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Awasthi D, Tang YH, Amer B, Baidoo EEK, Gin J, Chen Y, Petzold CJ, Kalyuzhnaya M, Singer SW. OUP accepted manuscript. J Ind Microbiol Biotechnol 2022; 49:6521446. [PMID: 35134957 PMCID: PMC9118986 DOI: 10.1093/jimb/kuac002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/19/2022] [Indexed: 11/15/2022]
Abstract
Rhamnolipids (RLs) are well-studied biosurfactants naturally produced by pathogenic strains of Pseudomonas aeruginosa. Current methods to produce RLs in native and heterologous hosts have focused on carbohydrates as production substrate; however, methane (CH4) provides an intriguing alternative as a substrate for RL production because it is low cost and may mitigate greenhouse gas emissions. Here, we demonstrate RL production from CH4 by Methylotuvimicrobium alcaliphilum DSM19304. RLs are inhibitory to M. alcaliphilum growth (<0.05 g/l). Adaptive laboratory evolution was performed by growing M. alcaliphilum in increasing concentrations of RLs, producing a strain that grew in the presence of 5 g/l of RLs. Metabolomics and proteomics of the adapted strain grown on CH4 in the absence of RLs revealed metabolic changes, increase in fatty acid production and secretion, alterations in gluconeogenesis, and increased secretion of lactate and osmolyte products compared with the parent strain. Expression of plasmid-borne RL production genes in the parent M. alcaliphilum strain resulted in cessation of growth and cell death. In contrast, the adapted strain transformed with the RL production genes showed no growth inhibition and produced up to 1 μM of RLs, a 600-fold increase compared with the parent strain, solely from CH4. This work has promise for developing technologies to produce fatty acid-derived bioproducts, including biosurfactants, from CH4.
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Affiliation(s)
- Deepika Awasthi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yung-Hsu Tang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bashar Amer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer Gin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marina Kalyuzhnaya
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Steven W Singer
- Correspondence should be addressed to: Steven W. Singer. Tel: 510-486-5556; Fax: 510-486-4252; E-mail:
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Abstract
Microbes with the capacity to use methane (CH4) as a carbon source (methanotrophs) have significant potential for the bioconversion of CH4-containing natural gas and anaerobic digestion-derived biogas to high value products. These organisms also play a vital role in the biogeochemical cycling of atmospheric CH4 by serving as the only known biological sink of this gas in terrestrial and aquatic ecosystems. Much is known regarding the enzymes and central metabolic pathways mediating CH4 utilization in these bacteria. However, large fundamental knowledge gaps exist regarding methanotroph physiology and responses to environmental stimuli, primarily due to a lack of efficient molecular tools to probe gene-function relationships. In this chapter, we describe several recently developed genetic tools and optimized genome editing methods that can be used for methanotroph metabolic engineering and to probe metabolic and physiological governing mechanisms in these unique bacteria.
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Affiliation(s)
- Sreemoye Nath
- Department of Biological Sciences, University of North Texas, Denton, TX, USA
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Jessica M Henard
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Calvin A Henard
- Department of Biological Sciences, University of North Texas, Denton, TX, USA.
- BioDiscovery Institute, University of North Texas, Denton, TX, USA.
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Johnson ZJ, Krutkin DD, Bohutskyi P, Kalyuzhnaya MG. Metals and methylotrophy: Via global gene expression studies. Methods Enzymol 2021; 650:185-213. [PMID: 33867021 DOI: 10.1016/bs.mie.2021.01.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A number of minerals, such as copper, cobalt, and rare earth elements (REE), are essential modulators of microbial one-carbon metabolism. This chapter provides an overview of the gene expression study design and analysis protocols for uncovering REE-induced changes in methylotrophic bacteria. By interrogating relationships and differences in total gene expression induced by mineral micronutrients, a deeper understanding of gene regulation at a systems scale can be gained. With careful design and execution of RNA-sequencing experiments, thorough processing and assessment of read quality can be utilized to assess and adjust for possible biases. By ensuring only quality data are utilized in downstream processes, differential gene expression, overrepresented analyses, and gene-set enrichment analyses provide reliable and reproducible representation of pathways and functions which are being affected by changes in environmental conditions.
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Affiliation(s)
- Zachary J Johnson
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Dennis D Krutkin
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Pavlo Bohutskyi
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Marina G Kalyuzhnaya
- Department of Biology, San Diego State University, San Diego, CA, United States.
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Ortega DR, Yang W, Subramanian P, Mann P, Kjær A, Chen S, Watts KJ, Pirbadian S, Collins DA, Kooger R, Kalyuzhnaya MG, Ringgaard S, Briegel A, Jensen GJ. Repurposing a chemosensory macromolecular machine. Nat Commun 2020; 11:2041. [PMID: 32341341 PMCID: PMC7184735 DOI: 10.1038/s41467-020-15736-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 03/23/2020] [Indexed: 12/20/2022] Open
Abstract
How complex, multi-component macromolecular machines evolved remains poorly understood. Here we reveal the evolutionary origins of the chemosensory machinery that controls flagellar motility in Escherichia coli. We first identify ancestral forms still present in Vibrio cholerae, Pseudomonas aeruginosa, Shewanella oneidensis and Methylomicrobium alcaliphilum, characterizing their structures by electron cryotomography and finding evidence that they function in a stress response pathway. Using bioinformatics, we trace the evolution of the system through γ-Proteobacteria, pinpointing key evolutionary events that led to the machine now seen in E. coli. Our results suggest that two ancient chemosensory systems with different inputs and outputs (F6 and F7) existed contemporaneously, with one (F7) ultimately taking over the inputs and outputs of the other (F6), which was subsequently lost. Bacterial chemosensory systems are grouped into 17 flagellar classes (F1-17). Here the authors employ electron cryotomography and comparative genomics to characterise the chemosensory arrays in γ-proteobacteria and identify a structural distinct form of F7 that was repurposed to a different biological role over the course of its evolution.
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Affiliation(s)
- Davi R Ortega
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, C1125, USA
| | - Wen Yang
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Poorna Subramanian
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, C1125, USA
| | - Petra Mann
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, D-35043, Marburg, Germany
| | - Andreas Kjær
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, C1125, USA.,Rex Richards Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Songye Chen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, C1125, USA
| | - Kylie J Watts
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Sahand Pirbadian
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, 90089, USA
| | - David A Collins
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
| | - Romain Kooger
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093, Zürich, Switzerland
| | - Marina G Kalyuzhnaya
- Department of Biology, Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
| | - Simon Ringgaard
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, D-35043, Marburg, Germany
| | - Ariane Briegel
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, C1125, USA. .,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA.
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Nariya S, Kalyuzhnaya MG. Hemerythrins enhance aerobic respiration in Methylomicrobium alcaliphilum 20ZR, a methane-consuming bacterium. FEMS Microbiol Lett 2020; 367:5735436. [PMID: 32053143 DOI: 10.1093/femsle/fnaa003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/03/2020] [Indexed: 01/04/2023] Open
Abstract
Numerous hemerythrins, di-iron proteins, have been identified in prokaryote genomes, but in most cases their function remains elusive. Bacterial hemerythrin homologs (bacteriohemerythrins, Bhrs) may contribute to various cellular functions, including oxygen sensing, metal binding and antibiotic resistance. It has been proposed that methanotrophic Bhrs support methane oxidation by supplying oxygen to a core enzyme, particulate methane monooxygenase. In this study, the consequences of the overexpression or deletion of the Bhr gene (bhr) in Methylomicrobiam alcaliphillum 20ZR were investigated. We found that the bhrknockout (20ZRΔbhr) displays growth kinetics and methane consumption rates similar to wild type. However, the 20ZRΔbhr accumulates elevated concentrations of acetate at aerobic conditions, indicating slowed respiration. The methanotrophic strain overproducing Bhr shows increased oxygen consumption and reduced carbon-conversion efficiency, while its methane consumption rates remain unchanged. These results suggest that the methanotrophic Bhr proteins specifically contribute to oxygen-dependent respiration, while they have minimal, if any, input of oxygen for the methane oxidation machinery.
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Affiliation(s)
- Snehal Nariya
- Biology Department, 5500 Campanile Drive, San Diego, CA, USA
| | - Marina G Kalyuzhnaya
- Biology Department, 5500 Campanile Drive, San Diego, CA, USA.,Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA
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