51
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Ogawa Y, Nishimura K, Obara K, Kamura T. Development of AlissAID system targeting GFP or mCherry fusion protein. PLoS Genet 2023; 19:e1010731. [PMID: 37315088 DOI: 10.1371/journal.pgen.1010731] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/04/2023] [Indexed: 06/16/2023] Open
Abstract
Conditional control of target proteins using the auxin-inducible degron (AID) system provides a powerful tool for investigating protein function in eukaryotes. Here, we established an Affinity-linker based super-sensitive auxin-inducible degron (AlissAID) system in budding yeast by using a single domain antibody (a nanobody). In this system, target proteins fused with GFP or mCherry were degraded depending on a synthetic auxin, 5-Adamantyl-IAA (5-Ad-IAA). In AlissAID system, nanomolar concentration of 5-Ad-IAA induces target degradation, thus minimizing the side effects from chemical compounds. In addition, in AlissAID system, we observed few basal degradations which was observed in other AID systems including ssAID system. Furthermore, AlissAID based conditional knockdown cell lines are easily generated by using budding yeast GFP Clone Collection. Target protein, which has antigen recognition sites exposed in cytosol or nucleus, can be degraded by the AlissAID system. From these advantages, the AlissAID system would be an ideal protein-knockdown system in budding yeast cells.
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Affiliation(s)
- Yoshitaka Ogawa
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kohei Nishimura
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Keisuke Obara
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Takumi Kamura
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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52
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Milholland KL, Gregor JB, Hoda S, Píriz-Antúnez S, Dueñas-Santero E, Vu BG, Patel KP, Moye-Rowley WS, de Aldana CRV, Correa-Bordes J, Briggs SD, Hall MC. Rapid, efficient auxin-inducible protein degradation in Candida pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541235. [PMID: 37293017 PMCID: PMC10245712 DOI: 10.1101/2023.05.17.541235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A variety of inducible protein degradation (IPD) systems have been developed as powerful tools for protein functional characterization. IPD systems provide a convenient mechanism for rapid inactivation of almost any target protein of interest. Auxin-inducible degradation (AID) is one of the most common IPD systems and has been established in diverse eukaryotic research model organisms. Thus far, IPD tools have not been developed for use in pathogenic fungal species. Here, we demonstrate that the original AID and the second generation AID2 systems work efficiently and rapidly in the human pathogenic yeasts Candida albicans and Candida glabrata . We developed a collection of plasmids that support AID system use in laboratory strains of these pathogens. These systems can induce >95% degradation of target proteins within minutes. In the case of AID2, maximal degradation was achieved at low nanomolar concentrations of the synthetic auxin analog 5-adamantyl-indole-3-acetic acid (5-Ad-IAA). Auxin-induced target degradation successfully phenocopied gene deletions in both species. The system should be readily adaptable to other fungal species and to clinical pathogen strains. Our results define the AID system as a powerful and convenient functional genomics tool for protein characterization in fungal pathogens.
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Affiliation(s)
- Kedric L. Milholland
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Justin B. Gregor
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Smriti Hoda
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | | | - Encarnación Dueñas-Santero
- Institute of Functional Biology and Genomics, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), Salamanca, Spain
| | - Bao Gia Vu
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Krishna P. Patel
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - W. Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Carlos R. Vázquez de Aldana
- Institute of Functional Biology and Genomics, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), Salamanca, Spain
| | - Jaime Correa-Bordes
- Department of Biomedical Sciences, Universidad de Extremadura, Badajoz, Spain
| | - Scott D. Briggs
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Mark C. Hall
- Department of Biochemistry and Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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53
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Phanindhar K, Mishra RK. Auxin-inducible degron system: an efficient protein degradation tool to study protein function. Biotechniques 2023; 74:186-198. [PMID: 37191015 DOI: 10.2144/btn-2022-0108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Targeted protein degradation, with its rapid protein depletion kinetics, allows the measurement of acute changes in the cell. The auxin-inducible degron (AID) system, rapidly degrades AID-tagged proteins only in the presence of auxin. The AID system being inducible makes the study of essential genes and dynamic processes like cell differentiation, cell cycle and genome organization feasible. The AID degradation system has been adapted to yeast, protozoans, C. elegans, Drosophila, zebrafish, mouse and mammalian cell lines. Using the AID system, researchers have unveiled novel functions for essential proteins at developmental stages that were previously difficult to investigate due to early lethality. This comprehensive review discusses the development, advancements, applications and drawbacks of the AID system and compares it with other available protein degradation systems.
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Affiliation(s)
- Kundurthi Phanindhar
- CSIR-Centre for Cellular & Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular & Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- Tata Institute for Genetics & Society (TIGS), Bangalore, 560065, India
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54
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Borrie MS, Kraycer PM, Gartenberg MR. Transcription-Driven Translocation of Cohesive and Non-Cohesive Cohesin In Vivo. Mol Cell Biol 2023; 43:254-268. [PMID: 37178128 PMCID: PMC10251789 DOI: 10.1080/10985549.2023.2199660] [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: 01/03/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 05/15/2023] Open
Abstract
Cohesin is a central architectural element of chromosomes that regulates numerous DNA-based events. The complex holds sister chromatids together until anaphase onset and organizes individual chromosomal DNAs into loops and self-associating domains. Purified cohesin diffuses along DNA in an ATP-independent manner but can be propelled by transcribing RNA polymerase. In conjunction with a cofactor, the complex also extrudes DNA loops in an ATP-dependent manner. In this study we examine transcription-driven translocation of cohesin under various conditions in yeast. To this end, obstacles of increasing size were tethered to DNA to act as roadblocks to complexes mobilized by an inducible gene. The obstacles were built from a GFP-lacI core fused to one or more mCherries. A chimera with four mCherries blocked cohesin passage in late G1. During M phase, the threshold barrier depended on the state of cohesion: non-cohesive complexes were also blocked by four mCherries whereas cohesive complexes were blocked by as few as three mCherries. Furthermore cohesive complexes that were stalled at obstacles, in turn, blocked the passage of non-cohesive complexes. That synthetic barriers capture mobilized cohesin demonstrates that transcription-driven complexes translocate processively in vivo. Together, this study reveals unexplored limitations to cohesin movement on chromosomes.
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Affiliation(s)
- Melinda S. Borrie
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Paul M. Kraycer
- Graduate Program in Cellular and Molecular Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Marc R. Gartenberg
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Member of The Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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55
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Campos A, Ramos F, Iglesias L, Delgado C, Merino E, Esperilla-Muñoz A, Correa-Bordes J, Clemente-Blanco A. Cdc14 phosphatase counteracts Cdk-dependent Dna2 phosphorylation to inhibit resection during recombinational DNA repair. Nat Commun 2023; 14:2738. [PMID: 37173316 PMCID: PMC10182099 DOI: 10.1038/s41467-023-38417-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Cyclin-dependent kinase (Cdk) stimulates resection of DNA double-strand breaks ends to generate single-stranded DNA (ssDNA) needed for recombinational DNA repair. Here we show in Saccharomyces cerevisiae that lack of the Cdk-counteracting phosphatase Cdc14 produces abnormally extended resected tracts at the DNA break ends, involving the phosphatase in the inhibition of resection. Over-resection in the absence of Cdc14 activity is bypassed when the exonuclease Dna2 is inactivated or when its Cdk consensus sites are mutated, indicating that the phosphatase restrains resection by acting through this nuclease. Accordingly, mitotically activated Cdc14 promotes Dna2 dephosphorylation to exclude it from the DNA lesion. Cdc14-dependent resection inhibition is essential to sustain DNA re-synthesis, thus ensuring the appropriate length, frequency, and distribution of the gene conversion tracts. These results establish a role for Cdc14 in controlling the extent of resection through Dna2 regulation and demonstrate that the accumulation of excessively long ssDNA affects the accurate repair of the broken DNA by homologous recombination.
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Affiliation(s)
- Adrián Campos
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain
| | - Facundo Ramos
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain
| | - Lydia Iglesias
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain
| | - Celia Delgado
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain
| | - Eva Merino
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain
| | | | - Jaime Correa-Bordes
- Departamento de Ciencias Biomédicas, Universidad de Extremadura, Badajoz, Spain
| | - Andrés Clemente-Blanco
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, Salamanca, Spain.
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56
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Bhat P, Aksenova V, Gazzara M, Rex EA, Aslam S, Haddad C, Gao S, Esparza M, Cagatay T, Batten K, El Zahed SS, Arnaoutov A, Zhong H, Shay JW, Tolbert BS, Dasso M, Lynch KW, García-Sastre A, Fontoura BMA. Influenza virus mRNAs encode determinants for nuclear export via the cellular TREX-2 complex. Nat Commun 2023; 14:2304. [PMID: 37085480 PMCID: PMC10121598 DOI: 10.1038/s41467-023-37911-0] [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: 09/06/2022] [Accepted: 04/05/2023] [Indexed: 04/23/2023] Open
Abstract
Nuclear export of influenza A virus (IAV) mRNAs occurs through the nuclear pore complex (NPC). Using the Auxin-Induced Degron (AID) system to rapidly degrade proteins, we show that among the nucleoporins localized at the nucleoplasmic side of the NPC, TPR is the key nucleoporin required for nuclear export of influenza virus mRNAs. TPR recruits the TRanscription and EXport complex (TREX)-2 to the NPC for exporting a subset of cellular mRNAs. By degrading components of the TREX-2 complex (GANP, Germinal-center Associated Nuclear Protein; PCID2, PCI domain containing 2), we show that influenza mRNAs require the TREX-2 complex for nuclear export and replication. Furthermore, we found that cellular mRNAs whose export is dependent on GANP have a small number of exons, a high mean exon length, long 3' UTR, and low GC content. Some of these features are shared by influenza virus mRNAs. Additionally, we identified a 45 nucleotide RNA signal from influenza virus HA mRNA that is sufficient to mediate GANP-dependent mRNA export. Thus, we report a role for the TREX-2 complex in nuclear export of influenza mRNAs and identified RNA determinants associated with the TREX-2-dependent mRNA export.
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Affiliation(s)
- Prasanna Bhat
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Matthew Gazzara
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Emily A Rex
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sadaf Aslam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Matthew Esparza
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tolga Cagatay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kimberly Batten
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sara S El Zahed
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexei Arnaoutov
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hualin Zhong
- Department of Biological Sciences, Hunter College, New York, NY, 10065, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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57
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Kakko N, Rantasalo A, Koponen T, Vidgren V, Kannisto M, Maiorova N, Nygren H, Mojzita D, Penttilä M, Jouhten P. Inducible Synthetic Growth Regulation Using the ClpXP Proteasome Enhances cis,cis-Muconic Acid and Glycolic Acid Yields in Saccharomyces cerevisiae. ACS Synth Biol 2023; 12:1021-1033. [PMID: 36976676 PMCID: PMC10127448 DOI: 10.1021/acssynbio.2c00467] [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: 09/01/2022] [Indexed: 03/29/2023]
Abstract
Engineered microbial cells can produce sustainable chemistry, but the production competes for resources with growth. Inducible synthetic control over the resource use would enable fast accumulation of sufficient biomass and then divert the resources to production. We developed inducible synthetic resource-use control overSaccharomyces cerevisiae by expressing a bacterial ClpXP proteasome from an inducible promoter. By individually targeting growth-essential metabolic enzymes Aro1, Hom3, and Acc1 to the ClpXP proteasome, cell growth could be efficiently repressed during cultivation. The ClpXP proteasome was specific to the target proteins, and there was no reduction in the targets when ClpXP was not induced. The inducible growth repression improved product yields from glucose (cis,cis-muconic acid) and per biomass (cis,cis-muconic acid and glycolic acid). The inducible ClpXP proteasome tackles uncertainties in strain optimization by enabling model-guided repression of competing, growth-essential, and metabolic enzymes. Most importantly, it allows improving production without compromising biomass accumulation when uninduced; therefore, it is expected to mitigate strain stability and low productivity challenges.
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Affiliation(s)
- Natalia Kakko
- VTT
Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
- School
of Chemical Engineering, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16300, Espoo FI-00076 AALTO, Finland
| | - Anssi Rantasalo
- VTT
Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Tino Koponen
- VTT
Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Virve Vidgren
- VTT
Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Matti Kannisto
- VTT
Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Natalia Maiorova
- VTT
Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Heli Nygren
- VTT
Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Dominik Mojzita
- VTT
Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
| | - Merja Penttilä
- VTT
Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
- School
of Chemical Engineering, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16300, Espoo FI-00076 AALTO, Finland
| | - Paula Jouhten
- VTT
Technical Research Centre of Finland Ltd, Espoo 02044 VTT, Finland
- School
of Chemical Engineering, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16300, Espoo FI-00076 AALTO, Finland
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58
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Terhorst A, Sandikci A, Whittaker CA, Szórádi T, Holt LJ, Neurohr GE, Amon A. The environmental stress response regulates ribosome content in cell cycle-arrested S. cerevisiae. Front Cell Dev Biol 2023; 11:1118766. [PMID: 37123399 PMCID: PMC10130656 DOI: 10.3389/fcell.2023.1118766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
Prolonged cell cycle arrests occur naturally in differentiated cells and in response to various stresses such as nutrient deprivation or treatment with chemotherapeutic agents. Whether and how cells survive prolonged cell cycle arrests is not clear. Here, we used S. cerevisiae to compare physiological cell cycle arrests and genetically induced arrests in G1-, meta- and anaphase. Prolonged cell cycle arrest led to growth attenuation in all studied conditions, coincided with activation of the Environmental Stress Response (ESR) and with a reduced ribosome content as determined by whole ribosome purification and TMT mass spectrometry. Suppression of the ESR through hyperactivation of the Ras/PKA pathway reduced cell viability during prolonged arrests, demonstrating a cytoprotective role of the ESR. Attenuation of cell growth and activation of stress induced signaling pathways also occur in arrested human cell lines, raising the possibility that the response to prolonged cell cycle arrest is conserved.
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Affiliation(s)
- Allegra Terhorst
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Arzu Sandikci
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Charles A. Whittaker
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tamás Szórádi
- Institute for Systems Genetics, New York University Langone Health, New York City, NY, United States
| | - Liam J. Holt
- Institute for Systems Genetics, New York University Langone Health, New York City, NY, United States
| | - Gabriel E. Neurohr
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
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59
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Rubio LS, Gross DS. Dynamic coalescence of yeast Heat Shock Protein genes bypasses the requirement for actin. Genetics 2023; 223:iyad006. [PMID: 36659814 PMCID: PMC10319981 DOI: 10.1093/genetics/iyad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 07/22/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Nuclear actin has been implicated in dynamic chromatin rearrangements in diverse eukaryotes. In mammalian cells, it is required to reposition double-strand DNA breaks to enable homologous recombination repair and to enhance transcription by facilitating RNA Pol II recruitment to gene promoters. In the yeast Saccharomyces cerevisiae, nuclear actin modulates interphase chromosome dynamics and is required to reposition the induced INO1 gene to the nuclear periphery. Here, we have investigated the role of actin in driving intergenic interactions between Heat Shock Factor 1 (Hsf1)-regulated Heat Shock Protein (HSP) genes in budding yeast. These genes, dispersed on multiple chromosomes, dramatically reposition following exposure of cells to acute thermal stress, leading to their clustering within dynamic biomolecular condensates. Using an auxin-induced degradation strategy, we found that conditional depletion of nucleators of either linear or branched F-actin (Bni1/Bnr1 and Arp2, respectively) had little or no effect on heat shock-induced HSP gene coalescence or transcription. In addition, we found that pretreatment of cells with latrunculin A, an inhibitor of both filamentous and monomeric actin, failed to affect intergenic interactions between activated HSP genes and their heat shock-induced intragenic looping and folding. Moreover, latrunculin A pretreatment had little effect on HSP gene expression at either RNA or protein levels. In notable contrast, we confirmed that repositioning of activated INO1 to the nuclear periphery and its proper expression do require actin. Collectively, our work suggests that transcriptional activation and 3D genome restructuring of thermally induced, Hsf1-regulated genes can occur in the absence of actin.
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Affiliation(s)
- Linda S Rubio
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - David S Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
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60
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Mariano NC, Rusin SF, Nasa I, Kettenbach AN. Inducible protein degradation as a strategy to identify Phosphoprotein Phosphatase 6 substrates in RAS-mutant colorectal cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534211. [PMID: 36993243 PMCID: PMC10055397 DOI: 10.1101/2023.03.25.534211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Protein phosphorylation is an essential regulatory mechanism that controls most cellular processes, including cell cycle progression, cell division, and response to extracellular stimuli, among many others, and is deregulated in many diseases. Protein phosphorylation is coordinated by the opposing activities of protein kinases and protein phosphatases. In eukaryotic cells, most serine/threonine phosphorylation sites are dephosphorylated by members of the Phosphoprotein Phosphatase (PPP) family. However, we only know for a few phosphorylation sites which specific PPP dephosphorylates them. Although natural compounds such as calyculin A and okadaic acid inhibit PPPs at low nanomolar concentrations, no selective chemical PPP inhibitors exist. Here, we demonstrate the utility of endogenous tagging of genomic loci with an auxin-inducible degron (AID) as a strategy to investigate specific PPP signaling. Using Protein Phosphatase 6 (PP6) as an example, we demonstrate how rapidly inducible protein degradation can be employed to identify dephosphorylation SITES and elucidate PP6 biology. Using genome editing, we introduce AID-tags into each allele of the PP6 catalytic subunit (PP6c) in DLD-1 cells expressing the auxin receptor Tir1. Upon rapid auxin-induced degradation of PP6c, we perform quantitative mass spectrometry-based proteomics and phosphoproteomics to identify PP6 substrates in mitosis. PP6 is an essential enzyme with conserved roles in mitosis and growth signaling. Consistently, we identify candidate PP6c-dependent phosphorylation sites on proteins implicated in coordinating the mitotic cell cycle, cytoskeleton, gene expression, and mitogen-activated protein kinase (MAPK) and Hippo signaling. Finally, we demonstrate that PP6c opposes the activation of large tumor suppressor 1 (LATS1) by dephosphorylating Threonine 35 (T35) on Mps One Binder (MOB1), thereby blocking the interaction of MOB1 and LATS1. Our analyses highlight the utility of combining genome engineering, inducible degradation, and multiplexed phosphoproteomics to investigate signaling by individual PPPs on a global level, which is currently limited by the lack of tools for specific interrogation.
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61
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Schindler N, Tonn M, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A, Luke B. Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun 2023; 14:1227. [PMID: 36869098 PMCID: PMC9984532 DOI: 10.1038/s41467-023-36866-6] [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: 06/12/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Single ribonucleoside monophosphates (rNMPs) are transiently present in eukaryotic genomes. The RNase H2-dependent ribonucleotide excision repair (RER) pathway ensures error-free rNMP removal. In some pathological conditions, rNMP removal is impaired. If these rNMPs hydrolyze during, or prior to, S phase, toxic single-ended double-strand breaks (seDSBs) can occur upon an encounter with replication forks. How such rNMP-derived seDSB lesions are repaired is unclear. We expressed a cell cycle phase restricted allele of RNase H2 to nick at rNMPs in S phase and study their repair. Although Top1 is dispensable, the RAD52 epistasis group and Rtt101Mms1-Mms22 dependent ubiquitylation of histone H3 become essential for rNMP-derived lesion tolerance. Consistently, loss of Rtt101Mms1-Mms22 combined with RNase H2 dysfunction leads to compromised cellular fitness. We refer to this repair pathway as nick lesion repair (NLR). The NLR genetic network may have important implications in the context of human pathologies.
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Affiliation(s)
- Natalie Schindler
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Matthias Tonn
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Vanessa Kellner
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,Department of Biology, New York University, New York, NY, USA
| | - Jia Jun Fung
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Arianna Lockhart
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Olga Vydzhak
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Stefanie Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anton Khmelinskii
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Brian Luke
- Johannes Gutenberg University Mainz, Institute for Developmental Neurology (IDN), Biozentrum 1, Hanns-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany. .,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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62
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Weiβ M, Chanou A, Schauer T, Tvardovskiy A, Meiser S, König AC, Schmidt T, Kruse E, Ummethum H, Trauner M, Werner M, Lalonde M, Hauck SM, Scialdone A, Hamperl S. Single-copy locus proteomics of early- and late-firing DNA replication origins identifies a role of Ask1/DASH complex in replication timing control. Cell Rep 2023; 42:112045. [PMID: 36701236 PMCID: PMC9989823 DOI: 10.1016/j.celrep.2023.112045] [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] [Received: 03/04/2022] [Revised: 11/28/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023] Open
Abstract
The chromatin environment at origins of replication is thought to influence DNA replication initiation in eukaryotic genomes. However, it remains unclear how and which chromatin features control the firing of early-efficient (EE) or late-inefficient (LI) origins. Here, we use site-specific recombination and single-locus chromatin isolation to purify EE and LI replication origins in Saccharomyces cerevisiae. Using mass spectrometry, we define the protein composition of native chromatin regions surrounding the EE and LI replication start sites. In addition to known origin interactors, we find the microtubule-binding Ask1/DASH complex as an origin-regulating factor. Strikingly, tethering of Ask1 to individual origin sites advances replication timing (RT) of the targeted chromosomal domain. Targeted degradation of Ask1 globally changes RT of a subset of origins, which can be reproduced by inhibiting microtubule dynamics. Thus, our findings mechanistically connect RT and chromosomal organization via Ask1/DASH with the microtubule cytoskeleton.
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Affiliation(s)
- Matthias Weiβ
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany
| | - Anna Chanou
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany
| | - Tamas Schauer
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Stefan Meiser
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Ann-Christine König
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Center for Environmental Health, Heidemannstrasse 1, 80939 München, Germany
| | - Tobias Schmidt
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany
| | - Elisabeth Kruse
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany
| | - Henning Ummethum
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany
| | - Manuel Trauner
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany
| | - Marcel Werner
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany
| | - Maxime Lalonde
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Center for Environmental Health, Heidemannstrasse 1, 80939 München, Germany
| | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Stephan Hamperl
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany.
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63
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González L, Kolbin D, Trahan C, Jeronimo C, Robert F, Oeffinger M, Bloom K, Michnick SW. Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation. Nat Commun 2023; 14:1135. [PMID: 36854718 PMCID: PMC9975218 DOI: 10.1038/s41467-023-36391-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 01/30/2023] [Indexed: 03/03/2023] Open
Abstract
Partitioning of active gene loci to the nuclear envelope (NE) is a mechanism by which organisms increase the speed of adaptation and metabolic robustness to fluctuating resources in the environment. In the yeast Saccharomyces cerevisiae, adaptation to nutrient depletion or other stresses, manifests as relocalization of active gene loci from nucleoplasm to the NE, resulting in more efficient transport and translation of mRNA. The mechanism by which this partitioning occurs remains a mystery. Here, we demonstrate that the yeast inositol depletion-responsive gene locus INO1 partitions to the nuclear envelope, driven by local histone acetylation-induced polymer-polymer phase separation from the nucleoplasmic phase. This demixing is consistent with recent evidence for chromatin phase separation by acetylation-mediated dissolution of multivalent histone association and fits a physical model where increased bending stiffness of acetylated chromatin polymer causes its phase separation from de-acetylated chromatin. Increased chromatin spring stiffness could explain nucleation of transcriptional machinery at active gene loci.
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Affiliation(s)
- Lidice González
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christian Trahan
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Marlene Oeffinger
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada.
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64
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González-Garrido C, Prado F. Parental histone distribution and location of the replication obstacle at nascent strands control homologous recombination. Cell Rep 2023; 42:112174. [PMID: 36862554 DOI: 10.1016/j.celrep.2023.112174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/09/2022] [Accepted: 02/10/2023] [Indexed: 03/03/2023] Open
Abstract
The advance and stability of replication forks rely on a tight co-regulation of DNA synthesis and nucleosome assembly. We show that mutants affected in parental histone recycling are impaired in the recombinational repair of the single-stranded DNA gaps generated in response to DNA adducts that hamper replication, which are then filled in by translesion synthesis. These recombination defects are in part due to an excess of parental nucleosomes at the invaded strand that destabilizes the sister chromatid junction formed after strand invasion through a Srs2-dependent mechanism. In addition, we show that a dCas9∗/R-loop is more recombinogenic when the dCas9∗/DNA-RNA hybrid interferes with the lagging than with the leading strand, and this recombination is particularly sensitive to problems in the deposition of parental histones at the strand that contains the hindrance. Therefore, parental histone distribution and location of the replication obstacle at the lagging or leading strand regulate homologous recombination.
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Affiliation(s)
- Cristina González-Garrido
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Félix Prado
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain.
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65
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Shively CA, Dong F, Mitra RD. A Suite of New Strain Construction Vectors for Gene Expression Knockdown in Budding Yeast. ACS Synth Biol 2023; 12:624-633. [PMID: 36650116 PMCID: PMC10406437 DOI: 10.1021/acssynbio.2c00547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Numerous tools for gene expression knockdown have been developed and characterized in the model organism Saccharomyces cerevisiae and extended to facilitate studies in multicellular models. To comparatively evaluate the efficacy of these approaches, we systematically applied seven such published constitutive and inducible knockdown strategies to a panel of essential genes encoding nuclear-localized proteins. In this effort, we created the CEAS (C-SWAT for Essential Allele Strains) collection, a suite of tagging vectors for improved utility and ease of strain construction. Of particular note, we adapted an improved auxin inducible degron (AID) protein degradation strategy previously available only in mammalian tissue culture for one-step strain construction in budding yeast by leveraging both the C-SWAT system and CRISPR/Cas9 editing. Taken together, this work presents a toolbox for endogenous gene expression knockdown and allows us to make recommendations on the efficacy and applicability of these tools for the perturbation of essential genes.
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Affiliation(s)
- Christian A Shively
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, United States.,The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, United States
| | - Fengping Dong
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, United States.,The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, United States
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, United States.,The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, United States.,McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, United States
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66
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Fenech EJ, Cohen N, Kupervaser M, Gazi Z, Schuldiner M. A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast. Mol Syst Biol 2023; 19:e11084. [PMID: 36651308 PMCID: PMC9912024 DOI: 10.15252/msb.202211084] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023] Open
Abstract
Identification of both stable and transient interactions is essential for understanding protein function and regulation. While assessing stable interactions is more straightforward, capturing transient ones is challenging. In recent years, sophisticated tools have emerged to improve transient interactor discovery, with many harnessing the power of evolved biotin ligases for proximity labelling. However, biotinylation-based methods have lagged behind in the model eukaryote, Saccharomyces cerevisiae, possibly due to the presence of several abundant, endogenously biotinylated proteins. In this study, we optimised robust biotin-ligation methodologies in yeast and increased their sensitivity by creating a bespoke technique for downregulating endogenous biotinylation, which we term ABOLISH (Auxin-induced BiOtin LIgase diminiSHing). We used the endoplasmic reticulum insertase complex (EMC) to demonstrate our approaches and uncover new substrates. To make these tools available for systematic probing of both stable and transient interactions, we generated five full-genome collections of strains in which every yeast protein is tagged with each of the tested biotinylation machineries, some on the background of the ABOLISH system. This comprehensive toolkit enables functional interactomics of the entire yeast proteome.
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Affiliation(s)
- Emma J Fenech
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Nir Cohen
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Meital Kupervaser
- The de Botton Protein Profiling Institute of the Nancy and Stephen Grand Israel National Centre for Personalized MedicineWeizmann Institute of ScienceRehovotIsrael
| | - Zohar Gazi
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Maya Schuldiner
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
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67
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Yin Z, Zhang Z, Lei Y, Klionsky DJ. Bidirectional roles of the Ccr4-Not complex in regulating autophagy before and after nitrogen starvation. Autophagy 2023; 19:415-425. [PMID: 35167422 PMCID: PMC9851207 DOI: 10.1080/15548627.2022.2036476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/12/2022] [Accepted: 01/28/2022] [Indexed: 01/22/2023] Open
Abstract
Macroautophagy/autophagy is a highly conserved catabolic process by which cytoplasmic constituents are delivered to the vacuole/lysosome for degradation and recycling. To maintain cellular homeostasis and prevent pathologies, the induction and amplitude of autophagy activity are finely controlled through regulation of ATG gene expression. Here we report that the Ccr4-Not complex in Saccharomyces cerevisiae has bidirectional roles in regulating autophagy before and after nutrient deprivation. Under nutrient-rich conditions, Ccr4-Not directly targets the mRNAs of several ATG genes in the core autophagy machinery to promote their degradation through deadenylation, thus contributing to maintaining autophagy at the basal level. Upon starvation, Ccr4-Not releases its repression of these ATG genes and switches its role to promote the expression of a different subset of ATG genes, which is required for sufficient autophagy induction and activity. These results reveal that the Ccr4-Not complex is indispensable to maintain autophagy at the appropriate amplitude in both basal and stress conditions.Abbreviations: AID, auxin-inducible degron; Ape1, aminopeptidase I; Atg, autophagy related; Cvt, cytoplasm-to-vacuole targeting; DMSO, dimethyl sulfoxide; IAA, indole-3-acetic acid; PA, protein A; RIP, RNA immunoprecipitation.
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Affiliation(s)
- Zhangyuan Yin
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Zhihai Zhang
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yuchen Lei
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J. Klionsky
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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68
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Hyle J, Djekidel MN, Williams J, Wright S, Shao Y, Xu B, Li C. Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation. Genome Biol 2023; 24:14. [PMID: 36698211 PMCID: PMC9878928 DOI: 10.1186/s13059-022-02843-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/29/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND CTCF is a well-established chromatin architectural protein that also plays various roles in transcriptional regulation. While CTCF biology has been extensively studied, how the domains of CTCF function to regulate transcription remains unknown. Additionally, the original auxin-inducible degron 1 (AID1) system has limitations in investigating the function of CTCF. RESULTS We employ an improved auxin-inducible degron technology, AID2, to facilitate the study of acute depletion of CTCF while overcoming the limitations of the previous AID system. As previously observed through the AID1 system and steady-state RNA analysis, the new AID2 system combined with SLAM-seq confirms that CTCF depletion leads to modest nascent and steady-state transcript changes. A CTCF domain sgRNA library screening identifies the zinc finger (ZF) domain as the region within CTCF with the most functional relevance, including ZFs 1 and 10. Removal of ZFs 1 and 10 reveals genomic regions that independently require these ZFs for DNA binding and transcriptional regulation. Notably, loci regulated by either ZF1 or ZF10 exhibit unique CTCF binding motifs specific to each ZF. CONCLUSIONS By extensively comparing the AID1 and AID2 systems for CTCF degradation in SEM cells, we confirm that AID2 degradation is superior for achieving miniAID-tagged protein degradation without the limitations of the AID1 system. The model we create that combines AID2 depletion of CTCF with exogenous overexpression of CTCF mutants allows us to demonstrate how peripheral ZFs intricately orchestrate transcriptional regulation in a cellular context for the first time.
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Affiliation(s)
- Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Justin Williams
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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69
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Meyer RE, Sartin A, Gish M, Harsha J, Wilkie E, Haworth D, LaVictoire R, Alberola I, Chuong HH, Gorbsky GJ, Dawson DS. Polyploid yeast are dependent on elevated levels of Mps1 for successful chromosome segregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523325. [PMID: 36712123 PMCID: PMC9882063 DOI: 10.1101/2023.01.09.523325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tumor cell lines with elevated chromosome numbers frequently have correlated elevations of Mps1 expression and these tumors are more dependent on Mps1 activity for their survival than control cell lines. Mps1 is a conserved kinase involved in controlling aspects of chromosome segregation in mitosis and meiosis. The mechanistic explanation for the Mps1-addiction of aneuploid cells is unknown. To address this question, we explored Mps1-dependence in yeast cells with increased sets of chromosomes. These experiments revealed that in yeast, increasing ploidy leads to delays and failures in orienting chromosomes on the mitotic spindle. Yeast cells with elevated numbers of chromosomes proved vulnerable to reductions of Mps1 activity. Cells with reduced Mps1 activity exhibit an extended prometaphase with longer spindles and delays in orienting the chromosomes. One known role of Mps1 is in recruiting Bub1 to the kinetochore in meiosis. We found that the Mps1-addiction of polyploid yeast cells is due in part to its role in Bub1 recruitment. Together, the experiments presented here demonstrate that increased ploidy renders cells more dependent on Mps1 for orienting chromosomes on the spindle. The phenomenon described here may be relevant in understanding why hyper-diploid cancer cells exhibit elevated reliance on Mps1 expression for successful chromosome segregation.
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Affiliation(s)
- Régis E Meyer
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Ashlea Sartin
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Madeline Gish
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Jillian Harsha
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Emily Wilkie
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Dawson Haworth
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Rebecca LaVictoire
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Isabel Alberola
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Hoa H Chuong
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Gary J Gorbsky
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Dean S Dawson
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
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70
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Ekal L, Hettema E. Targeted Modifications of the Yeast Genome to Study Peroxisomes. Methods Mol Biol 2023; 2643:217-232. [PMID: 36952189 DOI: 10.1007/978-1-0716-3048-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
PCR-based gene targeting enables rapid alteration of the Saccharomyces cerevisiae genome. Here we describe how this method can be applied for directed gene deletions, epitope and fluorescence protein tagging, and conditional gene expression, with a specific focus on peroxisomal proteins.
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Affiliation(s)
- Lakhan Ekal
- European Molecular Biology Laboratory, Hamburg, Germany.
| | - Ewald Hettema
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
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71
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Reusswig KU, Bittmann J, Peritore M, Courtes M, Pardo B, Wierer M, Mann M, Pfander B. Unscheduled DNA replication in G1 causes genome instability and damage signatures indicative of replication collisions. Nat Commun 2022; 13:7014. [PMID: 36400763 PMCID: PMC9674678 DOI: 10.1038/s41467-022-34379-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/24/2022] [Indexed: 11/19/2022] Open
Abstract
DNA replicates once per cell cycle. Interfering with the regulation of DNA replication initiation generates genome instability through over-replication and has been linked to early stages of cancer development. Here, we engineer genetic systems in budding yeast to induce unscheduled replication in a G1-like cell cycle state. Unscheduled G1 replication initiates at canonical S-phase origins. We quantifiy the composition of replisomes in G1- and S-phase and identified firing factors, polymerase α, and histone supply as factors that limit replication outside S-phase. G1 replication per se does not trigger cellular checkpoints. Subsequent replication during S-phase, however, results in over-replication and leads to chromosome breaks and chromosome-wide, strand-biased occurrence of RPA-bound single-stranded DNA, indicating head-to-tail replication collisions as a key mechanism generating genome instability upon G1 replication. Low-level, sporadic induction of G1 replication induces an identical response, indicating findings from synthetic systems are applicable to naturally occurring scenarios of unscheduled replication initiation.
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Affiliation(s)
- Karl-Uwe Reusswig
- grid.418615.f0000 0004 0491 845XDNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ,grid.38142.3c000000041936754XPresent Address: Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Present Address: Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215 USA
| | - Julia Bittmann
- grid.418615.f0000 0004 0491 845XDNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Martina Peritore
- grid.418615.f0000 0004 0491 845XDNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ,grid.7551.60000 0000 8983 7915Present Address: Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
| | - Mathilde Courtes
- grid.433120.7Institut de Génétique Humaine (IGH), Université de Montpellier – Centre National de la Recherche Scientifique, 34396 Montpellier, France
| | - Benjamin Pardo
- grid.433120.7Institut de Génétique Humaine (IGH), Université de Montpellier – Centre National de la Recherche Scientifique, 34396 Montpellier, France
| | - Michael Wierer
- grid.418615.f0000 0004 0491 845XProteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ,grid.5254.60000 0001 0674 042XPresent Address: Proteomics Research Infrastructure, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Matthias Mann
- grid.418615.f0000 0004 0491 845XProteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Boris Pfander
- grid.418615.f0000 0004 0491 845XDNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany ,grid.7551.60000 0000 8983 7915Present Address: Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany ,grid.6190.e0000 0000 8580 3777Present Address: Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, 50931 Cologne, Germany
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72
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Amodeo ME, Mitchell SPC, Pavan V, Kuehner JN. RNA polymerase II transcription attenuation at the yeast DNA repair gene DEF1 is biologically significant and dependent on the Hrp1 RNA-recognition motif. G3 (BETHESDA, MD.) 2022; 13:6782960. [PMID: 36315099 PMCID: PMC9836349 DOI: 10.1093/g3journal/jkac292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Premature transcription termination (i.e. attenuation) is a potent gene regulatory mechanism that represses mRNA synthesis. Attenuation of RNA polymerase II is more prevalent than once appreciated, targeting 10-15% of mRNA genes in yeast through higher eukaryotes, but its significance and mechanism remain obscure. In the yeast Saccharomyces cerevisiae, polymerase II attenuation was initially shown to rely on Nrd1-Nab3-Sen1 termination, but more recently our laboratory characterized a hybrid termination pathway involving Hrp1, an RNA-binding protein in the 3'-end cleavage factor. One of the hybrid attenuation gene targets is DEF1, which encodes a repair protein that promotes degradation of polymerase II stalled at DNA lesions. In this study, we characterized the chromosomal DEF1 attenuator and the functional role of Hrp1. DEF1 attenuator mutants overexpressed Def1 mRNA and protein, exacerbated polymerase II degradation, and hindered cell growth, supporting a biologically significant DEF1 attenuator function. Using an auxin-induced Hrp1 depletion system, we identified new Hrp1-dependent attenuators in MNR2, SNG1, and RAD3 genes. An hrp1-5 mutant (L205S) known to impair binding to cleavage factor protein Rna14 also disrupted attenuation, but surprisingly no widespread defect was observed for an hrp1-1 mutant (K160E) located in the RNA-recognition motif. We designed a new RNA recognition motif mutant (hrp1-F162W) that altered a highly conserved residue and was lethal in single copy. In a heterozygous strain, hrp1-F162W exhibited dominant-negative readthrough defects at several gene attenuators. Overall, our results expand the hybrid RNA polymerase II termination pathway, confirming that Hrp1-dependent attenuation controls multiple yeast genes and may function through binding cleavage factor proteins and/or RNA.
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Affiliation(s)
- Maria E Amodeo
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Shane P C Mitchell
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Vincent Pavan
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Jason N Kuehner
- Corresponding author: Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA.
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73
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Bensidoun P, Reiter T, Montpetit B, Zenklusen D, Oeffinger M. Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast. Mol Cell 2022; 82:3856-3871.e6. [PMID: 36220102 PMCID: PMC10300651 DOI: 10.1016/j.molcel.2022.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/24/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022]
Abstract
To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding into the nucleoplasm, is thought to function as a stable platform where mRNA-protein complexes (mRNPs) are rearranged and undergo quality control prior to export, ensuring that only mature mRNAs reach the cytoplasm. Here, we use proteomic, genetic, live-cell, and single-molecule resolution microscopy approaches in budding yeast to demonstrate that basket formation is dependent on RNA polymerase II transcription and subsequent mRNP processing. We further show that while all NPCs can bind Mlp1, baskets assemble only on a subset of nucleoplasmic NPCs, and these basket-containing NPCs associate a distinct protein and RNA interactome. Taken together, our data point toward NPC heterogeneity and an RNA-dependent mechanism for functionalization of NPCs in budding yeast through nuclear basket assembly.
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Affiliation(s)
- Pierre Bensidoun
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Taylor Reiter
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Ben Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Daniel Zenklusen
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada.
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
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74
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Hendy O, Serebreni L, Bergauer K, Muerdter F, Huber L, Nemčko F, Stark A. Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers. Mol Cell 2022; 82:3598-3612.e7. [PMID: 36113480 PMCID: PMC7614073 DOI: 10.1016/j.molcel.2022.08.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/13/2022] [Accepted: 08/17/2022] [Indexed: 01/21/2023]
Abstract
Gene transcription is a highly regulated process in all animals. In Drosophila, two major transcriptional programs, housekeeping and developmental, have promoters with distinct regulatory compatibilities and nucleosome organization. However, it remains unclear how the differences in chromatin structure relate to the distinct regulatory properties and which chromatin remodelers are required for these programs. Using rapid degradation of core remodeler subunits in Drosophila melanogaster S2 cells, we demonstrate that developmental gene transcription requires SWI/SNF-type complexes, primarily to maintain distal enhancer accessibility. In contrast, wild-type-level housekeeping gene transcription requires the Iswi and Ino80 remodelers to maintain nucleosome positioning and phasing at promoters. These differential remodeler dependencies relate to different DNA-sequence-intrinsic nucleosome affinities, which favor a default ON state for housekeeping but a default OFF state for developmental gene transcription. Overall, our results demonstrate how different transcription-regulatory strategies are implemented by DNA sequence, chromatin structure, and remodeler activity.
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Affiliation(s)
- Oliver Hendy
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Leonid Serebreni
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Katharina Bergauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Felix Muerdter
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Lukas Huber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Filip Nemčko
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Medical University of Vienna, Vienna BioCenter (VBC), Vienna 1030, Austria.
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75
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Figueiredo MRAD, Strader LC. Intrinsic and extrinsic regulators of Aux/IAA protein degradation dynamics. Trends Biochem Sci 2022; 47:865-874. [PMID: 35817652 PMCID: PMC9464691 DOI: 10.1016/j.tibs.2022.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 01/03/2023]
Abstract
The plant hormone auxin acts through regulated degradation of Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) proteins to regulate transcriptional events. In this review, we examine the composition and function of each Aux/IAA structural motif. We then focus on recent characterization of Aux/IAA N-terminal disordered regions, formation of secondary structure within these disordered regions, and post-translational modifications (PTMs) that affect Aux/IAA function and stability. We propose how structural variations between Aux/IAA family members may be tuned for differential transcriptional repression and degradation dynamics.
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76
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Sepers JJ, Verstappen NHM, Vo AA, Ragle JM, Ruijtenberg S, Ward JD, Boxem M. The mIAA7 degron improves auxin-mediated degradation in Caenorhabditiselegans. G3 (BETHESDA, MD.) 2022; 12:jkac222. [PMID: 36029236 PMCID: PMC9526053 DOI: 10.1093/g3journal/jkac222] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/15/2022] [Indexed: 04/08/2023]
Abstract
Auxin-inducible degradation is a powerful tool for the targeted degradation of proteins with spatiotemporal control. One limitation of the auxin-inducible degradation system is that not all proteins are degraded efficiently. Here, we demonstrate that an alternative degron sequence, termed mIAA7, improves the efficiency of degradation in Caenorhabditiselegans, as previously reported in human cells. We tested the depletion of a series of proteins with various subcellular localizations in different tissue types and found that the use of the mIAA7 degron resulted in faster depletion kinetics for 5 out of 6 proteins tested. The exception was the nuclear protein HIS-72, which was depleted with similar efficiency as with the conventional AID* degron sequence. The mIAA7 degron also increased the leaky degradation for 2 of the tested proteins. To overcome this problem, we combined the mIAA7 degron with the C. elegans AID2 system, which resulted in complete protein depletion without detectable leaky degradation. Finally, we show that the degradation of ERM-1, a highly stable protein that is challenging to deplete, could be improved further by using multiple mIAA7 degrons. Taken together, the mIAA7 degron further increases the power and applicability of the auxin-inducible degradation system. To facilitate the generation of mIAA7-tagged proteins using CRISPR/Cas9 genome engineering, we generated a toolkit of plasmids for the generation of dsDNA repair templates by PCR.
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Affiliation(s)
- Jorian J Sepers
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Noud H M Verstappen
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - An A Vo
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Suzan Ruijtenberg
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mike Boxem
- Division of Developmental Biology, Institute of Biodynamics and Biocomplexity, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
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77
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Li J, Dai C, Xie W, Zhang H, Huang X, Chronis C, Ye Y, Zhang W. A One-step strategy to target essential factors with auxin-inducible degron system in mouse embryonic stem cells. Front Cell Dev Biol 2022; 10:964119. [PMID: 36003152 PMCID: PMC9393215 DOI: 10.3389/fcell.2022.964119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
The self-renewal and pluripotency of embryonic stem cells (ESCs) are conferred by networks including transcription factors and histone modifiers. The Auxin-inducible degron (AID) system can rapidly and reversibly degrade its target proteins and is becoming a powerful tool to explore novel function of key pluripotent and histone modifier genes in ESCs. However, the low biallelic tagging efficiency and a basal degradation level of the current AID systems deem it unsuitable to target key pluripotent genes with tightly controlled expression levels. Here, we develop a one-step strategy to successfully target and repress the endogenous pluripotent genes in mouse ESCs and replace their expression with AID fused transgenes. Therefore, this work provides an efficient way for employing the AID system to uncover novel function of essential pluripotent and chromatin modifier genes in ESCs.
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Affiliation(s)
- Jingsheng Li
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
| | - Chunhong Dai
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
| | - Wenyan Xie
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
| | - Heyao Zhang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
| | - Xin Huang
- Department of Computational Biology St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Constantinos Chronis
- Department of Biochemistry and Molecular Genetics University of Illinois at Chicago, Chicago, IL, United States
| | - Ying Ye
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
- *Correspondence: Ying Ye, ; Wensheng Zhang,
| | - Wensheng Zhang
- Cam-Su Genomic Resource Center, Medical College of Soochow University, Suzhou, China
- Department of Physiology School of Basic Medical Sciences Binzhou Medical University, Yantai, China
- *Correspondence: Ying Ye, ; Wensheng Zhang,
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78
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Lehmayer L, Bernauer L, Emmerstorfer-Augustin A. ‘Applying the auxin-based degron system for the inducible, reversible and complete protein degradation in Komagataella phaffii’. iScience 2022; 25:104888. [PMID: 36043049 PMCID: PMC9420516 DOI: 10.1016/j.isci.2022.104888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 06/10/2022] [Accepted: 08/03/2022] [Indexed: 11/15/2022] Open
Abstract
The auxin-inducible degron (AID) system is a useful technique to rapidly deplete any protein of interest “on-demand.” In this study, we successfully established the AID system for the “biotech” yeast Komagataella phaffii. First, we tested different expression levels of TIR1 for auxin-induced degradation of the glycerol kinase Gut1. Moderate expression of TIR1 resulted in complete degradation of the target protein within several minutes. Second, we show that the absence of all three Wsc type sensors is detrimental to cell growth, which indicates that these are the dominant cell wall sensors this yeast. Third, down-regulation of Erg1, an essential enzyme of the ergosterol biosynthetic pathway, resulted in quick and efficient accumulation of squalene, a pharmaceutically relevant reagent. We conclude that AID is an extremely powerful tool that, for the first time, enables the analysis of gene essentiality and function in K. phaffii. Conditional AID mutants are generated in Komagataella phaffii expressing OsTIR1 Target proteins fused to AID are depleted rapidly on the addition of auxin The deletion of all three Wsc-type severely reduces the growth of K. phaffii Cells degrading Erg1 quickly and efficiently accumulated squalene
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Affiliation(s)
- Leonie Lehmayer
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14/II, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Lukas Bernauer
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14/II, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Anita Emmerstorfer-Augustin
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14/II, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- acib - Austrian Centre of Industrial Biotechnology, 8010 Graz, Austria
- Corresponding author
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79
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Lahiri V, Metur SP, Hu Z, Song X, Mari M, Hawkins WD, Bhattarai J, Delorme-Axford E, Reggiori F, Tang D, Dengjel J, Klionsky DJ. Post-transcriptional regulation of ATG1 is a critical node that modulates autophagy during distinct nutrient stresses. Autophagy 2022; 18:1694-1714. [PMID: 34836487 PMCID: PMC9298455 DOI: 10.1080/15548627.2021.1997305] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023] Open
Abstract
Macroautophagy/autophagy is a highly conserved nutrient-recycling pathway that eukaryotes utilize to combat diverse stresses including nutrient depletion. Dysregulation of autophagy disrupts cellular homeostasis leading to starvation susceptibility in yeast and disease development in humans. In yeast, the robust autophagy response to starvation is controlled by the upregulation of ATG genes, via regulatory processes involving multiple levels of gene expression. Despite the identification of several regulators through genetic studies, the predominant mechanism of regulation modulating the autophagy response to subtle differences in nutrient status remains undefined. Here, we report the unexpected finding that subtle changes in nutrient availability can cause large differences in autophagy flux, governed by hitherto unknown post-transcriptional regulatory mechanisms affecting the expression of the key autophagyinducing kinase Atg1 (ULK1/ULK2 in mammals). We have identified two novel post-transcriptional regulators of ATG1 expression, the kinase Rad53 and the RNA-binding protein Ded1 (DDX3 in mammals). Furthermore, we show that DDX3 regulates ULK1 expression post-transcriptionally, establishing mechanistic conservation and highlighting the power of yeast biology in uncovering regulatory mechanisms that can inform therapeutic approaches.
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Affiliation(s)
- Vikramjit Lahiri
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shree Padma Metur
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Zehan Hu
- Department of Biology, University of Fribourg, FribourgSwitzerland
| | - Xinxin Song
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, GroningenThe Netherlands
| | - Wayne D. Hawkins
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Janakraj Bhattarai
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, GroningenThe Netherlands
| | - Daolin Tang
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joern Dengjel
- Department of Biology, University of Fribourg, FribourgSwitzerland
| | - Daniel J. Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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80
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WASp modulates RPA function on single-stranded DNA in response to replication stress and DNA damage. Nat Commun 2022; 13:3743. [PMID: 35768435 PMCID: PMC9243104 DOI: 10.1038/s41467-022-31415-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Perturbation in the replication-stress response (RSR) and DNA-damage response (DDR) causes genomic instability. Genomic instability occurs in Wiskott-Aldrich syndrome (WAS), a primary immunodeficiency disorder, yet the mechanism remains largely uncharacterized. Replication protein A (RPA), a single-strand DNA (ssDNA) binding protein, has key roles in the RSR and DDR. Here we show that human WAS-protein (WASp) modulates RPA functions at perturbed replication forks (RFs). Following genotoxic insult, WASp accumulates at RFs, associates with RPA, and promotes RPA:ssDNA complexation. WASp deficiency in human lymphocytes destabilizes RPA:ssDNA-complexes, impairs accumulation of RPA, ATR, ETAA1, and TOPBP1 at genotoxin-perturbed RFs, decreases CHK1 activation, and provokes global RF dysfunction. las17 (yeast WAS-homolog)-deficient S. cerevisiae also show decreased ScRPA accumulation at perturbed RFs, impaired DNA recombination, and increased frequency of DNA double-strand break (DSB)-induced single-strand annealing (SSA). Consequently, WASp (or Las17)-deficient cells show increased frequency of DSBs upon genotoxic insult. Our study reveals an evolutionarily conserved, essential role of WASp in the DNA stress-resolution pathway, such that WASp deficiency provokes RPA dysfunction-coupled genomic instability. Cancer develops in Wiskott-Aldrich syndrome (WAS). Here the authors identify a role for WAS-protein (WASp) in the DNA stress-resolution pathway by promoting the function of Replication Protein A at replication forks after DNA damage.
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81
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Macdonald L, Taylor GC, Brisbane JM, Christodoulou E, Scott L, von Kriegsheim A, Rossant J, Gu B, Wood AJ. Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons. eLife 2022; 11:e77987. [PMID: 35736539 PMCID: PMC9273210 DOI: 10.7554/elife.77987] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Auxin-inducible degrons are a chemical genetic tool for targeted protein degradation and are widely used to study protein function in cultured mammalian cells. Here, we develop CRISPR-engineered mouse lines that enable rapid and highly specific degradation of tagged endogenous proteins in vivo. Most but not all cell types are competent for degradation. By combining ligand titrations with genetic crosses to generate animals with different allelic combinations, we show that degradation kinetics depend upon the dose of the tagged protein, ligand, and the E3 ligase substrate receptor TIR1. Rapid degradation of condensin I and II - two essential regulators of mitotic chromosome structure - revealed that both complexes are individually required for cell division in precursor lymphocytes, but not in their differentiated peripheral lymphocyte derivatives. This generalisable approach provides unprecedented temporal control over the dose of endogenous proteins in mouse models, with implications for studying essential biological pathways and modelling drug activity in mammalian tissues.
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Affiliation(s)
- Lewis Macdonald
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Gillian C Taylor
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Jennifer Margaret Brisbane
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Ersi Christodoulou
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Lucy Scott
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Janet Rossant
- Program in Developmental and Stem Cell Biology, Hospital for Sick ChildrenTorontoCanada
| | - Bin Gu
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State UniversityEast LansingUnited States
- Department of Biomedical Engineering; Michigan State UniversityEast LansingUnited States
- Institute for Quantitative Health Science and Engineering, Michigan State UniversityEast LansingUnited States
| | - Andrew J Wood
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
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82
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Chappleboim A, Joseph-Strauss D, Gershon O, Friedman N. Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown. Nucleic Acids Res 2022; 50:5864-5880. [PMID: 35640599 PMCID: PMC9177992 DOI: 10.1093/nar/gkac411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 01/02/2023] Open
Abstract
In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells' total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1-the main 5'-3' mRNA exonuclease-which was previously implicated in balancing mRNA levels. We captured the detailed dynamics of the adaptation to rapid degradation of Xrn1 and observed a significant accumulation of mRNA, followed by a delayed global reduction in transcription and a gradual return to baseline mRNA levels. We found that this transcriptional response is not unique to Xrn1 depletion; rather, it is induced earlier when upstream factors in the 5'-3' degradation pathway are perturbed. Our data suggest that the mRNA feedback mechanism monitors the accumulation of inputs to the 5'-3' exonucleolytic pathway rather than its outputs.
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Affiliation(s)
- Alon Chappleboim
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daphna Joseph-Strauss
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Omer Gershon
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Friedman
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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83
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Matsumoto S, Ono S, Shinoda S, Kakuta C, Okada S, Ito T, Numata T, Endo T. GET pathway mediates transfer of mislocalized tail-anchored proteins from mitochondria to the ER. J Cell Biol 2022; 221:213171. [PMID: 35442388 DOI: 10.1083/jcb.202104076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 01/18/2022] [Accepted: 03/14/2022] [Indexed: 11/22/2022] Open
Abstract
Tail-anchored (TA) membrane proteins have a potential risk to be mistargeted to the mitochondrial outer membrane (OM). Such mislocalized TA proteins can be extracted by the mitochondrial AAA-ATPase Msp1 from the OM and transferred to the ER for ER protein quality control involving ubiquitination by the ER-resident Doa10 complex. Yet it remains unclear how the extracted TA proteins can move to the ER crossing the aqueous cytosol and whether this transfer to the ER is essential for the clearance of mislocalized TA proteins. Here we show by time-lapse microscopy that mislocalized TA proteins, including an authentic ER-TA protein, indeed move from mitochondria to the ER in a manner strictly dependent on Msp1 expression. The Msp1-dependent mitochondria-to-ER transfer of TA proteins is blocked by defects in the GET system, and this block is not due to impaired Doa10 functions. Thus, the GET pathway facilitates the transfer of mislocalized TA proteins from mitochondria to the ER.
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Affiliation(s)
- Shunsuke Matsumoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.,Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Suzuka Ono
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Saori Shinoda
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Chika Kakuta
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Satoshi Okada
- Department of Biochemistry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Ito
- Department of Biochemistry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
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84
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METALIC reveals interorganelle lipid flux in live cells by enzymatic mass tagging. Nat Cell Biol 2022; 24:996-1004. [PMID: 35654841 PMCID: PMC9203272 DOI: 10.1038/s41556-022-00917-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 04/18/2022] [Indexed: 11/08/2022]
Abstract
The distinct activities of organelles depend on the proper function of their membranes. Coordinated membrane biogenesis of different organelles necessitates lipid transport from their site of synthesis to their destination. Several factors have been proposed to participate in lipid distribution, but despite its basic importance, in vivo evidence linking the absence of putative transport pathways to specific transport defects remains scarce. A reason for this scarcity is the near absence of in vivo lipid trafficking assays. Here we introduce a versatile method named METALIC (Mass tagging-Enabled TrAcking of Lipids In Cells) to track interorganelle lipid flux inside cells. In this strategy, two enzymes, one directed to a 'donor' and the other to an 'acceptor' organelle, add two distinct mass tags to lipids. Mass-spectrometry-based detection of lipids bearing the two mass tags is then used to quantify exchange between the two organelles. By applying this approach, we show that the ERMES and Vps13-Mcp1 complexes have transport activity in vivo, and unravel their relative contributions to endoplasmic reticulum-mitochondria lipid exchange.
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85
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Huynh MH, Carruthers VB. Toxoplasma gondii excretion of glycolytic products is associated with acidification of the parasitophorous vacuole during parasite egress. PLoS Pathog 2022; 18:e1010139. [PMID: 35512005 PMCID: PMC9113570 DOI: 10.1371/journal.ppat.1010139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/17/2022] [Accepted: 03/28/2022] [Indexed: 11/19/2022] Open
Abstract
The Toxoplasma gondii lytic cycle is a repetition of host cell invasion, replication, egress, and re-invasion into the next host cell. While the molecular players involved in egress have been studied in greater detail in recent years, the signals and pathways for triggering egress from the host cell have not been fully elucidated. A perforin-like protein, PLP1, has been shown to be necessary for permeabilizing the parasitophorous vacuole (PV) membrane or exit from the host cell. In vitro studies indicated that PLP1 is most active in acidic conditions, and indirect evidence using superecliptic pHluorin indicated that the PV pH drops prior to parasite egress. Using ratiometric pHluorin, a GFP variant that responds to changes in pH with changes in its bimodal excitation spectrum peaks, allowed us to directly measure the pH in the PV prior to and during egress by live-imaging microscopy. A statistically significant change was observed in PV pH during ionomycin or zaprinast induced egress in both wild-type RH and Δplp1 vacuoles compared to DMSO-treated vacuoles. Interestingly, if parasites are chemically paralyzed, a pH drop is still observed in RH but not in Δplp1 tachyzoites. This indicates that the pH drop is dependent on the presence of PLP1 or motility. Efforts to determine transporters, exchangers, or pumps that could contribute to the drop in PV pH identified two formate-nitrite transporters (FNTs). Auxin induced conditional knockdown and knockouts of FNT1 and FNT2 reduced the levels of lactate and pyruvate released by the parasites and lead to an abatement of vacuolar acidification. While additional transporters and molecules are undoubtedly involved, we provide evidence of a definitive reduction in vacuolar pH associated with induced and natural egress and characterize two transporters that contribute to the acidification. Toxoplasma gondii is a single celled intracellular parasite that infects many different animals, and it is thought to infect up to one third of the human population. This parasite must rupture out of its replicative compartment and the host cell to spread from one cell to another. Previous studies indicated that a decrease in pH occurs within the replicative compartment near the time of parasite exit from host cells, an event termed egress. However, it remained unknown whether the decrease in pH is directly tied to egress and, if so, what is responsible for the decrease in pH. Here we used a fluorescent reporter protein to directly measure pH within the replicative compartment during parasite egress. We found that pH decreases immediately prior to parasite egress and that this decrease is linked to parasite disruption of membranes. We also identified a family of transporters that release acidic products from parasite use of glucose for energy as contributing to the decrease in pH during egress. Our findings provide new insight that connects parasite glucose metabolism to acidification of its replicative compartment during egress from infected cells.
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Affiliation(s)
- My-Hang Huynh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Vern B. Carruthers
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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86
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Herod SG, Dyatel A, Hodapp S, Jovanovic M, Berchowitz LE. Clearance of an amyloid-like translational repressor is governed by 14-3-3 proteins. Cell Rep 2022; 39:110753. [PMID: 35508136 PMCID: PMC9156962 DOI: 10.1016/j.celrep.2022.110753] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/24/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Amyloids are fibrous protein aggregates associated with age-related diseases. While these aggregates are typically described as irreversible and pathogenic, some cells use reversible amyloid-like structures that serve important functions. The RNA-binding protein Rim4 forms amyloid-like assemblies that are essential for translational control during Saccharomyces cerevisiae meiosis. Rim4 amyloid-like assemblies are disassembled in a phosphorylation-dependent manner at meiosis II onset. By investigating Rim4 clearance, we elucidate co-factors that mediate clearance of amyloid-like assemblies in a physiological setting. We demonstrate that yeast 14-3-3 proteins bind to Rim4 assemblies and facilitate their subsequent phosphorylation and timely clearance. Furthermore, distinct 14-3-3 proteins play non-redundant roles in facilitating phosphorylation and clearance of amyloid-like Rim4. Additionally, we find that 14-3-3 proteins contribute to global protein aggregate homeostasis. Based on the role of 14-3-3 proteins in aggregate homeostasis and their interactions with disease-associated assemblies, we propose that these proteins may protect against pathological protein aggregates.
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Affiliation(s)
- S Grace Herod
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA; Taub Institute for Research on Alzheimer's and the Aging Brain, New York, NY, USA
| | - Annie Dyatel
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Stefanie Hodapp
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Luke E Berchowitz
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY, USA; Taub Institute for Research on Alzheimer's and the Aging Brain, New York, NY, USA.
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87
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Xie L, Dong P, Qi Y, Hsieh THS, English BP, Jung S, Chen X, De Marzio M, Casellas R, Chang HY, Zhang B, Tjian R, Liu Z. BRD2 compartmentalizes the accessible genome. Nat Genet 2022; 54:481-491. [PMID: 35410381 PMCID: PMC9099420 DOI: 10.1038/s41588-022-01044-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/01/2022] [Indexed: 12/15/2022]
Abstract
Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associated domains (TADs). While the formation of TADs is dependent on Cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after Cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on one hand by Cohesin and on the other by the BET homolog protein BRD4, both of which inhibit BRD2 binding to chromatin. Polymer simulation of our data supports a BRD2-Cohesin interplay model of nuclear topology, where genome compartmentalization results from a competition between loop extrusion and chromatin state-specific affinity interactions.
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88
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Pascual-Garcia P, Little SC, Capelson M. Nup98-dependent transcriptional memory is established independently of transcription. eLife 2022; 11:e63404. [PMID: 35289742 PMCID: PMC8923668 DOI: 10.7554/elife.63404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/26/2022] [Indexed: 12/31/2022] Open
Abstract
Cellular ability to mount an enhanced transcriptional response upon repeated exposure to external cues is termed transcriptional memory, which can be maintained epigenetically through cell divisions and can depend on a nuclear pore component Nup98. The majority of mechanistic knowledge on transcriptional memory has been derived from bulk molecular assays. To gain additional perspective on the mechanism and contribution of Nup98 to memory, we used single-molecule RNA FISH (smFISH) to examine the dynamics of transcription in Drosophila cells upon repeated exposure to the steroid hormone ecdysone. We combined smFISH with mathematical modeling and found that upon hormone exposure, cells rapidly activate a low-level transcriptional response, but simultaneously begin a slow transition into a specialized memory state characterized by a high rate of expression. Strikingly, our modeling predicted that this transition between non-memory and memory states is independent of the transcription stemming from initial activation. We confirmed this prediction experimentally by showing that inhibiting transcription during initial ecdysone exposure did not interfere with memory establishment. Together, our findings reveal that Nup98's role in transcriptional memory is to stabilize the forward rate of conversion from low to high expressing state, and that induced genes engage in two separate behaviors - transcription itself and the establishment of epigenetically propagated transcriptional memory.
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Affiliation(s)
- Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Shawn C Little
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Maya Capelson
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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89
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Wegmann S, Meister C, Renz C, Yakoub G, Wollscheid HP, Takahashi DT, Mikicic I, Beli P, Ulrich HD. Linkage reprogramming by tailor-made E3s reveals polyubiquitin chain requirements in DNA-damage bypass. Mol Cell 2022; 82:1589-1602.e5. [PMID: 35263628 PMCID: PMC9098123 DOI: 10.1016/j.molcel.2022.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/05/2022] [Accepted: 02/08/2022] [Indexed: 12/22/2022]
Abstract
A polyubiquitin chain can adopt a variety of shapes, depending on how the ubiquitin monomers are joined. However, the relevance of linkage for the signaling functions of polyubiquitin chains is often poorly understood because of our inability to control or manipulate this parameter in vivo. Here, we present a strategy for reprogramming polyubiquitin chain linkage by means of tailor-made, linkage- and substrate-selective ubiquitin ligases. Using the polyubiquitylation of the budding yeast replication factor PCNA in response to DNA damage as a model case, we show that altering the features of a polyubiquitin chain in vivo can change the fate of the modified substrate. We also provide evidence for redundancy between distinct but structurally similar linkages, and we demonstrate by proof-of-principle experiments that the method can be generalized to targets beyond PCNA. Our study illustrates a promising approach toward the in vivo analysis of polyubiquitin signaling.
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Affiliation(s)
- Sabrina Wegmann
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Cindy Meister
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Christian Renz
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - George Yakoub
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | | | - Diane T Takahashi
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, 10413 Illkirch, Strasbourg, France
| | - Ivan Mikicic
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany.
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90
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Tsirkas I, Dovrat D, Thangaraj M, Brouwer I, Cohen A, Paleiov Z, Meijler MM, Lenstra T, Aharoni A. Transcription-replication coordination revealed in single live cells. Nucleic Acids Res 2022; 50:2143-2156. [PMID: 35137218 PMCID: PMC8887460 DOI: 10.1093/nar/gkac069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/04/2022] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
The coexistence of DNA replication and transcription during S-phase requires their tight coordination to prevent harmful conflicts. While extensive research revealed important mechanisms for minimizing these conflicts and their consequences, little is known regarding how the replication and transcription machinery are coordinated in real-time. Here, we developed a live-cell imaging approach for the real-time monitoring of replisome progression and transcription dynamics during a transcription-replication encounter. We found a wave of partial transcriptional repression ahead of the moving replication fork, which may contribute to efficient fork progression through the transcribed gene. Real-time detection of conflicts revealed their negative impact on both processes, leading to fork stalling or slowdown as well as lower transcription levels during gene replication, with different trade-offs observed in defined subpopulations of cells. Our real-time measurements of transcription-replication encounters demonstrate how these processes can proceed simultaneously while maintaining genomic stability, and how conflicts can arise when coordination is impaired.
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Affiliation(s)
- Ioannis Tsirkas
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Manikandan Thangaraj
- The Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Ineke Brouwer
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute,1066CX Amsterdam, The Netherlands
| | - Amit Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Zohar Paleiov
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Michael M Meijler
- The Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Tineke Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute,1066CX Amsterdam, The Netherlands
| | - Amir Aharoni
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
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91
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Hills-Muckey K, Martinez MAQ, Stec N, Hebbar S, Saldanha J, Medwig-Kinney TN, Moore FEQ, Ivanova M, Morao A, Ward JD, Moss EG, Ercan S, Zinovyeva AY, Matus DQ, Hammell CM. An engineered, orthogonal auxin analog/AtTIR1(F79G) pairing improves both specificity and efficacy of the auxin degradation system in Caenorhabditis elegans. Genetics 2022; 220:iyab174. [PMID: 34739048 PMCID: PMC9097248 DOI: 10.1093/genetics/iyab174] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
The auxin-inducible degradation system in C. elegans allows for spatial and temporal control of protein degradation via heterologous expression of a single Arabidopsis thaliana F-box protein, transport inhibitor response 1 (AtTIR1). In this system, exogenous auxin (Indole-3-acetic acid; IAA) enhances the ability of AtTIR1 to function as a substrate recognition component that adapts engineered degron-tagged proteins to the endogenous C. elegans E3 ubiquitin ligases complex [SKR-1/2-CUL-1-F-box (SCF)], targeting them for degradation by the proteosome. While this system has been employed to dissect the developmental functions of many C. elegans proteins, we have found that several auxin-inducible degron (AID)-tagged proteins are constitutively degraded by AtTIR1 in the absence of auxin, leading to undesired loss-of-function phenotypes. In this manuscript, we adapt an orthogonal auxin derivative/mutant AtTIR1 pair [C. elegans AID version 2 (C.e.AIDv2)] that transforms the specificity of allosteric regulation of TIR1 from IAA to one that is dependent on an auxin derivative harboring a bulky aryl group (5-Ph-IAA). We find that a mutant AtTIR1(F79G) allele that alters the ligand-binding interface of TIR1 dramatically reduces ligand-independent degradation of multiple AID*-tagged proteins. In addition to solving the ectopic degradation problem for some AID-targets, the addition of 5-Ph-IAA to culture media of animals expressing AtTIR1(F79G) leads to more penetrant loss-of-function phenotypes for AID*-tagged proteins than those elicited by the AtTIR1-IAA pairing at similar auxin analog concentrations. The improved specificity and efficacy afforded by the mutant AtTIR1(F79G) allele expand the utility of the AID system and broaden the number of proteins that can be effectively targeted with it.
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Affiliation(s)
| | - Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Natalia Stec
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Shilpa Hebbar
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Joanne Saldanha
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Taylor N Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Frances E Q Moore
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Maria Ivanova
- Department of Molecular Biology, Rowan University, Stratford, NJ 08084, USA
| | - Ana Morao
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - J D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eric G Moss
- Department of Molecular Biology, Rowan University, Stratford, NJ 08084, USA
| | - Sevinc Ercan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Anna Y Zinovyeva
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
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92
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Negishi T, Kitagawa S, Horii N, Tanaka Y, Haruta N, Sugimoto A, Sawa H, Hayashi KI, Harata M, Kanemaki MT. The auxin-inducible degron 2 (AID2) system enables controlled protein knockdown during embryogenesis and development in Caenorhabditis elegans. Genetics 2022; 220:iyab218. [PMID: 34865044 PMCID: PMC9208642 DOI: 10.1093/genetics/iyab218] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/18/2021] [Indexed: 01/09/2023] Open
Abstract
Targeted protein degradation using the auxin-inducible degron (AID) system is garnering attention in the research field of Caenorhabditis elegans, because of the rapid and efficient target depletion it affords, which can be controlled by treating the animals with the phytohormone auxin. However, the current AID system has drawbacks, i.e., leaky degradation in the absence of auxin and the requirement for high auxin doses. Furthermore, it is challenging to deplete degron-fused proteins in embryos because of their eggshell, which blocks auxin permeability. Here, we apply an improved AID2 system utilizing AtTIR1(F79G) and 5-phenyl-indole-3-acetic acid (5-Ph-IAA) to C. elegans and demonstrated that it confers better degradation control vs the previous system by suppressing leaky degradation and inducing sharp degradation using 1,300-fold lower 5-Ph-IAA doses. We successfully degraded the endogenous histone H2A.Z protein fused to an mAID degron and disclosed its requirement in larval growth and reproduction, regardless of the presence of maternally inherited H2A.Z molecules. Moreover, we developed an eggshell-permeable 5-Ph-IAA analog, 5-Ph-IAA-AM, that affords an enhanced degradation in laid embryos. Our improved system will contribute to the disclosure of the roles of proteins in C. elegans, in particular those that are involved in embryogenesis and development, through temporally controlled protein degradation.
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Affiliation(s)
- Takefumi Negishi
- Multicellular Organization Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Saho Kitagawa
- Laboratory of Molecular Biology, Division of Life Science, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-0845, Japan
| | - Natsumi Horii
- Laboratory of Molecular Biology, Division of Life Science, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-0845, Japan
| | - Yuka Tanaka
- Department of Biochemistry, Okayama University of Science, Okayama 700-0005, Japan
| | - Nami Haruta
- Laboratory of Developmental Dynamics, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Asako Sugimoto
- Laboratory of Developmental Dynamics, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Hitoshi Sawa
- Multicellular Organization Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Ken-ichiro Hayashi
- Department of Biochemistry, Okayama University of Science, Okayama 700-0005, Japan
| | - Masahiko Harata
- Laboratory of Molecular Biology, Division of Life Science, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-0845, Japan
| | - Masato T Kanemaki
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
- Molecular Cell Engineering Laboratory, Department of Chromosome Science, National Institute of Genetics, ROIS, Mishima, Shizuoka 411-8540, Japan
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93
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Joo JH, Kang HA, Kim KP, Hong S. Meiotic prophase roles of Pds5 in recombination and chromosome condensation in budding yeast. J Microbiol 2022; 60:177-186. [PMID: 35102525 DOI: 10.1007/s12275-022-1635-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
Abstract
Genetic variation in eukaryotes is mediated during meiosis by the exchange of genetic material between homologous chromosomes to produce recombinant chromosomes. Cohesin is essential to promote proper chromosome segregation, chromosome morphogenesis, and recombination in meiotic cells. Cohesin consists of three main subunits-Smc1, Smc3, and the kleisin subunit Mcd1/Scc1 (Rec8 in meiosis)-and cohesin accessory factors. In Saccharomyces cerevisiae, the cohesin regulatory subunit Pds5 plays a role in homolog pairing, meiotic axis formation, and interhomolog recombination. In this study, we examine the prophase functions of Pds5 by performing physical analysis of recombination and three-dimensional high-resolution microscopy analysis to identify its roles in meiosis-specific recombination and chromosome morphogenesis. To investigate whether Pds5 plays a role in mitotic-like recombination, we inhibited Mek1 kinase activity, which resulted in switching to sister template bias by Rad51-dependent recombination. Reductions in double-strand breaks and crossover products and defective interhomolog recombination occurred in the absence of Pds5. Furthermore, recombination intermediates, including single-end invasion and double-Holliday junction, were reduced in the absence of Pds5 with Mek1 kinase inactivation compared to Mek1 kinase inactivation cells. Interestingly, the absence of Pds5 resulted in increasing numbers of chromosomes with hypercompaction of the chromosome axis. Thus, we suggest that Pds5 plays an essential role in recombination by suppressing the pairing of sister chromatids and abnormal compaction of the chromosome axis.
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Affiliation(s)
- Jeong Hwan Joo
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyun Ah Kang
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Keun Pil Kim
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Soogil Hong
- Department of Life Sciences, Chung-Ang University, Seoul, 06974, Republic of Korea.
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94
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Kanemaki MT. Ligand-induced degrons for studying nuclear functions. Curr Opin Cell Biol 2022; 74:29-36. [DOI: 10.1016/j.ceb.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 01/21/2023]
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95
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Oz T, Mengoli V, Rojas J, Jonak K, Braun M, Zagoriy I, Zachariae W. The Spo13/Meikin pathway confines the onset of gamete differentiation to meiosis II in yeast. EMBO J 2022; 41:e109446. [PMID: 35023198 PMCID: PMC8844990 DOI: 10.15252/embj.2021109446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 11/09/2022] Open
Abstract
Sexual reproduction requires genome haploidization by the two divisions of meiosis and a differentiation program to generate gametes. Here, we have investigated how sporulation, the yeast equivalent of gamete differentiation, is coordinated with progression through meiosis. Spore differentiation is initiated at metaphase II when a membrane-nucleating structure, called the meiotic plaque, is assembled at the centrosome. While all components of this structure accumulate already at entry into meiosis I, they cannot assemble because centrosomes are occupied by Spc72, the receptor of the γ-tubulin complex. Spc72 is removed from centrosomes by a pathway that depends on the polo-like kinase Cdc5 and the meiosis-specific kinase Ime2, which is unleashed by the degradation of Spo13/Meikin upon activation of the anaphase-promoting complex at anaphase I. Meiotic plaques are finally assembled upon reactivation of Cdk1 at entry into metaphase II. This unblocking-activation mechanism ensures that only single-copy genomes are packaged into spores and might serve as a paradigm for the regulation of other meiosis II-specific processes.
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Affiliation(s)
- Tugce Oz
- Laboratory of Chromosome Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Valentina Mengoli
- Laboratory of Chromosome Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Julie Rojas
- Laboratory of Chromosome Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Katarzyna Jonak
- Laboratory of Chromosome Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marianne Braun
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Ievgeniia Zagoriy
- Laboratory of Chromosome Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Zachariae
- Laboratory of Chromosome Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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96
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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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97
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Aksenova V, Arnaoutov A, Dasso M. Analysis of Nucleoporin Function Using Inducible Degron Techniques. Methods Mol Biol 2022; 2502:129-150. [PMID: 35412236 PMCID: PMC11098028 DOI: 10.1007/978-1-0716-2337-4_9] [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] [Indexed: 06/14/2023]
Abstract
Over the last decade, the use of auxin-inducible degrons (AID) to control the stability of target proteins has revolutionized the field of cell biology. AID-mediated degradation helps to overcome multiple hurdles that have been encountered in studying multisubunit protein complexes, like the nuclear pore complex (NPC), using classical biochemical and genetic methods. We have used the AID system for acute depletion of individual members of the NPC, called nucleoporins, in order to distinguish their roles both within established NPCs and during NPC assembly.Here, we describe a protocol for CRISPR/Cas9-mediated gene targeting of genes with the AID tag. As an example, we describe a step-by-step protocol for targeting of the NUP153 gene. We also provide recommendations for screening strategies and integration of the sequence encoding the Transport Inhibitor Response 1 (TIR1) protein, a E3-Ubiquitin ligase subunit necessary for AID-dependent protein degradation. In addition, we discuss applications of the NUP-AID system and functional assays for analysis of NUP-AID tagged cell lines.
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Affiliation(s)
- Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Alexei Arnaoutov
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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98
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Arsenault HE, Ghizzoni JM, Leech CM, Diers AR, Gesta S, Vishnudas VK, Narain NR, Sarangarajan R, Benanti JA. Ubc1 turnover contributes to the spindle assembly checkpoint in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2021; 11:jkab346. [PMID: 34586382 PMCID: PMC8664427 DOI: 10.1093/g3journal/jkab346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022]
Abstract
The spindle assembly checkpoint protects the integrity of the genome by ensuring that chromosomes are properly attached to the mitotic spindle before they are segregated during anaphase. Activation of the spindle checkpoint results in inhibition of the Anaphase-Promoting Complex (APC), an E3 ubiquitin ligase that triggers the metaphase-anaphase transition. Here, we show that levels of Ubc1, an E2 enzyme that functions in complex with the APC, modulate the response to spindle checkpoint activation in Saccharomyces cerevisiae. Overexpression of Ubc1 increased resistance to microtubule poisons, whereas Ubc1 shut-off sensitized cells. We also found that Ubc1 levels are regulated by the spindle checkpoint. Checkpoint activation or direct APC inhibition led to a decrease in Ubc1 levels, charging, and half-life. Additionally, stabilization of Ubc1 prevented its down-regulation by the spindle checkpoint and increased resistance to checkpoint-activating drugs. These results suggest that down-regulation of Ubc1 in response to spindle checkpoint signaling is necessary for a robust cell cycle arrest.
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Affiliation(s)
- Heather E Arsenault
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Julie M Ghizzoni
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Cassandra M Leech
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | | | | | | | | | - Jennifer A Benanti
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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99
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RNA-DNA hybrids regulate meiotic recombination. Cell Rep 2021; 37:110097. [PMID: 34879269 DOI: 10.1016/j.celrep.2021.110097] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/26/2021] [Accepted: 11/14/2021] [Indexed: 01/07/2023] Open
Abstract
RNA-DNA hybrids are often associated with genome instability and also function as a cellular regulator in many biological processes. In this study, we show that accumulated RNA-DNA hybrids cause multiple defects in budding yeast meiosis, including decreased sporulation efficiency and spore viability. Further analysis shows that these RNA-DNA hybrid foci colocalize with RPA/Rad51 foci on chromosomes. The efficient formation of RNA-DNA hybrid foci depends on Rad52 and ssDNA ends of meiotic DNA double-strand breaks (DSBs), and their number is correlated with DSB frequency. Interestingly, RNA-DNA hybrid foci and recombination foci show similar dynamics. The excessive accumulation of RNA-DNA hybrids around DSBs competes with Rad51/Dmc1, impairs homolog bias, and decreases crossover and noncrossover recombination. Furthermore, precocious removal of RNA-DNA hybrids by RNase H1 overexpression also impairs meiotic recombination similarly. Taken together, our results demonstrate that RNA-DNA hybrids form at ssDNA ends of DSBs to actively regulate meiotic recombination.
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100
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Hayashi H, Kishi T. A Set of Plasmid-Based Modules for Easy Switching of C-Terminal Epitope Tags in Saccharomyces cerevisiae. Microorganisms 2021; 9:2505. [PMID: 34946108 PMCID: PMC8707574 DOI: 10.3390/microorganisms9122505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Epitope tagging is a powerful strategy for analyzing the functions of targeted proteins. The use of this strategy has become more convenient with the development of the epitope switch, which is another type of epitope tagging designed to convert the previously tagged epitopes on the chromosome to other epitopes of interest. Various modules for C-terminal epitope switching have been developed and amplified using the one-step polymerase chain reaction (PCR) method before transformation. However, PCR amplification occasionally generates mutations that affect the fidelity of epitope switching. Here, we constructed several plasmids to isolate modules for epitope switching through digestion by restriction enzymes. The isolated modules contained DNA sequences for homologous recombination, various epitopes (13×Myc, 6×HA, GFP, Venus, YFP, mCherry, and CFP), and a transformation marker (Candida glabrata LEU2). The restriction enzyme-digested plasmids were used to directly transform the cells for epitope switching. We demonstrate the efficient and accurate switching of the MX6 module-based C-terminal tandem affinity purification tags to each aforementioned epitope. We believe that our plasmids can serve as powerful tools for the functional analysis of yeast proteins.
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Affiliation(s)
| | - Tsutomu Kishi
- College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan;
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