201
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Shao B, Yuan H, Zhang R, Wang X, Zhang S, Ouyang Q, Hao N, Luo C. Reconstructing the regulatory circuit of cell fate determination in yeast mating response. PLoS Comput Biol 2017; 13:e1005671. [PMID: 28742153 PMCID: PMC5546706 DOI: 10.1371/journal.pcbi.1005671] [Citation(s) in RCA: 5] [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: 03/28/2017] [Revised: 08/07/2017] [Accepted: 07/09/2017] [Indexed: 12/22/2022] Open
Abstract
Massive technological advances enabled high-throughput measurements of proteomic changes in biological processes. However, retrieving biological insights from large-scale protein dynamics data remains a challenging task. Here we used the mating differentiation in yeast Saccharomyces cerevisiae as a model and developed integrated experimental and computational approaches to analyze the proteomic dynamics during the process of cell fate determination. When exposed to a high dose of mating pheromone, the yeast cell undergoes growth arrest and forms a shmoo-like morphology; however, at intermediate doses, chemotropic elongated growth is initialized. To understand the gene regulatory networks that control this differentiation switch, we employed a high-throughput microfluidic imaging system that allows real-time and simultaneous measurements of cell growth and protein expression. Using kinetic modeling of protein dynamics, we classified the stimulus-dependent changes in protein abundance into two sources: global changes due to physiological alterations and gene-specific changes. A quantitative framework was proposed to decouple gene-specific regulatory modes from the growth-dependent global modulation of protein abundance. Based on the temporal patterns of gene-specific regulation, we established the network architectures underlying distinct cell fates using a reverse engineering method and uncovered the dose-dependent rewiring of gene regulatory network during mating differentiation. Furthermore, our results suggested a potential crosstalk between the pheromone response pathway and the target of rapamycin (TOR)-regulated ribosomal biogenesis pathway, which might underlie a cell differentiation switch in yeast mating response. In summary, our modeling approach addresses the distinct impacts of the global and gene-specific regulation on the control of protein dynamics and provides new insights into the mechanisms of cell fate determination. We anticipate that our integrated experimental and modeling strategies could be widely applicable to other biological systems. A systematic characterization of the proteomic changes during the process of cell differentiation is critical for understanding the underlying molecular mechanisms. However, protein expression can be largely affected by changes in cell physiological state, which hampers the detection of regulatory interactions. Here we proposed an integrated experimental and computational framework to reconstruct regulatory circuits in mating differentiation of budding yeast Saccharomyces cerevisiae, in which distinct cell fates are triggered by alteration in pheromone concentration. A modeling approach was developed to decouple gene-specific regulation from growth-dependent global regulation of protein expression, allowing us to reverse engineering the gene regulatory circuits underlying distinct cell fates. Our work highlights the importance of model-based analysis of proteomic data and delivers new insight into dose-dependent differentiation behavior of budding yeast.
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Affiliation(s)
- Bin Shao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Haiyu Yuan
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Rongfei Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xuan Wang
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
| | - Shuwen Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (CL); (NH)
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
- * E-mail: (CL); (NH)
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202
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Chang YL, Tseng SF, Huang YC, Shen ZJ, Hsu PH, Hsieh MH, Yang CW, Tognetti S, Canal B, Subirana L, Wang CW, Chen HT, Lin CY, Posas F, Teng SC. Yeast Cip1 is activated by environmental stress to inhibit Cdk1-G1 cyclins via Mcm1 and Msn2/4. Nat Commun 2017; 8:56. [PMID: 28676626 PMCID: PMC5496861 DOI: 10.1038/s41467-017-00080-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/01/2017] [Indexed: 12/20/2022] Open
Abstract
Upon environmental changes, proliferating cells delay cell cycle to prevent further damage accumulation. Yeast Cip1 is a Cdk1 and Cln2-associated protein. However, the function and regulation of Cip1 are still poorly understood. Here we report that Cip1 expression is co-regulated by the cell-cycle-mediated factor Mcm1 and the stress-mediated factors Msn2/4. Overexpression of Cip1 arrests cell cycle through inhibition of Cdk1–G1 cyclin complexes at G1 stage and the stress-activated protein kinase-dependent Cip1 T65, T69, and T73 phosphorylation may strengthen the Cip1and Cdk1–G1 cyclin interaction. Cip1 accumulation mainly targets Cdk1–Cln3 complex to prevent Whi5 phosphorylation and inhibit early G1 progression. Under osmotic stress, Cip1 expression triggers transient G1 delay which plays a functionally redundant role with another hyperosmolar activated CKI, Sic1. These findings indicate that Cip1 functions similarly to mammalian p21 as a stress-induced CDK inhibitor to decelerate cell cycle through G1 cyclins to cope with environmental stresses. A G1 cell cycle regulatory kinase Cip1 has been identified in budding yeast but how this is regulated is unclear. Here the authors identify cell cycle (Mcm1) and stress-mediated (Msn 2/4) transcription factors as regulating Cip1, causing stress induced CDK inhibition and delay in cell cycle progression.
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Affiliation(s)
- Ya-Lan Chang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Shun-Fu Tseng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.,Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, 11490, Taiwan
| | - Yu-Ching Huang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Zih-Jie Shen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Meng-Hsun Hsieh
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chia-Wei Yang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Silvia Tognetti
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Berta Canal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Laia Subirana
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Chien-Wei Wang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Hsiao-Tan Chen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chi-Ying Lin
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
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203
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Sharma S, Sourirajan A, Dev K. Role of Saccharomyces cerevisiae TAN1 (tRNA acetyltransferase) in eukaryotic initiation factor 2B (eIF2B)-mediated translation control and stress response. 3 Biotech 2017; 7:223. [PMID: 28677085 DOI: 10.1007/s13205-017-0857-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/17/2017] [Indexed: 10/19/2022] Open
Abstract
Eukaryotic initiation factor 2B (eIF2B) controls the first step of translation by catalyzing guanine nucleotide exchange on eukaryotic initiation factor 2 (eIF2). Mutations in the genes encoding eIF2B subunits inhibit the nucleotide exchange and eventually slow down the process of translation, causing vanishing white matter disease. We constructed a Saccharomyces cerevisiae genomic DNA library in YEp24 vector and screened it for the identification of extragenic suppressors of eIF2B mutations, corresponding to human eIF2B mutations. We found a suppressor-II (Sup-II) genomic clone, as suppressor of eIF2Bβ (gcd7-201) mutation. Identification of Sup-II reveals the presence of truncated SEC15, full-length TAN1 (tRNA acetyltransferase), full-length EMC4, full-length YGL230C (putative protein) and truncated SAP4 genes. Full-length TAN1 (tRNA acetyltransferase) gene, subcloned into pEG(KG) vector and overexpressed in gcd7-201 gcn2∆ strain, suppresses the slow-growth (Slg-) and general control derepression (Gcd-) phenotype of gcd7-201 gcn2∆ mutation, but YGL230C did not show any effect. A GST-Tan1p fusion protein of 60 kDa was detected by western blotting using α-GST antibodies. Interestingly, Tan1p overexpression also suppresses the temperature-sensitive (Ts-), Slg- and Gcd- phenotype of eIF2Bγ (gcd1-502) mutant. Role of Tan1p protein in eIF2B-mediated translation regulation was also studied. Results revealed that Tan1p overexpression confers resistance to GCD7 GCN2, gcd7-201 gcn2∆, GCD7 gcn2∆ growth defect under ethanol, H2O2 and caffeine stress. No resistance to DMSO-, NaCl- and DTT-mediated growth defect upon GCD7 gcn2∆, GCD7 GCN2, gcd7-201 gcn2∆ was observed by overexpression of TAN1. Hence, we proposed that Tan1p is involved directly or indirectly in regulating eIF2B-mediated translation.
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Affiliation(s)
- Sonum Sharma
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Anuradha Sourirajan
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Kamal Dev
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India.
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204
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Li J, Shen J, Sun Z, Li J, Li C, Li X, Zhang Y. Discovery of Several Novel Targets that Enhance β-Carotene Production in Saccharomyces cerevisiae. Front Microbiol 2017; 8:1116. [PMID: 28663749 PMCID: PMC5471310 DOI: 10.3389/fmicb.2017.01116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/31/2017] [Indexed: 11/13/2022] Open
Abstract
β-Carotene is the precursor of vitamin A, and also exhibits multiple pharmaceutical functions by itself. In comparison to chemical synthesis, the production of β-carotene in microbes by metabolic engineering strategy is relatively inexpensive. Identifying genes enhancing β-carotene production in microbes is important for engineering a strain of producing higher yields of β-carotene. Most of previous efforts in identifying the gene targets have focused on the isoprenoid pathway where the β-carotene biosynthesis belongs. However, due to the complex interactions between metabolic fluxes, seemingly irrelevant genes that are outside the isoprenoid pathway might also affect β-carotene biosynthesis. To this end, here we provided an example that several novel gene targets, which are outside the isoprenoid pathway, have improving effects on β-carotene synthesis in yeast cells, when they were over-expressed. Among these targets, the class E protein of the vacuolar protein-sorting pathway (Did2) led to the highest improvement in β-carotene yields, which was 2.1-fold to that of the corresponding control. This improvement was further explained by the observation that the overexpression of the DID2 gene generally boosted the transcriptions of β-carotene pathway genes. The mechanism by which the other targets improve the production of β-carotene is discussed.
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Affiliation(s)
- Jia Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Jia Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Zhiqiang Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Jing Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Changfu Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Xiaohua Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China.,University of Chinese Academy of SciencesBeijing, China
| | - Yansheng Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
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205
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MNRR1, a Biorganellar Regulator of Mitochondria. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:6739236. [PMID: 28685009 PMCID: PMC5480048 DOI: 10.1155/2017/6739236] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/09/2017] [Indexed: 12/12/2022]
Abstract
The central role of energy metabolism in cellular activities is becoming widely recognized. However, there are many gaps in our knowledge of the mechanisms by which mitochondria evaluate their status and call upon the nucleus to make adjustments. Recently, a protein family consisting of twin CX9C proteins has been shown to play a role in human pathophysiology. We focus here on two family members, the isoforms CHCHD2 (renamed MNRR1) and CHCHD10. The better studied isoform, MNRR1, has the unusual property of functioning in both the mitochondria and the nucleus and of having a different function in each. In the mitochondria, it functions by binding to cytochrome c oxidase (COX), which stimulates respiration. Its binding to COX is promoted by tyrosine-99 phosphorylation, carried out by ABL2 kinase (ARG). In the nucleus, MNRR1 binds to a novel promoter element in COX4I2 and itself, increasing transcription at 4% oxygen. We discuss mutations in both MNRR1 and CHCHD10 found in a number of chronic, mostly neurodegenerative, diseases. Finally, we propose a model of a graded response to hypoxic and oxidative stresses, mediated under different oxygen tensions by CHCHD10, MNRR1, and HIF1, which operate at intermediate and very low oxygen concentrations, respectively.
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206
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GSK-3β Homolog Rim11 and the Histone Deacetylase Complex Ume6-Sin3-Rpd3 Are Involved in Replication Stress Response Caused by Defects in Dna2. Genetics 2017; 206:829-842. [PMID: 28468907 DOI: 10.1534/genetics.116.198671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 04/18/2017] [Indexed: 01/22/2023] Open
Abstract
Lagging strand synthesis is mechanistically far more complicated than leading strand synthesis because it involves multistep processes and requires considerably more enzymes and protein factors. Due to this complexity, multiple fail-safe factors are required to ensure successful replication of the lagging strand DNA. We attempted to identify novel factors that are required in the absence of the helicase activity of Dna2, an essential enzyme in Okazaki-fragment maturation. In this article, we identified Rim11, a GSK-3β-kinase homolog, as a multicopy suppressor of dna2 helicase-dead mutant (dna2-K1080E). Subsequent epistasis analysis revealed that Ume6 (a DNA binding protein, a downstream substrate of Rim11) also acted as a multicopy suppressor of the dna2 allele. We found that the interaction of Ume6 with the conserved histone deacetylase complex Sin3-Rpd3 and the catalytic activity of Rpd3 were indispensable for the observed suppression of the dna2 mutant. Moreover, multicopy suppression by Rim11/Ume6 requires the presence of sister-chromatid recombination mediated by Rad52/Rad59 proteins, but not vice versa. Interestingly, the overexpression of Rim11 or Ume6 also suppressed the MMS sensitivity of rad59Δ. We also showed that the lethality of dna2 helicase-dead mutant was attributed to checkpoint activation and that decreased levels of deoxynucleotide triphosphates (dNTPs) by overexpressing Sml1 (an inhibitor of ribonucleotide reductase) rescued the dna2 mutant. We also present evidence that indicates Rim11/Ume6 works independently but in parallel with that of checkpoint inhibition, dNTP regulation, and sister-chromatid recombination. In conclusion, our results establish Rim11, Ume6, the histone deacetylase complex Sin3-Rpd3 and Sml1 as new factors important in the events of faulty lagging strand synthesis.
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207
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Kraus OZ, Grys BT, Ba J, Chong Y, Frey BJ, Boone C, Andrews BJ. Automated analysis of high-content microscopy data with deep learning. Mol Syst Biol 2017; 13:924. [PMID: 28420678 PMCID: PMC5408780 DOI: 10.15252/msb.20177551] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Existing computational pipelines for quantitative analysis of high‐content microscopy data rely on traditional machine learning approaches that fail to accurately classify more than a single dataset without substantial tuning and training, requiring extensive analysis. Here, we demonstrate that the application of deep learning to biological image data can overcome the pitfalls associated with conventional machine learning classifiers. Using a deep convolutional neural network (DeepLoc) to analyze yeast cell images, we show improved performance over traditional approaches in the automated classification of protein subcellular localization. We also demonstrate the ability of DeepLoc to classify highly divergent image sets, including images of pheromone‐arrested cells with abnormal cellular morphology, as well as images generated in different genetic backgrounds and in different laboratories. We offer an open‐source implementation that enables updating DeepLoc on new microscopy datasets. This study highlights deep learning as an important tool for the expedited analysis of high‐content microscopy data.
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Affiliation(s)
- Oren Z Kraus
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Ben T Grys
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jimmy Ba
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, Canada
| | - Yolanda Chong
- Cellular Pharmacology, Discovery Sciences, Janssen Pharmaceutical Companies, Johnson & Johnson, Beerse, Belgium
| | - Brendan J Frey
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Canadian Institute for Advanced Research, Program on Genetic Networks, Toronto, ON, Canada.,Canadian Institute for Advanced Research, Program on Learning in Machines & Brains, Toronto, ON, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Canadian Institute for Advanced Research, Program on Genetic Networks, Toronto, ON, Canada
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Canadian Institute for Advanced Research, Program on Genetic Networks, Toronto, ON, Canada
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208
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Cabrera M, Novarina D, Rempel IL, Veenhoff LM, Chang M. A simple microfluidic platform to study age-dependent protein abundance and localization changes in Saccharomyces cerevisiae. MICROBIAL CELL 2017; 4:169-174. [PMID: 28685142 PMCID: PMC5425278 DOI: 10.15698/mic2017.05.573] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The budding yeast Saccharomyces cerevisiae divides asymmetrically, with a smaller daughter cell emerging from its larger mother cell. While the daughter lineage is immortal, mother cells age with each cell division and have a finite lifespan. The replicative ageing of the yeast mother cell has been used as a model to study the ageing of mitotically active human cells. Several microfluidic platforms, which use fluid flow to selectively remove daughter cells, have recently been developed that can monitor cell physiology as mother cells age. However, these platforms are not trivial to set up and users often require many hours of training. In this study, we have developed a simple system, which combines a commercially available microfluidic platform (the CellASIC ONIX Microfluidic Platform) and a genetic tool to prevent the proliferation of daughter cells (the Mother Enrichment Program), to monitor protein abundance and localization changes during approximately the first half of the yeast replicative lifespan. We validated our system by observing known age-dependent changes, such as decreased Sir2 abundance, and have identified a protein with a previously unknown age-dependent change in localization.
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Affiliation(s)
- Margarita Cabrera
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Daniele Novarina
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Irina L Rempel
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
| | - Michael Chang
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, the Netherlands
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209
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Differential Proteome Analysis of a Flor Yeast Strain under Biofilm Formation. Int J Mol Sci 2017; 18:ijms18040720. [PMID: 28350350 PMCID: PMC5412306 DOI: 10.3390/ijms18040720] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/21/2017] [Accepted: 03/21/2017] [Indexed: 11/30/2022] Open
Abstract
Several Saccharomyces cerevisiae strains (flor yeasts) form a biofilm (flor velum) on the surface of Sherry wines after fermentation, when glucose is depleted. This flor velum is fundamental to biological aging of these particular wines. In this study, we identify abundant proteins in the formation of the biofilm of an industrial flor yeast strain. A database search to enrich flor yeast “biological process” and “cellular component” according to Gene Ontology Terminology (GO Terms) and, “pathways” was carried out. The most abundant proteins detected were largely involved in respiration, translation, stress damage prevention and repair, amino acid metabolism (glycine, isoleucine, leucine and arginine), glycolysis/gluconeogenesis and biosynthesis of vitamin B9 (folate). These proteins were located in cellular components as in the peroxisome, mitochondria, vacuole, cell wall and extracellular region; being these two last directly related with the flor formation. Proteins like Bgl2p, Gcv3p, Hyp2p, Mdh1p, Suc2p and Ygp1p were quantified in very high levels. This study reveals some expected processes and provides new and important information for the design of conditions and genetic constructions of flor yeasts for improving the cellular survival and, thus, to optimize biological aging of Sherry wine production.
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210
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Increased genome instability is not accompanied by sensitivity to DNA damaging agents in aged yeast cells. DNA Repair (Amst) 2017; 54:1-7. [PMID: 28384494 DOI: 10.1016/j.dnarep.2017.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 11/21/2022]
Abstract
The budding yeast Saccharomyces cerevisiae divides asymmetrically, producing a new daughter cell from the original mother cell. While daughter cells are born with a full lifespan, a mother cell ages with each cell division and can only generate on average 25 daughter cells before dying. Aged yeast cells exhibit genomic instability, which is also a hallmark of human aging. However, it is unclear how this genomic instability contributes to aging. To shed light on this issue, we investigated endogenous DNA damage in S. cerevisiae during replicative aging and tested for age-dependent sensitivity to exogenous DNA damaging agents. Using live-cell imaging in a microfluidic device, we show that aging yeast cells display an increase in spontaneous Rad52 foci, a marker of endogenous DNA damage. Strikingly, this elevated DNA damage is not accompanied by increased sensitivity of aged yeast cells to genotoxic agents nor by global changes in the proteome or transcriptome that would indicate a specific "DNA damage signature". These results indicate that DNA repair proficiency is not compromised in aged yeast cells, suggesting that yeast replicative aging and age-associated genomic instability is likely not a consequence of an inability to repair DNA damage.
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211
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Zhou N, Swamy KBS, Leu JY, McDonald MJ, Galafassi S, Compagno C, Piškur J. Coevolution with bacteria drives the evolution of aerobic fermentation in Lachancea kluyveri. PLoS One 2017; 12:e0173318. [PMID: 28282411 PMCID: PMC5345805 DOI: 10.1371/journal.pone.0173318] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 02/17/2017] [Indexed: 11/18/2022] Open
Abstract
The Crabtree positive yeasts, such as Saccharomyces cerevisiae, prefer fermentation to respiration, even under fully aerobic conditions. The selective pressures that drove the evolution of this trait remain controversial because of the low ATP yield of fermentation compared to respiration. Here we propagate experimental populations of the weak-Crabtree yeast Lachancea kluyveri, in competitive co-culture with bacteria. We find that L. kluyveri adapts by producing quantities of ethanol lethal to bacteria and evolves several of the defining characteristics of Crabtree positive yeasts. We use precise quantitative analysis to show that the rate advantage of fermentation over aerobic respiration is insufficient to provide an overall growth advantage. Thus, the rapid consumption of glucose and the utilization of ethanol are essential for the success of the aerobic fermentation strategy. These results corroborate that selection derived from competition with bacteria could have provided the impetus for the evolution of the Crabtree positive trait.
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Affiliation(s)
- Nerve Zhou
- Department of Biology, Lund University, Lund, Sweden
- * E-mail: (NZ); (KBSS)
| | - Krishna B. S. Swamy
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail: (NZ); (KBSS)
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Silvia Galafassi
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Concetta Compagno
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Jure Piškur
- Department of Biology, Lund University, Lund, Sweden
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212
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Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae. Proc Natl Acad Sci U S A 2017; 114:E2411-E2419. [PMID: 28265091 DOI: 10.1073/pnas.1612422114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Forkhead Box (Fox) proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which contributes to developmental defects, cancer, and aging. We recently identified Saccharomyces cerevisiae Forkhead 1 (Fkh1) and Forkhead 2 (Fkh2) as required for the clustering of a subset of replication origins in G1 phase and for the early initiation of these origins in the ensuing S phase, suggesting a mechanistic role linking the spatial organization of the origins and their activity. Here, we show that Fkh1 and Fkh2 share a unique structural feature of human FoxP proteins that enables FoxP2 and FoxP3 to form domain-swapped dimers capable of bridging two DNA molecules in vitro. Accordingly, Fkh1 self-associates in vitro and in vivo in a manner dependent on the conserved domain-swapping region, strongly suggestive of homodimer formation. Fkh1- and Fkh2-domain-swap-minus (dsm) mutations are functional as transcription factors yet are defective in replication origin timing control. Fkh1-dsm binds replication origins in vivo but fails to cluster them, supporting the conclusion that Fkh1 and Fkh2 dimers perform a structural role in the spatial organization of chromosomal elements with functional importance.
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213
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Votino C, Laudanna C, Parcesepe P, Giordano G, Remo A, Manfrin E, Pancione M. Aberrant BLM cytoplasmic expression associates with DNA damage stress and hypersensitivity to DNA-damaging agents in colorectal cancer. J Gastroenterol 2017; 52:327-340. [PMID: 27169843 DOI: 10.1007/s00535-016-1222-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/26/2016] [Indexed: 02/05/2023]
Abstract
BACKGROUND Bloom syndrome is a rare and recessive disorder characterized by loss-of-function mutations of the BLM gene, which encodes a RecQ 3'-5' DNA helicase. Despite its putative tumor suppressor function, the contribution of BLM to human sporadic colorectal cancer (CRC) remains poorly understood. METHODS The transcriptional regulation mechanism underlying BLM and related DNA damage response regulation in independent CRC subsets and a panel of derived cell lines was investigated by bioinformatics analysis, the transcriptomic profile, a CpG island promoter methylation assay, Western blot, and an immunolocalization assay. RESULTS In silico analysis of gene expression data sets revealed that BLM is overexpressed in poorly differentiated CRC and exhibits a close connection with shorter relapse-free survival even after adjustment for prognostic factors and pathways that respond to DNA damage response through ataxia telangiectasia mutated (ATM) signaling. Functional characterization demonstrated that CpG island promoter hypomethylation increases BLM expression and associates with cytoplasmic BLM mislocalization and increased DNA damage response both in clinical CRC samples and in derived cancer cell lines. The DNA-damaging agent S-adenosylmethionine suppresses BLM expression, leading to the inhibition of cell growth following accumulation of DNA damage. In tumor specimens, cytoplasmic accumulation of BLM correlates with DNA damage and γH2AX and phosphorylated ATM foci and predicts long-term progression-free survival in metastatic patients treated with irinotecan. CONCLUSIONS Taken together, the findings of this study provide the first evidence that cancer-linked DNA hypomethylation and cytosolic BLM mislocalization might reflect compromised levels of DNA-repair activity and enhanced hypersensitivity to DNA-damaging agents in CRC patients.
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Affiliation(s)
- Carolina Votino
- Department of Sciences and Technologies, University of Sannio, Via Port'Arsa, 11, 82100, Benevento, Italy
| | - Carmelo Laudanna
- Department of Experimental and Clinical Medicine "Gaetano Salvatore", University "Magna Grecia", 88100, Catanzaro, Italy
| | - Pietro Parcesepe
- Department of Surgery and Oncology, University of Verona, 37129, Verona, Italy
| | - Guido Giordano
- Medical Oncology Unit, Fatebenefratelli Hospital, 82100, Benevento, Italy
| | - Andrea Remo
- Department of Pathology, "Mater Salutis" Hospital, 37045, Legnago, VR, Italy
| | - Erminia Manfrin
- Medical Oncology Unit, Fatebenefratelli Hospital, 82100, Benevento, Italy
| | - Massimo Pancione
- Department of Sciences and Technologies, University of Sannio, Via Port'Arsa, 11, 82100, Benevento, Italy.
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University, Madrid, Spain.
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214
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Zhang R, Yuan H, Wang S, Ouyang Q, Chen Y, Hao N, Luo C. High-throughput single-cell analysis for the proteomic dynamics study of the yeast osmotic stress response. Sci Rep 2017; 7:42200. [PMID: 28181485 PMCID: PMC5299847 DOI: 10.1038/srep42200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/06/2017] [Indexed: 11/22/2022] Open
Abstract
Motorized fluorescence microscopy combined with high-throughput microfluidic chips is a powerful method to obtain information about different biological processes in cell biology studies. Generally, to observe different strains under different environments, high-throughput microfluidic chips require complex preparatory work. In this study, we designed a novel and easily operated high-throughput microfluidic system to observe 96 different GFP-tagged yeast strains in one switchable culture condition or 24 different GFP-tagged yeast strains in four parallel switchable culture conditions. A multi-pipette is the only additional equipment required for high-throughput patterning of cells in the chip. Only eight connections are needed to control 96 conditions. Using these devices, the proteomic dynamics of the yeast stress response pathway were carefully studied based on single-cell data. A new method to characterize the proteomic dynamics using a single cell’s data is proposed and compared to previous methods, and the new technique should be useful for studying underlying control networks. Our method provides an easy and systematic way to study signaling pathways at the single-cell level.
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Affiliation(s)
- Rongfei Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Haiyu Yuan
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Shujing Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yong Chen
- Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris, France
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
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215
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Meitinger F, Pereira G. The septin-associated kinase Gin4 recruits Gps1 to the site of cell division. Mol Biol Cell 2017; 28:883-889. [PMID: 28148650 PMCID: PMC5385937 DOI: 10.1091/mbc.e16-09-0687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 01/24/2023] Open
Abstract
Gps1 is a regulator of Rho GTPases during cell division. Cell cycle–regulated recruitment of Gps1 to the cell division site is under control of the conserved kinase Gin4 and the bud neck–associated protein Nba1. This biphasic recruitment is required for the spatiotemporal activation of Rho1 and inhibition of Cdc42. Cell cycle–dependent morphogenesis of unicellular organisms depends on the spatiotemporal control of cell polarity. Rho GTPases are the major players that guide cells through structural reorganizations such as cytokinesis (Rho1 dependent) and polarity establishment (Cdc42 dependent). In budding yeast, the protein Gps1 plays a pivotal role in both processes. Gps1 resides at the bud neck to maintain Rho1 localization and restrict Cdc42 activity during cytokinesis. Here we analyze how Gps1 is recruited to the bud neck during the cell cycle. We show that different regions of Gps1 and the septin-associated kinase Gin4 are involved in maintaining Gps1 at the bud neck from late G1 phase until midanaphase. From midanaphase, the targeting function of Gin4 is taken over by the bud neck–associated protein Nba1. Our data show that Gps1 is targeted to the cell division site in a biphasic manner, via Gin4 and Nba1, to control the spatiotemporal activation of Rho1 and inhibition of Cdc42.
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Affiliation(s)
- Franz Meitinger
- Centre for Organismal Studies and German Cancer Research Center, DKFZ-ZMBH Alliance, and Molecular Biology of Centrosomes and Cilia Unit, University of Heidelberg, 69120 Heidelberg, Germany
| | - Gislene Pereira
- Centre for Organismal Studies and German Cancer Research Center, DKFZ-ZMBH Alliance, and Molecular Biology of Centrosomes and Cilia Unit, University of Heidelberg, 69120 Heidelberg, Germany
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216
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Dayan IE, Arga KY, Ulgen KO. Multiomics Approach to Novel Therapeutic Targets for Cancer and Aging-Related Diseases: Role of Sld7 in Yeast Aging Network. ACTA ACUST UNITED AC 2017; 21:100-113. [DOI: 10.1089/omi.2016.0157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Irem E. Dayan
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
| | | | - Kutlu O. Ulgen
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
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217
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Kumar R. Separase: Function Beyond Cohesion Cleavage and an Emerging Oncogene. J Cell Biochem 2017; 118:1283-1299. [PMID: 27966791 DOI: 10.1002/jcb.25835] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 12/12/2016] [Indexed: 12/22/2022]
Abstract
Proper and timely segregation of genetic endowment is necessary for survival and perpetuation of every species. Mis-segregation of chromosomes and resulting aneuploidy leads to genetic instability, which can jeopardize the survival of an individual or population as a whole. Abnormality with segregation of genetic contents has been associated with several medical consequences including cancer, sterility, mental retardation, spontaneous abortion, miscarriages, and other birth related defects. Separase, by irreversible cleavage of cohesin complex subunit, paves the way for metaphase/anaphase transition during the cell cycle. Both over or reduced expression and altered level of separase have been associated with several medical consequences including cancer, as a result separase now emerges as an important oncogene and potential molecular target for medical intervenes. Recently, separase is also found to be essential in separation and duplication of centrioles. Here, I review the role of separase in mitosis, meiosis, non-canonical roles of separase, separase regulation, as a regulator of centriole disengagement, nonproteolytic roles, diverse substrates, structural insights, and association of separase with cancer. At the ends, I proposed a model which showed that separase is active throughout the cell cycle and there is a mere increase in separase activity during metaphase contrary to the common believes that separase is inactive throughout cell cycle except for metaphase. J. Cell. Biochem. 118: 1283-1299, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ravinder Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076, Maharashtra, India
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218
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Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response. G3-GENES GENOMES GENETICS 2017; 7:221-231. [PMID: 27883312 PMCID: PMC5217111 DOI: 10.1534/g3.116.034991] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast Saccharomyces cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis, and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times, and performed RNA sequencing (RNA-seq) analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold. The genes responded with varying kinetics suggesting that multiple regulatory pathways are involved. We identified most known oxygen-regulated genes and also uncovered new regulated genes. Reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed that the lysine methyltransferase EFM6 and the recombinase DMC1, both conserved in humans, are indeed oxygen-responsive. Looking more broadly, oxygen-regulated genes participate in expected processes like respiration and lipid metabolism, but also in unexpected processes like amino acid and vitamin metabolism. Using principle component analysis, we discovered that the hypoxic response largely occurs during the first 2 hr and then a new steady-state expression state is achieved. Moreover, we show that the oxygen-dependent genes are not part of the previously described environmental stress response (ESR) consisting of genes that respond to diverse types of stress. While hypoxia appears to cause a transient stress, the hypoxic response is mostly characterized by a transition to a new state of gene expression. In summary, our results reveal that hypoxia causes widespread and complex changes in gene expression to prepare the cell to function with little or no oxygen.
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219
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Santos RM, Nogueira FC, Brasil AA, Carvalho PC, Leprevost FV, Domont GB, Eleutherio EC. Quantitative proteomic analysis of the Saccharomyces cerevisiae industrial strains CAT-1 and PE-2. J Proteomics 2017; 151:114-121. [DOI: 10.1016/j.jprot.2016.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/25/2016] [Accepted: 08/25/2016] [Indexed: 10/21/2022]
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220
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Guerrero-Serrano G, Castanedo L, Cristóbal-Mondragón GR, Montalvo-Arredondo J, Riego-Ruíz L, DeLuna A, De Las Peñas A, Castaño I, Calera MR, Sánchez-Olea R. Npa3/ScGpn1 carboxy-terminal tail is dispensable for cell viability and RNA polymerase II nuclear targeting but critical for microtubule stability and function. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:451-462. [PMID: 27965115 DOI: 10.1016/j.bbamcr.2016.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 12/03/2016] [Accepted: 12/09/2016] [Indexed: 10/20/2022]
Abstract
Genetic deletion of the essential GTPase Gpn1 or replacement of the endogenous gene by partial loss of function mutants in yeast is associated with multiple cellular phenotypes, including in all cases a marked cytoplasmic retention of RNA polymerase II (RNAPII). Global inhibition of RNAPII-mediated transcription due to malfunction of Gpn1 precludes the identification and study of other cellular function(s) for this GTPase. In contrast to the single Gpn protein present in Archaea, eukaryotic Gpn1 possesses an extension of approximately 100 amino acids at the C-terminal end of the GTPase domain. To determine the importance of this C-terminal extension in Saccharomyces cerevisiae Gpn1, we generated yeast strains expressing either C-terminal truncated (gpn1ΔC) or full-length ScGpn1. We found that ScGpn1ΔC was retained in the cell nucleus, an event physiologically relevant as gpn1ΔC cells contained a higher nuclear fraction of the RNAPII CTD phosphatase Rtr1. gpn1ΔC cells displayed an increased size, a delay in mitosis exit, and an increased sensitivity to the microtubule polymerization inhibitor benomyl at the cell proliferation level and two cellular events that depend on microtubule function: RNAPII nuclear targeting and vacuole integrity. These phenotypes were not caused by inhibition of RNAPII, as in gpn1ΔC cells RNAPII nuclear targeting and transcriptional activity were unaffected. These data, combined with our description here of a genetic interaction between GPN1 and BIK1, a microtubule plus-end tracking protein with a mitotic function, strongly suggest that the ScGpn1 C-terminal tail plays a critical role in microtubule dynamics and mitotic progression in an RNAPII-independent manner.
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Affiliation(s)
- Gehenna Guerrero-Serrano
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Univesitaria, C.P. 78290, San Luis Potosí, San Luis Potosí, Mexico
| | - Leonardo Castanedo
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Univesitaria, C.P. 78290, San Luis Potosí, San Luis Potosí, Mexico
| | - Gema R Cristóbal-Mondragón
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Univesitaria, C.P. 78290, San Luis Potosí, San Luis Potosí, Mexico
| | - Javier Montalvo-Arredondo
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, C.P. 78216, San Luis Potosí, San Luis Potosí, Mexico
| | - Lina Riego-Ruíz
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, C.P. 78216, San Luis Potosí, San Luis Potosí, Mexico
| | - Alexander DeLuna
- LANGEBIO: Laboratorio Nacional de Genomica para la Biodiversidad, Km 9.6 Libramiento Norte Carretera León, C.P. 36821 Irapuato, Guanajuato, Mexico
| | - Alejandro De Las Peñas
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, C.P. 78216, San Luis Potosí, San Luis Potosí, Mexico
| | - Irene Castaño
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, C.P. 78216, San Luis Potosí, San Luis Potosí, Mexico
| | - Mónica R Calera
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Univesitaria, C.P. 78290, San Luis Potosí, San Luis Potosí, Mexico.
| | - Roberto Sánchez-Olea
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Univesitaria, C.P. 78290, San Luis Potosí, San Luis Potosí, Mexico.
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221
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Lebesgue N, Megyeri M, Cristobal A, Scholten A, Chuartzman SG, Voichek Y, Scheltema RA, Mohammed S, Futerman AH, Schuldiner M, Heck AJR, Lemeer S. Combining Deep Sequencing, Proteomics, Phosphoproteomics, and Functional Screens To Discover Novel Regulators of Sphingolipid Homeostasis. J Proteome Res 2016; 16:571-582. [PMID: 28152593 DOI: 10.1021/acs.jproteome.6b00691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Sphingolipids (SLs) are essential components of cell membranes and are broad-range bioactive signaling molecules. SL levels must be tightly regulated as imbalances affect cellular function and contribute to pathologies ranging from neurodegenerative and metabolic disorders to cancer and aging. Deciphering how SL homeostasis is maintained and uncovering new regulators is required for understanding lipid biology and for identifying new targets for therapeutic interventions. Here we combine omics technologies to identify the changes of the transcriptome, proteome, and phosphoproteome in the yeast Saccharomyces cerevisiae upon SL depletion induced by myriocin. Surprisingly, while SL depletion triggers important changes in the expression of regulatory proteins involved in SL homeostasis, the most dramatic regulation occurs at the level of the phosphoproteome, suggesting that maintaining SL homeostasis demands rapid responses. To discover which of the phosphoproteomic changes are required for the cell's first-line response to SL depletion, we overlaid our omics results with systematic growth screens for genes required during growth in myriocin. By following the rate of SL biosynthesis in those candidates that are both affecting growth and are phosphorylated in response to the drug, we uncovered Atg9, Stp4, and Gvp36 as putative new regulators of SL homeostasis.
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Affiliation(s)
- Nicolas Lebesgue
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Márton Megyeri
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel.,Department of Chemical Biology, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Alba Cristobal
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Arjen Scholten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Silvia G Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Yoav Voichek
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Anthony H Futerman
- Department of Chemical Biology, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center , Padualaan 8, 3584 CH Utrecht, The Netherlands
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222
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Specht EA, Braselmann E, Palmer AE. A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging. Annu Rev Physiol 2016; 79:93-117. [PMID: 27860833 DOI: 10.1146/annurev-physiol-022516-034055] [Citation(s) in RCA: 259] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescent tools have revolutionized our ability to probe biological dynamics, particularly at the cellular level. Fluorescent sensors have been developed on several platforms, utilizing either small-molecule dyes or fluorescent proteins, to monitor proteins, RNA, DNA, small molecules, and even cellular properties, such as pH and membrane potential. We briefly summarize the impressive history of tool development for these various applications and then discuss the most recent noteworthy developments in more detail. Particular emphasis is placed on tools suitable for single-cell analysis and especially live-cell imaging applications. Finally, we discuss prominent areas of need in future fluorescent tool development-specifically, advancing our capability to analyze and integrate the plethora of high-content data generated by fluorescence imaging.
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Affiliation(s)
- Elizabeth A Specht
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303; .,BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303
| | - Esther Braselmann
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303; .,BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303
| | - Amy E Palmer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303; .,BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303
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223
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Tarrant DJ, Stirpe M, Rowe M, Howard MJ, von der Haar T, Gourlay CW. Inappropriate expression of the translation elongation factor 1A disrupts genome stability and metabolism. J Cell Sci 2016; 129:4455-4465. [PMID: 27807005 PMCID: PMC5201016 DOI: 10.1242/jcs.192831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/26/2016] [Indexed: 02/02/2023] Open
Abstract
The translation elongation factor eEF1A is one of the most abundant proteins found within cells, and its role within protein synthesis is well documented. Levels of eEF1A are tightly controlled, with inappropriate expression linked to oncogenesis. However, the mechanisms by which increased eEF1A expression alters cell behaviour are unknown. Our analyses in yeast suggest that elevation of eEF1A levels leads to stabilisation of the spindle pole body and changes in nuclear organisation. Elevation of the eEF1A2 isoform also leads to altered nuclear morphology in cultured human cells, suggesting a conserved role in maintaining genome stability. Gene expression and metabolomic analyses reveal that the level of eEF1A is crucial for the maintenance of metabolism and amino acid levels in yeast, most likely because of its role in the control of vacuole function. Increased eEF1A2 levels trigger lysosome biogenesis in cultured human cells, also suggesting a conserved role within metabolic control mechanisms. Taken together, our data suggest that the control of eEF1A levels is important for the maintenance of a number of cell functions beyond translation and that its de-regulation might contribute to its oncogenic properties. Summary: The translation elongation factor eEF1A is elevated in some cancers. We use yeast and human cell models to show that eEF1A elevation leads to genome instability and metabolic alterations that might affect its oncogenic properties.
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Affiliation(s)
- Daniel J Tarrant
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Mariarita Stirpe
- Department of Biology and Biotechnology, Sapienza, University of Rome, 00185 Rome, Italy
| | - Michelle Rowe
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Mark J Howard
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Campbell W Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
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224
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Replication intermediates that escape Dna2 activity are processed by Holliday junction resolvase Yen1. Nat Commun 2016; 7:13157. [PMID: 27779184 PMCID: PMC5093310 DOI: 10.1038/ncomms13157] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 09/08/2016] [Indexed: 12/29/2022] Open
Abstract
Cells have evolved mechanisms to protect, restart and repair perturbed replication forks, allowing full genome duplication, even under replication stress. Interrogating the interplay between nuclease-helicase Dna2 and Holliday junction (HJ) resolvase Yen1, we find the Dna2 helicase activity acts parallel to homologous recombination (HR) in promoting DNA replication and chromosome detachment at mitosis after replication fork stalling. Yen1, but not the HJ resolvases Slx1-Slx4 and Mus81-Mms4, safeguards chromosome segregation by removing replication intermediates that escape Dna2. Post-replicative DNA damage checkpoint activation in Dna2 helicase-defective cells causes terminal G2/M arrest by precluding Yen1-dependent repair, whose activation requires progression into anaphase. These findings explain the exquisite replication stress sensitivity of Dna2 helicase-defective cells, and identify a non-canonical role for Yen1 in the processing of replication intermediates that is distinct from HJ resolution. The involvement of Dna2 helicase activity in completing replication may have implications for DNA2-associated pathologies, including cancer and Seckel syndrome.
DNA replication stress drives genome instability and cancer. Here, Ölmezer and colleagues show that the helicase activity of multifunctional enzyme Dna2 suppresses dead-end replication structures that impair chromosome segregation if not removed by Holliday junction resolvase Yen1 in yeast.
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225
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Lien PTK, Izumikawa K, Muroi K, Irie K, Suda Y, Irie K. Analysis of the Physiological Activities of Scd6 through Its Interaction with Hmt1. PLoS One 2016; 11:e0164773. [PMID: 27776129 PMCID: PMC5077174 DOI: 10.1371/journal.pone.0164773] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/30/2016] [Indexed: 01/26/2023] Open
Abstract
Scd6, a yeast homologue of human RAP55, is a component of messenger ribonucleoproteins (mRNPs) that repress translation by binding to translation initiation factors, and also is a decapping activator along with the binding partners Edc3 and Dhh1. Herein, we report that Scd6 is a substrate of the intrinsic protein arginine methyltransferase, Hmt1, in budding yeast Saccharomyces cerevisiae. Mass spectrometric analysis revealed that several arginine residues within the Scd6 RGG motif, which is important for mRNA binding, were methylated in Hmt1 dependent manner. Under stress conditions such as glucose starvation, Scd6 localized to cytoplasmic processing bodies (P-bodies) wherein translationally repressed mRNPs and untranslated mRNAs accumulate. Localization of Scd6 to P-bodies was impaired in hmt1 deletion mutant and in the presence of methylation-deficient substitution of Scd6. In addition, deletion of scd6 and dhh1 led to severe synthetic growth defect at high temperature. Methylation-deficient mutation of Scd6 suppressed the phenotypic defects of scd6 dhh1 double mutant, whereas methylation-mimic mutation did not, suggesting that the arginine methylation might negatively regulate Scd6 function relating to Dhh1. Therefore, the present data suggest that Hmt1-based arginine methylation is required for Scd6 localization and function.
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Affiliation(s)
- Pham Thi Kim Lien
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiichi Izumikawa
- Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Kei Muroi
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kaoru Irie
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yasuyuki Suda
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Live Cell Super-resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
- * E-mail:
| | - Kenji Irie
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
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226
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Kasavi C, Eraslan S, Oner ET, Kirdar B. An integrative analysis of transcriptomic response of ethanol tolerant strains to ethanol in Saccharomyces cerevisiae. MOLECULAR BIOSYSTEMS 2016; 12:464-76. [PMID: 26661334 DOI: 10.1039/c5mb00622h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The accumulation of ethanol is one of the main environmental stresses that Saccharomyces cerevisiae cells are exposed to in industrial alcoholic beverage and bioethanol production processes. Despite the known impacts of ethanol, the molecular mechanisms underlying ethanol tolerance are still not fully understood. Novel gene targets leading to ethanol tolerance were previously identified via a network approach and the investigations of the deletions of these genes resulted in the improved ethanol tolerance of pmt7Δ/pmt7Δ and yhl042wΔ/yhl042wΔ strains. In the present study, an integrative system based approach was used to investigate the global transcriptional changes in these two ethanol tolerant strains in response to ethanol and hence to elucidate the mechanisms leading to the observed tolerant phenotypes. In addition to strain specific biological processes, a number of common and already reported biological processes were found to be affected in the reference and both ethanol tolerant strains. However, the integrative analysis of the transcriptome with the transcriptional regulatory network and the ethanol tolerance network revealed that each ethanol tolerant strain had a specific organization of the transcriptomic response. Transcription factors around which most important changes occur were determined and active subnetworks in response to ethanol and functional clusters were identified in all strains.
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Affiliation(s)
- Ceyda Kasavi
- Department of Chemical Engineering, Boğaziçi University, Istanbul, Turkey.
| | - Serpil Eraslan
- Department of Chemical Engineering, Boğaziçi University, Istanbul, Turkey.
| | - Ebru Toksoy Oner
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Betul Kirdar
- Department of Chemical Engineering, Boğaziçi University, Istanbul, Turkey.
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227
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Styles EB, Founk KJ, Zamparo LA, Sing TL, Altintas D, Ribeyre C, Ribaud V, Rougemont J, Mayhew D, Costanzo M, Usaj M, Verster AJ, Koch EN, Novarina D, Graf M, Luke B, Muzi-Falconi M, Myers CL, Mitra RD, Shore D, Brown GW, Zhang Z, Boone C, Andrews BJ. Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci. Cell Syst 2016; 3:264-277.e10. [PMID: 27617677 PMCID: PMC5689480 DOI: 10.1016/j.cels.2016.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/27/2016] [Accepted: 08/11/2016] [Indexed: 01/12/2023]
Abstract
A significant challenge of functional genomics is to develop methods for genome-scale acquisition and analysis of cell biological data. Here, we present an integrated method that combines genome-wide genetic perturbation of Saccharomyces cerevisiae with high-content screening to facilitate the genetic description of sub-cellular structures and compartment morphology. As proof of principle, we used a Rad52-GFP marker to examine DNA damage foci in ∼20 million single cells from ∼5,000 different mutant backgrounds in the context of selected genetic or chemical perturbations. Phenotypes were classified using a machine learning-based automated image analysis pipeline. 345 mutants were identified that had elevated numbers of DNA damage foci, almost half of which were identified only in sensitized backgrounds. Subsequent analysis of Vid22, a protein implicated in the DNA damage response, revealed that it acts together with the Sgs1 helicase at sites of DNA damage and preferentially binds G-quadruplex regions of the genome. This approach is extensible to numerous other cell biological markers and experimental systems.
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Affiliation(s)
- Erin B Styles
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Karen J Founk
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Lee A Zamparo
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Sciences, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Tina L Sing
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Dogus Altintas
- Department of Molecular Biology, NCCR Program "Frontiers in Genetics", Institute of Genetics, Genomics, Geneva (iGE3), University of Geneva, 30, quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Cyril Ribeyre
- Department of Molecular Biology, NCCR Program "Frontiers in Genetics", Institute of Genetics, Genomics, Geneva (iGE3), University of Geneva, 30, quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Virginie Ribaud
- Department of Molecular Biology, NCCR Program "Frontiers in Genetics", Institute of Genetics, Genomics, Geneva (iGE3), University of Geneva, 30, quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Jacques Rougemont
- Laboratory of Computational Systems Biology, Ecole Polytéchnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - David Mayhew
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Michael Costanzo
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Matej Usaj
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Adrian J Verster
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Elizabeth N Koch
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniele Novarina
- Dipartimento di Bioscienze, Universita' degli Studi di Milano, 20122 Milano, Italy
| | - Marco Graf
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz 55128, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz 55128, Germany
| | - Marco Muzi-Falconi
- Dipartimento di Bioscienze, Universita' degli Studi di Milano, 20122 Milano, Italy
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robi David Mitra
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - David Shore
- Department of Molecular Biology, NCCR Program "Frontiers in Genetics", Institute of Genetics, Genomics, Geneva (iGE3), University of Geneva, 30, quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Grant W Brown
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Zhaolei Zhang
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.
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228
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Ledesma-Fernández E, Thorpe PH, de Bruin RAM. Bringing Functional Genomics into Focus. Cell Syst 2016; 3:214-216. [PMID: 27684184 DOI: 10.1016/j.cels.2016.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Styles et al. develop an optimized method that combines high-content microscopy and automated phenotypic analysis with genome-wide yeast genetics to identify genes in DNA damage repair.
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Affiliation(s)
| | - Peter H Thorpe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Robertus A M de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; The UCL Cancer Institute, University College London, London WC1E 6BT, UK.
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229
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Abstract
A clear definition of what constitutes “Big Data” is difficult to identify, but we find it most useful to define Big Data as a data collection that is complete. By this criterion, researchers on Caenorhabditis elegans have a long history of collecting Big Data, since the organism was selected with the idea of obtaining a complete biological description and understanding of development. The complete wiring diagram of the nervous system, the complete cell lineage, and the complete genome sequence provide a framework to phrase and test hypotheses. Given this history, it might be surprising that the number of “complete” data sets for this organism is actually rather small—not because of lack of effort, but because most types of biological experiments are not currently amenable to complete large-scale data collection. Many are also not inherently limited, so that it becomes difficult to even define completeness. At present, we only have partial data on mutated genes and their phenotypes, gene expression, and protein–protein interaction—important data for many biological questions. Big Data can point toward unexpected correlations, and these unexpected correlations can lead to novel investigations; however, Big Data cannot establish causation. As a result, there is much excitement about Big Data, but there is also a discussion on just what Big Data contributes to solving a biological problem. Because of its relative simplicity, C. elegans is an ideal test bed to explore this issue and at the same time determine what is necessary to build a multicellular organism from a single cell.
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Affiliation(s)
- Harald Hutter
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Donald Moerman
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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230
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Abstract
The demand for phenomics, a high-dimensional and high-throughput phenotyping method, has been increasing in many fields of biology. The budding yeast Saccharomyces cerevisiae, a unicellular model organism, provides an invaluable system for dissecting complex cellular processes using high-resolution phenotyping. Moreover, the addition of spatial and temporal attributes to subcellular structures based on microscopic images has rendered this cell phenotyping system more reliable and amenable to analysis. A well-designed experiment followed by appropriate multivariate analysis can yield a wealth of biological knowledge. Here we review recent advances in cell imaging and illustrate their broad applicability to eukaryotic cells by showing how these techniques have advanced our understanding of budding yeast.
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Affiliation(s)
- Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Yoshitaka Kimori
- Department of Imaging Science, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Hiroki Okada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
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231
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Roles of Rack1 Proteins in Fungal Pathogenesis. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4130376. [PMID: 27656651 PMCID: PMC5021465 DOI: 10.1155/2016/4130376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/16/2016] [Indexed: 01/21/2023]
Abstract
Pathogenic fungi cause diseases on various organisms. Despite their differences in life cycles, fungal pathogens use well-conserved proteins and pathways to regulate developmental and infection processes. In this review, we focus on Rack1, a multifaceted scaffolding protein involved in various biological processes. Rack1 is well conserved in eukaryotes and plays important roles in fungi, though limited studies have been conducted. To accelerate the study of Rack1 proteins in fungi, we review the functions of Rack1 proteins in model and pathogenic fungi and summarize recent progress on how Rack1 proteins are involved in fungal pathogenesis.
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232
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An Unsupervised kNN Method to Systematically Detect Changes in Protein Localization in High-Throughput Microscopy Images. PLoS One 2016; 11:e0158712. [PMID: 27442431 PMCID: PMC4956220 DOI: 10.1371/journal.pone.0158712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/13/2016] [Indexed: 11/19/2022] Open
Abstract
Despite the importance of characterizing genes that exhibit subcellular localization changes between conditions in proteome-wide imaging experiments, many recent studies still rely upon manual evaluation to assess the results of high-throughput imaging experiments. We describe and demonstrate an unsupervised k-nearest neighbours method for the detection of localization changes. Compared to previous classification-based supervised change detection methods, our method is much simpler and faster, and operates directly on the feature space to overcome limitations in needing to manually curate training sets that may not generalize well between screens. In addition, the output of our method is flexible in its utility, generating both a quantitatively ranked list of localization changes that permit user-defined cut-offs, and a vector for each gene describing feature-wise direction and magnitude of localization changes. We demonstrate that our method is effective at the detection of localization changes using the Δrpd3 perturbation in Saccharomyces cerevisiae, where we capture 71.4% of previously known changes within the top 10% of ranked genes, and find at least four new localization changes within the top 1% of ranked genes. The results of our analysis indicate that simple unsupervised methods may be able to identify localization changes in images without laborious manual image labelling steps.
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233
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Nuebel E, Manganas P, Tokatlidis K. Orphan proteins of unknown function in the mitochondrial intermembrane space proteome: New pathways and metabolic cross-talk. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2613-2623. [PMID: 27425144 PMCID: PMC5404111 DOI: 10.1016/j.bbamcr.2016.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 07/07/2016] [Accepted: 07/12/2016] [Indexed: 12/14/2022]
Abstract
The mitochondrial intermembrane space (IMS) is involved in protein transport, lipid homeostasis and metal ion exchange, while further acting in signalling pathways such as apoptosis. Regulation of these processes involves protein modifications, as well as stress-induced import or release of proteins and other signalling molecules. Even though the IMS is the smallest sub-compartment of mitochondria, its redox state seems to be tightly regulated. However, the way in which this compartment participates in the cross-talk between the multiple organelles and the cytosol is far from understood. Here we focus on newly identified IMS proteins that may represent future challenges in mitochondrial research. We present an overview of the import pathways, the recently discovered new components of the IMS proteome and how these relate to key aspects of cell signalling and progress made in stem cell and cancer research. A brief overview of the classic mitochondrial import pathways is featured Recent studies assigning a number of new proteins to the mitochondrial IMS are discussed Analysis of the expanded IMS proteomes can provide insights into organelle cross-talk and signalling pathways
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Affiliation(s)
- Esther Nuebel
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Phanee Manganas
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Kostas Tokatlidis
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
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234
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Bonner JN, Choi K, Xue X, Torres NP, Szakal B, Wei L, Wan B, Arter M, Matos J, Sung P, Brown GW, Branzei D, Zhao X. Smc5/6 Mediated Sumoylation of the Sgs1-Top3-Rmi1 Complex Promotes Removal of Recombination Intermediates. Cell Rep 2016; 16:368-378. [PMID: 27373152 PMCID: PMC5051638 DOI: 10.1016/j.celrep.2016.06.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/12/2016] [Accepted: 05/31/2016] [Indexed: 01/23/2023] Open
Abstract
Timely removal of DNA recombination intermediates is critical for genome stability. The DNA helicase-topoisomerase complex, Sgs1-Top3-Rmi1 (STR), is the major pathway for processing these intermediates to generate conservative products. However, the mechanisms that promote STR-mediated functions remain to be defined. Here we show that Sgs1 binds to poly-SUMO chains and associates with the Smc5/6 SUMO E3 complex in yeast. Moreover, these interactions contribute to the sumoylation of Sgs1, Top3, and Rmi1 upon the generation of recombination structures. We show that reduced STR sumoylation leads to accumulation of recombination structures, and impaired growth in conditions when these structures arise frequently, highlighting the importance of STR sumoylation. Mechanistically, sumoylation promotes STR inter-subunit interactions and accumulation at DNA repair centers. These findings expand the roles of sumoylation and Smc5/6 in genome maintenance by demonstrating that they foster STR functions in the removal of recombination intermediates.
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Affiliation(s)
- Jacob N Bonner
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Programs in Biochemistry, Cell, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Koyi Choi
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Programs in Biochemistry, Cell, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Xiaoyu Xue
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nikko P Torres
- Donnelly Centre and Department of Biochemistry, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Barnabas Szakal
- IFOM, The FIRC of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Lei Wei
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bingbing Wan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Meret Arter
- Institute of Biochemistry, Swiss Federal Institute of Technology in Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Joao Matos
- Institute of Biochemistry, Swiss Federal Institute of Technology in Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Grant W Brown
- Donnelly Centre and Department of Biochemistry, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Dana Branzei
- IFOM, The FIRC of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Programs in Biochemistry, Cell, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.
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235
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Promotion of Cell Viability and Histone Gene Expression by the Acetyltransferase Gcn5 and the Protein Phosphatase PP2A in Saccharomyces cerevisiae. Genetics 2016; 203:1693-707. [PMID: 27317677 DOI: 10.1534/genetics.116.189506] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/27/2016] [Indexed: 01/23/2023] Open
Abstract
Histone modifications direct chromatin-templated events in the genome and regulate access to DNA sequence information. There are multiple types of modifications, and a common feature is their dynamic nature. An essential step for understanding their regulation, therefore, lies in characterizing the enzymes responsible for adding and removing histone modifications. Starting with a dosage-suppressor screen in Saccharomyces cerevisiae, we have discovered a functional interaction between the acetyltransferase Gcn5 and the protein phosphatase 2A (PP2A) complex, two factors that regulate post-translational modifications. We find that RTS1, one of two genes encoding PP2A regulatory subunits, is a robust and specific high-copy suppressor of temperature sensitivity of gcn5∆ and a subset of other gcn5∆ phenotypes. Conversely, loss of both PP2A(Rts1) and Gcn5 function in the SAGA and SLIK/SALSA complexes is lethal. RTS1 does not restore global transcriptional defects in gcn5∆; however, histone gene expression is restored, suggesting that the mechanism of RTS1 rescue includes restoration of specific cell cycle transcripts. Pointing to new mechanisms of acetylation-phosphorylation cross-talk, RTS1 high-copy rescue of gcn5∆ growth requires two residues of H2B that are phosphorylated in human cells. These data highlight the potential significance of dynamic phosphorylation and dephosphorylation of these deeply conserved histone residues for cell viability.
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236
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Abstract
MOTIVATION High-content screening (HCS) technologies have enabled large scale imaging experiments for studying cell biology and for drug screening. These systems produce hundreds of thousands of microscopy images per day and their utility depends on automated image analysis. Recently, deep learning approaches that learn feature representations directly from pixel intensity values have dominated object recognition challenges. These tasks typically have a single centered object per image and existing models are not directly applicable to microscopy datasets. Here we develop an approach that combines deep convolutional neural networks (CNNs) with multiple instance learning (MIL) in order to classify and segment microscopy images using only whole image level annotations. RESULTS We introduce a new neural network architecture that uses MIL to simultaneously classify and segment microscopy images with populations of cells. We base our approach on the similarity between the aggregation function used in MIL and pooling layers used in CNNs. To facilitate aggregating across large numbers of instances in CNN feature maps we present the Noisy-AND pooling function, a new MIL operator that is robust to outliers. Combining CNNs with MIL enables training CNNs using whole microscopy images with image level labels. We show that training end-to-end MIL CNNs outperforms several previous methods on both mammalian and yeast datasets without requiring any segmentation steps. AVAILABILITY AND IMPLEMENTATION Torch7 implementation available upon request. CONTACT oren.kraus@mail.utoronto.ca.
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Affiliation(s)
- Oren Z Kraus
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, M5S 2E4, Canada The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, Canada
| | - Jimmy Lei Ba
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, M5S 2E4, Canada
| | - Brendan J Frey
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, M5S 2E4, Canada The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, Canada
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237
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Boone CHT, Grove RA, Adamcova D, Braga CP, Adamec J. Revealing oxidative damage to enzymes of carbohydrate metabolism in yeast: An integration of 2D DIGE, quantitative proteomics, and bioinformatics. Proteomics 2016; 16:1889-903. [PMID: 27193513 DOI: 10.1002/pmic.201500546] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/19/2016] [Accepted: 05/16/2016] [Indexed: 12/17/2022]
Abstract
Clinical usage of lidocaine, a pro-oxidant has been linked with severe, mostly neurological complications. The mechanism(s) causing these complications is independent of the blockade of voltage-gated sodium channels. The budding yeast Saccharomyces cerevisiae lacks voltage-gated sodium channels, thus provides an ideal system to investigate lidocaine-induced protein and pathway alterations. Whole-proteome alterations leading to these complications have not been identified. To address this, S. cerevisiae was grown to stationary phase and exposed to an LC50 dose of lidocaine. The differential proteomes of lidocaine treatment and control were resolved 6 h post exposure using 2D DIGE. Amine reactive dyes and carbonyl reactive dyes were used to assess protein abundance and protein oxidation, respectively. Quantitative analysis of these dyes (⩾ 1.5-fold alteration, p ⩽ 0.05) revealed a total of 33 proteoforms identified by MS differing in abundance and/or oxidation upon lidocaine exposure. Network analysis showed enrichment of apoptotic proteins and cell wall maintenance proteins, while the abundance of proteins central to carbohydrate metabolism, such as triosephosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase, and redox proteins superoxide dismutase and peroxiredoxin were significantly decreased. Enzymes of carbohydrate metabolism, such as phosphoglycerate kinase and enolase, the TCA cycle enzyme aconitase, and multiple ATP synthase subunits were found to be oxidatively modified. Also, the activity of aconitase was found to be decreased. Overall, these data suggest that toxic doses of lidocaine induce significant disruption of glycolytic pathways, energy production, and redox balance, potentially leading to cell malfunction and death.
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Affiliation(s)
- Cory H T Boone
- Redox Biology Center, Department of Biochemistry, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Ryan A Grove
- Redox Biology Center, Department of Biochemistry, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Dana Adamcova
- Redox Biology Center, Department of Biochemistry, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Camila P Braga
- Redox Biology Center, Department of Biochemistry, University of Nebraska - Lincoln, Lincoln, NE, USA.,Department of Chemistry and Biochemistry, Institute of Bioscience, São Paulo State University, Botucatu, SP, Brazil
| | - Jiri Adamec
- Redox Biology Center, Department of Biochemistry, University of Nebraska - Lincoln, Lincoln, NE, USA
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238
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Gilmore JM, Sardiu ME, Groppe BD, Thornton JL, Liu X, Dayebgadoh G, Banks CA, Slaughter BD, Unruh JR, Workman JL, Florens L, Washburn MP. WDR76 Co-Localizes with Heterochromatin Related Proteins and Rapidly Responds to DNA Damage. PLoS One 2016; 11:e0155492. [PMID: 27248496 PMCID: PMC4889050 DOI: 10.1371/journal.pone.0155492] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/30/2016] [Indexed: 12/21/2022] Open
Abstract
Proteins that respond to DNA damage play critical roles in normal and diseased states in human biology. Studies have suggested that the S. cerevisiae protein CMR1/YDL156w is associated with histones and is possibly associated with DNA repair and replication processes. Through a quantitative proteomic analysis of affinity purifications here we show that the human homologue of this protein, WDR76, shares multiple protein associations with the histones H2A, H2B, and H4. Furthermore, our quantitative proteomic analysis of WDR76 associated proteins demonstrated links to proteins in the DNA damage response like PARP1 and XRCC5 and heterochromatin related proteins like CBX1, CBX3, and CBX5. Co-immunoprecipitation studies validated these interactions. Next, quantitative imaging studies demonstrated that WDR76 was recruited to laser induced DNA damage immediately after induction, and we compared the recruitment of WDR76 to laser induced DNA damage to known DNA damage proteins like PARP1, XRCC5, and RPA1. In addition, WDR76 co-localizes to puncta with the heterochromatin proteins CBX1 and CBX5, which are also recruited to DNA damage but much less intensely than WDR76. This work demonstrates the chromatin and DNA damage protein associations of WDR76 and demonstrates the rapid response of WDR76 to laser induced DNA damage.
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Affiliation(s)
- Joshua M. Gilmore
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Mihaela E. Sardiu
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Brad D. Groppe
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Janet L. Thornton
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Xingyu Liu
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Gerald Dayebgadoh
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Charles A. Banks
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Brian D. Slaughter
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Jay R. Unruh
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Jerry L. Workman
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Michael P. Washburn
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas, 66160, United States of America
- * E-mail:
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239
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Bru S, Martínez-Laínez JM, Hernández-Ortega S, Quandt E, Torres-Torronteras J, Martí R, Canadell D, Ariño J, Sharma S, Jiménez J, Clotet J. Polyphosphate is involved in cell cycle progression and genomic stability in Saccharomyces cerevisiae. Mol Microbiol 2016; 101:367-80. [PMID: 27072996 DOI: 10.1111/mmi.13396] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 04/04/2016] [Accepted: 04/09/2016] [Indexed: 11/27/2022]
Abstract
Polyphosphate (polyP) is a linear chain of up to hundreds of inorganic phosphate residues that is necessary for many physiological functions in all living organisms. In some bacteria, polyP supplies material to molecules such as DNA, thus playing an important role in biosynthetic processes in prokaryotes. In the present study, we set out to gain further insight into the role of polyP in eukaryotic cells. We observed that polyP amounts are cyclically regulated in Saccharomyces cerevisiae, and those mutants that cannot synthesise (vtc4Δ) or hydrolyse polyP (ppn1Δ, ppx1Δ) present impaired cell cycle progression. Further analysis revealed that polyP mutants show delayed nucleotide production and increased genomic instability. Based on these findings, we concluded that polyP not only maintains intracellular phosphate concentrations in response to fluctuations in extracellular phosphate levels, but also muffles internal cyclic phosphate fluctuations, such as those produced by the sudden demand of phosphate to synthetize deoxynucleotides just before and during DNA duplication. We propose that the presence of polyP in eukaryotic cells is required for the timely and accurate duplication of DNA.
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Affiliation(s)
- Samuel Bru
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | | | - Sara Hernández-Ortega
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Eva Quandt
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Javier Torres-Torronteras
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Ramón Martí
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - David Canadell
- Department of Biochemistry and Molecular Biology and the Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joaquin Ariño
- Department of Biochemistry and Molecular Biology and the Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden
| | - Javier Jiménez
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Josep Clotet
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
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240
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Berry LK, Ólafsson G, Ledesma-Fernández E, Thorpe PH. Synthetic protein interactions reveal a functional map of the cell. eLife 2016; 5:e13053. [PMID: 27098839 PMCID: PMC4841780 DOI: 10.7554/elife.13053] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/17/2016] [Indexed: 11/13/2022] Open
Abstract
To understand the function of eukaryotic cells, it is critical to understand the role of protein-protein interactions and protein localization. Currently, we do not know the importance of global protein localization nor do we understand to what extent the cell is permissive for new protein associations - a key requirement for the evolution of new protein functions. To answer this question, we fused every protein in the yeast Saccharomyces cerevisiae with a partner from each of the major cellular compartments and quantitatively assessed the effects upon growth. This analysis reveals that cells have a remarkable and unanticipated tolerance for forced protein associations, even if these associations lead to a proportion of the protein moving compartments within the cell. Furthermore, the interactions that do perturb growth provide a functional map of spatial protein regulation, identifying key regulatory complexes for the normal homeostasis of eukaryotic cells.
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Affiliation(s)
- Lisa K Berry
- Mitotic Control Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Guðjón Ólafsson
- Mitotic Control Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Elena Ledesma-Fernández
- Mitotic Control Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Peter H Thorpe
- Mitotic Control Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
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241
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DNA damage regulation and its role in drug-related phenotypes in the malaria parasites. Sci Rep 2016; 6:23603. [PMID: 27033103 PMCID: PMC4817041 DOI: 10.1038/srep23603] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/10/2016] [Indexed: 11/29/2022] Open
Abstract
DNA of malaria parasites, Plasmodium falciparum, is subjected to extraordinary high levels of genotoxic insults during its complex life cycle within both the mosquito and human host. Accordingly, most of the components of DNA repair machinery are conserved in the parasite genome. Here, we investigated the genome-wide responses of P. falciparum to DNA damaging agents and provided transcriptional evidence of the existence of the double strand break and excision repair system. We also showed that acetylation at H3K9, H4K8, and H3K56 play a role in the direct and indirect response to DNA damage induced by an alkylating agent, methyl methanesulphonate (MMS). Artemisinin, the first line antimalarial chemotherapeutics elicits a similar response compared to MMS which suggests its activity as a DNA damaging agent. Moreover, in contrast to the wild-type P. falciparum, two strains (Dd2 and W2) previously shown to exhibit a mutator phenotype, fail to induce their DNA repair upon MMS-induced DNA damage. Genome sequencing of the two mutator strains identified point mutations in 18 DNA repair genes which may contribute to this phenomenon.
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242
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Kuzmin E, Costanzo M, Andrews B, Boone C. Synthetic Genetic Arrays: Automation of Yeast Genetics. Cold Spring Harb Protoc 2016; 2016:pdb.top086652. [PMID: 27037078 DOI: 10.1101/pdb.top086652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genome-sequencing efforts have led to great strides in the annotation of protein-coding genes and other genomic elements. The current challenge is to understand the functional role of each gene and how genes work together to modulate cellular processes. Genetic interactions define phenotypic relationships between genes and reveal the functional organization of a cell. Synthetic genetic array (SGA) methodology automates yeast genetics and enables large-scale and systematic mapping of genetic interaction networks in the budding yeast,Saccharomyces cerevisiae SGA facilitates construction of an output array of double mutants from an input array of single mutants through a series of replica pinning steps. Subsequent analysis of genetic interactions from SGA-derived mutants relies on accurate quantification of colony size, which serves as a proxy for fitness. Since its development, SGA has given rise to a variety of other experimental approaches for functional profiling of the yeast genome and has been applied in a multitude of other contexts, such as genome-wide screens for synthetic dosage lethality and integration with high-content screening for systematic assessment of morphology defects. SGA-like strategies can also be implemented similarly in a number of other cell types and organisms, includingSchizosaccharomyces pombe,Escherichia coli, Caenorhabditis elegans, and human cancer cell lines. The genetic networks emerging from these studies not only generate functional wiring diagrams but may also play a key role in our understanding of the complex relationship between genotype and phenotype.
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Affiliation(s)
- Elena Kuzmin
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Michael Costanzo
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Brenda Andrews
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
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243
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Styles EB, Friesen H, Boone C, Andrews BJ. High-Throughput Microscopy-Based Screening in Saccharomyces cerevisiae. Cold Spring Harb Protoc 2016; 2016:pdb.top087593. [PMID: 27037080 DOI: 10.1101/pdb.top087593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The budding yeastSaccharomyces cerevisiaehas served as the pioneer model organism for virtually all genome-scale methods, including genome sequencing, DNA microarrays, gene deletion collections, and a variety of proteomic platforms. Yeast has also provided a test-bed for the development of systematic fluorescence-based imaging screens to enable the analysis of protein localization and abundance in vivo. Especially important has been the integration of high-throughput microscopy with automated image-processing methods, which has allowed researchers to overcome issues associated with manual image analysis and acquire unbiased, quantitative data. Here we provide an introduction to automated imaging in budding yeast.
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Affiliation(s)
- Erin B Styles
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Helena Friesen
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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244
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Protein aggregation as a mechanism of adaptive cellular responses. Curr Genet 2016; 62:711-724. [DOI: 10.1007/s00294-016-0596-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 11/26/2022]
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245
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Silva S, Altmannova V, Luke-Glaser S, Henriksen P, Gallina I, Yang X, Choudhary C, Luke B, Krejci L, Lisby M. Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance. Genes Dev 2016; 30:700-17. [PMID: 26966248 PMCID: PMC4803055 DOI: 10.1101/gad.276204.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/17/2016] [Indexed: 11/25/2022]
Abstract
Mph1 is a member of the conserved FANCM family of DNA motor proteins that play key roles in genome maintenance processes underlying Fanconi anemia, a cancer predisposition syndrome in humans. Here, we identify Mte1 as a novel interactor of the Mph1 helicase in Saccharomyces cerevisiae. In vitro, Mte1 (Mph1-associated telomere maintenance protein 1) binds directly to DNA with a preference for branched molecules such as D loops and fork structures. In addition, Mte1 stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Deletion of MTE1 reduces crossover recombination and suppresses the sensitivity of mph1Δ mutant cells to replication stress. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres, and MTE1 deletion results in elongated telomeres. Taken together, our data indicate that Mte1 plays a role in regulation of crossover recombination, response to replication stress, and telomere maintenance.
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Affiliation(s)
- Sonia Silva
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | | | - Peter Henriksen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Irene Gallina
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Xuejiao Yang
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Brian Luke
- Institute of Molecular Biology gGmbH (IMB), 55128 Mainz, Germany
| | - Lumir Krejci
- Department of Biology, Masaryk University, CZ-62500 Brno, Czech Republic; National Centre for Biomolecular Research, Masaryk University, CZ-62500 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, CZ-656 91 Brno, Czech Republic; Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, CZ-656 91 Brno, Czech Republic
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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246
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Xue X, Papusha A, Choi K, Bonner JN, Kumar S, Niu H, Kaur H, Zheng XF, Donnianni RA, Lu L, Lichten M, Zhao X, Ira G, Sung P. Differential regulation of the anti-crossover and replication fork regression activities of Mph1 by Mte1. Genes Dev 2016; 30:687-99. [PMID: 26966246 PMCID: PMC4803054 DOI: 10.1101/gad.276139.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/17/2016] [Indexed: 02/03/2023]
Abstract
Xue et al. identified Mte1 as a multifunctional regulator of S. cerevisiae Mph1. Mte1 stimulates Mph1-mediated DNA replication fork regression and branch migration in a model substrate. Surprisingly, Mte1 antagonizes the D-loop-dissociative activity of Mph1–MHF and exerts a procrossover role in mitotic recombination. We identified Mte1 (Mph1-associated telomere maintenance protein 1) as a multifunctional regulator of Saccharomyces cerevisiae Mph1, a member of the FANCM family of DNA motor proteins important for DNA replication fork repair and crossover suppression during homologous recombination. We show that Mte1 interacts with Mph1 and DNA species that resemble a DNA replication fork and the D loop formed during recombination. Biochemically, Mte1 stimulates Mph1-mediated DNA replication fork regression and branch migration in a model substrate. Consistent with this activity, genetic analysis reveals that Mte1 functions with Mph1 and the associated MHF complex in replication fork repair. Surprisingly, Mte1 antagonizes the D-loop-dissociative activity of Mph1–MHF and exerts a procrossover role in mitotic recombination. We further show that the influence of Mte1 on Mph1 activities requires its binding to Mph1 and DNA. Thus, Mte1 differentially regulates Mph1 activities to achieve distinct outcomes in recombination and replication fork repair.
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Affiliation(s)
- Xiaoyu Xue
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Alma Papusha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Koyi Choi
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jacob N Bonner
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Sandeep Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hengyao Niu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Hardeep Kaur
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Xiao-Feng Zheng
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Roberto A Donnianni
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York 10032, USA
| | - Lucy Lu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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247
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Ianiri G, Idnurm A, Castoria R. Transcriptomic responses of the basidiomycete yeast Sporobolomyces sp. to the mycotoxin patulin. BMC Genomics 2016; 17:210. [PMID: 26956724 PMCID: PMC4784387 DOI: 10.1186/s12864-016-2550-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/28/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Patulin is a mycotoxin produced by Penicillium expansum, the causal agent of blue mold of stored pome fruits, and several other species of filamentous fungi. This mycotoxin has genotoxic, teratogenic and immunotoxic effects in mammals, and its presence in pome fruits and derived products represents a serious health hazard. Biocontrol agents in the Pucciniomycotina, such as the yeasts Sporobolomyces sp. strain IAM 13481 and Rhodosporidium kratochvilovae strain LS11, are able to resist patulin and degrade it into the less toxic compounds desoxypatulinic acid and ascladiol. RESULTS In this investigation we applied a transcriptomic approach based on RNAseq to annotate the genome of Sporobolomyces sp. IAM 13481 and then study the changes of gene expression in Sporobolomyces sp. exposed to patulin. Patulin treatment leads to ROS production and oxidative stress that result in the activation of stress response mechanisms controlled by transcription factors. Upregulated Sporobolomyces genes were those involved in oxidation-reduction and transport processes, suggesting the activation of defense mechanisms to resist patulin toxicity and expel the mycotoxin out of the cells. Other upregulated genes encoded proteins involved in metabolic processes such as those of the glutathione and thioredoxin systems, which are essential to restore the cellular redox homeostasis. Conversely, patulin treatment decreased the expression of genes involved in the processes of protein synthesis and modification, such as transcription, RNA processing, translation, protein phosphorylation and biosynthesis of amino acids. Also, genes encoding proteins involved in transport of ions, cell division and cell cycle were downregulated. This indicates a reduction of metabolic activity, probably due to the high energy requirement by the cells or metabolic arrest while recovering from the insult caused by patulin toxicity. CONCLUSIONS Complex mechanisms are activated in a biocontrol yeast in response to patulin. The genes identified in this study can pave the way to develop i) a biodetoxification process of patulin in juices and ii) a biosensor for the rapid and cost-effective detection of this mycotoxin.
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Affiliation(s)
- Giuseppe Ianiri
- Dipartimento di Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Via F. De Sanctis snc, 86100, Campobasso, Italy.
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, 64110, USA.
- Present address: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Alexander Idnurm
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, 64110, USA.
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Raffaello Castoria
- Dipartimento di Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Via F. De Sanctis snc, 86100, Campobasso, Italy.
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248
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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Feng J, Duan Y, Sun W, Qin Y, Zhuang Z, Zhu D, Sun X, Jiang L. CaTip41 regulates protein phosphatase 2A activity, CaRad53 deactivation and the recovery of DNA damage-induced filamentation to yeast form in Candida albicans. FEMS Yeast Res 2016; 16:fow009. [PMID: 26851402 DOI: 10.1093/femsyr/fow009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2016] [Indexed: 02/07/2023] Open
Abstract
Phosphorylation and dephosphorylation of the checkpoint kinase CaRad53 is crucial for fungal cells in response to genotoxic stresses. The protein phosphatase 2A (PP2A) CaPph3/CaPsy2 phosphatase complex is involved in CaRad53 dephosphorylation in Candida albicans. In view of the role of ScTip41/ScTap42 in regulating PP2A phosphatases in Saccharomyces cerevisiae, we have explored the function of CaTip41 in C. albicans. Here, we show that CaTIP41 is a functional ortholog of ScTIP41 in the sensitivity of S. cerevisiae cells to rapamycin. Deletion of CaTIP41 causes C. albicans cells to be sensitive to DNA damaging agents, methylmethane sulfonate (MMS) and cisplatin, and resistant to both rapamycin and caffeine. Accordingly, expression of CaTip41 increases in response to MMS and cisplatin. In addition, C. albicans cells lacking CaTIP41 show a delay in the recovery from MMS-induced filamentation to yeast form, decreased PP2A activity and a defect in deactivation of CaRad53 during recovery from DNA damage. Through yeast two-hybrid assay we show that CaTip41 interacts with either CaPph3, CaPsy2 or CaTap42. Therefore, CaTip41 plays regulatory roles in both the CaRad53 deactivation during recovery from DNA damage and the target of rapamycin signaling pathway.
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Affiliation(s)
- Jinrong Feng
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Yinong Duan
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Wei Sun
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Yongwei Qin
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Zhong Zhuang
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Dandan Zhu
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Xiaolei Sun
- Department of Pathogen Biology, School of Medicine, Nantong University, Nantong 226001, China
| | - Linghuo Jiang
- The National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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MTE1 Functions with MPH1 in Double-Strand Break Repair. Genetics 2016; 203:147-57. [PMID: 26920759 DOI: 10.1534/genetics.115.185454] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/22/2016] [Indexed: 11/18/2022] Open
Abstract
Double-strand DNA breaks occur upon exposure of cells to ionizing radiation and certain chemical agents or indirectly through replication fork collapse at DNA damage sites. If left unrepaired, double-strand breaks can cause genome instability and cell death, and their repair can result in loss of heterozygosity. In response to DNA damage, proteins involved in double-strand break repair by homologous recombination relocalize into discrete nuclear foci. We identified 29 proteins that colocalize with recombination repair protein Rad52 in response to DNA damage. Of particular interest, Ygr042w/Mte1, a protein of unknown function, showed robust colocalization with Rad52. Mte1 foci fail to form when the DNA helicase gene MPH1 is absent. Mte1 and Mph1 form a complex and are recruited to double-strand breaks in vivo in a mutually dependent manner. MTE1 is important for resolution of Rad52 foci during double-strand break repair and for suppressing break-induced replication. Together our data indicate that Mte1 functions with Mph1 in double-strand break repair.
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