1
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Li N, Gao N, Zhai Y. DDK promotes DNA replication initiation: Mechanistic and structural insights. Curr Opin Struct Biol 2023; 78:102504. [PMID: 36525878 DOI: 10.1016/j.sbi.2022.102504] [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: 08/31/2022] [Revised: 10/25/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022]
Abstract
DNA replication initiation in eukaryotes is tightly regulated through two cell-cycle specific processes, replication licensing to install inactive minichromosome maintenance (MCM) double-hexamers (DH) on origins in early G1 phase and origin firing to assemble and activate Cdc45-Mcm2-7-GINS (CMG) helicases upon S phase entry. Two kinases, cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), are responsible for driving the association of replication factors with the MCM-DH to form CMG helicases for origin melting and DNA unwinding and eventually replisomes for bi-directional DNA synthesis. In recent years, cryo-electron microscopy studies have generated a collection of structural snapshots for the stepwise assembly and remodeling of the replication initiation machineries, creating a framework for understanding the regulation of this fundamental process at a molecular level. Very recent progress is the structural characterization of the elusive MCM-DH-DDK complex, which provides insights into mechanisms of kinase activation, substrate recognition and selection, as well as molecular role of DDK-mediated MCM-DH phosphorylation in helicase activation.
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Affiliation(s)
- Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China; National Biomedical Imaging Center, Peking University, Beijing, China.
| | - Yuanliang Zhai
- School of Biological Sciences, The University of Hong Kong, Hong Kong.
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2
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Cheng J, Li N, Huo Y, Dang S, Tye BK, Gao N, Zhai Y. Structural Insight into the MCM double hexamer activation by Dbf4-Cdc7 kinase. Nat Commun 2022; 13:1396. [PMID: 35296675 PMCID: PMC8927117 DOI: 10.1038/s41467-022-29070-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/24/2022] [Indexed: 12/27/2022] Open
Abstract
The Dbf4-dependent kinase Cdc7 (DDK) regulates DNA replication initiation by phosphorylation of the MCM double hexamer (MCM-DH) to promote helicase activation. Here, we determine a series of cryo electron microscopy (cryo-EM) structures of yeast DDK bound to the MCM-DH. These structures, occupied by one or two DDKs, differ primarily in the conformations of the kinase core. The interactions of DDK with the MCM-DH are mediated exclusively by subunit Dbf4 straddling across the hexamer interface on the three N-terminal domains (NTDs) of subunits Mcm2, Mcm6, and Mcm4. This arrangement brings Cdc7 close to its only essential substrate, the N-terminal serine/threonine-rich domain (NSD) of Mcm4. Dbf4 further displaces the NSD from its binding site on Mcm4-NTD, facilitating an immediate targeting of this motif by Cdc7. Moreover, the active center of Cdc7 is occupied by a unique Dbf4 inhibitory loop, which is disengaged when the kinase core assumes wobbling conformations. This study elucidates the versatility of Dbf4 in regulating the ordered multisite phosphorylation of the MCM-DH by Cdc7 kinase during helicase activation.
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Affiliation(s)
- Jiaxuan Cheng
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yunjing Huo
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Bik-Kwoon Tye
- Institute for Advanced Study, The Hong Kong University of Science & Technology, Hong Kong, China. .,Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA.
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China. .,National Biomedical Imaging Center, Peking University, Beijing, 100871, China.
| | - Yuanliang Zhai
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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3
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The yeast Dbf4 Zn 2+ finger domain suppresses single-stranded DNA at replication forks initiated from a subset of origins. Curr Genet 2022; 68:253-265. [PMID: 35147742 PMCID: PMC8976809 DOI: 10.1007/s00294-022-01230-6] [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: 07/13/2021] [Revised: 12/23/2021] [Accepted: 01/06/2022] [Indexed: 11/25/2022]
Abstract
Dbf4 is the cyclin-like subunit for the Dbf4-dependent protein kinase (DDK), required for activating the replicative helicase at DNA replication origin that fire during S phase. Dbf4 also functions as an adaptor, targeting the DDK to different groups of origins and substrates. Here we report a genome-wide analysis of origin firing in a budding yeast mutant, dbf4-zn, lacking the Zn2+ finger domain within the C-terminus of Dbf4. At one group of origins, which we call dromedaries, we observe an unanticipated DNA replication phenotype: accumulation of single-stranded DNA spanning ± 5kbp from the center of the origins. A similar accumulation of single-stranded DNA at origins occurs more globally in pri1-m4 mutants defective for the catalytic subunit of DNA primase and rad53 mutants defective for the S phase checkpoint following DNA replication stress. We propose the Dbf4 Zn2+ finger suppresses single-stranded gaps at replication forks emanating from dromedary origins. Certain origins may impose an elevated requirement for the DDK to fully initiate DNA synthesis following origin activation. Alternatively, dbf4-zn may be defective for stabilizing/restarting replication forks emanating from dromedary origins during replication stress.
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4
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Liu Z, Hu S, Yun Z, Hu W, Zhang S, Luo D. Using dynamic cell communication improves treatment strategies of breast cancer. Cancer Cell Int 2021; 21:275. [PMID: 34034721 PMCID: PMC8145794 DOI: 10.1186/s12935-021-01979-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022] Open
Abstract
Several insights from the clinical treatment of breast cancer patients have revealed that only a portion of patients achieve the expected curative effect after traditional targeted therapy, that surgical treatment may promote the development of cancer metastasis, and that the optimal combination of neoadjuvant chemotherapy and traditional treatment is not clear. Therefore, a more precise classification of breast cancer and selection of treatment methods should be undertaken to improve the efficacy of clinical treatment. In the clinical treatment of breast cancer, cell communication molecules are often selected as therapeutic targets. However, various cell communications are not static. Their dynamic changes are related to communicating cells, communicating molecules, and various intertwined internal and external environmental factors. Understanding the dynamic microenvironment can help us improve therapeutic efficacy and provide new ways to more accurately determine the cancer status. Therefore, this review describes multiple types of cellular communication in the breast cancer microenvironment and incorporates internal and external environmental factors as variable signaling factors in cell communication. Using dynamic and developmental concepts, we summarize the functional changes in signaling molecules and cells to aid in the diagnosis and treatment of breast cancer.
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Affiliation(s)
- Zhibo Liu
- Second Clinic Medical College, The Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Yuzhong District, Chongqing, People's Republic of China
| | - Song Hu
- Thrombosis Center, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Zehui Yun
- Queen Mary School, School of Medicine, Nanchang University, Nanchang, People's Republic of China
| | - Wanshan Hu
- School of Medicine, Forth Clinic Medical College, Nanchang University, Nanchang, People's Republic of China
| | - Shuhua Zhang
- Jiangxi Cardiovascular Research Institute, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Aiguo Road, No. 152, Nanchang, 330006, Jiangxi, People's Republic of China.
| | - Daya Luo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Bayi Road, No. 461, Nanchang, 330006, People's Republic of China.
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5
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Huang J, Shen C, Ye R, Shi Y, Li W. The Effect of Early Maternal Separation Combined With Adolescent Chronic Unpredictable Mild Stress on Behavior and Synaptic Plasticity in Adult Female Rats. Front Psychiatry 2021; 12:539299. [PMID: 33746787 PMCID: PMC7973020 DOI: 10.3389/fpsyt.2021.539299] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 02/05/2021] [Indexed: 12/28/2022] Open
Abstract
Our aims were to evaluate the depression model of early maternal separation (MS) combined with adolescent chronic unpredictable mild stress (CUMS) in female adult SD rats to observe the behavior and the expressions of synaptic proteins in rats and to provide a reference for the screening of antidepressant drug activity. In our study, MS and CUMS were conducted to establish a dual stress model on female rats. Behavioral tests, including the sucrose preference test, open field test, and zero maze test, were used to detect depression-like and anxiety-like behavior of animals. Nissl staining was used to detect the number of neuronal cells in the hippocampus CA1 and DG regions of rats from each group. Synaptophysin (SYN), postsynaptic density-95 (PSD-95), and growth-associated protein-43 (GAP-43) expressions in the hippocampus were detected by western blot. Expression of the hippocampus SYN protein was further detected by immunohistochemistry. Rats in the MS+CUMS group presented more serious depression-like and anxiety-like behavior than in the MS group. Also, few Nissl bodies in the hippocampus CA1 and DG regions, less percentage of SYN-positive cells, and downregulated expressions of SYN, PSD-95, and GAP43 were found in the hippocampus of rats in MS+CUMS group. In conclusion, adult female rats that underwent MS and CUMS performed more critical depression-like and anxiety-like behaviors, and this process may be resulted from synaptic plasticity impairment.
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Affiliation(s)
- Jiawen Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chongkun Shen
- School of Fundamental Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ran Ye
- Heyuan People's Hospital, Heyuan, China.,School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yafei Shi
- School of Fundamental Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weirong Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.,Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
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6
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Abd Wahab S, Remus D. Antagonistic control of DDK binding to licensed replication origins by Mcm2 and Rad53. eLife 2020; 9:58571. [PMID: 32701054 PMCID: PMC7398698 DOI: 10.7554/elife.58571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic replication origins are licensed by the loading of the replicative DNA helicase, Mcm2-7, in inactive double hexameric form around DNA. Subsequent origin activation is under control of multiple protein kinases that either promote or inhibit origin activation, which is important for genome maintenance. Using the reconstituted budding yeast DNA replication system, we find that the flexible N-terminal extension (NTE) of Mcm2 promotes the stable recruitment of Dbf4-dependent kinase (DDK) to Mcm2-7 double hexamers, which in turn promotes DDK phosphorylation of Mcm4 and −6 and subsequent origin activation. Conversely, we demonstrate that the checkpoint kinase, Rad53, inhibits DDK binding to Mcm2-7 double hexamers. Unexpectedly, this function is not dependent on Rad53 kinase activity, suggesting steric inhibition of DDK by activated Rad53. These findings identify critical determinants of the origin activation reaction and uncover a novel mechanism for checkpoint-dependent origin inhibition.
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Affiliation(s)
- Syafiq Abd Wahab
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States.,Weill-Cornell Graduate School of Medical Sciences, New York, United States
| | - Dirk Remus
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States.,Weill-Cornell Graduate School of Medical Sciences, New York, United States
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7
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Wahab SA, Remus D. Antagonistic control of DDK binding to licensed replication origins by Mcm2 and Rad53.. [DOI: 10.1101/2020.05.04.077628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
ABSTRACTEukaryotic replication origins are licensed by the loading of the replicative DNA helicase, Mcm2-7, in inactive double hexameric form around DNA. Subsequent origin activation is under control of multiple protein kinases that either promote or inhibit origin activation, which is important for genome maintenance. Using the reconstituted budding yeast DNA replication system, we find that the flexible N-terminal tail of Mcm2 promotes the stable recruitment of Dbf4-dependent kinase (DDK) to Mcm2-7 double hexamers, which in turn promotes DDK phosphorylation of Mcm4 and -6 and subsequent origin activation. Conversely, we demonstrate that the checkpoint kinase, Rad53, inhibits DDK binding to Mcm2-7 double hexamers. Unexpectedly, this function is not dependent on Rad53 kinase activity, but requires Rad53 activation by trans-autophosphorylation, suggesting steric inhibition of DDK by activated Rad53. These findings identify critical determinants of the origin activation reaction and uncover a novel mechanism for checkpoint-dependent origin inhibition.
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8
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Almawi AW, Scotland MK, Randall JR, Liu L, Martin HK, Sacre L, Shen Y, Pillon MC, Simmons LA, Sutton MD, Guarné A. Binding of the regulatory domain of MutL to the sliding β-clamp is species specific. Nucleic Acids Res 2019; 47:4831-4842. [PMID: 30916336 PMCID: PMC6511837 DOI: 10.1093/nar/gkz115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 01/21/2019] [Accepted: 02/18/2019] [Indexed: 11/15/2022] Open
Abstract
The β-clamp is a protein hub central to DNA replication and fork management. Proteins interacting with the β-clamp harbor a conserved clamp-binding motif that is often found in extended regions. Therefore, clamp interactions have -almost exclusively- been studied using short peptides recapitulating the binding motif. This approach has revealed the molecular determinants that mediate the binding but cannot describe how proteins with clamp-binding motifs embedded in structured domains are recognized. The mismatch repair protein MutL has an internal clamp-binding motif, but its interaction with the β-clamp has different roles depending on the organism. In Bacillus subtilis, the interaction stimulates the endonuclease activity of MutL and it is critical for DNA mismatch repair. Conversely, disrupting the interaction between Escherichia coli MutL and the β-clamp only causes a mild mutator phenotype. Here, we determined the structures of the regulatory domains of E. coli and B. subtilis MutL bound to their respective β-clamps. The structures reveal different binding modes consistent with the binding to the β-clamp being a two-step process. Functional characterization indicates that, within the regulatory domain, only the clamp binding motif is required for the interaction between the two proteins. However, additional motifs beyond the regulatory domain may stabilize the interaction. We propose a model for the activation of the endonuclease activity of MutL in organisms lacking methyl-directed mismatch repair.
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Affiliation(s)
- Ahmad W Almawi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Michelle K Scotland
- Department of Biochemistry, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Witebsky Center for Microbial Pathogenesis and Immunology, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Justin R Randall
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Linda Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Heather K Martin
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lauralicia Sacre
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Yao Shen
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Monica C Pillon
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Lyle A Simmons
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Mark D Sutton
- Department of Biochemistry, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Witebsky Center for Microbial Pathogenesis and Immunology, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Genetics, Genomics and Bioinformatics Program, The Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Alba Guarné
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada
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9
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Deshpande I, Keusch JJ, Challa K, Iesmantavicius V, Gasser SM, Gut H. The Sir4 H-BRCT domain interacts with phospho-proteins to sequester and repress yeast heterochromatin. EMBO J 2019; 38:e101744. [PMID: 31515872 PMCID: PMC6792019 DOI: 10.15252/embj.2019101744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/24/2019] [Accepted: 08/11/2019] [Indexed: 12/22/2022] Open
Abstract
In Saccharomyces cerevisiae, the silent information regulator (SIR) proteins Sir2/3/4 form a complex that suppresses transcription in subtelomeric regions and at the homothallic mating-type (HM) loci. Here, we identify a non-canonical BRCA1 C-terminal domain (H-BRCT) in Sir4, which is responsible for tethering telomeres to the nuclear periphery. We show that Sir4 H-BRCT and the closely related Dbf4 H-BRCT serve as selective phospho-epitope recognition domains that bind to a variety of phosphorylated target peptides. We present detailed structural information about the binding mode of established Sir4 interactors (Esc1, Ty5, Ubp10) and identify several novel interactors of Sir4 H-BRCT, including the E3 ubiquitin ligase Tom1. Based on these findings, we propose a phospho-peptide consensus motif for interaction with Sir4 H-BRCT and Dbf4 H-BRCT. Ablation of the Sir4 H-BRCT phospho-peptide interaction disrupts SIR-mediated repression and perinuclear localization. In conclusion, the Sir4 H-BRCT domain serves as a hub for recruitment of phosphorylated target proteins to heterochromatin to properly regulate silencing and nuclear order.
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Affiliation(s)
- Ishan Deshpande
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of Natural SciencesUniversity of BaselBaselSwitzerland
- Present address:
Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCAUSA
| | - Jeremy J Keusch
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Kiran Challa
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | | | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of Natural SciencesUniversity of BaselBaselSwitzerland
| | - Heinz Gut
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
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10
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Julius J, Peng J, McCulley A, Caridi C, Arnak R, See C, Nugent CI, Feng W, Bachant J. Inhibition of spindle extension through the yeast S phase checkpoint is coupled to replication fork stability and the integrity of centromeric DNA. Mol Biol Cell 2019; 30:2771-2789. [PMID: 31509480 PMCID: PMC6789157 DOI: 10.1091/mbc.e19-03-0156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Budding yeast treated with hydroxyurea (HU) activate the S phase checkpoint kinase Rad53, which prevents DNA replication forks from undergoing aberrant structural transitions and nuclease processing. Rad53 is also required to prevent premature extension of the mitotic spindle that assembles during a HU-extended S phase. Here we present evidence that checkpoint restraint of spindle extension is directly coupled to Rad53 control of replication fork stability. In budding yeast, centromeres are flanked by replication origins that fire in early S phase. Mutations affecting the Zn2+-finger of Dbf4, an origin activator, preferentially reduce centromere-proximal origin firing in HU, corresponding with suppression of rad53 spindle extension. Inactivating Exo1 nuclease or displacing centromeres from origins provides a similar suppression. Conversely, short-circuiting Rad53 targeting of Dbf4, Sld3, and Dun1, substrates contributing to fork stability, induces spindle extension. These results reveal spindle extension in HU-treated rad53 mutants is a consequence of replication fork catastrophes at centromeres. When such catastrophes occur, centromeres become susceptible to nucleases, disrupting kinetochore function and spindle force balancing mechanisms. At the same time, our data indicate centromere duplication is not required to stabilize S phase spindle structure, leading us to propose a model for how monopolar kinetochore-spindle attachments may contribute to spindle force balance in HU.
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Affiliation(s)
- Jeff Julius
- Department of Molecular Cell Systems Biology, University of California, Riverside, Riverside, CA 92521
| | - Jie Peng
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Andrew McCulley
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Chris Caridi
- Department of Molecular Cell Systems Biology, University of California, Riverside, Riverside, CA 92521
| | - Remigiusz Arnak
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Colby See
- Department of Molecular Cell Systems Biology, University of California, Riverside, Riverside, CA 92521
| | - Constance I Nugent
- Department of Molecular Cell Systems Biology, University of California, Riverside, Riverside, CA 92521
| | - Wenyi Feng
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Jeff Bachant
- Department of Molecular Cell Systems Biology, University of California, Riverside, Riverside, CA 92521
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11
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Phospho-peptide binding domains in S. cerevisiae model organism. Biochimie 2019; 163:117-127. [PMID: 31194995 DOI: 10.1016/j.biochi.2019.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
Abstract
Protein phosphorylation is one of the main mechanisms by which signals are transmitted in eukaryotic cells, and it plays a crucial regulatory role in almost all cellular processes. In yeast, more than half of the proteins are phosphorylated in at least one site, and over 20,000 phosphopeptides have been experimentally verified. However, the functional consequences of these phosphorylation events for most of the identified phosphosites are unknown. A family of protein interaction domains selectively recognises phosphorylated motifs to recruit regulatory proteins and activate signalling pathways. Nine classes of dedicated modules are coded by the yeast genome: 14-3-3, FHA, WD40, BRCT, WW, PBD, and SH2. The recognition specificity relies on a few residues on the target protein and has coevolved with kinase specificity. In the present study, we review the current knowledge concerning yeast phospho-binding domains and their networks. We emphasise the relevance of both positive and negative amino acid selection to orchestrate the highly regulated outcomes of inter- and intra-molecular interactions. Finally, we hypothesise that only a small fraction of yeast phosphorylation events leads to the creation of a docking site on the target molecule, while many have a direct effect on the protein or, as has been proposed, have no function at all.
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12
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Wagner T, André-Leroux G, Hindie V, Barilone N, Lisa MN, Hoos S, Raynal B, Vulliez-Le Normand B, O'Hare HM, Bellinzoni M, Alzari PM. Structural insights into the functional versatility of an FHA domain protein in mycobacterial signaling. Sci Signal 2019; 12:12/580/eaav9504. [PMID: 31064884 DOI: 10.1126/scisignal.aav9504] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Forkhead-associated (FHA) domains are modules that bind to phosphothreonine (pThr) residues in signaling cascades. The FHA-containing mycobacterial protein GarA is a central element of a phosphorylation-dependent signaling pathway that redirects metabolic flux in response to amino acid starvation or cell growth requirements. GarA acts as a phosphorylation-dependent ON/OFF molecular switch. In its nonphosphorylated ON state, the GarA FHA domain engages in phosphorylation-independent interactions with various metabolic enzymes that orchestrate nitrogen flow, such as 2-oxoglutarate decarboxylase (KGD). However, phosphorylation at the GarA N-terminal region by the protein kinase PknB or PknG triggers autoinhibition through the intramolecular association of the N-terminal domain with the FHA domain, thus blocking all downstream interactions. To investigate these different FHA binding modes, we solved the crystal structures of the mycobacterial upstream (phosphorylation-dependent) complex PknB-GarA and the downstream (phosphorylation-independent) complex GarA-KGD. Our results show that the phosphorylated activation loop of PknB serves as a docking site to recruit GarA through canonical FHA-pThr interactions. However, the same GarA FHA-binding pocket targets an allosteric site on nonphosphorylated KGD, where a key element of recognition is a phosphomimetic aspartate. Further enzymatic and mutagenesis studies revealed that GarA acted as a dynamic allosteric inhibitor of KGD by preventing crucial motions in KGD that are necessary for catalysis. Our results provide evidence for physiological phosphomimetics, supporting numerous mutagenesis studies using such approaches, and illustrate how evolution can shape a single FHA-binding pocket to specifically interact with multiple phosphorylated and nonphosphorylated protein partners.
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Affiliation(s)
- Tristan Wagner
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Gwénaëlle André-Leroux
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Valérie Hindie
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Nathalie Barilone
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - María-Natalia Lisa
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Sylviane Hoos
- Institut Pasteur, Plateforme de Biophysique Moléculaire, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Bertrand Raynal
- Institut Pasteur, Plateforme de Biophysique Moléculaire, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Brigitte Vulliez-Le Normand
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Helen M O'Hare
- Leicester Tuberculosis Research Group (LTBRG) and Leicester Institute of Structural and Chemical Biology (LISCB), Department of Respiratory Science & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Marco Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.
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Xie C, He C, Jiang Y, Yu H, Cheng L, Nshogoza G, Ala MS, Tian C, Wu J, Shi Y, Li F. Structural insights into the recognition of phosphorylated Hop1 by Mek1. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1027-1038. [PMID: 30289413 DOI: 10.1107/s2059798318011993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/24/2018] [Indexed: 11/10/2022]
Abstract
The FHA domain-containing protein Mek1 is a meiosis-specific kinase that is involved in the regulation of interhomolog recombination in meiosis in Saccharomyces cerevisiae. The recruitment and activation of Mek1 require the phosphorylation of the chromosome axis protein Hop1 at Thr318 (pT318), which is necessary for recognition by the Mek1 FHA domain. Here, crystal structures of the Mek1 FHA domain in the apo state and in complex with the Hop1 pT318 peptide are presented, demonstrating that the hydrophobic residues Phe320 and Val321 at the pT+2 and pT+3 positions in the ligand contribute to the preferential recognition. It was further found that in Schizosaccharomyces pombe Mek1 FHA binds both pT15 in its N-terminal SQ/TQ cluster domain (SCD) and pT270 in the Hop1 SCD. The results revealed the structural basis for the preferential recognition of phosphorylated Hop1 by Mek1 in S. cerevisiae and facilitate the understanding of the interaction between the S. pombe Mek1 FHA domain and its binding targets.
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Affiliation(s)
- Changlin Xie
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Chao He
- Anhui Key Laboratory of Modern Biomanufacturing and School of Life Sciences, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Hailong Yu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Lin Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Moududee Sayed Ala
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Yunyu Shi
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
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14
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VanSchouwen B, Ahmed R, Milojevic J, Melacini G. Functional dynamics in cyclic nucleotide signaling and amyloid inhibition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1529-1543. [PMID: 28911813 DOI: 10.1016/j.bbapap.2017.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/29/2017] [Accepted: 09/07/2017] [Indexed: 12/28/2022]
Abstract
It is now established that understanding the molecular basis of biological function requires atomic resolution maps of both structure and dynamics. Here, we review several illustrative examples of functional dynamics selected from our work on cyclic nucleotide signaling and amyloid inhibition. Although fundamentally diverse, a central aspect common to both fields is that function can only be rationalized by considering dynamic equilibria between distinct states of the accessible free energy landscape. The dynamic exchange between ground and excited states of signaling proteins is essential to explain auto-inhibition and allosteric activation. The dynamic exchange between non-toxic monomeric species and toxic oligomers of amyloidogenic proteins provides a foundation to understand amyloid inhibition. NMR ideally probes both types of dynamic exchange at atomic resolution. Specifically, we will show how NMR was utilized to reveal the dynamical basis of cyclic nucleotide affinity, selectivity, agonism and antagonism in multiple eukaryotic cAMP and cGMP receptors. We will also illustrate how NMR revealed the mechanism of action of plasma proteins that act as extracellular chaperones and inhibit the self-association of the prototypical amyloidogenic Aβ peptide. The examples outlined in this review illustrate the widespread implications of functional dynamics and the power of NMR as an indispensable tool in molecular pharmacology and pathology.
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Affiliation(s)
- Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Julijana Milojevic
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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15
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Almawi AW, Matthews LA, Guarné A. FHA domains: Phosphopeptide binding and beyond. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 127:105-110. [DOI: 10.1016/j.pbiomolbio.2016.12.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/06/2016] [Indexed: 01/18/2023]
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16
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Complementary uses of small angle X-ray scattering and X-ray crystallography. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1623-1630. [PMID: 28743534 DOI: 10.1016/j.bbapap.2017.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/10/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Most proteins function within networks and, therefore, protein interactions are central to protein function. Although stable macromolecular machines have been extensively studied, dynamic protein interactions remain poorly understood. Small-angle X-ray scattering probes the size, shape and dynamics of proteins in solution at low resolution and can be used to study samples in a large range of molecular weights. Therefore, it has emerged as a powerful technique to study the structure and dynamics of biomolecular systems and bridge fragmented information obtained using high-resolution techniques. Here we review how small-angle X-ray scattering can be combined with other structural biology techniques to study protein dynamics. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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17
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Duncker BP. Mechanisms Governing DDK Regulation of the Initiation of DNA Replication. Genes (Basel) 2016; 8:genes8010003. [PMID: 28025497 PMCID: PMC5294998 DOI: 10.3390/genes8010003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 12/14/2022] Open
Abstract
The budding yeast Dbf4-dependent kinase (DDK) complex—comprised of cell division cycle (Cdc7) kinase and its regulatory subunit dumbbell former 4 (Dbf4)—is required to trigger the initiation of DNA replication through the phosphorylation of multiple minichromosome maintenance complex subunits 2-7 (Mcm2-7). DDK is also a target of the radiation sensitive 53 (Rad53) checkpoint kinase in response to replication stress. Numerous investigations have determined mechanistic details, including the regions of Mcm2, Mcm4, and Mcm6 phosphorylated by DDK, and a number of DDK docking sites. Similarly, the way in which the Rad53 forkhead-associated 1 (FHA1) domain binds to DDK—involving both canonical and non-canonical interactions—has been elucidated. Recent work has revealed mutual promotion of DDK and synthetic lethal with dpb11-1 3 (Sld3) roles. While DDK phosphorylation of Mcm2-7 subunits facilitates their interaction with Sld3 at origins, Sld3 in turn stimulates DDK phosphorylation of Mcm2. Details of a mutually antagonistic relationship between DDK and Rap1-interacting factor 1 (Rif1) have also recently come to light. While Rif1 is able to reverse DDK-mediated Mcm2-7 complex phosphorylation by targeting the protein phosphatase glycogen 7 (Glc7) to origins, there is evidence to suggest that DDK can counteract this activity by binding to and phosphorylating Rif1.
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Affiliation(s)
- Bernard P Duncker
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L3G1, Canada.
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