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Liu X, Zhang Y, Wen Z, Hao Y, Banks CAS, Cesare J, Bhattacharya S, Arvindekar S, Lange JJ, Xie Y, Garcia BA, Slaughter BD, Unruh JR, Viswanath S, Florens L, Workman JL, Washburn MP. An integrated structural model of the DNA damage-responsive H3K4me3 binding WDR76:SPIN1 complex with the nucleosome. Proc Natl Acad Sci U S A 2024; 121:e2318601121. [PMID: 39116123 PMCID: PMC11331135 DOI: 10.1073/pnas.2318601121] [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: 11/06/2023] [Accepted: 06/21/2024] [Indexed: 08/10/2024] Open
Abstract
Serial capture affinity purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross-linking mass spectrometry and computational approaches, one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone reader that recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were enriched with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in the DNA damage response. Since we detected 149 pairs of cross-links between WDR76, SPIN1, and histones, we then built an integrated structural model of the complex where SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Finally, we used the powerful Bayesian Integrative Modeling approach as implemented in the Integrative Modeling Platform to build a model of WDR76 and SPIN1 bound to the nucleosome.
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Affiliation(s)
- Xingyu Liu
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Zhihui Wen
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | - Joseph Cesare
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Medical Scientist Training Program, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66150
| | | | - Shreyas Arvindekar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University St. Louis School of Medicine, St. Louis, MO 63110
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University St. Louis School of Medicine, St. Louis, MO 63110
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Shruthi Viswanath
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | | | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO 64110
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Liu X, Zhang Y, Wen Z, Hao Y, Banks CAS, Lange JJ, Cesare J, Bhattacharya S, Slaughter BD, Unruh JR, Florens L, Workman JL, Washburn MP. Serial Capture Affinity Purification and Integrated Structural Modeling of the H3K4me3 Binding and DNA Damage Related WDR76:SPIN1 Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526478. [PMID: 36778327 PMCID: PMC9915617 DOI: 10.1101/2023.01.31.526478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
WDR76 is a multifunctional protein involved in many cellular functions. With a diverse and complicated protein interaction network, dissecting the structure and function of specific WDR76 complexes is needed. We previously demonstrated the ability of the Serial Capture Affinity Purification (SCAP) method to isolate specific complexes by introducing two proteins of interest as baits at the same time. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone marker reader that specifically recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to the SCAP analysis of the SPIN1:SPINDOC complex, H3K4me3 was copurified with the WDR76:SPIN1 complex. In combination with crosslinking mass spectrometry, we built an integrated structural model of the complex which revealed that SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Lastly, interaction network analysis of copurifying proteins revealed the potential role of the WDR76:SPIN1 complex in the DNA damage response. Teaser In contrast to the SPINDOC/SPIN1 complex, analyses reveal that the WDR76/SPIN1 complex interacts with core histones and is involved in DNA damage.
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HDA-2-Containing Complex Is Required for Activation of Catalase-3 Expression in Neurospora crassa. mBio 2022; 13:e0135122. [PMID: 35699373 PMCID: PMC9426557 DOI: 10.1128/mbio.01351-22] [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] [Indexed: 11/20/2022] Open
Abstract
It is essential for aerobic organisms to maintain the homeostasis of intracellular reactive oxygen species (ROS) for survival and adaptation to the environment. In line with other eukaryotes, the catalase of Neurospora crassa is an important enzyme for clearing ROS, and its expression is tightly regulated by the growth phase and various oxidative stresses. Our study reveals that, in N. crassa, histone deacetylase 2 (HDA-2) and its catalytic activity positively regulate the expression of the catalase-3 (cat-3) gene. HDA-2, SIF-2, and SNT-1 may form a subcomplex with such a regulation role. As expected, deletion of HDA-2 or SIF-2 subunit increased acetylation levels of histone H4, indicating that loss of HDA-2 complex fails to deacetylate H4 at the cat-3 locus. Furthermore, loss of HDA-2 or its catalytic activity led to dramatic decreases of TFIIB and RNA polymerase II (RNAP II) recruitment at the cat-3 locus and also resulted in high deposition of H2A.Z at the promoter and transcription start site (TSS) regions of the cat-3 gene. Collectively, this study strongly demonstrates that the HDA-2-containing complex activates the transcription of the cat-3 gene by facilitating preinitiation complex (PIC) assembly and antagonizing the inhibition of H2A.Z at the cat-3 locus through H4 acetylation. IMPORTANCE Clearance of reactive oxygen species (ROS) is critical to the survival of aerobic organisms. In the model filamentous fungus Neurospora crassa, catalase-3 (cat-3) expression is activated in response to H2O2-induced ROS stress. We found that histone deacetylase 2 (HDA-2) positively regulates cat-3 transcription in N. crassa; this is widely divergent from the classical repressive role of most histone deacetylases. Like HDA-2, the SIF-2 or SNT-1 subunit of HDA-2-containing complex plays a positive role in cat-3 transcription. Furthermore, we also found that HDA-2-containing complex provides an appropriate chromatin environment to facilitate PIC assembly and to antagonize the inhibition role of H2A.Z at the cat-3 locus through H4 acetylation. Taken together, our results establish a mechanism for how the HDA-2-containing complex regulates transcription of the cat-3 gene in N. crassa.
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Dayebgadoh G, Sardiu ME, Florens L, Washburn MP. Biochemical Reduction of the Topology of the Diverse WDR76 Protein Interactome. J Proteome Res 2019; 18:3479-3491. [PMID: 31353912 DOI: 10.1021/acs.jproteome.9b00373] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A hub protein in protein interaction networks will typically have a large number of diverse interactions. Determining the core interactions and the function of such a hub protein remains a significant challenge in the study of networks. Proteins with WD40 repeats represent a large class of proteins that can be hub proteins. WDR76 is a poorly characterized WD40 repeat protein with possible involvement in DNA damage repair, cell-cycle progression, apoptosis, gene expression regulation, and protein quality control. WDR76 has a large and diverse interaction network that has made its study challenging. Here we rigorously carry out a series of affinity purification coupled to mass spectrometry (AP-MS) analyses to map out the WDR76 interactome through different biochemical conditions. We apply AP-MS analysis coupled to size-exclusion chromatography to resolve WDR76-based protein complexes. Furthermore, we also show that WDR76 interacts with the CCT complex via its WD40 repeat domain and with DNA-PK-KU, PARP1, GAN, SIRT1, and histones outside of the WD40 domain. An evaluation of the stability of WDR76 interactions led to focused and streamlined reciprocal analyses that validate the interactions with GAN and SIRT1. Overall, the approaches used to study WDR76 would be valuable to study other proteins containing WD40 repeat domains, which are conserved in a large number of proteins in many organisms.
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Affiliation(s)
- Gerald Dayebgadoh
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| | - Mihaela E Sardiu
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| | - Laurence Florens
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States
| | - Michael P Washburn
- Stowers Institute for Medical Research , Kansas City , Missouri 64110 , United States.,Department of Pathology and Laboratory Medicine , The University of Kansas Medical Center , 3901 Rainbow Boulevard , Kansas City , Kansas 66160 , United States
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Mathew V, Tam AS, Milbury KL, Hofmann AK, Hughes CS, Morin GB, Loewen CJR, Stirling PC. Selective aggregation of the splicing factor Hsh155 suppresses splicing upon genotoxic stress. J Cell Biol 2017; 216:4027-4040. [PMID: 28978642 PMCID: PMC5716266 DOI: 10.1083/jcb.201612018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 07/17/2017] [Accepted: 08/22/2017] [Indexed: 12/15/2022] Open
Abstract
Upon genotoxic stress, dynamic relocalization events control DNA repair as well as alterations of the transcriptome and proteome, enabling stress recovery. How these events may influence one another is only partly known. Beginning with a cytological screen of genome stability proteins, we find that the splicing factor Hsh155 disassembles from its partners and localizes to both intranuclear and cytoplasmic protein quality control (PQC) aggregates under alkylation stress. Aggregate sequestration of Hsh155 occurs at nuclear and then cytoplasmic sites in a manner that is regulated by molecular chaperones and requires TORC1 activity signaling through the Sfp1 transcription factor. This dynamic behavior is associated with intron retention in ribosomal protein gene transcripts, a decrease in splicing efficiency, and more rapid recovery from stress. Collectively, our analyses suggest a model in which some proteins evicted from chromatin and undergoing transcriptional remodeling during stress are targeted to PQC sites to influence gene expression changes and facilitate stress recovery.
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Affiliation(s)
- Veena Mathew
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Karissa L Milbury
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Analise K Hofmann
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Christopher S Hughes
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Gregg B Morin
- Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Christopher J R Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada .,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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Gilmore JM, Sardiu ME, Groppe BD, Thornton JL, Liu X, Dayebgadoh G, Banks CA, Slaughter BD, Unruh JR, Workman JL, Florens L, Washburn MP. WDR76 Co-Localizes with Heterochromatin Related Proteins and Rapidly Responds to DNA Damage. PLoS One 2016; 11:e0155492. [PMID: 27248496 PMCID: PMC4889050 DOI: 10.1371/journal.pone.0155492] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/30/2016] [Indexed: 12/21/2022] Open
Abstract
Proteins that respond to DNA damage play critical roles in normal and diseased states in human biology. Studies have suggested that the S. cerevisiae protein CMR1/YDL156w is associated with histones and is possibly associated with DNA repair and replication processes. Through a quantitative proteomic analysis of affinity purifications here we show that the human homologue of this protein, WDR76, shares multiple protein associations with the histones H2A, H2B, and H4. Furthermore, our quantitative proteomic analysis of WDR76 associated proteins demonstrated links to proteins in the DNA damage response like PARP1 and XRCC5 and heterochromatin related proteins like CBX1, CBX3, and CBX5. Co-immunoprecipitation studies validated these interactions. Next, quantitative imaging studies demonstrated that WDR76 was recruited to laser induced DNA damage immediately after induction, and we compared the recruitment of WDR76 to laser induced DNA damage to known DNA damage proteins like PARP1, XRCC5, and RPA1. In addition, WDR76 co-localizes to puncta with the heterochromatin proteins CBX1 and CBX5, which are also recruited to DNA damage but much less intensely than WDR76. This work demonstrates the chromatin and DNA damage protein associations of WDR76 and demonstrates the rapid response of WDR76 to laser induced DNA damage.
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Affiliation(s)
- Joshua M. Gilmore
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Mihaela E. Sardiu
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Brad D. Groppe
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Janet L. Thornton
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Xingyu Liu
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Gerald Dayebgadoh
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Charles A. Banks
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Brian D. Slaughter
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Jay R. Unruh
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Jerry L. Workman
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
| | - Michael P. Washburn
- Stowers Institute for Medical Research, Kansas City, MO, 64110, United States of America
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas, 66160, United States of America
- * E-mail:
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