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Jacobus AP, Cavassana SD, de Oliveira II, Barreto JA, Rohwedder E, Frazzon J, Basso TP, Basso LC, Gross J. Optimal trade-off between boosted tolerance and growth fitness during adaptive evolution of yeast to ethanol shocks. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:63. [PMID: 38730312 PMCID: PMC11088041 DOI: 10.1186/s13068-024-02503-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/05/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND The selection of Saccharomyces cerevisiae strains with higher alcohol tolerance can potentially increase the industrial production of ethanol fuel. However, the design of selection protocols to obtain bioethanol yeasts with higher alcohol tolerance poses the challenge of improving industrial strains that are already robust to high ethanol levels. Furthermore, yeasts subjected to mutagenesis and selection, or laboratory evolution, often present adaptation trade-offs wherein higher stress tolerance is attained at the expense of growth and fermentation performance. Although these undesirable side effects are often associated with acute selection regimes, the utility of using harsh ethanol treatments to obtain robust ethanologenic yeasts still has not been fully investigated. RESULTS We conducted an adaptive laboratory evolution by challenging four populations (P1-P4) of the Brazilian bioethanol yeast, Saccharomyces cerevisiae PE-2_H4, through 68-82 cycles of 2-h ethanol shocks (19-30% v/v) and outgrowths. Colonies isolated from the final evolved populations (P1c-P4c) were subjected to whole-genome sequencing, revealing mutations in genes enriched for the cAMP/PKA and trehalose degradation pathways. Fitness analyses of the isolated clones P1c-P3c and reverse-engineered strains demonstrated that mutations were primarily selected for cell viability under ethanol stress, at the cost of decreased growth rates in cultures with or without ethanol. Under this selection regime for stress survival, the population P4 evolved a protective snowflake phenotype resulting from BUD3 disruption. Despite marked adaptation trade-offs, the combination of reverse-engineered mutations cyr1A1474T/usv1Δ conferred 5.46% higher fitness than the parental PE-2_H4 for propagation in 8% (v/v) ethanol, with only a 1.07% fitness cost in a culture medium without alcohol. The cyr1A1474T/usv1Δ strain and evolved P1c displayed robust fermentations of sugarcane molasses using cell recycling and sulfuric acid treatments, mimicking Brazilian bioethanol production. CONCLUSIONS Our study combined genomic, mutational, and fitness analyses to understand the genetic underpinnings of yeast evolution to ethanol shocks. Although fitness analyses revealed that most evolved mutations impose a cost for cell propagation, combination of key mutations cyr1A1474T/usv1Δ endowed yeasts with higher tolerance for growth in the presence of ethanol. Moreover, alleles selected for acute stress survival comprising the P1c genotype conferred stress tolerance and optimal performance under conditions simulating the Brazilian industrial ethanol production.
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Affiliation(s)
- Ana Paula Jacobus
- Bioenergy Research Institute, São Paulo State University, Rio Claro, Brazil
- SENAI Innovation Institute for Biotechnology, São Paulo, Brazil
| | | | | | | | - Ewerton Rohwedder
- Biological Science Department, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Jeverson Frazzon
- Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Thalita Peixoto Basso
- Department of Agri-Food Industry, Food and Nutrition, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Luiz Carlos Basso
- Biological Science Department, "Luiz de Queiroz" College of Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Jeferson Gross
- Bioenergy Research Institute, São Paulo State University, Rio Claro, Brazil.
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2
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Neagu AN, Bruno P, Johnson KR, Ballestas G, Darie CC. Biological Basis of Breast Cancer-Related Disparities in Precision Oncology Era. Int J Mol Sci 2024; 25:4113. [PMID: 38612922 PMCID: PMC11012526 DOI: 10.3390/ijms25074113] [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: 03/03/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Precision oncology is based on deep knowledge of the molecular profile of tumors, allowing for more accurate and personalized therapy for specific groups of patients who are different in disease susceptibility as well as treatment response. Thus, onco-breastomics is able to discover novel biomarkers that have been found to have racial and ethnic differences, among other types of disparities such as chronological or biological age-, sex/gender- or environmental-related ones. Usually, evidence suggests that breast cancer (BC) disparities are due to ethnicity, aging rate, socioeconomic position, environmental or chemical exposures, psycho-social stressors, comorbidities, Western lifestyle, poverty and rurality, or organizational and health care system factors or access. The aim of this review was to deepen the understanding of BC-related disparities, mainly from a biomedical perspective, which includes genomic-based differences, disparities in breast tumor biology and developmental biology, differences in breast tumors' immune and metabolic landscapes, ecological factors involved in these disparities as well as microbiomics- and metagenomics-based disparities in BC. We can conclude that onco-breastomics, in principle, based on genomics, proteomics, epigenomics, hormonomics, metabolomics and exposomics data, is able to characterize the multiple biological processes and molecular pathways involved in BC disparities, clarifying the differences in incidence, mortality and treatment response for different groups of BC patients.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iași, Carol I bvd. 20A, 700505 Iasi, Romania
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Kaya R Johnson
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Gabriella Ballestas
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY 13699-5810, USA
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3
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Piguet B, Houseley J. Transcription as source of genetic heterogeneity in budding yeast. Yeast 2024; 41:171-185. [PMID: 38196235 DOI: 10.1002/yea.3926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/10/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
Transcription presents challenges to genome stability both directly, by altering genome topology and exposing single-stranded DNA to chemical insults and nucleases, and indirectly by introducing obstacles to the DNA replication machinery. Such obstacles include the RNA polymerase holoenzyme itself, DNA-bound regulatory factors, G-quadruplexes and RNA-DNA hybrid structures known as R-loops. Here, we review the detrimental impacts of transcription on genome stability in budding yeast, as well as the mitigating effects of transcription-coupled nucleotide excision repair and of systems that maintain DNA replication fork processivity and integrity. Interactions between DNA replication and transcription have particular potential to induce mutation and structural variation, but we conclude that such interactions must have only minor effects on DNA replication by the replisome with little if any direct mutagenic outcome. However, transcription can significantly impair the fidelity of replication fork rescue mechanisms, particularly Break Induced Replication, which is used to restart collapsed replication forks when other means fail. This leads to de novo mutations, structural variation and extrachromosomal circular DNA formation that contribute to genetic heterogeneity, but only under particular conditions and in particular genetic contexts, ensuring that the bulk of the genome remains extremely stable despite the seemingly frequent interactions between transcription and DNA replication.
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4
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Schreurs M, Piampongsant S, Roncoroni M, Cool L, Herrera-Malaver B, Vanderaa C, Theßeling FA, Kreft Ł, Botzki A, Malcorps P, Daenen L, Wenseleers T, Verstrepen KJ. Predicting and improving complex beer flavor through machine learning. Nat Commun 2024; 15:2368. [PMID: 38531860 DOI: 10.1038/s41467-024-46346-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/21/2024] [Indexed: 03/28/2024] Open
Abstract
The perception and appreciation of food flavor depends on many interacting chemical compounds and external factors, and therefore proves challenging to understand and predict. Here, we combine extensive chemical and sensory analyses of 250 different beers to train machine learning models that allow predicting flavor and consumer appreciation. For each beer, we measure over 200 chemical properties, perform quantitative descriptive sensory analysis with a trained tasting panel and map data from over 180,000 consumer reviews to train 10 different machine learning models. The best-performing algorithm, Gradient Boosting, yields models that significantly outperform predictions based on conventional statistics and accurately predict complex food features and consumer appreciation from chemical profiles. Model dissection allows identifying specific and unexpected compounds as drivers of beer flavor and appreciation. Adding these compounds results in variants of commercial alcoholic and non-alcoholic beers with improved consumer appreciation. Together, our study reveals how big data and machine learning uncover complex links between food chemistry, flavor and consumer perception, and lays the foundation to develop novel, tailored foods with superior flavors.
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Affiliation(s)
- Michiel Schreurs
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, B-3001, Leuven, Belgium
| | - Supinya Piampongsant
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, B-3001, Leuven, Belgium
| | - Miguel Roncoroni
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, B-3001, Leuven, Belgium
| | - Lloyd Cool
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, B-3001, Leuven, Belgium
- Laboratory of Socioecology and Social Evolution, KU Leuven, Naamsestraat 59, B-3000, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, B-3001, Leuven, Belgium
| | - Christophe Vanderaa
- Laboratory of Socioecology and Social Evolution, KU Leuven, Naamsestraat 59, B-3000, Leuven, Belgium
| | - Florian A Theßeling
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001, Leuven, Belgium
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, B-3001, Leuven, Belgium
| | - Łukasz Kreft
- VIB Bioinformatics Core, VIB, Rijvisschestraat 120, B-9052, Ghent, Belgium
| | - Alexander Botzki
- VIB Bioinformatics Core, VIB, Rijvisschestraat 120, B-9052, Ghent, Belgium
| | | | - Luk Daenen
- AB InBev SA/NV, Brouwerijplein 1, B-3000, Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, KU Leuven, Naamsestraat 59, B-3000, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, B-3001, Leuven, Belgium.
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Gaston Geenslaan 1, B-3001, Leuven, Belgium.
- Leuven Institute for Beer Research (LIBR), Gaston Geenslaan 1, B-3001, Leuven, Belgium.
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5
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Yang T, Zhang S, Pan Y, Li X, Liu G, Sun H, Zhang R, Zhang C. Breeding of high-tolerance yeast by adaptive evolution and high-gravity brewing of mutant. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:686-697. [PMID: 37654243 DOI: 10.1002/jsfa.12959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/13/2023] [Accepted: 09/01/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Ethanol and osmotic stresses are the major limiting factors for brewing strong beer with high-gravity wort. Breeding of yeast strains with high osmotic and ethanol tolerance and studying very-high-gravity (VHG) brewing technology is of great significance for brewing strong beer. RESULTS This study used an optimized microbial microdroplet culture (MMC) system for adaptive laboratory evolution (ALE) of Saccharomyces cerevisiae YN81 to improve its tolerance to osmotic and ethanol stress. Meanwhile, we investigated the VHG and VHG with added ethanol (VHGAE) brewing processes for the evolved mutants in brewing strong beer. The results showed that three evolved mutants were obtained; among them, the growth performance of YN81mc-8.3 under 300, 340, 380, 420 and 460 g L-1 sucrose stresses was greater than that of the other strains. The ethanol tolerance of YN81mc-8.3 was 12%, which was 20% higher than that of YN81. During strong-beer brewing in a 100 L cylindrical cone-bottom tank, the sugar utilization and ethanol yield of YN81mc-8.3 outperformed those of YN81 in both the VHG and VHGAE brewing processes. Measurement of the diacetyl concentration showed that YN81mc-8.3 had a stronger diacetyl reduction ability; in particular, the real degree of fermentation of beers brewed by YN81mc-8.3 in VHG and VHGAE brewing processes was 75.35% and 66.71%, respectively - higher than those of the two samples brewed by YN81. Meanwhile, the visual, olfactive and gustative properties of the strong beer produced by YN81mc-8.3 were better than those of the other beers. CONCLUSION In this study, the mutant YN81mc-8.3 and the VHGAE brewing process were optimal and represented a better alternative strong-beer brewing process. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Tianyou Yang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Shishuang Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- College of Geology and Environment, Xi'an University of Science and Technology, Xi'an, China
| | - Yuru Pan
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Xu Li
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Gaifeng Liu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Haiyan Sun
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Rongxian Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Chaohui Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
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6
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Smenderovac E, Emilson C, Rheault K, Brazeau É, Morency MJ, Gagné P, Venier L, Martineau C. Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study. Sci Rep 2024; 14:1725. [PMID: 38242898 PMCID: PMC10798986 DOI: 10.1038/s41598-023-50541-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024] Open
Abstract
Soil sampling for environmental DNA in remote and semi-remote locations is often limited due to logistical constraints surrounding sample preservation, including no or limited access to a freezer. Freezing at - 20 °C is a common DNA preservation strategy, however, other methods such as desiccation, ethanol or commercial preservatives are available as potential alternative DNA preservation methods for room temperature storage. In this study, we assessed five preservation methods (CD1 solution, 95% Ethanol, Dry & Dry silica gel packs, RNAlater, LifeGuard) along with freezing at - 20 °C, against immediate extraction on organic and mineral soils for up to three weeks of preservation. We assessed direct effects on DNA concentration and quality, and used DNA metabarcoding to assess effects on bacterial and fungal communities. Drying with Dry & Dry led to no significant differences from immediate extraction. RNAlater led to lower DNA concentrations, but effects on community structures were comparable to freezing. CD1, LifeGuard and Ethanol either caused immediate significant shifts in community structure, degradation of DNA quality or changes in diversity metrics. Overall, our study supports the use of drying with silica gel packs as a cost-effective, and easily applied method for the short-term storage at room temperature for DNA-based microbial community analyses.
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Affiliation(s)
| | - Caroline Emilson
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | - Karelle Rheault
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | - Élodie Brazeau
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | | | - Patrick Gagné
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | - Lisa Venier
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
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7
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Porcher L, Vijayraghavan S, McCollum J, Mieczkowski PA, Saini N. Multiple DNA repair pathways prevent acetaldehyde-induced mutagenesis in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574575. [PMID: 38260495 PMCID: PMC10802451 DOI: 10.1101/2024.01.07.574575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Acetaldehyde is the primary metabolite of alcohol and is present in many environmental sources including tobacco smoke. Acetaldehyde is genotoxic, whereby it can form DNA adducts and lead to mutagenesis. Individuals with defects in acetaldehyde clearance pathways have increased susceptibility to alcohol-associated cancers. Moreover, a mutation signature specific to acetaldehyde exposure is widespread in alcohol and smoking-associated cancers. However, the pathways that repair acetaldehyde-induced DNA damage and thus prevent mutagenesis are vaguely understood. Here, we used Saccharomyces cerevisiae to systematically delete genes in each of the major DNA repair pathways to identify those that alter acetaldehyde-induced mutagenesis. We found that deletion of the nucleotide excision repair (NER) genes, RAD1 or RAD14, led to an increase in mutagenesis upon acetaldehyde exposure. Acetaldehyde-induced mutations were dependent on translesion synthesis as well as DNA inter-strand crosslink (ICL) repair in Δrad1 strains. Moreover, whole genome sequencing of the mutated isolates demonstrated an increase in C→A changes coupled with an enrichment of gCn→A changes in the acetaldehyde-treated Δrad1 isolates. The gCn→A mutation signature has been shown to be diagnostic of acetaldehyde exposure in yeast and in human cancers. We also demonstrated that the deletion of the two DNA-protein crosslink (DPC) repair proteases, WSS1 and DDI1, also led to increased acetaldehyde-induced mutagenesis. Defects in base excision repair (BER) led to a mild increase in mutagenesis, while defects in mismatch repair (MMR), homologous recombination repair (HR) and post replicative repair pathways did not impact mutagenesis upon acetaldehyde exposure. Our results in yeast were further corroborated upon analysis of whole exome sequenced liver cancers, wherein, tumors with defects in ERCC1 and ERCC4 (NER), FANCD2 (ICL repair) or SPRTN (DPC repair) carried a higher gCn→A mutation load than tumors with no deleterious mutations in these genes. Our findings demonstrate that multiple DNA repair pathways protect against acetaldehyde-induced mutagenesis.
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Affiliation(s)
- Latarsha Porcher
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, 29425, United States of America
| | - Sriram Vijayraghavan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, 29425, United States of America
| | - James McCollum
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, 29425, United States of America
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, 27599, United States of America
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, 29425, United States of America
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8
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Hoes L, Voordeckers K, Dok R, Boeckx B, Steemans B, Gopaul D, Pasero P, Govers SK, Lambrechts D, Nuyts S, Verstrepen KJ. Ethanol induces replication fork stalling and membrane stress in immortalized laryngeal cells. iScience 2023; 26:108564. [PMID: 38213791 PMCID: PMC10783606 DOI: 10.1016/j.isci.2023.108564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024] Open
Abstract
Although ethanol is a class I carcinogen and is linked to more than 700,000 cancer incidences, a clear understanding of the molecular mechanisms underlying ethanol-related carcinogenesis is still lacking. Further understanding of ethanol-related cell damage can contribute to reducing or treating alcohol-related cancers. Here, we investigated the effects of both short- and long-term exposure of human laryngeal epithelial cells to different ethanol concentrations. RNA sequencing shows that ethanol altered gene expression patterns in a time- and concentration-dependent way, affecting genes involved in ribosome biogenesis, cytoskeleton remodeling, Wnt signaling, and transmembrane ion transport. Additionally, ethanol induced a slower cell proliferation, a delayed cell cycle progression, and replication fork stalling. In addition, ethanol exposure resulted in morphological changes, which could be associated with membrane stress. Taken together, our data yields a comprehensive view of molecular changes associated with ethanol stress in epithelial cells of the upper aerodigestive tract.
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Affiliation(s)
- Lore Hoes
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Karin Voordeckers
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Rüveyda Dok
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Bart Steemans
- Laboratory of Microbial Systems Cell Biology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Diyavarshini Gopaul
- Institute of Human Genetics, CNRS, University of Montpellier, 34396 Montpellier, France
| | - Philippe Pasero
- Institute of Human Genetics, CNRS, University of Montpellier, 34396 Montpellier, France
| | - Sander K. Govers
- Laboratory of Microbial Systems Cell Biology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
- Department of Radiation Oncology, Leuven Cancer Institute, University Hospital Leuven, 3000 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
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9
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Li J, Stenberg S, Yue JX, Mikhalev E, Thompson D, Warringer J, Liti G. Genome instability footprint under rapamycin and hydroxyurea treatments. PLoS Genet 2023; 19:e1011012. [PMID: 37931001 PMCID: PMC10653606 DOI: 10.1371/journal.pgen.1011012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/16/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023] Open
Abstract
The mutational processes dictating the accumulation of mutations in genomes are shaped by genetic background, environment and their interactions. Accurate quantification of mutation rates and spectra under drugs has important implications in disease treatment. Here, we used whole-genome sequencing and time-resolved growth phenotyping of yeast mutation accumulation lines to give a detailed view of the mutagenic effects of rapamycin and hydroxyurea on the genome and cell growth. Mutation rates depended on the genetic backgrounds but were only marginally affected by rapamycin. As a remarkable exception, rapamycin treatment was associated with frequent chromosome XII amplifications, which compensated for rapamycin induced rDNA repeat contraction on this chromosome and served to maintain rDNA content homeostasis and fitness. In hydroxyurea, a wide range of mutation rates were elevated regardless of the genetic backgrounds, with a particularly high occurrence of aneuploidy that associated with dramatic fitness loss. Hydroxyurea also induced a high T-to-G and low C-to-A transversion rate that reversed the common G/C-to-A/T bias in yeast and gave rise to a broad range of structural variants, including mtDNA deletions. The hydroxyurea mutation footprint was consistent with the activation of error-prone DNA polymerase activities and non-homologues end joining repair pathways. Taken together, our study provides an in-depth view of mutation rates and signatures in rapamycin and hydroxyurea and their impact on cell fitness, which brings insights for assessing their chronic effects on genome integrity.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | - Dawn Thompson
- Ginkgo Bioworks, Boston, Massachusetts, United States of America
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Gianni Liti
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
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10
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Rubio LS, Mohajan S, Gross DS. Ethanol stress induces transient restructuring of the yeast genome yet stable formation of Hsf1 transcriptional condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560064. [PMID: 37808805 PMCID: PMC10557744 DOI: 10.1101/2023.09.28.560064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
In mammals, 3D genome topology has been linked to transcriptional states yet whether this link holds for other eukaryotes is unclear. Here we show that in budding yeast, Heat Shock Response (HSR) genes under the control of Heat Shock Factor (Hsf1) rapidly reposition in cells exposed to acute ethanol stress and engage in concerted, Hsf1-dependent intergenic interactions. Accompanying 3D genome reconfiguration is equally rapid formation of Hsf1-containing condensates. However, in contrast to the transience of Hsf1-driven intergenic interactions that peak within 10 min and dissipate within 1 h, Hsf1 condensates are stably maintained for hours. Moreover, under the same conditions, Pol II occupancy of HSR genes and RNA expression are detectable only later in the response and peak much later (>1 h). This contrasts with the coordinate response of HSR genes to thermal stress where Pol II occupancy, transcription, intergenic interactions, and formation of Hsf1 condensates are all rapid yet transient (peak within 2.5-10 min and dissipate within 1 h). Collectively, our data suggest that different stimuli drive distinct transcription, topologic, and phase-separation phenomena dependent on the same transcription factor and that transcription factor-containing condensates represent only part of the ensemble required for gene activation.
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Affiliation(s)
- Linda S Rubio
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130
| | - Suman Mohajan
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130
| | - David S Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130
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11
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Khemiri L, Kuja-Halkola R, Larsson H, Butwicka A, Tideman M, D'Onofrio BM, Latvala A, Lichtenstein P. Parental substance use disorder and risk of intellectual disability in offspring in Sweden: a national register study. EClinicalMedicine 2023; 63:102170. [PMID: 37680949 PMCID: PMC10480548 DOI: 10.1016/j.eclinm.2023.102170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
Background Intellectual disability (ID) is a disorder with unknown aetiology in many cases. Maternal alcohol use is a known risk factor for ID, but less is known about the importance of maternal and paternal substance use disorder (SUD) and risk of ID in offspring. Methods Data from multiple nationwide registers were used to create a cohort of children born from January 01, 1978 to December 31, 2002. All participants were born in Sweden, had available parental identification information and did not emigrate or die before age 12 (n = 1,940,820). Logistic regression modelling was performed with exposure defined as having a parent who received any SUD diagnosis, including alcohol use disorder (AUD) and drug use disorder (DUD). The outcome was registration of diagnosis of any form of ID. First, we analysed the risk of ID if parental SUD was registered prior to childbirth with stepwise adjustment of multiple covariates. Second, the effect of timing of SUD diagnosis in relation to childbirth was analysed. Findings Of 37,410 offspring with parental SUD registered prior to birth, 3.0% (n = 1110) had any form of ID compared to 1.2% (n = 23,168) of those 1,903,410 individuals without parental SUD prior birth. Parental SUD prior birth was associated with an increased risk of any form of ID (Odds Ratio [OR]: 2.3 [2.2-2.5]), with ORs similar for maternal (OR: 2.3 [2.1-2.5]) and paternal SUD (OR: 2.3 [2.1-2.5]). These ORs were reduced but remained statistically significant after adjusting for parental education, migration, psychiatric comorbidity, and co-parent SUD (OR parental SUD: 1.6 [1.5-1.8]; OR maternal SUD: 1.4 [1.2-1.5]; OR paternal SUD: 1.6 [1.5-1.7]). Parental SUD was associated with increased risk of ID in offspring irrespective of timing of diagnosis, but if mothers or fathers were diagnosed with AUD during pregnancy (OR maternal AUD: 5.0 [3.1-8.2]; OR paternal AUD: 2.8 [2.2-3.6]), the risk was significantly greater than if the AUD diagnosis was first registered after childbirth (OR maternal AUD: 1.9 [1.8-2.0]; OR paternal AUD: 1.6 [1.6-1.7]). Interpretation Both paternal and maternal SUD were associated with an increased risk of ID in offspring, with greatest risk observed when AUD was diagnosed during pregnancy. Possible mechanisms may involve shared genetic and environmental factors, including toxic effects from alcohol intake. These findings have clinical implications in suggesting that parental SUD in either parent represents a possibly modifiable risk factor to consider when developing prevention, diagnostics and treatment programs for children with ID. Funding Stockholm County Council, the Research Council of the Swedish Alcohol Retailing Monopoly, Fredrik and Ingrid Thurings stiftelse, Academy of Finland, the Swedish Research Council and the Swedish Research Council for Health, Working Life and Welfare, Nordforsk by the Nordic Council of Ministers and the Polish Medical Research Agency.
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Affiliation(s)
- Lotfi Khemiri
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
| | - Ralf Kuja-Halkola
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Larsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Agnieszka Butwicka
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health Services, Akershus University Hospital, Lørenskog, Norway
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
| | - Magnus Tideman
- Department of Social Sciences, Marie Cederschiöld University, Stockholm, Sweden
- School of Health and Welfare, Halmstad University, Halmstad, Sweden
| | - Brian M. D'Onofrio
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Antti Latvala
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Criminology and Legal Policy, University of Helsinki, Helsinki, Finland
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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12
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Patel D, Amiji H, Shropshire W, Condic N, Lermi NO, Sabha Y, John B, Hanson B, Karras GI. Ethanol Drives Evolution of Hsp90-Dependent Robustness by Redundancy in Yeast Domestication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.547572. [PMID: 37745611 PMCID: PMC10516021 DOI: 10.1101/2023.07.21.547572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Protein folding promotes and constrains adaptive evolution. We uncover this surprising duality in the role the protein-folding chaperone Hsp90 plays in mediating the interplay between proteome and the genome which acts to maintain the integrity of yeast metabolism in the face of proteotoxic stressors in anthropic niches. Of great industrial relevance, ethanol concentrations generated by fermentation in the making of beer and bread disrupt critical Hsp90-dependent nodes of metabolism and exert strong selective pressure for increased copy number of key genes encoding components of these nodes, yielding the classical genetic signatures of beer and bread domestication. This work establishes a mechanism of adaptive canalization in an ecology of major economic significance and highlights Hsp90-contingent variation as an important source of phantom heritability in complex traits.
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13
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Vijayraghavan S, Saini N. Aldehyde-Associated Mutagenesis─Current State of Knowledge. Chem Res Toxicol 2023. [PMID: 37363863 DOI: 10.1021/acs.chemrestox.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Aldehydes are widespread in the environment, with multiple sources such as food and beverages, industrial effluents, cigarette smoke, and additives. The toxic effects of exposure to several aldehydes have been observed in numerous studies. At the molecular level, aldehydes damage DNA, cross-link DNA and proteins, lead to lipid peroxidation, and are associated with increased disease risk including cancer. People genetically predisposed to aldehyde sensitivity exhibit severe health outcomes. In various diseases such as Fanconi's anemia and Cockayne syndrome, loss of aldehyde-metabolizing pathways in conjunction with defects in DNA repair leads to widespread DNA damage. Importantly, aldehyde-associated mutagenicity is being explored in a growing number of studies, which could offer key insights into how they potentially contribute to tumorigenesis. Here, we review the genotoxic effects of various aldehydes, focusing particularly on the DNA adducts underlying the mutagenicity of environmentally derived aldehydes. We summarize the chemical structures of the aldehydes and their predominant DNA adducts, discuss various methodologies, in vitro and in vivo, commonly used in measuring aldehyde-associated mutagenesis, and highlight some recent studies looking at aldehyde-associated mutation signatures and spectra. We conclude the Review with a discussion on the challenges and future perspectives of investigating aldehyde-associated mutagenesis.
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Affiliation(s)
- Sriram Vijayraghavan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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14
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Melde RH, Bao K, Sharp NP. Recent insights into the evolution of mutation rates in yeast. Curr Opin Genet Dev 2022; 76:101953. [PMID: 35834945 PMCID: PMC9491374 DOI: 10.1016/j.gde.2022.101953] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 02/08/2023]
Abstract
Mutation is the origin of all genetic variation, good and bad. The mutation process can evolve in response to mutations, positive or negative selection, and genetic drift, but how these forces contribute to mutation-rate variation is an unsolved problem at the heart of genetics research. Mutations can be challenging to measure, but genome sequencing and other tools have allowed for the collection of larger and more detailed datasets, particularly in the yeast-model system. We review key hypotheses for the evolution of mutation rates and describe recent advances in understanding variation in mutational properties within and among yeast species. The multidimensional spectrum of mutations is increasingly recognized as holding valuable clues about how this important process evolves.
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Affiliation(s)
- Robert H Melde
- Department of Genetics, University of Wisconsin-Madison, USA.
| | - Kevin Bao
- Department of Genetics, University of Wisconsin-Madison, USA
| | - Nathaniel P Sharp
- Department of Genetics, University of Wisconsin-Madison, USA. https://twitter.com/@sharpnath
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15
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Vijayraghavan S, Porcher L, Mieczkowski PA, Saini N. Acetaldehyde makes a distinct mutation signature in single-stranded DNA. Nucleic Acids Res 2022; 50:7451-7464. [PMID: 35776120 PMCID: PMC9303387 DOI: 10.1093/nar/gkac570] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/09/2022] [Accepted: 06/20/2022] [Indexed: 02/06/2023] Open
Abstract
Acetaldehyde (AA), a by-product of ethanol metabolism, is acutely toxic due to its ability to react with various biological molecules including DNA and proteins, which can greatly impede key processes such as replication and transcription and lead to DNA damage. As such AA is classified as a group 1 carcinogen by the International Agency for Research on Cancer (IARC). Previous in vitro studies have shown that AA generates bulky adducts on DNA, with signature guanine-centered (GG→TT) mutations. However, due to its weak mutagenicity, short chemical half-life, and the absence of powerful genetic assays, there is considerable variability in reporting the mutagenic effects of AA in vivo. Here, we used an established yeast genetic reporter system and demonstrate that AA treatment is highly mutagenic to cells and leads to strand-biased mutations on guanines (G→T) at a high frequency on single stranded DNA (ssDNA). We further demonstrate that AA-derived mutations occur through lesion bypass on ssDNA by the translesion polymerase Polζ. Finally, we describe a unique mutation signature for AA, which we then identify in several whole-genome and -exome sequenced cancers, particularly those associated with alcohol consumption. Our study proposes a key mechanism underlying carcinogenesis by acetaldehyde—mutagenesis of single-stranded DNA.
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Affiliation(s)
- Sriram Vijayraghavan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Latarsha Porcher
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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16
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Yuan T, Hu J, Zhu X, Yin H, Yin J. Oxidative stress-mediated up-regulation of ABC transporters in lung cancer cells. J Biochem Mol Toxicol 2022; 36:e23095. [PMID: 35478211 DOI: 10.1002/jbt.23095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 11/12/2022]
Abstract
This paper aimed to evaluate the role of oxidative stress in the regulation of ABC transporters in human lung cancer (A549) cells facing substrate (doxorubicin, DOX) and non-substrate (ethanol, ETH and hydrogen peroxide, HP) chemicals. After 24-h treatment, all the chemicals caused significant cytotoxicity as reflected by the reduction in cell viability and the increase in reactive oxygen species (ROS) levels. Depending on the rescuing effects of ROS scavenger including glutathione (GSH) and Vitamin C (VC), the toxicity dependence on oxidative stress were found to be HP>ETH>DOX. Addition of transporter inhibitors significantly enhanced the ROS levels and death-inducing effects of chemicals, indicating the universal detoxification function of ABC transporters. At moderate ROS levels (about 3-4 folds of control levels, caused by 10 μM DOX, 400 mM ETH, and 400 μM HP), all the three chemicals induced the gene expressions and activities of ABC transporters, but these values decreased at too high ROS levels (8.36 folds of control levels) caused by HP at LC50 (800 μM). Such induction could be attenuated by GSH and KCZ, and was completely abolished by 50 μM KCZ, indicating an important role of oxidative stress and pregnane X receptor (PXR) in the induction of ABC transporters. After all, this paper revealed a critical role of oxidative stress in the modulation of ABC transporters by either substrate or non-substrate chemicals during 24-h treatment. Such information should be beneficial for overcoming ABC transporter-mediated multidrug resistance (MDR). This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tongkuo Yuan
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, Jiangsu, 215163, PR China.,CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, PR China.,Jinan Guo Ke Medical Technology Development Co., Ltd, Jinan, 250001, PR China
| | - Jia Hu
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou, Jiangsu, 215123, PR China
| | - Xiaoming Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau SAR, China
| | - Huancai Yin
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, Jiangsu, 215163, PR China.,CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, PR China.,Jinan Guo Ke Medical Technology Development Co., Ltd, Jinan, 250001, PR China
| | - Jian Yin
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, Jiangsu, 215163, PR China.,CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, PR China.,Jinan Guo Ke Medical Technology Development Co., Ltd, Jinan, 250001, PR China
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17
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Substrates of the MAPK Slt2: Shaping Yeast Cell Integrity. J Fungi (Basel) 2022; 8:jof8040368. [PMID: 35448599 PMCID: PMC9031059 DOI: 10.3390/jof8040368] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/04/2023] Open
Abstract
The cell wall integrity (CWI) MAPK pathway of budding yeast Saccharomyces cerevisiae is specialized in responding to cell wall damage, but ongoing research shows that it participates in many other stressful conditions, suggesting that it has functional diversity. The output of this pathway is mainly driven by the activity of the MAPK Slt2, which regulates important processes for yeast physiology such as fine-tuning of signaling through the CWI and other pathways, transcriptional activation in response to cell wall damage, cell cycle, or determination of the fate of some organelles. To this end, Slt2 precisely phosphorylates protein substrates, modulating their activity, stability, protein interaction, and subcellular localization. Here, after recapitulating the methods that have been employed in the discovery of proteins phosphorylated by Slt2, we review the bona fide substrates of this MAPK and the growing set of candidates still to be confirmed. In the context of the complexity of MAPK signaling regulation, we discuss how Slt2 determines yeast cell integrity through phosphorylation of these substrates. Increasing data from large-scale analyses and the available methodological approaches pave the road to early identification of new Slt2 substrates and functions.
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18
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Nguyen L, Jager M, Lieshout R, de Ruiter PE, Locati MD, Besselink N, van der Roest B, Janssen R, Boymans S, de Jonge J, IJzermans JNM, Doukas M, Verstegen MMA, van Boxtel R, van der Laan LJW, Cuppen E, Kuijk E. Precancerous liver diseases do not cause increased mutagenesis in liver stem cells. Commun Biol 2021; 4:1301. [PMID: 34795391 PMCID: PMC8602268 DOI: 10.1038/s42003-021-02839-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/30/2021] [Indexed: 12/18/2022] Open
Abstract
Inflammatory liver disease increases the risk of developing primary liver cancer. The mechanism through which liver disease induces tumorigenesis remains unclear, but is thought to occur via increased mutagenesis. Here, we performed whole-genome sequencing on clonally expanded single liver stem cells cultured as intrahepatic cholangiocyte organoids (ICOs) from patients with alcoholic cirrhosis, non-alcoholic steatohepatitis (NASH), and primary sclerosing cholangitis (PSC). Surprisingly, we find that these precancerous liver disease conditions do not result in a detectable increased accumulation of mutations, nor altered mutation types in individual liver stem cells. This finding contrasts with the mutational load and typical mutational signatures reported for liver tumors, and argues against the hypothesis that liver disease drives tumorigenesis via a direct mechanism of induced mutagenesis. Disease conditions in the liver may thus act through indirect mechanisms to drive the transition from healthy to cancerous cells, such as changes to the microenvironment that favor the outgrowth of precancerous cells.
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Affiliation(s)
- Luan Nguyen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Myrthe Jager
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Mauro D Locati
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bastiaan van der Roest
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | | | | | | | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
- Hartwig Medical Foundation, Amsterdam, The Netherlands.
| | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
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19
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Jiang P, Ollodart AR, Sudhesh V, Herr AJ, Dunham MJ, Harris K. A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae. eLife 2021; 10:68285. [PMID: 34523420 PMCID: PMC8497059 DOI: 10.7554/elife.68285] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 09/14/2021] [Indexed: 12/23/2022] Open
Abstract
Although studies of Saccharomyces cerevisiae have provided many insights into mutagenesis and DNA repair, most of this work has focused on a few laboratory strains. Much less is known about the phenotypic effects of natural variation within S. cerevisiae’s DNA repair pathways. Here, we use natural polymorphisms to detect historical mutation spectrum differences among several wild and domesticated S. cerevisiae strains. To determine whether these differences are likely caused by genetic mutation rate modifiers, we use a modified fluctuation assay with a CAN1 reporter to measure de novo mutation rates and spectra in 16 of the analyzed strains. We measure a 10-fold range of mutation rates and identify two strains with distinctive mutation spectra. These strains, known as AEQ and AAR, come from the panel’s ‘Mosaic beer’ clade and share an enrichment for C > A mutations that is also observed in rare variation segregating throughout the genomes of several Mosaic beer and Mixed origin strains. Both AEQ and AAR are haploid derivatives of the diploid natural isolate CBS 1782, whose rare polymorphisms are enriched for C > A as well, suggesting that the underlying mutator allele is likely active in nature. We use a plasmid complementation test to show that AAR and AEQ share a mutator allele in the DNA repair gene OGG1, which excises 8-oxoguanine lesions that can cause C > A mutations if left unrepaired.
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Affiliation(s)
- Pengyao Jiang
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Anja R Ollodart
- Department of Genome Sciences, University of Washington, Seattle, United States.,Molecular and Cellular Biology Program, University of Washington, Seattle, United States
| | - Vidha Sudhesh
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Alan J Herr
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, United States.,Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
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20
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Hao W, Cui W, Cheng Z, Han L, Suo F, Liu Z, Zhou L, Zhou Z. Development of a base editor for protein evolution via in situ mutation in vivo. Nucleic Acids Res 2021; 49:9594-9605. [PMID: 34390349 PMCID: PMC8450078 DOI: 10.1093/nar/gkab673] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/21/2021] [Accepted: 07/24/2021] [Indexed: 12/16/2022] Open
Abstract
Protein evolution has significantly enhanced the development of life science. However, it is difficult to achieve in vitro evolution of some special proteins because of difficulties with heterologous expression, purification, and function detection. To achieve protein evolution via in situ mutation in vivo, we developed a base editor by fusing nCas with a cytidine deaminase in Bacillus subtilis through genome integration. The base editor introduced a cytidine-to-thymidine mutation of approximately 100% across a 5 nt editable window, which was much higher than those of other base editors. The editable window was expanded to 8 nt by extending the length of sgRNA, and conversion efficiency could be regulated by changing culture conditions, which was suitable for constructing a mutant protein library efficiently in vivo. As proof-of-concept, the Sec-translocase complex and bacitracin-resistance-related protein BceB were successfully evolved in vivo using the base editor. A Sec mutant with 3.6-fold translocation efficiency and the BceB mutants with different sensitivity to bacitracin were obtained. As the construction of the base editor does not rely on any additional or host-dependent factors, such base editors (BEs) may be readily constructed and applicable to a wide range of bacteria for protein evolution via in situ mutation.
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Affiliation(s)
- Wenliang Hao
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Wenjing Cui
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhongyi Cheng
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Laichuang Han
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Feiya Suo
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhongmei Liu
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Li Zhou
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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21
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Bradley AI, Marsh NM, Borror HR, Mostoller KE, Gama AI, Gardner RG. Acute ethanol stress induces sumoylation of conserved chromatin structural proteins in Saccharomyces cerevisiae. Mol Biol Cell 2021; 32:1121-1133. [PMID: 33788582 PMCID: PMC8351541 DOI: 10.1091/mbc.e20-11-0715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Stress is ubiquitous to life and can irreparably damage essential biomolecules and organelles in cells. To survive, organisms must sense and adapt to stressful conditions. One highly conserved adaptive stress response is through the posttranslational modification of proteins by the small ubiquitin-like modifier (SUMO). Here, we examine the effects of acute ethanol stress on protein sumoylation in the budding yeast Saccharomyces cerevisiae. We found that cells exhibit a transient sumoylation response after acute exposure to ≤7.5% vol/vol ethanol. By contrast, the sumoylation response becomes chronic at 10% ethanol exposure. Mass spectrometry analyses identified 18 proteins that are sumoylated after acute ethanol exposure, with 15 known to associate with chromatin. Upon further analysis, we found that the chromatin structural proteins Smc5 and Smc6 undergo ethanol-induced sumoylation that depends on the activity of the E3 SUMO ligase Mms21. Using cell-cycle arrest assays, we observed that Smc5 and Smc6 ethanol-induced sumoylation occurs during G1 and G2/M phases but not S phase. Acute ethanol exposure also resulted in the formation of Rad52 foci at levels comparable to Rad52 foci formation after exposure to the DNA alkylating agent methyl methanesulfonate (MMS). MMS exposure is known to induce the intra-S-phase DNA damage checkpoint via Rad53 phosphorylation, but ethanol exposure did not induce Rad53 phosphorylation. Ethanol abrogated the effect of MMS on Rad53 phosphorylation when added simultaneously. From these studies, we propose that acute ethanol exposure induces a change in chromatin leading to sumoylation of specific chromatin structural proteins.
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Affiliation(s)
- Amanda I Bradley
- Department of Pharmacology, University of Washington, Seattle, WA 98195.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195
| | - Nicole M Marsh
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | - Heather R Borror
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | | | - Amber I Gama
- Department of Pharmacology, University of Washington, Seattle, WA 98195
| | - Richard G Gardner
- Department of Pharmacology, University of Washington, Seattle, WA 98195.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195
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22
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Mardones W, Villarroel CA, Abarca V, Urbina K, Peña TA, Molinet J, Nespolo RF, Cubillos FA. Rapid selection response to ethanol in Saccharomyces eubayanus emulates the domestication process under brewing conditions. Microb Biotechnol 2021; 15:967-984. [PMID: 33755311 PMCID: PMC8913853 DOI: 10.1111/1751-7915.13803] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 01/02/2023] Open
Abstract
Although the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood. Domesticated yeasts for brewing, where short generation times and large phenotypic and genomic plasticity were attained in a few generations under selection, are prime examples. To experimentally emulate the lager yeast domestication process, we created a genetically complex (panmictic) artificial population of multiple Saccharomyces eubayanus genotypes, one of the parents of lager yeast. Then, we imposed a constant selection regime under a high ethanol concentration in 10 replicated populations during 260 generations (6 months) and compared them with propagated controls exposed solely to glucose. Propagated populations exhibited a selection differential of 60% in growth rate in ethanol, mostly explained by the proliferation of a single lineage (CL248.1) that competitively displaced all other clones. Interestingly, the outcome does not require the entire time‐course of adaptation, as four lineages monopolized the culture at generation 120. Sequencing demonstrated that de novo genetic variants were produced in all propagated lines, including SNPs, aneuploidies, INDELs and translocations. In addition, the different propagated populations showed correlated responses resembling the domestication syndrome: genomic rearrangements, faster fermentation rates, lower production of phenolic off‐flavours and lower volatile compound complexity. Expression profiling in beer wort revealed altered expression levels of genes related to methionine metabolism, flocculation, stress tolerance and diauxic shift, likely contributing to higher ethanol and fermentation stress tolerance in the evolved populations. Our study shows that experimental evolution can rebuild the brewing domestication process in ‘fast motion’ in wild yeast, and also provides a powerful tool for studying the genetics of the adaptation process in complex populations.
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Affiliation(s)
- Wladimir Mardones
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Carlos A Villarroel
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Valentina Abarca
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Kamila Urbina
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Tomás A Peña
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Jennifer Molinet
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Roberto F Nespolo
- Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile.,Institute of Environmental and Evolutionary Science, Universidad Austral de Chile, Valdivia, 5110566, Chile.,Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco A Cubillos
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
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23
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Schalck T, den Bergh BV, Michiels J. Increasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics. Microorganisms 2021; 9:249. [PMID: 33530454 PMCID: PMC7912173 DOI: 10.3390/microorganisms9020249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.
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Affiliation(s)
- Thomas Schalck
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
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24
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Shi M, Ren S, Chen H, Li J, Huang C, Li Y, Han Y, Li Y, Sun Z, Chen X, Xiong Z. Alcohol drinking inhibits NOTCH-PAX9 signaling in esophageal squamous epithelial cells. J Pathol 2021; 253:384-395. [PMID: 33314197 DOI: 10.1002/path.5602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/22/2020] [Accepted: 12/08/2020] [Indexed: 01/04/2023]
Abstract
Alcohol drinking has been established as a major risk factor for esophageal diseases. Our previous study showed that ethanol exposure inhibited PAX9 expression in human esophageal squamous epithelial cells in vitro and in vivo. In this study, we aimed to investigate the molecular pathways through which alcohol drinking suppresses PAX9 in esophageal squamous epithelial cells. We first demonstrated the inhibition of NOTCH by ethanol exposure in vitro. NOTCH regulated PAX9 expression in KYSE510 and KYSE410 cells in vitro and in vivo. RBPJ and NOTCH intracellular domain (NIC) D1 ChIP-PCR confirmed Pax9 as a direct downstream target of NOTCH signaling in mouse esophagus. NOTCH inhibition by alcohol drinking was further validated in mouse esophagus and human tissue samples. In conclusion, ethanol exposure inhibited NOTCH signaling and thus suppressed PAX9 expression in esophageal squamous epithelial cells in vitro and in vivo. Our data support a novel mechanism of alcohol-induced esophageal injury through the inhibition of NOTCH-PAX9 signaling. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Menghan Shi
- Beijing Stomatological Hospital, Capital Medical University, Beijing, PR China.,Cancer Research Program, Julius L Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, USA
| | - Shuang Ren
- Beijing Stomatological Hospital, Capital Medical University, Beijing, PR China.,Cancer Research Program, Julius L Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, USA
| | - Hao Chen
- Cancer Research Program, Julius L Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, USA
| | - Jing Li
- Cancer Research Program, Julius L Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, USA.,Department of Thoracic Surgery, Ningxia Medical University General Hospital, Yinchuan, PR China
| | - Caizhi Huang
- Cancer Research Program, Julius L Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, USA
| | - Yahui Li
- Cancer Research Program, Julius L Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, USA
| | - Yuning Han
- Department of Thoracic Surgery, Ningxia Medical University General Hospital, Yinchuan, PR China
| | - Yong Li
- Department of Thoracic Surgery, National Cancer Center, Cancer Hospital of Chinese Academy of Medical Sciences, Beijing, PR China
| | - Zheng Sun
- Beijing Stomatological Hospital, Capital Medical University, Beijing, PR China
| | - Xiaoxin Chen
- Cancer Research Program, Julius L Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, USA.,Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhaohui Xiong
- Cancer Research Program, Julius L Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, USA
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