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Wallace M, Cummings, Jr. DA, Roberts AG, Puri AW. A widespread methylotroph acyl-homoserine lactone synthase produces a new quorum sensing signal that regulates swarming in Methylobacterium fujisawaense. mBio 2024; 15:e0199923. [PMID: 38085021 PMCID: PMC10790750 DOI: 10.1128/mbio.01999-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/31/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Bacteria known as pink-pigmented facultative methylotrophs colonize many diverse environments on earth, play an important role in the carbon cycle, and in some cases promote plant growth. However, little is known about how these organisms interact with each other and their environment. In this work, we identify one of the chemical signals commonly used by these bacteria and discover that this signal controls swarming motility in the pink-pigmented facultative methylotroph Methylobacterium fujisawaense DSM5686. This work provides new molecular details about interactions between these important bacteria and will help scientists predict these interactions and the group behaviors they regulate from genomic sequencing information.
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Affiliation(s)
- Mike Wallace
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
| | - Dale A. Cummings, Jr.
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
| | - Andrew G. Roberts
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Aaron W. Puri
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
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2
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Beals DG, Puri AW. Linking methanotroph phenotypes to genotypes using a simple spatially resolved model ecosystem. ISME J 2024; 18:wrae060. [PMID: 38622932 PMCID: PMC11072679 DOI: 10.1093/ismejo/wrae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/20/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental context in laboratory settings. Laboratory-based model ecosystems offer a means to better account for environmental conditions compared with standard planktonic cultures and can help link genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs) within the methane-oxygen counter gradient typically found in the natural environment of these organisms. Culturing the methanotroph Methylomonas sp. strain LW13 in this system resulted in the formation of a distinct horizontal band at the intersection of the counter gradient, which we discovered was not due to increased numbers of bacteria at this location but instead to an increased amount of polysaccharides. We also discovered that different methanotrophic taxa form polysaccharide bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this band, we identified genes upregulated within the band and validated their involvement in growth and band formation within the model ecosystem using knockout strains. Notably, deletion of these genes did not negatively affect growth using standard planktonic culturing methods. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover bacterial phenotypes missing from standard laboratory conditions, and to link these phenotypes with their genetic determinants.
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Affiliation(s)
- Delaney G Beals
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, United States
| | - Aaron W Puri
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, United States
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3
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Suo Z, Cummings DA, Puri AW, Schaefer AL, Greenberg EP. A Mesorhizobium japonicum quorum sensing circuit that involves three linked genes and an unusual acyl-homoserine lactone signal. mBio 2023; 14:e0101023. [PMID: 37227303 PMCID: PMC10470506 DOI: 10.1128/mbio.01010-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Members of the genus Mesorhizobium, which are core components of the rhizosphere and specific symbionts of legume plants, possess genes for acyl-homoserine lactone (AHL) quorum sensing (QS). Here we show Mesorhizobium japonicum MAFF 303099 (formerly M. loti) synthesizes and responds to N-[(2E, 4E)-2,4-dodecadienoyl] homoserine lactone (2E, 4E-C12:2-HSL). We show that the 2E, 4E-C12:2-HSL QS circuit involves one of four luxR-luxI-type genes found in the sequenced genome of MAFF 303099. We refer to this circuit, which appears to be conserved among Mesorhizobium species, as R1-I1. We show that two other Mesorhizobium strains also produce 2E, 4E-C12:2-HSL. The 2E, 4E-C12:2-HSL is unique among known AHLs in its arrangement of two trans double bonds. The R1 response to 2E, 4E-C12:2-HSL is extremely selective in comparison with other LuxR homologs, and the trans double bonds appear critical for R1 signal recognition. Most well-studied LuxI-like proteins use S-adenosylmethionine and an acyl-acyl carrier protein as substrates for synthesis of AHLs. Others that form a subgroup of LuxI-type proteins use acyl-coenzyme A substrates rather than acyl-acyl carrier proteins. I1 clusters with the acyl-coenzyme A-type AHL synthases. We show that a gene linked to the I1 AHL synthase is involved in the production of the QS signal. The discovery of the unique I1 product enforces the view that further study of acyl-coenzyme A-dependent LuxI homologs will expand our knowledge of AHL diversity. The involvement of an additional enzyme in AHL generation leads us to consider this system a three-component QS circuit. IMPORTANCE We report a Mesorhizobium japonicum quorum sensing (QS) system involving a novel acyl-homoserine lactone (AHL) signal. This system is known to be involved in root nodule symbiosis with host plants. The chemistry of the newly described QS signal indicated that there may be a dedicated cellular enzyme involved in its synthesis in addition to the types known for production of other AHLs. Indeed, we report that an additional gene is required for synthesis of the unique signal, and we propose that this is a three-component QS circuit as opposed to the canonical two-component AHL QS circuits. The signaling system is exquisitely selective. The selectivity may be important when this species resides in the complex microbial communities around host plants and may make this system useful in various synthetic biology applications of QS circuits.
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Affiliation(s)
- Zehui Suo
- Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Dale A. Cummings
- Department of Chemistry and the Henry Eyring Center for Cell and Genomes Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Aaron W. Puri
- Department of Chemistry and the Henry Eyring Center for Cell and Genomes Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Amy L. Schaefer
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - E. Peter Greenberg
- Department of Microbiology, University of Washington, Seattle, Washington, USA
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4
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Nguyen NA, Cong Y, Hurrell RC, Arias N, Garg N, Puri AW, Schmidt EW, Agarwal V. A Silent Biosynthetic Gene Cluster from a Methanotrophic Bacterium Potentiates Discovery of a Substrate Promiscuous Proteusin Cyclodehydratase. ACS Chem Biol 2022; 17:1577-1585. [PMID: 35666841 PMCID: PMC9746716 DOI: 10.1021/acschembio.2c00251] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Natural product-encoding biosynthetic gene clusters (BGCs) within microbial genomes far outnumber the known natural products; chemical products from such BGCs remain cryptic. These silent BGCs hold promise not only for the elaboration of new natural products but also for the discovery of useful biosynthetic enzymes. Here, we describe a genome mining strategy targeted toward the discovery of substrate promiscuous natural product biosynthetic enzymes. In the genome of the methanotrophic bacterium Methylovulum psychrotolerans Sph1T, we discover a transcriptionally silent natural product BGC that encoded numerous ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. These cryptic RiPP natural products were accessed using heterologous expression of the substrate peptide and biosynthetic enzyme-encoded genes. In line with our genome mining strategy, the RiPP biosynthetic enzymes in this BGC were found to be substrate promiscuous, which allowed us to use them in a combinatorial fashion with a similarly substrate-tolerant cyanobactin biosynthetic enzyme to introduce head-to-tail macrocyclization in the proteusin family of RiPP natural products.
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Affiliation(s)
- Nguyet A. Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City UT, USA 84112
| | - Rachel C. Hurrell
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City UT, USA 84112
| | - Natalie Arias
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332
| | - Aaron W. Puri
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City UT, USA 84112
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City UT, USA 84112
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332,School of Biological Sciences, Georgia Institute of Technology, Atlanta GA, USA 30332,correspondence:
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5
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Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods 2021; 19:134-136. [PMID: 34862502 DOI: 10.1038/s41592-021-01339-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, Germany
| | - Vanessa V Phelan
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Deepa Acharya
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrew E Allen
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin P Bowen
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Deirdre Belle-Oudry
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Simon Boecker
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Dale A Cummings
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.,Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT, USA
| | - Jessica M Deutsch
- School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eoin Fahy
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mirtha Navarro-Hoyos
- BIoactivity for Sustainable Development Group (BIODESS), Department of Chemistry, University of Costa Rica, San Jose, Costa Rica
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Katherine Louie
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Michael M Meijler
- Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Rachel L Neve
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Trent R Northen
- DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Pullman
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Aaron W Puri
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.,Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT, USA
| | - Robin Schmid
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Monica Thukral
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Felipe Vasquez-Castro
- Centro Nacional de Innovaciones Biotecnologicas (CENIBiot), CeNAT-CONARE, 1174-1200, San Jose, Costa Rica
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. .,Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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6
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Abstract
Natural products are an essential source of bioactive compounds. Isotopic labeling is an effective way to identify natural products that incorporate a specific precursor; however, this approach is limited by the availability of isotopically enriched precursors. We used an inverse stable isotopic labeling approach to identify natural products by growing bacteria on a 13C-carbon source and then identifying 12C-precursor incorporation by mass spectrometry. We applied this approach to methylotrophs, ecologically important bacteria predicted to have significant yet underexplored biosynthetic potential. We demonstrate that this method identifies N-acyl homoserine lactone quorum sensing signals produced by diverse methylotrophs grown on three different one-carbon compounds. We then apply this approach to simultaneously detect five previously unidentified signals produced by a methylotroph and link these compounds to their synthases. We envision that this method can be used to identify other natural product classes synthesized by methylotrophs and other organisms that grow on relatively inexpensive 13C-carbon sources.
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Affiliation(s)
- Dale A. Cummings
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
| | - Alice I. Snelling
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
| | - Aaron W. Puri
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, United States
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8
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Fei Q, Puri AW, Smith H, Dowe N, Pienkos PT. Enhanced biological fixation of methane for microbial lipid production by recombinant Methylomicrobium buryatense. Biotechnol Biofuels 2018; 11:129. [PMID: 29755588 PMCID: PMC5934843 DOI: 10.1186/s13068-018-1128-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 04/23/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Due to the success of shale gas development in the US, the production cost of natural gas has been reduced significantly, which in turn has made methane (CH4), the major component of natural gas, a potential alternative substrate for bioconversion processes compared with other high-price raw material sources or edible feedstocks. Therefore, exploring effective ways to use CH4 for the production of biofuels is attractive. Biological fixation of CH4 by methanotrophic bacteria capable of using CH4 as their sole carbon and energy source has obtained great attention for biofuel production from this resource. RESULTS In this study, a fast-growing and lipid-rich methanotroph, Methylomicrobium buryatense 5GB1 and its glycogen-knock-out mutant (AP18) were investigated for the production of lipids derived from intracellular membranes, which are key precursors for the production of green diesel. The effects of culture conditions on cell growth and lipid production were investigated in high cell density cultivation with continuous feeding of CH4 and O2. The highest dry cell weight observed was 21.4 g/L and the maximum lipid productivity observed was 45.4 mg/L/h obtained in batch cultures, which corresponds to a 2-fold enhancement in cell density and 3-fold improvement in lipid production, compared with previous reported data from cultures of 5GB1. A 90% enhancement of lipid content was achieved by limiting the biosynthesis of glycogen in strain AP18. Increased CH4/O2 uptake and CO2 evaluation rates were observed in AP18 cultures suggesting that more carbon substrate and energy are needed for AP18 growth while producing lipids. The lipid produced by M. buryatense was estimated to have a cetane number of 75, which is 50% higher than biofuel standards requested by US and EU. CONCLUSIONS Cell growth and lipid production were significantly influenced by culture conditions for both 5GB1 and AP18. Enhanced lipid production in terms of titer, productivity, and content was achieved under high cell density culture conditions by blocking glycogen accumulation as a carbon sink in the strain AP18. Differences observed in CH4/O2 gas uptake and CO2 evolution rates as well as cell growth and glycogen accumulation between 5GB1 and AP18 suggest changes in the metabolic network between these strains. This bioconversion process provides a promising opportunity to transform CH4 into biofuel molecules and encourages further investigation to elucidate the remarkable CH4 biofixation mechanism used by these bacteria.
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Affiliation(s)
- Qiang Fei
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Aaron W. Puri
- Department of Chemical Engineering, University of Washington, Seattle, WA USA
| | - Holly Smith
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Nancy Dowe
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Philip. T. Pienkos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
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9
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Puri AW, Mevers E, Ramadhar TR, Petras D, Liu D, Piel J, Dorrestein PC, Greenberg EP, Lidstrom ME, Clardy J. Tundrenone: An Atypical Secondary Metabolite from Bacteria with Highly Restricted Primary Metabolism. J Am Chem Soc 2018; 140:2002-2006. [PMID: 29361220 PMCID: PMC5817624 DOI: 10.1021/jacs.7b12240] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Methane-oxidizing bacteria, aerobes
that utilize methane as their
sole carbon and energy source, are being increasingly studied for
their environmentally significant ability to remove methane from the
atmosphere. Their genomes indicate that they also have a robust and
unusual secondary metabolism. Bioinformatic analysis of the Methylobacter tundripaludum genome identified biosynthetic
gene clusters for several intriguing metabolites, and this report
discloses the structural and genetic characterization of tundrenone,
one of these metabolites. Tundrenone is a highly oxidized metabolite
that incorporates both a modified bicyclic chorismate-derived fragment
and a modified lipid tail bearing a β,γ-unsaturated α-hydroxy
ketone. Tundrenone has been genetically linked to its biosynthetic
gene cluster, and quorum sensing activates its production. M. tundripaludum’s genome and tundrenone’s
discovery support the idea that additional studies of methane-oxidizing
bacteria will reveal new naturally occurring molecular scaffolds and
the biosynthetic pathways that produce them.
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Affiliation(s)
- Aaron W Puri
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Timothy R Ramadhar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Darren Liu
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich , Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - E Peter Greenberg
- Department of Microbiology, University of Washington , Seattle, Washington 98195, United States
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States.,Department of Microbiology, University of Washington , Seattle, Washington 98195, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
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10
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Gilman A, Fu Y, Hendershott M, Chu F, Puri AW, Smith AL, Pesesky M, Lieberman R, Beck DAC, Lidstrom ME. Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C. PeerJ 2017; 5:e3945. [PMID: 29062611 PMCID: PMC5652258 DOI: 10.7717/peerj.3945] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 09/30/2017] [Indexed: 11/20/2022] Open
Abstract
The bacteria that grow on methane aerobically (methanotrophs) support populations of non-methanotrophs in the natural environment by excreting methane-derived carbon. One group of excreted compounds are short-chain organic acids, generated in highest abundance when cultures are grown under O2-starvation. We examined this O2-starvation condition in the methanotroph Methylomicrobium buryatense 5GB1. The M. buryatense 5GB1 genome contains homologs for all enzymes necessary for a fermentative metabolism, and we hypothesize that a metabolic switch to fermentation can be induced by low-O2 conditions. Under prolonged O2-starvation in a closed vial, this methanotroph increases the amount of acetate excreted about 10-fold, but the formate, lactate, and succinate excreted do not respond to this culture condition. In bioreactor cultures, the amount of each excreted product is similar across a range of growth rates and limiting substrates, including O2-limitation. A set of mutants were generated in genes predicted to be involved in generating or regulating excretion of these compounds and tested for growth defects, and changes in excretion products. The phenotypes and associated metabolic flux modeling suggested that in M. buryatense 5GB1, formate and acetate are excreted in response to redox imbalance. Our results indicate that even under O2-starvation conditions, M. buryatense 5GB1 maintains a metabolic state representing a combination of fermentation and respiration metabolism.
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Affiliation(s)
- Alexey Gilman
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America
| | - Yanfen Fu
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America
| | | | | | - Aaron W Puri
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America
| | | | - Mitchell Pesesky
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America
| | - Rose Lieberman
- Department of Biology, George Washington University, Washington, D.C., USA
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America.,eScience Institute, University of Washington, Seattle, WA, USA
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America.,Department of Microbiology, University of Washington, Seattle, WA, USA
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11
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Gilman A, Laurens LM, Puri AW, Chu F, Pienkos PT, Lidstrom ME. Bioreactor performance parameters for an industrially-promising methanotroph Methylomicrobium buryatense 5GB1. Microb Cell Fact 2015; 14:182. [PMID: 26572866 PMCID: PMC4647623 DOI: 10.1186/s12934-015-0372-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/29/2015] [Indexed: 11/22/2022] Open
Abstract
Background Methane is a feedstock of interest for the future, both from natural gas and from renewable biogas sources. Methanotrophic bacteria have the potential to enable commercial methane bioconversion to value-added products such as fuels and chemicals. A strain of interest for such applications is Methylomicrobium buryatense 5GB1, due to its robust growth characteristics. However, to take advantage of the potential of this methanotroph, it is important to generate comprehensive bioreactor-based datasets for different growth conditions to compare bioprocess parameters. Results Datasets of growth parameters, gas utilization rates, and products (total biomass, extracted fatty acids, glycogen, excreted acids) were obtained for cultures of M. buryatense 5GB1 grown in continuous culture under methane limitation and O2 limitation conditions. Additionally, experiments were performed involving unrestricted batch growth conditions with both methane and methanol as substrate. All four growth conditions show significant differences. The most notable changes are the high glycogen content and high formate excretion for cells grown on methanol (batch), and high O2:CH4 utilization ratio for cells grown under methane limitation. Conclusions The results presented here represent the most comprehensive published bioreactor datasets for a gamma-proteobacterial methanotroph. This information shows that metabolism by M. buryatense 5GB1 differs significantly for each of the four conditions tested. O2 limitation resulted in the lowest relative O2 demand and fed-batch growth on methane the highest. Future studies are needed to understand the metabolic basis of these differences. However, these results suggest that both batch and continuous culture conditions have specific advantages, depending on the product of interest. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0372-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexey Gilman
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Lieve M Laurens
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA.
| | - Aaron W Puri
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Frances Chu
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Philip T Pienkos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA.
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA. .,Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.
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12
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Bender KO, Garland M, Ferreyra JA, Hryckowian AJ, Child MA, Puri AW, Solow-Cordero DE, Higginbottom SK, Segal E, Banaei N, Shen A, Sonnenburg JL, Bogyo M. A small-molecule antivirulence agent for treating Clostridium difficile infection. Sci Transl Med 2015; 7:306ra148. [PMID: 26400909 DOI: 10.1126/scitranslmed.aac9103] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/04/2015] [Indexed: 12/22/2022]
Abstract
Clostridium difficile infection (CDI) is a worldwide health threat that is typically triggered by the use of broad-spectrum antibiotics, which disrupt the natural gut microbiota and allow this Gram-positive anaerobic pathogen to thrive. The increased incidence and severity of disease coupled with decreased response, high recurrence rates, and emergence of multiple antibiotic-resistant strains have created an urgent need for new therapies. We describe pharmacological targeting of the cysteine protease domain (CPD) within the C. difficile major virulence factor toxin B (TcdB). Through a targeted screen with an activity-based probe for this protease domain, we identified a number of potent CPD inhibitors, including one bioactive compound, ebselen, which is currently in human clinical trials for a clinically unrelated indication. This drug showed activity against both major virulence factors, TcdA and TcdB, in biochemical and cell-based studies. Treatment in a mouse model of CDI that closely resembles the human infection confirmed a therapeutic benefit in the form of reduced disease pathology in host tissues that correlated with inhibition of the release of the toxic glucosyltransferase domain (GTD). Our results show that this non-antibiotic drug can modulate the pathology of disease and therefore could potentially be developed as a therapeutic for the treatment of CDI.
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Affiliation(s)
- Kristina Oresic Bender
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - Megan Garland
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - Jessica A Ferreyra
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Matthew A Child
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - Aaron W Puri
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - David E Solow-Cordero
- Stanford University High-Throughput Bioscience Center, 1291 Welch Road, Stanford, CA 94305-5174, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Ehud Segal
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA. Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305-5107, USA
| | - Aimee Shen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324, USA. Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA.
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13
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Kalyuzhnaya MG, Puri AW, Lidstrom ME. Metabolic engineering in methanotrophic bacteria. Metab Eng 2015; 29:142-152. [PMID: 25825038 DOI: 10.1016/j.ymben.2015.03.010] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 02/26/2015] [Accepted: 03/17/2015] [Indexed: 12/19/2022]
Abstract
Methane, as natural gas or biogas, is the least expensive source of carbon for (bio)chemical synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can bring new sustainable solutions to a number of industries with large environmental footprints, such as natural gas/petroleum production, landfills, wastewater treatment, and livestock. Microbial biocatalysis with methane as a feedstock has been pursued off and on for almost a half century, with little enduring success. Today, biological engineering and systems biology provide new opportunities for metabolic system modulation and give new optimism to the concept of a methane-based bio-industry. Here we present an overview of the most recent advances pertaining to metabolic engineering of microbial methane utilization. Some ideas concerning metabolic improvements for production of acetyl-CoA and pyruvate, two main precursors for bioconversion, are presented. We also discuss main gaps in the current knowledge of aerobic methane utilization, which must be solved in order to release the full potential of methane-based biosystems.
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Affiliation(s)
- Marina G Kalyuzhnaya
- Biology Department, San Diego State University, San Diego, CA 92182-4614, United States; Department of Microbiology, University of Washington, Seattle, WA 98195, United States
| | - Aaron W Puri
- Department of Chemical Engineering, Seattle, WA 98195, United States
| | - Mary E Lidstrom
- Department of Chemical Engineering, Seattle, WA 98195, United States; Department of Microbiology, University of Washington, Seattle, WA 98195, United States.
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Abstract
Elucidating the molecular and biochemical details of bacterial infections can be challenging because of the many complex interactions that exist between a pathogen and its host. Consequently, many tools have been developed to aid the study of bacterial pathogenesis. Small molecules are a valuable complement to traditional genetic techniques because they can be used to rapidly perturb genetically intractable systems and to monitor post-translationally regulated processes. Activity-based probes are a subset of small molecules that covalently label an enzyme of interest based on its catalytic mechanism. These tools allow monitoring of enzyme activation within the context of a native biological system and can be used to dissect the biochemical details of enzyme function. This review describes the development and application of activity-based probes for examining aspects of bacterial infection on both sides of the host-pathogen interface.
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Affiliation(s)
- Aaron W Puri
- Department of Chemical and Systems Biology, ‡Department of Microbiology and Immunology, and §Department of Pathology, Stanford University School of Medicine , 300 Pasteur Drive, Stanford, California 94305, United States
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Xiao J, Broz P, Puri AW, Deu E, Morell M, Monack DM, Bogyo M. A coupled protein and probe engineering approach for selective inhibition and activity-based probe labeling of the caspases. J Am Chem Soc 2013; 135:9130-8. [PMID: 23701470 DOI: 10.1021/ja403521u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Caspases are cysteine proteases that play essential roles in apoptosis and inflammation. Unfortunately, their highly conserved active sites and overlapping substrate specificities make it difficult to use inhibitors or activity-based probes to study the function, activation, localization, and regulation of individual members of this family. Here we describe a strategy to engineer a caspase to contain a latent nucleophile that can be targeted by a probe containing a suitably placed electrophile, thereby allowing specific, irreversible inhibition and labeling of only the engineered protease. To accomplish this, we have identified a non-conserved residue on the small subunit of all caspases that is near the substrate-binding pocket and that can be mutated to a non-catalytic cysteine residue. We demonstrate that an active-site probe containing an irreversible binding acrylamide electrophile can specifically target this cysteine residue. Here we validate the approach using the apoptotic mediator, caspase-8, and the inflammasome effector, caspase-1. We show that the engineered enzymes are functionally identical to the wild-type enzymes and that the approach allows specific inhibition and direct imaging of the engineered targets in cells. Therefore, this method can be used to image localization and activation as well as the functional contributions of individual caspase proteases to the process of cell death or inflammation.
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Affiliation(s)
- Junpeng Xiao
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
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Puri AW, Broz P, Shen A, Monack DM, Bogyo M. Caspase-1 activity is required to bypass macrophage apoptosis upon Salmonella infection. Nat Chem Biol 2012; 8:745-7. [PMID: 22797665 PMCID: PMC3461347 DOI: 10.1038/nchembio.1023] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 06/11/2012] [Indexed: 01/14/2023]
Abstract
Here we report AWP28, an activity-based probe that can be used to biochemically monitor caspase-1 activation in response to pro-inflammatory stimuli. Using AWP28 we show that apoptosis is triggered upon bacterial infection in primary murine bone marrow macrophages lacking caspase-1. Furthermore we report that upon Salmonella infection, inflammasome-mediated caspase-1 activity is required to bypass apoptosis in favor of pro-inflammatory pyroptotic cell death.
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Affiliation(s)
- Aaron W Puri
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
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17
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Abstract
Understanding the ways in which pathogens invade and neutralize their hosts is of great interest from both an academic and a clinical perspective. However, in many cases genetic tools are unavailable or insufficient to fully characterize the detailed mechanisms of pathogenesis. Small molecule approaches are particularly powerful due to their ability to modulate specific biological functions in a highly controlled manner and their potential to broadly target conserved processes across species. Recently, two approaches that make use of small molecules, activity-based protein profiling and high-throughput phenotypic screening, have begun to find applications in the study of pathways involved in pathogenesis. In this Review we highlight ways in which these techniques have been applied to examine bacterial and parasitic pathogenesis and discuss possible ways in which these efforts can be expanded in the near future.
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Affiliation(s)
| | - Matthew Bogyo
- Chemical and Systems Biology
- Pathology
- Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Dr., Stanford, California 94305
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