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Doron L, Kerfeld CA. Bacterial microcompartments as a next-generation metabolic engineering tool: utilizing nature's solution for confining challenging catabolic pathways. Biochem Soc Trans 2024; 52:997-1010. [PMID: 38813858 DOI: 10.1042/bst20230229] [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: 02/23/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Advancements in synthetic biology have facilitated the incorporation of heterologous metabolic pathways into various bacterial chassis, leading to the synthesis of targeted bioproducts. However, total output from heterologous production pathways can suffer from low flux, enzyme promiscuity, formation of toxic intermediates, or intermediate loss to competing reactions, which ultimately hinder their full potential. The self-assembling, easy-to-modify, protein-based bacterial microcompartments (BMCs) offer a sophisticated way to overcome these obstacles by acting as an autonomous catalytic module decoupled from the cell's regulatory and metabolic networks. More than a decade of fundamental research on various types of BMCs, particularly structural studies of shells and their self-assembly, the recruitment of enzymes to BMC shell scaffolds, and the involvement of ancillary proteins such as transporters, regulators, and activating enzymes in the integration of BMCs into the cell's metabolism, has significantly moved the field forward. These advances have enabled bioengineers to design synthetic multi-enzyme BMCs to promote ethanol or hydrogen production, increase cellular polyphosphate levels, and convert glycerol to propanediol or formate to pyruvate. These pioneering efforts demonstrate the enormous potential of synthetic BMCs to encapsulate non-native multi-enzyme biochemical pathways for the synthesis of high-value products.
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Affiliation(s)
- Lior Doron
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, U.S.A
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Szaleniec M, Oleksy G, Sekuła A, Aleksić I, Pietras R, Sarewicz M, Krämer K, Pierik AJ, Heider J. Modeling the Initiation Phase of the Catalytic Cycle in the Glycyl-Radical Enzyme Benzylsuccinate Synthase. J Phys Chem B 2024; 128:5823-5839. [PMID: 38848492 PMCID: PMC11194802 DOI: 10.1021/acs.jpcb.4c01237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024]
Abstract
The reaction of benzylsuccinate synthase, the radical-based addition of toluene to a fumarate cosubstrate, is initiated by hydrogen transfer from a conserved cysteine to the nearby glycyl radical in the active center of the enzyme. In this study, we analyze this step by comprehensive computer modeling, predicting (i) the influence of bound substrates or products, (ii) the energy profiles of forward- and backward hydrogen-transfer reactions, (iii) their kinetic constants and potential mechanisms, (iv) enantiospecificity differences, and (v) kinetic isotope effects. Moreover, we support several of the computational predictions experimentally, providing evidence for the predicted H/D-exchange reactions into the product and at the glycyl radical site. Our data indicate that the hydrogen transfer reactions between the active site glycyl and cysteine are principally reversible, but their rates differ strongly depending on their stereochemical orientation, transfer of protium or deuterium, and the presence or absence of substrates or products in the active site. This is particularly evident for the isotope exchange of the remaining protium atom of the glycyl radical to deuterium, which appears dependent on substrate or product binding, explaining why the exchange is observed in some, but not all, glycyl-radical enzymes.
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Affiliation(s)
- Maciej Szaleniec
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Gabriela Oleksy
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
| | - Anna Sekuła
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Ivana Aleksić
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy
of Sciences, Kraków 31-201, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 31-007, Poland
| | - Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków 31-007, Poland
| | - Kai Krämer
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
| | - Antonio J. Pierik
- Biochemistry,
Faculty of ChemistryRPTU Kaiserslautern-Landau, Kaiserslautern D-67663, Germany
| | - Johann Heider
- Department
of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg 35043, Germany
- Synmikro-Center
for Synthetic Microbiology, Philipps University
Marburg, Marburg 35043, Germany
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3
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Kushkevych I, Martínková K, Mráková L, Giudici F, Baldi S, Novak D, Gajdács M, Vítězová M, Dordevic D, Amedei A, Rittmann SKMR. Comparison of microbial communities and the profile of sulfate-reducing bacteria in patients with ulcerative colitis and their association with bowel diseases: a pilot study. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:79-89. [PMID: 38486888 PMCID: PMC10939707 DOI: 10.15698/mic2024.03.817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 03/17/2024]
Abstract
Considerable evidence has accumulated regarding the molecular relationship between gut microbiota (GM) composition and the onset (clinical presentation and prognosis of ulcerative colitis (UC)). In addition, it is well documented that short-chain fatty acid (SCFA)-producing bacteria may play a fundamental role in maintaining an anti-inflammatory intestinal homeostasis, but sulfate- and sulfite reducing bacteria may be responsible for the production of toxic metabolites, such as hydrogen sulfide and acetate. Hence, the present study aimed to assess the GM composition - focusing on sulfate-reducing bacteria (SRB) - in patients with severe, severe-active and moderate UC. Each one of the six enrolled patients provided two stool samples in the following way: one sample was cultivated in a modified SRB-medium before 16S rRNA sequencing and the other was not cultivated. Comparative phylogenetic analysis was conducted on each sample. Percentage of detected gut microbial genera showed considerable variation based on the patients' disease severity and cultivation in the SRB medium. In detail, samples without cultivation from patients with moderate UC showed a high abundance of the genera Bacteroides, Bifidobacterium and Ruminococcus, but after SRB cultivation, the dominant genera were Bacteroides, Klebsiella and Bilophila. On the other hand, before SRB cultivation, the main represented genera in patients with severe UC were Escherichia-Shigella, Proteus, Methanothermobacter and Methanobacterium. However, after incubation in the SRB medium Bacteroides, Proteus, Alistipes and Lachnoclostridium were predominant. Information regarding GM compositional changes in UC patients may aid the development of novel therapeutic strategies (e.g., probiotic preparations containing specific bacterial strains) to counteract the mechanisms of virulence of harmful bacteria and the subsequent inflammatory response that is closely related to the pathogenesis of inflammatory bowel diseases.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Kristýna Martínková
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Lenka Mráková
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Francesco Giudici
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Simone Baldi
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - David Novak
- Department of Biochemistry, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Márió Gajdács
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, 6720 Szeged, Hungary
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Dani Dordevic
- Department of Plant Origin Food Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Simon K.-M. R. Rittmann
- Department of Functional and Evolutionary Ecology, Archaea Physiology & Biotechnology Group, Universität Wien, 1030 Wien, Austria
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Levent G, Božić A, Petrujkić BT, Callaway TR, Poole TL, Crippen TL, Harvey RB, Ochoa-García P, Corral-Luna A, Yeater KM, Anderson RC. Assessment of Potential Anti-Methanogenic and Antimicrobial Activity of Ethyl Nitroacetate, α-Lipoic Acid, Taurine and L-Cysteinesulfinic Acid In Vitro. Microorganisms 2023; 12:34. [PMID: 38257860 PMCID: PMC10819541 DOI: 10.3390/microorganisms12010034] [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: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Livestock producers need new technologies to maintain the optimal health and well-being of their animals while minimizing the risks of propagating and disseminating pathogenic and antimicrobial-resistant bacteria to humans or other animals. Where possible, these interventions should contribute to the efficiency and profitability of animal production to avoid passing costs on to consumers. In this study, we examined the potential of nitroethane, 3-nitro-1-propionate, ethyl nitroacetate, taurine and L-cysteinesulfinic acid to modulate rumen methane production, a digestive inefficiency that results in the loss of up to 12% of the host's dietary energy intake and a major contributor of methane as a greenhouse gas to the atmosphere. The potential for these compounds to inhibit the foodborne pathogens, Escherichia coli O157:H7 and Salmonella Typhimurium DT104, was also tested. The results from the present study revealed that anaerobically grown O157:H7 and DT104 treated with the methanogenic inhibitor, ethyl nitroacetate, at concentrations of 3 and 9 mM had decreased (p < 0.05) mean specific growth rates of O157:H7 (by 22 to 36%) and of DT104 (by 16 to 26%) when compared to controls (0.823 and 0.886 h-1, respectively). The growth rates of O157:H7 and DT104 were decreased (p < 0.05) from controls by 31 to 73% and by 41 to 78% by α-lipoic acid, which we also found to inhibit in vitro rumen methanogenesis up to 66% (p < 0.05). Ethyl nitroacetate was mainly bacteriostatic, whereas 9 mM α-lipoic acid decreased (p < 0.05) maximal optical densities (measured at 600 nm) of O157:H7 and DT104 by 25 and 42% compared to controls (0.448 and 0.451, respectively). In the present study, the other oxidized nitro and organosulfur compounds were neither antimicrobial nor anti-methanogenic.
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Affiliation(s)
- Gizem Levent
- School of Veterinary Medicine, Texas Tech University, Lubbock, TX 79409, USA;
| | - Aleksandar Božić
- Faculty of Agriculture, Department of Animal Science, University of Novi Sad, 21000 Novi Sad, Serbia;
| | - Branko T. Petrujkić
- Department of Nutrition and Botany, Faculty of Veterinary Medicine, University of Belgrade, 110000 Belgrade, Serbia;
| | - Todd R. Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30609, USA;
| | - Toni L. Poole
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (T.L.P.); (T.L.C.); (R.B.H.)
| | - Tawni L. Crippen
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (T.L.P.); (T.L.C.); (R.B.H.)
| | - Roger B. Harvey
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (T.L.P.); (T.L.C.); (R.B.H.)
| | - Pedro Ochoa-García
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua 31000, Mexico; (P.O.-G.); (A.C.-L.)
| | - Agustin Corral-Luna
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua 31000, Mexico; (P.O.-G.); (A.C.-L.)
| | - Kathleen M. Yeater
- United States Department of Agriculture/Agricultural Research Service, Office of the Area Director, 104 Ambrose Hill, Williamsburg, VA 20250, USA
| | - Robin C. Anderson
- United States Department of Agriculture/Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (T.L.P.); (T.L.C.); (R.B.H.)
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Zhang Y, Shen Y, Liufu N, Liu L, Li W, Shi Z, Zheng H, Mei X, Chen CY, Jiang Z, Abtahi S, Dong Y, Liang F, Shi Y, Cheng LL, Yang G, Kang JX, Wilkinson JE, Xie Z. Transmission of Alzheimer's disease-associated microbiota dysbiosis and its impact on cognitive function: evidence from mice and patients. Mol Psychiatry 2023; 28:4421-4437. [PMID: 37604976 DOI: 10.1038/s41380-023-02216-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/26/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023]
Abstract
Spouses of Alzheimer's disease (AD) patients are at a higher risk of developing incidental dementia. However, the causes and underlying mechanism of this clinical observation remain largely unknown. One possible explanation is linked to microbiota dysbiosis, a condition that has been associated with AD. However, it remains unclear whether gut microbiota dysbiosis can be transmitted from AD individuals to non-AD individuals and contribute to the development of AD pathogenesis and cognitive impairment. We, therefore, set out to perform both animal studies and clinical investigation by co-housing wild-type mice and AD transgenic mice, analyzing microbiota via 16S rRNA gene sequencing, measuring short-chain fatty acid amounts, and employing behavioral test, mass spectrometry, site-mutations and other methods. The present study revealed that co-housing between wild-type mice and AD transgenic mice or administrating feces of AD transgenic mice to wild-type mice resulted in AD-associated gut microbiota dysbiosis, Tau phosphorylation, and cognitive impairment in the wild-type mice. Gavage with Lactobacillus and Bifidobacterium restored these changes in the wild-type mice. The oral and gut microbiota of AD patient partners resembled that of AD patients but differed from healthy controls, indicating the transmission of microbiota. The underlying mechanism of these findings includes that the butyric acid-mediated acetylation of GSK3β at lysine 15 regulated its phosphorylation at serine 9, consequently impacting Tau phosphorylation. Pending confirmative studies, these results provide insight into a potential link between the transmission of AD-associated microbiota dysbiosis and development of cognitive impairment, which underscore the need for further research in this area.
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Affiliation(s)
- Yiying Zhang
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA.
| | - Yuan Shen
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
- Anesthesia and Brain Research Institute, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, PR China
- Mental Health Center affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Ning Liufu
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, 510120, PR China
| | - Ling Liu
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, 510120, PR China
| | - Wei Li
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Zhongyong Shi
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
- Anesthesia and Brain Research Institute, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, PR China
- Mental Health Center affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Hailin Zheng
- Anesthesia and Brain Research Institute, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, PR China
| | - Xinchun Mei
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
- Anesthesia and Brain Research Institute, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, PR China
- Mental Health Center affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, PR China
| | - Chih-Yu Chen
- Laboratory for Lipid Medicine and Technology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Zengliang Jiang
- Laboratory for Lipid Medicine and Technology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, PR China
| | - Shabnamsadat Abtahi
- Biostatistics Department and Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Yuanlin Dong
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Feng Liang
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Yujiang Shi
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China
| | - Leo L Cheng
- Departments of Radiology and Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Guang Yang
- Department of Anesthesiology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Jing X Kang
- Laboratory for Lipid Medicine and Technology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Jeremy E Wilkinson
- Biostatistics Department and Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Zhongcong Xie
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA.
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Doron L, Sutter M, Kerfeld CA. Characterization of a novel aromatic substrate-processing microcompartment in Actinobacteria. mBio 2023; 14:e0121623. [PMID: 37462359 PMCID: PMC10470539 DOI: 10.1128/mbio.01216-23] [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: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 09/02/2023] Open
Abstract
We have discovered a new cluster of genes that is found exclusively in the Actinobacteria phylum. This locus includes genes for the 2-aminophenol meta-cleavage pathway and the shell proteins of a bacterial microcompartment (BMC) and has been named aromatics (ARO) for its putative role in the breakdown of aromatic compounds. In this study, we provide details about the distribution and composition of the ARO BMC locus and conduct phylogenetic, structural, and functional analyses of the first two enzymes in the catabolic pathway: a unique 2-aminophenol dioxygenase, which is exclusively found alongside BMC shell genes in Actinobacteria, and a semialdehyde dehydrogenase, which works downstream of the dioxygenase. Genomic analysis reveals variations in the complexity of the ARO loci across different orders. Some loci are simple, containing shell proteins and enzymes for the initial steps of the catabolic pathway, while others are extensive, encompassing all the necessary genes for the complete breakdown of 2-aminophenol into pyruvate and acetyl-CoA. Furthermore, our analysis uncovers two subtypes of ARO BMC that likely degrade either 2-aminophenol or catechol, depending on the presence of a pathway-specific gene within the ARO locus. The precise precursor of 2-aminophenol, which serves as the initial substrate and/or inducer for the ARO pathway, remains unknown, as our model organism Micromonospora rosaria cannot utilize 2-aminophenol as its sole energy source. However, using enzymatic assays, we demonstrate the dioxygenase's ability to cleave both 2-aminophenol and catechol in vitro, in collaboration with the aldehyde dehydrogenase, to facilitate the rapid conversion of these unstable and toxic intermediates. IMPORTANCE Bacterial microcompartments (BMCs) are proteinaceous organelles that are widespread among bacteria and provide a competitive advantage in specific environmental niches. Studies have shown that the genetic information necessary to form functional BMCs is encoded in loci that contain genes encoding shell proteins and the enzymatic core. This allows the bioinformatic discovery of BMCs with novel functions and expands our understanding of the metabolic diversity of BMCs. ARO loci, found only in Actinobacteria, contain genes encoding for phylogenetically remote shell proteins and homologs of the meta-cleavage degradation pathway enzymes that were shown to convert central aromatic intermediates into pyruvate and acetyl-CoA in gamma Proteobacteria. By analyzing the gene composition of ARO BMC loci and characterizing two core enzymes phylogenetically, structurally, and functionally, we provide an initial functional characterization of the ARO BMC, the most unusual BMC identified to date, distinctive among the repertoire of studied BMCs.
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Affiliation(s)
- Lior Doron
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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Dukes HE, Tinker KA, Ottesen EA. Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics. Front Microbiol 2023; 14:1156809. [PMID: 37323917 PMCID: PMC10266427 DOI: 10.3389/fmicb.2023.1156809] [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: 02/01/2023] [Accepted: 05/08/2023] [Indexed: 06/17/2023] Open
Abstract
Omnivorous cockroaches host a complex hindgut microbiota comprised of insect-specific lineages related to those found in mammalian omnivores. Many of these organisms have few cultured representatives, thereby limiting our ability to infer the functional capabilities of these microbes. Here we present a unique reference set of 96 high-quality single cell-amplified genomes (SAGs) from bacterial and archaeal cockroach gut symbionts. We additionally generated cockroach hindgut metagenomic and metatranscriptomic sequence libraries and mapped them to our SAGs. By combining these datasets, we are able to perform an in-depth phylogenetic and functional analysis to evaluate the abundance and activities of the taxa in vivo. Recovered lineages include key genera within Bacteroidota, including polysaccharide-degrading taxa from the genera Bacteroides, Dysgonomonas, and Parabacteroides, as well as a group of unclassified insect-associated Bacteroidales. We also recovered a phylogenetically diverse set of Firmicutes exhibiting a wide range of metabolic capabilities, including-but not limited to-polysaccharide and polypeptide degradation. Other functional groups exhibiting high relative activity in the metatranscriptomic dataset include multiple putative sulfate reducers belonging to families in the Desulfobacterota phylum and two groups of methanogenic archaea. Together, this work provides a valuable reference set with new insights into the functional specializations of insect gut symbionts and frames future studies of cockroach hindgut metabolism.
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Affiliation(s)
- Helen E Dukes
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Kara A Tinker
- National Energy Technology Laboratory (NETL), Pittsburgh, PA, United States
| | - Elizabeth A Ottesen
- Department of Microbiology, University of Georgia, Athens, GA, United States
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8
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Felber J, Gross B, Rahrisch A, Waltersbacher E, Trips E, Schröttner P, Fitze G, Schultz J. Bacterial pathogens in pediatric appendicitis: a comprehensive retrospective study. Front Cell Infect Microbiol 2023; 13:1027769. [PMID: 37228669 PMCID: PMC10205019 DOI: 10.3389/fcimb.2023.1027769] [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: 08/25/2022] [Accepted: 03/30/2023] [Indexed: 05/27/2023] Open
Abstract
Background Appendicitis is a frequent condition, with peak incidences in the second decade of life. Its pathogenesis is under debate, but bacterial infections are crucial, and antibiotic treatment remains essential. Rare bacteria are accused of causing complications, and various calculated antibiotics are propagated, yet there is no comprehensive microbiological analysis of pediatric appendicitis. Here we review different pre-analytic pathways, identify rare and common bacterial pathogens and their antibiotic resistances, correlate clinical courses, and evaluate standard calculated antibiotics in a large pediatric cohort. Method We reviewed 579 patient records and microbiological results of intraoperative swabs in standard Amies agar media or fluid samples after appendectomies for appendicitis between May 2011 and April 2019. Bacteria were cultured and identified via VITEK 2 or MALDI-TOF MS. Minimal inhibitory concentrations were reevaluated according to EUCAST 2022. Results were correlated to clinical courses. Results Of 579 analyzed patients, in 372 patients we got 1330 bacterial growths with resistograms. 1259 times, bacteria could be identified to species level. 102 different bacteria could be cultivated. 49% of catarrhal and 52% of phlegmonous appendices resulted in bacterial growth. In gangrenous appendicitis, only 38% remained sterile, while this number reduced to 4% after perforation. Many fluid samples remained sterile even when unsterile swabs had been taken simultaneously. 40 common enteral genera were responsible for 76.5% of bacterial identifications in 96.8% of patients. However, 69 rare bacteria were found in 187 patients without specifically elevated risk for complications. Conclusion Amies agar gel swabs performed superior to fluid samples and should be a standard in appendectomies. Even catarrhal appendices were only sterile in 51%, which is interesting in view of a possible viral cause. According to our resistograms, the best in vitro antibiotic was imipenem with 88.4% susceptible strains, followed by piperacillin-tazobactam, cefuroxime with metronidazole, and ampicillin-sulbactam to which only 21.6% of bacteria were susceptible. Bacterial growths and higher resistances correlate to an elevated risk of complications. Rare bacteria are found in many patients, but there is no specific consequence regarding antibiotic susceptibility, clinical course, or complications. Prospective, comprehensive studies are needed to further elicit pediatric appendicitis microbiology and antibiotic treatment.
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Affiliation(s)
- Julia Felber
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Benedikt Gross
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Arend Rahrisch
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Eric Waltersbacher
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Evelyn Trips
- Coordination Centre for Clinical Trials, Faculty of Medicine Carl Gustav Carus, Technical University of Dresden, Dresden, Germany
| | - Percy Schröttner
- Institute for Microbiology and Virology, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Guido Fitze
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Jurek Schultz
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
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9
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Zhang Y, Shen Y, Liufu N, Liu L, Li W, Shi Z, Zheng H, Mei X, Chen CY, Jiang Z, Abtahi S, Dong Y, Liang F, Shi Y, Cheng L, Yang G, Kang JX, Wilkinson J, Xie Z. Transmission of Alzheimer's Disease-Associated Microbiota Dysbiosis and its Impact on Cognitive Function: Evidence from Mouse Models and Human Patients. RESEARCH SQUARE 2023:rs.3.rs-2790988. [PMID: 37162940 PMCID: PMC10168447 DOI: 10.21203/rs.3.rs-2790988/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Spouses of Alzheimer's disease (AD) patients are at higher risk of developing AD dementia, but the reasons and underlying mechanism are unknown. One potential factor is gut microbiota dysbiosis, which has been associated with AD. However, it remains unclear whether the gut microbiota dysbiosis can be transmitted to non-AD individuals and contribute to the development of AD pathogenesis and cognitive impairment. The present study found that co-housing wild-type mice with AD transgenic mice or giving them AD transgenic mice feces caused AD-associated gut microbiota dysbiosis, Tau phosphorylation, and cognitive impairment. Gavage with Lactobacillus and Bifidobacterium restored these changes. The oral and gut microbiota of AD patient partners resembled that of AD patients but differed from healthy controls, indicating the transmission of oral and gut microbiota and its impact on cognitive function. The underlying mechanism of these findings includes that the butyric acid-mediated acetylation of GSK3β at lysine 15 regulated its phosphorylation at serine 9, consequently impacting Tau phosphorylation. These results provide insight into a potential link between gut microbiota dysbiosis and AD and underscore the need for further research in this area.
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Affiliation(s)
| | - Yuan Shen
- Tenth People's Hospital of Tongji University
| | | | | | - Wei Li
- Massachusetts General Hospital
| | | | | | | | | | | | | | - Yuanlin Dong
- Geriatric Anesthesia Research Unit, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School
| | | | | | | | - Guang Yang
- Department of Anesthesiology, Columbia University
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10
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Yin N, Chang X, Xiao P, Zhou Y, Liu X, Xiong S, Wang P, Cai X, Sun G, Cui Y, Hu Z. Role of microbial iron reduction in arsenic metabolism from soil particle size fractions in simulated human gastrointestinal tract. ENVIRONMENT INTERNATIONAL 2023; 174:107911. [PMID: 37030286 DOI: 10.1016/j.envint.2023.107911] [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: 12/19/2022] [Revised: 03/03/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
Gut microbiota provides protection against arsenic (As) induced toxicity, and As metabolism is considered an important part of risk assessment associated with soil As exposures. However, little is known about microbial iron(III) reduction and its role in metabolism of soil-bound As in the human gut. Here, we determined the dissolution and transformation of As and Fe from incidental ingestion of contaminated soils as a function of particle size (<250 μm, 100-250 μm, 50-100 μm and < 50 μm). Colon incubation with human gut microbiota yielded a high degree of As reduction and methylation of up to 53.4 and 0.074 μg/(log CFU/mL)/hr, respectively; methylation percentage increased with increasing soil organic matter and decreasing soil pore size. We also found significant microbial Fe(III) reduction and high levels of Fe(II) (48 %-100 % of total soluble Fe) may promote the capacity of As methylation. Although no statistical change in Fe phases was observed with low Fe dissolution and high molar Fe/As ratios, higher As bioaccessibility of colon phase (avg. 29.4 %) was mainly contributed from reductive dissolution of As(V)-bearing Fe(III) (oxy)hydroxides. Our results suggest that As mobility and biotransformation by human gut microbiota (carrying arrA and arsC genes) are strongly controlled by microbial Fe(III) reduction coupled with soil particle size. This will expand our knowledge on oral bioavailability of soil As and health risks from exposure to contaminated soils.
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Affiliation(s)
- Naiyi Yin
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Xuhui Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Peng Xiao
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Yi Zhou
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Xiaotong Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Shimao Xiong
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Pengfei Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Xiaolin Cai
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Guoxin Sun
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.
| | - Yanshan Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.
| | - Zhengyi Hu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China
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11
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Sun Y, Gao S, Ye C, Zhao W. Gut microbiota dysbiosis in polycystic ovary syndrome: Mechanisms of progression and clinical applications. Front Cell Infect Microbiol 2023; 13:1142041. [PMID: 36909735 PMCID: PMC9998696 DOI: 10.3389/fcimb.2023.1142041] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/06/2023] [Indexed: 02/26/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrine diseases in women of childbearing age that leads to menstrual disorders and infertility. The pathogenesis of PCOS is complex and has not yet been fully clarified. Gut microbiota is associated with disorders of lipid, glucose, and steroid hormone metabolish. A large body of studies demonstrated that gut microbiota could regulate the synthesis and secretion of insulin, and affect androgen metabolism and follicle development, providing us a novel idea for unravelling the pathogenesis of PCOS. The relationship between gut microbiota and the pathogenesis of PCOS is particularly important. This study reviewed recent research advances in the roles of gut microbiota in the occurrence and development of PCOS. It is expected to provide a new direction for the treatment of PCOS based on gut microbiota.
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Affiliation(s)
- Yan Sun
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Shouyang Gao
- Department of Obstetrics and Gynecology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Cong Ye
- Department of Obstetrics and Gynecology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Weiliang Zhao
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Weiliang Zhao,
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12
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Modulation of Gut Microbiota and Neuroprotective Effect of a Yeast-Enriched Beer. Nutrients 2022; 14:nu14122380. [PMID: 35745108 PMCID: PMC9228237 DOI: 10.3390/nu14122380] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Beer is the most consumed alcoholic beverage worldwide. It is rich in nutrients, and with its microbial component it could play a role in gut microbiota modulation. Conflicting data are currently available regarding the consequences of alcohol and alcohol-containing beverages on dementia and age-associated disorders including Alzheimer’s disease (AD), a neurodegeneration characterized by protein aggregation, inflammatory processes and alterations of components of the gut–brain axis. The effects of an unfiltered and unpasteurized craft beer on AD molecular hallmarks, levels of gut hormones and composition of micro/mycobiota were dissected using 3xTg-AD mice. In addition, to better assess the role of yeasts, beer was enriched with the same Saccharomyces cerevisiae strain used for brewing. The treatment with the yeast-enriched beer ameliorated cognition and favored the reduction of Aβ(1-42) and pro-inflammatory molecules, also contributing to an increase in the concentration of anti-inflammatory cytokines. A significant improvement in the richness and presence of beneficial taxa in the gut bacterial population of the 3xTg-AD animals was observed. In addition, the fungal order, Sordariomycetes, associated with gut inflammatory conditions, noticeably decreased with beer treatments. These data demonstrate, for the first time, the beneficial effects of a yeast-enriched beer on AD signs, suggesting gut microbiota modulation as a mechanism of action.
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