Microbial Cell最新文献_第5页

Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast 条形码测序和高通量测定时间顺序寿命揭示老化相关基因在裂变酵母

IF 4.6 3区生物学

Microbial Cell Pub Date : 2021-03-04 DOI: 10.1101/2021.03.04.433786

Catalina-Andreea Romila, StJohn Townsend, M. Malecki, S. Kamrad, María Rodríguez-López, Olivia Hillson, Cristina Cotobal, M. Ralser, J. Bähler

{"title":"Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast","authors":"Catalina-Andreea Romila, StJohn Townsend, M. Malecki, S. Kamrad, María Rodríguez-López, Olivia Hillson, Cristina Cotobal, M. Ralser, J. Bähler","doi":"10.1101/2021.03.04.433786","DOIUrl":"https://doi.org/10.1101/2021.03.04.433786","url":null,"abstract":"Ageing-related processes are largely conserved, with simple organisms remaining the main platform to discover and dissect new ageing-associated genes. Yeasts provide potent model systems to study cellular ageing owing their amenability to systematic functional assays under controlled conditions. Even with yeast cells, however, ageing assays can be laborious and resource-intensive. Here we present improved experimental and computational methods to study chronological lifespan in Schizosaccharomyces pombe. We decoded the barcodes for 3206 mutants of the latest gene-deletion library, enabling the parallel profiling of ∼700 additional mutants compared to previous screens. We then applied a refined method of barcode sequencing (Bar-seq), addressing technical and statistical issues raised by persisting DNA in dead cells and sampling bottlenecks in aged cultures, to screen for mutants showing altered lifespan during stationary phase. This screen identified 341 long-lived mutants and 1246 short-lived mutants which point to many previously unknown ageing-associated genes, including 51 conserved but entirely uncharacterized genes. The ageing-associated genes showed coherent enrichments in processes also associated with human ageing, particularly with respect to ageing in non-proliferative brain cells. We also developed an automated colony-forming unit assay for chronological lifespan to facilitate medium- to high-throughput ageing studies by saving time and resources compared to the traditional assay. Results from the Bar-seq screen showed good agreement with this new assay, validating 33 genes not previously associated with cellular ageing. This study provides an effective methodological platform and identifies many new ageing-associated genes as a framework for analysing cellular ageing in yeast and beyond.","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":"8 1","pages":"146 - 160"},"PeriodicalIF":4.6,"publicationDate":"2021-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47081069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Broad-spectrum antifungal activities and mechanism of drimane sesquiterpenoids drimane倍半萜类化合物的广谱抗真菌活性及其作用机制

IF 4.6 3区生物学

Microbial Cell Pub Date : 2019-10-23 DOI: 10.1101/816082

Edruce Edouarzin, Connor Horn, Anuja Paduyal, Cunli Zhang, Jianyu Lu, Zongbo Tong, G. Giaever, C. Nislow, R. Veerapandian, D. Hua, Govindsamy Vediyappan

{"title":"Broad-spectrum antifungal activities and mechanism of drimane sesquiterpenoids","authors":"Edruce Edouarzin, Connor Horn, Anuja Paduyal, Cunli Zhang, Jianyu Lu, Zongbo Tong, G. Giaever, C. Nislow, R. Veerapandian, D. Hua, Govindsamy Vediyappan","doi":"10.1101/816082","DOIUrl":"https://doi.org/10.1101/816082","url":null,"abstract":"Eight drimane sesquiterpenoids including (-)-drimenol and (+)-albicanol were synthesized from (+)-sclareolide and evaluated for their antifungal activities. Three compounds, (-)-drimenol, (+)-albicanol, and (1R,2R,4aS,8aS)-2-hydroxy-2,5,5,8a-tetramethyl-decahydronaphthalene-1-carbaldehyde (4) showed strong activity against C. albicans. (-)-Drimenol, the strongest inhibitor of the three, (at concentrations of 8 – 64 μg/ml, causing 100% death of fungi), acts not only against C. albicans as a fungicidal manner, but also inhibits other fungi such as Aspergillus, Cryptococcus, Pneumocystis, Blastomyces, Fusarium, Rhizopus, Saksenaea and FLU resistant strains of C. albicans, C. glabrata, C. krusei, C. parapsilosis and C. auris. These observations suggest drimenol is a broad-spectrum antifungal agent. At high concentration (100 μg/ml), drimenol caused a rupture of the fungal cell wall/membrane. In a nematode model of C. albicans infection, drimenol rescued the worms from C. albicans-mediated death, indicating drimenol is tolerable and bioactive in a metazoan. Genome-wide fitness profiling assays of both S. cerevisiae (nonessential homozygous and essential heterozygous) and C. albicans (Tn-insertion mutants) collections revealed putative genes and pathways affected by drimenol. Using a C. albicans mutants spot assay, the Crk1 kinase associated gene products, Ret2, Cdc37, and novel putative targets orf19.759, orf19.1672, and orf19.4382 were revealed to be the potential targets of drimenol. Further, computational modeling results suggest possible modification of the structure of drimenol including the A ring for improving antifungal activity.","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":"7 1","pages":"146 - 159"},"PeriodicalIF":4.6,"publicationDate":"2019-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43221812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Yet another job for the bacterial ribosome 这是细菌核糖体的另一项工作

IF 4.6 3区生物学

Microbial Cell Pub Date : 2019-10-17 DOI: 10.15698/mic2019.11.698

Andrea Origi, Ana Natriashivili, Lara Knüpffer, C. Fehrenbach, Kärt Denks, Rosella Asti, H. Koch

引用次数: 3

Type II-Metacaspases are involved in cell stress but not in cell death in the unicellular green alga Dunaliella tertiolecta 在单细胞绿藻Dunaliella tertiolecta中，II型半胱天冬酶参与细胞应激，但不参与细胞死亡

IF 4.6 3区生物学

Microbial Cell Pub Date : 2019-10-07 DOI: 10.15698/mic2019.11.696

M. Mata, Armando Palma, C. García-Gómez, María López-Parages, V. Vázquez, Iván Cheng-Sánchez, F. Sarabia, F. López-Figueroa, C. Jiménez, M. Segovia

{"title":"Type II-Metacaspases are involved in cell stress but not in cell death in the unicellular green alga Dunaliella tertiolecta","authors":"M. Mata, Armando Palma, C. García-Gómez, María López-Parages, V. Vázquez, Iván Cheng-Sánchez, F. Sarabia, F. López-Figueroa, C. Jiménez, M. Segovia","doi":"10.15698/mic2019.11.696","DOIUrl":"https://doi.org/10.15698/mic2019.11.696","url":null,"abstract":"Ultraviolet radiation (UVR; 280–400 nm) has a great impact on aquatic ecosystems by affecting ecophysiological and biogeochemical processes as a consequence of the global change scenario generated by anthropogenic activities. We studied the effect of PAR (P)+UVA (A)+UVB (B) i.e. PAB, on the molecular physiology of the unicellular green alga Dunaliella tertiolecta for six days. We assessed the relationship between the triggered UVR stress response and metacaspases and caspase-like (CL)activities, which are proteases denoted to participate in cell death (CD) in phytoplankton. UVR inhibited cell growth and in vivo chlorophyll a fluorescence but did not cause cell death. Western blot analyses reflected that Type-II metacaspases (MCs) are present and appear to be involved in UVR induced-cell stress but not in dark-induced CD in D. tertiolecta. Enzyme kinetics revealed that cleavage of the MCs-reporter substrates RVRR, QRR, GRR, LKR, HEK, and VLK was 10-fold higher than WEHD, DEVD, IETD, and LETD CLs-substrates. The lowest apparent Michaelis-Menten constants (KMap) corresponded to RVRRase (37.5 μM) indicating a high affinity by the RVRR substrate. The inhibition of enzymatic activities by using inhibitors with different target sites for hydrolyses demonstrated that from all of the R/ Kase activities only RVRRase was a potential candidate for being a metacaspase. In parallel, zymograms and peptide-mass fingerprinting analyses revealed the identities of such Rase activities suggesting an indirect evidence of possible natural physiological substrates of MCs. We present evidence of type II-MCs not being involved in CD in D. tertiolecta, but rather in survival strategies under the stressful irradiance conditions applied in this study.","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":"6 1","pages":"494 - 508"},"PeriodicalIF":4.6,"publicationDate":"2019-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47318428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Transcriptomic and chemogenomic analyses unveil the essential role of Com2-regulon in response and tolerance of Saccharomyces cerevisiae to stress induced by sulfur dioxide 转录组学和化学基因组学分析揭示了com2调控在酿酒酵母对二氧化硫胁迫的响应和耐受中的重要作用

IF 4.6 3区生物学

Microbial Cell Pub Date : 2019-09-30 DOI: 10.15698/mic2019.11.697

Patrícia Lage, B. Sampaio-Marques, P. Ludovico, N. Mira, A. Mendes-Ferreira

{"title":"Transcriptomic and chemogenomic analyses unveil the essential role of Com2-regulon in response and tolerance of Saccharomyces cerevisiae to stress induced by sulfur dioxide","authors":"Patrícia Lage, B. Sampaio-Marques, P. Ludovico, N. Mira, A. Mendes-Ferreira","doi":"10.15698/mic2019.11.697","DOIUrl":"https://doi.org/10.15698/mic2019.11.697","url":null,"abstract":"During vinification Saccharomyces cerevisiae cells are frequently exposed to high concentrations of sulfur dioxide (SO2) that is used to avoid overgrowth of unwanted bacteria or fungi present in the must. Up to now the characterization of the molecular mechanisms by which S. cerevisiae responds and tolerates SO2 was focused on the role of the sulfite efflux pump Ssu1 and investigation on the involvement of other players has been scarce, especially at a genome-wide level. In this work, we uncovered the essential role of the poorly characterized transcription factor Com2 in tolerance and response of S. cerevisiae to stress induced by SO2 at the enologically relevant pH of 3.5. Transcriptomic analysis revealed that Com2 controls, directly or indirectly, the expression of more than 80% of the genes activated by SO2, a percentage much higher than the one that could be attributed to any other stress-responsive transcription factor. Large-scale phenotyping of the yeast haploid mutant collection led to the identification of 50 Com2-targets contributing to the protection against SO2 including all the genes that compose the sulfate reduction pathway (MET3, MET14, MET16, MET5, MET10) and the majority of the genes required for biosynthesis of lysine (LYS2, LYS21, LYS20, LYS14, LYS4, LYS5, LYS1 and LYS9) or arginine (ARG5,6, ARG4, ARG2, ARG3, ARG7, ARG8, ORT1 and CPA1). Other uncovered determinants of resistance to SO2 (not under the control of Com2) included genes required for function and assembly of the vacuolar proton pump and enzymes of the antioxidant defense, consistent with the observed cytosolic and mitochondrial accumulation of reactive oxygen species in SO2-stressed yeast cells.","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":"6 1","pages":"509 - 523"},"PeriodicalIF":4.6,"publicationDate":"2019-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45894582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Gut microbial metabolites in depression: understanding the biochemical mechanisms 抑郁症中的肠道微生物代谢物:了解生化机制

IF 4.6 3区生物学

Microbial Cell Pub Date : 2019-09-27 DOI: 10.15698/mic2019.10.693

G. Caspani, S. Kennedy, J. Foster, J. Swann

{"title":"Gut microbial metabolites in depression: understanding the biochemical mechanisms","authors":"G. Caspani, S. Kennedy, J. Foster, J. Swann","doi":"10.15698/mic2019.10.693","DOIUrl":"https://doi.org/10.15698/mic2019.10.693","url":null,"abstract":"Gastrointestinal and central function are intrinsically connected by the gut microbiota, an ecosystem that has co-evolved with the host to expand its biotransformational capabilities and interact with host physiological processes by means of its metabolic products. Abnormalities in this microbiota-gut-brain axis have emerged as a key component in the pathophysiology of depression, leading to more research attempting to understand the neuroactive potential of the products of gut microbial metabolism. This review explores the potential for the gut microbiota to contribute to depression and focuses on the role that microbially-derived molecules – neurotransmitters, short-chain fatty acids, indoles, bile acids, choline metabolites, lactate and vitamins – play in the context of emotional behavior. The future of gut-brain axis research lies is moving away from association, towards the mechanisms underlying the relationship between the gut bacteria and depressive behavior. We propose that direct and indirect mechanisms exist through which gut microbial metabolites affect depressive behavior: these include (i) direct stimulation of central receptors, (ii) peripheral stimulation of neural, endocrine, and immune mediators, and (iii) epigenetic regulation of histone acetylation and DNA methylation. Elucidating these mechanisms is essential to expand our understanding of the etiology of depression, and to develop new strategies to harness the beneficial psychotropic effects of these molecules. Overall, the review highlights the potential for dietary interventions to represent such novel therapeutic strategies for major depressive disorder.","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":"6 1","pages":"454 - 481"},"PeriodicalIF":4.6,"publicationDate":"2019-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.15698/mic2019.10.693","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45652772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 125

Proline metabolism regulates replicative lifespan in the yeast Saccharomyces cerevisiae 脯氨酸代谢调节酿酒酵母的繁殖寿命

IF 4.6 3区生物学

Microbial Cell Pub Date : 2019-09-24 DOI: 10.15698/mic2019.10.694

Y. Mukai, Yuka Kamei, Xu Liu, Sha Jiang, Yukiko Sugimoto, Noreen Suliani Mat Nanyan, D. Watanabe, H. Takagi

{"title":"Proline metabolism regulates replicative lifespan in the yeast Saccharomyces cerevisiae","authors":"Y. Mukai, Yuka Kamei, Xu Liu, Sha Jiang, Yukiko Sugimoto, Noreen Suliani Mat Nanyan, D. Watanabe, H. Takagi","doi":"10.15698/mic2019.10.694","DOIUrl":"https://doi.org/10.15698/mic2019.10.694","url":null,"abstract":"In many plants and microorganisms, intracellular proline has a protective role against various stresses, including heat-shock, oxidation and osmolarity. Environmental stresses induce cellular senescence in a variety of eukaryotes. Here we showed that intracellular proline regulates the replicative lifespan in the budding yeast Saccharomyces cerevisiae. Deletion of the proline oxidase gene PUT1 and expression of the γ-glutamate kinase mutant gene PRO1-I150T that is less sensitive to feedback inhibition accumulated proline and extended the replicative lifespan of yeast cells. Inversely, disruption of the proline biosynthetic genes PRO1, PRO2, and CAR2 decreased stationary proline level and shortened the lifespan of yeast cells. Quadruple disruption of the proline transporter genes unexpectedly did not change intracellular proline levels and replicative lifespan. Overexpression of the stress-responsive transcription activator gene MSN2 reduced intracellular proline levels by inducing the expression of PUT1, resulting in a short lifespan. Thus, the intracellular proline levels at stationary phase was positively correlated with the replicative lifespan. Furthermore, multivariate analysis of amino acids in yeast mutants deficient in proline metabolism showed characteristic metabolic profiles coincident with longevity: acidic and basic amino acids and branched-chain amino acids positively contributed to the replicative lifespan. These results allude to proline metabolism having a physiological role in maintaining the lifespan of yeast cells.","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":"6 1","pages":"482 - 490"},"PeriodicalIF":4.6,"publicationDate":"2019-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44171015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 15

The multiple functions of the numerous Chlamydia trachomatis secreted proteins: the tip of the iceberg 沙眼衣原体分泌蛋白的多种功能：冰山一角

IF 4.6 3区生物学

Microbial Cell Pub Date : 2019-08-21 DOI: 10.15698/mic2019.09.691

Joana N. Bugalhão, L. J. Mota

引用次数: 33

Diverse conditions support near-zero growth in yeast: Implications for the study of cell lifespan 多种条件支持酵母近乎零生长：对细胞寿命研究的启示

IF 4.6 3区生物学

Microbial Cell Pub Date : 2019-08-20 DOI: 10.15698/mic2019.09.690

Jordan Gulli, E. Cook, Eugene Kroll, Adam P. Rosebrock, A. Caudy, Frank Rosenzweig

{"title":"Diverse conditions support near-zero growth in yeast: Implications for the study of cell lifespan","authors":"Jordan Gulli, E. Cook, Eugene Kroll, Adam P. Rosebrock, A. Caudy, Frank Rosenzweig","doi":"10.15698/mic2019.09.690","DOIUrl":"https://doi.org/10.15698/mic2019.09.690","url":null,"abstract":"Baker's yeast has a finite lifespan and ages in two ways: a mother cell can only divide so many times (its replicative lifespan), and a non-dividing cell can only live so long (its chronological lifespan). Wild and laboratory yeast strains exhibit natural variation for each type of lifespan, and the genetic basis for this variation has been generalized to other eukaryotes, including metazoans. To date, yeast chronological lifespan has chiefly been studied in relation to the rate and mode of functional decline among non-dividing cells in nutrient-depleted batch culture. However, this culture method does not accurately capture two major classes of long-lived metazoan cells: cells that are terminally differentiated and metabolically active for periods that approximate animal lifespan (e.g. cardiac myocytes), and cells that are pluripotent and metabolically quiescent (e.g. stem cells). Here, we consider alternative ways of cultivating Saccharomyces cerevisiae so that these different metabolic states can be explored in non-dividing cells: (i) yeast cultured as giant colonies on semi-solid agar, (ii) yeast cultured in retentostats and provided sufficient nutrients to meet minimal energy requirements, and (iii) yeast encapsulated in a semisolid matrix and fed ad libitum in bioreactors. We review the physiology of yeast cultured under each of these conditions, and explore their potential to provide unique insights into determinants of chronological lifespan in the cells of higher eukaryotes.","PeriodicalId":18397,"journal":{"name":"Microbial Cell","volume":"6 1","pages":"397 - 413"},"PeriodicalIF":4.6,"publicationDate":"2019-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43562953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Inhibiting eukaryotic ribosome biogenesis: Mining new tools for basic research and medical applications. 抑制真核核糖体生物发生：为基础研究和医学应用挖掘新工具

IF 4.6 3区生物学

Microbial Cell Pub Date : 2019-08-20 DOI: 10.15698/mic2019.10.695

Lisa Kofler, Michael Prattes, Helmut Bergler

引用次数: 0