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Hamada T, Sutherland K, Ishikawa M, Saito J, Miyamoto N, Honma S, Shirato H, Honma KI. A novel method for measurements of sleep/wake states, feeding and drinking behaviors using the tracking technique of 3D positions in freely moving mice. Biochem Biophys Res Commun 2024; 732:150359. [PMID: 39032409 DOI: 10.1016/j.bbrc.2024.150359] [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: 05/31/2024] [Accepted: 07/04/2024] [Indexed: 07/23/2024]
Abstract
We have previously developed a 3D video tracking system which enables us to analyze long-term quantitative analysis of gene expression in freely moving mice. In the present study, we improved 3D video tracking and developed a system that analyzes more detailed behavioral data. We succeeded in simultaneously analyzing sleep-wake, feeding, and drinking behavior rhythms in the same individual using our tracking system. This system will make it possible to measure gene expression in each tissue in vivo in real time in relation to the various behavioral rhythms mentioned above.
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Affiliation(s)
- Toshiyuki Hamada
- Department of Pharmaceutical Sciences, International University of Health and Welfare, Ohtawara, Tochigi, 324-8501, Japan.
| | - Kenneth Sutherland
- Global Center for Biomedical Science and Engineering, Hokkaido University, North 15 West 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Masayori Ishikawa
- Department of Biomedical Science and Engineering, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, 060-0812, Japan
| | - Jun Saito
- Department of Pharmaceutical Sciences, International University of Health and Welfare, Ohtawara, Tochigi, 324-8501, Japan
| | - Naoki Miyamoto
- Division of Applied Quantum Science and Engineering, Faculty of Engineering, Hokkaido University, North15 West 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Sato Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, 060-8638, Japan
| | - Hiroki Shirato
- Global Center for Biomedical Science and Engineering, Hokkaido University, North 15 West 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Ken-Ichi Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, 060-8638, Japan
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2
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Arreaza-Gil V, Escobar-Martínez I, Soliz-Rueda JR, Suárez M, Muguerza B, Schellekens H, Torres-Fuentes C, Arola-Arnal A. Photoperiod effects on corticosterone and seasonal clocks in cafeteria-induced obese fischer 344 rats are influenced by gut microbiota. Sci Rep 2024; 14:22560. [PMID: 39343766 PMCID: PMC11439935 DOI: 10.1038/s41598-024-73289-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 09/15/2024] [Indexed: 10/01/2024] Open
Abstract
Seasonal rhythms are gaining attention given their impact on metabolic disorders development such as obesity gut microbiota is emerging as a key factor in mediating this link. However, the underlying mechanisms are still poorly understood. In this regard, corticosterone may play a role as it has been shown to be affected by gut bacteria and seasonal rhythms, and has been linked to obesity. Thus, this study aimed to investigate if seasonal rhythms effects on corticosterone are influenced by gut microbiota in obese rats and whether this may be related to seasonal and clock genes expression in the pituitary gland and colon. Fischer 344 male rats fed with cafeteria diet (CAF) were housed under different photoperiods for 9 weeks and treated with an antibiotic cocktail (ABX) in drinking water during the last 4 weeks. Rats fed with standard chow and CAF-fed rats without ABX were included as controls. ABX altered gut microbiota, corticosterone levels and seasonal clock expression in the pituitary depending on photoperiod conditions. These results suggest a link between gut bacteria, seasonal rhythms and corticosterone and a novel nutrigenomic target for obesity.
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Affiliation(s)
- Verónica Arreaza-Gil
- Nutrigenomics Research Group, Departament de Bioquímica I Biotecnologia, Universitat Rovira I Virgili, 43007, Tarragona, Spain
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Iván Escobar-Martínez
- Nutrigenomics Research Group, Departament de Bioquímica I Biotecnologia, Universitat Rovira I Virgili, 43007, Tarragona, Spain
| | - Jorge R Soliz-Rueda
- Nutrigenomics Research Group, Departament de Bioquímica I Biotecnologia, Universitat Rovira I Virgili, 43007, Tarragona, Spain
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Manuel Suárez
- Nutrigenomics Research Group, Departament de Bioquímica I Biotecnologia, Universitat Rovira I Virgili, 43007, Tarragona, Spain
| | - Begoña Muguerza
- Nutrigenomics Research Group, Departament de Bioquímica I Biotecnologia, Universitat Rovira I Virgili, 43007, Tarragona, Spain
| | - Harriet Schellekens
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
| | - Cristina Torres-Fuentes
- Nutrigenomics Research Group, Departament de Bioquímica I Biotecnologia, Universitat Rovira I Virgili, 43007, Tarragona, Spain.
| | - Anna Arola-Arnal
- Nutrigenomics Research Group, Departament de Bioquímica I Biotecnologia, Universitat Rovira I Virgili, 43007, Tarragona, Spain
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3
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San Martin A, Yanovsky MJ. Arabidopsis photoperiodic regulator CONSTANS feeds back to control the circadian clock. MOLECULAR PLANT 2024; 17:1338-1340. [PMID: 39148294 DOI: 10.1016/j.molp.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/17/2024]
Affiliation(s)
- Abril San Martin
- Instituto de Investigaciones Bioquímicas de Buenos Aires (Fundación Instituto Leloir-CONICET), Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - Marcelo Javier Yanovsky
- Instituto de Investigaciones Bioquímicas de Buenos Aires (Fundación Instituto Leloir-CONICET), Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina.
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4
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Rowson M, Jolly M, Dickson S, Gifford ML, Carré I. Timely symbiosis: circadian control of legume-rhizobia symbiosis. Biochem Soc Trans 2024; 52:1419-1430. [PMID: 38779952 PMCID: PMC11346424 DOI: 10.1042/bst20231307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Legumes house nitrogen-fixing endosymbiotic rhizobia in specialised polyploid cells within root nodules. This results in a mutualistic relationship whereby the plant host receives fixed nitrogen from the bacteria in exchange for dicarboxylic acids. This plant-microbe interaction requires the regulation of multiple metabolic and physiological processes in both the host and symbiont in order to achieve highly efficient symbiosis. Recent studies have showed that the success of symbiosis is influenced by the circadian clock of the plant host. Medicago and soybean plants with altered clock mechanisms showed compromised nodulation and reduced plant growth. Furthermore, transcriptomic analyses revealed that multiple genes with key roles in recruitment of rhizobia to plant roots, infection and nodule development were under circadian control, suggesting that appropriate timing of expression of these genes may be important for nodulation. There is also evidence for rhythmic gene expression of key nitrogen fixation genes in the rhizobium symbiont, and temporal coordination between nitrogen fixation in the bacterial symbiont and nitrogen assimilation in the plant host may be important for successful symbiosis. Understanding of how circadian regulation impacts on nodule establishment and function will identify key plant-rhizobial connections and regulators that could be targeted to increase the efficiency of this relationship.
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Affiliation(s)
- Monique Rowson
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Matthew Jolly
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Suzanna Dickson
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Miriam L. Gifford
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, The University of Warwick, Coventry CV4 7AL, U.K
| | - Isabelle Carré
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
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5
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Zeng Y, Guo Z, Wu M, Chen F, Chen L. Circadian rhythm regulates the function of immune cells and participates in the development of tumors. Cell Death Discov 2024; 10:199. [PMID: 38678017 PMCID: PMC11055927 DOI: 10.1038/s41420-024-01960-1] [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: 01/16/2024] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
Circadian rhythms are present in almost all cells and play a crucial role in regulating various biological processes. Maintaining a stable circadian rhythm is essential for overall health. Disruption of this rhythm can alter the expression of clock genes and cancer-related genes, and affect many metabolic pathways and factors, thereby affecting the function of the immune system and contributing to the occurrence and progression of tumors. This paper aims to elucidate the regulatory effects of BMAL1, clock and other clock genes on immune cells, and reveal the molecular mechanism of circadian rhythm's involvement in tumor and its microenvironment regulation. A deeper understanding of circadian rhythms has the potential to provide new strategies for the treatment of cancer and other immune-related diseases.
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Affiliation(s)
- Yuen Zeng
- Department of Immunology, School of Basic Medical Sciences, Air Force Medical University, Xi'an, China
| | - Zichan Guo
- Faculty of Life Sciences, Northwest University, Xi'an, China
| | - Mengqi Wu
- Department of Immunology, School of Basic Medical Sciences, Air Force Medical University, Xi'an, China
| | - Fulin Chen
- Faculty of Life Sciences, Northwest University, Xi'an, China
| | - Lihua Chen
- Department of Immunology, School of Basic Medical Sciences, Air Force Medical University, Xi'an, China.
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Zhu P, Peek CB. Circadian timing of satellite cell function and muscle regeneration. Curr Top Dev Biol 2024; 158:307-339. [PMID: 38670711 DOI: 10.1016/bs.ctdb.2024.01.017] [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: 04/28/2024]
Abstract
Recent research has highlighted an important role for the molecular circadian machinery in the regulation of tissue-specific function and stress responses. Indeed, disruption of circadian function, which is pervasive in modern society, is linked to accelerated aging, obesity, and type 2 diabetes. Furthermore, evidence supporting the importance of the circadian clock within both the mature muscle tissue and satellite cells to regulate the maintenance of muscle mass and repair capacity in response injury has recently emerged. Here, we review the discovery of circadian clocks within the satellite cell (a.k.a. adult muscle stem cell) and how they act to regulate metabolism, epigenetics, and myogenesis during both healthy and diseased states.
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Affiliation(s)
- Pei Zhu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States; Department of Medicine-Endocrinology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States.
| | - Clara B Peek
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States; Department of Medicine-Endocrinology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States.
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7
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Chiou YY, Lee CY, Yang HW, Cheng WC, Ji KD. Circadian modulation of glucose utilization via CRY1-mediated repression of Pdk1 expression. J Biol Chem 2024; 300:105637. [PMID: 38199564 PMCID: PMC10869264 DOI: 10.1016/j.jbc.2024.105637] [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: 11/15/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
Life adapts to daily environmental changes through circadian rhythms, exhibiting spontaneous oscillations of biological processes. These daily functional oscillations must match the metabolic requirements responding to the time of the day. We focus on the molecular mechanism of how the circadian clock regulates glucose, the primary resource for energy production and other biosynthetic pathways. The complex regulation of the circadian rhythm includes many proteins that control this process at the transcriptional and translational levels and by protein-protein interactions. We have investigated the action of one of these proteins, cryptochrome (CRY), whose elevated mRNA and protein levels repress the function of an activator in the transcription-translation feedback loop, and this activator causes elevated Cry1 mRNA. We used a genome-edited cell line model to investigate downstream genes affected explicitly by the repressor CRY. We found that CRY can repress glycolytic genes, particularly that of the gatekeeper, pyruvate dehydrogenase kinase 1 (Pdk1), decreasing lactate accumulation and glucose utilization. CRY1-mediated decrease of Pdk1 expression can also be observed in a breast cancer cell line MDA-MB-231, whose glycolysis is associated with Pdk1 expression. We also found that exogenous expression of CRY1 in the MDA-MB-231 decreases glucose usage and growth rate. Furthermore, reduced CRY1 levels and the increased phosphorylation of PDK1 substrate were observed when cells were grown in suspension compared to cells grown in adhesion. Our data supports a model that the transcription-translation feedback loop can regulate the glucose metabolic pathway through Pdk1 gene expression according to the time of the day.
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Affiliation(s)
- Yi-Ying Chiou
- Graduate Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
| | - Cing-Yun Lee
- Graduate Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Hao-Wei Yang
- Graduate Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Cheng Cheng
- Graduate Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Kun-Da Ji
- Graduate Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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8
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Jin Y, Wang Z, Huang S, Liu C, Wu X, Wang H. Identify and validate circadian regulators as potential prognostic markers and immune infiltrates in head and neck squamous cell carcinoma. Sci Rep 2023; 13:19939. [PMID: 37968308 PMCID: PMC10651996 DOI: 10.1038/s41598-023-46560-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a heterogeneity pathological malignant cancer with leading causes of morbidity and mortality. EGFR inhibitors, immune checkpoint inhibitors have become novel treatments. However, the mechanism still remained uncertain. Several studies have confirmed that the circadian rhythms induce multiple malignancies developing. We utilized multi-omics analysis to demonstrate the crosstalk between circadian clock genes and tumor microenvironment in HNSCC. Firstly, we performed the LASSO Cox regression analysis based on the 16 important clock genes. A 7-gene risk model was successfully established in TCGA and validated in GEO datasets. Next, CIBERSORT and ESTIMATE methods were performed to display the immune landscape of high risk and low risk groups, and the results showed that high abundance of mast cells activated, dendritic cells activated and neutrophils were positively correlated with poor OS. To further identify hub genes, Kaplan Meier plot was applied in all TCGA and GEO datasets and two hub genes (PER2, and PER3) were identified, especially PER3, which was found strongly associated with immune score, PDCD1, CD4 + and CD8 + T cells in HNSCCC. Moreover, to explore the innate mechanism of circadian-induced pathway, we constructed a circadian-related ceRNA regulatory network containing 34 lncRNAs, 3 miRNAs and 4 core circadian genes. In-vitro experiments also verified that Per2 or Per3 could suppressed the proliferation, migration and invasion of HNSC. This study unraveled the association between PER3 and prognosis in patients with HNSC and the innate mechanism remains to be elucidated.
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Affiliation(s)
- Yi Jin
- Department of Radiation Oncology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Key Laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Zhanwang Wang
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha, 410013, China
| | - Siwei Huang
- School of Humanities and Management, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China
| | - Chang Liu
- Department of Nuclear Medicine, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Xiangwei Wu
- Department of Radiation Oncology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Key Laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Hui Wang
- Department of Radiation Oncology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Key Laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China.
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9
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Siebieszuk A, Sejbuk M, Witkowska AM. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Int J Mol Sci 2023; 24:16169. [PMID: 38003359 PMCID: PMC10671191 DOI: 10.3390/ijms242216169] [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: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
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Affiliation(s)
- Adam Siebieszuk
- Department of Physiology, Faculty of Medicine, Medical University of Bialystok, Mickiewicza 2C, 15-222 Białystok, Poland;
| | - Monika Sejbuk
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| | - Anna Maria Witkowska
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
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10
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Tao Y, Qin Y, Chen S, Xu T, Lin J, Su D, Yu W, Chen X. Emerging trends and hot spots of sleep and genetic research: a bibliometric analysis of publications from 2002 to 2022 in the field. Front Neurol 2023; 14:1264177. [PMID: 38020599 PMCID: PMC10663257 DOI: 10.3389/fneur.2023.1264177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
Background Sleep is an important biological process and has been linked to many diseases; however, very little is known about which and how genes control and regulate sleep. Although technology has seen significant development, this issue has still not been adequately resolved. Therefore, we conducted a bibliometric analysis to assess the progress in research on sleep quality and associated genes over the past 2 decades. Through our statistical data and discussions, we aimed to provide researchers with better research directions and ideas, thus promoting the advancement of this field. Methods On December 29, 2022, we utilized bibliometric techniques, such as co-cited and cluster analysis and keyword co-occurrence, using tools such as CiteSpace, VOSviewer, and the Online Analysis Platform of Literature Metrology (http://bibliometric.com/), to conduct a thorough examination of the relevant publications extracted from the Web of Science Core Collection (WoSCC). Our analysis aimed to identify the emerging trends and hot spots in this field while also predicting their potential development in future. Results Cluster analysis of the co-cited literature revealed the most popular terms relating to sleep quality and associated genes in the manner of cluster labels; these included genome-wide association studies (GWAS), circadian rhythms, obstructive sleep apnea (OSA), DNA methylation, and depression. Keyword burst detection suggested that obstructive sleep apnea, circadian clock, circadian genes, and polygenic risk score were newly emergent research hot spots. Conclusion Based on this bibliometric analysis of the publications in the last 20 years, a comprehensive analysis of the literature clarified the contributions, changes in research hot spots, and evolution of research techniques regarding sleep quality and associated genes. This research can provide medical staff and researchers with revelations into future directions of the study on the pathological mechanisms of sleep-related diseases.
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Affiliation(s)
- Ying Tao
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Yi Qin
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Sifan Chen
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Tian Xu
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Junhui Lin
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Diansan Su
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Weifeng Yu
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
| | - Xuemei Chen
- Department of Anesthesiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Anesthesiology (Shanghai Jiao Tong University), Ministry of Education, Shanghai, China
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11
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de Barros Dantas LL, Eldridge BM, Dorling J, Dekeya R, Lynch DA, Dodd AN. Circadian regulation of metabolism across photosynthetic organisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:650-668. [PMID: 37531328 PMCID: PMC10953457 DOI: 10.1111/tpj.16405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.
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Affiliation(s)
| | - Bethany M. Eldridge
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Jack Dorling
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Richard Dekeya
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Deirdre A. Lynch
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Antony N. Dodd
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
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12
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Landman J, Verduyn Lunel SM, Kegel WK. Transcription factor competition facilitates self-sustained oscillations in single gene genetic circuits. PLoS Comput Biol 2023; 19:e1011525. [PMID: 37773967 PMCID: PMC10566692 DOI: 10.1371/journal.pcbi.1011525] [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: 02/20/2023] [Revised: 10/11/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
Genetic feedback loops can be used by cells to regulate internal processes or to keep track of time. It is often thought that, for a genetic circuit to display self-sustained oscillations, a degree of cooperativity is needed in the binding and unbinding of actor species. This cooperativity is usually modeled using a Hill function, regardless of the actual promoter architecture. Furthermore, genetic circuits do not operate in isolation and often transcription factors are shared between different promoters. In this work we show how mathematical modelling of genetic feedback loops can be facilitated with a mechanistic fold-change function that takes into account the titration effect caused by competing binding sites for transcription factors. The model shows how the titration effect facilitates self-sustained oscillations in a minimal genetic feedback loop: a gene that produces its own repressor directly without cooperative transcription factor binding. The use of delay-differential equations leads to a stability contour that predicts whether a genetic feedback loop will show self-sustained oscillations, even when taking the bursty nature of transcription into account.
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Affiliation(s)
- Jasper Landman
- Physics & Physical Chemistry of Foods, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Willem K. Kegel
- Van ‘t Hoff Laboratory for Physical & Colloid Chemistry, Utrecht University, Utrecht, the Netherlands
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13
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Cheng Y, Chi Y, Sun L, Wang GZ. Dominant constraints on the evolution of rhythmic gene expression. Comput Struct Biotechnol J 2023; 21:4301-4311. [PMID: 37692081 PMCID: PMC10492206 DOI: 10.1016/j.csbj.2023.08.035] [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: 03/27/2023] [Revised: 08/21/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023] Open
Abstract
Although the individual transcriptional regulators of the core circadian clock are distinct among different organisms, the autoregulatory feedback loops they form are conserved. This unified design principle explains how daily physiological activities oscillate across species. However, it is unknown whether analogous design principles govern the gene expression output of circadian clocks. In this study, we performed a comparative analysis of rhythmic gene expression in eight diverse species and identified four common distribution patterns of cycling gene expression across these species. We hypothesized that the maintenance of reduced energetic costs constrains the evolution of rhythmic gene expression. Our large-scale computational simulations support this hypothesis by showing that selection against high-energy expenditure completely regenerates all cycling gene patterns. Moreover, we find that the peaks of rhythmic expression have been subjected to this type of selective pressure. The results suggest that selective pressure from circadian regulation efficiently removes unnecessary gene products from the transcriptome, thereby significantly impacting its evolutionary path.
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Affiliation(s)
| | | | | | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Pehlivan S. The circadian systems genes and their importance of human health. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 137:1-15. [PMID: 37709372 DOI: 10.1016/bs.apcsb.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
The circadian rhythm is the timing mechanism that creates approximately 24-hour rhythms in cellular and bodily functions in almost all living species. These internal clock systems enable living organisms to predict and respond to daily changes in their environment, optimizing temporal physiology and behavior. Circadian rhythms are regulated by both genetic and environmental risk factors. Circadian rhythms play an important role in maintaining homeostasis at the systemic and tissue levels. Disruption of this rhythm lays the groundwork for human health and disease. Disruption in these rhythms increases the susceptibility to many diseases, such as cancer, psychiatric disorders, and neurodegenerative diseases. In this chapter, the characteristics of circadian rhythm and its relationship with diseases will be discussed.
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Affiliation(s)
- S Pehlivan
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey.
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15
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Xiong LI, Garfinkel A. Are physiological oscillations physiological? J Physiol 2023. [PMID: 37622389 DOI: 10.1113/jp285015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023] Open
Abstract
Despite widespread and striking examples of physiological oscillations, their functional role is often unclear. Even glycolysis, the paradigm example of oscillatory biochemistry, has seen questions about its oscillatory function. Here, we take a systems approach to argue that oscillations play critical physiological roles, such as enabling systems to avoid desensitization, to avoid chronically high and therefore toxic levels of chemicals, and to become more resistant to noise. Oscillation also enables complex physiological systems to reconcile incompatible conditions such as oxidation and reduction, by cycling between them, and to synchronize the oscillations of many small units into one large effect. In pancreatic β-cells, glycolytic oscillations synchronize with calcium and mitochondrial oscillations to drive pulsatile insulin release, critical for liver regulation of glucose. In addition, oscillation can keep biological time, essential for embryonic development in promoting cell diversity and pattern formation. The functional importance of oscillatory processes requires a re-thinking of the traditional doctrine of homeostasis, holding that physiological quantities are maintained at constant equilibrium values, a view that has largely failed in the clinic. A more dynamic approach will initiate a paradigm shift in our view of health and disease. A deeper look into the mechanisms that create, sustain and abolish oscillatory processes requires the language of nonlinear dynamics, well beyond the linearization techniques of equilibrium control theory. Nonlinear dynamics enables us to identify oscillatory ('pacemaking') mechanisms at the cellular, tissue and system levels.
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Affiliation(s)
- Lingyun Ivy Xiong
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Alan Garfinkel
- Departments of Medicine (Cardiology) and Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
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Rasaei N, Samadi M, Khadem A, Badrooj N, Hassan Zadeh M, Ghaffarian-Ensaf R, Gholami F, Mirzaei K. The association between cholesterol/saturated fat index (CSI) and quality of sleep, and circadian rhythm among overweight and obese women: a cross-sectional study. JOURNAL OF HEALTH, POPULATION, AND NUTRITION 2023; 42:75. [PMID: 37501196 PMCID: PMC10375646 DOI: 10.1186/s41043-023-00414-1] [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: 05/01/2023] [Accepted: 07/09/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND The decline in sleep quality is one of the main public health problems affecting the global population. Some studies have shown that a high-fat diet may be linked to changes in circadian rhythm and sleep quality. The cholesterol/saturated fatty acid index (CSI) determines the amount of cholesterol and saturated fatty acid (SFA) in people's dietary patterns and can affect the quality of sleep and circadian rhythm. However, to date, no studies have investigated the effect of this index on these two variables. Therefore, our aim was to investigate the relationship between CSI on circadian rhythm and sleep quality in obese and overweight women. METHOD This cross-sectional study included 378 adult women who were obese or overweight. Using accepted techniques, anthropometric measurements, blood pressure readings, and biochemical variables were evaluated. A validated and trustworthy semi-quantitative food frequency questionnaire (FFQ 147 items) was used to gauge dietary intake. The CSI was measured to find out how much cholesterol and saturated fats were in the diet. Additionally, to assess circadian rhythm and sleep quality, respectively, the valid morning-evening questionnaire (MEQ) and Pittsburgh sleep quality index (PSQI) questionnaires were utilized. RESULT The results of the multinomial logistic regression model of our analysis showed that a significant association was observed between circadian rhythm status with CSI score, and participants with one higher unit of CSI had a 7.3% more chance of being in the eveningness group than being in morningness category in the crude model (OR: 1.07; 95% CI 1.00, 1.14; P = 0.026). This association remains marginally significant when adjusting for age, energy intake, BMI, job status, thyroid, and smoking status (OR = 1.08; 95% CI 1.00, 1.16; P = 0.051). The binary logistic regression model showed that after controlling for potentially confounding variables, there was no significant association between sleep quality with CSI score, however, those with one higher unit of CSI had 1.6% more chance of having sleep problems (OR: 1.01; 95% CI 0.96, 1.06; P = 0.503). CONCLUSION Our results indicated a direct marginally significant association between CSI with evening type in overweight and obese women. Future studies are needed to clarify the precise link between circadian rhythm and sleep behavior with fatty acid quality index.
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Affiliation(s)
- Niloufar Rasaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O. Box: 14155-6117, Tehran, Iran
| | - Mahsa Samadi
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O. Box: 14155-6117, Tehran, Iran
| | - Alireza Khadem
- Department of Nutrition, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Negin Badrooj
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O. Box: 14155-6117, Tehran, Iran
| | - Mohadeseh Hassan Zadeh
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Fatemeh Gholami
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O. Box: 14155-6117, Tehran, Iran
| | - Khadijeh Mirzaei
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences (TUMS), P.O. Box: 14155-6117, Tehran, Iran.
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Li Q, Zhang S, Wang H, Wang Z, Zhang X, Wang Y, Yuan J. Association of rotating night shift work, CLOCK, MTNR1A, MTNR1B genes polymorphisms and their interactions with type 2 diabetes among steelworkers: a case-control study. BMC Genomics 2023; 24:232. [PMID: 37138267 PMCID: PMC10157991 DOI: 10.1186/s12864-023-09328-y] [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: 04/12/2022] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND The purpose of this study is to investigate the association of rotating night shift work, CLOCK, MTNR1A, MTNR1B genes polymorphisms and their interactions with type 2 diabetes among steelworkers. METHODS A case-control study was conducted in the Tangsteel company in Tangshan, China. The sample sizes of the case group and control group were 251 and 451, respectively. The logistic regression, log-linear model and generalized multifactor dimensionality (GMDR) method were used to investigate the interaction between circadian clock gene, melatonin receptor genes and rotating night shift work on type 2 diabetes among steelworkers. Relative excess risk due to interaction (RERI) and attributable proportions (AP) were used to evaluate additive interactions. RESULTS Rotating night shift work, current shift status, duration of night shifts, and average frequency of night shifts were associated with an increased risk of type 2 diabetes after adjustment for confounders. Rs1387153 variants in MTNR1B was found to be associated with an increased risk of type 2 diabetes, which was not found between MTNR1A gene rs2119882 locus, CLOCK gene rs1801260 locus and the risk of type 2 diabetes. The association between rotating night shift work and risk of type 2 diabetes appeared to be modified by MTNR1B gene rs1387153 locus (RERI = 0.98, (95% CI, 0.40-1.55); AP = 0.60, (95% CI, 0.07-1.12)). The interaction between MTNR1A gene rs2119882 locus and CLOCK gene rs1801260 locus was associated with the risk of type 2 diabetes (RERI = 1.07, (95% CI, 0.23-1.91); AP = 0.77, (95% CI, 0.36-1.17)). The complex interaction of the MTNR1A-MTNR1B-CLOCK-rotating night shift work model based on the GMDR methods may increase the risk of type 2 diabetes (P = 0.011). CONCLUSIONS Rotating night shift work and rs1387153 variants in MTNR1B were associated with an increased risk of type 2 diabetes among steelworkers. The complex interaction of MTNR1A-MTNR1B-CLOCK-rotating night shift work may increase the risk of type 2 diabetes.
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Affiliation(s)
- Qinglin Li
- Department of Epidemiology and Health Statistics, School of Public Health, North China University of Science and Technology, Hebei, Tangshan, People's Republic of China
| | - Shengkui Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, North China University of Science and Technology, Hebei, Tangshan, People's Republic of China
| | - Han Wang
- Tianjin Baodi District Center for Disease Control, Tianjin, People's Republic of China
| | - Zhende Wang
- Department of Public Health Crisis Management, School of Public Health, Shandong Province, Weifang Medical University, Weifang, People's Republic of China
| | - Xiaohong Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, North China University of Science and Technology, Hebei, Tangshan, People's Republic of China
| | - Yongbin Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Xinxiang Medical University, Henan Province, Xinxiang, People's Republic of China.
| | - Juxiang Yuan
- Department of Epidemiology and Health Statistics, School of Public Health, North China University of Science and Technology, Hebei, Tangshan, People's Republic of China.
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18
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Migliori ML, Goya ME, Lamberti ML, Silva F, Rota R, Bénard C, Golombek DA. Caenorhabditis elegans as a Promising Model Organism in Chronobiology. J Biol Rhythms 2023; 38:131-147. [PMID: 36680418 DOI: 10.1177/07487304221143483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Circadian rhythms represent an adaptive feature, ubiquitously found in nature, which grants living beings the ability to anticipate daily variations in their environment. They have been found in a multitude of organisms, ranging from bacteria to fungi, plants, and animals. Circadian rhythms are generated by endogenous clocks that can be entrained daily by environmental cycles such as light and temperature. The molecular machinery of circadian clocks includes a transcriptional-translational feedback loop that takes approximately 24 h to complete. Drosophila melanogaster has been a model organism of choice to understand the molecular basis of circadian clocks. However, alternative animal models are also being adopted, each offering their respective experimental advantages. The nematode Caenorhabditis elegans provides an excellent model for genetics and neuro-behavioral studies, which thanks to its ease of use and manipulation, as well as availability of genetic data and mutant strains, is currently used as a novel model for circadian research. Here, we aim to evaluate C. elegans as a model for chronobiological studies, focusing on its strengths and weaknesses while reviewing the available literature. Possible zeitgebers (including light and temperature) are also discussed. Determining the molecular bases and the neural circuitry involved in the central pacemaker of the C. elegans' clock will contribute to the understanding of its circadian system, becoming a novel model organism for the study of diseases due to alterations of the circadian cycle.
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Affiliation(s)
- María Laura Migliori
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - María Eugenia Goya
- European Institute for the Biology of Aging, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Francisco Silva
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Rosana Rota
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Claire Bénard
- Department of Biological Sciences, CERMO-FC Research Center, Universite du Québec à Montréal, Montreál, QC, Canada
| | - Diego Andrés Golombek
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
- Universidad de San Andrés, Victoria, Argentina
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Miro C, Docimo A, Barrea L, Verde L, Cernea S, Sojat AS, Marina LV, Docimo G, Colao A, Dentice M, Muscogiuri G. "Time" for obesity-related cancer: The role of the circadian rhythm in cancer pathogenesis and treatment. Semin Cancer Biol 2023; 91:99-109. [PMID: 36893964 DOI: 10.1016/j.semcancer.2023.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/21/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
The circadian rhythm is regulated by an intrinsic time-tracking system, composed both of a central and a peripheral clock, which influences the cycles of activities and sleep of an individual over 24 h. At the molecular level, the circadian rhythm begins when two basic helix-loop-helix/Per-ARNT-SIM (bHLH-PAS) proteins, BMAL-1 and CLOCK, interact with each other to produce BMAL-1/CLOCK heterodimers in the cytoplasm. The BMAL-1/CLOCK target genes encode for the repressor components of the clock, cryptochrome (Cry1 and Cry2) and the Period proteins (Per1, Per2 and Per3). It has been recently demonstrated that the disruption of circadian rhythm is associated with an increased risk of developing obesity and obesity-related diseases. In addition, it has been demonstrated that the disruption of the circadian rhythm plays a key role in tumorigenesis. Further, an association between the circadian rhythm disruptions and an increased incidence and progression of several types of cancer (e.g., breast, prostate, colorectal and thyroid cancer) has been found. As the perturbation of circadian rhythm has adverse metabolic consequences (e.g., obesity) and at the same time tumor promoter functions, this manuscript has the aim to report how the aberrant circadian rhythms affect the development and prognosis of different types of obesity-related cancers (breast, prostate, colon rectal and thyroid cancer) focusing on both human studies and on molecular aspects.
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Affiliation(s)
- Caterina Miro
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131 Naples, Italy
| | - Annamaria Docimo
- Dipartimento di Medicina Clinica e Chirurgia, Unità di Endocrinologia, Diabetologia ed Andrologia, Università Federico II, Naples, Italy
| | - Luigi Barrea
- Dipartimento di Scienze Umanistiche, Università Telematica Pegaso, 80143 Naples, Italy
| | - Ludovica Verde
- Department of Public Health, University of Federico II, 80131 Naples, Italy
| | - Simona Cernea
- George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Târgu Mures/Internal Medicine I, Târgu Mureş, Romania; Diabetes, Nutrition and Metabolic Diseases Outpatient Unit, Emergency County Clinical Hospital, Târgu Mureş, Romania
| | - Antoan Stefan Sojat
- National Centre for Infertility and Endocrinology of Gender, Clinic for Endocrinology Diabetes and Metabolic Diseases, University Clinical Centre of Serbia, Serbia
| | - Ljiljana V Marina
- National Centre for Infertility and Endocrinology of Gender, Clinic for Endocrinology Diabetes and Metabolic Diseases, University Clinical Centre of Serbia, Serbia
| | - Giovanni Docimo
- Department of Medical and Advanced Surgical Sciences, University of Campania "Luigi Vanvitelli", 80131 Naples, Italy
| | - Annamaria Colao
- Dipartimento di Medicina Clinica e Chirurgia, Unità di Endocrinologia, Diabetologia ed Andrologia, Università Federico II, Naples, Italy; UNESCO Chair "Education for Health and Sustainable Development", University of Naples "Federico II", Naples, Italy
| | - Monica Dentice
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131 Naples, Italy
| | - Giovanna Muscogiuri
- Dipartimento di Medicina Clinica e Chirurgia, Unità di Endocrinologia, Diabetologia ed Andrologia, Università Federico II, Naples, Italy; UNESCO Chair "Education for Health and Sustainable Development", University of Naples "Federico II", Naples, Italy.
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20
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Li W, Wang Z, Cao J, Dong Y, Chen Y. Perfecting the Life Clock: The Journey from PTO to TTFL. Int J Mol Sci 2023; 24:ijms24032402. [PMID: 36768725 PMCID: PMC9916482 DOI: 10.3390/ijms24032402] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
The ubiquity of biological rhythms in life implies that it results from selection in the evolutionary process. The origin of the biological clock has two possible hypotheses: the selective pressure hypothesis of the oxidative stress cycle and the light evasion hypothesis. Moreover, the biological clock gives life higher adaptability. Two biological clock mechanisms have been discovered: the negative feedback loop of transcription-translation (TTFL) and the post-translational oscillation mechanism (PTO). The TTFL mechanism is the most classic and relatively conservative circadian clock oscillation mechanism, commonly found in eukaryotes. We have introduced the TTFL mechanism of the classical model organisms. However, the biological clock of prokaryotes is based on the PTO mechanism. The Peroxiredoxin (PRX or PRDX) protein-based PTO mechanism circadian clock widely existing in eukaryotic and prokaryotic life is considered a more conservative oscillation mechanism. The coexistence of the PTO and TTFL mechanisms in eukaryotes prompted us to explain the relationship between the two. Finally, we speculated that there might be a driving force for the evolution of the biological clock. The biological clock may have an evolutionary trend from the PTO mechanism to the TTFL mechanism, resulting from the evolution of organisms adapting to the environment.
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Affiliation(s)
- Weitian Li
- College of Veterinary Medicine, China Agricultural University, Haidian, Beijing 100193, China
| | - Zixu Wang
- College of Veterinary Medicine, China Agricultural University, Haidian, Beijing 100193, China
| | - Jing Cao
- College of Veterinary Medicine, China Agricultural University, Haidian, Beijing 100193, China
| | - Yulan Dong
- College of Veterinary Medicine, China Agricultural University, Haidian, Beijing 100193, China
| | - Yaoxing Chen
- College of Veterinary Medicine, China Agricultural University, Haidian, Beijing 100193, China
- Department of Nutrition and Health, China Agricultural University, Haidian, Beijing 100193, China
- Correspondence: ; Tel.: +86-10-62733778
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21
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Nakaya M, Wakamatsu M, Motegi H, Tanaka A, Sutherland K, Ishikawa M, Ozaki M, Shirato H, Hamada K, Hamada T. A real-time measurement system for gene expression rhythms from deep tissues of freely moving mice under light-dark conditions. Biochem Biophys Rep 2022; 32:101344. [PMID: 36160030 PMCID: PMC9489493 DOI: 10.1016/j.bbrep.2022.101344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 10/24/2022] Open
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22
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Careno DA, Perez Santangelo S, Macknight RC, Yanovsky MJ. The 5'-3' mRNA Decay Pathway Modulates the Plant Circadian Network in Arabidopsis. PLANT & CELL PHYSIOLOGY 2022; 63:1709-1719. [PMID: 36066193 DOI: 10.1093/pcp/pcac126] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/18/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Circadian rhythms enable organisms to anticipate and adjust their physiology to periodic environmental changes. These rhythms are controlled by biological clocks that consist of a set of clock genes that regulate each other's expression. Circadian oscillations in messenger RNA (mRNA) levels require the regulation of mRNA production and degradation. While transcription factors controlling clock function have been well characterized from cyanobacteria to humans, the role of factors controlling mRNA decay is largely unknown. Here, we show that mutations in SM-LIKE PROTEIN 1 (LSM1) and exoribonucleases 4 (XRN4), components of the 5'-3' mRNA decay pathway, alter clock function in Arabidopsis. We found that lsm1 and xrn4 mutants display long-period phenotypes for clock gene expression. In xrn4, these circadian defects were associated with changes in circadian phases of expression, but not overall mRNA levels, of several core-clock genes. We then used noninvasive transcriptome-wide mRNA stability analysis to identify genes and pathways regulated by XRN4. Among genes affected in the xrn4 mutant at the transcriptional and posttranscriptional level, we found an enrichment in genes involved in auxin, ethylene and drought recovery. Large effects were not observed for canonical core-clock genes, although the mRNAs of several auxiliary clock genes that control the pace of the clock were stabilized in xrn4 mutants. Our results establish that the 5'-3' mRNA decay pathway constitutes a novel posttranscriptional regulatory layer of the circadian gene network, which probably acts through a combination of small effects on mRNA stability of several auxiliary and some core-clock genes.
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Affiliation(s)
- Daniel A Careno
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
| | | | | | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
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23
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Chen SP, Wang DF, Ma WF, Lin XL, Yang G. Knockout of cryptochrome 1 disturbs the locomotor circadian rhythm and development of Plutella xylostella. INSECT SCIENCE 2022. [PMID: 36380712 DOI: 10.1111/1744-7917.13150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/24/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Cryptochrome 1 (CRY1) functions as a light-responsive photoreceptor, which is crucial for circadian rhythms. The identity and function of CRY1 in Plutella xylostella remain unknown. In this study, cry1 was cloned and identified in P. xylostella. Then, a cry1-knockout strain (Cry1-KO) of P. xylostella with a 2-bp deletion was established from the strain Geneva 88 (G88) using the CRISPR/Cas9 technology. No daily temporal oscillation of cry1 was observed in G88 and Cry1-KO, and cry1 mean daily transcription of Cry1-KO was lower than that of G88. Both G88 and Cry1-KO demonstrated rhythmic locomotion under the light/dark condition with Cry1-KO being more active than G88 in the daytime, whereas Cry1-KO completely lost rhythmicity under constant darkness. The developmental period of pre-adult of Cry1-KO was longer than that of G88; the lifespan of the Cry1-KO male adult was shorter than that of G88; the fecundity of Cry1-KO was lower than that of G88; and Cry1-KO showed lower intrinsic rate of increase (r), net reproduction rate (R0 ), finite increase rate (λ), and longer mean generation time (T) than G88. Our results indicate that cry1 is involved in the regulation of locomotor circadian rhythm and development in P. xylostella, providing a potential target gene for controlling the pest and a basis for further investigation on circadian rhythms in lepidopterans.
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Affiliation(s)
- Shao-Ping Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Dan-Feng Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Wei-Feng Ma
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Xiao-Lu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
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Pollinator biological traits and ecological interactions mediate the impacts of mosquito-targeting malathion application. Sci Rep 2022; 12:17039. [PMID: 36220841 PMCID: PMC9554017 DOI: 10.1038/s41598-022-20823-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/19/2022] [Indexed: 12/29/2022] Open
Abstract
Mosquito adulticides are perceived by the public as detrimental to nontarget arthropods, contributing to declines of native and beneficial insects. However, the actual impact of adulticides on nontarget arthropods in nature needs to incorporate biological and ecological elements. Here, we investigated the effect of biological/behavioral traits (butterfly roosting at different heights, roosting in sites underneath foliage, bumblebee hive usage) and interactions (parasitism, predation) of pollinators (butterflies and bumblebees) that could mediate the impacts of malathion application in manipulative semi-field experiments in Florida, USA. Roosting height from the spray route had a significant negative relationship with mortality of butterflies treated with ULV malathion, with high survival at the highest roosting height (7 m), but butterflies roosting among vegetation did not have higher survival. Bumblebees with hive access had significantly higher survival than bumblebees without hive access. Host plants treated with ULV malathion significantly reduced parasitism of monarch eggs by Trichogramma platneri, but increased predation of monarch caterpillars by Polistes paper wasps. These data provide insight into the realistic impacts of adulticide applications on pollinators in nature which will enable mosquito control districts to better limit nontarget effects of adulticide treatments and may help to address concerns related to potential nontarget effects.
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Oravec MW, Greenham K. The adaptive nature of the plant circadian clock in natural environments. PLANT PHYSIOLOGY 2022; 190:968-980. [PMID: 35894658 PMCID: PMC9516730 DOI: 10.1093/plphys/kiac337] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/27/2022] [Indexed: 05/10/2023]
Abstract
The plant circadian clock coordinates developmental, physiological, and metabolic processes with diel changes in light and temperature throughout the year. The balance between the persistence and plasticity of the clock in response to predictable and unpredictable environmental changes may be key to the clock's adaptive nature across temporal and spatial scales. Studies under controlled conditions have uncovered critical signaling pathways involved in light and temperature perception by the clock; however, they don't account for the natural lag of temperature behind photoperiod. Studies in natural environments provide key insights into the clock's adaptive advantage under more complex natural settings. Here, we discuss the role of the circadian clock in light and temperature perception and signaling, how the clock integrates these signals for a coordinated and adaptive response, and the adaptive advantage conferred by the clock across time and space in natural environments.
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Affiliation(s)
- Madeline W Oravec
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108, USA
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26
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Okada M, Yang Z, Mas P. Circadian autonomy and rhythmic precision of the Arabidopsis female reproductive organ. Dev Cell 2022; 57:2168-2180.e4. [PMID: 36115345 DOI: 10.1016/j.devcel.2022.08.013] [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: 03/25/2022] [Revised: 07/12/2022] [Accepted: 08/26/2022] [Indexed: 11/03/2022]
Abstract
The plant circadian clock regulates essential biological processes including flowering time or petal movement. However, little is known about how the clock functions in flowers. Here, we identified the circadian components and transcriptional networks contributing to the generation of rhythms in pistils, the female reproductive organ. When detached from the rest of the flower, pistils sustain highly precise rhythms, indicating organ-specific circadian autonomy. Analyses of clock mutants and chromatin immunoprecipitation assays showed distinct expression patterns and specific regulatory functions for clock activators and repressors in pistils. Genetic interaction studies also suggested a hierarchy of the repressing activities that provide robustness and precision to the pistil clock. Globally, the circadian function in pistils primarily governs responses to environmental stimuli and photosynthesis and controls pistil growth and seed weight and production. Understanding the circadian intricacies in reproductive organs may prove useful for optimizing plant reproduction and productivity.
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Affiliation(s)
- Masaaki Okada
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Zhiyuan Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain.
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27
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Hickner PV, Mori A, Rund SSC, Severson DW. Quantitative Trait Locus Determining the Time of Blood Feeding in Culex pipiens (Diptera: Culicidae). JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:1500-1506. [PMID: 35976948 PMCID: PMC9473656 DOI: 10.1093/jme/tjac118] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 06/15/2023]
Abstract
Mosquitoes and other blood feeding arthropods are vectors of pathogens causing serious human diseases, such as Plasmodium spp. (malaria), Wuchereria bancrofti (lymphatic filariasis), Borrelia burgdorferi (Lyme disease), and viruses causing dengue, Zika, West Nile, chikungunya, and yellow fever. Among the most effective strategies for the prevention of vector-borne diseases are those aimed at reducing human-vector interactions, such as insecticide applications and insecticide-treated bed nets (ITNs). In some areas where ITNs are widely used, behavioral adaptations have resulted in mosquitoes shifting their time of blood feeding to earlier or later in the night when the bed nets are not being employed. Little is known about the genetic basis of these behavioral shifts. We conducted quantitative trait locus (QTL) analysis using two strains of Culex pipiens sensu lato with contrasting blood feeding behaviors, wherein the lab adapted Shasta strain blood feeds at any time of the day or night, while the newly established Trinidad strain feeds only at night. We identified a single locus on chromosome 2 associated with the observed variation in feeding times. None of the core clock genes period, timeless, clock, cycle, PAR-domain protein 1, vrille, discs overgrown, cryptochrome 1, or cryptochrome 2 were located within the QTL region. We then monitored locomotor behavior to determine if they differed in their flight activity. The highly nocturnal Trinidad strain showed little daytime activity while the day-feeding Shasta strain was active during the day, suggesting blood feeding behavior and flight activity are physiologically linked.
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Affiliation(s)
- Paul V Hickner
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Laboratory, Kerrville, TX 78028, USA
| | - Akio Mori
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Samuel S C Rund
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
- Center for Research Computing, University of Notre Dame, Notre Dame, IN 46556, USA
| | - David W Severson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Life Sciences, University of the West Indies, Saint Augustine, Trinidad, West Indies
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, South Bend, IN, USA
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28
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Singh A, Li C, Diernfellner ACR, Höfer T, Brunner M. Data-driven modelling captures dynamics of the circadian clock of Neurospora crassa. PLoS Comput Biol 2022; 18:e1010331. [PMID: 35951637 PMCID: PMC9397904 DOI: 10.1371/journal.pcbi.1010331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/23/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic circadian clocks are based on self-sustaining, cell-autonomous oscillatory feedback loops that can synchronize with the environment via recurrent stimuli (zeitgebers) such as light. The components of biological clocks and their network interactions are becoming increasingly known, calling for a quantitative understanding of their role for clock function. However, the development of data-driven mathematical clock models has remained limited by the lack of sufficiently accurate data. Here we present a comprehensive model of the circadian clock of Neurospora crassa that describe free-running oscillations in constant darkness and entrainment in light-dark cycles. To parameterize the model, we measured high-resolution time courses of luciferase reporters of morning and evening specific clock genes in WT and a mutant strain. Fitting the model to such comprehensive data allowed estimating parameters governing circadian phase, period length and amplitude, and the response of genes to light cues. Our model suggests that functional maturation of the core clock protein Frequency causes a delay in negative feedback that is critical for generating circadian rhythms. Circadian rhythms are endogenous autonomous clocks that emancipate daily rhythms in physiology and behavior. Lately, a large body of research has contributed to our understanding of clocks’ genetic and mechanistic basis across kingdoms of life, i.e., mammals, fungi, plants, and bacteria. Several mathematical models have made key contributions to our current understanding of the design principles of the Neurospora crassa circadian clock and conditions for self-sustained oscillations. However, previous models uncovered and described the principle properties of the clock in generic manner due to a lack of experimental data. In this study, we developed a mathematical model based on systems of differential equations to describe the core clock components and estimated model parameters from luciferase data that capture experimental observations. We demonstrate the model predictive control simulation emphasizing the importance of functional maturation of the core clock protein Frequency in generating circadian rhythms.
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Affiliation(s)
- Amit Singh
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Congxin Li
- Theoretical Systems Biology [B086] Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | | | - Thomas Höfer
- Theoretical Systems Biology [B086] Deutsches Krebsforschungszentrum, Heidelberg, Germany
- * E-mail: (TH); (MB)
| | - Michael Brunner
- Heidelberg University Biochemistry Center, Heidelberg, Germany
- * E-mail: (TH); (MB)
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29
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Tatsumoto M, Matsumura R, Endo T, Tokuda IT, Node K, Akashi M. Potential negative effect of total parenteral nutrition on the human circadian clock. Genes Cells 2022; 27:613-620. [DOI: 10.1111/gtc.12976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Muneto Tatsumoto
- Medical Safety Management Center Dokkyo Medical University Hospital 880 Kitakobayashi, Mibu, Shimotsuga Tochigi Japan
| | - Ritsuko Matsumura
- The Research Institute for Time Studies, Yamaguchi University 1677‐1 Yoshida, Yamaguchi Yamaguchi Japan
| | - Takuyuki Endo
- Department of Neurology Osaka Toneyama Medical Center 5‐1‐1 Toneyama, Toyonaka Osaka Japan
| | - Isao T. Tokuda
- Department of Mechanical Engineering Ritsumeikan University 1‐1‐1 Nojihigashi Kusatsu Shiga Japan
| | - Koichi Node
- Department of Cardiovascular Medicine Saga University 5‐1‐1 Nabeshima, Saga Saga Japan
| | - Makoto Akashi
- The Research Institute for Time Studies, Yamaguchi University 1677‐1 Yoshida, Yamaguchi Yamaguchi Japan
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30
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Gong J, Tang Y, Liu Y, Sun R, Li Y, Ma J, Zhang S, Zhang F, Chen Z, Liao X, Sun H, Lu Z, Zhao C, Gao S. The Central Circadian Clock Protein TaCCA1 Regulates Seedling Growth and Spike Development in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:946213. [PMID: 35923880 PMCID: PMC9340162 DOI: 10.3389/fpls.2022.946213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/20/2022] [Indexed: 05/14/2023]
Abstract
The biological functions of the circadian clock on growth and development have been well elucidated in model plants, while its regulatory roles in crop species, especially the roles on yield-related traits, are poorly understood. In this study, we characterized the core clock gene CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) homoeologs in wheat and studied their biological functions in seedling growth and spike development. TaCCA1 homoeologs exhibit typical diurnal expression patterns, which are positively regulated by rhythmic histone modifications including histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 9 acetylation (H3K9Ac), and histone H3 lysine 36 trimethylation (H3K36me3). TaCCA1s are preferentially located in the nucleus and tend to form both homo- and heterodimers. TaCCA1 overexpression (TaCCA1-OE) transgenic wheat plants show disrupted circadian rhythmicity coupling with reduced chlorophyll and starch content, as well as biomass at seedling stage, also decreased spike length, grain number per spike, and grain size at the ripening stage. Further studies using DNA affinity purification followed by deep sequencing [DNA affinity purification and sequencing (DAP-seq)] indicated that TaCCA1 preferentially binds to sequences similarly to "evening elements" (EE) motif in the wheat genome, particularly genes associated with photosynthesis, carbon utilization, and auxin homeostasis, and decreased transcriptional levels of these target genes are observed in TaCCA1-OE transgenic wheat plants. Collectively, our study provides novel insights into a circadian-mediated mechanism of gene regulation to coordinate photosynthetic and metabolic activities in wheat, which is important for optimal plant growth and crop yield formation.
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Affiliation(s)
- Jie Gong
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yimiao Tang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yongjie Liu
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Renwei Sun
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanhong Li
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinxiu Ma
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shengquan Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fengting Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zhaobo Chen
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiangzheng Liao
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hui Sun
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zefu Lu
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changping Zhao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shiqing Gao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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31
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An Y, Yuan B, Xie P, Gu Y, Liu Z, Wang T, Li Z, Xu Y, Liu Y. Decoupling PER phosphorylation, stability and rhythmic expression from circadian clock function by abolishing PER-CK1 interaction. Nat Commun 2022; 13:3991. [PMID: 35810166 PMCID: PMC9271041 DOI: 10.1038/s41467-022-31715-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
Robust rhythms of abundances and phosphorylation profiles of PERIOD proteins were thought be the master rhythms that drive mammalian circadian clock functions. PER stability was proposed to be a major determinant of period length. In mammals, CK1 forms stable complexes with PER. Here we identify the PER residues essential for PER-CK1 interaction. In cells and in mice, their mutation abolishes PER phosphorylation and CLOCK hyperphosphorylation, resulting in PER stabilization, arrhythmic PER abundance and impaired negative feedback process, indicating that PER acts as the CK1 scaffold in circadian feedback mechanism. Surprisingly, the mutant mice exhibit robust short period locomotor activity and other physiological rhythms but low amplitude molecular rhythms. PER-CK1 interaction has two opposing roles in regulating CLOCK-BMAL1 activity. These results indicate that the circadian clock can function independently of PER phosphorylation and abundance rhythms due to another PER-CRY-dependent feedback mechanism and that period length can be uncoupled from PER stability.
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Affiliation(s)
- Yang An
- Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing, 210061, China.,Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Baoshi Yuan
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Pancheng Xie
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China.,Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yue Gu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhiwei Liu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Tao Wang
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhihao Li
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Ying Xu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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32
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Highly Sensitive Tryptophan Fluorescence Probe for detecting Rhythmic Conformational changes of KaiC in the Cyanobacterial Circadian Clock System. Biochem J 2022; 479:1505-1515. [PMID: 35771042 PMCID: PMC9342895 DOI: 10.1042/bcj20210544] [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: 01/04/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022]
Abstract
KaiC, a core protein of the cyanobacterial circadian clock, consists of an N-terminal CI domain and a C-terminal CII domain, and assembles into a double-ring hexamer upon binding with ATP. KaiC rhythmically phosphorylates and dephosphorylates its own two adjacent residues Ser431 and Thr432 at the CII domain with a period of approximately 24h through assembly and disassembly with the other clock proteins, KaiA and/or KaiB. In this study, to understand how KaiC alters its conformation as the source of circadian rhythm, we investigated structural changes of an inner-radius side of the CII ring using time-resolved Trp fluorescence spectroscopy. A KaiC mutant harboring a Trp fluorescence probe at a position of 419 exhibited a robust circadian rhythm with little temperature sensitivity in the presence of KaiA and KaiB. Our fluorescence observations show a remarkable environmental change at the inner-radius side of the CII ring during circadian oscillation. Crystallographic analysis revealed that a side chain of Trp at the position of 419 was oriented toward a region undergoing a helix-coil transition, which is considered to be a key event to allosterically regulate the CI ring that plays a crucial role in determining the cycle period. The present study provides a dynamical insight into how KaiC generates circadian oscillation.
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33
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Jalal A, Sun J, Chen Y, Fan C, Liu J, Wang C. Evolutionary Analysis and Functional Identification of Clock-Associated PSEUDO-RESPONSE REGULATOR (PRRs) Genes in the Flowering Regulation of Roses. Int J Mol Sci 2022; 23:ijms23137335. [PMID: 35806340 PMCID: PMC9266954 DOI: 10.3390/ijms23137335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/27/2023] Open
Abstract
Pseudo-response regulators (PRRs) are the important genes for flowering in roses. In this work, clock PRRs were genome-wide identified using Arabidopsis protein sequences as queries, and their evolutionary analyses were deliberated intensively in Rosaceae in correspondence with angiosperms species. To draw a comparative network and flow of clock PRRs in roses, a co-expression network of flowering pathway genes was drawn using a string database, and their functional analysis was studied by silencing using VIGS and protein-to-protein interaction. We revealed that the clock PRRs were significantly expanded in Rosaceae and were divided into three major clades, i.e., PRR5/9 (clade 1), PRR3/7 (clade 2), and TOC1/PRR1 (clade 3), based on their phylogeny. Within the clades, five clock PRRs were identified in Rosa chinensis. Clock PRRs had conserved RR domain and shared similar features, suggesting the duplication occurred during evolution. Divergence analysis indicated the role of duplication events in the expansion of clock PRRs. The diverse cis elements and interaction of clock PRRs with miRNAs suggested their role in plant development. Co-expression network analysis showed that the clock PRRs from Rosa chinensis had a strong association with flowering controlling genes. Further silencing of RcPRR1b and RcPRR5 in Rosa chinensis using VIGS led to earlier flowering, confirming them as negative flowering regulators. The protein-to-protein interactions between RcPRR1a/RcPRR5 and RcCO suggested that RcPRR1a/RcPRR5 may suppress flowering by interfering with the binding of RcCO to the promoter of RcFT. Collectively, these results provided an understanding of the evolutionary profiles as well as the functional role of clock PRRs in controlling flowering in roses.
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34
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Neves AR, Albuquerque T, Quintela T, Costa D. Circadian rhythm and disease: Relationship, new insights, and future perspectives. J Cell Physiol 2022; 237:3239-3256. [PMID: 35696609 DOI: 10.1002/jcp.30815] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/25/2022] [Accepted: 06/02/2022] [Indexed: 02/01/2023]
Abstract
The circadian system is responsible for internal functions and regulation of the organism according to environmental cues (zeitgebers). Circadian rhythm dysregulation or chronodisruption has been associated with several diseases, from mental to autoimmune diseases, and with life quality change. Following this, some therapies have been developed to correct circadian misalignments, such as light therapy and chronobiotics. In this manuscript, we describe the circadian-related diseases so far investigated, and studies reporting relevant data on this topic, evidencing this relationship, are included. Despite the actual limitations in published work, there is clear evidence of the correlation between circadian rhythm dysregulation and disease origin/development, and, in this way, clock-related therapies emerge as great progress in the clinical field. Future improvements in such interventions can lead to the development of successful chronotherapy strategies, deeply contributing to enhanced therapeutic outcomes.
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Affiliation(s)
- Ana R Neves
- CICS-UBI-Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal
| | - Tânia Albuquerque
- CICS-UBI-Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal
| | - Telma Quintela
- CICS-UBI-Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal.,Unidade de Investigação para o Desenvolvimento do Interior (UDI-IPG), Instituto Politécnico da Guarda, Guarda, Portugal
| | - Diana Costa
- CICS-UBI-Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal
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35
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Nidhi, Kumar P, Pathania D, Thakur S, Sharma M. Environment-mediated mutagenetic interference on genetic stabilization and circadian rhythm in plants. Cell Mol Life Sci 2022; 79:358. [PMID: 35687153 PMCID: PMC11072124 DOI: 10.1007/s00018-022-04368-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/21/2022] [Accepted: 05/07/2022] [Indexed: 12/29/2022]
Abstract
Many mortal organisms on this planet have developed the potential to merge all internal as well as external environmental cues to regulate various processes running inside organisms and in turn make them adaptive to the environment through the circadian clock. This moving rotator controls processes like activation of hormonal, metabolic, or defense pathways, initiation of flowering at an accurate period, and developmental processes in plants to ensure their stability in the environment. All these processes that are under the control of this rotating wheel can be changed either by external environmental factors or by an unpredictable phenomenon called mutation that can be generated by either physical mutagens, chemical mutagens, or by internal genetic interruption during metabolic processes, which alters normal functionality of organisms like innate immune responses, entrainment of the clock, biomass reduction, chlorophyll formation, and hormonal signaling, despite its fewer positive roles in plants like changing plant type, loss of vernalization treatment to make them survivable in different latitudes, and defense responses during stress. In addition, with mutation, overexpression of gene components sometimes supresses mutation effect and promote normal circadian genes abundance in the cell, while sometimes it affects circadian functionality by generating arrhythmicity and shows that not only mutation but overexpression also effects normal functional activities of plant. Therefore, this review mainly summarizes the role of each circadian clock genes in regulating rhythmicity, and shows that how circadian outputs are controlled by mutations as well as overexpression phenomenon.
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Affiliation(s)
- Nidhi
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India
| | - Pradeep Kumar
- Central University of Himachal Pradesh, Dharmshala, India
| | - Diksha Pathania
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India
| | - Sourbh Thakur
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, Gliwice, Poland
| | - Mamta Sharma
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India.
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36
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In Vivo Bioluminescence Analyses of Circadian Rhythms in Arabidopsis thaliana Using a Microplate Luminometer. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2482:395-406. [PMID: 35610442 DOI: 10.1007/978-1-0716-2249-0_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Our understanding of the circadian clock function in plants has been markedly assisted by studies with the model species Arabidopsis thaliana. Molecular and genetics approaches have delivered a comprehensive view of the transcriptional regulatory networks underlying the Arabidopsis circadian system. The use of the luciferase as a reporter allowed the precise in vivo determination of circadian periods, phases, and amplitudes of clock promoter activities with unprecedented temporal resolution. An increasing repertoire of fine-tuned luciferases together with additional applications such as translational fusions or bioluminescence molecular complementation assays have considerably expanded our view of circadian protein expression and activity, far beyond transcriptional regulation. Further applications have focused on the in vivo simultaneous examination of rhythms in different parts of the plant. The use of intact versus excised plant organs has also provided a glimpse on both the organ-specific and autonomy of the clocks and the importance of long distance communication for circadian function. This chapter provides a basic protocol for in vivo high-throughput monitoring of circadian rhythms in Arabidopsis seedlings using bioluminescent reporters and a microplate luminometer.
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37
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The role of cell-autonomous circadian oscillation of Cry transcription in circadian rhythm generation. Cell Rep 2022; 39:110703. [PMID: 35443162 DOI: 10.1016/j.celrep.2022.110703] [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: 12/20/2021] [Revised: 02/17/2022] [Accepted: 03/29/2022] [Indexed: 11/21/2022] Open
Abstract
The current model of the mammalian circadian clock describes cell-autonomous and negative feedback-driven circadian oscillation of Cry and Per transcription as the core circadian rhythm generator. However, the actual contribution of this oscillation to circadian rhythm generation remains undefined. Here we perform targeted disruption of cis elements indispensable for cell-autonomous Cry oscillation. Mice lacking overt cell-autonomous Cry oscillation show robust circadian rhythms in locomotor activity. In addition, tissue-autonomous circadian rhythms are robust in the absence of overt Cry oscillation. Unexpectedly, although the absence of overt Cry oscillation leads to severe attenuation of Per oscillation at the cell-autonomous level, circadian rhythms in Per2 accumulation remain robust. As a mechanism to explain this counterintuitive result, Per2 half-life shows cell-autonomous circadian rhythms independent of Cry and Per oscillation. The cell-autonomous circadian clock may therefore remain partially functional even in the absence of overt Cry and Per oscillation because of circadian oscillation in Per2 degradation.
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Nakahata Y, Fukada Y. Molecular connections between circadian clock and health/aging. J Biochem 2022; 171:473-476. [PMID: 35383844 DOI: 10.1093/jb/mvac028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/11/2022] [Indexed: 11/14/2022] Open
Abstract
For decades, considerable efforts have been expended for solving the molecular mechanisms of disease progression. An important clue to tackle this question is the circadian clock. Recent findings have uncovered previously unknown molecular connections between circadian clock and disease incidence, consequently causing the aging process. Furthermore, "chronotherapy" is emerging as a new concept of optimizing the time of the day for drug administration according to target gene expressions in order to maximize therapeutic efficacy and minimize the side effects. This concept will help cure patients and prevent them from suffering evitable pain and side effects. This JB special issue "Molecular connections between circadian clock and health/aging" discusses how the circadian clocks link to health and aging from molecular to organismal levels.
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Affiliation(s)
- Yasukazu Nakahata
- Department of Neurobiology & Behavior, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan
| | - Yoshitaka Fukada
- Department of Biological Sciences, School of Science
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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Sheardown E, Mech AM, Petrazzini MEM, Leggieri A, Gidziela A, Hosseinian S, Sealy IM, Torres-Perez JV, Busch-Nentwich EM, Malanchini M, Brennan CH. Translational relevance of forward genetic screens in animal models for the study of psychiatric disease. Neurosci Biobehav Rev 2022; 135:104559. [PMID: 35124155 PMCID: PMC9016269 DOI: 10.1016/j.neubiorev.2022.104559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/10/2021] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Psychiatric disorders represent a significant burden in our societies. Despite the convincing evidence pointing at gene and gene-environment interaction contributions, the role of genetics in the etiology of psychiatric disease is still poorly understood. Forward genetic screens in animal models have helped elucidate causal links. Here we discuss the application of mutagenesis-based forward genetic approaches in common animal model species: two invertebrates, nematodes (Caenorhabditis elegans) and fruit flies (Drosophila sp.); and two vertebrates, zebrafish (Danio rerio) and mice (Mus musculus), in relation to psychiatric disease. We also discuss the use of large scale genomic studies in human populations. Despite the advances using data from human populations, animal models coupled with next-generation sequencing strategies are still needed. Although with its own limitations, zebrafish possess characteristics that make them especially well-suited to forward genetic studies exploring the etiology of psychiatric disorders.
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Affiliation(s)
- Eva Sheardown
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Aleksandra M Mech
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | | | - Adele Leggieri
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Agnieszka Gidziela
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Saeedeh Hosseinian
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Ian M Sealy
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jose V Torres-Perez
- UK Dementia Research Institute at Imperial College London and Department of Brain Sciences, Imperial College London, 86 Wood Lane, London W12 0BZ, UK
| | - Elisabeth M Busch-Nentwich
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Margherita Malanchini
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Caroline H Brennan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK.
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Casein kinase rolls the dice in clocks from bread mold to humans. Proc Natl Acad Sci U S A 2022; 119:e2201492119. [PMID: 35312371 PMCID: PMC9060467 DOI: 10.1073/pnas.2201492119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Zielinski MR, Gibbons AJ. Neuroinflammation, Sleep, and Circadian Rhythms. Front Cell Infect Microbiol 2022; 12:853096. [PMID: 35392608 PMCID: PMC8981587 DOI: 10.3389/fcimb.2022.853096] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/24/2022] [Indexed: 12/14/2022] Open
Abstract
Molecules involved in innate immunity affect sleep and circadian oscillators and vice versa. Sleep-inducing inflammatory molecules are activated by increased waking activity and pathogens. Pathologies that alter inflammatory molecules, such as traumatic brain injury, cancer, cardiovascular disease, and stroke often are associated with disturbed sleep and electroencephalogram power spectra. Moreover, sleep disorders, such as insomnia and sleep disordered breathing, are associated with increased dysregulation of inflammatory processes. Inflammatory molecules in both the central nervous system and periphery can alter sleep. Inflammation can also modulate cerebral vascular hemodynamics which is associated with alterations in electroencephalogram power spectra. However, further research is needed to determine the interactions of sleep regulatory inflammatory molecules and circadian clocks. The purpose of this review is to: 1) describe the role of the inflammatory cytokines interleukin-1 beta and tumor necrosis factor-alpha and nucleotide-binding domain and leucine-rich repeat protein-3 inflammasomes in sleep regulation, 2) to discuss the relationship between the vagus nerve in translating inflammatory signals between the periphery and central nervous system to alter sleep, and 3) to present information about the relationship between cerebral vascular hemodynamics and the electroencephalogram during sleep.
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Affiliation(s)
- Mark R. Zielinski
- Veterans Affairs (VA) Boston Healthcare System, West Roxbury, MA, United States,Harvard Medical School, West Roxbury, MA, United States,*Correspondence: Mark R. Zielinski,
| | - Allison J. Gibbons
- Veterans Affairs (VA) Boston Healthcare System, West Roxbury, MA, United States
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Yang C, Hwang C, Tsai N, Yang M. Expression of circadian clock genes in leukocytes of patients with Meniere's disease. Laryngoscope Investig Otolaryngol 2022; 7:584-591. [PMID: 35434324 PMCID: PMC9008173 DOI: 10.1002/lio2.757] [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: 09/05/2021] [Revised: 01/07/2022] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
Objectives The underlying etiology of Meniere's disease (MD) is not completely clear, but the precipitated triggers may alter the circadian clock in patients with MD. This study aims to survey the expression of circadian clock genes in peripheral blood (PB) leukocytes of MD patients. Methods We investigated the expression of nine circadian clock genes in the PB leukocytes of patients with MD and normal controls using real‐time quantitative reverse transcriptase‐polymerase chain reaction (qRT‐PCR). Results We observed significantly lower expression of PER1 gene and higher expression of CLOCK gene in MD patients than those in normal controls (p < 0.05). PER1 did not associate with the degree of dizziness handicap in the patients with MD, but a lower expression of PER1 was significantly correlated with higher pure tone average (PTA) and speech reception threshold of the affected ear (p < 0.05). Patients with PTA > 30 dB had significantly lower PER1 expression than those with PTA ≤30 dB in the affected ear (p < 0.05). Our qRT‐PCR result was validated by fewer positively stained leukocytes for PER1 protein in the MD patients using the immunocytochemical study. Conclusion Our study implies the alteration of the circadian clock in patients with MD. In particular, the downregulation of PER1 correlated with the degree of hearing loss in the affected ear. PER1 in PB leukocytes may be a potential marker for the progression of hearing loss in MD.
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Affiliation(s)
- Chao‐Hui Yang
- Department of Otolaryngology Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung Taiwan
| | - Chung‐Feng Hwang
- Department of Otolaryngology Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung Taiwan
| | - Nai‐Wen Tsai
- Department of Neurology Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung Taiwan
| | - Ming‐Yu Yang
- Department of Otolaryngology Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung Taiwan
- Graduate Institute of Clinical Medical Sciences College of Medicine, Chang Gung University Tao‐Yuan Taiwan
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Duncan O, Millar AH. Day and night isotope labelling reveal metabolic pathway specific regulation of protein synthesis rates in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:745-763. [PMID: 34997626 DOI: 10.1111/tpj.15661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Plants have a diurnal separation of metabolic fluxes and a need for differential maintenance of protein machinery in the day and night. To directly assess the output of the translation process and to estimate the ATP investment involved, the individual rates of protein synthesis and degradation of hundreds of different proteins need to be measured simultaneously. We quantified protein synthesis and degradation through pulse labelling with heavy hydrogen in Arabidopsis thaliana rosettes to allow such an assessment of ATP investment in leaf proteome homeostasis on a gene-by-gene basis. Light-harvesting complex proteins were synthesised and degraded much faster in the day (approximately 10:1), while carbon metabolism and vesicle trafficking components were translated at similar rates day or night. Few leaf proteins changed in abundance between the day and the night despite reduced protein synthesis rates at night, indicating that protein degradation rates are tightly coordinated. The data reveal how the pausing of photosystem synthesis and degradation at night allows the redirection of a decreased energy budget to a selective night-time maintenance schedule.
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Affiliation(s)
- Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, Perth, WA, Australia
- Western Australian Proteomics, The University Western Australia, Perth, WA, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, Perth, WA, Australia
- Western Australian Proteomics, The University Western Australia, Perth, WA, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
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Senesi P, Ferrulli A, Luzi L, Terruzzi I. Chrono-communication and cardiometabolic health: The intrinsic relationship and therapeutic nutritional promises. Front Endocrinol (Lausanne) 2022; 13:975509. [PMID: 36176473 PMCID: PMC9513421 DOI: 10.3389/fendo.2022.975509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Circadian rhythm, an innate 24-h biological clock, regulates several mammalian physiological activities anticipating daily environmental variations and optimizing available energetic resources. The circadian machinery is a complex neuronal and endocrinological network primarily organized into a central clock, suprachiasmatic nucleus (SCN), and peripheral clocks. Several small molecules generate daily circadian fluctuations ensuring inter-organ communication and coordination between external stimuli, i.e., light, food, and exercise, and body metabolism. As an orchestra, this complex network can be out of tone. Circadian disruption is often associated with obesity development and, above all, with diabetes and cardiovascular disease onset. Moreover, accumulating data highlight a bidirectional relationship between circadian misalignment and cardiometabolic disease severity. Food intake abnormalities, especially timing and composition of meal, are crucial cause of circadian disruption, but evidence from preclinical and clinical studies has shown that food could represent a unique therapeutic approach to promote circadian resynchronization. In this review, we briefly summarize the structure of circadian system and discuss the role playing by different molecules [from leptin to ghrelin, incretins, fibroblast growth factor 21 (FGF-21), growth differentiation factor 15 (GDF15)] to guarantee circadian homeostasis. Based on the recent data, we discuss the innovative nutritional interventions aimed at circadian re-synchronization and, consequently, improvement of cardiometabolic health.
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Affiliation(s)
- Pamela Senesi
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
- Department of Endocrinology, Nutrition and Metabolic Diseases, IRCCS MultiMedica, Milan, Italy
| | - Anna Ferrulli
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
- Department of Endocrinology, Nutrition and Metabolic Diseases, IRCCS MultiMedica, Milan, Italy
| | - Livio Luzi
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
- Department of Endocrinology, Nutrition and Metabolic Diseases, IRCCS MultiMedica, Milan, Italy
| | - Ileana Terruzzi
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
- Department of Endocrinology, Nutrition and Metabolic Diseases, IRCCS MultiMedica, Milan, Italy
- *Correspondence: Ileana Terruzzi,
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Hartsock MJ, Strnad HK, Spencer RL. Iterative Metaplasticity Across Timescales: How Circadian, Ultradian, and Infradian Rhythms Modulate Memory Mechanisms. J Biol Rhythms 2021; 37:29-42. [PMID: 34781753 DOI: 10.1177/07487304211058256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Work in recent years has provided strong evidence for the modulation of memory function and neuroplasticity mechanisms across circadian (daily), ultradian (shorter-than-daily), and infradian (longer-than-daily) timescales. Despite rapid progress, however, the field has yet to adopt a general framework to describe the overarching role of biological rhythms in memory. To this end, Iyer and colleagues introduced the term iterative metaplasticity, which they define as the "gating of receptivity to subsequent signals that repeats on a cyclic timebase." The central concept is that the cyclic regulation of molecules involved in neuroplasticity may produce cycles in neuroplastic capacity-that is, the ability of neural cells to undergo activity-dependent change. Although Iyer and colleagues focus on the circadian timescale, we think their framework may be useful for understanding how biological rhythms influence memory more broadly. In this review, we provide examples and terminology to explain how the idea of iterative metaplasticity can be readily applied across circadian, ultradian, and infradian timescales. We suggest that iterative metaplasticity may not only support the temporal niching of neuroplasticity processes but also serve an essential role in the maintenance of memory function.
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Affiliation(s)
- Matthew J Hartsock
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
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Lagercrantz U, Billhardt A, Rousku SN, Leso M, Reza SH, Eklund DM. DE-ETIOLATED1 has a role in the circadian clock of the liverwort Marchantia polymorpha. THE NEW PHYTOLOGIST 2021; 232:595-609. [PMID: 34320227 DOI: 10.1111/nph.17653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Previous studies of plant circadian clock evolution have often relied on clock models and genes defined in Arabidopsis. These studies identified homologues with seemingly conserved function, as well as frequent gene loss. In the present study, we aimed to identify candidate clock genes in the liverwort Marchantia polymorpha using a more unbiased approach. To identify genes with circadian rhythm we sequenced the transcriptomes of gemmalings in a time series in constant light conditions. Subsequently, we performed functional studies using loss-of-function mutants and gene expression reporters. Among the genes displaying circadian rhythm, a homologue to the transcriptional co-repressor Arabidopsis DE-ETIOLATED1 showed high amplitude and morning phase. Because AtDET1 is arrhythmic and associated with the morning gene function of AtCCA1/LHY, that lack a homologue in liverworts, we functionally studied DET1 in M. polymorpha. We found that the circadian rhythm of MpDET1 expression is disrupted in loss-of-function mutants of core clock genes and putative evening-complex genes. MpDET1 knock-down in turn results in altered circadian rhythm of nyctinastic thallus movement and clock gene expression. We could not detect any effect of MpDET1 knock-down on circadian response to light, suggesting that MpDET1 has a yet unknown function in the M. polymorpha circadian clock.
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Affiliation(s)
- Ulf Lagercrantz
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anja Billhardt
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Sabine N Rousku
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Martina Leso
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Salim Hossain Reza
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - D Magnus Eklund
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- Physiological Botany, Department of Organismal Biology, Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls Väg 24E, SE-756 51, Uppsala, Sweden
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Mofatteh M, Echegaray-Iturra F, Alamban A, Dalla Ricca F, Bakshi A, Aydogan MG. Autonomous clocks that regulate organelle biogenesis, cytoskeletal organization, and intracellular dynamics. eLife 2021; 10:e72104. [PMID: 34586070 PMCID: PMC8480978 DOI: 10.7554/elife.72104] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/14/2021] [Indexed: 12/27/2022] Open
Abstract
How do cells perceive time? Do cells use temporal information to regulate the production/degradation of their enzymes, membranes, and organelles? Does controlling biological time influence cytoskeletal organization and cellular architecture in ways that confer evolutionary and physiological advantages? Potential answers to these fundamental questions of cell biology have historically revolved around the discussion of 'master' temporal programs, such as the principal cyclin-dependent kinase/cyclin cell division oscillator and the circadian clock. In this review, we provide an overview of the recent evidence supporting an emerging concept of 'autonomous clocks,' which under normal conditions can be entrained by the cell cycle and/or the circadian clock to run at their pace, but can also run independently to serve their functions if/when these major temporal programs are halted/abrupted. We begin the discussion by introducing recent developments in the study of such clocks and their roles at different scales and complexities. We then use current advances to elucidate the logic and molecular architecture of temporal networks that comprise autonomous clocks, providing important clues as to how these clocks may have evolved to run independently and, sometimes at the cost of redundancy, have strongly coupled to run under the full command of the cell cycle and/or the circadian clock. Next, we review a list of important recent findings that have shed new light onto potential hallmarks of autonomous clocks, suggestive of prospective theoretical and experimental approaches to further accelerate their discovery. Finally, we discuss their roles in health and disease, as well as possible therapeutic opportunities that targeting the autonomous clocks may offer.
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Affiliation(s)
- Mohammad Mofatteh
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Fabio Echegaray-Iturra
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Andrew Alamban
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Francesco Dalla Ricca
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Anand Bakshi
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Mustafa G Aydogan
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
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Jiang J, Li B, He W, Huang C. Dietary serine supplementation: Friend or foe? Curr Opin Pharmacol 2021; 61:12-20. [PMID: 34547701 DOI: 10.1016/j.coph.2021.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/11/2021] [Accepted: 08/18/2021] [Indexed: 02/08/2023]
Abstract
Serine lies at a critical node in biological processes involved in supplying intermediates for redox homeostasis, nucleotide, or lipid biosynthesis and one-carbon metabolism-coupled methyl donor production. Recently, dietary serine supplementation has been reported to modulate cellular serine levels and ameliorate neurological abnormalities induced by serine deficiency. Moreover, growing evidence showed that serine supplementation also alleviates fatty liver, encephalopathy, diabetes mellitus, and related complications, indicating the possibility of serine supplementation as a complementary therapeutic option. However, considering the serine addiction observed in tumorigenesis and tumor development, limitations may exist regarding the application of dietary serine supplementation in patients with cancer. Here, we assess recent research toward the mechanistic understanding of serine supplementation in various diseases to improve our cognition on modulating serine levels in different patients.
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Affiliation(s)
- Jingwen Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, PR China
| | - Bowen Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, PR China
| | - Weifeng He
- State Key Laboratory of Trauma, Burn and Combined Injury, Institute of Burn Research, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, Chengdu, PR China; Chongqing Key Laboratory for Disease Proteomics, Chongqing, Chengdu, PR China.
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, PR China.
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From circadian clock mechanism to sleep disorders and jet lag: Insights from a computational approach. Biochem Pharmacol 2021; 191:114482. [DOI: 10.1016/j.bcp.2021.114482] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022]
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50
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Moseley RC, Motta F, Tuskan GA, Haase SB, Yang X. Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi. Cells 2021; 10:2217. [PMID: 34571864 PMCID: PMC8471846 DOI: 10.3390/cells10092217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 02/01/2023] Open
Abstract
The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in Kalanchoë fedtschenkoi. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.
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Affiliation(s)
- Robert C. Moseley
- Department of Biology, Duke University, Durham, NC 27708, USA; (R.C.M.); (S.B.H.)
| | - Francis Motta
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA;
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA;
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven B. Haase
- Department of Biology, Duke University, Durham, NC 27708, USA; (R.C.M.); (S.B.H.)
- Department of Medicine, Duke University, Durham, NC 27708, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA;
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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