1
|
Ma K, Xue B, Chu R, Zheng Y, Sharma S, Jiang L, Hu M, Xie Y, Hu Y, Tao T, Zhou Y, Liu D, Li Z, Yang Q, Chen Y, Wu S, Tong Y, Robinson RC, Yew WS, Jin X, Liu Y, Zhao H, Ang EL, Wei Y, Zhang Y. A Widespread Radical-Mediated Glycolysis Pathway. J Am Chem Soc 2024; 146:26187-26197. [PMID: 39283600 DOI: 10.1021/jacs.4c07718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Glycyl radical enzymes (GREs) catalyze mechanistically diverse radical-mediated reactions, playing important roles in the metabolism of anaerobic bacteria. The model bacterium Escherichia coli MG1655 contains two GREs of unknown function, YbiW and PflD, which are widespread among human intestinal bacteria. Here, we report that YbiW and PflD catalyze ring-opening C-O cleavage of 1,5-anhydroglucitol-6-phosphate (AG6P) and 1,5-anhydromannitol-6-phosphate (AM6P), respectively. The product of both enzymes, 1-deoxy-fructose-6-phosphate (DF6P), is then cleaved by the aldolases FsaA or FsaB to form glyceraldehyde-3-phosphate (G3P) and hydroxyacetone (HA), which are then reduced by the NADH-dependent dehydrogenase GldA to form 1,2-propanediol (1,2-PDO). Crystal structures of YbiW and PflD in complex with their substrates provided insights into the mechanism of radical-mediated C-O cleavage. This "anhydroglycolysis" pathway enables anaerobic growth of E. coli on 1,5-anhydroglucitol (AG) and 1,5-anhydromannitol (AM), and we probe the feasibility of harnessing this pathway for the production of 1,2-PDO, a highly demanded chiral chemical feedstock, from inexpensive starch. Discovery of the anhydroglycolysis pathway expands the known catalytic repertoire of GREs, clarifies the hitherto unknown physiological functions of the well-studied enzymes FsaA, FsaB, and GldA, and demonstrates how enzyme discovery efforts can cast light on prevalent yet overlooked metabolites in the microbiome.
Collapse
Affiliation(s)
- Kailiang Ma
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bo Xue
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, Singapore 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ruoxing Chu
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yuchun Zheng
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Shishir Sharma
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Li Jiang
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Min Hu
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yiren Xie
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yiling Hu
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Tiantian Tao
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China
| | - Yan Zhou
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Dazhi Liu
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Meining Pharma Inc., 2-401-1, Bldg 8, Huiying Industrial Park, No. 86 West Zhonghuan Road, Tianjin Pilot Free Trade Zone, Tianjin 300308, China
| | - Zhi Li
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Qiaoyu Yang
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yiwei Chen
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Songgu Wu
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China
| | - Yang Tong
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, Singapore 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Xinghua Jin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China
| | - Yanhong Liu
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Yan Zhang
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Carbon-Negative Synthetic Biology for Biomaterial Production from CO2 (CNSB), Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore 138602, Singapore
| |
Collapse
|
2
|
Deng WH, Liao RZ. Cysteine Radical and Glutamate Collaboratively Enable C-H Bond Activation and C-N Bond Cleavage in a Glycyl Radical Enzyme HplG. J Chem Inf Model 2024; 64:4168-4179. [PMID: 38745447 DOI: 10.1021/acs.jcim.4c00122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Hydroxyprolines are abundant in nature and widely utilized by many living organisms. Isomerization of trans-4-hydroxy-d-proline (t4D-HP) to generate 2-amino-4-ketopentanoate has been found to need a glycyl radical enzyme HplG, which catalyzes the cleavage of the C-N bond, while dehydration of trans-4-hydroxy-l-proline involves a homologous enzyme of HplG. Herein, molecular dynamics simulations and quantum mechanics/molecular mechanics (QM/MM) calculations are employed to understand the reaction mechanism of HplG. Two possible reaction pathways of HplG have been explored to decipher the origin of its chemoselectivity. The QM/MM calculations reveal that the isomerization proceeds via an initial hydrogen shift from the Cγ site of t4D-HP to a catalytic cysteine radical, followed by cleavage of the Cδ-N bond in t4D-HP to form a radical intermediate that captures a hydrogen atom from the cysteine. Activation of the Cδ-H bond in t4D-HP to bring about dehydration of t4D-HP possesses an extremely high energy barrier, thus rendering the dehydration pathway implausible in HplG. On the basis of the current calculations, conserved residue Glu429 plays a pivotal role in the isomerization pathway: the hydrogen bonding between it and t4D-HP weakens the hydroxyalkyl Cγ-Hγ bond, and it acts as a proton acceptor to trigger the cleavage of the C-N bond in t4D-HP. Our current QM/MM calculations rationalize the origin of the experimentally observed chemoselectivity of HplG and propose an H-bond-assisted bond activation strategy in radical-containing enzymes. These findings have general implications on radical-mediated enzymatic catalysis and expand our understanding of how nature wisely and selectively activates the C-H bond to modulate catalytic selectivity.
Collapse
Affiliation(s)
- Wen-Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
3
|
Rodríguez Del Río Á, Giner-Lamia J, Cantalapiedra CP, Botas J, Deng Z, Hernández-Plaza A, Munar-Palmer M, Santamaría-Hernando S, Rodríguez-Herva JJ, Ruscheweyh HJ, Paoli L, Schmidt TSB, Sunagawa S, Bork P, López-Solanilla E, Coelho LP, Huerta-Cepas J. Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature 2024; 626:377-384. [PMID: 38109938 PMCID: PMC10849945 DOI: 10.1038/s41586-023-06955-z] [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: 02/01/2022] [Accepted: 12/08/2023] [Indexed: 12/20/2023]
Abstract
Many of the Earth's microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain largely overlooked in most metagenomic studies1. Here we analysed 149,842 environmental genomes from multiple habitats2-6 and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel (FESNov) gene families exclusive to uncultivated prokaryotic taxa. All FESNov families span multiple species, exhibit strong signals of purifying selection and qualify as new orthologous groups, thus nearly tripling the number of bacterial and archaeal gene families described to date. The FESNov catalogue is enriched in clade-specific traits, including 1,034 novel families that can distinguish entire uncultivated phyla, classes and orders, probably representing synapomorphies that facilitated their evolutionary divergence. Using genomic context analysis and structural alignments we predicted functional associations for 32.4% of FESNov families, including 4,349 high-confidence associations with important biological processes. These predictions provide a valuable hypothesis-driven framework that we used for experimental validatation of a new gene family involved in cell motility and a novel set of antimicrobial peptides. We also demonstrate that the relative abundance profiles of novel families can discriminate between environments and clinical conditions, leading to the discovery of potentially new biomarkers associated with colorectal cancer. We expect this work to enhance future metagenomics studies and expand our knowledge of the genetic repertory of uncultivated organisms.
Collapse
Affiliation(s)
- Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Joaquín Giner-Lamia
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), Universidad de Sevilla-CSIC, Seville, Spain
| | - Carlos P Cantalapiedra
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Jorge Botas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Ziqi Deng
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Ana Hernández-Plaza
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Martí Munar-Palmer
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Saray Santamaría-Hernando
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - José J Rodríguez-Herva
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Emilia López-Solanilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Shanghai, China
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
| |
Collapse
|
4
|
Wang J, Chen L, Qin S, Xie M, Luo SZ, Li W. Advances in biosynthesis of peptide drugs: Technology and industrialization. Biotechnol J 2024; 19:e2300256. [PMID: 37884278 DOI: 10.1002/biot.202300256] [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: 05/31/2023] [Revised: 07/24/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023]
Abstract
Peptide drugs are developed from endogenous or synthetic peptides with specific biological activities. They have advantages of strong target specificity, high efficacy and low toxicity, thus showing great promise in the treatment of many diseases such as cancer, infections, and diabetes. Although an increasing number of peptide drugs have entered market in recent years, the preparation of peptide drug substances is yet a bottleneck problem for their industrial production. Comparing to the chemical synthesis method, peptide biosynthesis has advantages of simple synthesis, low cost, and low contamination. Therefore, the biosynthesis technology of peptide drugs has been widely used for manufacturing. Herein, we reviewed the development of peptide drugs and recent advances in peptide biosynthesis technology, in order to shed a light to the prospect of industrial production of peptide drugs based on biosynthesis technology.
Collapse
Affiliation(s)
- Jing Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
- College of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Long Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Song Qin
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
| | - Mingyuan Xie
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics, Sun Yat-Sen University, Guangzhou, China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
| |
Collapse
|
5
|
Lundahl MN, Yang H, Broderick WE, Hoffman BM, Broderick JB. Pyruvate formate-lyase activating enzyme: The catalytically active 5'-deoxyadenosyl radical caught in the act of H-atom abstraction. Proc Natl Acad Sci U S A 2023; 120:e2314696120. [PMID: 37956301 PMCID: PMC10665898 DOI: 10.1073/pnas.2314696120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/03/2023] [Indexed: 11/15/2023] Open
Abstract
Enzymes of the radical S-adenosyl-l-methionine (radical SAM, RS) superfamily, the largest in nature, catalyze remarkably diverse reactions initiated by H-atom abstraction. Glycyl radical enzyme activating enzymes (GRE-AEs) are a growing class of RS enzymes that generate the catalytically essential glycyl radical of GREs, which in turn catalyze essential reactions in anaerobic metabolism. Here, we probe the reaction of the GRE-AE pyruvate formate-lyase activating enzyme (PFL-AE) with the peptide substrate RVSG734YAV, which mimics the site of glycyl radical formation on the native substrate, pyruvate formate-lyase. Time-resolved freeze-quench electron paramagnetic resonance spectroscopy shows that at short mixing times reduced PFL-AE + SAM reacts with RVSG734YAV to form the central organometallic intermediate, Ω, in which the adenosyl 5'C is covalently bound to the unique iron of the [4Fe-4S] cluster. Freeze-trapping the reaction at longer times reveals the formation of the peptide G734• glycyl radical product. Of central importance, freeze-quenching at intermediate times reveals that the conversion of Ω to peptide glycyl radical is not concerted. Instead, homolysis of the Ω Fe-C5' bond generates the nominally "free" 5'-dAdo• radical, which is captured here by freeze-trapping. During cryoannealing at 77 K, the 5'-dAdo• directly abstracts an H-atom from the peptide to generate the G734• peptide radical trapped in the PFL-AE active site. These observations reveal the 5'-dAdo• radical to be a well-defined intermediate, caught in the act of substrate H-atom abstraction, providing new insights into the mechanistic steps of radical initiation by RS enzymes.
Collapse
Affiliation(s)
- Maike N. Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| |
Collapse
|
6
|
Cáceres JC, Dolmatch A, Greene BL. The Mechanism of Inhibition of Pyruvate Formate Lyase by Methacrylate. J Am Chem Soc 2023; 145:22504-22515. [PMID: 37797332 PMCID: PMC10591478 DOI: 10.1021/jacs.3c07256] [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: 07/08/2023] [Indexed: 10/07/2023]
Abstract
Pyruvate Formate Lyase (PFL) catalyzes acetyl transfer from pyruvate to coenzyme a by a mechanism involving multiple amino acid radicals. A post-translationally installed glycyl radical (G734· in Escherichia coli) is essential for enzyme activity and two cysteines (C418 and C419) are proposed to form thiyl radicals during turnover, yet their unique roles in catalysis have not been directly demonstrated with both structural and electronic resolution. Methacrylate is an isostructural analog of pyruvate and an informative irreversible inhibitor of pfl. Here we demonstrate the mechanism of inhibition of pfl by methacrylate. Treatment of activated pfl with methacrylate results in the conversion of the G734· to a new radical species, concomitant with enzyme inhibition, centered at g = 2.0033. Spectral simulations, reactions with methacrylate isotopologues, and Density Functional Theory (DFT) calculations support our assignment of the radical to a C2 tertiary methacryl radical. The reaction is specific for C418, as evidenced by mass spectrometry. The methacryl radical decays over time, reforming G734·, and the decay exhibits a H/D solvent isotope effect of 3.4, consistent with H-atom transfer from an ionizable donor, presumably the C419 sulfhydryl group. Acrylate also inhibits PFL irreversibly, and alkylates C418, but we did not observe an acryl secondary radical in H2O or in D2O within 10 s, consistent with our DFT calculations and the expected reactivity of a secondary versus tertiary carbon-centered radical. Together, the results support unique roles of the two active site cysteines of PFL and a C419 S-H bond dissociation energy between that of a secondary and tertiary C-H bond.
Collapse
Affiliation(s)
- Juan Carlos Cáceres
- Biomolecular
Science and Engineering Program, University
of California, Santa
Barbara, California 93106, United States
| | - August Dolmatch
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Brandon L. Greene
- Biomolecular
Science and Engineering Program, University
of California, Santa
Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| |
Collapse
|
7
|
Jenkins DJ, Woolston BM, Hood-Pishchany MI, Pelayo P, Konopaski AN, Quinn Peters M, France MT, Ravel J, Mitchell CM, Rakoff-Nahoum S, Whidbey C, Balskus EP. Bacterial amylases enable glycogen degradation by the vaginal microbiome. Nat Microbiol 2023; 8:1641-1652. [PMID: 37563289 PMCID: PMC10465358 DOI: 10.1038/s41564-023-01447-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 07/11/2023] [Indexed: 08/12/2023]
Abstract
The human vaginal microbiota is frequently dominated by lactobacilli and transition to a more diverse community of anaerobic microbes is associated with health risks. Glycogen released by lysed epithelial cells is believed to be an important nutrient source in the vagina. However, the mechanism by which vaginal bacteria metabolize glycogen is unclear, with evidence implicating both bacterial and human enzymes. Here we biochemically characterize six glycogen-degrading enzymes (GDEs), all of which are pullanases (PulA homologues), from vaginal bacteria that support the growth of amylase-deficient Lactobacillus crispatus on glycogen. We reveal variations in their pH tolerance, substrate preferences, breakdown products and susceptibility to inhibition. Analysis of vaginal microbiome datasets shows that these enzymes are expressed in all community state types. Finally, we confirm the presence and activity of bacterial and human GDEs in cervicovaginal fluid. This work establishes that bacterial GDEs can participate in the breakdown of glycogen, providing insight into metabolism that may shape the vaginal microbiota.
Collapse
Affiliation(s)
- Dominick J Jenkins
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Benjamin M Woolston
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - M Indriati Hood-Pishchany
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Paula Pelayo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - M Quinn Peters
- Department of Chemistry, Seattle University, Seattle, WA, USA
| | - Michael T France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Caroline M Mitchell
- Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Seth Rakoff-Nahoum
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| | | | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
8
|
Oberg N, Zallot R, Gerlt JA. EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. J Mol Biol 2023; 435:168018. [PMID: 37356897 PMCID: PMC10291204 DOI: 10.1016/j.jmb.2023.168018] [Citation(s) in RCA: 79] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/04/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
The Enzyme Function Initiative (EFI) provides a web resource with "genomic enzymology" web tools to leverage the protein (UniProt) and genome (European Nucleotide Archive; ENA; https://www.ebi.ac.uk/ena/) databases to assist the assignment of in vitro enzymatic activities and in vivo metabolic functions to uncharacterized enzymes (https://efi.igb.illinois.edu/). The tools enable (1) exploration of sequence-function space in enzyme families using sequence similarity networks (SSNs; EFI-EST), (2) easy access to genome context for bacterial, archaeal, and fungal proteins in the SSN clusters so that isofunctional families can be identified and their functions inferred from genome context (EFI-GNT); and (3) determination of the abundance of SSN clusters in NIH Human Metagenome Project metagenomes using chemically guided functional profiling (EFI-CGFP). We describe enhancements that enable SSNs to be generated from taxonomy categories, allowing higher resolution analyses of sequence-function space; we provide examples of the generation of taxonomy category-specific SSNs.
Collapse
Affiliation(s)
- Nils Oberg
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States
| | - Rémi Zallot
- Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - John A Gerlt
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States.
| |
Collapse
|
9
|
Yuan F, Su B, Yu Y, Wang J. Study and design of amino acid-based radical enzymes using unnatural amino acids. RSC Chem Biol 2023; 4:431-446. [PMID: 37292061 PMCID: PMC10246556 DOI: 10.1039/d2cb00250g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
Radical enzymes harness the power of reactive radical species by placing them in a protein scaffold, and they are capable of catalysing many important reactions. New native radical enzymes, especially those with amino acid-based radicals, in the category of non-heme iron enzymes (including ribonucleotide reductases), heme enzymes, copper enzymes, and FAD-radical enzymes have been discovered and characterized. We discussed recent research efforts to discover new native amino acid-based radical enzymes, and to study the roles of radicals in processes such as enzyme catalysis and electron transfer. Furthermore, design of radical enzymes in a small and simple scaffold not only allows us to study the radical in a well-controlled system and test our understanding of the native enzymes, but also allows us to create powerful enzymes. In the study and design of amino acid-based radical enzymes, the use of unnatural amino acids allows precise control of pKa values and reduction potentials of the residue, as well as probing the location of the radical through spectroscopic methods, making it a powerful research tool. Our understanding of amino acid-based radical enzymes will allow us to tailor them to create powerful catalysts and better therapeutics.
Collapse
Affiliation(s)
- Feiyan Yuan
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Binbin Su
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Yang Yu
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101 China
| |
Collapse
|
10
|
Barbour A, Smith L, Oveisi M, Williams M, Huang RC, Marks C, Fine N, Sun C, Younesi F, Zargaran S, Orugunty R, Horvath TD, Haidacher SJ, Haag AM, Sabharwal A, Hinz B, Glogauer M. Discovery of phosphorylated lantibiotics with proimmune activity that regulate the oral microbiome. Proc Natl Acad Sci U S A 2023; 120:e2219392120. [PMID: 37216534 PMCID: PMC10235938 DOI: 10.1073/pnas.2219392120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/15/2023] [Indexed: 05/24/2023] Open
Abstract
Lantibiotics are ribosomally synthesized and posttranslationally modified peptides (RiPPs) that are produced by bacteria. Interest in this group of natural products is increasing rapidly as alternatives to conventional antibiotics. Some human microbiome-derived commensals produce lantibiotics to impair pathogens' colonization and promote healthy microbiomes. Streptococcus salivarius is one of the first commensal microbes to colonize the human oral cavity and gastrointestinal tract, and its biosynthesis of RiPPs, called salivaricins, has been shown to inhibit the growth of oral pathogens. Herein, we report on a phosphorylated class of three related RiPPs, collectively referred to as salivaricin 10, that exhibit proimmune activity and targeted antimicrobial properties against known oral pathogens and multispecies biofilms. Strikingly, the immunomodulatory activities observed include upregulation of neutrophil-mediated phagocytosis, promotion of antiinflammatory M2 macrophage polarization, and stimulation of neutrophil chemotaxis-these activities have been attributed to the phosphorylation site identified on the N-terminal region of the peptides. Salivaricin 10 peptides were determined to be produced by S. salivarius strains found in healthy human subjects, and their dual bactericidal/antibiofilm and immunoregulatory activity may provide new means to effectively target infectious pathogens while maintaining important oral microbiota.
Collapse
Affiliation(s)
- Abdelahhad Barbour
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Leif Smith
- Department of Biology, College of Science, Texas A&M University, College Station, TX 77843
| | - Morvarid Oveisi
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - McKinley Williams
- Department of Biology, College of Science, Texas A&M University, College Station, TX 77843
| | - Ruo Chen Huang
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Cara Marks
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Noah Fine
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Chunxiang Sun
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Fereshteh Younesi
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
- Laboratory of Tissue Repair and Regeneration, Keenan Research Centre for Biomedical Science of the St. Michael's Hospital, Toronto, ON M5B 1T8, Canada
| | - Sina Zargaran
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | | | - Thomas D Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX 77030
| | - Sigmund J Haidacher
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX 77030
| | - Anthony M Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX 77030
| | - Amarpreet Sabharwal
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Boris Hinz
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
- Laboratory of Tissue Repair and Regeneration, Keenan Research Centre for Biomedical Science of the St. Michael's Hospital, Toronto, ON M5B 1T8, Canada
| | - Michael Glogauer
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
- Department of Dental Oncology, Maxillofacial and Ocular Prosthetics, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| |
Collapse
|
11
|
Kaulich E, McCubbin PTN, Schafer WR, Walker DS. Physiological insight into the conserved properties of Caenorhabditis elegans acid-sensing degenerin/epithelial sodium channels. J Physiol 2023; 601:1625-1653. [PMID: 36200489 PMCID: PMC10424705 DOI: 10.1113/jp283238] [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: 04/30/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022] Open
Abstract
Acid-sensing ion channels (ASICs) are members of the diverse family of degenerin/epithelial sodium channels (DEG/ENaCs). They perform a wide range of physiological roles in healthy organisms, including in gut function and synaptic transmission, but also play important roles in disease, as acidosis is a hallmark of painful inflammatory and ischaemic conditions. We performed a screen for acid sensitivity on all 30 subunits of the Caenorhabditis elegans DEG/ENaC family using two-electrode voltage clamp in Xenopus oocytes. We found two groups of acid-sensitive DEG/ENaCs characterised by being either inhibited or activated by increasing proton concentrations. Three of these acid-sensitive C. elegans DEG/ENaCs were activated by acidic pH, making them functionally similar to the vertebrate ASICs. We also identified three new members of the acid-inhibited DEG/ENaC group, giving a total of seven additional acid-sensitive channels. We observed sensitivity to the anti-hypertensive drug amiloride as well as modulation by the trace element zinc. Acid-sensitive DEG/ENaCs were found to be expressed in both neurons and non-neuronal tissue, highlighting the likely functional diversity of these channels. Our findings provide a framework to exploit the C. elegans channels as models to study the function of these acid-sensing channels in vivo, as well as to study them as potential targets for anti-helminthic drugs. KEY POINTS: Acidosis plays many roles in healthy physiology, including synaptic transmission and gut function, but is also a key feature of inflammatory pain, ischaemia and many other conditions. Cells monitor acidosis of their surroundings via pH-sensing channels, including the acid-sensing ion channels (ASICs). These are members of the degenerin/epithelial sodium channel (DEG/ENaC) family, along with, as the name suggests, vertebrate ENaCs and degenerins of the roundworm Caenorhabditis elegans. By screening all 30 C. elegans DEG/ENaCs for pH dependence, we describe, for the first time, three acid-activated members, as well as three additional acid-inhibited channels. We surveyed both groups for sensitivity to amiloride and zinc; like their mammalian counterparts, their currents can be blocked, enhanced or unaffected by these modulators. Likewise, they exhibit diverse ion selectivity. Our findings underline the diversity of acid-sensitive DEG/ENaCs across species and provide a comparative resource for better understanding the molecular basis of their function.
Collapse
Affiliation(s)
- Eva Kaulich
- Neurobiology DivisionMRC Laboratory of Molecular BiologyCambridgeUK
| | | | - William R. Schafer
- Neurobiology DivisionMRC Laboratory of Molecular BiologyCambridgeUK
- Department of BiologyKU LeuvenLeuvenBelgium
| | - Denise S. Walker
- Neurobiology DivisionMRC Laboratory of Molecular BiologyCambridgeUK
| |
Collapse
|
12
|
Beliaeva MA, Wilmanns M, Zimmermann M. Decipher enzymes from human microbiota for drug discovery and development. Curr Opin Struct Biol 2023; 80:102567. [PMID: 36963164 DOI: 10.1016/j.sbi.2023.102567] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 03/26/2023]
Abstract
The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.
Collapse
Affiliation(s)
- Mariia A Beliaeva
- European Molecular Biology Laboratory, Heidelberg, Germany; European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany. https://twitter.com/@MariiaABeliaeva
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany. https://twitter.com/@WilmannsGroup
| | | |
Collapse
|
13
|
Marshall A, McGrath JW, Graham R, McMullan G. Food for thought-The link between Clostridioides difficile metabolism and pathogenesis. PLoS Pathog 2023; 19:e1011034. [PMID: 36602960 PMCID: PMC9815643 DOI: 10.1371/journal.ppat.1011034] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Clostridioides difficile (C. difficile) is an opportunistic pathogen that leads to antibiotic-associated diarrhoea and is a leading cause of morbidity and mortality worldwide. Antibiotic usage is the main risk factor leading to C. difficile infection (CDI), as a dysbiotic gut environment allows colonisation and eventual pathology manifested by toxin production. Although colonisation resistance is mediated by the action of secondary bile acids inhibiting vegetative outgrowth, nutrient competition also plays a role in preventing CDI as the gut microbiota compete for nutrient niches inhibiting C. difficile growth. C. difficile is able to metabolise carbon dioxide, the amino acids proline, hydroxyproline, and ornithine, the cell membrane constituent ethanolamine, and the carbohydrates trehalose, cellobiose, sorbitol, and mucin degradation products as carbon and energy sources through multiple pathways. Zinc sequestration by the host response mediates metabolic adaptation of C. difficile by perhaps signalling an inflamed gut allowing it to acquire abundant nutrients. Persistence within the gut environment is also mediated by the by-products of metabolism through the production of p-cresol, which inhibit gut commensal species growth promoting dysbiosis. This review aims to explore and describe the various metabolic pathways of C. difficile, which facilitate its survival and pathogenesis within the colonised host gut.
Collapse
Affiliation(s)
- Andrew Marshall
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
- * E-mail:
| | - John W. McGrath
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Robert Graham
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Geoff McMullan
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| |
Collapse
|
14
|
Jäger C, Croft AK. If It Is Hard, It Is Worth Doing: Engineering Radical Enzymes from Anaerobes. Biochemistry 2022; 62:241-252. [PMID: 36121716 PMCID: PMC9850924 DOI: 10.1021/acs.biochem.2c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
With a pressing need for sustainable chemistries, radical enzymes from anaerobes offer a shortcut for many chemical transformations and deliver highly sought-after functionalizations such as late-stage C-H functionalization, C-C bond formation, and carbon-skeleton rearrangements, among others. The challenges in handling these oxygen-sensitive enzymes are reflected in their limited industrial exploitation, despite what they may deliver. With an influx of structures and mechanistic understanding, the scope for designed radical enzymes to deliver wanted processes becomes ever closer. Combined with new advances in computational methods and workflows for these complex systems, the outlook for an increased use of radical enzymes in future processes is exciting.
Collapse
|
15
|
Clark KA, Bushin LB, Seyedsayamdost MR. RaS-RiPPs in Streptococci and the Human Microbiome. ACS BIO & MED CHEM AU 2022; 2:328-339. [PMID: 35996476 PMCID: PMC9389541 DOI: 10.1021/acsbiomedchemau.2c00004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Radical S-adenosylmethionine (RaS) enzymes have
quickly advanced to one of the most abundant and versatile enzyme
superfamilies known. Their chemistry is predicated upon reductive
homolytic cleavage of a carbon–sulfur bond in cofactor S-adenosylmethionine forming an oxidizing carbon-based radical,
which can initiate myriad radical transformations. An emerging role
for RaS enzymes is their involvement in the biosynthesis of ribosomally
synthesized and post-translationally modified peptides (RiPPs), a
natural product family that has become known as RaS-RiPPs. These metabolites
are especially prevalent in human and mammalian microbiomes because
the complex chemistry of RaS enzymes gives rise to correspondingly
complex natural products with minimal cellular energy and genomic
fingerprint, a feature that is advantageous in microbes with small,
host-adapted genomes in competitive environments. Herein, we review
the discovery and characterization of RaS-RiPPs from the human microbiome
with a focus on streptococcal bacteria. We discuss the varied chemical
modifications that RaS enzymes introduce onto their peptide substrates
and the diverse natural products that they give rise to. The majority
of RaS-RiPPs remain to be discovered, providing an intriguing avenue
for future investigations at the intersection of metalloenzymology,
chemical ecology, and the human microbiome.
Collapse
Affiliation(s)
- Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Leah B Bushin
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
16
|
d-Proline Reductase Underlies Proline-Dependent Growth of Clostridioides difficile. J Bacteriol 2022; 204:e0022922. [PMID: 35862761 PMCID: PMC9380539 DOI: 10.1128/jb.00229-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Clostridioides difficile is a nosocomial pathogen that colonizes the gut and causes diarrhea, colitis, and severe inflammation. Recently, C. difficile has been shown to use toxin-mediated inflammation to promote host collagen degradation, which releases several amino acids into the environment. Amino acids act as electron donors and acceptors in Stickland metabolism, an anaerobic process involving redox reactions between pairs of amino acids. Proline, glycine, and hydroxyproline are the three main constituents of collagen and are assumed to act as electron acceptors, but their exact effects on the growth and physiology of C. difficile are still unclear. Using three standard culture media (supplemented brain heart infusion [BHIS], tryptone-yeast [TY], and C. difficile minimal medium [CDMM]) supplemented with proline, glycine, or hydroxyproline, we grew C. difficile strains R20291, JIR8094, and a panel of mutants unable to express the Stickland selenoenzymes d-proline reductase and glycine reductase. In the wild-type strains, growth yields in rich media (BHIS and TY) were higher with proline and hydroxyproline but not glycine; moreover, proline-stimulated growth yields required the activity of d-proline reductase, whereas hydroxyproline-stimulated growth yields were independent of its activity. While assumed to be a proline auxotroph, C. difficile could surprisingly grow in a defined medium (CDMM) without proline but only if d-proline reductase was absent. We believe the mere presence of this enzyme ultimately determines the organism's strict dependence on proline and likely defines the bioenergetic priorities for thriving in the host. Finally, we demonstrated that addition of proline and hydroxyproline to the culture medium could reduce toxin production but not in cells lacking selenoproteins. IMPORTANCE Stickland metabolism is a core facet of C. difficile physiology that likely plays a major role in host colonization. Here, we carefully delineate the effects of each amino acid on the growth of C. difficile with respect to the selenoenzymes d-proline reductase and glycine reductase. Moreover, we report that d-proline reductase forces C. difficile to strictly depend on proline for growth. Finally, we provide evidence that proline and hydroxyproline suppress toxin production and that selenoproteins are involved in this mechanism. Our findings highlight the significance of selenium-dependent Stickland reactions and may provide insight on what occurs during host infection, especially as it relates to the decision to colonize based on proline as a nutrient.
Collapse
|
17
|
Hanževački M, Croft AK, Jäger CM. Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme. J Chem Inf Model 2022; 62:3401-3414. [PMID: 35771966 PMCID: PMC9326890 DOI: 10.1021/acs.jcim.2c00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) playing a pivotal role in the metabolism of strict and facultative anaerobes. Its activation is carried out by a PFL-activating enzyme, a member of the radical S-adenosylmethionine (rSAM) superfamily of metalloenzymes, which introduces a glycyl radical into the Gly radical domain of PFL. The activation mechanism is still not fully understood and is structurally based on a complex with a short model peptide of PFL. Here, we present extensive molecular dynamics simulations in combination with quantum mechanics/molecular mechanics (QM/MM)-based kinetic and thermodynamic reaction evaluations of a more complete activation model comprising the 49 amino acid long C-terminus region of PFL. We reveal the benefits and pitfalls of the current activation model, providing evidence that the bound peptide conformation does not resemble the bound protein-protein complex conformation with PFL, with implications for the activation process. Substitution of the central glycine with (S)- and (R)-alanine showed excellent binding of (R)-alanine over unstable binding of (S)-alanine. Radical stabilization calculations indicate that a higher radical stability of the glycyl radical might not be the sole origin of the evolutionary development of GREs. QM/MM-derived radical formation kinetics further demonstrate feasible activation barriers for both peptide and C-terminus activation, demonstrating why the crystalized model peptide system is an excellent inhibitory system for natural activation. This new evidence supports the theory that GREs converged on glycyl radical formation due to the better conformational accessibility of the glycine radical loop, rather than the highest radical stability of the formed peptide radicals.
Collapse
Affiliation(s)
- Marko Hanževački
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, U.K
| |
Collapse
|
18
|
Duan Y, Wei Y, Xing M, Liu J, Jiang L, Lu Q, Liu X, Liu Y, Ang EL, Liao RZ, Yuchi Z, Zhao H, Zhang Y. Anaerobic Hydroxyproline Degradation Involving C-N Cleavage by a Glycyl Radical Enzyme. J Am Chem Soc 2022; 144:9715-9722. [PMID: 35611954 DOI: 10.1021/jacs.2c01673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxyprolines are highly abundant in nature as they are components of many structural proteins and osmolytes. Anaerobic degradation of trans-4-hydroxy-l-proline (t4L-HP) was previously found to involve the glycyl radical enzyme (GRE) t4L-HP dehydratase (HypD). Here, we report a pathway for anaerobic hydroxyproline degradation that involves a new GRE, trans-4-hydroxy-d-proline (t4D-HP) C-N-lyase (HplG). In this pathway, cis-4-hydroxy-l-proline (c4L-HP) is first isomerized to t4D-HP, followed by radical-mediated ring opening by HplG to give 2-amino-4-ketopentanoate (AKP), the first example of a ring opening reaction catalyzed by a GRE 1,2-eliminase. Subsequent cleavage by AKP thiolase (OrtAB) yields acetyl-CoA and d-alanine. We report a crystal structure of HplG in complex with t4D-HP at a resolution of 2.7 Å, providing insights into its catalytic mechanism. Different from HypD commonly identified in proline-reducing Clostridia, HplG is present in other types of fermenting bacteria, including propionate-producing bacteria, underscoring the diversity of enzymatic radical chemistry in the anaerobic microbiome.
Collapse
Affiliation(s)
- Yongxu Duan
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Meining Xing
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Qiang Lu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Xumei Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yanhong Liu
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| |
Collapse
|
19
|
Abstract
Some oxidoreductase enzymes use redox-active tyrosine, tryptophan, cysteine, and/or glycine residues as one-electron, high-potential redox (radical) cofactors. Amino-acid radical cofactors typically perform one of four tasks-they work in concert with a metallocofactor to carry out a multielectron redox process, serve as storage sites for oxidizing equivalents, activate the substrate molecules, or move oxidizing equivalents over long distances. It is challenging to experimentally resolve the thermodynamic and kinetic redox properties of a single-amino-acid residue. The inherently reactive and highly oxidizing properties of amino-acid radicals increase the experimental barriers further still. This review describes a family of stable and well-structured model proteins that was made specifically to study tyrosine and tryptophan oxidation-reduction. The so-called α3X model protein system was combined with very-high-potential protein film voltammetry, transient absorption spectroscopy, and theoretical methods to gain a comprehensive description of the thermodynamic and kinetic properties of protein tyrosine and tryptophan radicals.
Collapse
Affiliation(s)
- Cecilia Tommos
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA;
| |
Collapse
|
20
|
Liu Y, Chen H, Van Treuren W, Hou BH, Higginbottom SK, Dodd D. Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites. Nat Microbiol 2022; 7:695-706. [PMID: 35505245 PMCID: PMC9089323 DOI: 10.1038/s41564-022-01109-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/24/2022] [Indexed: 11/30/2022]
Abstract
Gut bacteria face a key problem in how they capture enough energy to sustain their growth and physiology. The gut bacterium Clostridium sporogenes obtains its energy by utilizing amino acids in pairs, coupling the oxidation of one to the reduction of another-the Stickland reaction. Oxidative pathways produce ATP via substrate-level phosphorylation, whereas reductive pathways are thought to balance redox. In the present study, we investigated whether these reductive pathways are also linked to energy generation and the production of microbial metabolites that may circulate and impact host physiology. Using metabolomics, we find that, during growth in vitro, C. sporogenes produces 15 metabolites, 13 of which are present in the gut of C. sporogenes-colonized mice. Four of these compounds are reductive Stickland metabolites that circulate in the blood of gnotobiotic mice and are also detected in plasma from healthy humans. Gene clusters for reductive Stickland pathways suggest involvement of electron transfer proteins, and experiments in vitro demonstrate that reductive metabolism is coupled to ATP formation and not just redox balance. Genetic analysis points to the broadly conserved Rnf complex as a key coupling site for energy transduction. Rnf complex mutants show aberrant amino acid metabolism in a defined medium and are attenuated for growth in the mouse gut, demonstrating a role of the Rnf complex in Stickland metabolism and gut colonization. Our findings reveal that the production of circulating metabolites by a commensal bacterium within the host gut is linked to an ATP-yielding redox process.
Collapse
Affiliation(s)
- Yuanyuan Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Haoqing Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bi-Huei Hou
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dodd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
21
|
Williams TJ, Allen MA, Panwar P, Cavicchioli R. Into the darkness: the ecologies of novel 'microbial dark matter' phyla in an Antarctic lake. Environ Microbiol 2022; 24:2576-2603. [PMID: 35466505 PMCID: PMC9324843 DOI: 10.1111/1462-2920.16026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022]
Abstract
Uncultivated microbial clades ('microbial dark matter') are inferred to play important but uncharacterized roles in nutrient cycling. Using Antarctic lake (Ace Lake, Vestfold Hills) metagenomes, 12 metagenome-assembled genomes (MAGs; 88%-100% complete) were generated for four 'dark matter' phyla: six MAGs from Candidatus Auribacterota (=Aureabacteria, SURF-CP-2), inferred to be hydrogen- and sulfide-producing fermentative heterotrophs, with individual MAGs encoding bacterial microcompartments (BMCs), gas vesicles, and type IV pili; one MAG (100% complete) from Candidatus Hinthialibacterota (=OLB16), inferred to be a facultative anaerobe capable of dissimilatory nitrate reduction to ammonia, specialized for mineralization of complex organic matter (e.g. sulfated polysaccharides), and encoding BMCs, flagella, and Tad pili; three MAGs from Candidatus Electryoneota (=AABM5-125-24), previously reported to include facultative anaerobes capable of dissimilatory sulfate reduction, and here inferred to perform sulfite oxidation, reverse tricarboxylic acid cycle for autotrophy, and possess numerous proteolytic enzymes; two MAGs from Candidatus Lernaellota (=FEN-1099), inferred to be capable of formate oxidation, amino acid fermentation, and possess numerous enzymes for protein and polysaccharide degradation. The presence of 16S rRNA gene sequences in public metagenome datasets (88%-100% identity) suggests these 'dark matter' phyla contribute to sulfur cycling, degradation of complex organic matter, ammonification and/or chemolithoautotrophic CO2 fixation in diverse global environments.
Collapse
Affiliation(s)
- Timothy J. Williams
- School of Biotechnology and Biomolecular SciencesUNSW SydneySydneyNSW2052Australia
| | - Michelle A. Allen
- School of Biotechnology and Biomolecular SciencesUNSW SydneySydneyNSW2052Australia
| | - Pratibha Panwar
- School of Biotechnology and Biomolecular SciencesUNSW SydneySydneyNSW2052Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular SciencesUNSW SydneySydneyNSW2052Australia
| |
Collapse
|
22
|
The Autonomous Glycyl Radical Protein GrcA Restores Activity to Inactive Full-Length Pyruvate Formate-Lyase In Vivo. J Bacteriol 2022; 204:e0007022. [PMID: 35377165 DOI: 10.1128/jb.00070-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During glucose fermentation, Escherichia coli and many other microorganisms employ the glycyl radical enzyme (GRE) pyruvate formate-lyase (PflB) to catalyze the coenzyme A-dependent cleavage of pyruvate to formate and acetyl-coenzyme A (CoA). Due to its extreme reactivity, the radical in PflB must be controlled carefully and, once generated, is particularly susceptible to dioxygen. Exposure to oxygen of the radical on glycine residue 734 of PflB results in cleavage of the polypeptide chain and consequent inactivation of the enzyme. Two decades ago, a small 14-kDa protein called YfiD (now called autonomous glycyl radical cofactor [GrcA]) was shown to be capable of restoring activity to O2-inactivated PflB in vitro; however, GrcA has never been shown to have this function in vivo. By constructing a strain with a chromosomally encoded PflB enzyme variant with a G734A residue exchange, we could show that cells retained near-wild type fermentative growth, as well as formate and H2 production; H2 is derived by enzymatic disproportionation of formate. Introducing a grcA deletion mutation into this strain completely prevented formate and H2 generation and reduced anaerobic growth. We could show that the conserved glycine at position 102 on GrcA was necessary for GrcA to restore PflB activity and that this recovered activity depended on the essential cysteine residues 418 and 419 in the active site of PflB. Together, our findings demonstrate that GrcA is capable of restoring in vivo activity to inactive full-length PflB and support a model whereby GrcA displaces the C-terminal glycyl radical domain to rescue the catalytic function of PflB. IMPORTANCE Many facultative anaerobic microorganisms use glycyl radical enzymes (GREs) to catalyze chemically challenging reactions under anaerobic conditions. Pyruvate formate-lyase (PflB) is a GRE that catalyzes cleavage of the carbon-carbon bond of pyruvate during glucose fermentation. The problem is that glycyl radicals are destroyed readily, especially by oxygen. To protect and restore activity to inactivated PflB, bacteria like Escherichia coli have a small autonomous glycyl radical cofactor protein called GrcA, which functions to rescue inactivated PflB. To date, this proposed function of GrcA has only been demonstrated in vitro. Our data reveal that GrcA rescues and restores enzyme activity to an inactive full-length form of PflB in vivo. These results have important implications for the evolution of radical-based enzyme mechanisms.
Collapse
|
23
|
The Stickland Reaction Precursor trans-4-Hydroxy-l-Proline Differentially Impacts the Metabolism of Clostridioides difficile and Commensal Clostridia. mSphere 2022; 7:e0092621. [PMID: 35350846 PMCID: PMC9044972 DOI: 10.1128/msphere.00926-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
An intact gut microbiota confers colonization resistance against Clostridioides difficile through a variety of mechanisms, likely including competition for nutrients. Recently, proline was identified as an important environmental amino acid that C. difficile uses to support growth and cause significant disease. A posttranslationally modified form, trans-4-hydroxyproline, is highly abundant in collagen, which is degraded by host proteases in response to C. difficile toxin activity. The ability to dehydrate trans-4-hydroxyproline via the HypD glycyl radical enzyme is widespread among gut microbiota, including C. difficile and members of the commensal Clostridia, suggesting that this amino acid is an important nutrient in the host environment. Therefore, we constructed a C. difficile ΔhypD mutant and found that it was modestly impaired in fitness in a mouse model of infection, and was associated with an altered microbiota when compared to mice challenged with the wild-type strain. Changes in the microbiota between the two groups were largely driven by members of the Lachnospiraceae family and the Clostridium genus. We found that C. difficile and type strains of three commensal Clostridia had significant alterations to their metabolic gene expression in the presence of trans-4-hydroxyproline in vitro. The proline reductase (prd) genes were elevated in C. difficile, consistent with the hypothesis that trans-4-hydroxyproline is used by C. difficile to supply proline for energy metabolism. Similar transcripts were also elevated in some commensal Clostridia tested, although each strain responded differently. This suggests that the uptake and utilization of other nutrients by the commensal Clostridia may be affected by trans-4-hydroxyproline metabolism, highlighting how a common nutrient may be a signal to each organism to adapt to a unique niche. Further elucidation of the differences between them in the presence of hydroxyproline and other key nutrients will be important in determining their role in nutrient competition against C. difficile. IMPORTANCE Proline is an essential environmental amino acid that C. difficile uses to support growth and cause significant disease. A posttranslationally modified form, hydroxyproline, is highly abundant in collagen, which is degraded by host proteases in response to C. difficile toxin activity. The ability to dehydrate hydroxyproline via the HypD glycyl radical enzyme is widespread among gut microbiota, including C. difficile and members of the commensal Clostridia, suggesting that this amino acid is an important nutrient in the host environment. We found that C. difficile and three commensal Clostridia strains had significant, but different, alterations to their metabolic gene expression in the presence of hydroxyproline in vitro. This suggests that the uptake and utilization of other nutrients by the commensal Clostridia may be affected by hydroxyproline metabolism, highlighting how a common nutrient may be a signal to each organism to adapt to a unique niche. Further elucidation of the differences between them in the presence of hydroxyproline and other key nutrients will be important to determining their role in nutrient competition against C. difficile.
Collapse
|
24
|
Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases. Int J Mol Sci 2022; 23:ijms23063043. [PMID: 35328479 PMCID: PMC8950772 DOI: 10.3390/ijms23063043] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Among carbohydrate active enzymes, glycoside phosphorylases (GPs) are valuable catalysts for white biotechnologies, due to their exquisite capacity to efficiently re-modulate oligo- and poly-saccharides, without the need for costly activated sugars as substrates. The reversibility of the phosphorolysis reaction, indeed, makes them attractive tools for glycodiversification. However, discovery of new GP functions is hindered by the difficulty in identifying them in sequence databases, and, rather, relies on extensive and tedious biochemical characterization studies. Nevertheless, recent advances in automated tools have led to major improvements in GP mining, activity predictions, and functional screening. Implementation of GPs into innovative in vitro and in cellulo bioproduction strategies has also made substantial advances. Herein, we propose to discuss the latest developments in the strategies employed to efficiently discover GPs and make the best use of their exceptional catalytic properties for glycoside bioproduction.
Collapse
|
25
|
Yan D, Cao L, Zhou M, Mohimani H. TransDiscovery: Discovering Biotransformation from Human Microbiota by Integrating Metagenomic and Metabolomic Data. Metabolites 2022; 12:metabo12020119. [PMID: 35208194 PMCID: PMC8877437 DOI: 10.3390/metabo12020119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 12/27/2022] Open
Abstract
The human microbiome is a complex community of microorganisms, their enzymes, and the molecules they produce or modify. Recent studies show that imbalances in human microbial ecosystems can cause disease. Our microbiome affects our health through the products of biochemical reactions catalyzed by microbial enzymes (microbial biotransformations). Despite their significance, currently, there are no systematic strategies for identifying these chemical reactions, their substrates and molecular products, and their effects on health and disease. We present TransDiscovery, a computational algorithm that integrates molecular networks (connecting related molecules with similar mass spectra), association networks (connecting co-occurring molecules and microbes) and knowledge bases of microbial enzymes to discover microbial biotransformations, their substrates, and their products. After searching the metabolomics and metagenomics data from the American Gut Project and the Global Foodomic Project, TranDiscovery identified 17 potentially novel biotransformations from the human gut microbiome, along with the corresponding microbial species, substrates, and products.
Collapse
|
26
|
The Interaction among Microbiota, Epigenetic Regulation, and Air Pollutants in Disease Prevention. J Pers Med 2021; 12:jpm12010014. [PMID: 35055330 PMCID: PMC8777767 DOI: 10.3390/jpm12010014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/09/2021] [Accepted: 12/22/2021] [Indexed: 12/12/2022] Open
Abstract
Environmental pollutants can influence microbiota variety, with important implications for the general wellbeing of organisms. In subjects at high-risk of cancer, gut, and lung microbiota are distinct from those of low-risk subjects, and disease progression is associated with microbiota alterations. As with many inflammatory diseases, it is the combination of specific host and environmental factors in certain individuals that provokes disease outcomes. The microbiota metabolites influence activity of epigenetic enzymes. The knowledge of the mechanisms of action of environmental pollution now includes not only the alteration of the gut microbiota but also the interaction between different human microbiota niches such as the lung–gut axis. The epigenetic regulations can reprogram differentiated cells in response to environmental changes. The microbiota can play a major role in the progression and suppression of several epigenetic diseases. Accordingly, the maintenance of a balanced microbiota by monitoring the environmental stimuli provides a novel preventive approach for disease prevention. Metagenomics technologies can be utilized to establish new mitigation approaches for diseases induced by polluted environments. The purpose of this review is to examine the effects of particulate matter exposure on the progression of disease outcomes as related to the alterations of gut and lung microbial communities and consequent epigenetic modifications.
Collapse
|
27
|
Deng WH, Lu Y, Liao RZ. Revealing the Mechanism of Isethionate Sulfite-Lyase by QM/MM Calculations. J Chem Inf Model 2021; 61:5871-5882. [PMID: 34806370 DOI: 10.1021/acs.jcim.1c00978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Isethionate sulfite-lyase (IseG) is a recently characterized glycyl radical enzyme (GRE) that catalyzes radical-mediated C-S bond cleavage of isethionate to produce acetaldehyde and sulfite. Herein, we use quantum mechanical/molecular mechanical (QM/MM) calculations to investigate the detailed catalytic reaction mechanism of IseG. Our calculations indicate that a previously proposed direct 1,2-elimination mechanism is disfavored. Instead, we suggest a new 1,2-migration mechanism for this enzymatic reaction: a key stepwise 1,2-SO3- radical migration occurs after the catalytically active cysteinyl radical grabs a hydrogen atom from isethionate, followed by hydrogen atom transfer from cysteine to a 1-hydroxylethane-1-sulfonate radical intermediate. Finally, the elimination of sulfite from 1-hydroxylethane-1-sulfonate to result in the final product is likely to occur outside the enzyme. Glu468 in the active site is found to help orient the substrate rather than grabbing a proton from the hydroxyl group of the substrate. Our findings help reveal the mechanisms of radical-mediated C-S bond cleavage of organosulfonates catalyzed by GREs and expand the understanding of radical-based enzymatic catalysis.
Collapse
Affiliation(s)
- Wen-Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - You Lu
- Scientific Computing Department, UKRI STFC Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| |
Collapse
|
28
|
Lin S, Zhang H, Wang X, Lin T, Chen Z, Liu J, Wang J. Abundance of Lipopolysaccharide Heptosyltransferase I in Human Gut Microbiome and Its Association With Cardiovascular Disease and Liver Cirrhosis. Front Microbiol 2021; 12:756976. [PMID: 34917047 PMCID: PMC8669917 DOI: 10.3389/fmicb.2021.756976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Lipopolysaccharide (LPS) is a potent endotoxin on the outer membrane of gram-negative bacteria. Heptosyltransferase I (HpeI) takes part in the synthesis of LPS. In this study, we first collected the protein sequences of HpeI homologs from the human microbiome. The collected HpeI sequences was classified based on sequence similarity, and seven clusters of HpeI were obtained. Among these clusters, proteins from Cluster 3 were abundant in the human mouth, while Clusters 1, 6, and 7 were abundant in the human gut. In addition, proteins from Cluster 1 were mainly from the order of Enterobacterales, while Cluster 6 and 7 were from Burkholderiales. The correlation analysis indicated that the total abundance of HpeIs was increased in patients with cardiovascular disease and liver cirrhosis, and HpeI in Cluster 1 contributed to this increase. These data suggest that HpeI homologs in Cluster 1 can be recognized as biomarkers for cardiovascular disease and liver cirrhosis, and that reducing the bacterial load in Cluster 1 may contribute to disease therapy.
Collapse
Affiliation(s)
- Shujin Lin
- Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Hui Zhang
- Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Xueke Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Ting Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Zihan Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Jingfeng Liu
- Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Jianmin Wang
- Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China
| |
Collapse
|
29
|
Fregulia P, Neves ALA, Dias RJP, Campos MM. A review of rumen parameters in bovines with divergent feed efficiencies: What do these parameters tell us about improving animal productivity and sustainability? Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
30
|
Neves ALA, Yu J, Suzuki Y, Baez-Magana M, Arutyunova E, O'Hara E, McAllister T, Ominski KH, Lemieux MJ, Guan LL. Accelerated discovery of novel glycoside hydrolases using targeted functional profiling and selective pressure on the rumen microbiome. MICROBIOME 2021; 9:229. [PMID: 34814938 PMCID: PMC8609826 DOI: 10.1186/s40168-021-01147-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Carbohydrate-active enzymes (CAZymes) form the most widespread and structurally diverse set of enzymes involved in the breakdown, biosynthesis, or modification of lignocellulose that can be found in living organisms. However, the structural diversity of CAZymes has rendered the targeted discovery of novel enzymes extremely challenging, as these proteins catalyze many different chemical reactions and are sourced by a vast array of microbes. Consequently, many uncharacterized members of CAZyme families of interest have been overlooked by current methodologies (e.g., metagenomic screening) used to discover lignocellulolytic enzymes. RESULTS In the present study, we combined phenotype-based selective pressure on the rumen microbiota with targeted functional profiling to guide the discovery of unknown CAZymes. In this study, we found 61 families of glycoside hydrolases (GH) (out of 182 CAZymes) from protein sequences deposited in the CAZy database-currently associated with more than 20,324 microbial genomes. Phenotype-based selective pressure on the rumen microbiome showed that lignocellulolytic bacteria (e.g., Fibrobacter succinogenes, Butyrivibrio proteoclasticus) and three GH families (e.g., GH11, GH13, GH45) exhibited an increased relative abundance in the rumen of feed efficient cattle when compared to their inefficient counterparts. These results paved the way for the application of targeted functional profiling to screen members of the GH11 and GH45 families against a de novo protein reference database comprised of 1184 uncharacterized enzymes, which led to the identification of 18 putative xylanases (GH11) and three putative endoglucanases (GH45). The biochemical proof of the xylanolytic activity of the newly discovered enzyme validated the computational simulations and demonstrated the stability of the most abundant xylanase. CONCLUSIONS These findings contribute to the discovery of novel enzymes for the breakdown, biosynthesis, or modification of lignocellulose and demonstrate that the rumen microbiome is a source of promising enzyme candidates for the biotechnology industry. The combined approaches conceptualized in this study can be adapted to any microbial environment, provided that the targeted microbiome is easy to manipulate and facilitates enrichment for the microbes of interest. Video Abstract.
Collapse
Affiliation(s)
- André L A Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870, Frederiksberg C, Denmark
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G2P5, Canada
| | - Jiangkun Yu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G2P5, Canada
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yutaka Suzuki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 0608589, Japan
| | - Marisol Baez-Magana
- Centro Multisciplinario de Estudios en Biotecnologia, Facultad de Veterinaria y Zootecnia Universidad Michoacana de San Nicolas de Hidalgo, 58893, Morelia, Michoacan, Mexico
| | - Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada
| | - Eóin O'Hara
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G2P5, Canada
| | - Tim McAllister
- Lethbridge Research Center, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J4P4, Canada
| | - Kim H Ominski
- Department of Animal Science & National Centre for Livestock and the Environment (NCLE), University of Manitoba, Winnipeg, MB, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2R3, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G2P5, Canada.
| |
Collapse
|
31
|
Dai Z, Wu Z, Zhu W, Wu G. Amino Acids in Microbial Metabolism and Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1354:127-143. [PMID: 34807440 DOI: 10.1007/978-3-030-85686-1_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amino acids (AAs) not only serve as building blocks for protein synthesis in microorganisms but also play important roles in their metabolism, survival, inter-species crosstalk, and virulence. Different AAs have their distinct functions in microbes of the digestive tract and this in turn has important impacts on host nutrition and physiology. Deconjugation and re-conjugation of glycine- or taurine- conjugated bile acids in the process of their enterohepatic recycling is a good example of the bacterial adaptation to harsh gut niches, inter-kingdom cross-talk with AA metabolism, and cell signaling as the critical control point. It is also a big challenge for scientists to modulate the homeostasis of the pools of AAs and their metabolites in the digestive tract with the aim to improve nutrition and regulate AA metabolism related to anti-virulence reactions. Diversity of the metabolic pathways of AAs and their multi-functions in modulating bacterial growth and survival in the digestive tract should be taken into consideration in recommending nutrient requirements for animals. Thus, the concept of functional amino acids can guide not only microbiological studies but also nutritional and physiological investigations. Cutting edge discoveries in this research area will help to better understand the mechanisms responsible for host-microbe interactions and develop new strategies for improving the nutrition, health, and well-being of both animals and humans.
Collapse
Affiliation(s)
- Zhaolai Dai
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Weiyun Zhu
- National Center for International Research On Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Guoyao Wu
- Department of Animal Science, Texas A&M University, College Station, 77843, TX, USA
| |
Collapse
|
32
|
Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein. J Biol Chem 2021; 297:101423. [PMID: 34801558 PMCID: PMC8683613 DOI: 10.1016/j.jbc.2021.101423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Pyruvate formate-lyase (PFL) is a glycyl radical enzyme (GRE) that converts pyruvate and coenzyme A into acetyl-CoA and formate in a reaction that is crucial to the primary metabolism of many anaerobic bacteria. The glycyl radical cofactor, which is posttranslationally installed by a radical S-adenosyl-L-methionine (SAM) activase, is a simple and effective catalyst, but is also susceptible to oxidative damage in microaerobic environments. Such damage occurs at the glycyl radical cofactor, resulting in cleaved PFL (cPFL). Bacteria have evolved a spare part protein termed YfiD that can be used to repair cPFL. Previously, we obtained a structure of YfiD by NMR spectroscopy and found that the N-terminus of YfiD was disordered and that the C-terminus of YfiD duplicates the structure of the C-terminus of PFL, including a β-strand that is not removed by the oxygen-induced cleavage. We also showed that cPFL is highly susceptible to proteolysis, suggesting that YfiD rescue of cPFL competes with protein degradation. Here, we probe the mechanism by which YfiD can bind and restore activity to cPFL through enzymatic and spectroscopic studies. Our data show that the disordered N-terminal region of YfiD is important for YfiD glycyl radical installation but not for catalysis, and that the duplicate β-strand does not need to be cleaved from cPFL for YfiD to bind. In fact, truncation of this PFL region prevents YfiD rescue. Collectively our data suggest the molecular mechanisms by which YfiD activation is precluded both when PFL is not damaged and when it is highly damaged.
Collapse
|
33
|
Li Y, Cao H, Wang X, Guo L, Ding X, Zhao W, Zhang F. Diet-mediated metaorganismal relay biotransformation: health effects and pathways. Crit Rev Food Sci Nutr 2021:1-19. [PMID: 34802351 DOI: 10.1080/10408398.2021.2004993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In recent years, the concept of metaorganism expands our insight into how diet-microbe-host interactions contribute to human health and diseases. We realized that many biological metabolic processes in the host can be summarized into metaorganismal relay pathways, in which metabolites such as trimethylamine-N‑oxide, short-chain fatty acids and bile acids act as double-edged swords (beneficial or harmful effects) in the initiation and progression of diseases. Pleiotropic effects of metabolites are derived from several influencing factors including dose level, targeted organ of effect, action duration and species of these metabolites. Based on the pleiotropic effects of metabolites, personalized therapeutic approaches including microecological agents, enzymatic regulators and changes in dietary habits to govern related metabolite production may provide a new insight in promoting human health. In this review, we summarize our current knowledge of metaorganismal relay pathways and elaborate on the pleiotropic effects of metabolites in these pathways, with special emphasis on related therapeutic nutritional interventions.
Collapse
Affiliation(s)
- Yanmin Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hong Cao
- Department of Nutrition, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Xiaoqian Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Lichun Guo
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoying Ding
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Feng Zhang
- Department of Nutrition, Affiliated Hospital of Jiangnan University, Wuxi, China
| |
Collapse
|
34
|
McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
Collapse
Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| |
Collapse
|
35
|
Wei B, Wang YK, Yu JB, Wang SJ, Yu YL, Xu XW, Wang H. Discovery of novel glycoside hydrolases from C-glycoside-degrading bacteria using sequence similarity network analysis. J Microbiol 2021; 59:931-940. [PMID: 34554454 DOI: 10.1007/s12275-021-1292-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 11/25/2022]
Abstract
C-Glycosides are an important type of natural product with significant bioactivities, and the C-glycosidic bonds of C-glycosides can be cleaved by several intestinal bacteria, as exemplified by the human faeces-derived puerarin-degrading bacterium Dorea strain PUE. However, glycoside hydrolases in these bacteria, which may be involved in the C-glycosidic bond cleavage of C-glycosides, remain largely unknown. In this study, the genomes of the closest phylogenetic neighbours of five puerarin-degrading intestinal bacteria (including Dorea strain PUE) were retrieved, and the protein-coding genes in the genomes were subjected to sequence similarity network (SSN) analysis. Only four clusters of genes were annotated as glycoside hydrolases and observed in the genome of D. longicatena DSM 13814T (the closest phylogenetic neighbour of Dorea strain PUE); therefore, genes from D. longicatena DSM 13814T belonging to these clusters were selected to overexpress recombinant proteins (CG1, CG2, CG3, and CG4) in Escherichia coli BL21(DE3). In vitro assays indicated that CG4 efficiently cleaved the O-glycosidic bond of daidzin and showed moderate β-D-glucosidase and β-D-xylosidase activity. CG2 showed weak activity in hydrolyzing daidzin and pNP-β-D-fucopyranoside, while CG3 was identified as a highly selective and efficient α-glycosidase. Interestingly, CG3 and CG4 could be selectively inhibited by daidzein, explaining their different performance in kinetic studies. Molecular docking studies predicted the molecular determinants of CG2, CG3, and CG4 in substrate selectivity and inhibition propensity. The present study identified three novel and distinctive glycoside hydrolases, highlighting the potential of SSN in the discovery of novel enzymes from genomic data.
Collapse
Affiliation(s)
- Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, 310014, P. R. China
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, P. R. China
| | - Ya-Kun Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Jin-Biao Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Si-Jia Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
- Center for Human Nutrition, David Geffen School of Medicine, University of California, Los Angeles, California, 90024, USA
| | - Yan-Lei Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, P. R. China.
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, P. R. China.
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, 310014, P. R. China.
| |
Collapse
|
36
|
Medema MH, de Rond T, Moore BS. Mining genomes to illuminate the specialized chemistry of life. Nat Rev Genet 2021; 22:553-571. [PMID: 34083778 PMCID: PMC8364890 DOI: 10.1038/s41576-021-00363-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
All organisms produce specialized organic molecules, ranging from small volatile chemicals to large gene-encoded peptides, that have evolved to provide them with diverse cellular and ecological functions. As natural products, they are broadly applied in medicine, agriculture and nutrition. The rapid accumulation of genomic information has revealed that the metabolic capacity of virtually all organisms is vastly underappreciated. Pioneered mainly in bacteria and fungi, genome mining technologies are accelerating metabolite discovery. Recent efforts are now being expanded to all life forms, including protists, plants and animals, and new integrative omics technologies are enabling the increasingly effective mining of this molecular diversity.
Collapse
Affiliation(s)
- Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
37
|
Discovery and mining of enzymes from the human gut microbiome. Trends Biotechnol 2021; 40:240-254. [PMID: 34304905 DOI: 10.1016/j.tibtech.2021.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022]
Abstract
Advances in technological and bioinformatics approaches have led to the generation of a plethora of human gut metagenomic datasets. Metabolomics has also provided substantial data regarding the small metabolites produced and modified by the microbiota. Comparatively, the microbial enzymes mediating the transformation of metabolites have not been intensively investigated. Here, we discuss the recent efforts and technologies used for discovering and mining enzymes from the human gut microbiota. The wealth of knowledge on metabolites, reactions, genome sequences, and structures of proteins, may drive the development of strategies for enzyme mining. Ongoing efforts to annotate gut microbiota enzymes will explain catalytic mechanisms that may guide the clinical applications of the gut microbiome for diagnostic and therapeutic purposes.
Collapse
|
38
|
Yang Z, Kulik HJ. Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of trans-4-Hydroxy-l-Proline Dehydratase. J Phys Chem B 2021; 125:7774-7784. [PMID: 34236200 DOI: 10.1021/acs.jpcb.1c05320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzyme trans-4-hydroxy-l-proline (Hyp) dehydratase (HypD) is among the most abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is considered a promising antibiotic target for the prominent antibiotic-resistant pathogen Clostridium difficile. Although an enzymatic mechanism has been proposed, the role of the greater HypD protein environment in mediating radical reactivity is not well understood. To fill this gap in understanding, we investigate HypD across multiple time- and length-scales using electronic structure modeling and classical molecular dynamics. We observe that the Hyp substrate protonation state significantly alters both its enzyme-free reactivity and its dynamics within the enzyme active site. Accurate coupled-cluster modeling suggests the deprotonated form of Hyp to be the most reactive protonation state for C5-Hpro-S activation. In the protein environment, hydrophobic interactions modulate the positioning of the Cys434 radical to enhance the reactivity of C5-Hpro-S abstraction. Long-time dynamics reveal that changing Hyp protonation states triggers the switching of a Leu643-gated water tunnel, a functional feature that has not yet been observed for members of the GRE superfamily.
Collapse
Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
39
|
Abstract
![]()
The genomic era has dramatically changed how we discover and investigate
microbial biochemistry. In particular, the exponential expansion in
the number of sequenced microbial genomes provides investigators with
a vast wealth of sequence data to exploit for the discovery of biochemical
functions and mechanisms, as well as novel enzymes and metabolites.
In contrast to early biochemical work, which was largely characterized
by “forward” approaches that proceed from biomass to
enzyme to gene, the availability of genome sequences enables the discovery
of new microbial metabolic activities, enzymes, and metabolites by
“reverse” approaches that originate with genetic information
or by approaches that incorporate features of both forward and reverse
methodologies. In the genomic era, the canonical organization of microbial
genomes into gene clusters presents a singular opportunity for the
utilization of genomic data. Specifically, genomic context (information
gleaned from the genes surrounding a gene of interest in the chromosome)
is a powerful tool for chemical discovery in microbial systems because
of the functional and/or physiological relationship that usually exists
between genes found within a gene cluster. This means that the investigator
can use this inferred link to generate hypotheses about the functions
of individual genes in the cluster or even the function of the entire
cluster itself. Here, we discuss how analysis of genomic context in
combination with a mechanistic understanding of enzymes can facilitate
numerous facets of microbial biochemical research including the identification
of biosynthetic gene clusters, the discovery of important and novel
enzymes, the elucidation of natural product structures, and the identification
of new metabolic pathways. We highlight work from our laboratory using
genomic context to discover and study biosynthetic pathways that produce
natural products, including the cylindrocyclophanes, nitrogen–nitrogen
bond-containing metabolites, and the gut microbial genotoxin colibactin.
Although use of genomic context is most commonly associated with studies
of natural product biosynthesis, we also show that it can be applied
to the study of primary metabolism. We illustrate this with examples
from our work studying the members of the glycyl radical enzyme superfamily
involved in choline and 4-hydroxyproline degradation in the human
gut. Looking forward, we envision increased opportunities to use such
information, with the combination of biochemical knowledge and computational
tools poised to fuel a new revolution in our ability to connect genes
and their biochemical functions. In particular, we note a need for
methods that computationally formalize the functional association
between genes when such associations are not obvious from manual gene
annotations. Such tools will drastically augment the feasibility and
scope of gene cluster analysis and accelerate the discovery of new
microbial enzymes, metabolites, and metabolic processes.
Collapse
Affiliation(s)
- Duncan J. Kountz
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
40
|
Lu Q, Wei Y, Lin L, Liu J, Duan Y, Li Y, Zhai W, Liu Y, Ang EL, Zhao H, Yuchi Z, Zhang Y. The Glycyl Radical Enzyme Arylacetate Decarboxylase from Olsenella scatoligenes. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qiang Lu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yongxu Duan
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yaxin Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Weixiang Zhai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| |
Collapse
|
41
|
Abstract
Sulfonates include diverse natural products and anthropogenic chemicals and are widespread in the environment. Many bacteria can degrade sulfonates and obtain sulfur, carbon, and energy for growth, playing important roles in the biogeochemical sulfur cycle. Cleavage of the inert sulfonate C-S bond involves a variety of enzymes, cofactors, and oxygen-dependent and oxygen-independent catalytic mechanisms. Sulfonate degradation by strictly anaerobic bacteria was recently found to involve C-S bond cleavage through O2-sensitive free radical chemistry, catalyzed by glycyl radical enzymes (GREs). The associated discoveries of new enzymes and metabolic pathways for sulfonate metabolism in diverse anaerobic bacteria have enriched our understanding of sulfonate chemistry in the anaerobic biosphere. An anaerobic environment of particular interest is the human gut microbiome, where sulfonate degradation by sulfate- and sulfite-reducing bacteria (SSRB) produces H2S, a process linked to certain chronic diseases and conditions.
Collapse
Affiliation(s)
- Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology; and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China;
| |
Collapse
|
42
|
Dawson CD, Irwin SM, Backman LRF, Le C, Wang JX, Vennelakanti V, Yang Z, Kulik HJ, Drennan CL, Balskus EP. Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase. Cell Chem Biol 2021; 28:1333-1346.e7. [PMID: 33773110 PMCID: PMC8473560 DOI: 10.1016/j.chembiol.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 02/04/2021] [Accepted: 03/03/2021] [Indexed: 01/07/2023]
Abstract
Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound. In comparison with other GREs, alternate positioning of the active site β strands allows for distinct residue positions to contribute to substrate binding. These structural differences, combined with sequence variations, create a highly tailored active site for the binding of the negatively charged isethionate substrate. Through the kinetic analysis of 14 IslA variants and computational analyses, we probe the mechanism by which radical chemistry is used for C-S bond cleavage. This work further elucidates the structural basis of chemistry within the GRE superfamily and will inform structure-based inhibitor design of IsIA and thus of microbial hydrogen sulfide production.
Collapse
Affiliation(s)
- Christopher D Dawson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephania M Irwin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Lindsey R F Backman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chip Le
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Jennifer X Wang
- Harvard Center for Mass Spectrometry, Faculty of Arts and Sciences Division of Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Vyshnavi Vennelakanti
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Catherine L Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02139, USA.
| |
Collapse
|
43
|
Kim KH, Chun BH, Kim J, Jeon CO. Identification of biogenic amine-producing microbes during fermentation of ganjang, a Korean traditional soy sauce, through metagenomic and metatranscriptomic analyses. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107681] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
44
|
Plichta DR, Somani J, Pichaud M, Wallace ZS, Fernandes AD, Perugino CA, Lähdesmäki H, Stone JH, Vlamakis H, Chung DC, Khanna D, Pillai S, Xavier RJ. Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis. Genome Med 2021; 13:35. [PMID: 33648559 PMCID: PMC7919092 DOI: 10.1186/s13073-021-00853-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/11/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Immunoglobulin G4-related disease (IgG4-RD) and systemic sclerosis (SSc) are rare autoimmune diseases characterized by the presence of CD4+ cytotoxic T cells in the blood as well as inflammation and fibrosis in various organs, but they have no established etiologies. Similar to other autoimmune diseases, the gut microbiome might encode disease-triggering or disease-sustaining factors. METHODS The gut microbiomes from IgG4-RD and SSc patients as well as healthy individuals with no recent antibiotic treatment were studied by metagenomic sequencing of stool DNA. De novo assembly-based taxonomic and functional characterization, followed by association and accessory gene set enrichment analysis, were applied to describe microbiome changes associated with both diseases. RESULTS Microbiomes of IgG4-RD and SSc patients distinctly separated from those of healthy controls: numerous opportunistic pathogenic Clostridium and typically oral Streptococcus species were significantly overabundant, while Alistipes, Bacteroides, and butyrate-producing species were depleted in the two diseases compared to healthy controls. Accessory gene content analysis in these species revealed an enrichment of Th17-activating Eggerthella lenta strains in IgG4-RD and SSc and a preferential colonization of a homocysteine-producing strain of Clostridium bolteae in SSc. Overabundance of the classical mevalonate pathway, hydroxyproline dehydratase, and fibronectin-binding protein in disease microbiomes reflects potential functional differences in host immune recognition and extracellular matrix utilization associated with fibrosis. Strikingly, the majority of species that were differentially abundant in IgG4-RD and SSc compared to controls showed the same directionality in both diseases. Compared with multiple sclerosis and rheumatoid arthritis, the gut microbiomes of IgG4-RD and SSc showed similar signatures; in contrast, the most differentially abundant taxa were not the facultative anaerobes consistently identified in inflammatory bowel diseases, suggesting the microbial signatures of IgG4-RD and SSc do not result from mucosal inflammation and decreased anaerobism. CONCLUSIONS These results provide an initial characterization of gut microbiome ecology in fibrosis-prone IgG4-RD and SSc and reveal microbial functions that offer insights into the pathophysiology of these rare diseases.
Collapse
Affiliation(s)
| | - Juhi Somani
- Department of Computer Science, Aalto University, 02150, Espoo, Finland
| | | | - Zachary S Wallace
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
- Clinical Epidemiology Program and Rheumatology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ana D Fernandes
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Cory A Perugino
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, 02150, Espoo, Finland
| | - John H Stone
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel C Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Risk Assessment, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dinesh Khanna
- University of Michigan Scleroderma Program, Ann Arbor, MI, USA
| | - Shiv Pillai
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
| |
Collapse
|
45
|
Shanahan ER, McMaster JJ, Staudacher HM. Conducting research on diet-microbiome interactions: A review of current challenges, essential methodological principles, and recommendations for best practice in study design. J Hum Nutr Diet 2021; 34:631-644. [PMID: 33639033 DOI: 10.1111/jhn.12868] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/07/2021] [Accepted: 01/19/2021] [Indexed: 12/21/2022]
Abstract
Diet is one of the strongest modulators of the gut microbiome. However, the complexity of the interactions between diet and the microbial community emphasises the need for a robust study design and continued methodological development. This review aims to summarise considerations for conducting high-quality diet-microbiome research, outline key challenges unique to the field, and provide advice for addressing these in a practical manner useful to dietitians, microbiologists, gastroenterologists and other diet-microbiome researchers. Searches of databases and references from relevant articles were conducted using the primary search terms 'diet', 'diet intervention', 'dietary analysis', 'microbiome' and 'microbiota', alone or in combination. Publications were considered relevant if they addressed methods for diet and/or microbiome research, or were a human study relevant to diet-microbiome interactions. Best-practice design in diet-microbiome research requires appropriate consideration of the study population and careful choice of trial design and data collection methodology. Ongoing challenges include the collection of dietary data that accurately reflects intake at a timescale relevant to microbial community structure and metabolism, measurement of nutrients in foods pertinent to microbes, improving ability to measure and understand microbial metabolic and functional properties, adequately powering studies, and the considered analysis of multivariate compositional datasets. Collaboration across the disciplines of nutrition science and microbiology is crucial for high-quality diet-microbiome research. Improvements in our understanding of the interaction between nutrient intake and microbial metabolism, as well as continued methodological innovation, will facilitate development of effective evidence-based personalised dietary treatments.
Collapse
Affiliation(s)
- Erin R Shanahan
- School of Life and Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | | | - Heidi M Staudacher
- IMPACT (The Institute for Mental and Physical Health and Clinical Translation) Food & Mood Centre, Deakin University, Geelong, VIC, Australia
| |
Collapse
|
46
|
Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium. Microorganisms 2021; 9:microorganisms9020371. [PMID: 33673352 PMCID: PMC7918557 DOI: 10.3390/microorganisms9020371] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
Clostridioides difficile is an anaerobic pathogen that causes significant morbidity and mortality. Understanding the mechanisms of colonization resistance against C. difficile is important for elucidating the mechanisms by which C. difficile is able to colonize the gut after antibiotics. Commensal Clostridium play a key role in colonization resistance. They are able to modify bile acids which alter the C. difficile life cycle. Commensal Clostridium also produce other inhibitory metabolites including antimicrobials and short chain fatty acids. They also compete with C. difficile for vital nutrients such as proline. Understanding the mechanistic effects that these metabolites have on C. difficile and other gut pathogens is important for the development of new therapeutics against C. difficile infection (CDI), which are urgently needed.
Collapse
|
47
|
Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota. Nat Commun 2021; 12:462. [PMID: 33469019 PMCID: PMC7815924 DOI: 10.1038/s41467-020-20746-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/17/2020] [Indexed: 01/04/2023] Open
Abstract
Clostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile. Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile. We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation. The effects of antibiotics on the gut microbiota can lead to enhanced colonization of Clostridioides difficile (C. difficile) and toxin-mediated pathogenesis. Here, using defined toxin-mutant strains and a murine model, the authors provide insights into how toxin-induced inflammation alters C. difficile metabolism, host tissue gene expression and gut microbiota, together influencing a beneficial niche for infection.
Collapse
|
48
|
Zallot R, Oberg N, Gerlt JA. Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools. Curr Opin Biotechnol 2021; 69:77-90. [PMID: 33418450 DOI: 10.1016/j.copbio.2020.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/08/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022]
Abstract
The continuing expansion of protein and genome sequence databases is an opportunity to identify novel enzymes with biotechnological applications. Whether applied to enzymology, chemical biology, systems biology, and microbiology, database mining must be 'user-friendly' so that experimentalists can devise focused strategies to discover the in vitro activities and in vivo functions of uncharacterized enzymes. We developed a suite of genomic enzymology tools (https://efi.igb.illinois.edu/) to (1) generate sequence similarity networks (SSNs) for exploration of sequence-function space in protein families (EFI-EST) and (2) provide genome context for members of protein families (EFI-GNT). Integrated analysis of this complementary information allows to generate testable hypotheses about new functions. After a brief overview of EFI-EST and EFI-GNT, we describe applications that illustrate their use.
Collapse
Affiliation(s)
- Remi Zallot
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States; Institute of Life Sciences, Swansea University Medical School, Swansea SA2 8PP, Wales, United Kingdom
| | - Nils Oberg
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - John A Gerlt
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States; Departments of Biochemistry and Chemistry, University of Illinois, Urbana, Illinois 61801, United States.
| |
Collapse
|
49
|
Stack TMM, Gerlt JA. Discovery of novel pathways for carbohydrate metabolism. Curr Opin Chem Biol 2020; 61:63-70. [PMID: 33197748 DOI: 10.1016/j.cbpa.2020.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 01/09/2023]
Abstract
Closing the gap between the increasing availability of complete genome sequences and the discovery of novel enzymes in novel metabolic pathways is a significant challenge. Here, we review recent examples of assignment of in vitro enzymatic activities and in vivo metabolic functions to uncharacterized proteins, with a focus on enzymes and metabolic pathways involved in the catabolism and biosynthesis of monosaccharides and polysaccharides. The most effective approaches are based on analyses of sequence-function space in protein families that provide clues for the predictions of the functions of the uncharacterized enzymes. As summarized in this Opinion, this approach allows the discovery of the catabolism of new molecules, new pathways for common molecules, and new enzymatic chemistries.
Collapse
Affiliation(s)
- Tyler M M Stack
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, United States
| | - John A Gerlt
- Carl. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, United States; Departments of Biochemistry and Chemistry, University of Illinois, Urbana, IL 61801, United States.
| |
Collapse
|
50
|
Williamson A, Leiros HKS. Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds. Nucleic Acids Res 2020; 48:8225-8242. [PMID: 32365176 PMCID: PMC7470946 DOI: 10.1093/nar/gkaa307] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
DNA ligases are diverse enzymes with essential functions in replication and repair of DNA; here we review recent advances in their structure and distribution and discuss how this contributes to understanding their biological roles and technological potential. Recent high-resolution crystal structures of DNA ligases from different organisms, including DNA-bound states and reaction intermediates, have provided considerable insight into their enzymatic mechanism and substrate interactions. All cellular organisms possess at least one DNA ligase, but many species encode multiple forms some of which are modular multifunctional enzymes. New experimental evidence for participation of DNA ligases in pathways with additional DNA modifying enzymes is defining their participation in non-redundant repair processes enabling elucidation of their biological functions. Coupled with identification of a wealth of DNA ligase sequences through genomic data, our increased appreciation of the structural diversity and phylogenetic distribution of DNA ligases has the potential to uncover new biotechnological tools and provide new treatment options for bacterial pathogens.
Collapse
Affiliation(s)
- Adele Williamson
- School of Science, University of Waikato, Hamilton 3240, New Zealand.,Department of Chemistry, UiT The Arctic University of Norway, Tromsø N-9037, Norway
| | | |
Collapse
|