1
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Chen Y, Liu Z, Zhang Y, Ye M, Chen Y, Gao J, Song J, Yang H, Wu C, Yao W, Bai X, Fan M, Feng S, Wang Y, Zhang L, Ge L, Feng D, Yi C. Two distinct regulatory pathways govern Cct2-Atg8 binding in the process of solid aggrephagy. EMBO Rep 2024; 25:4749-4776. [PMID: 39322741 PMCID: PMC11549370 DOI: 10.1038/s44319-024-00275-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 08/30/2024] [Accepted: 09/13/2024] [Indexed: 09/27/2024] Open
Abstract
CCT2 serves as an aggrephagy receptor that plays a crucial role in the clearance of solid aggregates, yet the underlying molecular mechanisms by which CCT2 regulates solid aggrephagy are not fully understood. Here we report that the binding of Cct2 to Atg8 is governed by two distinct regulatory mechanisms: Atg1-mediated Cct2 phosphorylation and the interaction between Cct2 and Atg11. Atg1 phosphorylates Cct2 at Ser412 and Ser470, and disruption of these phosphorylation sites impairs solid aggrephagy by hindering Cct2-Atg8 binding. Additionally, we observe that Atg11, an adaptor protein involved in selective autophagy, directly associates with Cct2 through its CC4 domain. Deficiency in this interaction significantly weakens the association of Cct2 with Atg8. The requirement of Atg1-mediated Cct2 phosphorylation and of Atg11 for CCT2-LC3C binding and subsequent aggrephagy is conserved in mammalian cells. These findings provide insights into the crucial roles of Atg1-mediated Cct2 phosphorylation and Atg11-Cct2 binding as key mediators governing the interaction between Cct2 and Atg8 during the process of solid aggrephagy.
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Affiliation(s)
- Yuting Chen
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhaojie Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yi Zhang
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Miao Ye
- Xinyuan Institute of Medicine and Biotechnology, School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yingcong Chen
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianhua Gao
- School of Medical Technology, Jiangxi Medical College, Shangrao, China
| | - Juan Song
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
| | - Huan Yang
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Choufei Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
| | - Weijing Yao
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xue Bai
- Mass Spectrometry & Metabolomics Core Facility, Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, China
| | - Mingzhu Fan
- Mass Spectrometry & Metabolomics Core Facility, Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, China
| | - Shan Feng
- Mass Spectrometry & Metabolomics Core Facility, Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, China
| | - Yigang Wang
- Xinyuan Institute of Medicine and Biotechnology, School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Liqin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Du Feng
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.
| | - Cong Yi
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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2
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Ganesan I, Pfanner N, Wiedemann N. Screen for temperature-sensitive mutants of non-essential yeast genes. Methods Enzymol 2024; 707:611-634. [PMID: 39488393 DOI: 10.1016/bs.mie.2024.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2024]
Abstract
Yeast deletion mutants of crucial genes are often associated with a number of secondary defects, which hamper the analysis of primary protein function. Therefore, temperature-sensitive mutants are valuable tools to evaluate protein function in a focused and often reversible manner. However, temperature-sensitive mutants are uncommon for non-essential genes that nevertheless may have strong defects. Here we describe a screening method for generating temperature-sensitive mutants of non-essential genes in synthetic lethal backgrounds of Saccharomyces cerevisiae. As proof of principle, we describe a successful screen for the yeast mitochondrial inner membrane protease iAAA subunit Yme1 utilizing two screening approaches: a random mutagenesis and rational design approach. We then describe how candidate temperature-sensitive mutants are validated.
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Affiliation(s)
- Iniyan Ganesan
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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3
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Bykov YS, Schuldiner M. Analysis of mitochondrial biogenesis and protein localization by genetic screens and automated imaging. Methods Enzymol 2024; 706:97-123. [PMID: 39455236 DOI: 10.1016/bs.mie.2024.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2024]
Abstract
Budding yeast is a laboratory model of a simple eukaryotic cell. Its compact genome is very easy to edit. This allowed to create systematic collections (libraries) of yeast strains where every gene is either perturbed or tagged. Here we review how such collections were used to study mitochondrial biology by doing genetic screens. First, we introduce the principles of yeast genome editing and the basics of its life cycle that are useful for genetic experiments. Then we overview what yeast strain collections were created over the past years. We also describe the creation and the usage of the new generation of SWAP-Tag (SWAT) collections that allow to create custom libraries. We outline the principles of changing the genetic background of whole collections in parallel, and the basics of synthetic genetic array (SGA) approach. Then we review the discoveries that were made using different types of genetic screens focusing on general mitochondrial functions, proteome, and protein targeting pathways. The development of new collections and screening techniques will continue to bring valuable insight into the function of mitochondria and other organelles.
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Affiliation(s)
- Yury S Bykov
- Quantitative Cell Biology, Rhineland-Palatinate Technical University, Kaiserslautern, Germany.
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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4
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Wang C, Quadrado M, Mireau H. Temperature-sensitive splicing defects in Arabidopsis mitochondria caused by mutations in the ROOT PRIMORDIUM DEFECTIVE 1 gene. Nucleic Acids Res 2024; 52:4575-4587. [PMID: 38364869 PMCID: PMC11077063 DOI: 10.1093/nar/gkae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/06/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Group II introns in plant organelles have lost splicing autonomy and require the assistance of nuclear-encoded trans-factors whose roles remain to be elucidated. These factors can be mono- or poly-specific with respect to the number of introns whose splicing they facilitate. Poly-acting splicing factors are often essential and their genetic identification may benefit from the use of conditional mutations. Temperature-sensitive (TS) mutations in the ROOT PRIMORDIUM DEFECTIVE 1 (RPD1) gene were initially selected for their inhibitory effect on root formation in Arabidopsis. Further analysis revealed that RPD1 encodes a mitochondria-targeted RNA-binding protein family member, suggesting a role in mitochondrial gene expression and making its role in root formation enigmatic. We analysed the function of RPD1 and found that it is required for the removal of 9 mitochondrial group II introns and that the identified TS mutations affect the splicing function of RPD1. These results support that the inhibition of adventitious root formation at non-permissive temperature results from a reduction in RPD1 activity and thus mitochondrial activity. We further show that RPD1 physically associates in vivo with the introns whose splicing it facilitates. Preliminary mapping indicates that RPD1 may not bind to the same regions within all of its intron targets, suggesting potential variability in its influence on splicing activation.
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Affiliation(s)
- Chuande Wang
- School of Agriculture and Biology, Joint Center for Single cell Biology/Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai Jiao Tong University, Shanghai, China
| | - Martine Quadrado
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Hakim Mireau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
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5
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Liu H, Sun M, Zhang J. Genomic estimates of mutation and substitution rates contradict the evolutionary speed hypothesis of the latitudinal diversity gradient. Proc Biol Sci 2023; 290:20231787. [PMID: 37876195 PMCID: PMC10598419 DOI: 10.1098/rspb.2023.1787] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
The latitudinal diversity gradient (LDG) refers to a decrease in biodiversity from the equator to the poles. The evolutionary speed hypothesis, backed by the metabolic theory of ecology, asserts that nucleotide mutation and substitution rates per site per year are higher and thereby speciation rates are higher at higher temperatures, generating the LDG. However, prior empirical investigations of the relationship between the temperature and mutation or substitution rate were based on a few genes and the results were mixed. We here revisit this relationship using genomic data. No significant correlation between the temperature and mutation rate is found in 13 prokaryotes or in 107 eukaryotes. An analysis of 234 diverse trios of bacterial taxa indicates that the synonymous substitution rate is not significantly associated with the growth temperature. The same data, however, reveal a significant negative association between the nonsynonymous substitution rate and temperature, which is explainable by a larger fraction of detrimental nonsynonymous mutations at higher temperatures due to a stronger demand for protein stability. We conclude that the evolutionary speed hypothesis of the LDG is unsupported by genomic data and advise that future mechanistic studies of the LDG should focus on other hypotheses.
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Affiliation(s)
- Haoxuan Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Evolutionary & Organismal Biology and the Fourth Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou 310058, People's Republic of China
| | - Mengyi Sun
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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6
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Schramm T, Lubrano P, Pahl V, Stadelmann A, Verhülsdonk A, Link H. Mapping temperature-sensitive mutations at a genome scale to engineer growth switches in Escherichia coli. Mol Syst Biol 2023; 19:e11596. [PMID: 37642940 PMCID: PMC10568205 DOI: 10.15252/msb.202311596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
Temperature-sensitive (TS) mutants are a unique tool to perturb and engineer cellular systems. Here, we constructed a CRISPR library with 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins. 1,269 of these mutants showed temperature-sensitive growth in a time-resolved competition assay. We reconstructed 94 TS mutants and measured their metabolism under growth arrest at 42°C using metabolomics. Metabolome changes were strong and mutant-specific, showing that metabolism of nongrowing E. coli is perturbation-dependent. For example, 24 TS mutants of metabolic enzymes overproduced the direct substrate metabolite due to a bottleneck in their associated pathway. A strain with TS homoserine kinase (ThrBF267D ) produced homoserine for 24 h, and production was tunable by temperature. Finally, we used a TS subunit of DNA polymerase III (DnaXL289Q ) to decouple growth from arginine overproduction in engineered E. coli. These results provide a strategy to identify TS mutants en masse and demonstrate their large potential to produce bacterial metabolites with nongrowing cells.
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Affiliation(s)
- Thorben Schramm
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
- Present address:
Department of Biology, Institute of Molecular Systems BiologyETH ZurichZürichSwitzerland
| | - Paul Lubrano
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
| | - Vanessa Pahl
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
| | - Amelie Stadelmann
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
| | - Andreas Verhülsdonk
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
| | - Hannes Link
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence “Controlling Microbes to Fight Infections”University of TübingenTübingenGermany
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7
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Kumar A, Stirling PC. Turning up the heat on essential E. coli genes. Mol Syst Biol 2023; 19:e11933. [PMID: 37718698 PMCID: PMC10568200 DOI: 10.15252/msb.202311933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023] Open
Abstract
Temperature-sensitive (TS) alleles create tunable thermoswitches to deplete essential cellular activities and are used to dissect gene function. In their recent study, Link and colleagues (Schramm et al 2023) use a CRISPR-based approach to systematically create TS alleles across essential genes in E. coli.
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Affiliation(s)
- Arun Kumar
- Terry Fox LaboratoryBC Cancer Research InstituteVancouverBCCanada
| | - Peter C Stirling
- Terry Fox LaboratoryBC Cancer Research InstituteVancouverBCCanada
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8
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Amin A, Wu R, Khan MA, Cheung MH, Liang Y, Liu C, Zhu G, Yu ZL, Liang C. An essential Noc3p dimerization cycle mediates ORC double-hexamer formation in replication licensing. Life Sci Alliance 2023; 6:e202201594. [PMID: 36599624 PMCID: PMC9813392 DOI: 10.26508/lsa.202201594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023] Open
Abstract
Replication licensing, a prerequisite of DNA replication, helps to ensure once-per-cell-cycle genome duplication. Some DNA replication-initiation proteins are sequentially loaded onto replication origins to form pre-replicative complexes (pre-RCs). ORC and Noc3p bind replication origins throughout the cell cycle, providing a platform for pre-RC assembly. We previously reported that cell cycle-dependent ORC dimerization is essential for the chromatin loading of the symmetric MCM double-hexamers. Here, we used Saccharomyces cerevisiae separation-of-function NOC3 mutants to confirm the separable roles of Noc3p in DNA replication and ribosome biogenesis. We also show that an essential and cell cycle-dependent Noc3p dimerization cycle regulates the ORC dimerization cycle. Noc3p dimerizes at the M-to-G1 transition and de-dimerizes in S-phase. The Noc3p dimerization cycle coupled with the ORC dimerization cycle enables replication licensing, protects nascent sister replication origins after replication initiation, and prevents re-replication. This study has revealed a new mechanism of replication licensing and elucidated the molecular mechanism of Noc3p as a mediator of ORC dimerization in pre-RC formation.
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Affiliation(s)
- Aftab Amin
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Rentian Wu
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Man Hei Cheung
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanting Liang
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Changdong Liu
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Guang Zhu
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhi-Ling Yu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Chun Liang
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- EnKang Pharmaceuticals (Guangzhou), Ltd., Guangzhou, China
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9
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Inactive Proteasomes Routed to Autophagic Turnover Are Confined within the Soluble Fraction of the Cell. Biomolecules 2022; 13:biom13010077. [PMID: 36671462 PMCID: PMC9855985 DOI: 10.3390/biom13010077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
Previous studies demonstrated that dysfunctional yeast proteasomes accumulate in the insoluble protein deposit (IPOD), described as the final deposition site for amyloidogenic insoluble proteins and that this compartment also mediates proteasome ubiquitination, a prerequisite for their targeted autophagy (proteaphagy). Here, we examined the solubility state of proteasomes subjected to autophagy as a result of their inactivation, or under nutrient starvation. In both cases, only soluble proteasomes could serve as a substrate to autophagy, suggesting a modified model whereby substrates for proteaphagy are dysfunctional proteasomes in their near-native soluble state, and not as previously believed, those sequestered at the IPOD. Furthermore, the insoluble fraction accumulating in the IPOD represents an alternative pathway, enabling the removal of inactive proteasomes that escaped proteaphagy when the system became saturated. Altogether, we suggest that the relocalization of proteasomes to soluble aggregates represents a general stage of proteasome recycling through autophagy.
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10
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Wagner A, Schosserer M. The epitranscriptome in ageing and stress resistance: A systematic review. Ageing Res Rev 2022; 81:101700. [PMID: 35908668 DOI: 10.1016/j.arr.2022.101700] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 01/31/2023]
Abstract
Modifications of RNA, collectively called the "epitranscriptome", might provide novel biomarkers and innovative targets for interventions in geroscience but are just beginning to be studied in the context of ageing and stress resistance. RNA modifications modulate gene expression by affecting translation initiation and speed, miRNA binding, RNA stability, and RNA degradation. Nonetheless, the precise underlying molecular mechanisms and physiological consequences of most alterations of the epitranscriptome are still only poorly understood. We here systematically review different types of modifications of rRNA, tRNA and mRNA, the methodology to analyze them, current challenges in the field, and human disease associations. Furthermore, we compiled evidence for a connection between individual enzymes, which install RNA modifications, and lifespan in yeast, worm and fly. We also included resistance to different stressors and competitive fitness as search criteria for genes potentially relevant to ageing. Promising candidates identified by this approach include RCM1/NSUN5, RRP8, and F33A8.4/ZCCHC4 that introduce base methylations in rRNA, the methyltransferases DNMT2 and TRM9/ALKBH8, as well as factors involved in the thiolation or A to I editing in tRNA, and finally the m6A machinery for mRNA.
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Affiliation(s)
- Anja Wagner
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Schosserer
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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11
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Berg MD, Zhu Y, Loll-Krippleber R, San Luis BJ, Genereaux J, Boone C, Villén J, Brown GW, Brandl CJ. Genetic background and mistranslation frequency determine the impact of mistranslating tRNASerUGG. G3 GENES|GENOMES|GENETICS 2022; 12:6588684. [PMID: 35587152 PMCID: PMC9258585 DOI: 10.1093/g3journal/jkac125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/07/2022] [Indexed: 12/02/2022]
Abstract
Transfer RNA variants increase the frequency of mistranslation, the misincorporation of an amino acid not specified by the “standard” genetic code, to frequencies approaching 10% in yeast and bacteria. Cells cope with these variants by having multiple copies of each tRNA isodecoder and through pathways that deal with proteotoxic stress. In this study, we define the genetic interactions of the gene encoding tRNASerUGG,G26A, which mistranslates serine at proline codons. Using a collection of yeast temperature-sensitive alleles, we identify negative synthetic genetic interactions between the mistranslating tRNA and 109 alleles representing 91 genes, with nearly half of the genes having roles in RNA processing or protein folding and turnover. By regulating tRNA expression, we then compare the strength of the negative genetic interaction for a subset of identified alleles under differing amounts of mistranslation. The frequency of mistranslation correlated with the impact on cell growth for all strains analyzed; however, there were notable differences in the extent of the synthetic interaction at different frequencies of mistranslation depending on the genetic background. For many of the strains, the extent of the negative interaction with tRNASerUGG,G26A was proportional to the frequency of mistranslation or only observed at intermediate or high frequencies. For others, the synthetic interaction was approximately equivalent at all frequencies of mistranslation. As humans contain similar mistranslating tRNAs, these results are important when analyzing the impact of tRNA variants on disease, where both the individual’s genetic background and the expression of the mistranslating tRNA variant need to be considered.
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Affiliation(s)
- Matthew D Berg
- Department of Biochemistry, The University of Western Ontario , London, ON N6A 5C1, Canada
- Department of Genome Sciences, University of Washington , Seattle, WA 98195, USA
| | - Yanrui Zhu
- Department of Biochemistry, The University of Western Ontario , London, ON N6A 5C1, Canada
| | - Raphaël Loll-Krippleber
- Department of Biochemistry, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 3E1, Canada
| | - Bryan-Joseph San Luis
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 1A8, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario , London, ON N6A 5C1, Canada
| | - Charles Boone
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 1A8, Canada
| | - Judit Villén
- Department of Genome Sciences, University of Washington , Seattle, WA 98195, USA
| | - Grant W Brown
- Department of Biochemistry, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 3E1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario , London, ON N6A 5C1, Canada
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12
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Phenomics approaches to understand genetic networks and gene function in yeast. Biochem Soc Trans 2022; 50:713-721. [PMID: 35285506 PMCID: PMC9162466 DOI: 10.1042/bst20210285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 01/03/2023]
Abstract
Over the past decade, major efforts have been made to systematically survey the characteristics or phenotypes associated with genetic variation in a variety of model systems. These so-called phenomics projects involve the measurement of 'phenomes', or the set of phenotypic information that describes an organism or cell, in various genetic contexts or states, and in response to external factors, such as environmental signals. Our understanding of the phenome of an organism depends on the availability of reagents that enable systematic evaluation of the spectrum of possible phenotypic variation and the types of measurements that can be taken. Here, we highlight phenomics studies that use the budding yeast, a pioneer model organism for functional genomics research. We focus on genetic perturbation screens designed to explore genetic interactions, using a variety of phenotypic read-outs, from cell growth to subcellular morphology.
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13
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Xavier JB, Monk JM, Poudel S, Norsigian CJ, Sastry AV, Liao C, Bento J, Suchard MA, Arrieta-Ortiz ML, Peterson EJ, Baliga NS, Stoeger T, Ruffin F, Richardson RA, Gao CA, Horvath TD, Haag AM, Wu Q, Savidge T, Yeaman MR. Mathematical models to study the biology of pathogens and the infectious diseases they cause. iScience 2022; 25:104079. [PMID: 35359802 PMCID: PMC8961237 DOI: 10.1016/j.isci.2022.104079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mathematical models have many applications in infectious diseases: epidemiologists use them to forecast outbreaks and design containment strategies; systems biologists use them to study complex processes sustaining pathogens, from the metabolic networks empowering microbial cells to ecological networks in the microbiome that protects its host. Here, we (1) review important models relevant to infectious diseases, (2) draw parallels among models ranging widely in scale. We end by discussing a minimal set of information for a model to promote its use by others and to enable predictions that help us better fight pathogens and the diseases they cause.
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Affiliation(s)
- Joao B. Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | | | - Saugat Poudel
- Department of Bioengineering, UC San Diego, San Diego, CA, USA
| | | | - Anand V. Sastry
- Department of Bioengineering, UC San Diego, San Diego, CA, USA
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Jose Bento
- Computer Science Department, Boston College, Chestnut Hill, MA, USA
| | - Marc A. Suchard
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | | | | | | | - Thomas Stoeger
- Department of Chemical and Biological Engineering; Northwestern University, Evanston, IL 60208, USA
- Successful Clinical Response in Pneumonia Therapy (SCRIPT) Systems Biology Center, Northwestern University, Chicago, IL, USA
| | - Felicia Ruffin
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Reese A.K. Richardson
- Department of Chemical and Biological Engineering; Northwestern University, Evanston, IL 60208, USA
- Successful Clinical Response in Pneumonia Therapy (SCRIPT) Systems Biology Center, Northwestern University, Chicago, IL, USA
| | - Catherine A. Gao
- Successful Clinical Response in Pneumonia Therapy (SCRIPT) Systems Biology Center, Northwestern University, Chicago, IL, USA
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Thomas D. Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Anthony M. Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Qinglong Wu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Michael R. Yeaman
- David Geffen School of Medicine at UCLA & Lundquist Institute for Infection & Immunity at Harbor UCLA Medical Center, Los Angeles, CA, USA
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14
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Zhang XR, Zhao L, Suo F, Gao Y, Wu Q, Qi X, Du LL. An improved auxin-inducible degron system for fission yeast. G3 (BETHESDA, MD.) 2022; 12:6440046. [PMID: 34849776 PMCID: PMC8727963 DOI: 10.1093/g3journal/jkab393] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/25/2021] [Indexed: 01/09/2023]
Abstract
Conditional degron technologies, which allow a protein of interest to be degraded in an inducible manner, are important tools for biological research, and are especially useful for creating conditional loss-of-function mutants of essential genes. The auxin-inducible degron (AID) technology, which utilizes plant auxin signaling components to control protein degradation in nonplant species, is a widely used small-molecular-controlled degradation method in yeasts and animals. However, the currently available AID systems still have room for further optimization. Here, we have improved the AID system for the fission yeast Schizosaccharomyces pombe by optimizing all three components: the AID degron, the small-molecule inducer, and the inducer-responsive F-box protein. We chose a 36-amino-acid sequence of the Arabidopsis IAA17 protein as the degron and employed three tandem copies of it to enhance efficiency. To minimize undesirable side effects of the inducer, we adopted a bulky analog of auxin, 5-adamantyl-IAA, and paired it with the F-box protein OsTIR1 that harbors a mutation (F74A) at the auxin-binding pocket. 5-adamantyl-IAA, when utilized with OsTIR1-F74A, is effective at concentrations thousands of times lower than auxin used in combination with wild-type OsTIR1. We tested our improved AID system on 10 essential genes and achieved inducible lethality for all of them, including ones that could not be effectively inactivated using a previously published AID system. Our improved AID system should facilitate the construction of conditional loss-of-function mutants in fission yeast.
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Affiliation(s)
- Xiao-Ran Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lei Zhao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yadong Gao
- National Institute of Biological Sciences, Beijing 102206, China.,School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, China
| | - Qingcui Wu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xiangbing Qi
- National Institute of Biological Sciences, Beijing 102206, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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15
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Maity S, Ghosh A, Chakraborty K. Integrating an ER Stress Reporter for Monitoring Genome-Wide UPR-ER in Budding Yeast. Methods Mol Biol 2022; 2378:189-201. [PMID: 34985701 DOI: 10.1007/978-1-0716-1732-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Genetic interaction studies have been instrumental in understanding and organizing cellular pathways. This has been helpful in identifying and arranging genes according to pathways, identifying novel pathways, ascribing gene function, and providing information regarding redundant and antagonistic pathways. Synthetic Genetic Array (SGA) uses growth to identify genome scale gene interaction networks. While this has provided most of the genetic interaction data available, SGA coupled to other reporters have the potential to identify components of pathways that specifically affect the probed reporter. The method described here utilizes SGA principles to understand conserved elements of endoplasmic reticulum (ER) homeostasis in the presence and absence of ER stress. The use of a fluorescent reporter of ER stress allows quantitative measurements and provides a handle to measure the proteostasis capacity of the ER in a high-throughput manner. The integration of such a fluorescent reporter in the background of different mutant/deletion strains is sufficient to identify genetic modules in a high-throughput manner.
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Affiliation(s)
- Shuvadeep Maity
- Department of Biological Sciences, Birla Institute of Technology and Sciences (BITs)-Pilani, Hyderabad, Telangana, India.
| | - Asmita Ghosh
- Department of Neurosciences, Centre Hospitalier de l'Universite de Montreal (CHUM) Research Center, Montreal, QC, Canada
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India
| | - Kausik Chakraborty
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi, India.
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16
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Shi R, Hou W, Wang ZQ, Xu X. Biogenesis of Iron-Sulfur Clusters and Their Role in DNA Metabolism. Front Cell Dev Biol 2021; 9:735678. [PMID: 34660592 PMCID: PMC8514734 DOI: 10.3389/fcell.2021.735678] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/06/2021] [Indexed: 12/02/2022] Open
Abstract
Iron–sulfur (Fe/S) clusters (ISCs) are redox-active protein cofactors that their synthesis, transfer, and insertion into target proteins require many components. Mitochondrial ISC assembly is the foundation of all cellular ISCs in eukaryotic cells. The mitochondrial ISC cooperates with the cytosolic Fe/S protein assembly (CIA) systems to accomplish the cytosolic and nuclear Fe/S clusters maturation. ISCs are needed for diverse cellular functions, including nitrogen fixation, oxidative phosphorylation, mitochondrial respiratory pathways, and ribosome assembly. Recent research advances have confirmed the existence of different ISCs in enzymes that regulate DNA metabolism, including helicases, nucleases, primases, DNA polymerases, and glycosylases. Here we outline the synthesis of mitochondrial, cytosolic and nuclear ISCs and highlight their functions in DNA metabolism.
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Affiliation(s)
- Ruifeng Shi
- Shenzhen University-Friedrich Schiller Universität Jena Joint Ph.D. Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
| | - Wenya Hou
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany.,Faculty of Biological Sciences, Friedrich-Schiller-University Jena, Jena, Germany
| | - Xingzhi Xu
- Shenzhen University-Friedrich Schiller Universität Jena Joint Ph.D. Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, China.,Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, China
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17
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Berg MD, Zhu Y, Ruiz BY, Loll-Krippleber R, Isaacson J, San Luis BJ, Genereaux J, Boone C, Villén J, Brown GW, Brandl CJ. The amino acid substitution affects cellular response to mistranslation. G3-GENES GENOMES GENETICS 2021; 11:6310018. [PMID: 34568909 PMCID: PMC8473984 DOI: 10.1093/g3journal/jkab218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 01/24/2023]
Abstract
Mistranslation, the misincorporation of an amino acid not specified by the "standard" genetic code, occurs in all organisms. tRNA variants that increase mistranslation arise spontaneously and engineered tRNAs can achieve mistranslation frequencies approaching 10% in yeast and bacteria. Interestingly, human genomes contain tRNA variants with the potential to mistranslate. Cells cope with increased mistranslation through multiple mechanisms, though high levels cause proteotoxic stress. The goal of this study was to compare the genetic interactions and the impact on transcriptome and cellular growth of two tRNA variants that mistranslate at a similar frequency but create different amino acid substitutions in Saccharomyces cerevisiae. One tRNA variant inserts alanine at proline codons whereas the other inserts serine for arginine. Both tRNAs decreased growth rate, with the effect being greater for arginine to serine than for proline to alanine. The tRNA that substituted serine for arginine resulted in a heat shock response. In contrast, heat shock response was minimal for proline to alanine substitution. Further demonstrating the significance of the amino acid substitution, transcriptome analysis identified unique up- and down-regulated genes in response to each mistranslating tRNA. Number and extent of negative synthetic genetic interactions also differed depending upon type of mistranslation. Based on the unique responses observed for these mistranslating tRNAs, we predict that the potential of mistranslation to exacerbate diseases caused by proteotoxic stress depends on the tRNA variant. Furthermore, based on their unique transcriptomes and genetic interactions, different naturally occurring mistranslating tRNAs have the potential to negatively influence specific diseases.
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Affiliation(s)
- Matthew D Berg
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 3K7, Canada.,Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Yanrui Zhu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Bianca Y Ruiz
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Raphaël Loll-Krippleber
- Department of Biochemistry, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S, Canada
| | - Joshua Isaacson
- Department of Biology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Bryan-Joseph San Luis
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Charles Boone
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S, Canada
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Grant W Brown
- Department of Biochemistry, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 3K7, Canada
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18
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A CRISPR Interference Screen of Essential Genes Reveals that Proteasome Regulation Dictates Acetic Acid Tolerance in Saccharomyces cerevisiae. mSystems 2021; 6:e0041821. [PMID: 34313457 PMCID: PMC8407339 DOI: 10.1128/msystems.00418-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
CRISPR interference (CRISPRi) is a powerful tool to study cellular physiology under different growth conditions, and this technology provides a means for screening changed expression of essential genes. In this study, a Saccharomyces cerevisiae CRISPRi library was screened for growth in medium supplemented with acetic acid. Acetic acid is a growth inhibitor challenging the use of yeast for the industrial conversion of lignocellulosic biomasses. Tolerance to acetic acid that is released during biomass hydrolysis is crucial for cell factories to be used in biorefineries. The CRISPRi library screened consists of >9,000 strains, where >98% of all essential and respiratory growth-essential genes were targeted with multiple guide RNAs (gRNAs). The screen was performed using the high-throughput, high-resolution Scan-o-matic platform, where each strain is analyzed separately. Our study identified that CRISPRi targeting of genes involved in vesicle formation or organelle transport processes led to severe growth inhibition during acetic acid stress, emphasizing the importance of these intracellular membrane structures in maintaining cell vitality. In contrast, strains in which genes encoding subunits of the 19S regulatory particle of the 26S proteasome were downregulated had increased tolerance to acetic acid, which we hypothesize is due to ATP salvage through an increased abundance of the 20S core particle that performs ATP-independent protein degradation. This is the first study where high-resolution CRISPRi library screening paves the way to understanding and bioengineering the robustness of yeast against acetic acid stress. IMPORTANCE Acetic acid is inhibitory to the growth of the yeast Saccharomyces cerevisiae, causing ATP starvation and oxidative stress, which leads to the suboptimal production of fuels and chemicals from lignocellulosic biomass. In this study, where each strain of a CRISPRi library was characterized individually, many essential and respiratory growth-essential genes that regulate tolerance to acetic acid were identified, providing a new understanding of the stress response of yeast and new targets for the bioengineering of industrial yeast. Our findings on the fine-tuning of the expression of proteasomal genes leading to increased tolerance to acetic acid suggest that this could be a novel strategy for increasing stress tolerance, leading to improved strains for the production of biobased chemicals.
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19
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Minaker SW, Kofoed MC, Hieter P, Stirling PC. A nuclear proteome localization screen reveals the exquisite specificity of Gpn2 in RNA polymerase biogenesis. Cell Cycle 2021; 20:1361-1373. [PMID: 34180355 DOI: 10.1080/15384101.2021.1943879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The GPN proteins are a conserved family of GTP-binding proteins that are involved in the assembly and subsequent import of RNA polymerase II and III. In this study, we sought to ascertain the specificity of yeast GPN2 for RNA polymerases by screening the localization of a collection of 1350 GFP-tagged nuclear proteins in WT or GPN2 mutant cells. We found that the strongest mislocalization occurred for RNA polymerase II and III subunits and only a handful of other RNAPII associated proteins were altered in GPN2 mutant cells. Our screen identified Ess1, an Rpb1 C-terminal domain (CTD) prolyl isomerase, as mislocalized in GPN2 mutants. Building on this observation we tested for effects of mutations in other factors which regulate Rpb1-CTD phosphorylation status. This uncovered significant changes in nuclear-cytoplasmic distribution of Rpb1-GFP in strains with disrupted RNA polymerase CTD kinases or phosphatases. Overall, this screen shows the exquisite specificity of GPN2 for RNA polymerase transport, and reveals a previously unappreciated role for CTD modification in RNAPII nuclear localization.
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Affiliation(s)
- Sean W Minaker
- Terry Fox Laboratories, BC Cancer Research Institute, Vancouver, Canada
| | - Megan C Kofoed
- Michael Smith Laboratory, University of British Columbia, Vancouver, Canada
| | - Philip Hieter
- Michael Smith Laboratory, University of British Columbia, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter C Stirling
- Terry Fox Laboratories, BC Cancer Research Institute, Vancouver, Canada
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20
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Salim D, Bradford WD, Rubinstein B, Gerton JL. DNA replication, transcription, and H3K56 acetylation regulate copy number and stability at tandem repeats. G3-GENES GENOMES GENETICS 2021; 11:6174693. [PMID: 33729510 DOI: 10.1093/g3journal/jkab082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/26/2021] [Indexed: 11/13/2022]
Abstract
Tandem repeats are inherently unstable and exhibit extensive copy number polymorphisms. Despite mounting evidence for their adaptive potential, the mechanisms associated with regulation of the stability and copy number of tandem repeats remain largely unclear. To study copy number variation at tandem repeats, we used two well-studied repetitive arrays in the budding yeast genome, the ribosomal DNA (rDNA) locus, and the copper-inducible CUP1 gene array. We developed powerful, highly sensitive, and quantitative assays to measure repeat instability and copy number and used them in multiple high-throughput genetic screens to define pathways involved in regulating copy number variation. These screens revealed that rDNA stability and copy number are regulated by DNA replication, transcription, and histone acetylation. Through parallel studies of both arrays, we demonstrate that instability can be induced by DNA replication stress and transcription. Importantly, while changes in stability in response to stress are observed within a few cell divisions, a change in steady state repeat copy number requires selection over time. Further, H3K56 acetylation is required for regulating transcription and transcription-induced instability at the CUP1 array, and restricts transcription-induced amplification. Our work suggests that the modulation of replication and transcription is a direct, reversible strategy to alter stability at tandem repeats in response to environmental stimuli, which provides cells rapid adaptability through copy number variation. Additionally, histone acetylation may function to promote the normal adaptive program in response to transcriptional stress. Given the omnipresence of DNA replication, transcription, and chromatin marks like histone acetylation, the fundamental mechanisms we have uncovered significantly advance our understanding of the plasticity of tandem repeats more generally.
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Affiliation(s)
- Devika Salim
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States of America.,Open University, Milton Keynes MK7 6BJ, United Kingdom
| | - William D Bradford
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States of America
| | - Boris Rubinstein
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States of America
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States of America.,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, United States of America
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21
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Comparative parallel analysis of RNA ends identifies mRNA substrates of a tRNA splicing endonuclease-initiated mRNA decay pathway. Proc Natl Acad Sci U S A 2021; 118:2020429118. [PMID: 33649230 DOI: 10.1073/pnas.2020429118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Eukaryotes share a conserved messenger RNA (mRNA) decay pathway in which bulk mRNA is degraded by exoribonucleases. In addition, it has become clear that more specialized mRNA decay pathways are initiated by endonucleolytic cleavage at particular sites. The transfer RNA (tRNA) splicing endonuclease (TSEN) has been studied for its ability to remove introns from pre-tRNAs. More recently it has been shown that single amino acid mutations in TSEN cause pontocerebellar hypoplasia. Other recent studies indicate that TSEN has other functions, but the nature of these functions has remained obscure. Here we show that yeast TSEN cleaves a specific subset of mRNAs that encode mitochondrial proteins, and that the cleavage sites are in part determined by their sequence. This provides an explanation for the counterintuitive mitochondrial localization of yeast TSEN. To identify these mRNA target sites, we developed a "comPARE" (comparative parallel analysis of RNA ends) bioinformatic approach that should be easily implemented and widely applicable to the study of endoribonucleases. The similarity of tRNA endonuclease-initiated decay to regulated IRE1-dependent decay of mRNA suggests that mRNA specificity by colocalization may be an important determinant for the degradation of localized mRNAs in a variety of eukaryotic cells.
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22
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Kuzmin E, Andrews BJ, Boone C. Trigenic Synthetic Genetic Array (τ-SGA) Technique for Complex Interaction Analysis. Methods Mol Biol 2021; 2212:377-400. [PMID: 33733368 DOI: 10.1007/978-1-0716-0947-7_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Complex genetic interactions occur when mutant alleles of multiple genes combine to elicit an unexpected phenotype, which could not be predicted given the expectation based on the combination of phenotypes associated with individual mutant alleles. Trigenic Synthetic Genetic Array (τ-SGA) methodology was developed for the systematic analysis of complex interactions involving combinations of three gene perturbations. With a series of replica pinning steps of the τ-SGA procedure, haploid triple mutants are constructed through automated mating and meiotic recombination. For example, a double-mutant query strain carrying two mutant alleles of interest, such as a deletion allele of a nonessential gene and a conditional temperature-sensitive allele of an essential gene, is crossed to an input array of yeast mutants, such as the diagnostic array set of ~1200 mutants, to generate an output array of triple mutants. The colony-size measurements of the resulting triple mutants are used to estimate cellular fitness and quantify trigenic interactions by incorporating corresponding single- and double-mutant fitness estimates. Trigenic interaction networks can be further analyzed for functional modules using various clustering and enrichment analysis tools. Complex genetic interactions are rich in functional information and provide insight into the genotype-to-phenotype relationship, genome size, and speciation.
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Affiliation(s)
- Elena Kuzmin
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Brenda J Andrews
- The Donnelly Centre, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Charles Boone
- The Donnelly Centre, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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23
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Chemical-Genetic Interactions with the Proline Analog L-Azetidine-2-Carboxylic Acid in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2020; 10:4335-4345. [PMID: 33082270 PMCID: PMC7718759 DOI: 10.1534/g3.120.401876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Non-proteinogenic amino acids, such as the proline analog L-azetidine-2-carboxylic acid (AZC), are detrimental to cells because they are mis-incorporated into proteins and lead to proteotoxic stress. Our goal was to identify genes that show chemical-genetic interactions with AZC in Saccharomyces cerevisiae and thus also potentially define the pathways cells use to cope with amino acid mis-incorporation. Screening the yeast deletion and temperature sensitive collections, we found 72 alleles with negative chemical-genetic interactions with AZC treatment and 12 alleles that suppress AZC toxicity. Many of the genes with negative chemical-genetic interactions are involved in protein quality control pathways through the proteasome. Genes involved in actin cytoskeleton organization and endocytosis also had negative chemical-genetic interactions with AZC. Related to this, the number of actin patches per cell increases upon AZC treatment. Many of the same cellular processes were identified to have interactions with proteotoxic stress caused by two other amino acid analogs, canavanine and thialysine, or a mistranslating tRNA variant that mis-incorporates serine at proline codons. Alleles that suppressed AZC-induced toxicity functioned through the amino acid sensing TOR pathway or controlled amino acid permeases required for AZC uptake. Further suggesting the potential of genetic changes to influence the cellular response to proteotoxic stress, overexpressing many of the genes that had a negative chemical-genetic interaction with AZC suppressed AZC toxicity.
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24
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Peck Justice SA, Barron MP, Qi GD, Wijeratne HRS, Victorino JF, Simpson ER, Vilseck JZ, Wijeratne AB, Mosley AL. Mutant thermal proteome profiling for characterization of missense protein variants and their associated phenotypes within the proteome. J Biol Chem 2020; 295:16219-16238. [PMID: 32878984 PMCID: PMC7705321 DOI: 10.1074/jbc.ra120.014576] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
Temperature-sensitive (TS) missense mutants have been foundational for characterization of essential gene function. However, an unbiased approach for analysis of biochemical and biophysical changes in TS missense mutants within the context of their functional proteomes is lacking. We applied MS-based thermal proteome profiling (TPP) to investigate the proteome-wide effects of missense mutations in an application that we refer to as mutant thermal proteome profiling (mTPP). This study characterized global impacts of temperature sensitivity-inducing missense mutations in two different subunits of the 26S proteasome. The majority of alterations identified by RNA-Seq and global proteomics were similar between the mutants, which could suggest that a similar functional disruption is occurring in both missense variants. Results from mTPP, however, provide unique insights into the mechanisms that contribute to the TS phenotype in each mutant, revealing distinct changes that were not obtained using only steady-state transcriptome and proteome analyses. Computationally, multisite λ-dynamics simulations add clear support for mTPP experimental findings. This work shows that mTPP is a precise approach to measure changes in missense mutant-containing proteomes without the requirement for large amounts of starting material, specific antibodies against proteins of interest, and/or genetic manipulation of the biological system. Although experiments were performed under permissive conditions, mTPP provided insights into the underlying protein stability changes that cause dramatic cellular phenotypes observed at nonpermissive temperatures. Overall, mTPP provides unique mechanistic insights into missense mutation dysfunction and connection of genotype to phenotype in a rapid, nonbiased fashion.
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Affiliation(s)
- Sarah A Peck Justice
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Monica P Barron
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Guihong D Qi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - H R Sagara Wijeratne
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - José F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ed R Simpson
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA; Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University, Indianapolis, Indiana, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jonah Z Vilseck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Aruna B Wijeratne
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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25
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Zhu Y, Berg MD, Yang P, Loll-Krippleber R, Brown GW, Brandl CJ. Mistranslating tRNA identifies a deleterious S213P mutation in theSaccharomyces cerevisiaeeco1-1allele. Biochem Cell Biol 2020; 98:624-630. [DOI: 10.1139/bcb-2020-0151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Mistranslation occurs when an amino acid not specified by the standard genetic code is incorporated during translation. Since the ribosome does not read the amino acid, tRNA variants aminoacylated with a non-cognate amino acid or containing a non-cognate anticodon dramatically increase the frequency of mistranslation. In a systematic genetic analysis, we identified a suppression interaction between tRNASerUGG, G26A, which mistranslates proline codons by inserting serine, and eco1-1, a temperature sensitive allele of the gene encoding an acetyltransferase required for sister chromatid cohesion. The suppression was partial, with a tRNA that inserts alanine at proline codons and not apparent for a tRNA that inserts serine at arginine codons. Sequencing of the eco1-1 allele revealed a mutation that would convert the highly conserved serine 213 within β7 of the GCN5-related N-acetyltransferase core to proline. Mutation of P213 in eco1-1 back to the wild-type serine restored the function of the enzyme at elevated temperatures. Our results indicate the utility of mistranslating tRNA variants to identify functionally relevant mutations and identify eco1 as a reporter for mistranslation. We propose that mistranslation could be used as a tool to treat genetic disease.
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Affiliation(s)
- Yanrui Zhu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Phoebe Yang
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Raphaël Loll-Krippleber
- Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Grant W. Brown
- Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Christopher J. Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability. Cell Rep 2020; 28:1551-1563.e7. [PMID: 31390568 PMCID: PMC6693559 DOI: 10.1016/j.celrep.2019.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 03/18/2019] [Accepted: 07/01/2019] [Indexed: 01/19/2023] Open
Abstract
THO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here, we show that human THO interacts with MFAP1 (microfibrillar-associated protein 1), a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing γH2AX foci and DNA breaks. This phenotype is not dependent on either transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381 cause similar transcription-independent genome instability, supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses. MFAP1 depletion affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role.
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Xue A, Robbins N, Cowen LE. Advances in fungal chemical genomics for the discovery of new antifungal agents. Ann N Y Acad Sci 2020; 1496:5-22. [PMID: 32860238 DOI: 10.1111/nyas.14484] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022]
Abstract
Invasive fungal infections have escalated from a rare curiosity to a major cause of human mortality around the globe. This is in part due to a scarcity in the number of antifungal drugs available to combat mycotic disease, making the discovery of novel bioactive compounds and determining their mode of action of utmost importance. The development and application of chemical genomic assays using the model yeast Saccharomyces cerevisiae has provided powerful methods to identify the mechanism of action of diverse molecules in a living cell. Furthermore, complementary assays are continually being developed in fungal pathogens, most notably Candida albicans and Cryptococcus neoformans, to elucidate compound mechanism of action directly in the pathogen of interest. Collectively, the suite of chemical genetic assays that have been developed in multiple fungal species enables the identification of candidate drug target genes, as well as genes involved in buffering drug target pathways, and genes involved in general cellular responses to small molecules. In this review, we examine current yeast chemical genomic assays and highlight how such resources provide powerful tools that can be utilized to bolster the antifungal pipeline.
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Affiliation(s)
- Alice Xue
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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28
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Milbury KL, Paul B, Lari A, Fowler C, Montpetit B, Stirling PC. Exonuclease domain mutants of yeast DIS3 display genome instability. Nucleus 2020; 10:21-32. [PMID: 30724665 PMCID: PMC6380420 DOI: 10.1080/19491034.2019.1578600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, are linked to multiple myeloma. Here we report that a cancer-associated DIS3 allele, dis3E729K, provides evidence for DIS3 functioning in mitotic fidelity in yeast. This dis3E729K allele does not induce defects in 7S→5.8S rRNA processing, although it elicits a requirement for P-body function. While it does not significantly influence cell cycle progression alone, the allele reduces the efficiency of cell cycle arrest in strains with defects in kinetochore assembly. Finally, point mutations in the exonuclease domains of yeast Dis3 elicit genome instability phenotypes; however, these DIS3 mutations do not increase DNA damage or RNA processing defects that lead to the accumulation of polyadenylated RNA in the nucleus. These data suggest that specific DIS3 activities support mitotic fidelity in yeast.
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Affiliation(s)
- Karissa L Milbury
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Biplab Paul
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Azra Lari
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Claire Fowler
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Ben Montpetit
- b Department of Cell Biology , University of Alberta , Edmonton , Canada.,c Department of Viticulture and Enology , University of California , Davis , CA , USA
| | - Peter C Stirling
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada.,d Department of Medical Genetics , University of British Columbia , Vancouver , BC , Canada
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Schramm T, Lempp M, Beuter D, Sierra SG, Glatter T, Link H. High-throughput enrichment of temperature-sensitive argininosuccinate synthetase for two-stage citrulline production in E. coli. Metab Eng 2020; 60:14-24. [PMID: 32179161 PMCID: PMC7225747 DOI: 10.1016/j.ymben.2020.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/03/2020] [Accepted: 03/08/2020] [Indexed: 12/20/2022]
Abstract
Controlling metabolism of engineered microbes is important to modulate cell growth and production during a bioprocess. For example, external parameters such as light, chemical inducers, or temperature can act on metabolism of production strains by changing the abundance or activity of enzymes. Here, we created temperature-sensitive variants of an essential enzyme in arginine biosynthesis of Escherichia coli (argininosuccinate synthetase, ArgG) and used them to dynamically control citrulline overproduction and growth of E. coli. We show a method for high-throughput enrichment of temperature-sensitive ArgG variants with a fluorescent TIMER protein and flow cytometry. With 90 of the thus derived ArgG variants, we complemented an ArgG deletion strain showing that 90% of the strains exhibit temperature-sensitive growth and 69% of the strains are auxotrophic for arginine at 42 °C and prototrophic at 30 °C. The best temperature-sensitive ArgG variant enabled precise and tunable control of cell growth by temperature changes. Expressing this variant in a feedback-dysregulated E. coli strain allowed us to realize a two-stage bioprocess: a 33 °C growth-phase for biomass accumulation and a 39 °C stationary-phase for citrulline production. With this two-stage strategy, we produced 3 g/L citrulline during 45 h cultivation in a 1-L bioreactor. These results show that temperature-sensitive enzymes can be created en masse and that they may function as metabolic valves in engineered bacteria. Method to enrich temperature-sensitive enzymes en masse. Temperature-sensitive enzymes function as metabolic valve. Temperature controlled two-stage production of citrulline.
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Affiliation(s)
- Thorben Schramm
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Martin Lempp
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Dominik Beuter
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Silvia González Sierra
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany.
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Karmon O, Ben Aroya S. Spatial Organization of Proteasome Aggregates in the Regulation of Proteasome Homeostasis. Front Mol Biosci 2020; 6:150. [PMID: 31998748 PMCID: PMC6962763 DOI: 10.3389/fmolb.2019.00150] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 12/06/2019] [Indexed: 12/23/2022] Open
Abstract
Misfolded proteins and insoluble aggregates are continuously produced in the cell and can result in severe stress that threatens cellular fitness and viability if not managed effectively. Accordingly, organisms have evolved several protective protein quality control (PQC) machineries to address these threats. In eukaryotes, the ubiquitin–proteasome system (UPS) plays a vital role in the disposal of intracellular misfolded, damaged, or unneeded proteins. Although ubiquitin-mediated proteasomal degradation of many proteins plays a key role in the PQC system, cells must also dispose of the proteasomes themselves when their subunits are assembled improperly, or when they dysfunction under various conditions, e.g., as a result of genomic mutations, diverse stresses, or treatment with proteasome inhibitors. Here, we review recent studies that identified the regulatory pathways that mediate proteasomes sorting under various stress conditions, and the elimination of its dysfunctional subunits. Following inactivation of the 26S proteasome, UPS-mediated degradation of its own misassembled subunits is the favored disposal pathway. However, the cytosolic cell-compartment-specific aggregase, Hsp42 mediates an alternative pathway, the accumulation of these subunits in cytoprotective compartments, where they become extensively modified with ubiquitin, and are directed by ubiquitin receptors for autophagic clearance (proteaphagy). We also discuss the sorting mechanisms that the cell uses under nitrogen stress, and to distinguish between dysfunctional proteasome aggregates and proteasome storage granules (PSGs), reversible assemblies of membrane-free cytoplasmic condensates that form in yeast upon carbon starvation and help protect proteasomes from autophagic degradation. Regulated proteasome subunit homeostasis is thus controlled through cellular probing of the level of proteasome assembly, and the interplay between UPS-mediated degradation or sorting of misfolded proteins into distinct cellular compartments.
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Affiliation(s)
- Ofri Karmon
- The Mina and Everard Goodman, Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shay Ben Aroya
- The Mina and Everard Goodman, Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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31
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Upadhyay RK. Markers for Global Climate Change and Its Impact on Social, Biological and Ecological Systems: A Review. ACTA ACUST UNITED AC 2020. [DOI: 10.4236/ajcc.2020.93012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Van Bergen NJ, Guo Y, Al-Deri N, Lipatova Z, Stanga D, Zhao S, Murtazina R, Gyurkovska V, Pehlivan D, Mitani T, Gezdirici A, Antony J, Collins F, Willis MJH, Coban Akdemir ZH, Liu P, Punetha J, Hunter JV, Jhangiani SN, Fatih JM, Rosenfeld JA, Posey JE, Gibbs RA, Karaca E, Massey S, Ranasinghe TG, Sleiman P, Troedson C, Lupski JR, Sacher M, Segev N, Hakonarson H, Christodoulou J. Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability. Brain 2020; 143:112-130. [PMID: 31794024 PMCID: PMC6935753 DOI: 10.1093/brain/awz374] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/20/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022] Open
Abstract
The conserved transport protein particle (TRAPP) complexes regulate key trafficking events and are required for autophagy. TRAPPC4, like its yeast Trs23 orthologue, is a core component of the TRAPP complexes and one of the essential subunits for guanine nucleotide exchange factor activity for Rab1 GTPase. Pathogenic variants in specific TRAPP subunits are associated with neurological disorders. We undertook exome sequencing in three unrelated families of Caucasian, Turkish and French-Canadian ethnicities with seven affected children that showed features of early-onset seizures, developmental delay, microcephaly, sensorineural deafness, spastic quadriparesis and progressive cortical and cerebellar atrophy in an effort to determine the genetic aetiology underlying neurodevelopmental disorders. All seven affected subjects shared the same identical rare, homozygous, potentially pathogenic variant in a non-canonical, well-conserved splice site within TRAPPC4 (hg19:chr11:g.118890966A>G; TRAPPC4: NM_016146.5; c.454+3A>G). Single nucleotide polymorphism array analysis revealed there was no haplotype shared between the tested Turkish and Caucasian families suggestive of a variant hotspot region rather than a founder effect. In silico analysis predicted the variant to cause aberrant splicing. Consistent with this, experimental evidence showed both a reduction in full-length transcript levels and an increase in levels of a shorter transcript missing exon 3, suggestive of an incompletely penetrant splice defect. TRAPPC4 protein levels were significantly reduced whilst levels of other TRAPP complex subunits remained unaffected. Native polyacrylamide gel electrophoresis and size exclusion chromatography demonstrated a defect in TRAPP complex assembly and/or stability. Intracellular trafficking through the Golgi using the marker protein VSVG-GFP-ts045 demonstrated significantly delayed entry into and exit from the Golgi in fibroblasts derived from one of the affected subjects. Lentiviral expression of wild-type TRAPPC4 in these fibroblasts restored trafficking, suggesting that the trafficking defect was due to reduced TRAPPC4 levels. Consistent with the recent association of the TRAPP complex with autophagy, we found that the fibroblasts had a basal autophagy defect and a delay in autophagic flux, possibly due to unsealed autophagosomes. These results were validated using a yeast trs23 temperature sensitive variant that exhibits constitutive and stress-induced autophagic defects at permissive temperature and a secretory defect at restrictive temperature. In summary we provide strong evidence for pathogenicity of this variant in a member of the core TRAPP subunit, TRAPPC4 that associates with vesicular trafficking and autophagy defects. This is the first report of a TRAPPC4 variant, and our findings add to the growing number of TRAPP-associated neurological disorders.
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Affiliation(s)
- Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Yiran Guo
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - Noraldin Al-Deri
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Daniela Stanga
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Sarah Zhao
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Rakhilya Murtazina
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Valeriya Gyurkovska
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, 34303, Turkey
| | - Jayne Antony
- TY Nelson Department of Neurology and Neurosurgery, Children’s Hospital at Westmead, Sydney, Australia
| | - Felicity Collins
- Western Sydney Genetics Program, Children’s Hospital at Westmead, Sydney, Australia
- Medical Genomics Department, Royal Prince Alfred Hospital, Sydney, Australia
| | - Mary J H Willis
- Department of Pediatrics, Naval Medical Center San Diego, San Diego, California, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Thisara G Ranasinghe
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Patrick Sleiman
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - Chris Troedson
- TY Nelson Department of Neurology and Neurosurgery, Children’s Hospital at Westmead, Sydney, Australia
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Hakon Hakonarson
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, VIC, Australia
- Kids Research, The Children’s Hospital at Westmead, Sydney, NSW, Australia
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Natarajan N, Foresti O, Wendrich K, Stein A, Carvalho P. Quality Control of Protein Complex Assembly by a Transmembrane Recognition Factor. Mol Cell 2019; 77:108-119.e9. [PMID: 31679820 PMCID: PMC6941229 DOI: 10.1016/j.molcel.2019.10.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/27/2019] [Accepted: 10/01/2019] [Indexed: 01/08/2023]
Abstract
The inner nuclear membrane (INM) is continuous with the endoplasmic reticulum (ER) but harbors a distinctive proteome essential for nuclear functions. In yeast, the Asi1/Asi2/Asi3 ubiquitin ligase complex safeguards the INM proteome through the clearance of mislocalized ER membrane proteins. How the Asi complex selectively targets mislocalized proteins and coordinates its activity with other ER functions, such as protein biogenesis, is unclear. Here, we uncover a link between INM proteome identity and membrane protein complex assembly in the remaining ER. We show that lone proteins and complex subunits failing to assemble in the ER access the INM for Asi-mediated degradation. Substrates are recognized by direct binding of Asi2 to their transmembrane domains for subsequent ubiquitination by Asi1/Asi3 and membrane extraction. Our data suggest a model in which spatial segregation of membrane protein complex assembly and quality control improves assembly efficiency and reduces the levels of orphan subunits. Quality control of unassembled subunits of membrane complexes is restricted to the INM The Asi complex promotes degradation of folded but unassembled membrane proteins Binding of Asi2 to membrane domain of unassembled subunits mediates their recognition INM quality control maintains complex subunits within near-stoichiometric levels
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Affiliation(s)
- Nivedita Natarajan
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ombretta Foresti
- Cell and Developmental Biology Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - Kim Wendrich
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Alexander Stein
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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Harari Y, Gershon L, Alonso-Perez E, Klein S, Berneman Y, Choudhari K, Singh P, Sau S, Liefshitz B, Kupiec M. Telomeres and stress in yeast cells: When genes and environment interact. Fungal Biol 2019; 124:311-315. [PMID: 32389293 DOI: 10.1016/j.funbio.2019.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/27/2022]
Abstract
Telomeres are structures composed of simple DNA repeats and specific proteins that protect the eukaryotic chromosomal ends from degradation, and facilitate the replication of the genome. They are central to the maintenance of the genome integrity, and play important roles in the development of cancer and in the process of aging in humans. The yeast Saccharomyces cerevisiae has greatly contributed to our understanding of basic telomere biology. Our laboratory has carried out systematic screen for mutants that affect telomere length, and identified ∼500 genes that, when mutated, affect telomere length. Remarkably, all ∼500 TLM (Telomere Length Maintenance) genes participate in a very tight homeostatic process, and it is enough to mutate one of them to change the steady-state telomere length. Despite this complex network of balances, it is also possible to change telomere length in yeast by applying several types of external stresses. We summarize our insights about the molecular mechanisms by which genes and environment interact to affect telomere length.
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Affiliation(s)
- Yaniv Harari
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Lihi Gershon
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Elisa Alonso-Perez
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Shir Klein
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Yael Berneman
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Karan Choudhari
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Pragyan Singh
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Soumitra Sau
- Amity Institute of Biotechnology, Amity University Kolkata, Kolkata, India
| | - Batia Liefshitz
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Martin Kupiec
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel.
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Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rps2 in Saccharomyces cerevisiae. Mol Cell Biol 2019; 39:MCB.00094-19. [PMID: 31182640 DOI: 10.1128/mcb.00094-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/03/2019] [Indexed: 01/31/2023] Open
Abstract
Eukaryotic ribosome biogenesis requires the action of approximately 200 trans-acting factors and the incorporation of 79 ribosomal proteins (RPs). The delivery of RPs to preribosomes is a major challenge for the cell because RPs are often highly basic and contain intrinsically disordered regions prone to nonspecific interactions and aggregation. To counteract this, eukaryotes developed dedicated chaperones for certain RPs that promote their solubility and expression, often by binding eukaryote-specific extensions of the RPs. Rps2 (uS5) is a universally conserved RP that assembles into nuclear pre-40S subunits. However, a chaperone for Rps2 had not been identified. Our laboratory previously characterized Tsr4 as a 40S biogenesis factor of unknown function. Here, we report that Tsr4 cotranslationally associates with Rps2. Rps2 harbors a eukaryote-specific N-terminal extension that is critical for its interaction with Tsr4. Moreover, Tsr4 perturbation resulted in decreased Rps2 levels and phenocopied Rps2 depletion. Despite Rps2 joining nuclear pre-40S particles, Tsr4 appears to be restricted to the cytoplasm. Thus, we conclude that Tsr4 is a cytoplasmic chaperone dedicated to Rps2.
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Natali F, Rancati G. The Mutator Phenotype: Adapting Microbial Evolution to Cancer Biology. Front Genet 2019; 10:713. [PMID: 31447882 PMCID: PMC6691094 DOI: 10.3389/fgene.2019.00713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 07/05/2019] [Indexed: 01/07/2023] Open
Abstract
The mutator phenotype hypothesis was postulated almost 40 years ago to reconcile the observation that while cancer cells display widespread mutational burden, acquisition of mutations in non-transformed cells is a rare event. Moreover, it also suggested that cancer evolution could be fostered by increased genome instability. Given the evolutionary conservation throughout the tree of life and the genetic tractability of model organisms, yeast and bacterial species pioneered studies to dissect the functions of genes required for genome maintenance (caretaker genes) or for cell growth control (gatekeeper genes). In this review, we first provide an overview of what we learned from model organisms about the roles of these genes and the genome instability that arises as a consequence of their dysregulation. We then discuss our current understanding of how mutator phenotypes shape the evolution of bacteria and yeast species. We end by bringing clinical evidence that lessons learned from single-cell organisms can be applied to tumor evolution.
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Affiliation(s)
- Federica Natali
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Giulia Rancati
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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Volpe M, Levinton N, Rosenstein N, Prag G, Ben-Aroya S. Regulation of the anaphase promoting complex/cyclosome by the degradation of its unassembled catalytic subunit, Apc11. FASEB J 2019; 33:9752-9761. [PMID: 31162950 DOI: 10.1096/fj.201802300r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
One of the challenges encountered by the protein quality control machinery is the need to ensure that members of multiprotein complexes are available in the correct proportions. In this study, we demonstrate that the ubiquitin proteasome system (UPS) mediates the degradation of Apc11, the catalytic core subunit of the anaphase promoting complex/cyclosome (APC/C). In vitro studies have shown that Apc11, together with its E2 enzyme, is sufficient to ubiquitinate substrates independently of the APC/C. Here, we establish that this can occur in living yeast cells. We show that the tight controls regulating the function of the fully assembled APC/C can be circumvented when its substrates are ubiquitinated by the excess levels of Apc11 independently of the assembled complex. We thus suggest that the UPS-mediated degradation of Apc11 is an overlooked mechanism ensuring that proper function of the APC/C is limited to suitably delimited holoenzymes and that an imbalance in protein expression may result in detrimental gain-of-function activity, rather than merely the disruption of protein complex stoichiometry.-Volpe, M., Levinton, N., Rosenstein, N., Prag, G., Ben-Aroya, S. Regulation of the anaphase promoting complex/cyclosome by the degradation of its unassembled catalytic subunit, Apc11.
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Affiliation(s)
- Marina Volpe
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Nelly Levinton
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Gali Prag
- The Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
| | - Shay Ben-Aroya
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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Simpkins SW, Deshpande R, Nelson J, Li SC, Piotrowski JS, Ward HN, Yashiroda Y, Osada H, Yoshida M, Boone C, Myers CL. Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments. Nat Protoc 2019; 14:415-440. [PMID: 30635653 DOI: 10.1038/s41596-018-0099-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The construction of genome-wide mutant collections has enabled high-throughput, high-dimensional quantitative characterization of gene and chemical function, particularly via genetic and chemical-genetic interaction experiments. As the throughput of such experiments increases with improvements in sequencing technology and sample multiplexing, appropriate tools must be developed to handle the large volume of data produced. Here, we describe how to apply our approach to high-throughput, fitness-based profiling of pooled mutant yeast collections using the BEAN-counter software pipeline (Barcoded Experiment Analysis for Next-generation sequencing) for analysis. The software has also successfully processed data from Schizosaccharomyces pombe, Escherichia coli, and Zymomonas mobilis mutant collections. We provide general recommendations for the design of large-scale, multiplexed barcode sequencing experiments. The procedure outlined here was used to score interactions for ~4 million chemical-by-mutant combinations in our recently published chemical-genetic interaction screen of nearly 14,000 chemical compounds across seven diverse compound collections. Here we selected a representative subset of these data on which to demonstrate our analysis pipeline. BEAN-counter is open source, written in Python, and freely available for academic use. Users should be proficient at the command line; advanced users who wish to analyze larger datasets with hundreds or more conditions should also be familiar with concepts in analysis of high-throughput biological data. BEAN-counter encapsulates the knowledge we have accumulated from, and successfully applied to, our multiplexed, pooled barcode sequencing experiments. This protocol will be useful to those interested in generating their own high-dimensional, quantitative characterizations of gene or chemical function in a high-throughput manner.
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Affiliation(s)
- Scott W Simpkins
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Justin Nelson
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Sheena C Li
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Jeff S Piotrowski
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.,Yumanity Therapeutics, Cambridge, MA, USA
| | - Henry Neil Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Charles Boone
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.,Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Chad L Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota Twin Cities, Minneapolis, MN, USA. .,Department of Computer Science and Engineering, University of Minnesota Twin Cities, Minneapolis, MN, USA.
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39
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Auxin-Inducible Depletion of the Essentialome Suggests Inhibition of TORC1 by Auxins and Inhibition of Vrg4 by SDZ 90-215, a Natural Antifungal Cyclopeptide. G3-GENES GENOMES GENETICS 2019; 9:829-840. [PMID: 30670608 PMCID: PMC6404609 DOI: 10.1534/g3.118.200748] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Gene knockout and knockdown strategies have been immensely successful probes of gene function, but small molecule inhibitors (SMIs) of gene products allow much greater time resolution and are particularly useful when the targets are essential for cell replication or survival. SMIs also serve as lead compounds for drug discovery. However, discovery of selective SMIs is costly and inefficient. The action of SMIs can be modeled simply by tagging gene products with an auxin-inducible degron (AID) that triggers rapid ubiquitylation and proteasomal degradation of the tagged protein upon exposure of live cells to auxin. To determine if this approach is broadly effective, we AID-tagged over 750 essential proteins in Saccharomyces cerevisiae and observed growth inhibition by low concentrations of auxin in over 66% of cases. Polytopic transmembrane proteins in the plasma membrane, Golgi complex, and endoplasmic reticulum were efficiently depleted if the AID-tag was exposed to cytoplasmic OsTIR1 ubiquitin ligase. The auxin analog 1-napthylacetic acid (NAA) was as potent as auxin on AID-tags, but surprisingly NAA was more potent than auxin at inhibiting target of rapamycin complex 1 (TORC1) function. Auxin also synergized with known SMIs when acting on the same essential protein, indicating that AID-tagged strains can be useful for SMI screening. Auxin synergy, resistance mutations, and cellular assays together suggest the essential GMP/GDP-mannose exchanger in the Golgi complex (Vrg4) as the target of a natural cyclic peptide of unknown function (SDZ 90-215). These findings indicate that AID-tagging can efficiently model the action of SMIs before they are discovered and can facilitate SMI discovery.
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Abstract
The ability to rapidly assess chromosome instability (CIN) has enabled profiling of most yeast genes for potential effects on genome stability. The A-like faker (ALF) assay is one of several qualitative and quantitative marker loss assays that indirectly measure loss or conversion of genetic material using a counterselection step. The ALF assay relies on the ability to count spurious mating events that occur upon loss of the MATα locus of haploid Saccharomyces cerevisiae strains. Here, we describe the deployment of the ALF assay for both rapid and simple qualitative, and more in-depth quantitative analysis allowing determination of absolute ALF frequencies.
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Affiliation(s)
- Carolina A Novoa
- Terry Fox Laboratory, BC Cancer Agency, 675 W. 10th Ave, Vancouver, Canada
| | - J Sidney Ang
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, BC Cancer Agency, 675 W. 10th Ave, Vancouver, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.
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41
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Cheng L, Liu CX, Jiang S, Hou S, Huang JG, Chen ZQ, Sun YY, Qi H, Jiang HW, Wang JF, Zhou YM, Czajkowsky DM, Dai J, Tao SC. Cell Lysate Microarray for Mapping the Network of Genetic Regulators for Histone Marks. Mol Cell Proteomics 2018; 17:1720-1736. [PMID: 29871872 DOI: 10.1074/mcp.ra117.000550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/22/2018] [Indexed: 11/06/2022] Open
Abstract
Proteins, as the major executer for cell progresses and functions, its abundance and the level of post-translational modifications, are tightly monitored by regulators. Genetic perturbation could help us to understand the relationships between genes and protein functions. Herein, to explore the impact of the genome-wide interruption on certain protein, we developed a cell lysate microarray on kilo-conditions (CLICK) with 4837 knockout (YKO) and 322 temperature-sensitive (ts) mutant strains of yeast (Saccharomyces cerevisiae). Taking histone marks as examples, a general workflow was established for the global identification of upstream regulators. Through a single CLICK array test, we obtained a series of regulators for H3K4me3, which covers most of the known regulators in S. cerevisiae We also noted that several group of proteins are involved in negatively regulation of H3K4me3. Further, we discovered that Cab4p and Cab5p, two key enzymes of CoA biosynthesis, play central roles in histone acylation. Because of its general applicability, CLICK array could be easily adopted to rapid and global identification of upstream protein/enzyme(s) that regulate/modify the level of a protein or the posttranslational modification of a non-histone protein.
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Affiliation(s)
- Li Cheng
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China.,§Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Cheng-Xi Liu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Shuangying Jiang
- §Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Sha Hou
- §Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Jin-Guo Huang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Zi-Qing Chen
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yang-Yang Sun
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Huan Qi
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - He-Wei Jiang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jing-Fang Wang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yi-Ming Zhou
- ¶Beijing NeoAntigen Biotechnology Co. Ltd, Beijing, 102206, PR China
| | - Daniel M Czajkowsky
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Junbiao Dai
- §Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China;
| | - Sheng-Ce Tao
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China;
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Yeast KEOPS complex regulates telomere length independently of its t 6A modification function. J Genet Genomics 2018; 45:247-257. [PMID: 29804714 DOI: 10.1016/j.jgg.2018.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/15/2018] [Accepted: 03/23/2018] [Indexed: 11/24/2022]
Abstract
In Saccharomyces cerevisiae, the highly conserved Sua5 and KEOPS complex (including five subunits Kae1, Bud32, Cgi121, Pcc1 and Gon7) catalyze a universal tRNA modification, namely N6-threonylcarbamoyladenosine (t6A), and regulate telomere replication and recombination. However, whether telomere regulation function of Sua5 and KEOPS complex depends on the t6A modification activity remains unclear. Here we show that Sua5 and KEOPS regulate telomere length in the same genetic pathway. Interestingly, the telomere length regulation by KEOPS is independent of its t6A biosynthesis activity. Cytoplasmic overexpression of Qri7, a functional counterpart of KEOPS in mitochondria, restores cytosolic tRNA t6A modification and cell growth, but is not sufficient to rescue telomere length in the KEOPS mutant kae1Δ cells, indicating that a t6A modification-independent function is responsible for the telomere regulation. The results of our in vitro biochemical and in vivo genetic assays suggest that telomerase RNA TLC1 might not be modified by Sua5 and KEOPS. Moreover, deletion of KEOPS subunits results in a dramatic reduction of telomeric G-overhang, suggesting that KEOPS regulates telomere length by promoting G-overhang generation. These findings support a model in which KEOPS regulates telomere replication independently of its function on tRNA modification.
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43
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Chuartzman SG, Schuldiner M. Database for High Throughput Screening Hits (dHITS): a simple tool to retrieve gene specific phenotypes from systematic screens done in yeast. Yeast 2018; 35:477-483. [PMID: 29574976 PMCID: PMC6055851 DOI: 10.1002/yea.3312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/04/2018] [Accepted: 03/07/2018] [Indexed: 12/21/2022] Open
Abstract
In the last decade several collections of Saccharomyces cerevisiae yeast strains have been created. In these collections every gene is modified in a similar manner such as by a deletion or the addition of a protein tag. Such libraries have enabled a diversity of systematic screens, giving rise to large amounts of information regarding gene functions. However, often papers describing such screens focus on a single gene or a small set of genes and all other loci affecting the phenotype of choice (‘hits’) are only mentioned in tables that are provided as supplementary material and are often hard to retrieve or search. To help unify and make such data accessible, we have created a Database of High Throughput Screening Hits (dHITS). The dHITS database enables information to be obtained about screens in which genes of interest were found as well as the other genes that came up in that screen – all in a readily accessible and downloadable format. The ability to query large lists of genes at the same time provides a platform to easily analyse hits obtained from transcriptional analyses or other screens. We hope that this platform will serve as a tool to facilitate investigation of protein functions to the yeast community.
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Affiliation(s)
- Silvia G Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
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44
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Morrison AJ. Genome maintenance functions of the INO80 chromatin remodeller. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0289. [PMID: 28847826 DOI: 10.1098/rstb.2016.0289] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2017] [Indexed: 12/15/2022] Open
Abstract
Chromatin modification is conserved in all eukaryotes and is required to facilitate and regulate DNA-templated processes. For example, chromatin manipulation, such as histone post-translational modification and nucleosome positioning, play critical roles in genome stability pathways. The INO80 chromatin-remodelling complex, which regulates the abundance and positioning of nucleosomes, is particularly important for proper execution of inducible responses to DNA damage. This review discusses the participation and activity of the INO80 complex in DNA repair and cell cycle checkpoint pathways, with emphasis on the Saccharomyces cerevisiae model system. Furthermore, the role of ATM/ATR kinases, central regulators of DNA damage signalling, in the regulation of INO80 function will be reviewed. In addition, emerging themes of chromatin remodelling in mitotic stability pathways and chromosome segregation will be introduced. These studies are critical to understanding the dynamic chromatin landscape that is rapidly and reversibly modified to maintain the integrity of the genome.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Ashby J Morrison
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
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45
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Reactive oxygen species stress increases accumulation of tyrosyl-DNA phsosphodiesterase 1 within mitochondria. Sci Rep 2018. [PMID: 29523818 PMCID: PMC5844879 DOI: 10.1038/s41598-018-22547-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a nuclear and mitochondrial protein that in nuclei and in vitro repairs blocked 3' DNA termini such as 3' phosphotyrosine conjugates resulting from stalling of topoisomerase I-DNA intermediates. Its mutation also causes spinocerebellar ataxia with axonal neuropathy type 1 (SCAN1). Because Tdp1 colocalizes with mitochondria following oxidative stress, we hypothesized that Tdp1 repairs mitochondrial DNA (mtDNA) and that mtDNA damage mediates entry of Tdp1 into the mitochondria. To test this, we used S. cerevisiae mutants, cultured mouse and human cells, and a Tdp1 knockout mouse. H2O2- and rotenone-induced cellular and intramitochondrial reactive oxygen species (ROS) activated oxidant-responsive kinases P38 and ERK1, and the translocation of Tdp1 from the nucleus to the mitochondria via the TIM/TOM complex. This translocation occurred independently of mtDNA. Within the mitochondria, Tdp1 interacted with Ligase III and reduced mtDNA mutations. Tdp1-deficient tissues had impaired mitochondrial respiration and decreased viability. These observations suggest that Tdp1 maintains mtDNA integrity and support the hypothesis that mitochondrial dysfunction contributes to the pathology of SCAN1.
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46
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Cova M, López-Gutiérrez B, Artigas-Jerónimo S, González-Díaz A, Bandini G, Maere S, Carretero-Paulet L, Izquierdo L. The Apicomplexa-specific glucosamine-6-phosphate N-acetyltransferase gene family encodes a key enzyme for glycoconjugate synthesis with potential as therapeutic target. Sci Rep 2018; 8:4005. [PMID: 29507322 PMCID: PMC5838249 DOI: 10.1038/s41598-018-22441-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/22/2018] [Indexed: 02/06/2023] Open
Abstract
Apicomplexa form a phylum of obligate parasitic protozoa of great clinical and veterinary importance. These parasites synthesize glycoconjugates for their survival and infectivity, but the enzymatic steps required to generate the glycosylation precursors are not completely characterized. In particular, glucosamine-phosphate N-acetyltransferase (GNA1) activity, needed to produce the essential UDP-N-acetylglucosamine (UDP-GlcNAc) donor, has not been identified in any Apicomplexa. We scanned the genomes of Plasmodium falciparum and representatives from six additional main lineages of the phylum for proteins containing the Gcn5-related N-acetyltransferase (GNAT) domain. One family of GNAT-domain containing proteins, composed by a P. falciparum sequence and its six apicomplexan orthologs, rescued the growth of a yeast temperature-sensitive GNA1 mutant. Heterologous expression and in vitro assays confirmed the GNA1 enzymatic activity in all lineages. Sequence, phylogenetic and synteny analyses suggest an independent origin of the Apicomplexa-specific GNA1 family, parallel to the evolution of a different GNA1 family in other eukaryotes. The inability to disrupt an otherwise modifiable gene target suggests that the enzyme is essential for P. falciparum growth. The relevance of UDP-GlcNAc for parasite viability, together with the independent evolution and unique sequence features of Apicomplexa GNA1, highlights the potential of this enzyme as a selective therapeutic target against apicomplexans.
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Affiliation(s)
- Marta Cova
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Borja López-Gutiérrez
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Sara Artigas-Jerónimo
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Aida González-Díaz
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Giulia Bandini
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, USA
| | - Steven Maere
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, B-9052, Ghent, Belgium
| | - Lorenzo Carretero-Paulet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052, Ghent, Belgium.
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, B-9052, Ghent, Belgium.
| | - Luis Izquierdo
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.
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47
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Ben-Shimon L, Paul VD, David-Kadoch G, Volpe M, Stümpfig M, Bill E, Mühlenhoff U, Lill R, Ben-Aroya S. Fe-S cluster coordination of the chromokinesin KIF4A alters its sub-cellular localization during mitosis. J Cell Sci 2018; 131:jcs.211433. [DOI: 10.1242/jcs.211433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/11/2018] [Indexed: 11/20/2022] Open
Abstract
Fe-S clusters act as co-factors of proteins with diverse functions, e.g. in DNA repair. Down-regulation of the cytosolic iron-sulfur protein assembly (CIA) machinery promotes genomic instability by the inactivation of multiple DNA repair pathways. Furthermore, CIA deficiencies are associated with so far unexplained mitotic defects. Here, we show that CIA2B and MMS19, constituents of the CIA targeting complex involved in facilitating Fe-S cluster insertion into cytosolic and nuclear target proteins, co-localize with components of the mitotic machinery. Down-regulation of CIA2B and MMS19 impairs the mitotic cycle. We identify the chromokinesin KIF4A as a mitotic component involved in these effects. KIF4A binds a Fe-S cluster in vitro through its conserved cysteine-rich domain. We demonstrate in vivo that this domain is required for the mitosis-related KIF4A localization and for the mitotic defects associated with KIF4A knockout. KIF4A is the first identified mitotic component carrying such a post-translational modification. These findings suggest that the lack of Fe-S clusters in KIF4A upon down-regulation of the CIA targeting complex contributes to the mitotic defects.
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Affiliation(s)
- Lilach Ben-Shimon
- The Nano Center, Building 206 room B-840, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Viktoria D. Paul
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
- LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Strasse, 35043 Marburg, Germany
| | - Galit David-Kadoch
- The Nano Center, Building 206 room B-840, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Marina Volpe
- The Nano Center, Building 206 room B-840, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Martin Stümpfig
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim-Ruhr, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, 35032 Marburg, Germany
- LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Strasse, 35043 Marburg, Germany
| | - Shay Ben-Aroya
- The Nano Center, Building 206 room B-840, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
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48
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Reporter-Based Synthetic Genetic Array Analysis: A Functional Genomics Approach for Investigating Transcript or Protein Abundance Using Fluorescent Proteins in Saccharomyces cerevisiae. Methods Mol Biol 2018; 1672:613-629. [PMID: 29043651 DOI: 10.1007/978-1-4939-7306-4_40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Fluorescent reporter genes have long been used to quantify various cell features such as transcript and protein abundance. Here, we describe a method, reporter synthetic genetic array (R-SGA) analysis, which allows for the simultaneous quantification of any fluorescent protein readout in thousands of yeast strains using an automated pipeline. R-SGA combines a fluorescent reporter system with standard SGA analysis and can be used to examine any array-based strain collection available to the yeast community. This protocol describes the R-SGA methodology for screening different arrays of yeast mutants including the deletion collection, a collection of temperature-sensitive strains for the assessment of essential yeast genes and a collection of inducible overexpression strains. We also present an alternative pipeline for the analysis of R-SGA output strains using flow cytometry of cells in liquid culture. Data normalization for both pipelines is discussed.
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49
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Comyn SA, Mayor T. A Method to Monitor Protein Turnover by Flow Cytometry and to Screen for Factors that Control Degradation by Fluorescence-Activated Cell Sorting. Methods Mol Biol 2018; 1844:137-153. [PMID: 30242708 DOI: 10.1007/978-1-4939-8706-1_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The protein quality control network consists of multiple proteins or protein complexes that monitor proteome integrity by mediating protein folding and the removal of proteins that cannot be folded. An integral component of this network is the ubiquitin-proteasome system, which controls the degradation of thousands of cellular proteins. A number of questions remain unanswered regarding the degradation of misfolded proteins. For example, how are substrates recognized and triaged? What are the identities of the components involved? And finally, what substrates are targeted by any given component of the quality control network? Finding answers to these questions is what inspires our work in protein quality control. Further characterization of protein quality control mechanisms requires methods that can reliably quantify turnover rates of model substrates. One such method is based on flow cytometry. Here, we present protocols detailing how to assess protein stability with flow cytometry and how fluorescence-activated cell sorting (FACS) can be used to screen for factors important for protein quality control and protein turnover.
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Affiliation(s)
- Sophie A Comyn
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
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Ghanegolmohammadi F, Yoshida M, Ohnuki S, Sukegawa Y, Okada H, Obara K, Kihara A, Suzuki K, Kojima T, Yachie N, Hirata D, Ohya Y. Systematic analysis of Ca 2+ homeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles. Mol Biol Cell 2017; 28:3415-3427. [PMID: 28566553 PMCID: PMC5687040 DOI: 10.1091/mbc.e17-04-0216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 12/20/2022] Open
Abstract
We investigated the global landscape of Ca2+ homeostasis in budding yeast based on high-dimensional chemical-genetic interaction profiles. The morphological responses of 62 Ca2+-sensitive (cls) mutants were quantitatively analyzed with the image processing program CalMorph after exposure to a high concentration of Ca2+ After a generalized linear model was applied, an analysis of covariance model was used to detect significant Ca2+-cls interactions. We found that high-dimensional, morphological Ca2+-cls interactions were mixed with positive (86%) and negative (14%) chemical-genetic interactions, whereas one-dimensional fitness Ca2+-cls interactions were all negative in principle. Clustering analysis with the interaction profiles revealed nine distinct gene groups, six of which were functionally associated. In addition, characterization of Ca2+-cls interactions revealed that morphology-based negative interactions are unique signatures of sensitized cellular processes and pathways. Principal component analysis was used to discriminate between suppression and enhancement of the Ca2+-sensitive phenotypes triggered by inactivation of calcineurin, a Ca2+-dependent phosphatase. Finally, similarity of the interaction profiles was used to reveal a connected network among the Ca2+ homeostasis units acting in different cellular compartments. Our analyses of high-dimensional chemical-genetic interaction profiles provide novel insights into the intracellular network of yeast Ca2+ homeostasis.
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Affiliation(s)
| | - Mitsunori Yoshida
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Yuko Sukegawa
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
- AIST-UTokyo Advanced Operand-Measurement Technology Open Innovation Laboratory, Kashiwa 277-0882, Japan
| | - Hiroki Okada
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058
| | - Keisuke Obara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Kuninori Suzuki
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
- Bioimaging Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Tetsuya Kojima
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Nozomu Yachie
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan
- PRESTO, Japan Science and Technology Agency, Tokyo 102-0076, Japan
| | - Dai Hirata
- Research and Development Department, Asahi Sake Brewing Co., Nagaoka 949-5494, Japan
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
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