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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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Tamaru Y, Nakanishi S, Tanaka K, Umetsu M, Nakazawa H, Sugiyama A, Ito T, Shimokawa N, Takagi M. Recent research advances on non-linear phenomena in various biosystems. J Biosci Bioeng 2023:S1389-1723(23)00107-X. [PMID: 37246137 DOI: 10.1016/j.jbiosc.2023.03.012] [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: 09/02/2022] [Revised: 03/03/2023] [Accepted: 03/22/2023] [Indexed: 05/30/2023]
Abstract
All biological phenomena can be classified as open, dissipative and non-linear. Moreover, the most typical phenomena are associated with non-linearity, dissipation and openness in biological systems. In this review article, four research topics on non-linear biosystems are described to show the examples from various biological systems. First, membrane dynamics of a lipid bilayer for the cell membrane is described. Since the cell membrane separates the inside of the cell from the outside, self-organizing systems that form spatial patterns on membranes often depend on non-linear dynamics. Second, various data banks based on recent genomics analysis supply the data including vast functional proteins from many organisms and their variable species. Since the proteins existing in nature are only a very small part of the space represented by amino acid sequence, success of mutagenesis-based molecular evolution approach crucially depends on preparing a library with high enrichment of functional proteins. Third, photosynthetic organisms depend on ambient light, the regular and irregular changes of which have a significant impact on photosynthetic processes. The light-driven process proceeds through many redox couples in the cyanobacteria constituting chain of redox reactions. Forth topics focuses on a vertebrate model, the zebrafish, which can help to understand, predict and control the chaos of complex biological systems. In particular, during early developmental stages, developmental differentiation occurs dynamically from a fertilized egg to divided and mature cells. These exciting fields of complexity, chaos, and non-linear science have experienced impressive growth in recent decades. Finally, future directions for non-liner biosystems are presented.
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Affiliation(s)
- Yutaka Tamaru
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie 514-8507, Japan.
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kenya Tanaka
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Aruto Sugiyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masahiro Takagi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Hatano J, Kusama S, Tanaka K, Kohara A, Miyake C, Nakanishi S, Shimakawa G. NADPH production in dark stages is critical for cyanobacterial photocurrent generation: a study using mutants deficient in oxidative pentose phosphate pathway. PHOTOSYNTHESIS RESEARCH 2022; 153:113-120. [PMID: 35182311 DOI: 10.1007/s11120-022-00903-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Live cyanobacteria and algae integrated onto an extracellular electrode can generate a light-induced current (i.e., a photocurrent). Although the photocurrent is expected to be correlated with the redox environment of the photosynthetic cells, the relationship between the photocurrent and the cellular redox state is poorly understood. Here, we investigated the effect of the reduced nicotinamide adenine dinucleotide phosphate [NADP(H)] redox level of cyanobacterial cells (before light exposure) on the photocurrent using several mutants (Δzwf, Δgnd, and ΔglgP) deficient in the oxidative pentose phosphate (OPP) pathway, which is the metabolic pathway that produces NADPH in darkness. The NAD(P)H redox level and photocurrent in the cyanobacterium Synechocystis sp. PCC 6803 were measured noninvasively. Dysfunction of the OPP pathway led to oxidation of the photosynthetic NADPH pool in darkness. In addition, photocurrent induction was retarded and the current density was lower in Δzwf, Δgnd, and ΔglgP than in wild-type cells. Exogenously added glucose compensated the phenotype of ΔglgP and drove the OPP pathway in the mutant, resulting in an increase in the photocurrent. The results indicated that NADPH accumulated by the OPP pathway before illumination is a key factor for the generation of a photocurrent. In addition, measuring the photocurrent can be a non-invasive approach to estimate the cellular redox level related to NADP(H) pool in cyanobacteria.
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Affiliation(s)
- Jiro Hatano
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan
| | - Shoko Kusama
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan
| | - Kenya Tanaka
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan
- Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Ayaka Kohara
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Chikahiro Miyake
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan.
- Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Ginga Shimakawa
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan.
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan.
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Light exposure mediates circadian rhythms of rhizosphere microbial communities. THE ISME JOURNAL 2021; 15:2655-2664. [PMID: 33746202 PMCID: PMC8397761 DOI: 10.1038/s41396-021-00957-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 02/01/2023]
Abstract
Microbial community circadian rhythms have a broad influence on host health and even though light-induced environmental fluctuations could regulate microbial communities, the contribution of light to the circadian rhythms of rhizosphere microbial communities has received little attention. To address this gap, we monitored diel changes in the microbial communities in rice (Oryza sativa L.) rhizosphere soil under light-dark and constant dark regimes, identifying microbes with circadian rhythms caused by light exposure and microbial circadian clocks, respectively. While rhizosphere microbial communities displayed circadian rhythms under light-dark and constant dark regimes, taxa possessing circadian rhythms under the two conditions were dissimilar. Light exposure concealed microbial circadian clocks as a regulatory driver, leading to fewer ecological niches in light versus dark communities. These findings disentangle regulation mechanisms for circadian rhythms in the rice rhizosphere microbial communities and highlight the role of light-induced regulation of rhizosphere microbial communities.
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Kaneko M, Ishihara K, Nakanishi S. Redox-Active Polymers Connecting Living Microbial Cells to an Extracellular Electrical Circuit. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001849. [PMID: 32734709 DOI: 10.1002/smll.202001849] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial electrochemical systems in which metabolic electrons in living microbes have been extracted to or injected from an extracellular electrical circuit have attracted considerable attention as environmentally-friendly energy conversion systems. Since general microbes cannot exchange electrons with extracellular solids, electron mediators are needed to connect living cells to an extracellular electrode. Although hydrophobic small molecules that can penetrate cell membranes are commonly used as electron mediators, they cannot be dissolved at high concentrations in aqueous media. The use of hydrophobic mediators in combination with small hydrophilic redox molecules can substantially increase the efficiency of the extracellular electron transfer process, but this method has side effects, in some cases, such as cytotoxicity and environmental pollution. In this Review, recently-developed redox-active polymers are highlighted as a new type of electron mediator that has less cytotoxicity than many conventional electron mediators. Owing to the design flexibility of polymer structures, important parameters that affect electron transport properties, such as redox potential, the balance of hydrophobicity and hydrophilicity, and electron conductivity, can be systematically regulated.
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Affiliation(s)
- Masahiro Kaneko
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kazuhiko Ishihara
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
- Graduate School of Engineering Science Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
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