1
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Trivellin C, Torello Pianale L, Olsson L. Robustness quantification of a mutant library screen revealed key genetic markers in yeast. Microb Cell Fact 2024; 23:218. [PMID: 39098937 PMCID: PMC11298085 DOI: 10.1186/s12934-024-02490-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Microbial robustness is crucial for developing cell factories that maintain consistent performance in a challenging environment such as large-scale bioreactors. Although tools exist to assess and understand robustness at a phenotypic level, the underlying metabolic and genetic mechanisms are not well defined, which limits our ability to engineer more strains with robust functions. RESULTS This study encompassed four steps. (I) Fitness and robustness were analyzed from a published dataset of yeast mutants grown in multiple environments. (II) Genes and metabolic processes affecting robustness or fitness were identified, and 14 of these genes were deleted in Saccharomyces cerevisiae CEN.PK113-7D. (III) The mutants bearing gene deletions were cultivated in three perturbation spaces mimicking typical industrial processes. (IV) Fitness and robustness were determined for each mutant in each perturbation space. We report that robustness varied according to the perturbation space. We identified genes associated with increased robustness such as MET28, linked to sulfur metabolism; as well as genes associated with decreased robustness, including TIR3 and WWM1, both involved in stress response and apoptosis. CONCLUSION The present study demonstrates how phenomics datasets can be analyzed to reveal the relationship between phenotypic response and associated genes. Specifically, robustness analysis makes it possible to study the influence of single genes and metabolic processes on stable microbial performance in different perturbation spaces. Ultimately, this information can be used to enhance robustness in targeted strains.
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Affiliation(s)
- Cecilia Trivellin
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Luca Torello Pianale
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
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2
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Gutbier U, Korp J, Scheufler L, Ostermann K. Genetic modules for α-factor pheromone controlled growth regulation of Saccharomyces cerevisiae. Eng Life Sci 2024; 24:e2300235. [PMID: 39113811 PMCID: PMC11300815 DOI: 10.1002/elsc.202300235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 03/29/2024] [Accepted: 05/05/2024] [Indexed: 08/10/2024] Open
Abstract
Saccharomyces cerevisiae is a commonly used microorganism in the biotechnological industry. For the industrial heterologous production of compounds, it is of great advantage to work with growth-controllable yeast strains. In our work, we utilized the natural pheromone system of S. cerevisiae and generated a set of different strains possessing an α-pheromone controllable growth behavior. Naturally, the α-factor pheromone is involved in communication between haploid S. cerevisiae cells. Perception of the pheromone initiates several cellular changes, enabling the cells to prepare for an upcoming mating event. We exploited this natural pheromone response system and developed two different plasmid-based modules, in which the target genes, MET15 and FAR1, are under control of the α-factor sensitive FIG1 promoter for a controlled expression in S. cerevisiae. Whereas expression of MET15 led to a growth induction, FAR1 expression inhibited growth. The utilization of low copy number or high copy number plasmids for target gene expression and different concentrations of α-factor allow a finely adjustable control of yeast growth rate.
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Affiliation(s)
- Uta Gutbier
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
- Else Kröner Fresenius Center for Digital HealthFaculty of Medicine Carl Gustav CarusTUD Dresden University of TechnologyDresdenGermany
| | - Juliane Korp
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
| | - Lennart Scheufler
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
| | - Kai Ostermann
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
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3
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Pannafino G, Chen JJ, Mithani V, Payero L, Gioia M, Crickard JB, Alani E. The Dmc1 recombinase physically interacts with and promotes the meiotic crossover functions of the Mlh1-Mlh3 endonuclease. Genetics 2024; 227:iyae066. [PMID: 38657110 PMCID: PMC11228845 DOI: 10.1093/genetics/iyae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker's yeast approximately 80% of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates to perform its role in crossover resolution. We performed a gene dosage screen in baker's yeast to identify novel genetic interactors with Mlh1-Mlh3. Specifically, we looked for genes whose lowered dosage reduced meiotic crossing over using sensitized mlh3 alleles that disrupt the stability of the Mlh1-Mlh3 complex and confer defects in mismatch repair but do not disrupt meiotic crossing over. To our surprise we identified genetic interactions between MLH3 and DMC1, the recombinase responsible for recombination between homologous chromosomes during meiosis. We then showed that Mlh3 physically interacts with Dmc1 in vitro and in vivo. Partial complementation of Mlh3 crossover functions was observed when MLH3 was expressed under the control of the CLB1 promoter (NDT80 regulon), suggesting that Mlh3 function can be provided late in meiotic prophase at some functional cost. A model for how Dmc1 could facilitate Mlh1-Mlh3's role in crossover resolution is presented.
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Affiliation(s)
- Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Viraj Mithani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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4
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Flyckt KS, Roesler K, Haug Collet K, Jaureguy L, Booth R, Thatcher SR, Everard JD, Ripp KG, Liu ZB, Shen B, Wayne LL. A Novel Soybean Diacylglycerol Acyltransferase 1b Variant with Three Amino Acid Substitutions Increases Seed Oil Content. PLANT & CELL PHYSIOLOGY 2024; 65:872-884. [PMID: 37982755 PMCID: PMC11209548 DOI: 10.1093/pcp/pcad148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/24/2023] [Accepted: 11/17/2023] [Indexed: 11/21/2023]
Abstract
Improving soybean (Glycine max) seed composition by increasing the protein and oil components will add significant value to the crop and enhance environmental sustainability. Diacylglycerol acyltransferase (DGAT) catalyzes the final rate-limiting step in triacylglycerol biosynthesis and has a major impact on seed oil accumulation. We previously identified a soybean DGAT1b variant modified with 14 amino acid substitutions (GmDGAT1b-MOD) that increases total oil content by 3 percentage points when overexpressed in soybean seeds. In the present study, additional GmDGAT1b variants were generated to further increase oil with a reduced number of substitutions. Variants with one to four amino acid substitutions were screened in the model systems Saccharomyces cerevisiae and transient Nicotiana benthamiana leaf. Promising GmDGAT1b variants resulting in high oil accumulation in the model systems were selected for overexpression in soybeans. One GmDGAT1b variant with three novel amino acid substitutions (GmDGAT1b-3aa) increased total soybean oil to levels near the previously discovered GmDGAT1b-MOD variant. In a multiple location field trial, GmDGAT1b-3aa transgenic events had significantly increased oil and protein by up to 2.3 and 0.6 percentage points, respectively. The modeling of the GmDGAT1b-3aa protein structure provided insights into the potential function of the three substitutions. These findings will guide efforts to improve soybean oil content and overall seed composition by CRISPR editing.
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Affiliation(s)
- Kayla S Flyckt
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston 50131, USA
| | - Keith Roesler
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston 50131, USA
| | | | | | - Russ Booth
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston 50131, USA
| | | | - John D Everard
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston 50131, USA
| | - Kevin G Ripp
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston 50131, USA
| | - Zhan-Bin Liu
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston 50131, USA
| | - Bo Shen
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston 50131, USA
| | - Laura L Wayne
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston 50131, USA
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5
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Saha D, Gregor JB, Hoda S, Eastman KE, Navarrete M, Wisecaver JH, Briggs SD. Candida glabrata maintains two Hap1 homologs, Zcf27 and Zcf4, for distinct roles in ergosterol gene regulation to mediate sterol homeostasis under azole and hypoxic conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599910. [PMID: 38979343 PMCID: PMC11230168 DOI: 10.1101/2024.06.20.599910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Candida glabrata exhibits innate resistance to azole antifungal drugs but also has the propensity to rapidly develop clinical drug resistance. Azole drugs, which target Erg11, is one of the three major classes of antifungals used to treat Candida infections. Despite their widespread use, the mechanism controlling azole-induced ERG gene expression and drug resistance in C. glabrata has primarily revolved around Upc2 and/or Pdr1. In this study, we determined the function of two zinc cluster transcription factors, Zcf27 and Zcf4, as direct but distinct regulators of ERG genes. Our phylogenetic analysis revealed C. glabrata Zcf27 and Zcf4 as the closest homologs to Saccharomyces cerevisiae Hap1. Hap1 is a known zinc cluster transcription factor in S. cerevisiae in controlling ERG gene expression under aerobic and hypoxic conditions. Interestingly, when we deleted HAP1 or ZCF27 in either S. cerevisiae or C. glabrata, respectively, both deletion strains showed altered susceptibility to azole drugs, whereas the strain deleted for ZCF4 did not exhibit azole susceptibility. We also determined that the increased azole susceptibility in a zcf27Δ strain is attributed to decreased azole-induced expression of ERG genes, resulting in decreased levels of total ergosterol. Surprisingly, Zcf4 protein expression is barely detected under aerobic conditions but is specifically induced under hypoxic conditions. However, under hypoxic conditions, Zcf4 but not Zcf27 was directly required for the repression of ERG genes. This study provides the first demonstration that Zcf27 and Zcf4 have evolved to serve distinct roles allowing C. glabrata to adapt to specific host and environmental conditions.
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Affiliation(s)
| | | | | | | | | | | | - Scott D. Briggs
- Department of Biochemistry
- Purdue University Institute for Cancer Research
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6
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Yan W, Li Y, Louis EJ, Kyriacou CP, Hu Y, Cordell RL, Xie X. Quantitative genetic analysis of attractiveness of yeast products to Drosophila. Genetics 2024; 227:iyae048. [PMID: 38560786 PMCID: PMC11151935 DOI: 10.1093/genetics/iyae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
An attractive perfume is a complex mixture of compounds, some of which may be unpleasant on their own. This is also true for the volatile combinations from yeast fermentation products in vineyards and orchards when assessed by Drosophila. Here, we used crosses between a yeast strain with an attractive fermentation profile and another strain with a repulsive one and tested fly responses using a T-maze. QTL analysis reveals allelic variation in four yeast genes, namely PTC6, SAT4, YFL040W, and ARI1, that modulated expression levels of volatile compounds [assessed by gas chromatography-mass spectrometry (GC-MS)] and in different combinations, generated various levels of attractiveness. The parent strain that is more attractive to Drosophila has repulsive alleles at two of the loci, while the least attractive parent has attractive alleles. Behavioral assays using artificial mixtures mimicking the composition of odors from fermentation validated the results of GC-MS and QTL mapping, thereby directly connecting genetic variation in yeast to attractiveness in flies. This study can be used as a basis for dissecting the combination of olfactory receptors that mediate the attractiveness/repulsion of flies to yeast volatiles and may also serve as a model for testing the attractiveness of pest species such as Drosophila suzukii to their host fruit.
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Affiliation(s)
- Weiru Yan
- Institute of Genetics, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
- Department of Genetics & Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Yishen Li
- Department of Genetics & Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Edward J Louis
- Department of Genetics & Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | - Yue Hu
- Department of Genetics & Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Rebecca L Cordell
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Xiaodong Xie
- Institute of Genetics, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
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7
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Moyung K, Li Y, Hartemink AJ, MacAlpine DM. Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595391. [PMID: 38826400 PMCID: PMC11142231 DOI: 10.1101/2024.05.24.595391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Epigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy throughout the genome. Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely unexplored on a comprehensive scale. We address this by employing a factor-agnostic, reverse-genetics approach that uses MNase-seq to capture genome-wide TF and nucleosome occupancies in response to the individual deletion of 201 transcriptional regulators in Saccharomyces cerevisiae, thereby assaying nearly one million mutant-gene interactions. We develop a principled approach to identify and quantify chromatin changes genome-wide, observing differences in TF and nucleosome occupancy that recapitulate well-established pathways identified by gene expression data. We also discover distinct chromatin signatures associated with the up- and downregulation of genes, and use these signatures to reveal regulatory mechanisms previously unexplored in expression-based studies. Finally, we demonstrate that chromatin features are predictive of transcriptional activity and leverage these features to reconstruct chromatin-based transcriptional regulatory networks. Overall, these results illustrate the power of an approach combining genetic perturbation with high-resolution epigenomic profiling; the latter enables a close examination of the interplay between TFs and nucleosomes genome-wide, providing a deeper, more mechanistic understanding of the complex relationship between chromatin organization and transcription.
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Affiliation(s)
- Kevin Moyung
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | - Yulong Li
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
- Department of Computer Science, Duke University, Durham, NC 27708
| | - Alexander J. Hartemink
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Computer Science, Duke University, Durham, NC 27708
| | - David M. MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
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8
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Kazmirchuk TDD, Burnside DJ, Wang J, Jagadeesan SK, Al-Gafari M, Silva E, Potter T, Bradbury-Jost C, Ramessur NB, Ellis B, Takallou S, Hajikarimlou M, Moteshareie H, Said KB, Samanfar B, Fletcher E, Golshani A. Cymoxanil disrupts RNA synthesis through inhibiting the activity of dihydrofolate reductase. Sci Rep 2024; 14:11695. [PMID: 38778133 PMCID: PMC11111663 DOI: 10.1038/s41598-024-62563-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024] Open
Abstract
The agricultural fungicide cymoxanil (CMX) is commonly used in the treatment of plant pathogens, such as Phytophthora infestans. Although the use of CMX is widespread throughout the agricultural industry and internationally, the exact mechanism of action behind this fungicide remains unclear. Therefore, we sought to elucidate the biocidal mechanism underlying CMX. This was accomplished by first performing a large-scale chemical-genomic screen comprising the 4000 haploid non-essential gene deletion array of the yeast Saccharomyces cerevisiae. We found that gene families related to de novo purine biosynthesis and ribonucleoside synthesis were enriched in the presence of CMX. These results were confirmed through additional spot-test and colony counting assays. We next examined whether CMX affects RNA biosynthesis. Using qRT-PCR and expression assays, we found that CMX appears to target RNA biosynthesis possibly through the yeast dihydrofolate reductase (DHFR) enzyme Dfr1. To determine whether DHFR is a target of CMX, we performed an in-silico molecular docking assay between CMX and yeast, human, and P. infestans DHFR. The results suggest that CMX directly interacts with the active site of all tested forms of DHFR using conserved residues. Using an in vitro DHFR activity assay we observed that CMX inhibits DHFR activity in a dose-dependent relationship.
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Affiliation(s)
| | - Daniel J Burnside
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Jiashu Wang
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Sasi Kumar Jagadeesan
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Mustafa Al-Gafari
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Eshan Silva
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Taylor Potter
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Calvin Bradbury-Jost
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Nishka Beersing Ramessur
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Brittany Ellis
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Sarah Takallou
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Maryam Hajikarimlou
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Houman Moteshareie
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Kamaleldin B Said
- Department of Pathology and Microbiology, University of Hail, 55476, Hail, Saudi Arabia
| | - Bahram Samanfar
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, Canada
| | - Eugene Fletcher
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada
| | - Ashkan Golshani
- Department of Biology and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, K1S 5B6, Canada.
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9
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Desroches Altamirano C, Kang MK, Jordan MA, Borianne T, Dilmen I, Gnädig M, von Appen A, Honigmann A, Franzmann TM, Alberti S. eIF4F is a thermo-sensing regulatory node in the translational heat shock response. Mol Cell 2024; 84:1727-1741.e12. [PMID: 38547866 DOI: 10.1016/j.molcel.2024.02.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/18/2023] [Accepted: 02/29/2024] [Indexed: 05/05/2024]
Abstract
Heat-shocked cells prioritize the translation of heat shock (HS) mRNAs, but the underlying mechanism is unclear. We report that HS in budding yeast induces the disassembly of the eIF4F complex, where eIF4G and eIF4E assemble into translationally arrested mRNA ribonucleoprotein particles (mRNPs) and HS granules (HSGs), whereas eIF4A promotes HS translation. Using in vitro reconstitution biochemistry, we show that a conformational rearrangement of the thermo-sensing eIF4A-binding domain of eIF4G dissociates eIF4A and promotes the assembly with mRNA into HS-mRNPs, which recruit additional translation factors, including Pab1p and eIF4E, to form multi-component condensates. Using extracts and cellular experiments, we demonstrate that HS-mRNPs and condensates repress the translation of associated mRNA and deplete translation factors that are required for housekeeping translation, whereas HS mRNAs can be efficiently translated by eIF4A. We conclude that the eIF4F complex is a thermo-sensing node that regulates translation during HS.
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Affiliation(s)
- Christine Desroches Altamirano
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Moo-Koo Kang
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Mareike A Jordan
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Tom Borianne
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Irem Dilmen
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Maren Gnädig
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Alexander von Appen
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Alf Honigmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.
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10
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Cachera P, Kurt NC, Røpke A, Strucko T, Mortensen UH, Jensen MK. Genome-wide host-pathway interactions affecting cis-cis-muconic acid production in yeast. Metab Eng 2024; 83:75-85. [PMID: 38428729 DOI: 10.1016/j.ymben.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/11/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
Abstract
The success of forward metabolic engineering depends on a thorough understanding of the behaviour of a heterologous metabolic pathway within its host. We have recently described CRI-SPA, a high-throughput gene editing method enabling the delivery of a metabolic pathway to all strains of the Saccharomyces cerevisiae knock-out library. CRI-SPA systematically quantifies the effect of each modified gene present in the library on product synthesis, providing a complete map of host:pathway interactions. In its first version, CRI-SPA relied on the colour of the product betaxanthins to quantify strains synthesis ability. However, only a few compounds produce a visible or fluorescent phenotype limiting the scope of our approach. Here, we adapt CRI-SPA to onboard a biosensor reporting the interactions between host genes and the synthesis of the colourless product cis-cis-muconic acid (CCM). We phenotype >9,000 genotypes, including both gene knock-out and overexpression, by quantifying the fluorescence of yeast colonies growing in high-density agar arrays. We identify novel metabolic targets belonging to a broad range of cellular functions and confirm their positive impact on CCM biosynthesis. In particular, our data suggests a new interplay between CCM biosynthesis and cytosolic redox through their common interaction with the oxidative pentose phosphate pathway. Our genome-wide exploration of host:pathway interaction opens novel strategies for improved production of CCM in yeast cell factories.
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Affiliation(s)
- Paul Cachera
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nikolaj Can Kurt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas Røpke
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tomas Strucko
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Uffe H Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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11
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Ross RL, Santiago-Tirado FH. Advanced genetic techniques in fungal pathogen research. mSphere 2024; 9:e0064323. [PMID: 38470131 PMCID: PMC11036804 DOI: 10.1128/msphere.00643-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Although fungi have been important model organisms for solving genetic, molecular, and ecological problems, recently, they are also becoming an important source of infectious disease. Despite their high medical burden, fungal pathogens are understudied, and relative to other pathogenic microbes, less is known about how their gene functions contribute to disease. This is due, in part, to a lack of powerful genetic tools to study these organisms. In turn, this has resulted in inappropriate treatments and diagnostics and poor disease management. There are a variety of reasons genetic studies were challenging in pathogenic fungi, but in recent years, most of them have been overcome or advances have been made to circumvent these barriers. In this minireview, we highlight how recent advances in genetic studies in fungal pathogens have resulted in the discovery of important biology and potential new antifungals and have created the tools to comprehensively study these important pathogens.
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Affiliation(s)
- Robbi L. Ross
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Felipe H. Santiago-Tirado
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
- Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana, USA
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12
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Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024:10.1038/s41576-024-00711-3. [PMID: 38565962 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
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Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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13
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Nadal-Ribelles M, Solé C, de Nadal E, Posas F. The rise of single-cell transcriptomics in yeast. Yeast 2024; 41:158-170. [PMID: 38403881 DOI: 10.1002/yea.3934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/24/2024] [Accepted: 02/15/2024] [Indexed: 02/27/2024] Open
Abstract
The field of single-cell omics has transformed our understanding of biological processes and is constantly advancing both experimentally and computationally. One of the most significant developments is the ability to measure the transcriptome of individual cells by single-cell RNA-seq (scRNA-seq), which was pioneered in higher eukaryotes. While yeast has served as a powerful model organism in which to test and develop transcriptomic technologies, the implementation of scRNA-seq has been significantly delayed in this organism, mainly because of technical constraints associated with its intrinsic characteristics, namely the presence of a cell wall, a small cell size and little amounts of RNA. In this review, we examine the current technologies for scRNA-seq in yeast and highlight their strengths and weaknesses. Additionally, we explore opportunities for developing novel technologies and the potential outcomes of implementing single-cell transcriptomics and extension to other modalities. Undoubtedly, scRNA-seq will be invaluable for both basic and applied yeast research, providing unique insights into fundamental biological processes.
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Affiliation(s)
- Mariona Nadal-Ribelles
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carme Solé
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulalia de Nadal
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francesc Posas
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
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14
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Peng H, Darlington APS, South EJ, Chen HH, Jiang W, Ledesma-Amaro R. A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities. Nat Microbiol 2024; 9:848-863. [PMID: 38326570 PMCID: PMC10914607 DOI: 10.1038/s41564-023-01596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 12/18/2023] [Indexed: 02/09/2024]
Abstract
Engineered microbial consortia often have enhanced system performance and robustness compared with single-strain biomanufacturing production platforms. However, few tools are available for generating co-cultures of the model and key industrial host Saccharomyces cerevisiae. Here we engineer auxotrophic and overexpression yeast strains that can be used to create co-cultures through exchange of essential metabolites. Using these strains as modules, we engineered two- and three-member consortia using different cross-feeding architectures. Through a combination of ensemble modelling and experimentation, we explored how cellular (for example, metabolite production strength) and environmental (for example, initial population ratio, population density and extracellular supplementation) factors govern population dynamics in these systems. We tested the use of the toolkit in a division of labour biomanufacturing case study and show that it enables enhanced and tuneable antioxidant resveratrol production. We expect this toolkit to become a useful resource for a variety of applications in synthetic ecology and biomanufacturing.
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Affiliation(s)
- Huadong Peng
- Department of Bioengineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alexander P S Darlington
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry, UK
| | - Eric J South
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Hao-Hong Chen
- Department of Bioengineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Wei Jiang
- Department of Bioengineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College London, London, UK.
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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15
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Smith JR, Martini A, Gibney PA. Utilizing functional genomics in Saccharomyces cerevisiae to characterize food preservative compounds: A pilot study. J Food Sci 2024; 89:1196-1210. [PMID: 38224173 DOI: 10.1111/1750-3841.16906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/17/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
Chemical preservatives are ubiquitously used to suppress the growth of or kill microorganisms across numerous industries, including the food industry. Utilizing yeast functional genomic techniques, genes and their functions can be observed at a genomic scale to elucidate how environmental stressors (e.g., chemical preservatives) impact microbial survival. These types of chemical genomics approaches can reveal genetic mutations that result in preservative resistance or sensitivity, assist in identification of preservative mechanism of action, and can be used to compare different preservatives for rational design of preservative mixtures. In this proof-of-concept study, we performed deletion and high-copy genetic expression screens to identify mutants that confer drug resistance to sodium benzoate, potassium sorbate, rosemary extract, and Natamax. By observing overlapping mutant genes between genetic screens, we were able to identify functional overlap between chemical preservatives and begin to explain mechanisms of action for these compounds.
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Affiliation(s)
- Jeremy R Smith
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Austin Martini
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Patrick A Gibney
- Department of Food Science, Cornell University, Ithaca, New York, USA
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16
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Sapède E, Sugawara N, Tyers RG, Nakajima Y, Afreen MF, Romero Escobar J, Haber JE. Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing in Saccharomyces cerevisiae. PLoS Genet 2024; 20:e1010527. [PMID: 38315739 PMCID: PMC10868807 DOI: 10.1371/journal.pgen.1010527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/15/2024] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Single-strand annealing (SSA) is initiated when a double strand break (DSB) occurs between two flanking repeated sequences, resulting in a deletion that leaves a single copy of the repeat. We studied budding yeast strains carrying two 200-bp URA3 sequences separated by 2.6 kb of spacer DNA (phage lambda) in which a site-specific DSB can be created by HO or Cas9 endonucleases. Repeat-mediated deletion requires removal of long 3'-ended single-stranded tails (flaps) by Rad1-Rad10 with the assistance of Msh2-Msh3, Saw1 and Slx4. A natural 3% divergence of unequally spaced heterologies between these repeats (designated F and A) causes a significant reduction in the frequency of SSA repair. This decrease is caused by heteroduplex rejection in which mismatches (MMs) in the annealed intermediate are recognized by the MutS (Msh2 and Msh6) components of the MM repair (MMR) pathway coupled to unwinding of the duplex by the Sgs1-Rmi1-Top3 helicase. MutL homologs, Mlh1-Pms1 (MutL), are not required for rejection but play their expected role in mismatch correction. Remarkably, heteroduplex rejection is very low in strains where the divergent repeats were immediately adjacent (Tailless strains) and the DSB was induced by Cas9. These results suggest that the presence of nonhomologous tails strongly stimulates heteroduplex rejection in SSA. DNA sequencing analysis of SSA products from the FA Tailed strain showed a gradient of correction favoring the sequence opposite each 3' end of the annealed strand. Mismatches located in the center of the repair intermediate were corrected by Msh2-Msh6 mediated mismatch correction, while correction of MMs at the extremity of the SSA intermediate often appears to use a different mechanism, possibly by 3' nonhomologous tail removal that includes part of the homologous sequence. In contrast, in FA Tailless strains there was a uniform repair of the MMs across the repeat. A distinctive pattern of correction was found in the absence of MSH2, in both Tailed and Tailless strains, different from the spectrum seen in a msh3Δ msh6Δ double mutant. Previous work has shown that SSA is Rad51-independent but dependent on the strand annealing activity of Rad52. However Rad52 becomes dispensable in a Tailless construct where the DSB is induced by Cas9 or in transformation of a plasmid where SSA occurs in the absence of nonhomologous tails.
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Affiliation(s)
- Elena Sapède
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Neal Sugawara
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Randall G. Tyers
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Yuko Nakajima
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Mosammat Faria Afreen
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jesselin Romero Escobar
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - James E. Haber
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
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17
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Samakkarn W, Vandecruys P, Moreno MRF, Thevelein J, Ratanakhanokchai K, Soontorngun N. New biomarkers underlying acetic acid tolerance in the probiotic yeast Saccharomyces cerevisiae var. boulardii. Appl Microbiol Biotechnol 2024; 108:153. [PMID: 38240846 PMCID: PMC10799125 DOI: 10.1007/s00253-023-12946-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 01/22/2024]
Abstract
Evolutionary engineering experiments, in combination with omics technologies, revealed genetic markers underpinning the molecular mechanisms behind acetic acid stress tolerance in the probiotic yeast Saccharomyces cerevisiae var. boulardii. Here, compared to the ancestral Ent strain, evolved yeast strains could quickly adapt to high acetic acid levels (7 g/L) and displayed a shorter lag phase of growth. Bioinformatic-aided whole-genome sequencing identified genetic changes associated with enhanced strain robustness to acetic acid: a duplicated sequence in the essential endocytotic PAN1 gene, mutations in a cell wall mannoprotein (dan4Thr192del), a lipid and fatty acid transcription factor (oaf1Ser57Pro) and a thiamine biosynthetic enzyme (thi13Thr332Ala). Induction of PAN1 and its associated endocytic complex SLA1 and END3 genes was observed following acetic acid treatment in the evolved-resistant strain when compared to the ancestral strain. Genome-wide transcriptomic analysis of the evolved Ent acid-resistant strain (Ent ev16) also revealed a dramatic rewiring of gene expression among genes associated with cellular transport, metabolism, oxidative stress response, biosynthesis/organization of the cell wall, and cell membrane. Some evolved strains also displayed better growth at high acetic acid concentrations and exhibited adaptive metabolic profiles with altered levels of secreted ethanol (4.0-6.4% decrease), glycerol (31.4-78.5% increase), and acetic acid (53.0-60.3% increase) when compared to the ancestral strain. Overall, duplication/mutations and transcriptional alterations are key mechanisms driving improved acetic acid tolerance in probiotic strains. We successfully used adaptive evolutionary engineering to rapidly and effectively elucidate the molecular mechanisms behind important industrial traits to obtain robust probiotic yeast strains for myriad biotechnological applications. KEY POINTS: •Acetic acid adaptation of evolutionary engineered robust probiotic yeast S. boulardii •Enterol ev16 with altered genetic and transcriptomic profiles survives in up to 7 g/L acetic acid •Improved acetic acid tolerance of S. boulardii ev16 with mutated PAN1, DAN4, OAF1, and THI13 genes.
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Affiliation(s)
- Wiwan Samakkarn
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Paul Vandecruys
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Leuven, Flanders, Belgium
| | - Maria Remedios Foulquié Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Leuven, Flanders, Belgium
| | - Johan Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Leuven, Flanders, Belgium
- NovelYeast Bv, Open Bio-Incubator, Erasmus High School, (Jette), Brussels, Belgium
| | - Khanok Ratanakhanokchai
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Nitnipa Soontorngun
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
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18
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Gaikani HK, Stolar M, Kriti D, Nislow C, Giaever G. From beer to breadboards: yeast as a force for biological innovation. Genome Biol 2024; 25:10. [PMID: 38178179 PMCID: PMC10768129 DOI: 10.1186/s13059-023-03156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
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Affiliation(s)
- Hamid Kian Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Monika Stolar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
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19
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Lino BR, Van Deventer JA. Genome-Wide Screen for Enhanced Noncanonical Amino Acid Incorporation in Yeast. Methods Mol Biol 2024; 2760:219-251. [PMID: 38468092 DOI: 10.1007/978-1-0716-3658-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Expanding the genetic code beyond the 20 canonical amino acids enables access to a wide range of chemical functionality that is inaccessible within conventionally biosynthesized proteins. The vast majority of efforts to expand the genetic code have focused on the orthogonal translation systems required to achieve the genetically encoded addition of noncanonical amino acids (ncAAs) into proteins. There remain tremendous opportunities for identifying genetic and genomic factors that enhance ncAA incorporation. Here we describe genome-wide screening strategies to identify factors that enable more efficient addition of ncAAs to biosynthesized proteins. These unbiased screens can reveal previously unknown genes or mutations that can enhance ncAA incorporation and deepen our understanding of the translation apparatus.
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Affiliation(s)
- Briana R Lino
- Chemical and Biological Engineering Department, Tufts University, Medford, MA, USA
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA, USA.
- Biomedical Engineering Department, Tufts University, Medford, MA, USA.
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20
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Murphy RO, Beckmann JF. Using Baker's Yeast to Determine Functions of Novel Wolbachia (and Other Prokaryotic) Effectors. Methods Mol Biol 2024; 2739:321-336. [PMID: 38006560 DOI: 10.1007/978-1-0716-3553-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
Yeasts are single-celled eukaryotic organisms classified as fungi, mostly in the phylum Ascomycota. Of about 1500 named species, Saccharomyces cerevisiae, also known as baker's yeast, domesticated by humans in the context of cooking and brewing, is a profound genetic tool for exploring functions of novel effector proteins from Wolbachia and prokaryotes in general. Wolbachia is a Gram-negative alpha-proteobacterium that infects up to ~75% of all insects as an obligate intracellular microbe (Jeyaprakash A, Hoy MA, Insect Mol Biol 9:393-405, 2000). Wolbachia's lifestyle presents unique challenges for researchers. Wolbachia cannot be axenically cultured and has never been genetically manipulated. Furthermore, many Wolbachia genes have no known function or well-annotated orthologs in other genomes. Yet given the effects of Wolbachia on host phenotypes, which have considerable practical applications for pest control, they undoubtedly involve secreted effector proteins that interact with host gene products. Studying these effectors is challenging with Wolbachia's current genetic limitations. However, some of the constraints to working with Wolbachia can be overcome by expressing candidate proteins in S. cerevisiae. This approach capitalizes on yeast's small genome (~6500 genes), typical eukaryotic cellular organization, and the sophisticated suite of genetic tools available for its manipulation in culture. Thus, yeast can serve as a powerful mock eukaryotic host background to study Wolbachia effector function. Specifically, yeast is used for recombinant protein expression, drug discovery, protein localization studies, protein interaction mapping (yeast two-hybrid system), modeling chromosomal evolution, and examining interactions between proteins responsible for complex phenotypes in less tractable prokaryotic systems. As an example, the paired genes responsible for Wolbachia-mediated cytoplasmic incompatibility (CI) encode novel proteins with limited homology to other known proteins, and no obvious function. This article details how S. cerevisiae was used as an initial staging ground to explore the molecular basis of one of Wolbachia's trademark phenotypes (CI).
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Affiliation(s)
- Richard O Murphy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - John F Beckmann
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA.
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21
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Lang OW, Srivastava D, Pugh BF, Lai WKM. GenoPipe: identifying the genotype of origin within (epi)genomic datasets. Nucleic Acids Res 2023; 51:12054-12068. [PMID: 37933851 PMCID: PMC10711449 DOI: 10.1093/nar/gkad950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/19/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023] Open
Abstract
Confidence in experimental results is critical for discovery. As the scale of data generation in genomics has grown exponentially, experimental error has likely kept pace despite the best efforts of many laboratories. Technical mistakes can and do occur at nearly every stage of a genomics assay (i.e. cell line contamination, reagent swapping, tube mislabelling, etc.) and are often difficult to identify post-execution. However, the DNA sequenced in genomic experiments contains certain markers (e.g. indels) encoded within and can often be ascertained forensically from experimental datasets. We developed the Genotype validation Pipeline (GenoPipe), a suite of heuristic tools that operate together directly on raw and aligned sequencing data from individual high-throughput sequencing experiments to characterize the underlying genome of the source material. We demonstrate how GenoPipe validates and rescues erroneously annotated experiments by identifying unique markers inherent to an organism's genome (i.e. epitope insertions, gene deletions and SNPs).
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Affiliation(s)
- Olivia W Lang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Divyanshi Srivastava
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, 16801, USA
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - William K M Lai
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY 14850, USA
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22
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Dolan M, St. John N, Zaidi F, Doyle F, Fasullo M. High-throughput screening of the Saccharomyces cerevisiae genome for 2-amino-3-methylimidazo [4,5-f] quinoline resistance identifies colon cancer-associated genes. G3 (BETHESDA, MD.) 2023; 13:jkad219. [PMID: 37738679 PMCID: PMC11025384 DOI: 10.1093/g3journal/jkad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 10/25/2022] [Accepted: 09/15/2023] [Indexed: 09/24/2023]
Abstract
Heterocyclic aromatic amines (HAAs) are potent carcinogenic agents found in charred meats and cigarette smoke. However, few eukaryotic resistance genes have been identified. We used Saccharomyces cerevisiae (budding yeast) to identify genes that confer resistance to 2-amino-3-methylimidazo[4,5-f] quinoline (IQ). CYP1A2 and NAT2 activate IQ to become a mutagenic nitrenium compound. Deletion libraries expressing human CYP1A2 and NAT2 or no human genes were exposed to either 400 or 800 µM IQ for 5 or 10 generations. DNA barcodes were sequenced using the Illumina HiSeq 2500 platform and statistical significance was determined for exactly matched barcodes. We identified 424 ORFs, including 337 genes of known function, in duplicate screens of the "humanized" collection for IQ resistance; resistance was further validated for a select group of 51 genes by growth curves, competitive growth, or trypan blue assays. Screens of the library not expressing human genes identified 143 ORFs conferring resistance to IQ per se. Ribosomal protein and protein modification genes were identified as IQ resistance genes in both the original and "humanized" libraries, while nitrogen metabolism, DNA repair, and growth control genes were also prominent in the "humanized" library. Protein complexes identified included the casein kinase 2 (CK2) and histone chaperone (HIR) complex. Among DNA Repair and checkpoint genes, we identified those that function in postreplication repair (RAD18, UBC13, REV7), base excision repair (NTG1), and checkpoint signaling (CHK1, PSY2). These studies underscore the role of ribosomal protein genes in conferring IQ resistance, and illuminate DNA repair pathways for conferring resistance to activated IQ.
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Affiliation(s)
- Michael Dolan
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Nick St. John
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Faizan Zaidi
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Francis Doyle
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Michael Fasullo
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
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23
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Sonal, Yuan AE, Yang X, Shou W. Collective production of hydrogen sulfide gas enables budding yeast lacking MET17 to overcome their metabolic defect. PLoS Biol 2023; 21:e3002439. [PMID: 38060626 PMCID: PMC10729969 DOI: 10.1371/journal.pbio.3002439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 12/19/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023] Open
Abstract
Assimilation of sulfur is vital to all organisms. In S. cerevisiae, inorganic sulfate is first reduced to sulfide, which is then affixed to an organic carbon backbone by the Met17 enzyme. The resulting homocysteine can then be converted to all other essential organosulfurs such as methionine, cysteine, and glutathione. This pathway has been known for nearly half a century, and met17 mutants have long been classified as organosulfur auxotrophs, which are unable to grow on sulfate as their sole sulfur source. Surprisingly, we found that met17Δ could grow on sulfate, albeit only at sufficiently high cell densities. We show that the accumulation of hydrogen sulfide gas underpins this density-dependent growth of met17Δ on sulfate and that the locus YLL058W (HSU1) enables met17Δ cells to assimilate hydrogen sulfide. Hsu1 protein is induced during sulfur starvation and under exposure to high sulfide concentrations in wild-type cells, and the gene has a pleiotropic role in sulfur assimilation. In a mathematical model, the low efficiency of sulfide assimilation in met17Δ can explain the observed density-dependent growth of met17Δ on sulfate. Thus, having uncovered and explained the paradoxical growth of a commonly used "auxotroph," our findings may impact the design of future studies in yeast genetics, metabolism, and volatile-mediated microbial interactions.
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Affiliation(s)
- Sonal
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Alex E. Yuan
- University of Washington, Seattle, Washington, United States of America
| | - Xueqin Yang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Wenying Shou
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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Stasiowski E, O’Laughlin R, Holness S, Csicsery N, Hasty J, Hao N. A Microfluidic Platform for Screening Gene Expression Dynamics across Yeast Strain Libraries. Bio Protoc 2023; 13:e4883. [PMID: 38023791 PMCID: PMC10665637 DOI: 10.21769/bioprotoc.4883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/16/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The relative ease of genetic manipulation in S. cerevisiae is one of its greatest strengths as a model eukaryotic organism. Researchers have leveraged this quality of the budding yeast to study the effects of a variety of genetic perturbations, such as deletion or overexpression, in a high-throughput manner. This has been accomplished by producing a number of strain libraries that can contain hundreds or even thousands of distinct yeast strains with unique genetic alterations. While these strategies have led to enormous increases in our understanding of the functions and roles that genes play within cells, the techniques used to screen genetically modified libraries of yeast strains typically rely on plate or sequencing-based assays that make it difficult to analyze gene expression changes over time. Microfluidic devices, combined with fluorescence microscopy, can allow gene expression dynamics of different strains to be captured in a continuous culture environment; however, these approaches often have significantly lower throughput compared to traditional techniques. To address these limitations, we have developed a microfluidic platform that uses an array pinning robot to allow for up to 48 different yeast strains to be transferred onto a single device. Here, we detail a validated methodology for constructing and setting up this microfluidic device, starting with the photolithography steps for constructing the wafer, then the soft lithography steps for making polydimethylsiloxane (PDMS) microfluidic devices, and finally the robotic arraying of strains onto the device for experiments. We have applied this device for dynamic screens of a protein aggregation library; however, this methodology has the potential to enable complex and dynamic screens of yeast libraries for a wide range of applications. Key features • Major steps of this protocol require access to specialized equipment (i.e., microfabrication tools typically found in a cleanroom facility and an array pinning robot). • Construction of microfluidic devices with multiple different feature heights using photolithography and soft lithography with PDMS. • Robotic spotting of up to 48 different yeast strains onto microfluidic devices.
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Affiliation(s)
- Elizabeth Stasiowski
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Richard O’Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Shayna Holness
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Nicholas Csicsery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA
| | - Nan Hao
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA
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25
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Pannafino G, Chen JJ, Mithani V, Payero L, Gioia M, Brooks Crickard J, Alani E. The Dmc1 recombinase physically interacts with and promotes the meiotic crossover functions of the Mlh1-Mlh3 endonuclease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566911. [PMID: 38014100 PMCID: PMC10680668 DOI: 10.1101/2023.11.13.566911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker's yeast approximately 80 percent of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction (dHJ) intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates and whether it interacts with other meiotic factors prior to its role in crossover resolution. We performed a haploinsufficiency screen in baker's yeast to identify novel genetic interactors with Mlh1-Mlh3 using sensitized mlh3 alleles that disrupt the stability of the Mlh1-Mlh3 complex and confer defects in mismatch repair but do not disrupt meiotic crossing over. We identified several genetic interactions between MLH3 and DMC1, the recombinase responsible for recombination between homologous chromosomes during meiosis. We then showed that Mlh3 physically interacts with Dmc1 in vitro and at times in meiotic prophase when Dmc1 acts as a recombinase. Interestingly, restricting MLH3 expression to roughly the time of crossover resolution resulted in a mlh3 null-like phenotype for crossing over. Our data are consistent with a model in which Dmc1 nucleates a polymer of Mlh1-Mlh3 to promote crossing over.
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Affiliation(s)
- Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Viraj Mithani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
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Alhajouj S, Turkolmez S, Abalkhail T, Alwan ZHO, James Gilmour D, Mitchell PJ, Hettema EH. Efficient PCR-based gene targeting in isolates of the nonconventional yeast Debaryomyces hansenii. Yeast 2023; 40:550-564. [PMID: 37870109 DOI: 10.1002/yea.3902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 10/24/2023] Open
Abstract
Debaryomyces hansenii is a yeast with considerable biotechnological potential as an osmotolerant, stress-tolerant oleaginous microbe. However, targeted genome modification tools are limited and require a strain with auxotrophic markers. Gene targeting by homologous recombination has been reported to be inefficient, but here we describe a set of reagents and a method that allows gene targeting at high efficiency in wild-type isolates. It uses a simple polymerase chain reaction (PCR)-based amplification that extends a completely heterologous selectable marker with 50 bp flanks identical to the target site in the genome. Transformants integrate the PCR product through homologous recombination at high frequency (>75%). We illustrate the potential of this method by disrupting genes at high efficiency and by expressing a heterologous protein from a safe chromosomal harbour site. These methods should stimulate and facilitate further analysis of D. hansenii strains and open the way to engineer strains for biotechnology.
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Affiliation(s)
- Sondos Alhajouj
- School of Bioscience, University of Sheffield, Sheffield, UK
| | - Selva Turkolmez
- School of Bioscience, University of Sheffield, Sheffield, UK
| | - Tarad Abalkhail
- School of Bioscience, University of Sheffield, Sheffield, UK
- Future address: Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Phil J Mitchell
- School of Bioscience, University of Sheffield, Sheffield, UK
| | - Ewald H Hettema
- School of Bioscience, University of Sheffield, Sheffield, UK
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27
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Gygi JS, Liu X, Levi BP, Paulo JA. Proteome-wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing. Proteomics 2023:e2300303. [PMID: 37882342 PMCID: PMC11045664 DOI: 10.1002/pmic.202300303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023]
Abstract
The GET pathway is associated with post-translational delivery of tail-anchored (TA) proteins to the endoplasmic reticulum (ER) in yeast, as well as other eukaryotes. Moreover, dysfunction of the GET pathway has been associated with various pathological conditions (i.e., neurodegenerative disorders, cardiovascular ailments, and protein misfolding diseases). In this study, we used yeast deletion strains of Get complex members (specifically, Get1, Get2, Get3, Get4, and Get5) coupled with sample multiplexing-based quantitative mass spectrometry to profile protein abundance on a proteome-wide scale across the five individual deletion strains. Our dataset consists of over 4500 proteins, which corresponds to >75% of the yeast proteome. The data reveal several dozen proteins that are differentially abundant in one or more deletion strains, some of which are membrane-associated, yet the abundance of many TA proteins remained unchanged. This study provides valuable insights into the roles of these Get genes, and the potential for alternative pathways which help maintain cellular function despite the disruption of the GET pathway.
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Affiliation(s)
- Joel S Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin P Levi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
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28
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Bleckmann A, Spitzlberger N, Denninger P, Ehrnsberger HF, Wang L, Bruckmann A, Reich S, Holzinger P, Medenbach J, Grasser KD, Dresselhaus T. Cytosolic RGG RNA-binding proteins are temperature sensitive flowering time regulators in Arabidopsis. Biol Chem 2023; 404:1069-1084. [PMID: 37674329 DOI: 10.1515/hsz-2023-0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
mRNA translation is tightly regulated by various classes of RNA-binding proteins (RBPs) during development and in response to changing environmental conditions. In this study, we characterize the arginine-glycine-glycine (RGG) motif containing RBP family of Arabidopsis thaliana representing homologues of the multifunctional translation regulators and ribosomal preservation factors Stm1 from yeast (ScStm1) and human SERBP1 (HsSERBP1). The Arabidopsis genome encodes three RGG proteins named AtRGGA, AtRGGB and AtRGGC. While AtRGGA is ubiquitously expressed, AtRGGB and AtRGGC are enriched in dividing cells. All AtRGGs localize almost exclusively to the cytoplasm and bind with high affinity to ssRNA, while being capable to interact with most nucleic acids, except dsRNA. A protein-interactome study shows that AtRGGs interact with ribosomal proteins and proteins involved in RNA processing and transport. In contrast to ScStm1, AtRGGs are enriched in ribosome-free fractions in polysome profiles, suggesting additional plant-specific functions. Mutant studies show that AtRGG proteins differentially regulate flowering time, with a distinct and complex temperature dependency for each AtRGG protein. In conclusion, we suggest that AtRGGs function in fine-tuning translation efficiency to control flowering time and potentially other developmental processes in response to environmental changes.
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Affiliation(s)
- Andrea Bleckmann
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Nicole Spitzlberger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Philipp Denninger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Hans F Ehrnsberger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Lele Wang
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Stefan Reich
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Philipp Holzinger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Jan Medenbach
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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29
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Chen V, Johnson MS, Hérissant L, Humphrey PT, Yuan DC, Li Y, Agarwala A, Hoelscher SB, Petrov DA, Desai MM, Sherlock G. Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments. eLife 2023; 12:e92899. [PMID: 37861305 PMCID: PMC10629826 DOI: 10.7554/elife.92899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/21/2023] Open
Abstract
Adaptation is driven by the selection for beneficial mutations that provide a fitness advantage in the specific environment in which a population is evolving. However, environments are rarely constant or predictable. When an organism well adapted to one environment finds itself in another, pleiotropic effects of mutations that made it well adapted to its former environment will affect its success. To better understand such pleiotropic effects, we evolved both haploid and diploid barcoded budding yeast populations in multiple environments, isolated adaptive clones, and then determined the fitness effects of adaptive mutations in 'non-home' environments in which they were not selected. We find that pleiotropy is common, with most adaptive evolved lineages showing fitness effects in non-home environments. Consistent with other studies, we find that these pleiotropic effects are unpredictable: they are beneficial in some environments and deleterious in others. However, we do find that lineages with adaptive mutations in the same genes tend to show similar pleiotropic effects. We also find that ploidy influences the observed adaptive mutational spectra in a condition-specific fashion. In some conditions, haploids and diploids are selected with adaptive mutations in identical genes, while in others they accumulate mutations in almost completely disjoint sets of genes.
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Affiliation(s)
- Vivian Chen
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Milo S Johnson
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityBostonUnited States
| | - Lucas Hérissant
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Parris T Humphrey
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - David C Yuan
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Yuping Li
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Atish Agarwala
- Department of Physics, Stanford UniversityStanfordUnited States
| | | | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Quantitative Biology Initiative, Harvard UniversityCambridgeUnited States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard UniversityBostonUnited States
- Department of Physics, Harvard UniversityCambridgeUnited States
| | - Gavin Sherlock
- Department of Genetics, Stanford UniversityStanfordUnited States
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30
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Davis C, Spaller BL, Choi E, Kurrasch J, Chong H, Elsasser S, Finley D, Matouschek A. A strict requirement in proteasome substrates for spacing between ubiquitin tag and degradation initiation elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552540. [PMID: 37609285 PMCID: PMC10441315 DOI: 10.1101/2023.08.08.552540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Proteins are typically targeted to the proteasome for degradation through the attachment of ubiquitin chains and the proteasome initiates degradation at a disordered region within the target protein. Yet some proteins with ubiquitin chains and disordered regions escape degradation. Here we investigate how the position of the ubiquitin chain on the target protein relative to the disordered region modulates degradation and show that the distance between the two determines whether a protein is degraded efficiently. This distance depends on the type of the degradation tag and is likely a result of the separation on the proteasome between the receptor that binds the tag and the site that engages the disordered region.
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31
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Avecilla G, Spealman P, Matthews J, Caudal E, Schacherer J, Gresham D. Copy number variation alters local and global mutational tolerance. Genome Res 2023; 33:1340-1353. [PMID: 37652668 PMCID: PMC10547251 DOI: 10.1101/gr.277625.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/07/2023] [Indexed: 09/02/2023]
Abstract
Copy number variants (CNVs), duplications and deletions of genomic sequences, contribute to evolutionary adaptation but can also confer deleterious effects and cause disease. Whereas the effects of amplifying individual genes or whole chromosomes (i.e., aneuploidy) have been studied extensively, much less is known about the genetic and functional effects of CNVs of differing sizes and structures. Here, we investigated Saccharomyces cerevisiae (yeast) strains that acquired adaptive CNVs of variable structures and copy numbers following experimental evolution in glutamine-limited chemostats. Although beneficial in the selective environment, CNVs result in decreased fitness compared with the euploid ancestor in rich media. We used transposon mutagenesis to investigate mutational tolerance and genome-wide genetic interactions in CNV strains. We find that CNVs increase mutational target size, confer increased mutational tolerance in amplified essential genes, and result in novel genetic interactions with unlinked genes. We validated a novel genetic interaction between different CNVs and BMH1 that was common to multiple strains. We also analyzed global gene expression and found that transcriptional dosage compensation does not affect most genes amplified by CNVs, although gene-specific transcriptional dosage compensation does occur for ∼12% of amplified genes. Furthermore, we find that CNV strains do not show previously described transcriptional signatures of aneuploidy. Our study reveals the extent to which local and global mutational tolerance is modified by CNVs with implications for genome evolution and CNV-associated diseases, such as cancer.
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Affiliation(s)
- Grace Avecilla
- Department of Biology, New York University, New York, New York 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Pieter Spealman
- Department of Biology, New York University, New York, New York 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Julia Matthews
- Department of Biology, New York University, New York, New York 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Elodie Caudal
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
- Institut Universitaire de France (IUF), 75231 Paris Cedex 05, France
| | - David Gresham
- Department of Biology, New York University, New York, New York 10003, USA;
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
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Kessi-Pérez EI, Acuña E, Bastías C, Fundora L, Villalobos-Cid M, Romero A, Khaiwal S, De Chiara M, Liti G, Salinas F, Martínez C. Single nucleotide polymorphisms associated with wine fermentation and adaptation to nitrogen limitation in wild and domesticated yeast strains. Biol Res 2023; 56:43. [PMID: 37507753 PMCID: PMC10385942 DOI: 10.1186/s40659-023-00453-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
For more than 20 years, Saccharomyces cerevisiae has served as a model organism for genetic studies and molecular biology, as well as a platform for biotechnology (e.g., wine production). One of the important ecological niches of this yeast that has been extensively studied is wine fermentation, a complex microbiological process in which S. cerevisiae faces various stresses such as limited availability of nitrogen. Nitrogen deficiencies in grape juice impair fermentation rate and yeast biomass production, leading to sluggish or stuck fermentations, resulting in considerable economic losses for the wine industry. In the present work, we took advantage of the "1002 Yeast Genomes Project" population, the most complete catalogue of the genetic variation in the species and a powerful resource for genotype-phenotype correlations, to study the adaptation to nitrogen limitation in wild and domesticated yeast strains in the context of wine fermentation. We found that wild and domesticated yeast strains have different adaptations to nitrogen limitation, corroborating their different evolutionary trajectories. Using a combination of state-of-the-art bioinformatic (GWAS) and molecular biology (CRISPR-Cas9) methodologies, we validated that PNP1, RRT5 and PDR12 are implicated in wine fermentation, where RRT5 and PDR12 are also involved in yeast adaptation to nitrogen limitation. In addition, we validated SNPs in these genes leading to differences in fermentative capacities and adaptation to nitrogen limitation. Altogether, the mapped genetic variants have potential applications for the genetic improvement of industrial yeast strains.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Eric Acuña
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Camila Bastías
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Leyanis Fundora
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Manuel Villalobos-Cid
- Departamento de Ingeniería Informática, Program for the Development of Sustainable Production Systems (PDSPS), Facultad de Ingeniería, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Andrés Romero
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sakshi Khaiwal
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | | | - Gianni Liti
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | - Francisco Salinas
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.
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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] [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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Lahiri P, Martin MS, Lino BR, Scheck RA, Van Deventer JA. Dual Noncanonical Amino Acid Incorporation Enabling Chemoselective Protein Modification at Two Distinct Sites in Yeast. Biochemistry 2023; 62:2098-2114. [PMID: 37377426 PMCID: PMC11146674 DOI: 10.1021/acs.biochem.2c00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Incorporation of more than one noncanonical amino acid (ncAA) within a single protein endows the resulting construct with multiple useful features such as augmented molecular recognition or covalent cross-linking capabilities. Herein, for the first time, we demonstrate the incorporation of two chemically distinct ncAAs into proteins biosynthesized in Saccharomyces cerevisiae. To complement ncAA incorporation in response to the amber (TAG) stop codon in yeast, we evaluated opal (TGA) stop codon suppression using three distinct orthogonal translation systems. We observed selective TGA readthrough without detectable cross-reactivity from host translation components. Readthrough efficiency at TGA was modulated by factors including the local nucleotide environment, gene deletions related to the translation process, and the identity of the suppressor tRNA. These observations facilitated systematic investigation of dual ncAA incorporation in both intracellular and yeast-displayed protein constructs, where we observed efficiencies up to 6% of wild-type protein controls. The successful display of doubly substituted proteins enabled the exploration of two critical applications on the yeast surface─(A) antigen binding functionality and (B) chemoselective modification with two distinct chemical probes through sequential application of two bioorthogonal click chemistry reactions. Lastly, by utilizing a soluble form of a doubly substituted construct, we validated the dual incorporation system using mass spectrometry and demonstrated the feasibility of conducting selective labeling of the two ncAAs sequentially using a "single-pot" approach. Overall, our work facilitates the addition of a 22nd amino acid to the genetic code of yeast and expands the scope of applications of ncAAs for basic biological research and drug discovery.
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Affiliation(s)
- Priyanka Lahiri
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Meghan S. Martin
- Chemistry Department, Tufts University, Medford, Massachusetts 02155, USA
| | - Briana R. Lino
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Rebecca A. Scheck
- Chemistry Department, Tufts University, Medford, Massachusetts 02155, USA
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
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Lewis GR, Marshall WF. Mitochondrial networks through the lens of mathematics. Phys Biol 2023; 20:051001. [PMID: 37290456 PMCID: PMC10347554 DOI: 10.1088/1478-3975/acdcdb] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/10/2023]
Abstract
Mitochondria serve a wide range of functions within cells, most notably via their production of ATP. Although their morphology is commonly described as bean-like, mitochondria often form interconnected networks within cells that exhibit dynamic restructuring through a variety of physical changes. Further, though relationships between form and function in biology are well established, the extant toolkit for understanding mitochondrial morphology is limited. Here, we emphasize new and established methods for quantitatively describing mitochondrial networks, ranging from unweighted graph-theoretic representations to multi-scale approaches from applied topology, in particular persistent homology. We also show fundamental relationships between mitochondrial networks, mathematics, and physics, using ideas of graph planarity and statistical mechanics to better understand the full possible morphological space of mitochondrial network structures. Lastly, we provide suggestions for how examination of mitochondrial network form through the language of mathematics can inform biological understanding, and vice versa.
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Affiliation(s)
- Greyson R Lewis
- Biophysics Graduate Program, University of California—San Francisco, San Francisco, CA, United States of America
- NSF Center for Cellular Construction, Department of Biochemistry and Biophysics, UCSF, 600 16th St., San Francisco, CA, United States of America
- Department of Biochemistry and Biophysics, Center for Cellular Construction, University of California San Francisco, San Francisco, CA, United States of America
| | - Wallace F Marshall
- NSF Center for Cellular Construction, Department of Biochemistry and Biophysics, UCSF, 600 16th St., San Francisco, CA, United States of America
- Department of Biochemistry and Biophysics, Center for Cellular Construction, University of California San Francisco, San Francisco, CA, United States of America
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36
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Hrach VL, King WR, Nelson LD, Conklin S, Pollock JA, Patton-Vogt J. The acyltransferase Gpc1 is both a target and an effector of the unfolded protein response in Saccharomyces cerevisiae. J Biol Chem 2023; 299:104884. [PMID: 37269946 PMCID: PMC10331479 DOI: 10.1016/j.jbc.2023.104884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023] Open
Abstract
The unfolded protein response (UPR) is sensitive to proteotoxic and membrane bilayer stress, both of which are sensed by the ER protein Ire1. When activated, Ire1 splices HAC1 mRNA, producing a transcription factor that targets genes involved in proteostasis and lipid metabolism, among others. The major membrane lipid phosphatidylcholine (PC) is subject to phospholipase-mediated deacylation, producing glycerophosphocholine (GPC), followed by reacylation of GPC through the PC deacylation/reacylation pathway (PC-DRP). The reacylation events occur via a two-step process catalyzed first by the GPC acyltransferase Gpc1, followed by acylation of the lyso-PC molecule by Ale1. However, whether Gpc1 is critical for ER bilayer homeostasis is unclear. Using an improved method for C14-choline-GPC radiolabeling, we first show that loss of Gpc1 results in abrogation of PC synthesis through PC-DRP and that Gpc1 colocalizes with the ER. We then probe the role of Gpc1 as both a target and an effector of the UPR. Exposure to the UPR-inducing compounds tunicamycin, DTT, and canavanine results in a Hac1-dependent increase in GPC1 message. Further, cells lacking Gpc1 exhibit increased sensitivity to those proteotoxic stressors. Inositol limitation, known to induce the UPR via bilayer stress, also induces GPC1 expression. Finally, we show that loss of GPC1 induces the UPR. A gpc1Δ mutant displays upregulation of the UPR in strains expressing a mutant form of Ire1 that is unresponsive to unfolded proteins, indicating that bilayer stress is responsible for the observed upregulation. Collectively, our data indicate an important role for Gpc1 in yeast ER bilayer homeostasis.
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Affiliation(s)
- Victoria Lee Hrach
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - William R King
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Laura D Nelson
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Shane Conklin
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - John A Pollock
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA.
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Marmiroli M, Birarda G, Gallo V, Villani M, Zappettini A, Vaccari L, Marmiroli N, Pagano L. Cadmium Sulfide Quantum Dots, Mitochondrial Function and Environmental Stress: A Mechanistic Reconstruction through In Vivo Cellular Approaches in Saccharomyces cerevisiae. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1944. [PMID: 37446460 DOI: 10.3390/nano13131944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023]
Abstract
Research on the effects of engineered nanomaterials (ENMs) on mitochondria, which represent one of the main actors in cell function, highlighted effects on ROS production, gametogenesis and organellar genome replication. Specifically, the mitochondrial effects of cadmium sulfide quantum dots (CdS QDs) exposure can be observed through the variation in enzymatic kinetics at the level of the respiratory chain and also by analyzing modifications of reagent and products in term of the bonds created and disrupted during the reactions through Fourier-transform infrared spectroscopy (FTIR). This study investigated both in intact cells and in isolated mitochondria to observe the response to CdS QDs treatment at the level of electron transport chain in the wild-type yeast Saccharomyces cerevisiae and in the deletion mutant Δtom5, whose function is implicated in nucleo-mitochondrial protein trafficking. The changes observed in wild type and Δtom5 strains in terms of an increase or decrease in enzymatic activity (ranging between 1 and 2 folds) also differed according to the genetic background of the strains and the respiratory chain functionality during the CdS QDs treatment performed. Results were confirmed by FTIR, where a clear difference between the QD effects in the wild type and in the mutant strain, Δtom5, was observed. The utilization of these genetic and biochemical approaches is instrumental to clarify the mitochondrial mechanisms implicated in response to these types of ENMs and to the stress response that follows the exposure.
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Affiliation(s)
- Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Giovanni Birarda
- Elettra, Sincrotrone Trieste, Strada Statale 14-km 163.5 in AREA Science Park, Basovizza, 34149 Trieste, Italy
| | - Valentina Gallo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marco Villani
- Istituto dei Materiali per l'Elettronica e il Magnetismo, Consiglio Nazionale delle Ricerche (IMEM-CNR), 43124 Parma, Italy
| | - Andrea Zappettini
- Istituto dei Materiali per l'Elettronica e il Magnetismo, Consiglio Nazionale delle Ricerche (IMEM-CNR), 43124 Parma, Italy
| | - Lisa Vaccari
- Elettra, Sincrotrone Trieste, Strada Statale 14-km 163.5 in AREA Science Park, Basovizza, 34149 Trieste, Italy
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Consorzio Interuniversitario Nazionale per le Scienze Ambientali (CINSA), University of Parma, 43124 Parma, Italy
| | - Luca Pagano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Consorzio Interuniversitario Nazionale per le Scienze Ambientali (CINSA), University of Parma, 43124 Parma, Italy
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38
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Recio PS, Mitra NJ, Shively CA, Song D, Jaramillo G, Lewis KS, Chen X, Mitra R. Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode. Nucleic Acids Res 2023; 51:5006-5021. [PMID: 37125648 PMCID: PMC10250231 DOI: 10.1093/nar/gkad320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 05/02/2023] Open
Abstract
Gene expression changes are orchestrated by transcription factors (TFs), which bind to DNA to regulate gene expression. It remains surprisingly difficult to predict basic features of the transcriptional process, including in vivo TF occupancy. Existing thermodynamic models of TF function are often not concordant with experimental measurements, suggesting undiscovered biology. Here, we analyzed one of the most well-studied TFs, the yeast zinc cluster Gal4, constructed a Shea-Ackers thermodynamic model to describe its binding, and compared the results of this model to experimentally measured Gal4p binding in vivo. We found that at many promoters, the model predicted no Gal4p binding, yet substantial binding was observed. These outlier promoters lacked canonical binding motifs, and subsequent investigation revealed Gal4p binds unexpectedly to DNA sequences with high densities of its half site (CGG). We confirmed this novel mode of binding through multiple experimental and computational paradigms; we also found most other zinc cluster TFs we tested frequently utilize this binding mode, at 27% of their targets on average. Together, these results demonstrate a novel mode of binding where zinc clusters, the largest class of TFs in yeast, bind DNA sequences with high densities of half sites.
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Affiliation(s)
- Pamela S Recio
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Nikhil J Mitra
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Christian A Shively
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - David Song
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Grace Jaramillo
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Kristine Shady Lewis
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Xuhua Chen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
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39
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Turco G, Chang C, Wang RY, Kim G, Stoops EH, Richardson B, Sochat V, Rust J, Oughtred R, Thayer N, Kang F, Livstone MS, Heinicke S, Schroeder M, Dolinski KJ, Botstein D, Baryshnikova A. Global analysis of the yeast knockout phenome. SCIENCE ADVANCES 2023; 9:eadg5702. [PMID: 37235661 DOI: 10.1126/sciadv.adg5702] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Genome-wide phenotypic screens in the budding yeast Saccharomyces cerevisiae, enabled by its knockout collection, have produced the largest, richest, and most systematic phenotypic description of any organism. However, integrative analyses of this rich data source have been virtually impossible because of the lack of a central data repository and consistent metadata annotations. Here, we describe the aggregation, harmonization, and analysis of ~14,500 yeast knockout screens, which we call Yeast Phenome. Using this unique dataset, we characterized two unknown genes (YHR045W and YGL117W) and showed that tryptophan starvation is a by-product of many chemical treatments. Furthermore, we uncovered an exponential relationship between phenotypic similarity and intergenic distance, which suggests that gene positions in both yeast and human genomes are optimized for function.
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Affiliation(s)
- Gina Turco
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Christie Chang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | | | - Griffin Kim
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Brianna Richardson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Vanessa Sochat
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Rust
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Rose Oughtred
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | | | - Fan Kang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Michael S Livstone
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Sven Heinicke
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Mark Schroeder
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kara J Dolinski
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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40
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Hara Y, Kuraku S. The impact of local genomic properties on the evolutionary fate of genes. eLife 2023; 12:82290. [PMID: 37223962 DOI: 10.7554/elife.82290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Functionally indispensable genes are likely to be retained and otherwise to be lost during evolution. This evolutionary fate of a gene can also be affected by factors independent of gene dispensability, including the mutability of genomic positions, but such features have not been examined well. To uncover the genomic features associated with gene loss, we investigated the characteristics of genomic regions where genes have been independently lost in multiple lineages. With a comprehensive scan of gene phylogenies of vertebrates with a careful inspection of evolutionary gene losses, we identified 813 human genes whose orthologs were lost in multiple mammalian lineages: designated 'elusive genes.' These elusive genes were located in genomic regions with rapid nucleotide substitution, high GC content, and high gene density. A comparison of the orthologous regions of such elusive genes across vertebrates revealed that these features had been established before the radiation of the extant vertebrates approximately 500 million years ago. The association of human elusive genes with transcriptomic and epigenomic characteristics illuminated that the genomic regions containing such genes were subject to repressive transcriptional regulation. Thus, the heterogeneous genomic features driving gene fates toward loss have been in place and may sometimes have relaxed the functional indispensability of such genes. This study sheds light on the complex interplay between gene function and local genomic properties in shaping gene evolution that has persisted since the vertebrate ancestor.
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Affiliation(s)
- Yuichiro Hara
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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41
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Weller CA, Andreev I, Chambers MJ, Park M, Bloom JS, Sadhu MJ. Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity. Genome Res 2023; 33:729-740. [PMID: 37127330 PMCID: PMC10317115 DOI: 10.1101/gr.277515.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
Understanding the genetic causes of trait variation is a primary goal of genetic research. One way that individuals can vary genetically is through variable pangenomic genes: genes that are only present in some individuals in a population. The presence or absence of entire genes could have large effects on trait variation. However, variable pangenomic genes can be missed in standard genotyping workflows, owing to reliance on aligning short-read sequencing to reference genomes. A popular method for studying the genetic basis of trait variation is linkage mapping, which identifies quantitative trait loci (QTLs), regions of the genome that harbor causative genetic variants. Large-scale linkage mapping in the budding yeast Saccharomyces cerevisiae has found thousands of QTLs affecting myriad yeast phenotypes. To enable the resolution of QTLs caused by variable pangenomic genes, we used long-read sequencing to generate highly complete de novo genome assemblies of 16 diverse yeast isolates. With these assemblies, we resolved QTLs for growth on maltose, sucrose, raffinose, and oxidative stress to specific genes that are absent from the reference genome but present in the broader yeast population at appreciable frequency. Copies of genes also duplicate onto chromosomes where they are absent in the reference genome, and we found that these copies generate additional QTLs whose resolution requires pangenome characterization. Our findings show the need for highly complete genome assemblies to identify the genetic basis of trait variation.
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Affiliation(s)
- Cory A Weller
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ilya Andreev
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael J Chambers
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Morgan Park
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Joshua S Bloom
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
- Institute for Quantitative and Computational Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Meru J Sadhu
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
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42
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Messner CB, Demichev V, Muenzner J, Aulakh SK, Barthel N, Röhl A, Herrera-Domínguez L, Egger AS, Kamrad S, Hou J, Tan G, Lemke O, Calvani E, Szyrwiel L, Mülleder M, Lilley KS, Boone C, Kustatscher G, Ralser M. The proteomic landscape of genome-wide genetic perturbations. Cell 2023; 186:2018-2034.e21. [PMID: 37080200 PMCID: PMC7615649 DOI: 10.1016/j.cell.2023.03.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 01/20/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Functional genomic strategies have become fundamental for annotating gene function and regulatory networks. Here, we combined functional genomics with proteomics by quantifying protein abundances in a genome-scale knockout library in Saccharomyces cerevisiae, using data-independent acquisition mass spectrometry. We find that global protein expression is driven by a complex interplay of (1) general biological properties, including translation rate, protein turnover, the formation of protein complexes, growth rate, and genome architecture, followed by (2) functional properties, such as the connectivity of a protein in genetic, metabolic, and physical interaction networks. Moreover, we show that functional proteomics complements current gene annotation strategies through the assessment of proteome profile similarity, protein covariation, and reverse proteome profiling. Thus, our study reveals principles that govern protein expression and provides a genome-spanning resource for functional annotation.
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Affiliation(s)
- Christoph B Messner
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland
| | - Vadim Demichev
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QW, UK
| | - Julia Muenzner
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Simran K Aulakh
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Natalie Barthel
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Annika Röhl
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | | | - Anna-Sophia Egger
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Stephan Kamrad
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Jing Hou
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Guihong Tan
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Oliver Lemke
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Enrica Calvani
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Lukasz Szyrwiel
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Michael Mülleder
- Charité Universitätsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, Germany
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QW, UK
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S3E1, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada; RIKEN Center for Sustainable Resource Science, Wako, 351-0198 Saitama, Japan
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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43
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Chen N, Yang S, You D, Shen J, Ruan B, Wu M, Zhang J, Luo X, Tang H. Systematic genetic modifications of cell wall biosynthesis enhanced the secretion and surface-display of polysaccharide degrading enzymes in Saccharomyces cerevisiae. Metab Eng 2023; 77:273-282. [PMID: 37100192 DOI: 10.1016/j.ymben.2023.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/31/2023] [Accepted: 04/15/2023] [Indexed: 04/28/2023]
Abstract
Saccharomyces cerevisiae is a robust cell factory to secrete or surface-display cellulase and amylase for the conversion of agricultural residues into valuable chemicals. Engineering the secretory pathway is a well-known strategy for overproducing these enzymes. Although cell wall biosynthesis can be tightly linked to the secretory pathway by regulation of all involved processes, the effect of its modifications on protein production has not been extensively studied. In this study, we systematically studied the effect of engineering cell wall biosynthesis on the activity of cellulolytic enzyme β-glucosidase (BGL1) by comparing seventy-nine gene knockout S. cerevisiae strains and newly identified that inactivation of DFG5, YPK1, FYV5, CCW12 and KRE1 obviously improved BGL1 secretion and surface-display. Combinatorial modifications of these genes, particularly double deletion of FVY5 and CCW12, along with the use of rich medium, increased the activity of secreted and surface-displayed BGL1 by 6.13-fold and 7.99-fold, respectively. Additionally, we applied this strategy to improve the activity of the cellulolytic cellobiohydrolase and amylolytic α-amylase. Through proteomic analysis coupled with reverse engineering, we found that in addition to the secretory pathway, regulation of translation processes may also involve in improving enzyme activity by engineering cell wall biosynthesis. Our work provides new insight into the construction of a yeast cell factory for efficient production of polysaccharide degrading enzymes.
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Affiliation(s)
- Nanzhu Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shuo Yang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology, 3501 Daxue Road, Jinan, 250353, China
| | - Dawei You
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Junfeng Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Banlai Ruan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Mei Wu
- Synceres Biosciences (Shenzhen) Co., Ltd, Nanshan Medical Device Industrial Park, Nanhai Avenue, Shenzhen, 518067, China
| | - Jianzhi Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Hongting Tang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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44
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Wang L, Tonsager AJ, Zheng W, Wang Y, Stessman D, Fang W, Stenback KE, Campbell A, Tanvir R, Zhang J, Cothron S, Wan D, Meng Y, Spalding MH, Nikolau BJ, Li L. Single-cell genetic models to evaluate orphan gene function: The case of QQS regulating carbon and nitrogen allocation. FRONTIERS IN PLANT SCIENCE 2023; 14:1126139. [PMID: 37051080 PMCID: PMC10084940 DOI: 10.3389/fpls.2023.1126139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
We demonstrate two synthetic single-cell systems that can be used to better understand how the acquisition of an orphan gene can affect complex phenotypes. The Arabidopsis orphan gene, Qua-Quine Starch (QQS) has been identified as a regulator of carbon (C) and nitrogen (N) partitioning across multiple plant species. QQS modulates this important biotechnological trait by replacing NF-YB (Nuclear Factor Y, subunit B) in its interaction with NF-YC. In this study, we expand on these prior findings by developing Chlamydomonas reinhardtii and Saccharomyces cerevisiae strains, to refactor the functional interactions between QQS and NF-Y subunits to affect modulations in C and N allocation. Expression of QQS in C. reinhardtii modulates C (i.e., starch) and N (i.e., protein) allocation by affecting interactions between NF-YC and NF-YB subunits. Studies in S. cerevisiae revealed similar functional interactions between QQS and the NF-YC homolog (HAP5), modulating C (i.e., glycogen) and N (i.e., protein) allocation. However, in S. cerevisiae both the NF-YA (HAP2) and NF-YB (HAP3) homologs appear to have redundant functions to enable QQS and HAP5 to affect C and N allocation. The genetically tractable systems that developed herein exhibit the plasticity to modulate highly complex phenotypes.
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Affiliation(s)
- Lei Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Andrew J. Tonsager
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Wenguang Zheng
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Yingjun Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Dan Stessman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Wei Fang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Kenna E. Stenback
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Alexis Campbell
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Rezwan Tanvir
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Jinjiang Zhang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
- Mississippi School for Mathematics and Science, Columbus, MS, United States
| | - Samuel Cothron
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Dongli Wan
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yan Meng
- Department of Agriculture, Alcorn State University, Lorman, MS, United States
| | - Martin H. Spalding
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Basil J. Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
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45
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Lang O, Srivastava D, Pugh BF, Lai WK. GenoPipe: identifying the genotype of origin within (epi)genomic datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532660. [PMID: 36993164 PMCID: PMC10055126 DOI: 10.1101/2023.03.14.532660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Confidence in experimental results is critical for discovery. As the scale of data generation in genomics has grown exponentially, experimental error has likely kept pace despite the best efforts of many laboratories. Technical mistakes can and do occur at nearly every stage of a genomics assay (i.e., cell line contamination, reagent swapping, tube mislabelling, etc.) and are often difficult to identify post-execution. However, the DNA sequenced in genomic experiments contains certain markers (e.g., indels) encoded within and can often be ascertained forensically from experimental datasets. We developed the Genotype validation Pipeline (GenoPipe), a suite of heuristic tools that operate together directly on raw and aligned sequencing data from individual high-throughput sequencing experiments to characterize the underlying genome of the source material. We demonstrate how GenoPipe validates and rescues erroneously annotated experiments by identifying unique markers inherent to an organism’s genome (i.e., epitope insertions, gene deletions, and SNPs).
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46
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Daraghmi MM, Miller JM, Bailey CG, Doss EM, Kalinski AL, Smaldino PJ, Rubenstein EM. Macro-ER-phagy receptors Atg39p and Atg40p confer resistance to aminoglycoside hygromycin B in S. cerevisiae. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000738. [PMID: 36818312 PMCID: PMC9932795 DOI: 10.17912/micropub.biology.000738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/24/2023]
Abstract
Receptor-mediated autophagic turnover of portions of the endoplasmic reticulum (ER) is mediated by macro-ER-phagy. We hypothesized macro-ER-phagy promotes proteotoxic stress resistance. We predicted Saccharomyces cerevisiae lacking macro-ER-phagy receptors would exhibit enhanced sensitivity to hygromycin B, which reduces translational fidelity and is expected to globally disrupt protein homeostasis, including at the ER. We observed that loss of either of two yeast macro-ER-phagy receptors (Atg39p or Atg40p) compromised cellular resistance to hygromycin B to a similar extent as loss of ER-associated degradation (ERAD) ubiquitin ligases Hrd1p and Doa10p. Our data are consistent with a model whereby macro-ER-phagy and ERAD collaborate to mediate ER protein quality control. Disruptions of macro-ER-phagy have been linked to neuropathy, dementia, and cancer. A dampened capacity to mediate protein quality control may contribute to these conditions.
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Affiliation(s)
| | | | | | | | | | | | - Eric M. Rubenstein
- Department of Biology, Ball State University
,
Correspondence to: Eric M. Rubenstein (
)
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47
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Li B, Zeis P, Zhang Y, Alekseenko A, Fürst E, Sanchez YP, Lin G, Tekkedil MM, Piazza I, Steinmetz LM, Pelechano V. Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation. Nat Commun 2023; 14:910. [PMID: 36801853 PMCID: PMC9936472 DOI: 10.1038/s41467-023-36586-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Chromatin organization has been shown to play a role in the faster response of primed cells. However, the contribution of post-transcriptional regulation is not yet explored. Here we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose. We find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. Our work shows that gene-specific differences in intrinsic nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that primed cells present altered levels of RNA degradation machinery and that both nuclear and cytoplasmic mRNA decay modulate transcriptional memory. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.
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Affiliation(s)
- Bingnan Li
- Department of Diagnostics, Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Patrice Zeis
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Yujie Zhang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Alisa Alekseenko
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Eliska Fürst
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Yerma Pareja Sanchez
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Gen Lin
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,AbbVie Pte Ltd, Singapore, Singapore
| | - Manu M Tekkedil
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
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48
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Brown JI, Alibhai J, Zhu E, Frankel A. Methylarginine efflux in nutrient-deprived yeast mitigates disruption of nitric oxide synthesis. Amino Acids 2023; 55:215-233. [PMID: 36454288 DOI: 10.1007/s00726-022-03220-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022]
Abstract
Protein arginine N-methyltransferases (PRMTs) have emerged as important actors in the eukaryotic stress response with implications in human disease, aging, and cell signaling. Intracellular free methylarginines contribute to cellular stress through their interaction with nitric oxide synthase (NOS). The arginine-dependent production of nitric oxide (NO), which is strongly inhibited by methylarginines, serves as a protective small molecule against oxidative stress in eukaryotic cells. NO signaling is highly conserved between higher and lower eukaryotes, although a canonical NOS homologue has yet to be identified in yeast. Since stress signaling pathways are well conserved among eukaryotes, yeast is an ideal model organism to study the implications of PRMTs and methylarginines during stress. We sought to explore the roles and fates of methylarginines in Saccharomyces cerevisiae. We starved methyltransferase-, autophagy-, and permease-related yeast knockouts by incubating them in water and monitored methylarginine production. We found that under starvation, methylarginines are expelled from yeast cells. We found that autophagy-deficient cells have an impaired ability to efflux methylarginines, which suggests that methylarginine-containing proteins are degraded via autophagy. For the first time, we determine that yeast take up methylarginines less readily than arginine, and we show that methylarginines impact yeast NO production. This study reveals that yeast circumvent a potential methylarginine toxicity by expelling them after autophagic degradation of arginine-modified proteins.
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Affiliation(s)
- Jennifer I Brown
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Jenah Alibhai
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Erica Zhu
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.
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49
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Žun G, Doberšek K, Petrovič U. Construction and evaluation of gRNA arrays for multiplex CRISPR-Cas9. Yeast 2023; 40:32-41. [PMID: 36536407 PMCID: PMC10107897 DOI: 10.1002/yea.3833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 11/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Endonuclease system CRISPR-Cas9 represents a powerful toolbox for the budding yeast's Saccharomyces cerevisiae genome perturbation. The resulting double-strand breaks are preferentially repaired via highly efficient homologous recombination, which subsequently leads to marker-free genome editing. The goal of this study was to evaluate precise targeting of multiple loci simultaneously. To construct an array of independently expressing guide RNAs (gRNAs), the genes encoding them were assembled through a BioBrick construction procedure. We designed a multiplex CRISPR-Cas9 system for targeting 6 marker genes, whereby the gRNA array was expressed from a single plasmid. To evaluate the performance of the gRNA array, the activity of the designed system was assessed by the success rate of the introduction of perturbations within the target loci: successful gRNA expression, followed by target DNA double-strand breaks formation and their repair by homologous recombination led to premature termination of the coding sequence of the marker genes, resulting in the prevention of growth of the transformants on the corresponding selection media. In conclusion, we successfully introduced up to five simultaneous perturbations within single cells of yeast S. cerevisiae using the multiplex CRISPR-Cas9 system. While this has been done before, we here present an alternative sequential BioBrick assembly with the capability to accommodate many highly similar gRNA-expression cassettes, and an exhaustive evaluation of their performance.
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Affiliation(s)
- Gašper Žun
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Katja Doberšek
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaLjubljanaSlovenia
| | - Uroš Petrovič
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
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50
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Holland K, Blazeck J. High throughput mutagenesis and screening for yeast engineering. J Biol Eng 2022; 16:37. [PMID: 36575525 PMCID: PMC9793380 DOI: 10.1186/s13036-022-00315-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/03/2022] [Indexed: 12/28/2022] Open
Abstract
The eukaryotic yeast Saccharomyces cerevisiae is a model host utilized for whole cell biocatalytic conversions, protein evolution, and scientific inquiries into the pathogenesis of human disease. Over the past decade, the scale and pace of such studies has drastically increased alongside the advent of novel tools for both genome-wide studies and targeted genetic mutagenesis. In this review, we will detail past and present (e.g., CRISPR/Cas) genome-scale screening platforms, typically employed in the context of growth-based selections for improved whole cell phenotype or for mechanistic interrogations. We will further highlight recent advances that enable the rapid and often continuous evolution of biomolecules with improved function. Additionally, we will detail the corresponding advances in high throughput selection and screening strategies that are essential for assessing or isolating cellular and protein improvements. Finally, we will describe how future developments can continue to advance yeast high throughput engineering.
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Affiliation(s)
- Kendreze Holland
- grid.213917.f0000 0001 2097 4943Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia USA ,grid.213917.f0000 0001 2097 4943Bioengineering Program, Georgia Institute of Technology, Atlanta, Georgia USA
| | - John Blazeck
- grid.213917.f0000 0001 2097 4943Bioengineering Program, Georgia Institute of Technology, Atlanta, Georgia USA ,grid.213917.f0000 0001 2097 4943School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia USA
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