Lopez
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, Seattle, Washington
| | - Michael C Kruer
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
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21
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Lairón-Peris M, Pérez-Través L, Muñiz-Calvo S, Guillamón JM, Heras JM, Barrio E, Querol A. Differential Contribution of the Parental Genomes to a S. cerevisiae × S. uvarum Hybrid, Inferred by Phenomic, Genomic, and Transcriptomic Analyses, at Different Industrial Stress Conditions. Front Bioeng Biotechnol 2020; 8:129. [PMID: 32195231 PMCID: PMC7062649 DOI: 10.3389/fbioe.2020.00129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/10/2020] [Indexed: 01/09/2023] Open
Abstract
In European regions of cold climate, S. uvarum can replace S. cerevisiae in wine fermentations performed at low temperatures. S. uvarum is a cryotolerant yeast that produces more glycerol, less acetic acid and exhibits a better aroma profile. However, this species exhibits a poor ethanol tolerance compared with S. cerevisiae. In the present study, we obtained by rare mating (non-GMO strategy), and a subsequent sporulation, an interspecific S. cerevisiae × S. uvarum spore-derivative hybrid that improves or maintains a combination of parental traits of interest for the wine industry, such as good fermentation performance, increased ethanol tolerance, and high glycerol and aroma productions. Genomic sequencing analysis showed that the artificial spore-derivative hybrid is an allotriploid, which is very common among natural hybrids. Its genome contains one genome copy from the S. uvarum parental genome and two heterozygous copies of the S. cerevisiae parental genome, with the exception of a monosomic S. cerevisiae chromosome III, where the sex-determining MAT locus is located. This genome constitution supports that the original hybrid from which the spore was obtained likely originated by a rare-mating event between a mating-competent S. cerevisiae diploid cell and either a diploid or a haploid S. uvarum cell of the opposite mating type. Moreover, a comparative transcriptomic analysis reveals that each spore-derivative hybrid subgenome is regulating different processes during the fermentation, in which each parental species has demonstrated to be more efficient. Therefore, interactions between the two subgenomes in the spore-derivative hybrid improve those differential species-specific adaptations to the wine fermentation environments, already present in the parental species.
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Affiliation(s)
- María Lairón-Peris
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - Laura Pérez-Través
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - Sara Muñiz-Calvo
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - José Manuel Guillamón
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | | | - Eladio Barrio
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
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22
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Manzano CM, Nakahata DH, Tenorio JC, Lustri WR, Resende Nogueira FA, Aleixo NA, da Silva Gomes PS, Pavan FR, Grecco JA, Ribeiro CM, Corbi PP. Silver complexes with fluoroanthranilic acid isomers: Spectroscopic characterization, antimycobacterial activity and cytotoxic studies over a panel of tumor cells. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2019.119293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Zhu M, Sun L, Lu X, Zong H, Zhuge B. Establishment of a transient CRISPR-Cas9 genome editing system in Candida glycerinogenes for co-production of ethanol and xylonic acid. J Biosci Bioeng 2019; 128:283-289. [DOI: 10.1016/j.jbiosc.2019.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
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24
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Parnell EJ, Stillman DJ. Multiple Negative Regulators Restrict Recruitment of the SWI/SNF Chromatin Remodeler to the HO Promoter in Saccharomyces cerevisiae. Genetics 2019; 212:1181-1204. [PMID: 31167839 PMCID: PMC6707452 DOI: 10.1534/genetics.119.302359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/30/2019] [Indexed: 01/22/2023] Open
Abstract
Activation of the Saccharomyces cerevisiae HO promoter is highly regulated, requiring the ordered recruitment of activators and coactivators and allowing production of only a few transcripts in mother cells within a short cell cycle window. We conducted genetic screens to identify the negative regulators of HO expression necessary to limit HO transcription. Known repressors of HO (Ash1 and Rpd3) were identified, as well as several additional chromatin-associated factors including the Hda1 histone deacetylase, the Isw2 chromatin remodeler, and the corepressor Tup1 We also identified clusters of HO promoter mutations that suggested roles for the Dot6/Tod6 (PAC site) and Ume6 repression pathways. We used ChIP assays with synchronized cells to validate the involvement of these factors and map the association of Ash1, Dot6, and Ume6 with the HO promoter to a brief window in the cell cycle between binding of the initial activating transcription factor and initiation of transcription. We found that Ash1 and Ume6 each recruit the Rpd3 histone deacetylase to HO, and their effects are additive. In contrast, Rpd3 was not recruited significantly to the PAC site, suggesting this site has a distinct mechanism for repression. Increases in HO expression and SWI/SNF recruitment were all additive upon loss of Ash1, Ume6, and PAC site factors, indicating the convergence of independent pathways for repression. Our results demonstrate that multiple protein complexes are important for limiting the spread of SWI/SNF-mediated nucleosome eviction across the HO promoter, suggesting that regulation requires a delicate balance of activities that promote and repress transcription.
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Affiliation(s)
- Emily J Parnell
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - David J Stillman
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
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25
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Erpf PE, Stephenson CJ, Fraser JA. amdS as a dominant recyclable marker in Cryptococcus neoformans. Fungal Genet Biol 2019; 131:103241. [PMID: 31220607 DOI: 10.1016/j.fgb.2019.103241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/13/2019] [Accepted: 06/13/2019] [Indexed: 02/04/2023]
Abstract
While the fungal pathogen Cryptoccocus neoformans is a leading cause of death in immunocompromised individuals, the molecular toolkit currently available to study this important pathogen is extremely limited. To enable an unprecedented level of control over manipulation of the genome, we have developed a dominant recyclable marker by expanding on the classic studies of the amdS gene by Michael J. Hynes and John Pateman. The ascomycete Aspergillus nidulans employs the acetamidase AmdS to hydrolyse acetamide to ammonium and acetate, which serve as a nitrogen and carbon source, respectively. Acetamidase activity has never been reported in the Basidiomycota. Here we have successfully demonstrated that acetamide can be utilized as a good nitrogen source in C. neoformans heterologously expressing amdS and that this activity does not influence virulence, enabling it to be used as a basic dominant selectable marker. The expression of this gene in C. neoformans also causes sensitivity to fluoroacetamide, permitting counterselection. Taking advantage of this toxicity we have modified our basic marker to create a comprehensive series of powerful and reliable tools to successfully delete multiple genes in the one strain, generate markerless strains with modifications such as fluorescent protein fusions at native genomic loci, and establish whether a gene is essential in C. neoformans.
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26
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Shor E, Schuyler J, Perlin DS. A Novel, Drug Resistance-Independent, Fluorescence-Based Approach To Measure Mutation Rates in Microbial Pathogens. mBio 2019; 10:e00120-19. [PMID: 30808701 DOI: 10.1128/mBio.00120-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Measurements of mutation rates—i.e., how often proliferating cells acquire mutations in their DNA—are essential for understanding cellular processes that maintain genome stability. Many traditional mutation rate measurement assays are based on detecting mutations that cause resistance to a particular drug. Such assays typically work well for laboratory strains but have significant limitations when comparing clinical or environmental isolates that have various intrinsic levels of drug tolerance, which confounds the interpretation of results. Here we report the development and validation of a novel method of measuring mutation rates, which detects mutations that cause loss of fluorescence rather than acquisition of drug resistance. Using this method, we measured the mutation rates of clinical isolates of fungal pathogen Candida glabrata. This assay can be adapted to other organisms and used to compare mutation rates in contexts where unequal drug sensitivity is anticipated. All evolutionary processes are underpinned by a cellular capacity to mutate DNA. To identify factors affecting mutagenesis, it is necessary to compare mutation rates between different strains and conditions. Drug resistance-based mutation reporters are used extensively to measure mutation rates, but they are suitable only when the compared strains have identical drug tolerance levels—a condition that is not satisfied under many “real-world” circumstances, e.g., when comparing mutation rates among a series of environmental or clinical isolates. Candida glabrata is a fungal pathogen that shows a high degree of genetic diversity and fast emergence of antifungal drug resistance. To enable meaningful comparisons of mutation rates among C. glabrata clinical isolates, we developed a novel fluorescence-activated cell sorting-based approach to measure the mutation rate of a chromosomally integrated GFP gene. We found that in Saccharomyces cerevisiae this approach recapitulated the reported mutation rate of a wild-type strain and the mutator phenotype of a shu1Δ mutant. In C. glabrata, the GFP reporter captured the mutation rate increases caused either by a genotoxic agent or by deletion of DNA mismatch repair gene MSH2, as well as the specific mutational signature associated with msh2Δ. Finally, the reporter was used to measure the mutation rates of C. glabrata clinical isolates carrying different alleles of MSH2. Together, these results show that fluorescence-based mutation reporters can be used to measure mutation rates in microbes under conditions of unequal drug susceptibility to reveal new insights about drivers of mutagenesis.
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27
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Coelho MC, Pinto RM, Murray AW. Heterozygous mutations cause genetic instability in a yeast model of cancer evolution. Nature 2019; 566:275-278. [PMID: 30700905 DOI: 10.1038/s41586-019-0887-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 12/18/2018] [Indexed: 12/26/2022]
Abstract
Genetic instability, a heritable increase in the rate of genetic mutation, accelerates evolutionary adaptation1 and is widespread in cancer2,3. In mammals, instability can arise from damage to both copies of genes involved in DNA metabolism and cell cycle regulation4 or from inactivation of one copy of a gene whose product is present in limiting amounts (haploinsufficiency5); however, it has proved difficult to determine the relative importance of these two mechanisms. In Escherichia coli6, the application of repeated, strong selection enriches for genetic instability. Here we have used this approach to evolve genetic instability in diploid cells of the budding yeast Saccharomyces cerevisiae, and have isolated clones with increased rates of point mutation, mitotic recombination, and chromosome loss. We identified candidate, heterozygous, instability-causing mutations; engineering these mutations, as heterozygotes, into the ancestral diploid strain caused genetic instability. Mutations that inactivated one copy of haploinsufficient genes were more common than those that dominantly altered the function of the mutated gene copy. The mutated genes were enriched for genes functioning in transport, protein quality control, and DNA metabolism, and have revealed new targets for genetic instability7-11, including essential genes. Although only a minority (10 out of 57 genes with orthologues or close homologues) of the targets we identified have homologous human genes that have been implicated in cancer2, the remainder are candidates to contribute to human genetic instability. To test this hypothesis, we inactivated six examples in a near-haploid human cell line; five of these mutations increased instability. We conclude that single genetic events cause genetic instability in diploid yeast cells, and propose that similar, heterozygous mutations in mammalian homologues initiate genetic instability in cancer.
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Affiliation(s)
- Miguel C Coelho
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA. .,Molecular and Cell Biology, Harvard University, Cambridge, MA, USA. .,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Ricardo M Pinto
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Andrew W Murray
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA. .,Molecular and Cell Biology, Harvard University, Cambridge, MA, USA.
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28
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García-Ríos E, Guillén A, de la Cerda R, Pérez-Través L, Querol A, Guillamón JM. Improving the Cryotolerance of Wine Yeast by Interspecific Hybridization in the Genus Saccharomyces. Front Microbiol 2019; 9:3232. [PMID: 30671041 PMCID: PMC6331415 DOI: 10.3389/fmicb.2018.03232] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/12/2018] [Indexed: 12/02/2022] Open
Abstract
Fermentations carried out at low temperatures (10–15°C) enhance the production and retention of flavor volatiles, but also increase the chances of slowing or arresting the process. Notwithstanding, as Saccharomyces cerevisiae is the main species responsible for alcoholic fermentation, other species of the genus Saccharomyces, such as cryophilic species Saccharomyces eubayanus, Saccharomyces kudriavzevii and Saccharomyces uvarum, are better adapted to low-temperature fermentations during winemaking. In this work, a Saccharomyces cerevisiae × S. uvarum hybrid was constructed to improve the enological features of a wine S. cerevisiae strain at low temperature. Fermentations of white grape musts were performed, and the phenotypic differences between parental and hybrid strains under different temperature conditions were examined. This work demonstrates that hybridization constitutes an effective approach to obtain yeast strains with desirable physiological features, like low-temperature fermentation capacity, which genetically depend on the expression of numerous genes (polygenic character). As this interspecific hybridization approach is not considered a GMO, the genetically improved strains can be quickly transferred to the wine industry.
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Affiliation(s)
- Estéfani García-Ríos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Alba Guillén
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Roberto de la Cerda
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Laura Pérez-Través
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos - Consejo Superior de Investigaciones Científicas, Valencia, Spain
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29
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Kruis AJ, Gallone B, Jonker T, Mars AE, van Rijswijck IMH, Wolkers-Rooijackers JCM, Smid EJ, Steensels J, Verstrepen KJ, Kengen SWM, van der Oost J, Weusthuis RA. Contribution of Eat1 and Other Alcohol Acyltransferases to Ester Production in Saccharomyces cerevisiae. Front Microbiol 2018; 9:3202. [PMID: 30622529 PMCID: PMC6308380 DOI: 10.3389/fmicb.2018.03202] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/10/2018] [Indexed: 12/16/2022] Open
Abstract
Esters are essential for the flavor and aroma of fermented products, and are mainly produced by alcohol acyl transferases (AATs). A recently discovered AAT family named Eat (Ethanol acetyltransferase) contributes to ethyl acetate synthesis in yeast. However, its effect on the synthesis of other esters is unknown. In this study, the role of the Eat family in ester synthesis was compared to that of other Saccharomyces cerevisiae AATs (Atf1p, Atf2p, Eht1p, and Eeb1p) in silico and in vivo. A genomic study in a collection of industrial S. cerevisiae strains showed that variation of the primary sequence of the AATs did not correlate with ester production. Fifteen members of the EAT family from nine yeast species were overexpressed in S. cerevisiae CEN.PK2-1D and were able to increase the production of acetate and propanoate esters. The role of Eat1p was then studied in more detail in S. cerevisiae CEN.PK2-1D by deleting EAT1 in various combinations with other known S. cerevisiae AATs. Between 6 and 11 esters were produced under three cultivation conditions. Contrary to our expectations, a strain where all known AATs were disrupted could still produce, e.g., ethyl acetate and isoamyl acetate. This study has expanded our understanding of ester synthesis in yeast but also showed that some unknown ester-producing mechanisms still exist.
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Affiliation(s)
- Aleksander J Kruis
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands.,Bioprocess Engineering, Wageningen University and Research, Wageningen, Netherlands
| | - Brigida Gallone
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.,VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics, Department of M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Timo Jonker
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Astrid E Mars
- Biobased Products, Wageningen University and Research, Wageningen, Netherlands
| | - Irma M H van Rijswijck
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | | | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Jan Steensels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics, Department of M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics, Department of M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Wageningen, Netherlands
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30
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Ohkuni K, Pasupala N, Peek J, Holloway GL, Sclar GD, Levy-Myers R, Baker RE, Basrai MA, Kerscher O. SUMO-Targeted Ubiquitin Ligases (STUbLs) Reduce the Toxicity and Abnormal Transcriptional Activity Associated With a Mutant, Aggregation-Prone Fragment of Huntingtin. Front Genet 2018; 9:379. [PMID: 30279700 PMCID: PMC6154015 DOI: 10.3389/fgene.2018.00379] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/27/2018] [Indexed: 01/01/2023] Open
Abstract
Cell viability and gene expression profiles are altered in cellular models of neurodegenerative disorders such as Huntington’s Disease (HD). Using the yeast model system, we show that the SUMO-targeted ubiquitin ligase (STUbL) Slx5 reduces the toxicity and abnormal transcriptional activity associated with a mutant, aggregation-prone fragment of huntingtin (Htt), the causative agent of HD. We demonstrate that expression of an aggregation-prone Htt construct with 103 glutamine residues (103Q), but not the non-expanded form (25Q), results in severe growth defects in slx5Δ and slx8Δ cells. Since Slx5 is a nuclear protein and because Htt expression affects gene transcription, we assessed the effect of STUbLs on the transcriptional properties of aggregation-prone Htt. Expression of Htt 25Q and 55Q fused to the Gal4 activation domain (AD) resulted in reporter gene auto-activation. Remarkably, the auto-activation of Htt constructs was abolished by expression of Slx5 fused to the Gal4 DNA-binding domain (BD-Slx5). In support of these observations, RNF4, the human ortholog of Slx5, curbs the aberrant transcriptional activity of aggregation-prone Htt in yeast and a variety of cultured human cell lines. Functionally, we find that an extra copy of SLX5 specifically reduces Htt aggregates in the cytosol as well as chromatin-associated Htt aggregates in the nucleus. Finally, using RNA sequencing, we identified and confirmed specific targets of Htt’s transcriptional activity that are modulated by Slx5. In summary, this study of STUbLs uncovers a conserved pathway that counteracts the accumulation of aggregating, transcriptionally active Htt (and possibly other poly-glutamine expanded proteins) on chromatin in both yeast and in mammalian cells.
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Affiliation(s)
- Kentaro Ohkuni
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Nagesh Pasupala
- Biology Department, College of William & Mary, Williamsburg, VA, United States
| | - Jennifer Peek
- Biology Department, College of William & Mary, Williamsburg, VA, United States
| | | | - Gloria D Sclar
- Biology Department, College of William & Mary, Williamsburg, VA, United States
| | - Reuben Levy-Myers
- Biology Department, College of William & Mary, Williamsburg, VA, United States
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Oliver Kerscher
- Biology Department, College of William & Mary, Williamsburg, VA, United States
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31
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Murdoch I, Powers S, Welch A. Fluorinated Phenylalanine Precursor Resistance in Yeast. Fermentation 2018; 4:41. [DOI: 10.3390/fermentation4020041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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32
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Chen L, Chen M, Ma C, Zeng AP. Discovery of feed-forward regulation in L-tryptophan biosynthesis and its use in metabolic engineering of E. coli for efficient tryptophan bioproduction. Metab Eng 2018; 47:434-444. [DOI: 10.1016/j.ymben.2018.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 10/17/2022]
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33
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Barajas‐Lopez JDD, Moreno JR, Gamez‐Arjona FM, Pardo JM, Punkkinen M, Zhu J, Quintero FJ, Fujii H. Upstream kinases of plant SnRKs are involved in salt stress tolerance. Plant J 2018; 93:107-118. [PMID: 29094495 PMCID: PMC5814739 DOI: 10.1111/tpj.13761] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 10/21/2017] [Accepted: 10/24/2017] [Indexed: 05/03/2023]
Abstract
Sucrose non-fermenting 1-related protein kinases (SnRKs) are important for plant growth and stress responses. This family has three clades: SnRK1, SnRK2 and SnRK3. Although plant SnRKs are thought to be activated by upstream kinases, the overall mechanism remains obscure. Geminivirus Rep-Interacting Kinase (GRIK)1 and GRIK2 phosphorylate SnRK1s, which are involved in sugar/energy sensing, and the grik1-1 grik2-1 double mutant shows growth retardation under regular growth conditions. In this study, we established another Arabidopsis mutant line harbouring a different allele of gene GRIK1 (grik1-2 grik2-1) that grows similarly to the wild-type, enabling us to evaluate the function of GRIKs under stress conditions. In the grik1-2 grik2-1 double mutant, phosphorylation of SnRK1.1 was reduced, but not eliminated, suggesting that the grik1-2 mutation is a weak allele. In addition to high sensitivity to glucose, the grik1-2 grik2-1 mutant was sensitive to high salt, indicating that GRIKs are also involved in salinity signalling pathways. Salt Overly Sensitive (SOS)2, a member of the SnRK3 subfamily, is a critical mediator of the response to salinity. GRIK1 phosphorylated SOS2 in vitro, resulting in elevated kinase activity of SOS2. The salt tolerance of sos2 was restored to normal levels by wild-type SOS2, but not by a mutated form of SOS2 lacking the T168 residue phosphorylated by GRIK1. Activation of SOS2 by GRIK1 was also demonstrated in a reconstituted system in yeast. Our results indicate that GRIKs phosphorylate and activate SnRK1 and other members of the SnRK3 family, and that they play important roles in multiple signalling pathways in vivo.
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Affiliation(s)
| | - Jose Ramon Moreno
- Instituto de Recursos Naturales y Agrobiología de SevillaConsejo Superior de Investigaciones Cientificas41012SevillaSpain
| | - Francisco M. Gamez‐Arjona
- Instituto de Recursos Naturales y Agrobiología de SevillaConsejo Superior de Investigaciones Cientificas41012SevillaSpain
| | - Jose M. Pardo
- Instituto de Bioquímica Vegetal y FotosíntesisConsejo Superior de Investigaciones Cientificas41092SevillaSpain
| | - Matleena Punkkinen
- Molecular Plant Biology UnitDepartment of BiochemistryUniversity of Turku20014TurkuFinland
| | - Jian‐Kang Zhu
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteINUSA
- Shanghai Center for Plant Stress BiologyShanghai Institutes for Biological SciencesCenter of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200032China
| | - Francisco J. Quintero
- Instituto de Bioquímica Vegetal y FotosíntesisConsejo Superior de Investigaciones Cientificas41092SevillaSpain
| | - Hiroaki Fujii
- Molecular Plant Biology UnitDepartment of BiochemistryUniversity of Turku20014TurkuFinland
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Cao S, Smith LL, Padilla-Lopez SR, Guida BS, Blume E, Shi J, Morton SU, Brownstein CA, Beggs AH, Kruer MC, Agrawal PB. Homozygous EEF1A2 mutation causes dilated cardiomyopathy, failure to thrive, global developmental delay, epilepsy and early death. Hum Mol Genet 2017; 26:3545-3552. [PMID: 28911200 PMCID: PMC5886049 DOI: 10.1093/hmg/ddx239] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/09/2017] [Accepted: 06/20/2017] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic elongation factor 1A (EEF1A), is encoded by two distinct isoforms, EEF1A1 and EEF1A2; whereas EEF1A1 is expressed almost ubiquitously, EEF1A2 expression is limited such that it is only detectable in skeletal muscle, heart, brain and spinal cord. Currently, the role of EEF1A2 in normal cardiac development and function is unclear. There have been several reports linking de novo dominant EEF1A2 mutations to neurological issues in humans. We report a pair of siblings carrying a homozygous missense mutation p.P333L in EEF1A2 who exhibited global developmental delay, failure to thrive, dilated cardiomyopathy and epilepsy, ultimately leading to death in early childhood. A third sibling also died of a similar presentation, but DNA was unavailable to confirm the mutation. Functional genomic analysis was performed in S. cerevisiae and zebrafish. In S. cerevisiae, there was no evidence for a dominant-negative effect. Previously identified putative de novo mutations failed to complement yeast strains lacking the EEF1A ortholog showing a major growth defect. In contrast, the introduction of the mutation seen in our family led to a milder growth defect. To evaluate its function in zebrafish, we knocked down eef1a2 expression using translation blocking and splice-site interfering morpholinos. EEF1A2-deficient zebrafish had skeletal muscle weakness, cardiac failure and small heads. Human EEF1A2 wild-type mRNA successfully rescued the morphant phenotype, but mutant RNA did not. Overall, EEF1A2 appears to be critical for normal heart function in humans, and its deficiency results in clinical abnormalities in neurologic function as well as in skeletal and cardiac muscle defects.
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Affiliation(s)
- Siqi Cao
- Division of Newborn Medicine
- Division of Genetics and Genomics
- The Manton Center for Orphan Disease Research
| | | | - Sergio R. Padilla-Lopez
- Department of Child Health, Barrow Neurological Institute, Phoenix Children's Hospital, University of Arizona College of Medicine, Phoenix, AZ 85013, USA
| | - Brandon S. Guida
- Department of Child Health, Barrow Neurological Institute, Phoenix Children's Hospital, University of Arizona College of Medicine, Phoenix, AZ 85013, USA
| | - Elizabeth Blume
- Department of Cardiology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jiahai Shi
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR
| | | | | | - Alan H. Beggs
- Division of Genetics and Genomics
- The Manton Center for Orphan Disease Research
| | - Michael C. Kruer
- Department of Child Health, Barrow Neurological Institute, Phoenix Children's Hospital, University of Arizona College of Medicine, Phoenix, AZ 85013, USA
| | - Pankaj B. Agrawal
- Division of Newborn Medicine
- Division of Genetics and Genomics
- The Manton Center for Orphan Disease Research
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35
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Yin Y, Dominska M, Yim E, Petes TD. High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast. eLife 2017; 6. [PMID: 28714850 PMCID: PMC5531827 DOI: 10.7554/elife.28069] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/14/2017] [Indexed: 12/13/2022] Open
Abstract
In yeast, DNA breaks are usually repaired by homologous recombination (HR). An early step for HR pathways is formation of a heteroduplex, in which a single-strand from the broken DNA molecule pairs with a strand derived from an intact DNA molecule. If the two strands of DNA are not identical, there will be mismatches within the heteroduplex DNA (hetDNA). In wild-type strains, these mismatches are repaired by the mismatch repair (MMR) system, producing a gene conversion event. In strains lacking MMR, the mismatches persist. Most previous studies involving hetDNA formed during mitotic recombination were restricted to one locus. Below, we present a global mapping of hetDNA formed in the MMR-defective mlh1 strain. We find that many recombination events are associated with repair of double-stranded DNA gaps and/or involve Mlh1-independent mismatch repair. Many of our events are not explicable by the simplest form of the double-strand break repair model of recombination. DOI:http://dx.doi.org/10.7554/eLife.28069.001
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Affiliation(s)
- Yi Yin
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, United States
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, United States
| | - Eunice Yim
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, United States
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, United States
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36
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Gnügge R, Rudolf F. Saccharomyces cerevisiaeShuttle vectors. Yeast 2017; 34:205-221. [DOI: 10.1002/yea.3228] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 01/25/2023] Open
Affiliation(s)
- Robert Gnügge
- D-BSSE; ETH Zurich and Swiss Institute of Bioinformatics; Zurich Switzerland
- Life Science Zurich PhD Program on Molecular and Translational Biomedicine; Zurich Switzerland
- Competence Centre for Personalized Medicine; Zurich Switzerland
| | - Fabian Rudolf
- D-BSSE; ETH Zurich and Swiss Institute of Bioinformatics; Zurich Switzerland
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Dalton JP, Uy B, Phummarin N, Copp BR, Denny WA, Swift S, Wiles S. Effect of common and experimental anti-tuberculosis treatments on Mycobacterium tuberculosis growing as biofilms. PeerJ 2016; 4:e2717. [PMID: 27904808 PMCID: PMC5126618 DOI: 10.7717/peerj.2717] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 10/25/2016] [Indexed: 01/01/2023] Open
Abstract
Much is known regarding the antibiotic susceptibility of planktonic cultures of Mycobacterium tuberculosis, the bacterium responsible for the lung disease tuberculosis (TB). As planktonically-grown M. tuberculosis are unlikely to be entirely representative of the bacterium during infection, we set out to determine how effective a range of anti-mycobacterial treatments were against M. tuberculosis growing as a biofilm, a bacterial phenotype known to be more resistant to antibiotic treatment. Light levels from bioluminescently-labelled M. tuberculosis H37Rv (strain BSG001) were used as a surrogate for bacterial viability, and were monitored before and after one week of treatment. After treatment, biofilms were disrupted, washed and inoculated into fresh broth and plated onto solid media to rescue any surviving bacteria. We found that in this phenotypic state M. tuberculosis was resistant to the majority of the compounds tested. Minimum inhibitory concentrations (MICs) increased by 20-fold to greater than 1,000-fold, underlying the potential of this phenotype to cause significant problems during treatment.
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Affiliation(s)
- James P Dalton
- Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand; Bioluminescent Superbugs Lab, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Benedict Uy
- Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand; Bioluminescent Superbugs Lab, University of Auckland, Auckland, New Zealand
| | - Narisa Phummarin
- School of Chemical Sciences, University of Auckland , Auckland , New Zealand
| | - Brent R Copp
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand; School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - William A Denny
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand; Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Simon Swift
- Molecular Medicine and Pathology, University of Auckland , Auckland , New Zealand
| | - Siouxsie Wiles
- Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand; Bioluminescent Superbugs Lab, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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38
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Amich J, Bignell E. Amino acid biosynthetic routes as drug targets for pulmonary fungal pathogens: what is known and why do we need to know more? Curr Opin Microbiol 2016; 32:151-158. [DOI: 10.1016/j.mib.2016.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/07/2016] [Accepted: 06/09/2016] [Indexed: 11/29/2022]
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Kuwahara H, Alazmi M, Cui X, Gao X. MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. Nucleic Acids Res 2016; 44:W217-25. [PMID: 27131375 PMCID: PMC4987905 DOI: 10.1093/nar/gkw342] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.
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Affiliation(s)
- Hiroyuki Kuwahara
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia
| | - Meshari Alazmi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia
| | - Xuefeng Cui
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955, Saudi Arabia
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40
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Hudson LE, Stewart TP, Fasken MB, Corbett AH, Lamb TJ. Transformation of Probiotic Yeast and Their Recovery from Gastrointestinal Immune Tissues Following Oral Gavage in Mice. J Vis Exp 2016:e53453. [PMID: 26890281 PMCID: PMC4781741 DOI: 10.3791/53453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Development of recombinant oral therapy would allow for more direct targeting of the mucosal immune system and improve the ability to combat gastrointestinal disorders. Adapting probiotic yeast in particular for this approach carries several advantages. These strains have not only the potential to synthesize a wide variety of complex heterologous proteins but are also capable of surviving and protecting those proteins during transit through the intestine. Critically, however, this approach requires expertise in many diverse laboratory techniques not typically used in tandem. Furthermore, although individual protocols for yeast transformation are well characterized for commonly used laboratory strains, emphasis is placed here on alternative approaches and the importance of optimizing transformation for less well characterized probiotic strains. Detailing these methods will help facilitate discussion as to the best approaches for testing probiotic yeast as oral drug delivery vehicles and indeed serve to advance the development of this novel strategy for gastrointestinal therapy.
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Affiliation(s)
- Lauren E Hudson
- Department of Pediatrics, Emory University School of Medicine
| | - Taryn P Stewart
- Department of Pediatrics, Emory University School of Medicine
| | - Milo B Fasken
- Department of Biochemistry, Emory University School of Medicine
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine
| | - Tracey J Lamb
- Department of Pediatrics, Emory University School of Medicine;
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41
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Feliziani C, Valdez Taubas J, Moyano S, Quassollo G, Poprawski JE, Wendland B, Touz MC. Vestiges of Ent3p/Ent5p function in the giardial epsin homolog. Biochim Biophys Acta 2016; 1863:749-59. [PMID: 26851076 DOI: 10.1016/j.bbamcr.2016.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/12/2016] [Accepted: 02/01/2016] [Indexed: 11/29/2022]
Abstract
An accurate way to characterize the functional potential of a protein is to analyze recognized protein domains encoded by the genes in a given group. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated trafficking. In this work, we investigate the function of the single ENTH-containing protein from the protist Giardia lamblia by testing its function in Saccharomyces cerevisiae. This protein, named GlENTHp (for G. lamblia ENTH protein), is involved in Giardia in endocytosis and in protein trafficking from the ER to the vacuoles, fulfilling the function of the ENTH proteins epsin and epsinR, respectively. There are two orthologs of epsin, Ent1p and Ent2p, and two orthologs of epsinR, Ent3p and Ent5p in S. cerevisiae. Although the expression of GlENTHp neither complemented growth in the ent1Δent2Δ mutant nor restored the GFP-Cps1 vacuolar trafficking defect in ent3Δent5Δ, it interfered with the normal function of Ent3/5 in the wild-type strain. The phenotype observed is linked to a defect in Cps1 localization and α-factor mating pheromone maturation. The finding that GlENTHp acts as dominant negative epsinR in yeast cells reinforces the phylogenetic data showing that GlENTHp belongs to the epsinR subfamily present in eukaryotes prior to their evolution into different taxa.
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Affiliation(s)
- Constanza Feliziani
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli, 2434, Córdoba, Argentina
| | - Javier Valdez Taubas
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC (UNC-CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Sofía Moyano
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli, 2434, Córdoba, Argentina
| | - Gonzalo Quassollo
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli, 2434, Córdoba, Argentina
| | - Joanna E Poprawski
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Mudd Hall Room 35, Baltimore, USA
| | - Beverly Wendland
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Mudd Hall Room 35, Baltimore, USA
| | - Maria C Touz
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Friuli, 2434, Córdoba, Argentina.
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Abstract
The field of fluorescent proteins (FPs) is constantly developing. The use of FPs changed the field of life sciences completely, starting a new era of direct observation and quantification of cellular processes. The broad spectrum of FPs (see Fig. 1) with a wide range of characteristics allows their use in many different experiments. This review discusses the use of FPs for imaging in budding yeast (Saccharomyces cerevisiae) and fission yeast Schizosaccharomyces pombe). The information included in this review is relevant for both species unless stated otherwise.
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Affiliation(s)
- Maja Bialecka-Fornal
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94158, USA
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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Fernandes JDS, Martho K, Tofik V, Vallim MA, Pascon RC. The Role of Amino Acid Permeases and Tryptophan Biosynthesis in Cryptococcus neoformans Survival. PLoS One 2015; 10:e0132369. [PMID: 26162077 PMCID: PMC4498599 DOI: 10.1371/journal.pone.0132369] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/14/2015] [Indexed: 01/25/2023] Open
Abstract
Metabolic diversity is an important factor during microbial adaptation to different environments. Among metabolic processes, amino acid biosynthesis has been demonstrated to be relevant for survival for many microbial pathogens, whereas the association between pathogenesis and amino acid uptake and recycling are less well-established. Cryptococcus neoformans is an opportunistic fungal pathogen with many habitats. As a result, it faces frequent metabolic shifts and challenges during its life cycle. Here we studied the C. neoformans tryptophan biosynthetic pathway and found that the pathway is essential. RNAi indicated that interruptions in the biosynthetic pathway render strains inviable. However, auxotroph complementation can be partially achieved by tryptophan uptake when a non preferred nitrogen source and lower growth temperature are applied, suggesting that amino acid permeases may be the target of nitrogen catabolism repression (NCR). We used bioinformatics to search for amino acid permeases in the C. neoformans and found eight potential global permeases (AAP1 to AAP8). The transcriptional profile of them revealed that they are subjected to regulatory mechanisms which are known to respond to nutritional status in other fungi, such as (i) quality of nitrogen (Nitrogen Catabolism Repression, NCR) and carbon sources (Carbon Catabolism Repression, CCR), (ii) amino acid availability in the extracellular environment (SPS-sensing) and (iii) nutritional deprivation (Global Amino Acid Control, GAAC). This study shows that C. neoformans has fewer amino acid permeases than other model yeasts, and that these proteins may be subjected to complex regulatory mechanisms. Our data suggest that the C. neoformans tryptophan biosynthetic pathway is an excellent pharmacological target. Furthermore, inhibitors of this pathway cause Cryptococcus growth arrest in vitro.
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Affiliation(s)
- João Daniel Santos Fernandes
- Departamento de Ciências Biológicas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Campus Diadema, Laboratório de Interações Microbianas (Laboratory 29), Rua Arthur Ridel, 275, 09972–270, Bairro Eldorado, Diadema, SP, Brazil
- Universidade de São Paulo, Avenida Prof. Lineu Prestes, 2415 Edifício ICB – III, Cidade Universitária, CEP 05508–900, São Paulo, SP, Brazil
| | - Kevin Martho
- Departamento de Ciências Biológicas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Campus Diadema, Laboratório de Interações Microbianas (Laboratory 29), Rua Arthur Ridel, 275, 09972–270, Bairro Eldorado, Diadema, SP, Brazil
| | - Veridiana Tofik
- Departamento de Ciências Biológicas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Campus Diadema, Laboratório de Interações Microbianas (Laboratory 29), Rua Arthur Ridel, 275, 09972–270, Bairro Eldorado, Diadema, SP, Brazil
| | - Marcelo A. Vallim
- Departamento de Ciências Biológicas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Campus Diadema, Laboratório de Interações Microbianas (Laboratory 29), Rua Arthur Ridel, 275, 09972–270, Bairro Eldorado, Diadema, SP, Brazil
| | - Renata C. Pascon
- Departamento de Ciências Biológicas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Campus Diadema, Laboratório de Interações Microbianas (Laboratory 29), Rua Arthur Ridel, 275, 09972–270, Bairro Eldorado, Diadema, SP, Brazil
- * E-mail:
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MacDonald C, Piper RC. Puromycin- and methotrexate-resistance cassettes and optimized Cre-recombinase expression plasmids for use in yeast. Yeast 2015; 32:423-38. [PMID: 25688547 DOI: 10.1002/yea.3069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 02/03/2015] [Accepted: 02/07/2015] [Indexed: 11/07/2022] Open
Abstract
Here we expand the set of tools for genetically manipulating Saccharomyces cerevisiae. We show that puromycin-resistance can be achieved in yeast through expression of a bacterial puromycin-resistance gene optimized to the yeast codon bias, which in turn serves as an easy-to-use dominant genetic marker suitable for gene disruption. We have constructed a similar DNA cassette expressing yeast codon-optimized mutant human dihydrofolate reductase (DHFR), which confers resistance to methotrexate and can also be used as a dominant selectable marker. Both of these drug-resistant marker cassettes are flanked by loxP sites, allowing for their excision from the genome following expression of Cre-recombinase. Finally, we have created a series of plasmids for low-level constitutive expression of Cre-recombinase in yeast that allows for efficient excision of loxP-flanked markers.
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Affiliation(s)
- Chris MacDonald
- Department of Molecular Physiology and Biophysics, University of Iowa, IA, USA
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Watts SG, Crowder JJ, Coffey SZ, Rubenstein EM. Growth-based determination and biochemical confirmation of genetic requirements for protein degradation in Saccharomyces cerevisiae. J Vis Exp 2015:e52428. [PMID: 25742191 DOI: 10.3791/52428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Regulated protein degradation is crucial for virtually every cellular function. Much of what is known about the molecular mechanisms and genetic requirements for eukaryotic protein degradation was initially established in Saccharomyces cerevisiae. Classical analyses of protein degradation have relied on biochemical pulse-chase and cycloheximide-chase methodologies. While these techniques provide sensitive means for observing protein degradation, they are laborious, time-consuming, and low-throughput. These approaches are not amenable to rapid or large-scale screening for mutations that prevent protein degradation. Here, a yeast growth-based assay for the facile identification of genetic requirements for protein degradation is described. In this assay, a reporter enzyme required for growth under specific selective conditions is fused to an unstable protein. Cells lacking the endogenous reporter enzyme but expressing the fusion protein can grow under selective conditions only when the fusion protein is stabilized (i.e. when protein degradation is compromised). In the growth assay described here, serial dilutions of wild-type and mutant yeast cells harboring a plasmid encoding a fusion protein are spotted onto selective and non-selective medium. Growth under selective conditions is consistent with degradation impairment by a given mutation. Increased protein abundance should be biochemically confirmed. A method for the rapid extraction of yeast proteins in a form suitable for electrophoresis and western blotting is also demonstrated. A growth-based readout for protein stability, combined with a simple protocol for protein extraction for biochemical analysis, facilitates rapid identification of genetic requirements for protein degradation. These techniques can be adapted to monitor degradation of a variety of short-lived proteins. In the example presented, the His3 enzyme, which is required for histidine biosynthesis, was fused to Deg1-Sec62. Deg1-Sec62 is targeted for degradation after it aberrantly engages the endoplasmic reticulum translocon. Cells harboring Deg1-Sec62-His3 were able to grow under selective conditions when the protein was stabilized.
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Affiliation(s)
| | | | - Samuel Z Coffey
- Department of Biology, Ball State University; Division of Nephrology, Cincinnati Children's Hospital
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Song P, Liu S, Guo X, Bai X, He X, Zhang B. Scarless gene deletion in methylotrophic Hansenula polymorpha by using mazF as counter-selectable marker. Anal Biochem 2015; 468:66-74. [DOI: 10.1016/j.ab.2014.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/02/2014] [Accepted: 09/08/2014] [Indexed: 10/24/2022]
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Briones-Martin-Del-Campo M, Orta-Zavalza E, Cañas-Villamar I, Gutiérrez-Escobedo G, Juárez-Cepeda J, Robledo-Márquez K, Arroyo-Helguera O, Castaño I, De Las Peñas A. The superoxide dismutases of Candida glabrata protect against oxidative damage and are required for lysine biosynthesis, DNA integrity and chronological life survival. Microbiology (Reading) 2014; 161:300-310. [PMID: 25479837 DOI: 10.1099/mic.0.000006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The fungal pathogen Candida glabrata has a well-defined oxidative stress response, is extremely resistant to oxidative stress and can survive inside phagocytic cells. In order to further our understanding of the oxidative stress response in C. glabrata, we characterized the superoxide dismutases (SODs) Cu,ZnSOD (Sod1) and MnSOD (Sod2). We found that Sod1 is the major contributor to total SOD activity and is present in cytoplasm, whereas Sod2 is a mitochondrial protein. Both SODs played a central role in the oxidative stress response but Sod1 was more important during fermentative growth and Sod2 during respiration and growth in non-fermentable carbon sources. Interestingly, C. glabrata cells lacking both SODs showed auxotrophy for lysine, a high rate of spontaneous mutation and reduced chronological lifespan. Thus, our study reveals that SODs play an important role in metabolism, lysine biosynthesis, DNA protection and aging in C. glabrata.
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Affiliation(s)
- Marcela Briones-Martin-Del-Campo
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4a Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Emmanuel Orta-Zavalza
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4a Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Israel Cañas-Villamar
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4a Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Guadalupe Gutiérrez-Escobedo
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4a Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Jacqueline Juárez-Cepeda
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4a Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Karina Robledo-Márquez
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4a Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Omar Arroyo-Helguera
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4a Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Irene Castaño
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4a Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Alejandro De Las Peñas
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, no. 2055, Col. Lomas 4a Sección, San Luis Potosí, San Luis Potosí 78216, Mexico
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48
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Solis-Escalante D, Kuijpers NGA, van der Linden FH, Pronk JT, Daran JM, Daran-Lapujade P. Efficient simultaneous excision of multiple selectable marker cassettes using I-SceI-induced double-strand DNA breaks in Saccharomyces cerevisiae. FEMS Yeast Res 2014; 14:741-54. [PMID: 24833416 DOI: 10.1111/1567-1364.12162] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/09/2014] [Accepted: 05/11/2014] [Indexed: 12/26/2022] Open
Abstract
Large strain construction programs and functional analysis studies are becoming commonplace in Saccharomyces cerevisiae and involve construction of strains that carry multiple selectable marker genes. Extensive strain engineering is, however, severely hampered by the limited number of recyclable marker genes and by the reduced genome stability that occurs upon repeated use of heterologous recombinase-based marker removal methods. The present study proposes an efficient method to recycle multiple markers in S. cerevisiae simultaneously, thereby circumventing shortcomings of existing techniques and substantially accelerating the process of selection-excision. This method relies on artificial generation of double-strand breaks around the selection marker cassette by the meganuclease I-SceI and the subsequent repair of these breaks by the yeast homologous recombination machinery, guided by direct repeats. Simultaneous removal of up to three marker cassettes was achieved with high efficiencies (up to 56%), suggesting that I-SceI-based marker removal has the potential to co-excise an even larger number of markers. This locus- and marker-independent method can be used for both dominant and auxotrophy-complementing marker genes. Seven pDS plasmids carrying various selectable markers, which can be used for PCR-based generation of deletion cassettes suited for I-SceI marker recycling, are described and made available to the scientific community.
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49
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Abstract
Genetic defects in DNA polymerase accuracy, proofreading, or mismatch repair (MMR) induce mutator phenotypes that accelerate adaptation of microbes and tumor cells. Certain combinations of mutator alleles synergistically increase mutation rates to levels that drive extinction of haploid cells. The maximum tolerated mutation rate of diploid cells is unknown. Here, we define the threshold for replication error-induced extinction (EEX) of diploid Saccharomyces cerevisiae. Double-mutant pol3 alleles that carry mutations for defective DNA polymerase-δ proofreading (pol3-01) and accuracy (pol3-L612M or pol3-L612G) induce strong mutator phenotypes in heterozygous diploids (POL3/pol3-01,L612M or POL3/pol3-01,L612G). Both pol3-01,L612M and pol3-01,L612G alleles are lethal in the homozygous state; cells with pol3-01,L612M divide up to 10 times before arresting at random stages in the cell cycle. Antimutator eex mutations in the pol3 alleles suppress this lethality (pol3-01,L612M,eex or pol3-01,L612G,eex). MMR defects synergize with pol3-01,L612M,eex and pol3-01,L612G,eex alleles, increasing mutation rates and impairing growth. Conversely, inactivation of the Dun1 S-phase checkpoint kinase suppresses strong pol3-01,L612M,eex and pol3-01,L612G,eex mutator phenotypes as well as the lethal pol3-01,L612M phenotype. Our results reveal that the lethal error threshold in diploids is 10 times higher than in haploids and likely determined by homozygous inactivation of essential genes. Pronounced loss of fitness occurs at mutation rates well below the lethal threshold, suggesting that mutator-driven cancers may be susceptible to drugs that exacerbate replication errors.
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50
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Abstract
For genetic manipulation of yeast, numerous selection marker genes have been employed. These include prototrophic markers, markers conferring drug resistance, autoselection markers, and counterselectable markers. This chapter describes the different classes of selection markers and provides a number of examples for different applications.
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Affiliation(s)
- Verena Siewers
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden,
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