1
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Hirth A, Fatti E, Netz E, Acebron SP, Papageorgiou D, Švorinić A, Cruciat CM, Karaulanov E, Gopanenko A, Zhu T, Sinning I, Krijgsveld J, Kohlbacher O, Niehrs C. DEAD box RNA helicases are pervasive protein kinase interactors and activators. Genome Res 2024; 34:952-966. [PMID: 38986579 PMCID: PMC11293542 DOI: 10.1101/gr.278264.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
DEAD box (DDX) RNA helicases are a large family of ATPases, many of which have unknown functions. There is emerging evidence that besides their role in RNA biology, DDX proteins may stimulate protein kinases. To investigate if protein kinase-DDX interaction is a more widespread phenomenon, we conducted three orthogonal large-scale screens, including proteomics analysis with 32 RNA helicases, protein array profiling, and kinome-wide in vitro kinase assays. We retrieved Ser/Thr protein kinases as prominent interactors of RNA helicases and report hundreds of binary interactions. We identified members of ten protein kinase families, which bind to, and are stimulated by, DDX proteins, including CDK, CK1, CK2, DYRK, MARK, NEK, PRKC, SRPK, STE7/MAP2K, and STE20/PAK family members. We identified MARK1 in all screens and validated that DDX proteins accelerate the MARK1 catalytic rate. These findings indicate pervasive interactions between protein kinases and DEAD box RNA helicases, and provide a rich resource to explore their regulatory relationships.
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Affiliation(s)
- Alexander Hirth
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls University of Heidelberg, 69120 Heidelberg, Germany
| | - Edoardo Fatti
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls University of Heidelberg, 69120 Heidelberg, Germany
| | - Eugen Netz
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
| | - Sergio P Acebron
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Dimitris Papageorgiou
- Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Andrea Švorinić
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls University of Heidelberg, 69120 Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Cristina-Maria Cruciat
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | | | | | - Tianheng Zhu
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls University of Heidelberg, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Christof Niehrs
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany;
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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2
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Qian J, Peng M, Li Y, Liu W, Zou X, Chen H, Zhou S, Xiao S, Zhou J. Case report: A germline CHEK1 c.613 + 2T>C leads to a splicing error in a family with multiple cancer patients. Front Oncol 2024; 14:1380093. [PMID: 38686193 PMCID: PMC11056527 DOI: 10.3389/fonc.2024.1380093] [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: 02/01/2024] [Accepted: 03/21/2024] [Indexed: 05/02/2024] Open
Abstract
Background Genome instability plays a crucial role in promoting tumor development. Germline mutations in genes responsible for DNA repair are often associated with familial cancer syndromes. A noticeable exception is the CHEK1 gene. Despite its well-established role in homologous recombination, germline mutations in CHEK1 are rarely reported. Case presentation In this report, we present a patient diagnosed with ovarian clear cell carcinoma who has a family history of cancer. Her relatives include a grandfather with esophageal cancer, a father with gastric cancer, and an uncle with a brain tumor. The patient carried a typical genomic profile of clear cell carcinoma including mutations in KRAS, PPP2R1A, and PIK3R1. Importantly, her paired peripheral blood cells harbored a germline CHEK1 mutation, CHEK1 exon 6 c.613 + 2T>C, which was also found in her father. Unfortunately, the CHEK1 status of her grandfather and uncle remains unknown due to the unavailability of their specimens. Further evaluation via RT-PCR confirmed a splicing error in the CHEK1 gene, resulting in truncation at the kinase domain region, indicative of a loss-of-function mutation. Conclusion This case highlights a rare germline CHEK1 mutation within a family with a history of cancer. The confirmed splicing error at the mRNA level underscores the functional consequences of this mutation. Documenting such cases is vital for future evaluation of inheritance patterns, clinical penetrance of the mutation, and its association with specific cancer types.
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Affiliation(s)
- Jun Qian
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Min Peng
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yanan Li
- Molecular Genetics Laboratory, Suzhou Sano Precision Medicine Ltd., Suzhou, China
| | - Wei Liu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xinwei Zou
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huafei Chen
- Molecular Genetics Laboratory, Suzhou Sano Precision Medicine Ltd., Suzhou, China
| | - Sujuan Zhou
- Molecular Genetics Laboratory, Suzhou Sano Precision Medicine Ltd., Suzhou, China
| | - Sheng Xiao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Jinhua Zhou
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
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3
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Saldanha J, Rageul J, Patel JA, Kim H. The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork. Int J Mol Sci 2023; 24:10488. [PMID: 37445667 PMCID: PMC10341514 DOI: 10.3390/ijms241310488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.
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Affiliation(s)
- Joanne Saldanha
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jinal A Patel
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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4
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Gillespie DA. When more is less: heritable gain‐of‐function chk1 mutations impair human fertility. FEBS J 2022; 290:1719-1724. [PMID: 35231158 DOI: 10.1111/febs.16415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022]
Abstract
Heritable loss-of-function mutations in genes encoding key regulators of DNA repair and genome stability can result in degenerative progeroid and/or cancer predisposition syndromes; however, such mutations have never been found to affect the Chk1 protein kinase, despite its central role in DNA damage signalling and checkpoint activation. Remarkably, two recent reports now demonstrate that heritable, gain-of-function mutations within the Chk1 C-terminal regulatory domain can cause female infertility in humans. In vitro, oocytes from individuals heterozygous for such mutant Chk1 alleles fail to undergo the first mitotic division after fertilization owing to arrest in G2 phase of the cell cycle. This arrest results from inhibition of the master regulator of mitosis, the cyclin-dependent kinase CDK1, through the same molecular mechanisms that are engaged by activated Chk1 to impose G2 checkpoint arrest in somatic cells bearing DNA damage. Remarkably, the failure of this first zygotic division in heterozygotes in vitro can be rescued through treatment with selective Chk1 inhibitor drugs, allowing development of apparently normal blastocysts and offering hope that a pharmacological solution to this cause of infertility may be possible.
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Affiliation(s)
- David A. Gillespie
- Instituto de Tecnologías Biomédicas Centro de Investigaciones Biomédicas de Canarias Facultad de Medicina Campus Ciencias de la Salud Universidad de La Laguna España
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5
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Zhang H, Chen T, Wu K, Hou Z, Zhao S, Zhang C, Gao Y, Gao M, Chen ZJ, Zhao H. Dominant mutations in CHK1 cause pronuclear fusion failure and zygote arrest that can be rescued by CHK1 inhibitor. Cell Res 2021; 31:814-817. [PMID: 33953335 PMCID: PMC8249641 DOI: 10.1038/s41422-021-00507-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/08/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Honghui Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Tailai Chen
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China.,Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Keliang Wu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Zhenzhen Hou
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Shigang Zhao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Chuanxin Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Yuan Gao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Ming Gao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China. .,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China. .,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China. .,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China. .,Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Han Zhao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China. .,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China. .,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China.
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6
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Maternal heterozygous mutation in CHEK1 leads to mitotic arrest in human zygotes. Protein Cell 2021; 13:148-154. [PMID: 33948904 PMCID: PMC8783945 DOI: 10.1007/s13238-021-00844-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2021] [Indexed: 11/04/2022] Open
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7
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Day M, Parry-Morris S, Houghton-Gisby J, Oliver AW, Pearl LH. Structural basis for recruitment of the CHK1 DNA damage kinase by the CLASPIN scaffold protein. Structure 2021; 29:531-539.e3. [PMID: 33789090 PMCID: PMC8204404 DOI: 10.1016/j.str.2021.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/11/2021] [Accepted: 03/10/2021] [Indexed: 01/08/2023]
Abstract
CHK1 is a protein kinase that functions downstream of activated ATR to phosphorylate multiple targets as part of intra-S and G2/M DNA damage checkpoints. Its role in allowing cells to survive replicative stress has made it an important target for anti-cancer drug discovery. Activation of CHK1 by ATR depends on their mutual interaction with CLASPIN, a natively unstructured protein that interacts with CHK1 through a cluster of phosphorylation sites in its C-terminal half. We have now determined the crystal structure of the kinase domain of CHK1 bound to a high-affinity motif from CLASPIN. Our data show that CLASPIN engages a conserved site on CHK1 adjacent to the substrate-binding cleft, involved in phosphate sensing in other kinases. The CLASPIN motif is not phosphorylated by CHK1, nor does it affect phosphorylation of a CDC25 substrate peptide, suggesting that it functions purely as a scaffold for CHK1 activation by ATR. Novel crystal forms of the CHK1 kinase domain are reported Nucleotide-bound CHK1 structure Phosphorylated CLASPIN peptide-bound CHK1 structure CHK1-CLASPIN interaction does not affect kinase kinetics
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Affiliation(s)
- Matthew Day
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Sarah Parry-Morris
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Jack Houghton-Gisby
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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8
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Neizer-Ashun F, Bhattacharya R. Reality CHEK: Understanding the biology and clinical potential of CHK1. Cancer Lett 2020; 497:202-211. [PMID: 32991949 DOI: 10.1016/j.canlet.2020.09.016] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/26/2020] [Accepted: 09/20/2020] [Indexed: 12/13/2022]
Abstract
The DNA damage response enables cells to cope with various stresses that threaten genomic integrity. A critical component of this response is the serine/threonine kinase CHK1 which is encoded by the CHEK1 gene. Originally identified as a regulator of the G2/M checkpoint, CHK1 has since been shown to play important roles in DNA replication, mitotic progression, DNA repair, and overall cell cycle regulation. However, the potential of CHK1 as a cancer therapy has not been realized clinically. Herein we expound our current understanding of the principal roles of CHK1 and highlight different avenues for CHK1 targeting in cancer therapy.
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Affiliation(s)
- Fiifi Neizer-Ashun
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104, United States
| | - Resham Bhattacharya
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104, United States; Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, United States; Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104, United States.
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9
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Mai NT, Lan NT, Vu TY, Duong PTM, Tung NT, Phung HTT. Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations. J Mol Graph Model 2020; 100:107648. [PMID: 32653524 DOI: 10.1016/j.jmgm.2020.107648] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/29/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Checkpoint kinase 1 (CHK1) is a serine/threonine-protein kinase that is involved in cell cycle regulation in eukaryotes. Inhibition of CHK1 is thus considered as a promising approach in cancer therapy. In this study, the fast pulling of ligand (FPL) process was applied to predict the relative binding affinities of CHK1 inhibitors using non-equilibrium molecular dynamics (MD) simulations. The work of external harmonic forces to pull the ligand out of the binding cavity strongly correlated with the experimental binding affinity of CHK1 inhibitors with the correlation coefficient of R = -0.88 and an overall root mean square error (RMSE) of 0.99 kcal/mol. The data indicate that the FPL method is highly accurate in predicting the relative binding free energies of CHK1 inhibitors with an affordable CPU time. A new set of molecules were designed based on the molecular modeling of interactions between the known inhibitor and CHK1 as inhibitory candidates. Molecular docking and FPL results exhibited that the binding affinities of developed ligands were similar to the known inhibitor in interaction with the catalytic site of CHK1, producing very potential CHK1 inhibitors of that the inhibitory activities should be further evaluated in vitro.
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Affiliation(s)
- Nguyen Thi Mai
- Laboratory of Theoretical and Computational Biophysics, Ho Chi Minh City, Viet Nam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Ngo Thi Lan
- Institute of Materials Science & Graduate University of Science and Technology, Academy of Science and Technology, Hanoi, Viet Nam
| | - Thien Y Vu
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Phuong Thi Mai Duong
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Nguyen Thanh Tung
- Institute of Materials Science & Graduate University of Science and Technology, Academy of Science and Technology, Hanoi, Viet Nam.
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam.
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10
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Cassidy KB, Bang S, Kurokawa M, Gerber SA. Direct regulation of Chk1 protein stability by E3 ubiquitin ligase HUWE1. FEBS J 2020; 287:1985-1999. [PMID: 31713291 PMCID: PMC7226928 DOI: 10.1111/febs.15132] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 08/19/2019] [Accepted: 11/09/2019] [Indexed: 12/14/2022]
Abstract
The HECT E3 ubiquitin ligase HUWE1 is required for a wide array of important functions in cell biology. Although HUWE1 is known to play a role in DNA damage signaling, the mechanism(s) that underlie this function remain elusive. HUWE1 regulates effectors of DNA replication and genotoxic stress tolerance. However, the loss of HUWE1 can also result in the accrual of significant endogenous DNA damage due to insufficient remediation of replication stress induced by an overabundance of key substrates. We discovered that HUWE1 depletion leads to a significant increase in levels of the single-strand break effector kinase Chk1, independent of the DNA damage response, activation of apical DNA damage repair (DDR) signaling kinases (ATM and ATR), and the tumor suppressor p53. We also identified multiple lysine residues on Chk1 that are polyubiquitinated by HUWE1 in vitro, many of which are within the kinase domain. HUWE1 knockdown also markedly prolonged the protein half-life of Chk1 in steady-state conditions and resulted in greater stabilization of Chk1 protein than depletion of Cul4A, an E3 ubiquitin ligase previously described to control Chk1 abundance. Moreover, prolonged replication stress induced by hydroxyurea or camptothecin resulted in a reduction of Chk1 protein levels, which was rescued by HUWE1 knockdown. Our study indicates that HUWE1 plays a significant role in the regulation of the DDR signaling pathway by directly modulating the abundance of Chk1 protein.
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Affiliation(s)
- Katelyn B. Cassidy
- Department of Molecular & Systems Biology, Geisel School of Medicine, Hanover, NH 03755
| | - Scott Bang
- Department of Biological Sciences, Kent State University, Kent, OH 44242
| | - Manabu Kurokawa
- Department of Molecular & Systems Biology, Geisel School of Medicine, Hanover, NH 03755
- Department of Biological Sciences, Kent State University, Kent, OH 44242
- Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, NH 03756
| | - Scott A. Gerber
- Department of Molecular & Systems Biology, Geisel School of Medicine, Hanover, NH 03755
- Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, NH 03756
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11
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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12
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Chk1 KA1 domain auto-phosphorylation stimulates biological activity and is linked to rapid proteasomal degradation. Sci Rep 2018; 8:17536. [PMID: 30510197 PMCID: PMC6277497 DOI: 10.1038/s41598-018-35616-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/24/2018] [Indexed: 11/08/2022] Open
Abstract
The DNA damage-activated protein kinase Chk1 is known to undergo auto-phosphorylation, however the sites and functional significance of this modification remain poorly understood. We have identified two novel Chk1 auto-phosphorylation sites, threonines 378 and 382 (T378/382), located in a highly conserved motif within the C-terminal Kinase Associated 1 (KA1) domain. T378/382 occur within optimal consensus Chk1 phosphorylation motifs and substitution with phospho-mimetic aspartic acid residues results in a constitutively active mutant Chk1 kinase (Chk1-DD) that arrests cell cycle progression in G2 phase of the cell cycle in the absence of DNA damage. Remarkably, the mutant Chk1-DD protein is also subject to very rapid proteasomal degradation, with a half-life approximately one tenth that of wild-type Chk1. Consistent with this, T378/T382 auto-phosphorylation also accelerates the proteasomal degradation of constitutively active Chk1 KA1 domain structural mutants. T378/382 auto-phosphorylation and accelerated degradation of wild-type Chk1 occurs at low levels during unperturbed growth, but surprisingly, is not augmented in response to genotoxic stress. Taken together, these observations demonstrate that Chk1 T378/T382 auto-phosphorylation within the KA1 domain is linked to kinase activation and rapid proteasomal degradation, and suggest a non-canonical mechanism of regulation.
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Emptage RP, Lemmon MA, Ferguson KM, Marmorstein R. Structural Basis for MARK1 Kinase Autoinhibition by Its KA1 Domain. Structure 2018; 26:1137-1143.e3. [PMID: 30099988 DOI: 10.1016/j.str.2018.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/04/2018] [Accepted: 05/15/2018] [Indexed: 10/28/2022]
Abstract
The kinase associated-1 (KA1) domain is found at the C-terminus of multiple Ser/Thr protein kinases from yeast to humans, and has been assigned autoinhibitory, membrane-binding, and substrate-targeting roles. Here, we report the crystal structure of the MARK1 kinase/UBA domain bound to its autoinhibitory KA1 domain, revealing an unexpected interface at the αD helix and contacts with both the N- and C-lobes of the kinase domain. We confirm the binding interface location in kinetic studies of variants mutated on the kinase domain surface. Together with other MARK kinase structures, the data implicate that the KA1 domain blocks peptide substrate binding. The structure highlights the kinase-specific autoinhibitory binding modes of different KA1 domains, and provides potential new avenues by which to intervene therapeutically in Alzheimer's disease and cancers in which MARK1 or related kinases are implicated.
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Affiliation(s)
- Ryan P Emptage
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Mark A Lemmon
- Department of Pharmacology and Cancer Biology Institute, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kathryn M Ferguson
- Department of Pharmacology and Cancer Biology Institute, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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