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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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Beale AD, Hayter EA, Crosby P, Valekunja UK, Edgar RS, Chesham JE, Maywood ES, Labeed FH, Reddy AB, Wright KP, Lilley KS, Bechtold DA, Hastings MH, O'Neill JS. Mechanisms and physiological function of daily haemoglobin oxidation rhythms in red blood cells. EMBO J 2023; 42:e114164. [PMID: 37554073 PMCID: PMC10548169 DOI: 10.15252/embj.2023114164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/16/2023] [Accepted: 07/16/2023] [Indexed: 08/10/2023] Open
Abstract
Cellular circadian rhythms confer temporal organisation upon physiology that is fundamental to human health. Rhythms are present in red blood cells (RBCs), the most abundant cell type in the body, but their physiological function is poorly understood. Here, we present a novel biochemical assay for haemoglobin (Hb) oxidation status which relies on a redox-sensitive covalent haem-Hb linkage that forms during SDS-mediated cell lysis. Formation of this linkage is lowest when ferrous Hb is oxidised, in the form of ferric metHb. Daily haemoglobin oxidation rhythms are observed in mouse and human RBCs cultured in vitro, or taken from humans in vivo, and are unaffected by mutations that affect circadian rhythms in nucleated cells. These rhythms correlate with daily rhythms in core body temperature, with temperature lowest when metHb levels are highest. Raising metHb levels with dietary sodium nitrite can further decrease daytime core body temperature in mice via nitric oxide (NO) signalling. These results extend our molecular understanding of RBC circadian rhythms and suggest they contribute to the regulation of body temperature.
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Affiliation(s)
| | - Edward A Hayter
- Centre for Biological Timing, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Priya Crosby
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzCAUSA
| | - Utham K Valekunja
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Institute for Translational Medicine and Therapeutics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Rachel S Edgar
- Department of Infectious DiseasesImperial College LondonLondonUK
| | | | | | - Fatima H Labeed
- Faculty of Engineering and Physical SciencesUniversity of SurreyGuildfordUK
| | - Akhilesh B Reddy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Institute for Translational Medicine and Therapeutics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Kenneth P Wright
- Department of Integrative Physiology, Sleep and Chronobiology LaboratoryUniversity of Colorado BoulderBoulderCOUSA
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - David A Bechtold
- Centre for Biological Timing, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
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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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Fujii J, Homma T, Kobayashi S, Warang P, Madkaikar M, Mukherjee MB. Erythrocytes as a preferential target of oxidative stress in blood. Free Radic Res 2021; 55:562-580. [PMID: 33427524 DOI: 10.1080/10715762.2021.1873318] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Red blood cells (RBC) are specifically differentiated to transport oxygen and carbon dioxide in the blood and they lack most organelles, including mitochondria. The autoxidation of hemoglobin constitutes a major source of reactive oxygen species (ROS). Nitric oxide, which is produced by endothelial nitric oxide synthase (NOS3) or via the hemoglobin-mediated conversion of nitrite, interacts with ROS and results in the production of reactive nitrogen oxide species. Herein we present an overview of anemic diseases that are closely related to oxidative damage. Because the compensation of proteins by means of gene expression does not proceed in enucleated cells, antioxidative and redox systems play more important roles in maintaining the homeostasis of RBC against oxidative insult compared to ordinary cells. Defects in hemoglobin and enzymes that are involved in energy production and redox reactions largely trigger oxidative damage to RBC. The results of studies using genetically modified mice suggest that antioxidative enzymes, notably superoxide dismutase 1 and peroxiredoxin 2, play essential roles in coping with oxidative damage in erythroid cells, and their absence limits erythropoiesis, the life-span of RBC and consequently results in the development of anemia. The degeneration of the machinery involved in the proteolytic removal of damaged proteins appears to be associated with hemolytic events. The ubiquitin-proteasome system is the dominant machinery, not only for the proteolytic removal of damaged proteins in erythroid cells but also for the development of erythropoiesis. Hence, despite the fact that it is less abundant in RBC compared to ordinary cells, the aberrant ubiquitin-proteasome system may be associated with the development of anemic diseases via the accumulation of damaged proteins, as typified in sickle cell disease, and impaired erythropoiesis.
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Affiliation(s)
- Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata, Japan
| | - Takujiro Homma
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata, Japan
| | - Sho Kobayashi
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata, Japan
| | - Prashant Warang
- ICMR - National Institute of Immunohaematology, Mumbai, India
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Millius A, Ode KL, Ueda HR. A period without PER: understanding 24-hour rhythms without classic transcription and translation feedback loops. F1000Res 2019; 8. [PMID: 31031966 PMCID: PMC6468715 DOI: 10.12688/f1000research.18158.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/09/2019] [Indexed: 01/08/2023] Open
Abstract
Since Ronald Konopka and Seymour Benzer's discovery of the gene Period in the 1970s, the circadian rhythm field has diligently investigated regulatory mechanisms and intracellular transcriptional and translation feedback loops involving Period, and these investigations culminated in a 2017 Nobel Prize in Physiology or Medicine for Michael W. Young, Michael Rosbash, and Jeffrey C. Hall. Although research on 24-hour behavior rhythms started with Period, a series of discoveries in the past decade have shown us that post-transcriptional regulation and protein modification, such as phosphorylation and oxidation, are alternatives ways to building a ticking clock.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Laboratory of Systems Immunology and Laboratory of Host Defense, Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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Yamada Y, Prosser RA. Copper in the suprachiasmatic circadian clock: A possible link between multiple circadian oscillators. Eur J Neurosci 2018; 51:47-70. [PMID: 30269387 DOI: 10.1111/ejn.14181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 09/05/2018] [Accepted: 09/17/2018] [Indexed: 01/07/2023]
Abstract
The mammalian circadian clock in the suprachiasmatic nucleus (SCN) is very robust, able to coordinate our daily physiological and behavioral rhythms with exquisite accuracy. Simultaneously, the SCN clock is highly sensitive to environmental timing cues such as the solar cycle. This duality of resiliency and sensitivity may be sustained in part by a complex intertwining of three cellular oscillators: transcription/translation, metabolic/redox, and membrane excitability. We suggest here that one of the links connecting these oscillators may be forged from copper (Cu). Cellular Cu levels are highly regulated in the brain and peripherally, and Cu affects cellular metabolism, redox state, cell signaling, and transcription. We have shown that both Cu chelation and application induce nighttime phase shifts of the SCN clock in vitro and that these treatments affect glutamate, N-methyl-D-aspartate receptor, and associated signaling processes differently. More recently we found that Cu induces mitogen-activated protein kinase-dependent phase shifts, while the mechanisms by which Cu removal induces phase shifts remain unclear. Lastly, we have found that two Cu transporters are expressed in the SCN, and that one of these transporters (ATP7A) exhibits a day/night rhythm. Our results suggest that Cu homeostasis is tightly regulated in the SCN, and that changes in Cu levels may serve as a time cue for the circadian clock. We discuss these findings in light of the existing literature and current models of multiple coupled circadian oscillators in the SCN.
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Affiliation(s)
- Yukihiro Yamada
- Department of Biochemistry & Cellular and Molecular Biology, NeuroNET Research Center, University of Tennessee, Knoxville, Tennessee
| | - Rebecca A Prosser
- Department of Biochemistry & Cellular and Molecular Biology, NeuroNET Research Center, University of Tennessee, Knoxville, Tennessee
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Double Knockout of Peroxiredoxin 4 (Prdx4) and Superoxide Dismutase 1 (Sod1) in Mice Results in Severe Liver Failure. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:2812904. [PMID: 30050648 PMCID: PMC6040270 DOI: 10.1155/2018/2812904] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/04/2018] [Accepted: 04/30/2018] [Indexed: 12/16/2022]
Abstract
Mice that are deficient in superoxide dismutase 1 (Sod1), an antioxidative enzyme, are susceptible to developing liver steatosis. Peroxiredoxin 4 (Prdx4) catalyzes disulfide bond formation in proteins via the action of hydrogen peroxide and hence decreases oxidative stress and supports oxidative protein folding for the secretion of lipoproteins. Because elevated reactive oxygen species induce endoplasmic reticulum stress, this negative chain reaction is likely involved in the development of nonalcoholic fatty liver diseases and more advanced steatohepatitis (NASH). In the current study, we generated Prdx4 and Sod1 double knockout (DKO; Prdx4-/ySod1-/-) mice and examined whether the combined deletion of Prdx4 and Sod1 aggravated liver pathology compared to single knockout and wild-type mice. The secretion of triglyceride-rich lipoprotein was strikingly impaired in the DKO mice, leading to aggravated liver steatosis. Simultaneously, the activation of caspase-3 in the liver was observed. The hyperoxidation of Prdxs, a hallmark of oxidative stress, occurred in different isoforms that are uniquely associated with Sod1-/- and Prdx4-/y mice, and the effect was additive in DKO mouse livers. Because DKO mice spontaneously develop severe liver failure at a relatively young stage, they have the potential for use as a model for hepatic disorders and for testing other potential treatments.
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Abstract
Mounting evidence in recent years supports the extensive interaction between the circadian and redox systems. The existence of such a relationship is not surprising because most organisms, be they diurnal or nocturnal, display daily oscillations in energy intake, locomotor activity, and exposure to exogenous and internally generated oxidants. The transcriptional clock controls the levels of many antioxidant proteins and redox-active cofactors, and, conversely, the cellular redox poise has been shown to feed back to the transcriptional oscillator via redox-sensitive transcription factors and enzymes. However, the circadian cycles in the S-sulfinylation of the peroxiredoxin (PRDX) proteins constituted the first example of an autonomous circadian redox oscillation, which occurred independently of the transcriptional clock. Importantly, the high phylogenetic conservation of these rhythms suggests that they might predate the evolution of the transcriptional oscillator, and therefore could be a part of a primordial circadian redox/metabolic oscillator. This discovery forced the reappraisal of the dogmatic transcription-centered view of the clockwork and opened a new avenue of research. Indeed, the investigation into the links between the circadian and redox systems is still in its infancy, and many important questions remain to be addressed.
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Wang Y, Pati P, Xu Y, Chen F, Stepp DW, Huo Y, Rudic RD, Fulton DJR. Endotoxin Disrupts Circadian Rhythms in Macrophages via Reactive Oxygen Species. PLoS One 2016; 11:e0155075. [PMID: 27168152 PMCID: PMC4863972 DOI: 10.1371/journal.pone.0155075] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/24/2016] [Indexed: 12/04/2022] Open
Abstract
The circadian clock is a transcriptional network that functions to regulate the expression of genes important in the anticipation of changes in cellular and organ function. Recent studies have revealed that the recognition of pathogens and subsequent initiation of inflammatory responses are strongly regulated by a macrophage-intrinsic circadian clock. We hypothesized that the circadian pattern of gene expression might be influenced by inflammatory stimuli and that loss of circadian function in immune cells can promote pro-inflammatory behavior. To investigate circadian rhythms in inflammatory cells, peritoneal macrophages were isolated from mPer2luciferase transgenic mice and circadian oscillations were studied in response to stimuli. Using Cosinor analysis, we found that LPS significantly altered the circadian period in peritoneal macrophages from mPer2luciferase mice while qPCR data suggested that the pattern of expression of the core circadian gene (Bmal1) was disrupted. Inhibition of TLR4 offered protection from the LPS-induced impairment in rhythm, suggesting a role for toll-like receptor signaling. To explore the mechanisms involved, we inhibited LPS-stimulated NO and superoxide. Inhibition of NO synthesis with L-NAME had no effect on circadian rhythms. In contrast, inhibition of superoxide with Tempol or PEG-SOD ameliorated the LPS-induced changes in circadian periodicity. In gain of function experiments, we found that overexpression of NOX5, a source of ROS, could significantly disrupt circadian function in a circadian reporter cell line (U2OS) whereas iNOS overexpression, a source of NO, was ineffective. To assess whether alteration of circadian rhythms influences macrophage function, peritoneal macrophages were isolated from Bmal1-KO and Per-TKO mice. Compared to WT macrophages, macrophages from circadian knockout mice exhibited altered balance between NO and ROS release, increased uptake of oxLDL and increased adhesion and migration. These results suggest that pro-inflammatory stimuli can disrupt circadian rhythms in macrophages and that impaired circadian rhythms may contribute to cardiovascular diseases by altering macrophage behavior.
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Affiliation(s)
- Yusi Wang
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, United States of America
| | - Paramita Pati
- Department of Pharmacology, Medical College of Georgia at Augusta University, Augusta, Georgia, United States of America
| | - Yiming Xu
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, United States of America
| | - Feng Chen
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, United States of America
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - David W. Stepp
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, United States of America
| | - Yuqing Huo
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, United States of America
| | - R. Daniel Rudic
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, United States of America
- * E-mail: (DF); (RDR)
| | - David J. R. Fulton
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, United States of America
- * E-mail: (DF); (RDR)
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Putker M, O’Neill JS. Reciprocal Control of the Circadian Clock and Cellular Redox State - a Critical Appraisal. Mol Cells 2016; 39:6-19. [PMID: 26810072 PMCID: PMC4749875 DOI: 10.14348/molcells.2016.2323] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 11/26/2015] [Indexed: 12/16/2022] Open
Abstract
Redox signalling comprises the biology of molecular signal transduction mediated by reactive oxygen (or nitrogen) species. By specific and reversible oxidation of redox-sensitive cysteines, many biological processes sense and respond to signals from the intracellular redox environment. Redox signals are therefore important regulators of cellular homeostasis. Recently, it has become apparent that the cellular redox state oscillates in vivo and in vitro, with a period of about one day (circadian). Circadian time-keeping allows cells and organisms to adapt their biology to resonate with the 24-hour cycle of day/night. The importance of this innate biological time-keeping is illustrated by the association of clock disruption with the early onset of several diseases (e.g. type II diabetes, stroke and several forms of cancer). Circadian regulation of cellular redox balance suggests potentially two distinct roles for redox signalling in relation to the cellular clock: one where it is regulated by the clock, and one where it regulates the clock. Here, we introduce the concepts of redox signalling and cellular timekeeping, and then critically appraise the evidence for the reciprocal regulation between cellular redox state and the circadian clock. We conclude there is a substantial body of evidence supporting circadian regulation of cellular redox state, but that it would be premature to conclude that the converse is also true. We therefore propose some approaches that might yield more insight into redox control of cellular timekeeping.
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Affiliation(s)
- Marrit Putker
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH,
UK
| | - John Stuart O’Neill
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH,
UK
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A brief history of circadian time: The emergence of redox oscillations as a novel component of biological rhythms. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.pisc.2015.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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