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Kwak JS, León-Tapia MÁ, Diblasi C, Manousi D, Grønvold L, Sandvik GK, Saitou M. Functional and regulatory diversification of Period genes responsible for circadian rhythm in vertebrates. G3 (BETHESDA, MD.) 2024; 14:jkae162. [PMID: 39028850 PMCID: PMC11457068 DOI: 10.1093/g3journal/jkae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular rhythms through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes at the copy number and sequence levels, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3, which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa.
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Affiliation(s)
- Jun Soung Kwak
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - M Ángel León-Tapia
- Colección Nacional de Mamíferos, Pabellón Nacional de la Biodiversidad, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
| | - Celian Diblasi
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Domniki Manousi
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Lars Grønvold
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Guro Katrine Sandvik
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Marie Saitou
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Ås, Norway
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Farré R, Rodríguez-Lázaro MA, Otero J, Gavara N, Sunyer R, Farré N, Gozal D, Almendros I. Low-cost, open-source device for simultaneously subjecting rodents to different circadian cycles of light, food, and temperature. Front Physiol 2024; 15:1356787. [PMID: 38434139 PMCID: PMC10904513 DOI: 10.3389/fphys.2024.1356787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/05/2024] [Indexed: 03/05/2024] Open
Abstract
Exposure of experimental rodents to controlled cycles of light, food, and temperature is important when investigating alterations in circadian cycles that profoundly influence health and disease. However, applying such stimuli simultaneously is difficult in practice. We aimed to design, build, test, and open-source describe a simple device that subjects a conventional mouse cage to independent cycles of physiologically relevant environmental variables. The device is based on a box enclosing the rodent cage to modify the light, feeding, and temperature environments. The device provides temperature-controlled air conditioning (heating or cooling) by a Peltier module and includes programmable feeding and illumination. All functions are set by a user-friendly front panel for independent cycle programming. Bench testing with a model simulating the CO2 production of mice in the cage showed: a) suitable air renewal (by measuring actual ambient CO2), b) controlled realistic illumination at the mouse enclosure (measured by a photometer), c) stable temperature control, and d) correct cycling of light, feeding, and temperature. The cost of all the supplies (retail purchased by e-commerce) was <300 US$. Detailed technical information is open-source provided, allowing for any user to reliably reproduce or modify the device. This approach can considerably facilitate circadian research since using one of the described low-cost devices for any mouse group with a given light-food-temperature paradigm allows for all the experiments to be performed simultaneously, thereby requiring no changes in the light/temperature of a general-use laboratory.
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Affiliation(s)
- Ramon Farré
- Unit of Biophysics and Bioengineering, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
- Institut Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
| | - Miguel A. Rodríguez-Lázaro
- Unit of Biophysics and Bioengineering, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Jorge Otero
- Unit of Biophysics and Bioengineering, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
- The Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Núria Gavara
- Unit of Biophysics and Bioengineering, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- The Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Raimon Sunyer
- Unit of Biophysics and Bioengineering, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - Núria Farré
- Discipline of Cardiology, Saolta University Healthcare Group, Galway, Ireland
- School of Medicine, University of Galway, Galway, Ireland
| | - David Gozal
- Office of the Dean, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Isaac Almendros
- Unit of Biophysics and Bioengineering, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Barcelona, Spain
- Institut Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
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Fyie LR, Westby KM, Meuti ME. Light pollution disrupts circadian clock gene expression in two mosquito vectors during their overwintering dormancy. Sci Rep 2024; 14:2398. [PMID: 38287057 PMCID: PMC10824765 DOI: 10.1038/s41598-024-52794-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/23/2024] [Indexed: 01/31/2024] Open
Abstract
Artificial light at night (ALAN) is an increasingly important form of environmental disturbance as it alters Light:Dark cycles that regulate daily and seasonal changes in physiology and phenology. The Northern house mosquito (Culex pipiens) and the tiger mosquito (Aedes albopictus) enter an overwintering dormancy known as diapause that is cued by short days. These two species differ in diapause strategy: Cx. pipiens diapause as adult females while Ae. albopictus enter a maternally-programmed, egg diapause. Previous studies found that ALAN inhibits diapause in both species, but the mechanism is unknown. As the circadian clock is implicated in the regulation of diapause in many insects, we examined whether exposure to ALAN altered the daily expression of core circadian cloc genes (cycle, Clock, period, timeless, cryptochrome 1, cryptochrome 2, and Par domain protein 1) in these two species when reared under short-day, diapause-inducing conditions. We found that exposure to ALAN altered the abundance of several clock genes in adult females of both species, but that clock gene rhythmicity was maintained for most genes. ALAN also had little effect on clock gene abundance in mature oocytes that were dissected from female Ae. albopictus that were reared under short day conditions. Our findings indicate that ALAN may inhibit diapause initiation through the circadian clock in two medically-important mosquitoes.
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Affiliation(s)
- Lydia R Fyie
- Department of Entomology, The Ohio State University, 2021 Coffey Rd, Columbus, OH, 43210, USA.
| | - Katie M Westby
- Tyson Research Center, Washington University in St. Louis, 6750 Tyson Valley Road, Eureka, MO, 63025, USA
| | - Megan E Meuti
- Department of Entomology, The Ohio State University, 2021 Coffey Rd, Columbus, OH, 43210, USA
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Lyu J, Zhuang Y, Lin Y. Circadian regulation of translation. RNA Biol 2024; 21:14-24. [PMID: 39324589 PMCID: PMC11441039 DOI: 10.1080/15476286.2024.2408524] [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] [Revised: 09/09/2024] [Accepted: 09/16/2024] [Indexed: 09/27/2024] Open
Abstract
Most, if not all organisms exhibit robust rhythmicity of their biological functions, allowing a perpetual adaptation to external clues within the daily 24 hours-cycle. Studies on circadian rhythm regulation primarily focused on transcriptional level, considering mRNA levels to represent the primary determinant of oscillations of intracellular protein levels. However, a plethora of emerging evidence suggests that post-transcriptional regulation, particularly rhythmic mRNA translation, is not solely reliant on the oscillation of transcription. Instead, the circadian regulation of mRNA translation plays a critical role as well. A comprehensive understanding of these mechanisms underlying rhythmic translation and its regulation should bridge the gap in rhythm regulation beyond RNA fluctuations in research, and greatly enhance our comprehension of rhythm generation and maintenance. In this review, we summarize the major mechanisms of circadian regulation of translation, including regulation of translation initiation, elongation, and the alteration in rhythmic translation to external stresses, such as endoplasmic reticulum (ER) stress and ageing. We also illuminate the complex interplay between phase separation and mRNA translation. Together, we have summarized various facets of mRNA translation in circadian regulation, to set on forthcoming studies into the intricate regulatory mechanisms underpinning circadian rhythms and their implications for associated disorders.
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Affiliation(s)
- Jiali Lyu
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yanrong Zhuang
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yi Lin
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
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Pang X, Chen L, Xu G. New Awareness of the Interplay Between the Gut Microbiota and Circadian Rhythms. Pol J Microbiol 2023; 72:355-363. [PMID: 38095865 PMCID: PMC10725168 DOI: 10.33073/pjm-2023-046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/27/2023] [Indexed: 12/17/2023] Open
Abstract
Circadian rhythms influence various aspects of the biology and physiology of the host, such as food intake and sleep/wake cycles. In recent years, an increasing amount of genetic and epidemiological data has shown that the light/dark cycle is the main cue that regulates circadian rhythms. Other factors, including sleep/wake cycles and food intake, have necessary effects on the composition and rhythms of the gut microbiota. Interestingly, the gut microbiota can affect the circadian rhythm of hosts in turn through contact-dependent and contact-independent mechanisms. Furthermore, the gut microbiota has been shown to regulate the sleep/wake cycles through gut-brain-microbiota interaction. In addition to diabetes, the gut microbiota can also intervene in the progression of neuro- degenerative diseases through the gut-brain-microbiota interaction, and also in other diseases such as hypertension and rheumatoid arthritis, where it is thought to have a spare therapeutic potential. Even though fecal microbiota transplantation has good potential for treating many diseases, the risk of spreading intestinal pathogens should not be ignored.
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Affiliation(s)
- Xiaoxiao Pang
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, China
| | - Long Chen
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, China
| | - Guoxin Xu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, China
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