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Warnock JL, Ball JA, Najmi SM, Henes M, Vazquez A, Koshnevis S, Wieden HJ, Conn GL, Ghalei H. Differential roles of putative arginine fingers of AAA + ATPases Rvb1 and Rvb2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593962. [PMID: 38798342 PMCID: PMC11118528 DOI: 10.1101/2024.05.13.593962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The evolutionarily conserved AAA+ ATPases Rvb1 and Rvb2 proteins form a heteromeric complex (Rvb1/2) required for assembly or remodeling of macromolecular complexes in essential cellular processes ranging from chromatin remodeling to ribosome biogenesis. Rvb1 and Rvb2 have a high degree of sequence and structural similarity, and both contain the classical features of ATPases of their clade, including an N-terminal AAA+ subdomain with the Walker A motif, an insertion domain that typically interacts with various binding partners, and a C-terminal AAA+ subdomain containing a Walker B motif, the Sensor I and II motifs, and an arginine finger. In this study, we find that despite the high degree of structural similarity, Rvb1 and Rvb2 have distinct active sites that impact their activities and regulation within the Rvb1/2 complex. Using a combination of biochemical and genetic approaches, we show that replacing the homologous arginine fingers of Rvb1 and Rvb2 with different amino acids not only has distinct effects on the catalytic activity of the complex, but also impacts cell growth, and the Rvb1/2 interactions with binding partners. Using molecular dynamics simulations, we find that changes near the active site of Rvb1 and Rvb2 cause long-range effects on the protein dynamics in the insertion domain, suggesting a molecular basis for how enzymatic activity within the catalytic site of ATP hydrolysis can be relayed to other domains of the Rvb1/2 complex to modulate its function. Further, we show the impact that the arginine finger variants have on snoRNP biogenesis and validate the findings from molecular dynamics simulations using a targeted genetic screen. Together, our results reveal new aspects of the regulation of the Rvb1/2 complex by identifying a relay of long-range molecular communication from the ATPase active site of the complex to the binding site of cofactors. Most importantly, our findings suggest that despite high similarity and cooperation within the same protein complex, the two proteins have evolved with unique properties critical for the regulation and function of the Rvb1/2 complex.
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Affiliation(s)
- Jennifer L. Warnock
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Jacob A. Ball
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Saman M. Najmi
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Mina Henes
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
- Graduate Program in Biochemistry, Cell & Developmental Biology (BCDB), Emory University, Atlanta, Georgia, USA
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Amanda Vazquez
- Department of Microbiology, Faculty of Science, University of Manitoba, Manitoba, Canada
| | - Sohail Koshnevis
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Hans-Joachim Wieden
- Department of Microbiology, Faculty of Science, University of Manitoba, Manitoba, Canada
| | - Graeme L. Conn
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
| | - Homa Ghalei
- Emory University School of Medicine, Department of Biochemistry, Atlanta, Georgia, USA
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2
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Zhang H, Chen C, Zhang EE, Huang X. TDP-43 deficiency in suprachiasmatic nucleus perturbs rhythmicity of neuroactivity in prefrontal cortex. iScience 2024; 27:109522. [PMID: 38585660 PMCID: PMC10995886 DOI: 10.1016/j.isci.2024.109522] [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: 09/25/2023] [Revised: 12/28/2023] [Accepted: 03/14/2024] [Indexed: 04/09/2024] Open
Abstract
Individuals within the amyotrophic lateral sclerosis and frontotemporal dementia disease spectrum (ALS/FTD) often experience disruptive mental behaviors and sleep-wake disturbances. The hallmark of ALS/FTD is the pathological involvement of TAR DNA-binding protein 43 (TDP-43). Understanding the role of TDP-43 in the circadian clock holds promise for addressing these behavioral abnormalities. In this study, we unveil TDP-43 as a pivotal regulator of the circadian clock. TDP-43 knockdown induces intracellular arrhythmicity, disrupts transcriptional activation regulation, and diminishes clock genes expression. Moreover, our experiments in adult mouse reveal that TDP-43 knockdown, specifically within the suprachiasmatic nucleus (SCN), induces locomotor arrhythmia, arrhythmic c-Fos expression, and depression-like behavior. This observation offers valuable insights into the substantial impact of TDP-43 on the behavioral aberrations associated with ALS/FTD. In summary, our study illuminates the significance of TDP-43 in circadian regulation, shedding light on the circadian regulatory mechanisms that may elucidate the pathological underpinnings of ALS/FTD.
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Affiliation(s)
- Hongxia Zhang
- Department of Medical Microbiology, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- National Institute of Biological Sciences, Beijing 102206, China
| | - Chen Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | | | - Xiaotian Huang
- Department of Medical Microbiology, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
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3
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Zhou Q, Wang R, Su Y, Wang B, Zhang Y, Qin X. The molecular circadian rhythms regulating the cell cycle. J Cell Biochem 2024; 125:e30539. [PMID: 38372014 DOI: 10.1002/jcb.30539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/25/2024] [Accepted: 02/02/2024] [Indexed: 02/20/2024]
Abstract
The circadian clock controls the expression of a large proportion of protein-coding genes in mammals and can modulate a wide range of physiological processes. Recent studies have demonstrated that disruption or dysregulation of the circadian clock is involved in the development and progression of several diseases, including cancer. The cell cycle is considered to be the fundamental process related to cancer. Accumulating evidence suggests that the circadian clock can control the expression of a large number of genes related to the cell cycle. This article reviews the mechanism of cell cycle-related genes whose chromatin regulatory elements are rhythmically occupied by core circadian clock transcription factors, while their RNAs are rhythmically expressed. This article further reviews the identified oscillatory cell cycle-related genes in higher organisms such as baboons and humans. The potential functions of these identified genes in regulating cell cycle progression are also discussed. Understanding how the molecular clock controls the expression of cell cycle genes will be beneficial for combating and treating cancer.
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Affiliation(s)
- Qin Zhou
- Institute of Health Sciences and Technology, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Ruohan Wang
- Institute of Health Sciences and Technology, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Yunxia Su
- Institute of Health Sciences and Technology, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Bowen Wang
- Institute of Health Sciences and Technology, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Yunfei Zhang
- Modern Experiment Technology Center, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Ximing Qin
- Institute of Health Sciences and Technology, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
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4
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Liao M, Gao X, Chen C, Li Q, Guo Q, Huang H, Zhang E, Ju D. Integrated neural tracing and in-situ barcoded sequencing reveals the logic of SCN efferent circuits in regulating circadian behaviors. SCIENCE CHINA. LIFE SCIENCES 2024; 67:518-528. [PMID: 38057622 DOI: 10.1007/s11427-023-2420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/30/2023] [Indexed: 12/08/2023]
Abstract
The circadian clock coordinates rhythms in numerous physiological processes to maintain organismal homeostasis. Since the suprachiasmatic nucleus (SCN) is widely accepted as the circadian pacemaker, it is critical to understand the neural mechanisms by which rhythmic information is transferred from the SCN to peripheral clocks. Here, we present the first comprehensive map of SCN efferent connections and suggest a molecular logic underlying these projections. The SCN projects broadly to most major regions of the brain, rather than solely to the hypothalamus and thalamus. The efferent projections from different subtypes of SCN neurons vary in distance and intensity, and blocking synaptic transmission of these circuits affects circadian rhythms in locomotion and feeding to different extents. We also developed a barcoding system to integrate retrograde tracing with in-situ sequencing, allowing us to link circuit anatomy and spatial patterns of gene expression. Analyses using this system revealed that brain regions functioning downstream of the SCN receive input from multiple neuropeptidergic cell types within the SCN, and that individual SCN neurons generally project to a single downstream brain region. This map of SCN efferent connections provides a critical foundation for future investigations into the neural circuits underlying SCN-mediated rhythms in physiology. Further, our new barcoded tracing method provides a tool for revealing the molecular logic of neuronal circuits within heterogeneous brain regions.
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Affiliation(s)
- Meimei Liao
- College of Biological Sciences, China Agriculture University, Beijing, 100193, China
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Xinwei Gao
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Chen Chen
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Qi Li
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
- Tsinghua Institute of Multidisciplinar^ Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Qingchun Guo
- Chinese Institute for Brain Research, Beijing, 102206, China
- School of Biomedical Engineering, Capital Medical University, Beijing, 100069, China
| | - He Huang
- Department of Anesthesiology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 401336, China
| | - Erquan Zhang
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
- Tsinghua Institute of Multidisciplinar^ Biomedical Research, Tsinghua University, Beijing, 102206, China
| | - Dapeng Ju
- Department of Anesthesiology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 401336, China.
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5
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Zhao H, Han G, Jiang Z, Gao D, Zhang H, Yang L, Ma T, Gao L, Wang A, Chao HW, Li Q, Jin Y, Chen H. Identification of BMAL1-Regulated circadian genes in mouse liver and their potential association with hepatocellular carcinoma: Gys2 and Upp2 as promising candidates. Biochem Biophys Res Commun 2024; 696:149422. [PMID: 38183795 DOI: 10.1016/j.bbrc.2023.149422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024]
Abstract
Identification and functional analysis of key genes regulated by the circadian clock system will provide a comprehensive understanding of the underlying mechanisms through which circadian clock disruption impairs the health of living organisms. The initial phase involved bioinformatics analysis, drawing insights from three RNA-seq datasets (GSE184303, GSE114400, and GSE199061) derived from wild-type mouse liver tissues, which encompassed six distinct time points across a day. As expected, 536 overlapping genes exhibiting rhythmic expression patterns were identified. By intersecting these genes with differentially expressed genes (DEGs) originating from liver RNA-seq data at two representative time points (circadian time, CT: CT2 and CT14) in global Bmal1 knockout mice (Bmal1-/-), hepatocyte-specific Bmal1 knockout mice (L-Bmal1-/-), and their corresponding control groups, 80 genes potentially regulated by BMAL1 (referred to as BMAL1-regulated genes, BRGs) were identified. These genes were significantly enriched in glycolipid metabolism, immune response, and tumorigenesis pathways. Eight BRGs (Nr1d1, Cry1, Gys2, Homer2, Serpina6, Slc2a2, Nmrk1, and Upp2) were selected to validate their expression patterns in both control and L-Bmal1-/- mice livers over 24 h. Real-time quantitative polymerase chain reaction results demonstrated a comprehensive loss of rhythmic expression patterns in the eight selected BRGs in L-Bmal1-/- mice, in contrast to the discernible rhythmic patterns observed in the livers of control mice. Additionally, significant reductions in the expression levels of these selected BRGs, excluding Cry1, were also observed in L-Bmal1-/- mice livers. Chromatin immunoprecipitation (ChIP)-seq (GSE13505 and GSE39860) and JASPAR analyses validated the rhythmic binding of BMAL1 to the promoter and intron regions of these genes. Moreover, the progression of conditions, from basic steatosis to non-alcoholic fatty liver disease, and eventual malignancy, demonstrated a continuous gradual decline in Bmal1 transcripts in the human liver. Combining the aforementioned BRGs with DEGs derived from human liver cancer datasets identified Gys2 and Upp2 as potential node genes bridging the circadian clock system and hepatocellular carcinoma (HCC). In addition, CCK8 and wound healing assays demonstrated that the overexpression of human GYS2 and UPP2 proteins inhibited the proliferation and migration of HepG2 cells, accompanied by elevated expression of p53, a tumor suppressor protein. In summary, this study systematically identified rhythmic genes in the mouse liver, and a subset of circadian genes potentially regulated by BMAL1. Two circadian genes, Gys2 and Upp2, have been proposed and validated as potential candidates for advancing the prevention and treatment of HCC.
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Affiliation(s)
- Hongcong Zhao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guohao Han
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhou Jiang
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, Sichuan, 610000, China
| | - Dengke Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haisen Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Luda Yang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tiantian Ma
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lei Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Aihua Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China; Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hsu-Wen Chao
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, 11031, China; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan, 11031, China; Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, 80708, China.
| | - Qian Li
- Medical Experiment Centre, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, 712000, China
| | - Yaping Jin
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Huatao Chen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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6
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Mannar D, Ahmed S, Subramaniam S. AAA ATPase protein-protein interactions as therapeutic targets in cancer. Curr Opin Cell Biol 2024; 86:102291. [PMID: 38056141 DOI: 10.1016/j.ceb.2023.102291] [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: 06/30/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023]
Abstract
AAA ATPases are a conserved group of enzymes that couple ATP hydrolysis to diverse activities critical for cellular homeostasis by targeted protein-protein interactions. Some of these interactions are potential therapeutic targets because of their role in cancers which rely on increased AAA ATPase activities for maintenance of genomic stability. Two well-characterized members of this family are p97/VCP and RUVBL ATPases where there is a growing understanding of their structure and function, as well as an emerging landscape of selective inhibitors. Here we highlight recent progress in this field, with particular emphasis on structural advances enabled by cryo-electron microscopy (cryo-EM).
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Affiliation(s)
- Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sana Ahmed
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Gandeeva Therapeutics, Inc., Burnaby, BC V5C 6N5, Canada.
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7
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López-Perrote A, Serna M, Llorca O. Maturation and Assembly of mTOR Complexes by the HSP90-R2TP-TTT Chaperone System: Molecular Insights and Mechanisms. Subcell Biochem 2024; 104:459-483. [PMID: 38963496 DOI: 10.1007/978-3-031-58843-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The mechanistic target of rapamycin (mTOR) is a master regulator of cell growth and metabolism, integrating environmental signals to regulate anabolic and catabolic processes, regulating lipid synthesis, growth factor-induced cell proliferation, cell survival, and migration. These activities are performed as part of two distinct complexes, mTORC1 and mTORC2, each with specific roles. mTORC1 and mTORC2 are elaborated dimeric structures formed by the interaction of mTOR with specific partners. mTOR functions only as part of these large complexes, but their assembly and activation require a dedicated and sophisticated chaperone system. mTOR folding and assembly are temporarily separated with the TELO2-TTI1-TTI2 (TTT) complex assisting the cotranslational folding of mTOR into a native conformation. Matured mTOR is then transferred to the R2TP complex for assembly of active mTORC1 and mTORC2 complexes. R2TP works in concert with the HSP90 chaperone to promote the incorporation of additional subunits to mTOR and dimerization. This review summarizes our current knowledge on how the HSP90-R2TP-TTT chaperone system facilitates the maturation and assembly of active mTORC1 and mTORC2 complexes, discussing interactions, structures, and mechanisms.
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Affiliation(s)
- Andrés López-Perrote
- Spanish National Cancer Research Centre (CNIO), Structural Biology Programme, Melchor Fernández Almagro 3, Madrid, Spain.
| | - Marina Serna
- Spanish National Cancer Research Centre (CNIO), Structural Biology Programme, Melchor Fernández Almagro 3, Madrid, Spain
| | - Oscar Llorca
- Spanish National Cancer Research Centre (CNIO), Structural Biology Programme, Melchor Fernández Almagro 3, Madrid, Spain.
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8
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Xu W, Li X. Regulation of Pol II Pausing during Daily Gene Transcription in Mouse Liver. BIOLOGY 2023; 12:1107. [PMID: 37626993 PMCID: PMC10452108 DOI: 10.3390/biology12081107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
Cell autonomous circadian oscillation is present in central and various peripheral tissues. The intrinsic tissue clock and various extrinsic cues drive gene expression rhythms. Transcription regulation is thought to be the main driving force for gene rhythms. However, how transcription rhythms arise remains to be fully characterized due to the fact that transcription is regulated at multiple steps. In particular, Pol II recruitment, pause release, and premature transcription termination are critical regulatory steps that determine the status of Pol II pausing and transcription output near the transcription start site (TSS) of the promoter. Recently, we showed that Pol II pausing exhibits genome-wide changes during daily transcription in mouse liver. In this article, we review historical as well as recent findings on the regulation of transcription rhythms by the circadian clock and other transcription factors, and the potential limitations of those results in explaining rhythmic transcription at the TSS. We then discuss our results on the genome-wide characteristics of daily changes in Pol II pausing, the possible regulatory mechanisms involved, and their relevance to future research on circadian transcription regulation.
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Affiliation(s)
| | - Xiaodong Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China;
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9
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Xiang S, Li M, Li S. The circadian clock of anti-tumor immunity. Chin J Nat Med 2023; 21:481-482. [PMID: 37517816 DOI: 10.1016/s1875-5364(23)60431-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Indexed: 08/01/2023]
Affiliation(s)
- Shuting Xiang
- Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Mingxi Li
- Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Suxin Li
- Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China.
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Gao D, Ma T, Gao L, Zhang J, Zhang H, Zhang L, Dong H, Li Y, Zhao L, Liu W, Zhao H, Li D, Zhou D, Wang A, Jin Y, Chen H. Autophagy activation attenuates the circadian clock oscillators in U2OS cells via the ATG5 pathway. Cell Signal 2023; 101:110502. [PMID: 36280090 DOI: 10.1016/j.cellsig.2022.110502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/30/2022] [Accepted: 10/17/2022] [Indexed: 11/28/2022]
Abstract
The circadian clock and autophagy are essential biological mechanisms involved in regulating many physiological processes. Accumulating evidence has revealed that autophagic activity is regulated by the circadian clock system. However, whether autophagy regulates the circadian clock system remains unclear. In this study, rapamycin and AICAR, two classical activators of autophagy, were used to create autophagy activation models in BMAL1-dLuc U2OS cell line. The results showed that the mRNA expression of MAP1LC3B and ATG5 were significantly upregulated after autophagy activation, whereas the mRNA expression of circadian clock genes (BMAL1, PER2, REV-ERBα, and DBP) were significantly decreased. Consistent with these data, the relative ratio of LC3-II/LC3-I and the protein level of ATG5 were increased after rapamycin or AICAR treatment. In contrast, BMAL1 and REV-ERBα levels were decreased. Notably, the mRNA expression of circadian clock genes (BMAL1, PER2, REV-ERBα, and DBP) and autophagy-related genes (MAP1LC3B and ATG5) showed rhythmic expression patterns in both untreated and rapamycin/AICAR-treated U2OS cells. Moreover, the autophagy inhibitor 3-methyladenine partially reversed the inhibitory effects of autophagy on circadian clock genes expression and BMAL1-Luc oscillations. Another critical finding was that ATG5 knockout alleviates the inhibitory effect of rapamycin-mediated autophagy activation on the circadian clock oscillators in U2OS cells. Collectively, our data indicate that autophagy activation attenuates the circadian clock oscillators in U2OS cells via the ATG5 pathway.
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Affiliation(s)
- Dengke Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Tiantian Ma
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lei Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China; College of Agriculture and Animal Husbandry, Qing Hai University, Xining, Qinghai, China
| | - Jing Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Haisen Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Linlin Zhang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hao Dong
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yating Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lijia Zhao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wei Liu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hongcong Zhao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dan Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dong Zhou
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Aihua Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China; Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yaping Jin
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Huatao Chen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China.
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11
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A signalling pathway for transcriptional regulation of sleep amount in mice. Nature 2022; 612:519-527. [PMID: 36477534 DOI: 10.1038/s41586-022-05510-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
In mice and humans, sleep quantity is governed by genetic factors and exhibits age-dependent variation1-3. However, the core molecular pathways and effector mechanisms that regulate sleep duration in mammals remain unclear. Here, we characterize a major signalling pathway for the transcriptional regulation of sleep in mice using adeno-associated virus-mediated somatic genetics analysis4. Chimeric knockout of LKB1 kinase-an activator of AMPK-related protein kinase SIK35-7-in adult mouse brain markedly reduces the amount and delta power-a measure of sleep depth-of non-rapid eye movement sleep (NREMS). Downstream of the LKB1-SIK3 pathway, gain or loss-of-function of the histone deacetylases HDAC4 and HDAC5 in adult brain neurons causes bidirectional changes of NREMS amount and delta power. Moreover, phosphorylation of HDAC4 and HDAC5 is associated with increased sleep need, and HDAC4 specifically regulates NREMS amount in posterior hypothalamus. Genetic and transcriptomic studies reveal that HDAC4 cooperates with CREB in both transcriptional and sleep regulation. These findings introduce the concept of signalling pathways targeting transcription modulators to regulate daily sleep amount and demonstrate the power of somatic genetics in mouse sleep research.
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12
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Wang H, Li B, Zuo L, Wang B, Yan Y, Tian K, Zhou R, Wang C, Chen X, Jiang Y, Zheng H, Qin F, Zhang B, Yu Y, Liu CP, Xu Y, Gao J, Qi Z, Deng W, Ji X. The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors. Nat Commun 2022; 13:5703. [PMID: 36171202 PMCID: PMC9519968 DOI: 10.1038/s41467-022-33433-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
RNA polymerase II (Pol II) apparatuses are compartmentalized into transcriptional clusters. Whether protein factors control these clusters remains unknown. In this study, we find that the ATPase-associated with diverse cellular activities (AAA + ) ATPase RUVBL2 co-occupies promoters with Pol II and various transcription factors. RUVBL2 interacts with unphosphorylated Pol II in chromatin to promote RPB1 carboxy-terminal domain (CTD) clustering and transcription initiation. Rapid depletion of RUVBL2 leads to a decrease in the number of Pol II clusters and inhibits nascent RNA synthesis, and tethering RUVBL2 to an active promoter enhances Pol II clustering at the promoter. We also identify target genes that are directly linked to the RUVBL2-Pol II axis. Many of these genes are hallmarks of cancers and encode proteins with diverse cellular functions. Our results demonstrate an emerging activity for RUVBL2 in regulating Pol II cluster formation in the nucleus. RNA polymerase II (Pol II) transcription factories play a central role in gene expression and 3D chromatin organization. Here, the authors demonstrate that RUVBL2 directly regulates Pol II clustering at active gene promoters.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.,Department of Pathogenic Biology, Chengdu Medical College, Chengdu, 610500, China
| | - Boyuan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Linyu Zuo
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Bo Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences (CLS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Yan
- Institute for TCM-X; MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist (Beijing National Research Center for Information Science and Technology); Department of Automation, Tsinghua University, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Rong Zhou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Fangfei Qin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Bin Zhang
- Departments of Pathology and Laboratory Medicine, and Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA
| | - Yang Yu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao-Pei Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Juntao Gao
- Institute for TCM-X; MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist (Beijing National Research Center for Information Science and Technology); Department of Automation, Tsinghua University, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Zhi Qi
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences (CLS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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13
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ISX-9 potentiates CaMKIIδ-mediated BMAL1 activation to enhance circadian amplitude. Commun Biol 2022; 5:750. [PMID: 35902736 PMCID: PMC9334596 DOI: 10.1038/s42003-022-03725-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 07/15/2022] [Indexed: 11/09/2022] Open
Abstract
Circadian dysregulation associates with numerous diseases including metabolic dysfunction, sleep disorder, depression and aging. Given that declined circadian amplitude is a trait commonly found with compromised health, interventions that design in precluding circadian amplitude from dampening will aid to mitigate complex, circadian-related diseases. Here we identify a neurogenic small molecule ISX-9 that is able to support persistent and higher amplitude of circadian oscillations. ISX-9 improves diurnal metabolic rhythms in middle-aged mice. Moreover, the ISX-9-treated mice show better sleep homeostasis with increased delta power during the day time and higher locomotive activity in the dark period. ISX-9 augments CaMKIIδ expression and increases BMAL1 activity via eliciting CaMKIIδ-mediated phosphorylation on BMAL1 residues S513/S515/S516, accordingly composes a positive feedback effect on enhancing circadian amplitude. CaMKIIδ-targeting, and the use of ISX-9 may serve as decent choices for treating circadian-related disorders.
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14
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Mammalian PERIOD2 regulates H2A.Z incorporation in chromatin to orchestrate circadian negative feedback. Nat Struct Mol Biol 2022; 29:549-562. [PMID: 35606517 DOI: 10.1038/s41594-022-00777-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/11/2022] [Indexed: 11/08/2022]
Abstract
Mammalian circadian oscillators are built on a feedback loop in which the activity of the transcription factor CLOCK-BMAL1 is repressed by the PER-CRY complex. Here, we show that murine Per-/- fibroblasts display aberrant nucleosome occupancy around transcription start sites (TSSs) and at promoter-proximal and distal CTCF sites due to impaired histone H2A.Z deposition. Knocking out H2A.Z mimicked the Per null chromatin state and disrupted cellular rhythms. We found that endogenous mPER2 complexes retained CTCF as well as the specific H2A.Z-deposition chaperone YL1-a component of the ATP-dependent remodeler SRCAP and p400-TIP60 complex. While depleting YL1 or mutating chaperone-binding sites on H2A.Z lengthened the circadian period, H2A.Z deletion abrogated BMAL1 chromatin recruitment and promoted its proteasomal degradation. We propose that a PER2-mediated H2A.Z deposition pathway (1) compacts CLOCK-BMAL1 binding sites to establish negative feedback, (2) organizes circadian chromatin landscapes using CTCF and (3) bookmarks genomic loci for BMAL1 binding to impinge on the positive arm of the subsequent cycle.
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15
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Hatori M, Hirota T. Cell-Based Phenotypic Screens to Discover Circadian Clock-Modulating Compounds. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2482:95-104. [PMID: 35610421 DOI: 10.1007/978-1-0716-2249-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There is increasing demand to control circadian clock functions in a conditional manner for deeper understanding of the circadian system as well as for potential treatment of clock-related diseases. Small-molecule compounds provide powerful tools to reveal novel functions of target proteins in the circadian clock mechanism, and can be great therapeutic candidates. Here we describe the detailed methods of measuring cellular circadian rhythms in a high-throughput manner for chemical screening to identify compounds that affect circadian rhythms by targeting clock-related proteins.
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Affiliation(s)
- Megumi Hatori
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.
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16
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Radhi M, Ashraf S, Lawrence S, Tranholm AA, Wellham PAD, Hafeez A, Khamis AS, Thomas R, McWilliams D, de Moor CH. A Systematic Review of the Biological Effects of Cordycepin. Molecules 2021; 26:5886. [PMID: 34641429 PMCID: PMC8510467 DOI: 10.3390/molecules26195886] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
We conducted a systematic review of the literature on the effects of cordycepin on cell survival and proliferation, inflammation, signal transduction and animal models. A total of 1204 publications on cordycepin were found by the cut-off date of 1 February 2021. After application of the exclusion criteria, 791 papers remained. These were read and data on the chosen subjects were extracted. We found 192 papers on the effects of cordycepin on cell survival and proliferation and calculated a median inhibitory concentration (IC50) of 135 µM. Cordycepin consistently repressed cell migration (26 papers) and cellular inflammation (53 papers). Evaluation of 76 papers on signal transduction indicated consistently reduced PI3K/mTOR/AKT and ERK signalling and activation of AMPK. In contrast, the effects of cordycepin on the p38 and Jun kinases were variable, as were the effects on cell cycle arrest (53 papers), suggesting these are cell-specific responses. The examination of 150 animal studies indicated that purified cordycepin has many potential therapeutic effects, including the reduction of tumour growth (37 papers), repression of pain and inflammation (9 papers), protecting brain function (11 papers), improvement of respiratory and cardiac conditions (8 and 19 papers) and amelioration of metabolic disorders (8 papers). Nearly all these data are consistent with cordycepin mediating its therapeutic effects through activating AMPK, inhibiting PI3K/mTOR/AKT and repressing the inflammatory response. We conclude that cordycepin has excellent potential as a lead for drug development, especially for age-related diseases. In addition, we discuss the remaining issues around the mechanism of action, toxicity and biodistribution of cordycepin.
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Affiliation(s)
- Masar Radhi
- Pain Centre Versus Arthritis, University of Nottingham, Nottingham NG7 2RD, UK; (M.R.); (A.A.T.); (D.M.)
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK; (S.L.); (P.A.D.W.); (A.H.); (A.S.K.)
| | - Sadaf Ashraf
- Aberdeen Centre for Arthritis and Musculoskeletal Health, Institute of Medical Sciences, Aberdeen AB25 2ZD, UK;
| | - Steven Lawrence
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK; (S.L.); (P.A.D.W.); (A.H.); (A.S.K.)
| | - Asta Arendt Tranholm
- Pain Centre Versus Arthritis, University of Nottingham, Nottingham NG7 2RD, UK; (M.R.); (A.A.T.); (D.M.)
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK; (S.L.); (P.A.D.W.); (A.H.); (A.S.K.)
| | - Peter Arthur David Wellham
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK; (S.L.); (P.A.D.W.); (A.H.); (A.S.K.)
| | - Abdul Hafeez
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK; (S.L.); (P.A.D.W.); (A.H.); (A.S.K.)
| | - Ammar Sabah Khamis
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK; (S.L.); (P.A.D.W.); (A.H.); (A.S.K.)
| | - Robert Thomas
- The Primrose Oncology Unit, Bedford Hospital NHS Trust, Bedford MK42 9DJ, UK;
- Department of Oncology, Addenbrooke’s Cambridge University Hospitals NHS Trust, Cambridge CB2 0QQ, UK
| | - Daniel McWilliams
- Pain Centre Versus Arthritis, University of Nottingham, Nottingham NG7 2RD, UK; (M.R.); (A.A.T.); (D.M.)
- NIHR Nottingham Biomedical Research Centre (BRC), Nottingham NG5 1PB, UK
| | - Cornelia Huiberdina de Moor
- Pain Centre Versus Arthritis, University of Nottingham, Nottingham NG7 2RD, UK; (M.R.); (A.A.T.); (D.M.)
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK; (S.L.); (P.A.D.W.); (A.H.); (A.S.K.)
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17
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Li MD, Xin H, Yuan Y, Yang X, Li H, Tian D, Zhang H, Zhang Z, Han TL, Chen Q, Duan G, Ju D, Chen K, Deng F, He W. Circadian Clock-Controlled Checkpoints in the Pathogenesis of Complex Disease. Front Genet 2021; 12:721231. [PMID: 34557221 PMCID: PMC8452875 DOI: 10.3389/fgene.2021.721231] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/16/2021] [Indexed: 12/26/2022] Open
Abstract
The circadian clock coordinates physiology, metabolism, and behavior with the 24-h cycles of environmental light. Fundamental mechanisms of how the circadian clock regulates organ physiology and metabolism have been elucidated at a rapid speed in the past two decades. Here we review circadian networks in more than six organ systems associated with complex disease, which cluster around metabolic disorders, and seek to propose critical regulatory molecules controlled by the circadian clock (named clock-controlled checkpoints) in the pathogenesis of complex disease. These include clock-controlled checkpoints such as circadian nuclear receptors in liver and muscle tissues, chemokines and adhesion molecules in the vasculature. Although the progress is encouraging, many gaps in the mechanisms remain unaddressed. Future studies should focus on devising time-dependent strategies for drug delivery and engagement in well-characterized organs such as the liver, and elucidating fundamental circadian biology in so far less characterized organ systems, including the heart, blood, peripheral neurons, and reproductive systems.
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Affiliation(s)
- Min-Dian Li
- Department of Cardiology and the Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Haoran Xin
- Department of Cardiology and the Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yinglin Yuan
- Medical Center of Hematology, The Xinqiao Hospital of Army Medical University, Chongqing, China
| | - Xinqing Yang
- Department of Anesthesiology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hongli Li
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dingyuan Tian
- Department of Cardiology and the Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Hua Zhang
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhihui Zhang
- Department of Cardiology and the Center for Circadian Metabolism and Cardiovascular Disease, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Ting-Li Han
- Department of Obstetrics and Gynaecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qing Chen
- Key Lab of Medical Protection for Electromagnetic Radiation, Ministry of Education of China, Institute of Toxicology, College of Preventive Medicine, Army Medical University (Third Military Medical University), Chongqing, China
| | - Guangyou Duan
- Department of Anesthesiology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Dapeng Ju
- Department of Anesthesiology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ka Chen
- Research Center for Nutrition and Food Safety, Institute of Military Preventive Medicine, Army Medical University, Chongqing, China
| | - Fang Deng
- Key Laboratory of Extreme Environmental Medicine, Department of Pathophysiology, College of High Altitude Military Medicine, Ministry of Education of China, Army Medical University (Third Military Medical University), Chongqing, China.,Key Laboratory of High Altitude Medicine, PLA, Army Medical University (Third Military Medical University), Chongqing, China
| | - Wenyan He
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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18
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Zhang G, Li S, Cheng KW, Chou TF. AAA ATPases as therapeutic targets: Structure, functions, and small-molecule inhibitors. Eur J Med Chem 2021; 219:113446. [PMID: 33873056 PMCID: PMC8165034 DOI: 10.1016/j.ejmech.2021.113446] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/21/2021] [Accepted: 03/30/2021] [Indexed: 01/07/2023]
Abstract
ATPases Associated with Diverse Cellular Activity (AAA ATPase) are essential enzymes found in all organisms. They are involved in various processes such as DNA replication, protein degradation, membrane fusion, microtubule serving, peroxisome biogenesis, signal transduction, and the regulation of gene expression. Due to the importance of AAA ATPases, several researchers identified and developed small-molecule inhibitors against these enzymes. We discuss six AAA ATPases that are potential drug targets and have well-developed inhibitors. We compare available structures that suggest significant differences of the ATP binding pockets among the AAA ATPases with or without ligand. The distances from ADP to the His20 in the His-Ser-His motif and the Arg finger (Arg353 or Arg378) in both RUVBL1/2 complex structures bound with or without ADP have significant differences, suggesting dramatically different interactions of the binding site with ADP. Taken together, the inhibitors of six well-studied AAA ATPases and their structural information suggest further development of specific AAA ATPase inhibitors due to difference in their structures. Future chemical biology coupled with proteomic approaches could be employed to develop variant specific, complex specific, and pathway specific inhibitors or activators for AAA ATPase proteins.
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Affiliation(s)
- Gang Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
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19
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Ribeiro RFN, Cavadas C, Silva MMC. Small-molecule modulators of the circadian clock: Pharmacological potentials in circadian-related diseases. Drug Discov Today 2021; 26:1620-1641. [PMID: 33781946 DOI: 10.1016/j.drudis.2021.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/20/2021] [Accepted: 03/16/2021] [Indexed: 12/29/2022]
Abstract
Disruption of circadian oscillations has a wide-ranging impact on health, with the potential to induce the development of clock-related diseases. Small-molecule modulators of the circadian clock (SMMCC) target core or noncore clock proteins, modulating physiological effects as a consequence of agonist, inverse agonist, or antagonist interference. These pharmacological modulators are usually identified using chemical screening of large libraries of active compounds. However, target-based screens, chemical optimization, and circadian crystallography have recently assisted in the identification of these compounds. In this review, we focus on established and novel SMMCCs targeting both core and noncore clock proteins, identifying their circadian targets, detailed circadian effects, and specific physiological effects. In addition, we discuss their therapeutic potential for the treatment of diverse clock-related disorders (such as metabolic-associated disorders, autoimmune diseases, mood disorders, and cancer) and as chronotherapeutics. Future perspectives are also considered, such as clinical trials, and potential safety hazards, including those in the absence of clinical trials.
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Affiliation(s)
- Rodrigo F N Ribeiro
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Cláudia Cavadas
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
| | - Maria Manuel C Silva
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
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20
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López-Perrote A, Hug N, González-Corpas A, Rodríguez CF, Serna M, García-Martín C, Boskovic J, Fernandez-Leiro R, Caceres JF, Llorca O. Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM. eLife 2020; 9:63042. [PMID: 33205750 PMCID: PMC7707835 DOI: 10.7554/elife.63042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades aberrant mRNAs and also regulates the expression of a wide range of physiological transcripts. RUVBL1 and RUVBL2 AAA-ATPases form an hetero-hexameric ring that is part of several macromolecular complexes such as INO80, SWR1, and R2TP. Interestingly, RUVBL1-RUVBL2 ATPase activity is required for NMD activation by an unknown mechanism. Here, we show that DHX34, an RNA helicase regulating NMD initiation, directly interacts with RUVBL1-RUVBL2 in vitro and in cells. Cryo-EM reveals that DHX34 induces extensive changes in the N-termini of every RUVBL2 subunit in the complex, stabilizing a conformation that does not bind nucleotide and thereby down-regulates ATP hydrolysis of the complex. Using ATPase-deficient mutants, we find that DHX34 acts exclusively on the RUVBL2 subunits. We propose a model, where DHX34 acts to couple RUVBL1-RUVBL2 ATPase activity to the assembly of factors required to initiate the NMD response.
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Affiliation(s)
- Andres López-Perrote
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburghx, Edinburgh, United Kingdom
| | - Ana González-Corpas
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Carlos F Rodríguez
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marina Serna
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Carmen García-Martín
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jasminka Boskovic
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Rafael Fernandez-Leiro
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Javier F Caceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburghx, Edinburgh, United Kingdom
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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21
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Dauden MI, López-Perrote A, Llorca O. RUVBL1-RUVBL2 AAA-ATPase: a versatile scaffold for multiple complexes and functions. Curr Opin Struct Biol 2020; 67:78-85. [PMID: 33129013 DOI: 10.1016/j.sbi.2020.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022]
Abstract
RUVBL1 and RUVBL2 are two highly conserved AAA+ ATPases that form a hetero-hexameric complex that participates in a wide range of unrelated cellular processes, including chromatin remodeling, Fanconi Anemia (FA), nonsense-mediated mRNA decay (NMD), and assembly and maturation of several large macromolecular complexes such as RNA polymerases, the box C/D small nucleolar ribonucleoprotein (snoRNP) and mTOR complexes. How the RUVBL1-RUVBL2 complex works in such a variety of processes, sometimes antagonistic, has been obscure for a long time. Recent cryo-electron microscopy (cryo-EM) studies have started to reveal how RUVBL1-RUVBL2 forms a scaffold for complex protein-protein interactions and how the structure and ATPase activity of RUVBL1-RUVBL2 can be affected and regulated by the interaction with clients.
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Affiliation(s)
- Maria I Dauden
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Andrés López-Perrote
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain.
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Mahesh G, Rivas GBS, Caster C, Ost EB, Amunugama R, Jones R, Allen DL, Hardin PE. Proteomic analysis of Drosophila CLOCK complexes identifies rhythmic interactions with SAGA and Tip60 complex component NIPPED-A. Sci Rep 2020; 10:17951. [PMID: 33087840 PMCID: PMC7578830 DOI: 10.1038/s41598-020-75009-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
Circadian clocks keep time via ~ 24 h transcriptional feedback loops. In Drosophila, CLOCK-CYCLE (CLK-CYC) activators and PERIOD-TIMELESS (PER-TIM) repressors are feedback loop components whose transcriptional status varies over a circadian cycle. Although changes in the state of activators and repressors has been characterized, how their status is translated to transcriptional activity is not understood. We used mass spectrometry to identify proteins that interact with GFP-tagged CLK (GFP-CLK) in fly heads at different times of day. Many expected and novel interacting proteins were detected, of which several interacted rhythmically and were potential regulators of protein levels, activity or transcriptional output. Genes encoding these proteins were tested to determine if they altered circadian behavior via RNAi knockdown in clock cells. The NIPPED-A protein, a scaffold for the SAGA and Tip60 histone modifying complexes, interacts with GFP-CLK as transcription is activated, and reducing Nipped-A expression lengthens circadian period. RNAi analysis of other SAGA complex components shows that the SAGA histone deubiquitination (DUB) module lengthened period similarly to Nipped-A RNAi knockdown and weakened rhythmicity, whereas reducing Tip60 HAT expression drastically weakened rhythmicity. These results suggest that CLK-CYC binds NIPPED-A early in the day to promote transcription through SAGA DUB and Tip60 HAT activity.
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Affiliation(s)
- Guruswamy Mahesh
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Gustavo B S Rivas
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Courtney Caster
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | - Evan B Ost
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA
| | | | | | | | - Paul E Hardin
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, TX, 77843, USA.
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Affiliation(s)
- Dapeng Ju
- National Institute of Biological Sciences, Beijing 102206, China
| | - Eric Erquan Zhang
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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Shortening jet-lag recovery. Nat Rev Drug Discov 2020; 19:388. [DOI: 10.1038/d41573-020-00085-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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