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Ohsawa S, Schwaiger M, Iesmantavicius V, Hashimoto R, Moriyama H, Matoba H, Hirai G, Sodeoka M, Hashimoto A, Matsuyama A, Yoshida M, Yashiroda Y, Bühler M. Nitrogen signaling factor triggers a respiration-like gene expression program in fission yeast. EMBO J 2024:10.1038/s44318-024-00224-z. [PMID: 39256560 DOI: 10.1038/s44318-024-00224-z] [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: 03/01/2024] [Revised: 08/08/2024] [Accepted: 08/16/2024] [Indexed: 09/12/2024] Open
Abstract
Microbes have evolved intricate communication systems that enable individual cells of a population to send and receive signals in response to changes in their immediate environment. In the fission yeast Schizosaccharomyces pombe, the oxylipin nitrogen signaling factor (NSF) is part of such communication system, which functions to regulate the usage of different nitrogen sources. Yet, the pathways and mechanisms by which NSF acts are poorly understood. Here, we show that NSF physically interacts with the mitochondrial sulfide:quinone oxidoreductase Hmt2 and that it prompts a change from a fermentation- to a respiration-like gene expression program without any change in the carbon source. Our results suggest that NSF activity is not restricted to nitrogen metabolism alone and that it could function as a rheostat to prepare a population of S. pombe cells for an imminent shortage of their preferred nutrients.
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Affiliation(s)
- Shin Ohsawa
- Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056, Basel, Switzerland
| | - Michaela Schwaiger
- Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056, Basel, Switzerland
- Swiss Institute of Bioinformatics, 4056, Basel, Switzerland
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056, Basel, Switzerland
| | - Rio Hashimoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8538, Tokyo, Japan
| | - Hiromitsu Moriyama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8538, Tokyo, Japan
| | - Hiroaki Matoba
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi Higashi-ku, 812-8582, Fukuoka, Japan
| | - Go Hirai
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi Higashi-ku, 812-8582, Fukuoka, Japan
- Catalysis and Integrated Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
| | - Mikiko Sodeoka
- Catalysis and Integrated Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
| | - Atsushi Hashimoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
| | - Akihisa Matsuyama
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan
- Office of University Professors, The University of Tokyo, Bunkyo-ku, 113-8657, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, 113-8657, Tokyo, Japan
| | - Yoko Yashiroda
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan.
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Saitama, Japan.
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056, Basel, Switzerland.
- University of Basel, Petersplatz 10, 4003, Basel, Switzerland.
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2
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Bakhshi Sichani S, Khorshid M, Yongabi D, Urbán CT, Schreurs M, Verstrepen KJ, Lettinga MP, Schöning MJ, Lieberzeit P, Wagner P. Design of a Multiparametric Biosensing Platform and Its Validation in a Study on Spontaneous Cell Detachment from Temperature Gradients. ACS Sens 2024; 9:3967-3978. [PMID: 39079008 DOI: 10.1021/acssensors.4c00732] [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: 08/24/2024]
Abstract
This article reports on a bioanalytical sensor device that hosts three different transducer principles: impedance spectroscopy, quartz-crystal microbalance with dissipation monitoring, and the thermal-current-based heat-transfer method. These principles utilize a single chip, allowing one to perform either microbalance and heat transfer measurements in parallel or heat transfer and impedance measurements. When taking specific precautions, the three measurement modalities can even be used truly simultaneously. The probed parameters are distinctly different, so that one may speak about multiparametric or "orthogonal" sensing without crosstalk between the sensing circuits. Hence, this sensor allows one to identify which of these label-free sensing principles performs best for a given bioanalytical application in terms of a high signal amplitude and signal-to-noise ratio. As a proof-of-concept, the three-parameter sensor was validated by studying the spontaneous, collective detachment of eukaryotic cells in the presence of a temperature gradient between the QCM chip and the supernatant liquid. In addition to heat transfer, detachment can also be monitored by the impedance- and QCM-related signals. These features allow for the distinguishing between different yeast strains that differ in their flocculation genes, and the sensor device enables proliferation monitoring of yeast colonies over time.
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Affiliation(s)
- Soroush Bakhshi Sichani
- Laboratory for Soft Matter and Biophysics, ZMB, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Mehran Khorshid
- Laboratory for Soft Matter and Biophysics, ZMB, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Derick Yongabi
- Laboratory for Soft Matter and Biophysics, ZMB, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Csongor Tibor Urbán
- Laboratory for Soft Matter and Biophysics, ZMB, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
| | - Michiel Schreurs
- Laboratory for Genetics and Genomics, VIB - KU Leuven Center for Microbiology, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, VIB - KU Leuven Center for Microbiology, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Minne Paul Lettinga
- Laboratory for Soft Matter and Biophysics, ZMB, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
- Biomolecular Systems and Processes IBI-4, Institute of Biological Information Processing, Research Center Jülich, Wilhelm-Johnen-Straße, D-52428 Jülich, Germany
| | - Michael J Schöning
- Institute for Nano- and Biotechnologies, Aachen University of Applied Sciences, Heinrich-Mussmann-Straße 1, D-52428 Jülich, Germany
| | - Peter Lieberzeit
- Department of Physical Chemistry, Faculty for Chemistry, University of Vienna, Währinger Strasse 42, AT-1090 Vienna, Austria
| | - Patrick Wagner
- Laboratory for Soft Matter and Biophysics, ZMB, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200 D, B-3001 Leuven, Belgium
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Gutbier U, Korp J, Scheufler L, Ostermann K. Genetic modules for α-factor pheromone controlled growth regulation of Saccharomyces cerevisiae. Eng Life Sci 2024; 24:e2300235. [PMID: 39113811 PMCID: PMC11300815 DOI: 10.1002/elsc.202300235] [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: 08/15/2023] [Revised: 03/29/2024] [Accepted: 05/05/2024] [Indexed: 08/10/2024] Open
Abstract
Saccharomyces cerevisiae is a commonly used microorganism in the biotechnological industry. For the industrial heterologous production of compounds, it is of great advantage to work with growth-controllable yeast strains. In our work, we utilized the natural pheromone system of S. cerevisiae and generated a set of different strains possessing an α-pheromone controllable growth behavior. Naturally, the α-factor pheromone is involved in communication between haploid S. cerevisiae cells. Perception of the pheromone initiates several cellular changes, enabling the cells to prepare for an upcoming mating event. We exploited this natural pheromone response system and developed two different plasmid-based modules, in which the target genes, MET15 and FAR1, are under control of the α-factor sensitive FIG1 promoter for a controlled expression in S. cerevisiae. Whereas expression of MET15 led to a growth induction, FAR1 expression inhibited growth. The utilization of low copy number or high copy number plasmids for target gene expression and different concentrations of α-factor allow a finely adjustable control of yeast growth rate.
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Affiliation(s)
- Uta Gutbier
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
- Else Kröner Fresenius Center for Digital HealthFaculty of Medicine Carl Gustav CarusTUD Dresden University of TechnologyDresdenGermany
| | - Juliane Korp
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
| | - Lennart Scheufler
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
| | - Kai Ostermann
- Faculty of BiologyResearch Group Biological Sensor‐Actuator‐SystemsTUD Dresden University of TechnologyDresdenGermany
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4
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Liu H, Zhang X, Chen W, Wang C. The regulatory functions of oxylipins in fungi: A review. J Basic Microbiol 2023; 63:1073-1084. [PMID: 37357952 DOI: 10.1002/jobm.202200721] [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: 12/29/2022] [Revised: 03/02/2023] [Accepted: 03/09/2023] [Indexed: 06/27/2023]
Abstract
Quorum sensing (QS) is a communication mechanism between microorganisms originally found in bacteria. In recent years, an important QS mechanism has been discovered in the field of fungi, namely, the lipoxygenase compound oxylipin of arachidonic acid acts as a QS molecule in life cycle control, particularly in the sexual and asexual development of fungi. However, the role of oxylipins in mediating eukaryotic communication has not been previously described. In this paper, we review the regulatory role of oxylipins and the underlying mechanisms and discuss the potential for application in major fungi. The role of oxylipin as a fungal quorum-sensing molecule is the main focus of the review. Besides, the quorum regulation of fungal morphological transformation, biofilm formation, virulence factors, secondary metabolism, infection, symbiosis, and other physiological behaviors are discussed. Moreover, future prospectives and applications are elaborated as well.
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Affiliation(s)
- Huiqian Liu
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Xizi Zhang
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Wei Chen
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Chengtao Wang
- Key Laboratory of Geriatric Nutrition and Health, Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
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5
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Bordet F, Romanet R, Bahut F, Ballester J, Eicher C, Peña C, Ferreira V, Gougeon R, Julien-Ortiz A, Roullier-Gall C, Alexandre H. Expanding the diversity of Chardonnay aroma through the metabolic interactions of Saccharomyces cerevisiae cocultures. Front Microbiol 2023; 13:1032842. [PMID: 36845971 PMCID: PMC9947296 DOI: 10.3389/fmicb.2022.1032842] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/02/2022] [Indexed: 02/11/2023] Open
Abstract
Yeast co-inoculations in winemaking are often studied in the framework of modulating the aromatic profiles of wines. Our study aimed to investigate the impact of three cocultures and corresponding pure cultures of Saccharomyces cerevisiae on the chemical composition and the sensory profile of Chardonnay wine. Coculture makes it possible to obtain completely new aromatic expressions that do not exist in the original pure cultures attributed to yeast interactions. Esters, fatty acids and phenol families were identified as affected. The sensory profiles and metabolome of the cocultures, corresponding pure cultures and associated wine blends from both pure cultures were found to be different. The coculture did not turn out to be the addition of the two pure culture wines, indicating the impact of interaction. High resolution mass spectrometry revealed thousands of cocultures biomarkers. The metabolic pathways involved in these wine composition changes were highlighted, most of them belonging to nitrogen metabolism.
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Affiliation(s)
- Fanny Bordet
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France,Lallemand SAS, Blagnac, France,*Correspondence: Fanny Bordet,
| | - Rémy Romanet
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France
| | - Florian Bahut
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France,Lallemand SAS, Blagnac, France
| | - Jordi Ballester
- Centre des Sciences du Goût et de l’Alimentation, CNRS, INRAE, Institut Agro, Université Bourgogne Franche-Comté, Dijon, France
| | - Camille Eicher
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France
| | - Cristina Peña
- Dpt. Química Analítica, Facultad de Ciencias, University of Zaragoza, Zaragoza, Spain
| | - Vicente Ferreira
- Dpt. Química Analítica, Facultad de Ciencias, University of Zaragoza, Zaragoza, Spain
| | - Régis Gougeon
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France,DIVVA (Développement Innovation Vigne Vin Aliments) Platform/PAM UMR, IUVV, Dijon, France
| | | | - Chloé Roullier-Gall
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France
| | - Hervé Alexandre
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France
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6
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Rojas V, Larrondo LF. Coupling Cell Communication and Optogenetics: Implementation of a Light-Inducible Intercellular System in Yeast. ACS Synth Biol 2023; 12:71-82. [PMID: 36534043 PMCID: PMC9872819 DOI: 10.1021/acssynbio.2c00338] [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: 06/28/2022] [Indexed: 12/23/2022]
Abstract
Cell communication is a widespread mechanism in biology, allowing the transmission of information about environmental conditions. In order to understand how cell communication modulates relevant biological processes such as survival, division, differentiation, and apoptosis, different synthetic systems based on chemical induction have been successfully developed. In this work, we coupled cell communication and optogenetics in the budding yeast Saccharomyces cerevisiae. Our approach is based on two strains connected by the light-dependent production of α-factor pheromone in one cell type, which induces gene expression in the other type. After the individual characterization of the different variants of both strains, the optogenetic intercellular system was evaluated by combining the cells under contrasting illumination conditions. Using luciferase as a reporter gene, specific co-cultures at a 1:1 ratio displayed activation of the response upon constant blue light, which was not observed for the same cell mixtures grown in darkness. Then, the system was assessed at several dark/blue-light transitions, where the response level varies depending on the moment in which illumination was delivered. Furthermore, we observed that the amplitude of response can be tuned by modifying the initial ratio between both strains. Finally, the two-population system showed higher fold inductions in comparison with autonomous strains. Altogether, these results demonstrated that external light information is propagated through a diffusible signaling molecule to modulate gene expression in a synthetic system involving microbial cells, which will pave the road for studies allowing optogenetic control of population-level dynamics.
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Affiliation(s)
- Vicente Rojas
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Luis F. Larrondo
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
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7
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Chiu PC, Nakamura Y, Nishimura S, Tabuchi T, Yashiroda Y, Hirai G, Matsuyama A, Yoshida M. Ferrichrome, a fungal-type siderophore, confers high ammonium tolerance to fission yeast. Sci Rep 2022; 12:17411. [PMID: 36302945 PMCID: PMC9613971 DOI: 10.1038/s41598-022-22108-0] [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: 07/01/2022] [Accepted: 10/10/2022] [Indexed: 01/12/2023] Open
Abstract
Microorganisms and plants produce siderophores, which function to transport environmental iron into cells as well as participate in cellular iron use and deposition. Their biological functions are diverse although their role in primary metabolism is poorly understood. Ferrichrome is a fungal-type siderophore synthesized by nonribosomal peptide synthetase (NRPS). Herein we show that ferrichrome induces adaptive growth of fission yeast on high ammonium media. Ammonium is a preferred nitrogen source as it suppresses uptake and catabolism of less preferred nitrogen sources such as leucine through a mechanism called nitrogen catabolite repression (NCR). Therefore, the growth of fission yeast mutant cells with leucine auxotrophy is suppressed in the presence of high concentrations of ammonium. This growth suppression was canceled by ferrichrome in a manner dependent on the amino acid transporter Cat1. Additionally, growth retardation of wild-type cells by excess ammonium was exacerbated by deleting the NRPS gene sib1, which is responsible for the biosynthesis of ferrichrome, suggesting that intrinsically produced ferrichrome functions in suppressing the metabolic action of ammonium. Furthermore, ferrichrome facilitated the growth of both wild-type and sib1-deficient cells under low glucose conditions. These results suggest that intracellular iron regulates primary metabolism, including NCR, which is mediated by siderophores.
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Affiliation(s)
- Po-Chang Chiu
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Yuri Nakamura
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Shinichi Nishimura
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan ,grid.26999.3d0000 0001 2151 536XCollaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Toshitsugu Tabuchi
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Yoko Yashiroda
- grid.509461.f0000 0004 1757 8255RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198 Japan
| | - Go Hirai
- grid.509461.f0000 0004 1757 8255RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198 Japan ,grid.177174.30000 0001 2242 4849Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 Japan
| | - Akihisa Matsuyama
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan ,grid.509461.f0000 0004 1757 8255RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198 Japan
| | - Minoru Yoshida
- grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan ,grid.26999.3d0000 0001 2151 536XCollaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657 Japan ,grid.509461.f0000 0004 1757 8255RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198 Japan
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Abdul Hamid NW, Nadarajah K. Microbe Related Chemical Signalling and Its Application in Agriculture. Int J Mol Sci 2022; 23:ijms23168998. [PMID: 36012261 PMCID: PMC9409198 DOI: 10.3390/ijms23168998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
The agriculture sector has been put under tremendous strain by the world’s growing population. The use of fertilizers and pesticides in conventional farming has had a negative impact on the environment and human health. Sustainable agriculture attempts to maintain productivity, while protecting the environment and feeding the global population. The importance of soil-dwelling microbial populations in overcoming these issues cannot be overstated. Various processes such as rhizospheric competence, antibiosis, release of enzymes, and induction of systemic resistance in host plants are all used by microbes to influence plant-microbe interactions. These processes are largely founded on chemical signalling. Producing, releasing, detecting, and responding to chemicals are all part of chemical signalling. Different microbes released distinct sorts of chemical signal molecules which interacts with the environment and hosts. Microbial chemicals affect symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm growth, to name a few. We present an in-depth overview of chemical signalling between bacteria-bacteria, bacteria-fungi, and plant-microbe and the diverse roles played by these compounds in plant microbe interactions. These compounds’ current and potential uses and significance in agriculture have been highlighted.
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Singh D, Lee SH, Lee CH. Non-obligate pairwise metabolite cross-feeding suggests ammensalic interactions between Bacillus amyloliquefaciens and Aspergillus oryzae. Commun Biol 2022; 5:232. [PMID: 35293898 PMCID: PMC8924192 DOI: 10.1038/s42003-022-03181-7] [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: 09/10/2021] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial-fungal metabolite trade-offs determine their ecological interactions. We designed a non-obligate pairwise metabolite cross-feeding (MCF) between Bacillus amyloliquefaciens and Aspergillus oryzae. Cross-feeding Aspergillus metabolites (MCF-1) affected higher growth and biofilm formation in Bacillus. LC-MS/MS-based multivariate analyses (MVA) showed variations in the endogenous metabolite profiles between the cross-fed and control Bacillus. We observed and validated that Aspergillus-derived oxylipins were rapidly depleted in Bacillus cultures concomitant with lowered secretion of cyclic lipopeptides (CLPs). Conversely, Bacillus extracts cross-fed to Aspergillus (MCF-2) diminished its mycelial growth and conidiation. Fungistatic effects of Bacillus-derived cyclic surfactins were temporally reduced following their hydrolytic linearization. MVA highlighted disparity between the cross-fed (MCF-2) and control Aspergillus cultures with marked variations in the oxylipin levels. We conclude that the pairwise MCF selectively benefitted Bacillus while suppressing Aspergillus, which suggests their ammensalic interaction. Widening this experimental pipeline across tailored communities may help model and simulate BFIs in more complex microbiomes. Metabolite trade-offs between Bacillus amyloliquefaciens and Aspergillus oryzae selectively benefit the bacterial partner and suppress fungal growth, showcasing their ammensalic interaction.
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Affiliation(s)
- Digar Singh
- Department of Bioscience and Biotechnology, Konkuk University, 05029, Seoul, Korea
| | - Sang Hee Lee
- Department of Bioscience and Biotechnology, Konkuk University, 05029, Seoul, Korea
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, 05029, Seoul, Korea.
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Analysis of Volatile Molecules Present in the Secretome of the Fungal Pathogen Candida glabrata. Molecules 2021; 26:molecules26133881. [PMID: 34202061 PMCID: PMC8270331 DOI: 10.3390/molecules26133881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/15/2021] [Accepted: 06/21/2021] [Indexed: 01/04/2023] Open
Abstract
Candida albicans, Candida glabrata, Candida parapsilosis and Candida tropicalis are the four most common human fungal pathogens isolated that can cause superficial and invasive infections. It has been shown that specific metabolites present in the secretomes of these fungal pathogens are important for their virulence. C. glabrata is the second most common isolate world-wide and has an innate resistance to azoles, xenobiotics and oxidative stress that allows this fungal pathogen to evade the immune response and persist within the host. Here, we analyzed and compared the C. glabrata secretome with those of C. albicans, C. parapsilosis, C. tropicalis and the non-pathogenic yeast Saccharomyces cerevisiae. In C. glabrata, we identified a different number of metabolites depending on the growth media: 12 in synthetic complete media (SC), 27 in SC-glutamic acid and 23 in rich media (YPD). C. glabrata specific metabolites are 1-dodecene (0.09 ± 0.11%), 2,5-dimethylundecane (1.01 ± 0.19%), 3,7-dimethyldecane (0.14 ± 0.15%), and octadecane (0.4 ± 0.53%). The metabolites that are shared with C. albicans, C. glabrata, C. parapsilosis, C. tropicalis and S. cerevisiae are phenylethanol, which is synthesized from phenylalanine, and eicosane and nonanoic acid (identified as trimethylsilyl ester), which are synthesized from fatty acid metabolism. Phenylethanol is the most abundant metabolite in all fungi tested: 26.36 ± 17.42% (C. glabrata), 46.77 ± 15.58% (C. albicans), 49.76 ± 18.43% (C. tropicalis), 5.72 ± 0.66% (C. parapsilosis.) and 44.58 ± 27.91% (S. cerevisiae). The analysis of C. glabrata's secretome will allow us to further our understanding of the possible role these metabolites could play in its virulence.
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11
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PapRIV, a BV-2 microglial cell activating quorum sensing peptide. Sci Rep 2021; 11:10723. [PMID: 34021199 PMCID: PMC8140105 DOI: 10.1038/s41598-021-90030-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/06/2021] [Indexed: 11/21/2022] Open
Abstract
Quorum sensing peptides (QSPs) are bacterial peptides produced by Gram-positive bacteria to communicate with their peers in a cell-density dependent manner. These peptides do not only act as interbacterial communication signals, but can also have effects on the host. Compelling evidence demonstrates the presence of a gut-brain axis and more specifically, the role of the gut microbiota in microglial functioning. The aim of this study is to investigate microglial activating properties of a selected QSP (PapRIV) which is produced by Bacillus cereus species. PapRIV showed in vitro activating properties of BV-2 microglia cells and was able to cross the in vitro Caco-2 cell model and reach the brain. In vivo peptide presence was also demonstrated in mouse plasma. The peptide caused induction of IL-6, TNFα and ROS expression and increased the fraction of ameboid BV-2 microglia cells in an NF-κB dependent manner. Different metabolites were identified in serum, of which the main metabolite still remained active. PapRIV is thus able to cross the gastro-intestinal tract and the blood–brain barrier and shows in vitro activating properties in BV-2 microglia cells, hereby indicating a potential role of this quorum sensing peptide in gut-brain interaction.
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Chen S, Huang J, Qin H, He G, Zhou R, Yang Y, Qiu C, Zhang S. Evolving the core microbial community in pit mud based on bioturbation of fortified Daqu. Can J Microbiol 2020; 67:396-405. [PMID: 33064956 DOI: 10.1139/cjm-2020-0290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Directional stress is an effective measure to change the community structure and improve the bioactivity of pit mud (PM). In this study, the addition of fortified Daqu to artificial PM (APM) was intended to disturb the microbial community and further affect metabolites. To evaluate the effect of fortified Daqu on culturing APM, the microbial communities of APM with or without the addition of fortified Daqu were investigated by fluorescence in situ hybridization and Illumina MiSeq. The results indicated that microbes (Clostridium sp., Clostridium kluyveri, hydrogenotrophic methanogens, and acetotrophic methanogens) related to the production of key aroma compounds increased notably when fortified Daqu was added. In particular, the hydrogenotrophic and acetotrophic methanogens increased by 6.19- and 4.63-fold after 30 days of culture. Subsequently, metabolites (organic acids, volatile compounds) were also analyzed by HPLC (high-performance liquid chromatography) and HS-SPME-GC-MS (headspace solid phase microextraction - gas chromatography - mass spectrometry). The results showed that the content of butyric acid and hexanoic acid was significantly higher when fortified Daqu was added to APM. In addition, the proportion of esters and phenols was also higher than in APM without fortified Daqu. A survey of the microbial compositions of APMs with or without added fortified Daqu indicated that the microbial community evolves into a functional community favoring liquor brewing. We have developed a novel process by disturbing the community diversity.
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Affiliation(s)
- Suqi Chen
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, China
| | - Hui Qin
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China
| | - Guiqiang He
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.,Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, China
| | - Yan Yang
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China
| | - Chuanfeng Qiu
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China
| | - Suyi Zhang
- National Engineering Research Center of Solid-State Manufacturing, Luzhou 646000, China
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Jiranek V, Bauer F, Takagi H. Editorial: yeast ecology and interaction. FEMS Yeast Res 2019; 19:5673069. [DOI: 10.1093/femsyr/foz073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 10/20/2019] [Indexed: 12/12/2022] Open
Affiliation(s)
- Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, PMB 1 Glen Osmond, SA 5064, Australia
| | - Florian Bauer
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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