1
|
Shaw AE, Whitted JE, Mihelich MN, Reitman HJ, Timmerman AJ, Schauer GD. Revised Mechanism of Hydroxyurea Induced Cell Cycle Arrest and an Improved Alternative. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.02.583010. [PMID: 38496404 PMCID: PMC10942336 DOI: 10.1101/2024.03.02.583010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Replication stress describes various types of endogenous and exogenous challenges to DNA replication in S-phase. Stress during this critical process results in helicase-polymerase decoupling at replication forks, triggering the S-phase checkpoint, which orchestrates global replication fork stalling and delayed entry into G2. The replication stressor most often used to induce the checkpoint response is hydroxyurea (HU), a chemotherapeutic agent. The primary mechanism of S-phase checkpoint activation by HU has thus far been considered to be a reduction of dNTP synthesis by inhibition of ribonucleotide reductase (RNR), leading to helicase-polymerase decoupling and subsequent activation of the checkpoint, mediated by the replisome associated effector kinase Mrc1. In contrast, we observe that HU causes cell cycle arrest in budding yeast independent of both the Mrc1-mediated replication checkpoint response and the Psk1-Mrc1 oxidative signaling pathway. We demonstrate a direct relationship between HU incubation and reactive oxygen species (ROS) production in yeast nuclei. We further observe that ROS strongly inhibits the in vitro polymerase activity of replicative polymerases (Pols), Pol α, Pol δ, and Pol ε, causing polymerase complex dissociation and subsequent loss of DNA substrate binding, likely through oxidation of their integral iron sulfur Fe-S clusters. Finally, we present "RNR-deg," a genetically engineered alternative to HU in yeast with greatly increased specificity of RNR inhibition, allowing researchers to achieve fast, nontoxic, and more readily reversible checkpoint activation compared to HU, avoiding harmful ROS generation and associated downstream cellular effects that may confound interpretation of results.
Collapse
Affiliation(s)
- Alisa E Shaw
- Department of Biochemistry and Molecular Biology, Colorado State University, CO, USA
| | - Jackson E Whitted
- Department of Biochemistry and Molecular Biology, Colorado State University, CO, USA
| | - Mattias N Mihelich
- Department of Biochemistry and Molecular Biology, Colorado State University, CO, USA
| | - Hannah J Reitman
- Department of Biochemistry and Molecular Biology, Colorado State University, CO, USA
| | - Adam J Timmerman
- Department of Biochemistry and Molecular Biology, Colorado State University, CO, USA
| | - Grant D Schauer
- Department of Biochemistry and Molecular Biology, Colorado State University, CO, USA
| |
Collapse
|
2
|
Xiao Z, Lin H, Drake HF, Diaz J, Zhou HC, Pellois JP. Investigating the Cell Entry Mechanism, Disassembly, and Toxicity of the Nanocage PCC-1: Insights into Its Potential as a Drug Delivery Vehicle. J Am Chem Soc 2023; 145:27690-27701. [PMID: 38069810 PMCID: PMC10863074 DOI: 10.1021/jacs.3c09918] [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: 09/09/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023]
Abstract
The porous coordination cage PCC-1 represents a new platform potentially useful for the cellular delivery of drugs with poor cell permeability and solubility. PCC-1 is a metal-organic polyhedron constructed from zinc metal ions and organic ligands through coordination bonds. PCC-1 possesses an internal cavity that is suitable for drug encapsulation. To better understand the biocompatibility of PCC-1 with human cells, the cell entry mechanism, disassembly, and toxicity of the nanocage were investigated. PCC-1 localizes in the nuclei and cytoplasm within minutes upon incubation with cells, independent of endocytosis and cargo, suggesting direct plasma membrane translocation of the nanocage carrying its guest in its internal cavity. Furthermore, the rates of cell entry correlate to extracellular concentrations, indicating that PCC-1 is likely diffusing passively through the membrane despite its relatively large size. Once inside cells, PCC-1 disintegrates into zinc metal ions and ligands over a period of several hours, each component being cleared from cells within 1 day. PCC-1 is relatively safe for cells at low micromolar concentrations but becomes inhibitory to cell proliferation and toxic above a concentration or incubation time threshold. However, cells surviving these conditions can return to homeostasis 3-5 days after exposure. Overall, these findings demonstrate that PCC-1 enters live cells by crossing biological membranes spontaneously. This should prove useful to deliver drugs that lack this capacity on their own, provided that the dosage and exposure time are controlled to avoid toxicity.
Collapse
Affiliation(s)
- Zhifeng Xiao
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hengyu Lin
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hannah F. Drake
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Joshua Diaz
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Hong-Cai Zhou
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jean-Philippe Pellois
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
3
|
de Alteriis E, Incerti G, Cartenì F, Chiusano ML, Colantuono C, Palomba E, Termolino P, Monticolo F, Esposito A, Bonanomi G, Capparelli R, Iannaccone M, Foscari A, Landi C, Parascandola P, Sanchez M, Tirelli V, de Falco B, Lanzotti V, Mazzoleni S. Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:292-295. [PMID: 38053574 PMCID: PMC10695634 DOI: 10.15698/mic2023.12.810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including 1H-NMR metabolomic fingerprint, that the growth rate decline in Saccharomyces cerevisiae fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the entire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the observed growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the functional role of exDNA produced by living cells.
Collapse
Affiliation(s)
- Elisabetta de Alteriis
- Department of Biology, University of Naples “Federico II”, Via Cinthia 26, 80126 Naples, Italy
| | - Guido Incerti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Fabrizio Cartenì
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Emanuela Palomba
- Institute of Biosciences and Bioresources CNR, Via Università 133, 80055 Portici (NA), Italy
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources CNR, Via Università 133, 80055 Portici (NA), Italy
| | - Francesco Monticolo
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Alfonso Esposito
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Giuliano Bonanomi
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Task Force Microbiome - University of Naples “Federico II“
| | - Rosanna Capparelli
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Marco Iannaccone
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Laboratory of Biotechnological Processes for Energy and Industry, ENEA, Via Anguillarese, 301, - 00123 Rome, Italy
| | - Alessandro Foscari
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Carmine Landi
- Department of Industrial Engineering, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy-
| | - Palma Parascandola
- Department of Industrial Engineering, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy-
| | - Massimo Sanchez
- Istituto Superiore di Sanità (ISS) Core Facilities, Viale Regina Elena 299, 00161 Rome, Italy
| | - Valentina Tirelli
- Istituto Superiore di Sanità (ISS) Core Facilities, Viale Regina Elena 299, 00161 Rome, Italy
| | - Bruna de Falco
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Virginia Lanzotti
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples “Federico II”, via Università 100, 80055 Portici (NA), Italy
- Task Force Microbiome - University of Naples “Federico II“
| |
Collapse
|
4
|
Schwarz LV, Sandri FK, Scariot F, Delamare APL, Valera MJ, Carrau F, Echeverrigaray S. High nitrogen concentration causes G2/M arrest in Hanseniaspora vineae. Yeast 2023; 40:640-650. [PMID: 37997429 DOI: 10.1002/yea.3911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Yeasts have been widely used as a model to better understand cell cycle mechanisms and how nutritional and genetic factors can impact cell cycle progression. While nitrogen scarcity is well known to modulate cell cycle progression, the relevance of nitrogen excess for microorganisms has been overlooked. In our previous work, we observed an absence of proper entry into the quiescent state in Hanseniaspora vineae and identified a potential link between this behavior and nitrogen availability. Furthermore, the Hanseniaspora genus has gained attention due to a significant loss of genes associated with DNA repair and cell cycle. Thus, the aim of our study was to investigate the effects of varying nitrogen concentrations on H. vineae's cell cycle progression. Our findings demonstrated that nitrogen excess, regardless of the source, disrupts cell cycle progression and induces G2/M arrest in H. vineae after reaching the stationary phase. Additionally, we observed a viability decline in H. vineae cells in an ammonium-dependent manner, accompanied by increased production of reactive oxygen species, mitochondrial hyperpolarization, intracellular acidification, and DNA fragmentation. Overall, our study highlights the events of the cell cycle arrest in H. vineae induced by nitrogen excess and attempts to elucidate the possible mechanism triggering this absence of proper entry into the quiescent state.
Collapse
Affiliation(s)
- Luisa Vivian Schwarz
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul, Rio Grande do Sul, Brazil
| | - Fernanda Knaach Sandri
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul, Rio Grande do Sul, Brazil
| | - Fernando Scariot
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul, Rio Grande do Sul, Brazil
| | | | - Maria Jose Valera
- Enology and Fermentation Biotechnology Area, Departamento Ciencia y Tecnología Alimentos, Facultad de Química, Universidad de la Republica, Montevideo, Uruguay
| | - Francisco Carrau
- Enology and Fermentation Biotechnology Area, Departamento Ciencia y Tecnología Alimentos, Facultad de Química, Universidad de la Republica, Montevideo, Uruguay
| | - Sergio Echeverrigaray
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul, Rio Grande do Sul, Brazil
| |
Collapse
|
5
|
Mołoń M, Stępień K, Kielar P, Vasileva B, Lozanska B, Staneva D, Ivanov P, Kula-Maximenko M, Molestak E, Tchórzewski M, Miloshev G, Georgieva M. Actin-Related Protein 4 and Linker Histone Sustain Yeast Replicative Ageing. Cells 2022; 11:cells11172754. [PMID: 36078161 PMCID: PMC9454676 DOI: 10.3390/cells11172754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Ageing is accompanied by dramatic changes in chromatin structure organization and genome function. Two essential components of chromatin, the linker histone Hho1p and actin-related protein 4 (Arp4p), have been shown to physically interact in Saccharomyces cerevisiae cells, thus maintaining chromatin dynamics and function, as well as genome stability and cellular morphology. Disrupting this interaction has been proven to influence the stability of the yeast genome and the way cells respond to stress during chronological ageing. It has also been proven that the abrogated interaction between these two chromatin proteins elicited premature ageing phenotypes. Alterations in chromatin compaction have also been associated with replicative ageing, though the main players are not well recognized. Based on this knowledge, here, we examine how the interaction between Hho1p and Arp4p impacts the ageing of mitotically active yeast cells. For this purpose, two sets of strains were used—haploids (WT(n), arp4, hho1Δ and arp4 hho1Δ) and their heterozygous diploid counterparts (WT(2n), ARP4/arp4, HHO1/hho1Δ and ARP4 HHO1/arp4 hho1Δ)—for the performance of extensive morphological and physiological analyses during replicative ageing. These analyses included a comparative examination of the yeast cells’ chromatin structure, proliferative and reproductive potential, and resilience to stress, as well as polysome profiles and chemical composition. The results demonstrated that the haploid chromatin mutants arp4 and arp4 hho1Δ demonstrated a significant reduction in replicative and total lifespan. These findings lead to the conclusion that the importance of a healthy interaction between Arp4p and Hho1p in replicative ageing is significant. This is proof of the concomitant importance of Hho1p and Arp4p in chronological and replicative ageing.
Collapse
Affiliation(s)
- Mateusz Mołoń
- Department of Biochemistry and Cell Biology, Institute of Biology and Biotechnology, University of Rzeszow, 35-601 Rzeszow, Poland
- Correspondence: (M.M.); (M.G.)
| | - Karolina Stępień
- Department of Biochemistry and Cell Biology, Institute of Biology and Biotechnology, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Patrycja Kielar
- Department of Biochemistry and Cell Biology, Institute of Biology and Biotechnology, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Bela Vasileva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
| | - Bonka Lozanska
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
| | - Dessislava Staneva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
| | - Penyo Ivanov
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
| | - Monika Kula-Maximenko
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Eliza Molestak
- Department of Molecular Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - Marek Tchórzewski
- Department of Molecular Biology, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - George Miloshev
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
| | - Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology “Acad. R. Tsanev”, Bulgarian Academy of Sciences, 1123 Sofia, Bulgaria
- Correspondence: (M.M.); (M.G.)
| |
Collapse
|
6
|
Aging hampers neutrophil extracellular traps (NETs) efficacy. Aging Clin Exp Res 2022; 34:2345-2353. [PMID: 35920993 PMCID: PMC9637667 DOI: 10.1007/s40520-022-02201-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/17/2022] [Indexed: 11/16/2022]
Abstract
Background NETosis is a neutrophil-mediated defense mechanism during which DNA and enzymes are extruded forming a network (NETs) trapping and killing different pathogens. NETosis is reduced in both mice and humans during aging. Aims We explored the difference in the efficacy of NETs released in elderly (> 65 years) versus adults (20–50 years) subjects in inhibiting Staphylococcus aureus growth and activating the growth of keratinocytes. Methods Neutrophil granulocytes, obtained from venous blood both in healthy elderly and adult subjects, were stimulated by LPS (0–250 µg/ml) to induce the formation of NET. NETs were quantified by SYBR Green staining and growth inhibition of S. aureus was evaluated by disk diffusion test. Furthermore, NETs (0–500 ng/ml) were added to immortalized human keratinocytes (HaCaT cells), and their proliferation was evaluated by MTT assay after 24 h. Finally, the DNA size of NETs was evaluated by flow cytometry after SYBR Green staining. Results Greater production of NETs was observed in elderly subjects than in adults, but these NETs showed reduced bactericidal capacity and HaCaT cells’ proliferation stimulation. The activities of the NETs are related to the size of the extruded DNA threads, and when NETs size was analyzed, DNA from elderly showed a higher size compared to that obtained by adults. Discussion Unexpected results showed aging-related NETs structural modification resulting in both a lower antimicrobial activity and keratinocyte proliferation stimulation compared to NETs obtained from adults. Conclusions The NETs DNA size observed in elderly subjects has not been previously reported and could be part of other pathogenic mechanisms observed in aging.
Collapse
|
7
|
Schwarz LV, Valera MJ, Delamare APL, Carrau F, Echeverrigaray S. A peculiar cell cycle arrest at g2/m stage during the stationary phase of growth in the wine yeas Hanseniaspora vineae. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100129. [PMID: 35909624 PMCID: PMC9325883 DOI: 10.1016/j.crmicr.2022.100129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022] Open
Abstract
Cell cycle progress variations among Hanseniaspora species. H. vineae shows an unusual cell cycle progress. H. vineae undergoes G2/M arrest in stationary phase.
Yeasts of the genus Hanseniaspora gained notoriety in the last years due to their contribution to wine quality, and their loss of several genes, mainly related to DNA repair and cell cycle processes. Based on genomic data from many members of this genus, they have been classified in two well defined clades: the “faster-evolving linage” (FEL) and the “slower-evolving lineage” (SEL). In this context, we had detected that H. vineae exhibited a rapid loss of cell viability in some conditions during the stationary phase compared to H. uvarum and S. cerevisiae. The present work aimed to evaluate the viability and cell cycle progression of representatives of Hanseniaspora species along their growth in an aerobic and discontinuous system. Cell growth, viability and DNA content were determined by turbidity, Trypan Blue staining, and flow cytometry, respectively. Results showed that H. uvarum and H. opuntiae (representing FEL group), and H. osmophila (SEL group) exhibited a typical G1/G0 (1C DNA) arrest during the stationary phase, as S. cerevisiae. Conversely, the three strains studied here of H. vineae (SEL group) arrested at G2/M stages of cell cycle (2C DNA), and lost viability rapidly when enter the stationary phase. These results showed that H. vineae have a unique cell cycle behavior that will contribute as a new eukaryotic model for future studies of genetic determinants of yeast cell cycle control and progression.
Collapse
|
8
|
Palomba E, Tirelli V, de Alteriis E, Parascandola P, Landi C, Mazzoleni S, Sanchez M. A cytofluorimetric analysis of a Saccharomyces cerevisiae population cultured in a fed-batch bioreactor. PLoS One 2021; 16:e0248382. [PMID: 34111115 PMCID: PMC8191950 DOI: 10.1371/journal.pone.0248382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/27/2021] [Indexed: 11/18/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is a reference model system and one of the widely used microorganisms in many biotechnological processes. In industrial yeast applications, combined strategies aim to maximize biomass/product yield, with the fed-batch culture being one of the most frequently used. Flow cytometry (FCM) is widely applied in biotechnological processes and represents a key methodology to monitor cell population dynamics. We propose here an application of FCM in the analysis of yeast cell cycle along the time course of a typical S. cerevisiae fed-batch culture. We used two different dyes, SYTOX Green and SYBR Green, with the aim to better define each stage of cell cycle during S. cerevisiae fed-batch culture. The results provide novel insights in the use of FCM cell cycle analysis for the real-time monitoring of S. cerevisiae bioprocesses.
Collapse
Affiliation(s)
- Emanuela Palomba
- Department of Research Infrastructures for marine biological resources (RIMAR), Stazione Zoologica “Anton Dohrn”, Villa Comunale, Napoli, Italy
| | | | | | - Palma Parascandola
- Department of Industrial Engineering, University of Salerno, Salerno, Italy
| | - Carmine Landi
- Department of Industrial Engineering, University of Salerno, Salerno, Italy
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples “Federico II”, Naples, Italy
| | - Massimo Sanchez
- Istituto Superiore di Sanità (ISS) Core Facilities, Rome, Italy
| |
Collapse
|
9
|
Xu H, Zhu Y, Du M, Wang Y, Ju S, Ma R, Jiao Z. Subcellular mechanism of microbial inactivation during water disinfection by cold atmospheric-pressure plasma. WATER RESEARCH 2021; 188:116513. [PMID: 33091801 DOI: 10.1016/j.watres.2020.116513] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/15/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Although the identification of effective reactive oxygen species (ROS) generated by plasma has been extensively studied, yet the subcellular mechanism of microbial inactivation has never been clearly elucidated in plasma disinfection processes. In this study, subcellular mechanism of yeast cell inactivation during plasma-liquid interaction was revealed in terms of comprehensive factors including cell morphology, membrane permeability, lipid peroxidation, membrane potential, intracellular redox homeostasis (intracellular ROS and H2O2, and antioxidant system (SOD, CAT and GSH)), intracellular ionic equilibrium (intracellular H+ and K+) and energy metabolism (mitochondrial membrane potential, intracellular Ca2+ and ATP level). The ROS analysis show that ·OH, 1O2, ·O2-and H2O2 were generated in this plasma-liquid interaction system and ·O2-served as the precursor of 1O2. Additionally, the solution pH was reduced. Plasma can effectively inactivate yeast cells mainly via apoptosis by damaging cell membrane, intracellular redox and ion homeostasis and energy metabolism as well as causing DNA fragmentation. ROS scavengers (l-His, d-Man and SOD) and pH buffer (phosphate buffer solution, PBS) were employed to investigate the role of five antimicrobial factors (·OH, 1O2, ·O2-, H2O2 and low pH) in plasma sterilization. Results show that they have different influences on the aforementioned cell physiological activities. The ·OH and 1O2 contributed most to the yeast inactivation. The ·OH mainly attacked cell membrane and increased cell membrane permeability. The disturb of cell energy metabolism was mainly attributed to 1O2. The damage of cell membrane as well as extracellular low pH could break the intracellular ionic equilibrium and further reduce cell membrane potential. The remarkable increase of intracellular H2O2 was mainly due to the influx of extracellular H2O2 via destroyed cell membrane, which played a little role in yeast inactivation during 10-min plasma treatment. These findings provide comprehensive insights into the antimicrobial mechanism of plasma, which can promote the development of plasma as an alternative water disinfection strategy.
Collapse
Affiliation(s)
- Hangbo Xu
- Henan Key Laboratory of Ion-beam Bioengineering, College of Agricultural Science, Zhengzhou University, Zhengzhou 450052, China
| | - Yupan Zhu
- Henan Key Laboratory of Ion-beam Bioengineering, College of Agricultural Science, Zhengzhou University, Zhengzhou 450052, China
| | - Mengru Du
- Henan Key Laboratory of Ion-beam Bioengineering, College of Agricultural Science, Zhengzhou University, Zhengzhou 450052, China
| | - Yuqi Wang
- Henan Key Laboratory of Ion-beam Bioengineering, College of Agricultural Science, Zhengzhou University, Zhengzhou 450052, China
| | - Siyao Ju
- Henan Key Laboratory of Ion-beam Bioengineering, College of Agricultural Science, Zhengzhou University, Zhengzhou 450052, China
| | - Ruonan Ma
- Henan Key Laboratory of Ion-beam Bioengineering, College of Agricultural Science, Zhengzhou University, Zhengzhou 450052, China.
| | - Zhen Jiao
- Henan Key Laboratory of Ion-beam Bioengineering, College of Agricultural Science, Zhengzhou University, Zhengzhou 450052, China.
| |
Collapse
|
10
|
Zhang J, Martinez-Gomez K, Heinzle E, Wahl SA. Metabolic switches from quiescence to growth in synchronized Saccharomyces cerevisiae. Metabolomics 2019; 15:121. [PMID: 31468142 PMCID: PMC6715666 DOI: 10.1007/s11306-019-1584-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 08/09/2019] [Indexed: 12/27/2022]
Abstract
INTRODUCTION The switch from quiescence (G0) into G1 and cell cycle progression critically depends on specific nutrients and metabolic capabilities. Conversely, metabolic networks are regulated by enzyme-metabolite interaction and transcriptional regulation that lead to flux modifications to support cell growth. How cells process and integrate environmental information into coordinated responses is challenging to analyse and not yet described quantitatively. OBJECTIVES To quantitatively monitor the central carbon metabolism during G0 exit and the first 2 h after reentering the cell cycle from synchronized Saccharomyces cerevisiae. METHODS Dynamic tailored 13C metabolic flux analysis was used to observe the intracellular metabolite flux changes, and the metabolome and proteome were observed to identify regulatory mechanisms. RESULTS G0 cells responded immediately to an extracellular increase of glucose. The intracellular metabolic flux changed in time and specific events were observed. High fluxes into trehalose and glycogen synthesis were observed during the G0 exit. Both fluxes then decreased, reaching a minimum at t = 65 min. Here, storage degradation contributed significantly (i.e. 21%) to the glycolytic flux. In contrast to these changes, the glucose uptake rate remained constant after the G0 exit. The flux into the oxidative pentose phosphate pathway was highest (29-fold increase, 36.4% of the glucose uptake) at t = 65 min, while it was very low at other time points. The maximum flux seems to correlate with a late G1 state preparing for the S phase transition. In the G1/S phase (t = 87 min), anaplerotic reactions such as glyoxylate shunt increased. Protein results show that during this transition, proteins belonging to clusters related with ribosome biogenesis and assembly, and initiation transcription factors clusters were continuously synthetised. CONCLUSION The intracellular flux distribution changes dynamically and these major rearrangements highlight the coordinate reorganization of metabolic flux to meet requirements for growth during different cell state.
Collapse
Affiliation(s)
- Jinrui Zhang
- 0000 0001 2097 4740grid.5292.cDepartment of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Karla Martinez-Gomez
- 0000 0001 2167 7588grid.11749.3aBiochemical Engineering, Saarland University, Campus A 1.5, 66123 Saarbrücken, Germany
| | - Elmar Heinzle
- 0000 0001 2167 7588grid.11749.3aBiochemical Engineering, Saarland University, Campus A 1.5, 66123 Saarbrücken, Germany
| | - Sebastian Aljoscha Wahl
- 0000 0001 2097 4740grid.5292.cDepartment of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
11
|
Al-Halhouli A, Albagdady A, Al-Faqheri W, Kottmeier J, Meinen S, Frey LJ, Krull R, Dietzel A. Enhanced inertial focusing of microparticles and cells by integrating trapezoidal microchambers in spiral microfluidic channels. RSC Adv 2019; 9:19197-19204. [PMID: 35516901 PMCID: PMC9064905 DOI: 10.1039/c9ra03587g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/12/2019] [Indexed: 11/21/2022] Open
Abstract
In this work, manipulating width and equilibrium position of fluorescent microparticles in spiral microchannel fractionation devices by embedding microchambers along the last turn of a spiral is reported. Microchambers with different shapes and sizes were tested at Reynolds numbers between 15.7 and 156.6 (100-1000 μL min-1) to observe focusing of 2, 5 and 10 μm fluorescent microparticles. This paper also discusses the fabrication process of the microfluidic chips with femtosecond laser ablation on glass wafers, as well as a particle imaging velocimetry (μPIV) study of microparticle trajectories inside a microchamber. It could be demonstrated with an improved final design with inclined microchamber side walls, that the 2 μm particle equilibrium position is shifted towards the inner wall by ∼27 μm and the focusing line's width is reduced by ∼18 μm. Finally, Saccharomyces cerevisiae yeast cells were tested in the final chip and a cell focusing efficiency of 99.1% is achieved.
Collapse
Affiliation(s)
| | - Ahmed Albagdady
- NanoLab, School of Applied Technical Sciences, German Jordanian University Amman Jordan
| | - Wisam Al-Faqheri
- MicroNano Mechatronic Lab, Mechanical, Automotive & Materials Engineering, University of Windsor Windsor ON Canada
| | - Jonathan Kottmeier
- Institut für Mikrotechnik, Technische Universität Braunschweig Braunschweig Germany
| | - Sven Meinen
- Institut für Mikrotechnik, Technische Universität Braunschweig Braunschweig Germany
| | - Lasse Jannis Frey
- Zentrum für Pharmaverfahrenstechnik, Technische Universität Braunschweig Braunschweig Germany
| | - Rainer Krull
- Zentrum für Pharmaverfahrenstechnik, Technische Universität Braunschweig Braunschweig Germany
| | - Andreas Dietzel
- Institut für Mikrotechnik, Technische Universität Braunschweig Braunschweig Germany
| |
Collapse
|
12
|
Cryptococcus neoformans, Unlike Candida albicans, Forms Aneuploid Clones Directly from Uninucleated Cells under Fluconazole Stress. mBio 2018; 9:mBio.01290-18. [PMID: 30514783 PMCID: PMC6282203 DOI: 10.1128/mbio.01290-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heteroresistance to fluconazole (FLC) in Cryptococcus is a transient adaptive resistance which is lost upon release from the drug pressure. It is known that clones heteroresistant to FLC invariably contain disomic chromosomes, but how disomy is formed remains unclear. Previous reports suggested that the aneuploid heteroresistant colonies in Cryptococcus emerge from multinucleated cells, resembling the case in Candida albicans Although a small number of cells containing multiple nuclei appear in a short time after FLC treatment, we provide evidence that the heteroresistant colonies in the presence of FLC arise from uninucleate cells without involving multinuclear/multimeric stages. We found that fidelity of chromosome segregation in mitosis plays an important role in regulation of FLC heteroresistance frequency in C. neoformans Although FLC-resistant colonies occurred at a very low frequency, we were able to modulate the frequency of heteroresistance by overexpressing SMC1, which encodes a protein containing an SMC domain in chromosome segregation. Using time-lapse microscopy, we captured the entire process of colony formation from a single cell in the presence of FLC. All the multinucleated cells formed within a few hours of FLC exposure failed to multiply after a few cell divisions, and the cells able to proliferate to form colonies were all uninucleate without exception. Furthermore, no nuclear fusion event or asymmetric survival between mother and daughter cells, a hallmark of chromosome nondisjunction in haploid organisms, was observed. Therefore, the mechanisms of aneuploidy formation in C. neoformans appear different from most common categories of aneuploid formation known for yeasts.IMPORTANCE The gold standard of cryptococcosis treatment consists of induction therapy with amphotericin B followed by lifelong maintenance therapy with fluconazole (FLC). However, prolonged exposure to FLC induces the emergence of clones heteroresistant to azoles. All the heteroresistant clones thus far analyzed have been shown to be aneuploids, but how the aneuploid is formed remains unclear. Aneuploidy in fungi and other eukaryotic cells is known to result most commonly from chromosome missegregation during cell division due to defects in any one of the multiple components and processes that are required for the formation of two genetically identical daughter cells. Although formation of multinucleated cells has been observed in cells exposed to FLC, evidence for the emergence of drug-resistant aneuploid populations directly from such cells has been lacking. We show the evidence that the aneuploid in fluconazole-heteroresistant clones of Cryptococcus neoformans is derived neither from multinucleated cells nor from chromosome missegregation.
Collapse
|
13
|
Glycolytic Functions Are Conserved in the Genome of the Wine Yeast Hanseniaspora uvarum, and Pyruvate Kinase Limits Its Capacity for Alcoholic Fermentation. Appl Environ Microbiol 2017; 83:AEM.01580-17. [PMID: 28887422 DOI: 10.1128/aem.01580-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/03/2017] [Indexed: 01/11/2023] Open
Abstract
Hanseniaspora uvarum (anamorph Kloeckera apiculata) is a predominant yeast on wine grapes and other fruits and has a strong influence on wine quality, even when Saccharomyces cerevisiae starter cultures are employed. In this work, we sequenced and annotated approximately 93% of the H. uvarum genome. Southern and synteny analyses were employed to construct a map of the seven chromosomes present in a type strain. Comparative determinations of specific enzyme activities within the fermentative pathway in H. uvarum and S. cerevisiae indicated that the reduced capacity of the former yeast for ethanol production is caused primarily by an ∼10-fold-lower activity of the key glycolytic enzyme pyruvate kinase. The heterologous expression of the encoding gene, H. uvarumPYK1 (HuPYK1), and two genes encoding the phosphofructokinase subunits, HuPFK1 and HuPFK2, in the respective deletion mutants of S. cerevisiae confirmed their functional homology.IMPORTANCEHanseniaspora uvarum is a predominant yeast species on grapes and other fruits. It contributes significantly to the production of desired as well as unfavorable aroma compounds and thus determines the quality of the final product, especially wine. Despite this obvious importance, knowledge on its genetics is scarce. As a basis for targeted metabolic modifications, here we provide the results of a genomic sequencing approach, including the annotation of 3,010 protein-encoding genes, e.g., those encoding the entire sugar fermentation pathway, key components of stress response signaling pathways, and enzymes catalyzing the production of aroma compounds. Comparative analyses suggest that the low fermentative capacity of H. uvarum compared to that of Saccharomyces cerevisiae can be attributed to low pyruvate kinase activity. The data reported here are expected to aid in establishing H. uvarum as a non-Saccharomyces yeast in starter cultures for wine and cider fermentations.
Collapse
|
14
|
Duc C, Pradal M, Sanchez I, Noble J, Tesnière C, Blondin B. A set of nutrient limitations trigger yeast cell death in a nitrogen-dependent manner during wine alcoholic fermentation. PLoS One 2017; 12:e0184838. [PMID: 28922393 PMCID: PMC5602661 DOI: 10.1371/journal.pone.0184838] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/29/2017] [Indexed: 12/27/2022] Open
Abstract
Yeast cell death can occur during wine alcoholic fermentation. It is generally considered to result from ethanol stress that impacts membrane integrity. This cell death mainly occurs when grape musts processing reduces lipid availability, resulting in weaker membrane resistance to ethanol. However the mechanisms underlying cell death in these conditions remain unclear. We examined cell death occurrence considering yeast cells ability to elicit an appropriate response to a given nutrient limitation and thus survive starvation. We show here that a set of micronutrients (oleic acid, ergosterol, pantothenic acid and nicotinic acid) in low, growth-restricting concentrations trigger cell death in alcoholic fermentation when nitrogen level is high. We provide evidence that nitrogen signaling is involved in cell death and that either SCH9 deletion or Tor inhibition prevent cell death in several types of micronutrient limitation. Under such limitations, yeast cells fail to acquire any stress resistance and are unable to store glycogen. Unexpectedly, transcriptome analyses did not reveal any major changes in stress genes expression, suggesting that post-transcriptional events critical for stress response were not triggered by micronutrient starvation. Our data point to the fact that yeast cell death results from yeast inability to trigger an appropriate stress response under some conditions of nutrient limitations most likely not encountered by yeast in the wild. Our conclusions provide a novel frame for considering both cell death and the management of nutrients during alcoholic fermentation.
Collapse
Affiliation(s)
- Camille Duc
- UMR SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France.,Lallemand SAS, Blagnac, France
| | - Martine Pradal
- UMR SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Isabelle Sanchez
- UMR SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Catherine Tesnière
- UMR SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Bruno Blondin
- UMR SPO, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| |
Collapse
|
15
|
FLO5 gene controls flocculation phenotype and adhesive properties in a Saccharomyces cerevisiae sparkling wine strain. Sci Rep 2017; 7:10786. [PMID: 28883485 PMCID: PMC5589750 DOI: 10.1038/s41598-017-09990-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
Flocculation is an important feature for yeast survival in adverse conditions. The natural diversity of flocculating genes in Saccharomyces cerevisiae can also be exploited in several biotechnological applications. Flocculation is mainly regulated by the expression of genes belonging to the FLO family. These genes have a similar function, but their specific contribution to flocculation ability is still unclear. In this study, the distribution of FLO1, FLO5 and FLO8 genes in four S. cerevisiae wine strains was investigated. Subsequently, both FLO1 and FLO5 genes were separately deleted in a flocculent S. cerevisiae wine strain. After gene disruption, flocculation ability and agar adhesion were evaluated. FLO1 and FLO5 genes inheritance was also monitored. All strains presented different lengths for FLO1 and FLO5 genes. Results confirm that in S. cerevisiae strain F6789, the FLO5 gene drives flocculation and influences adhesive properties. Flocculation ability monitoring after a cross with a non-flocculent strain revealed that FLO5 is the gene responsible for flocculation development.
Collapse
|
16
|
Dos Santos LV, Carazzolle MF, Nagamatsu ST, Sampaio NMV, Almeida LD, Pirolla RAS, Borelli G, Corrêa TLR, Argueso JL, Pereira GAG. Unraveling the genetic basis of xylose consumption in engineered Saccharomyces cerevisiae strains. Sci Rep 2016; 6:38676. [PMID: 28000736 PMCID: PMC5175268 DOI: 10.1038/srep38676] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/11/2016] [Indexed: 11/21/2022] Open
Abstract
The development of biocatalysts capable of fermenting xylose, a five-carbon sugar abundant in lignocellulosic biomass, is a key step to achieve a viable production of second-generation ethanol. In this work, a robust industrial strain of Saccharomyces cerevisiae was modified by the addition of essential genes for pentose metabolism. Subsequently, taken through cycles of adaptive evolution with selection for optimal xylose utilization, strains could efficiently convert xylose to ethanol with a yield of about 0.46 g ethanol/g xylose. Though evolved independently, two strains carried shared mutations: amplification of the xylose isomerase gene and inactivation of ISU1, a gene encoding a scaffold protein involved in the assembly of iron-sulfur clusters. In addition, one of evolved strains carried a mutation in SSK2, a member of MAPKKK signaling pathway. In validation experiments, mutating ISU1 or SSK2 improved the ability to metabolize xylose of yeast cells without adaptive evolution, suggesting that these genes are key players in a regulatory network for xylose fermentation. Furthermore, addition of iron ion to the growth media improved xylose fermentation even by non-evolved cells. Our results provide promising new targets for metabolic engineering of C5-yeasts and point to iron as a potential new additive for improvement of second-generation ethanol production.
Collapse
Affiliation(s)
- Leandro Vieira Dos Santos
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil.,GranBio/BioCelere, Campinas, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Sheila Tiemi Nagamatsu
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Nádia Maria Vieira Sampaio
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins-CO, 80523-1618, USA
| | | | | | - Guilherme Borelli
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins-CO, 80523-1618, USA
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil.,GranBio/BioCelere, Campinas, Brazil
| |
Collapse
|
17
|
Kumar R, Srivastava S. Quantitative proteomic comparison of stationary/G0 phase cells and tetrads in budding yeast. Sci Rep 2016; 6:32031. [PMID: 27558777 PMCID: PMC4997312 DOI: 10.1038/srep32031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/02/2016] [Indexed: 02/08/2023] Open
Abstract
Most of the microbial cells on earth under natural conditions exist in a dormant condition, commonly known as quiescent state. Quiescent cells exhibit low rates of transcription and translation suggesting that cellular abundance of proteins may be similar in quiescent cells. Therefore, this study aim to compare the proteome of budding yeast cells from two quiescent states viz. stationary phase/G0 and tetrads. Using iTRAQ (isobaric tag for relative and absolute quantitation) based quantitative proteomics we identified 289 proteins, among which around 40 proteins exhibited ±1.5 fold change consistently from the four biological replicates. Proteomics data was validated by western blot and denstiometric analysis of Hsp12 and Spg4. Level of budding yeast 14-3-3 proteins was found to be similar in both the quiescent states, whereas Hsp12 and Spg4 expressed only during stress. FACS (fluorescence-activated cell sorting) analysis showed that budding yeast cells were arrested at G1 stages both in tetrads as well as in stationary phase. We also observed that quiescent states did not express Ime1 (inducer of meiosis). Taken together, our present study demonstrates that the cells in quiescent state may have similar proteome, and accumulation of proteins like Hsp12, Hsp26, and Spg4 may play an important role in retaining viability of the cells during dormancy.
Collapse
Affiliation(s)
- Ravinder Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, Maharashtra, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, Maharashtra, India
| |
Collapse
|
18
|
The fungicide Mancozeb induces metacaspase-dependent apoptotic cell death in Saccharomyces cerevisiae BY4741. Apoptosis 2016; 21:866-72. [DOI: 10.1007/s10495-016-1251-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
19
|
Brion C, Pflieger D, Souali-Crespo S, Friedrich A, Schacherer J. Differences in environmental stress response among yeasts is consistent with species-specific lifestyles. Mol Biol Cell 2016; 27:1694-705. [PMID: 27009200 PMCID: PMC4865325 DOI: 10.1091/mbc.e15-12-0816] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/15/2016] [Indexed: 12/19/2022] Open
Abstract
Defining how organisms respond to environmental change has always been an important step toward understanding their adaptive capacity and physiology. Variation in transcription during stress has been widely described in model species, especially in the yeast Saccharomyces cerevisiae, which helped to shape general rules regarding how cells cope with environmental constraints, as well as to decipher the functions of many genes. Comparison of the environmental stress response (ESR) across species is essential to obtaining better insight into the common and species-specific features of stress defense. In this context, we explored the transcriptional landscape of the yeast Lachancea kluyveri (formerly Saccharomyces kluyveri) in response to diverse stresses, using RNA sequencing. We investigated variation in gene expression and observed a link between genetic plasticity and environmental sensitivity. We identified the ESR genes in this species and compared them to those already found in S. cerevisiae We observed common features between the two species, as well as divergence in the regulatory networks involved. Of interest, some changes were related to differences in species lifestyle. Thus we were able to decipher how adaptation to stress has evolved among different yeast species. Finally, by analyzing patterns of coexpression, we were able to propose potential biological functions for 42% of genes and also annotate 301 genes for which no function could be assigned by homology. This large data set allowed for the characterization of the evolution of gene regulation and provides an efficient tool for assessing gene function.
Collapse
Affiliation(s)
- Christian Brion
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg 67083, France
| | - David Pflieger
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg 67083, France
| | - Sirine Souali-Crespo
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg 67083, France
| | - Anne Friedrich
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg 67083, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR7156, Strasbourg 67083, France
| |
Collapse
|
20
|
Accelerating Mutational Load Is Not Due to Synergistic Epistasis or Mutator Alleles in Mutation Accumulation Lines of Yeast. Genetics 2015; 202:751-63. [PMID: 26596348 DOI: 10.1534/genetics.115.182774] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/20/2015] [Indexed: 11/18/2022] Open
Abstract
Much of our knowledge about the fitness effects of new mutations has been gained from mutation accumulation (MA) experiments. Yet the fitness effect of single mutations is rarely measured in MA experiments. This raises several issues, notably for inferring epistasis for fitness. The acceleration of fitness decline in MA lines has been taken as evidence for synergistic epistasis, but establishing the role of epistasis requires measuring the fitness of genotypes carrying known numbers of mutations. Otherwise, accelerating fitness loss could be explained by increased genetic mutation rates. Here we segregated mutations accumulated over 4800 generations in haploid and diploid MA lines of the yeast Saccharomyces cerevisiae. We found no correspondence between an accelerated fitness decline and synergistic epistasis among deleterious mutations in haploid lines. Pairs of mutations showed no overall epistasis. Furthermore, several lines of evidence indicate that genetic mutation rates did not increase in the MA lines. Crucially, segregant fitness analyses revealed that MA accelerated in both haploid and diploid lines, even though the fitness of diploid lines was nearly constant during the MA experiment. This suggests that the accelerated fitness decline in haploids was caused by cryptic environmental factors that increased mutation rates in all lines during the last third of the lines' transfers. In addition, we provide new estimates of deleterious mutation rates, including lethal mutations, and highlight that nearly all the mutational load we observed was due to one or two mutations having a large effect on fitness.
Collapse
|
21
|
Tapsoba F, Legras JL, Savadogo A, Dequin S, Traore AS. Diversity of Saccharomyces cerevisiae strains isolated from Borassus akeassii palm wines from Burkina Faso in comparison to other African beverages. Int J Food Microbiol 2015. [DOI: 10.1016/j.ijfoodmicro.2015.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
22
|
do Carmo Silva L, Tamayo Ossa DP, Castro SVDC, Bringel Pires L, Alves de Oliveira CM, Conceição da Silva C, Coelho NP, Bailão AM, Parente-Rocha JA, Soares CMDA, Ruiz OH, Ochoa JGM, Pereira M. Transcriptome Profile of the Response of Paracoccidioides spp. to a Camphene Thiosemicarbazide Derivative. PLoS One 2015; 10:e0130703. [PMID: 26114868 PMCID: PMC4483234 DOI: 10.1371/journal.pone.0130703] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/23/2015] [Indexed: 01/06/2023] Open
Abstract
Paracoccidioidomycosis (PCM) is a systemic granulomatous human mycosis caused by fungi of the genus Paracoccidioides, which is geographically restricted to Latin America. Inhalation of spores, the infectious particles of the fungus, is a common route of infection. The PCM treatment of choice is azoles such as itraconazole, but sulfonamides and amphotericin B are used in some cases despite their toxicity to mammalian cells. The current availability of treatments highlights the need to identify and characterize novel targets for antifungal treatment of PCM as well as the need to search for new antifungal compounds obtained from natural sources or by chemical synthesis. To this end, we evaluated the antifungal activity of a camphene thiosemicarbazide derivative (TSC-C) compound on Paracoccidioides yeast. To determine the response of Paracoccidioides spp. to TSC-C, we analyzed the transcriptional profile of the fungus after 8 h of contact with the compound. The results demonstrate that Paracoccidioides lutzii induced the expression of genes related to metabolism; cell cycle and DNA processing; biogenesis of cellular components; cell transduction/signal; cell rescue, defense and virulence; cellular transport, transport facilities and transport routes; energy; protein synthesis; protein fate; transcription; and other proteins without classification. Additionally, we observed intensely inhibited genes related to protein synthesis. Analysis by fluorescence microscopy and flow cytometry revealed that the compound induced the production of reactive oxygen species. Using an isolate with down-regulated SOD1 gene expression (SOD1-aRNA), we sought to determine the function of this gene in the defense of Paracoccidioides yeast cells against the compound. Mutant cells were more susceptible to TSC-C, demonstrating the importance of this gene in response to the compound. The results presented herein suggest that TSC-C is a promising candidate for PCM treatment.
Collapse
Affiliation(s)
- Lívia do Carmo Silva
- Laboratório de Biologia Molecular, Instituto de Patologia Tropical e Saúde Pública Universidade Federal de Goiás, Goiânia, Brazil
| | - Diana Patrícia Tamayo Ossa
- Unidad de Biología Celular y Molecular, Corporación para Investigaciones Biológicas (CIB) and Facultad de Medicina Universidad de Antioquia, Medellín, Colombia
| | | | - Ludmila Bringel Pires
- Laboratório de Produtos Naturais, Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil
| | | | - Cleuza Conceição da Silva
- Laboratório de Fitoquímica e Síntese Orgânica, Departamento de Química, Universidade Estadual de Maringá, Paraná, Brazil
| | - Narcimário Pereira Coelho
- Laboratório de Fitoquímica e Síntese Orgânica, Departamento de Química, Universidade Estadual de Maringá, Paraná, Brazil
| | - Alexandre Melo Bailão
- Laboratório de Biologia Molecular, Instituto de Patologia Tropical e Saúde Pública Universidade Federal de Goiás, Goiânia, Brazil
| | - Juliana Alves Parente-Rocha
- Laboratório de Biologia Molecular, Instituto de Patologia Tropical e Saúde Pública Universidade Federal de Goiás, Goiânia, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Patologia Tropical e Saúde Pública Universidade Federal de Goiás, Goiânia, Brazil
| | - Orville Hernández Ruiz
- Unidad de Biología Celular y Molecular, Corporación para Investigaciones Biológicas (CIB) and Facultad de Medicina Universidad de Antioquia, Medellín, Colombia
| | - Juan G. McEwen Ochoa
- Unidad de Biología Celular y Molecular, Corporación para Investigaciones Biológicas (CIB) and Facultad de Medicina Universidad de Antioquia, Medellín, Colombia
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Instituto de Patologia Tropical e Saúde Pública Universidade Federal de Goiás, Goiânia, Brazil
- * E-mail:
| |
Collapse
|
23
|
Population structure and comparative genome hybridization of European flor yeast reveal a unique group of Saccharomyces cerevisiae strains with few gene duplications in their genome. PLoS One 2014; 9:e108089. [PMID: 25272156 PMCID: PMC4182726 DOI: 10.1371/journal.pone.0108089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/11/2014] [Indexed: 02/03/2023] Open
Abstract
Wine biological aging is a wine making process used to produce specific beverages in several countries in Europe, including Spain, Italy, France, and Hungary. This process involves the formation of a velum at the surface of the wine. Here, we present the first large scale comparison of all European flor strains involved in this process. We inferred the population structure of these European flor strains from their microsatellite genotype diversity and analyzed their ploidy. We show that almost all of these flor strains belong to the same cluster and are diploid, except for a few Spanish strains. Comparison of the array hybridization profile of six flor strains originating from these four countries, with that of three wine strains did not reveal any large segmental amplification. Nonetheless, some genes, including YKL221W/MCH2 and YKL222C, were amplified in the genome of four out of six flor strains. Finally, we correlated ICR1 ncRNA and FLO11 polymorphisms with flor yeast population structure, and associate the presence of wild type ICR1 and a long Flo11p with thin velum formation in a cluster of Jura strains. These results provide new insight into the diversity of flor yeast and show that combinations of different adaptive changes can lead to an increase of hydrophobicity and affect velum formation.
Collapse
|