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Hying ZT, Miller TJ, Loh CY, Bazurto JV. Glycine betaine metabolism is enabled in Methylorubrum extorquens PA1 by alterations to dimethylglycine dehydrogenase. Appl Environ Microbiol 2024; 90:e0209023. [PMID: 38534142 PMCID: PMC11267896 DOI: 10.1128/aem.02090-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/22/2024] [Indexed: 03/28/2024] Open
Abstract
Low nutrient availability is a key characteristic of the phyllosphere (the aerial surface of plants). Phyllospheric bacteria utilize a wide array of carbon sources generated by plant hosts. Glycine betaine (GB) is a plant-derived compound that can be metabolized by certain members of the phyllosphere microbiota. Metabolism of glycine betaine generates formaldehyde, an intermediate of methylotrophic metabolism, leading us to investigate how the ubiquitous plant colonizing bacterium Methylorubrum extorquens PA1 might metabolize GB encountered in its native environment. M. extorquens PA1 cannot utilize GB as a sole carbon source. Through suppressor mutation analysis, we show that M. extorquens PA1 encodes a conserved GB utilization pathway that can be activated by single point mutations conferring GB utilization as a carbon source. We identified the gene cluster encoding the GB catabolic enzymes and found that gene expression was induced in the presence of GB. We show that utilization of GB is conserved among representative Methylobacterium species and generates the one-carbon metabolism intermediate formaldehyde, which M. extorquens utilizes as a source of energy. Our results support a model where suppressor mutations in Mext_3745 or ftsH (Mext_4840) prevent the degradation of the dimethylglycine dehydrogenase subunit DgcB by the membrane integral protease FtsH, conferring the ability to utilize GB by either (i) restoring stable membrane topology of DgcB or (ii) decreasing FtsH protease activity, respectively. Both mutations alleviate the bottleneck at the second step of GB degradation catalyzed by DgcAB.IMPORTANCEOvercoming low nutrient availability is a challenge many bacteria encounter in the environment. Facultative methylotrophs are able to utilize one-carbon and multi-carbon compounds as carbon and energy sources. The utilization of plant-derived glycine betaine (GB) represents a possible source of multi-carbon and one-carbon substrates. The metabolism of glycine betaine produces formaldehyde and glycine, which may be used simultaneously by facultative methylotrophs. However, the genes required for the utilization of GB in the ubiquitous plant-associated bacterium Methylorubrum extorquens have yet to be identified or described. Our work identifies and validates the genes required for glycine betaine metabolism in M. extorquens and shows that it directly intersects with methylotrophic metabolism through the production of formaldehyde.
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Affiliation(s)
- Zachary T. Hying
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Tyler J. Miller
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Chin Yi Loh
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Jannell V. Bazurto
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
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2
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Bruger EL, Hying ZT, Singla D, Márquez Reyes NL, Pandey SK, Patel JS, Bazurto JV. Enhanced catabolism of glycine betaine and derivatives provides improved osmotic stress protection in Methylorubrum extorquens PA1. Appl Environ Microbiol 2024; 90:e0031024. [PMID: 38934615 PMCID: PMC11323934 DOI: 10.1128/aem.00310-24] [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: 02/22/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Integration of metabolites into the overall metabolic network of a cell requires careful coordination dependent upon the ultimate usage of the metabolite. Different stoichiometric needs, and thus pathway fluxes, must exist for compounds destined for diverse uses, such as carbon sources, nitrogen sources, or stress-protective agents. Herein, we expand upon our previous work that highlighted the nature of glycine betaine (GB) metabolism in Methylobacteria to examine the utilization of GB-derivative compounds dimethylglycine (DMG) and sarcosine into Methylorubrum extorquens in different metabolic capacities, including as sole nitrogen and/or carbon sources. We isolated gain-of-function mutations that allowed M. extorquens PA1 to utilize dimethylglycine as a carbon source and dimethylglycine and sarcosine as nitrogen source. Characterization of mutants demonstrated selection for variants of the AraC-like regulator Mext_3735 that confer constitutive expression of the GB metabolic gene cluster, allowing direct utilization of the downstream GB derivatives. Finally, among the distinct isolates examined, we found that catabolism of the osmoprotectant used for selection (GB or dimethylglycine) enhanced osmotic stress resistance provided in the presence of that particular osmolyte. Thus, access to the carbon and nitrogen and osmoprotective effects of GB and DMG are made readily accessible through adaptive mutations. In M. extorquens PA1, the limitations to exploiting this group of compounds appear to exist predominantly at the levels of gene regulation and functional activity, rather than being constrained by transport or toxicity.IMPORTANCEOsmotic stress is a common challenge for bacteria colonizing the phyllosphere, where glycine betaine (GB) can be found as a prevalent osmoprotectant. Though Methylorubrum extorquens PA1 cannot use GB or its demethylation products, dimethylglycine (DMG) and sarcosine, as a sole carbon source, utilization is highly selectable via single nucleotide changes for both GB and DMG growth. The innate inability to use these compounds is due to limited flux through steps in the pathway and regulatory constraints. Herein, the characterization of the transcriptional regulator, Mext_3735 (GbdR), expands our understanding of the various roles in which GB derivatives can be used in M. extorquens PA1. Interestingly, increased catabolism of GB and derivatives does not interfere with, but rather improves, the ability of cells to thrive under increased salt stress conditions, suggesting that metabolic flux improves stress tolerance rather than providing a distinct tension between uses.
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Affiliation(s)
- Eric L. Bruger
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Zachary T. Hying
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Deepanshu Singla
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Nicole L. Márquez Reyes
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Shubham Kumar Pandey
- Department of Chemical
and Biological Engineering, University of
Idaho, Moscow,
Idaho, USA
| | - Jagdish Suresh Patel
- Department of Chemical
and Biological Engineering, University of
Idaho, Moscow,
Idaho, USA
| | - Jannell V. Bazurto
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
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3
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Zhang C, Zhou DF, Wang MY, Song YZ, Zhang C, Zhang MM, Sun J, Yao L, Mo XH, Ma ZX, Yuan XJ, Shao Y, Wang HR, Dong SH, Bao K, Lu SH, Sadilek M, Kalyuzhnaya MG, Xing XH, Yang S. Phosphoribosylpyrophosphate synthetase as a metabolic valve advances Methylobacterium/Methylorubrum phyllosphere colonization and plant growth. Nat Commun 2024; 15:5969. [PMID: 39013920 PMCID: PMC11252147 DOI: 10.1038/s41467-024-50342-9] [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: 11/02/2023] [Accepted: 07/06/2024] [Indexed: 07/18/2024] Open
Abstract
The proficiency of phyllosphere microbiomes in efficiently utilizing plant-provided nutrients is pivotal for their successful colonization of plants. The methylotrophic capabilities of Methylobacterium/Methylorubrum play a crucial role in this process. However, the precise mechanisms facilitating efficient colonization remain elusive. In the present study, we investigate the significance of methanol assimilation in shaping the success of mutualistic relationships between methylotrophs and plants. A set of strains originating from Methylorubrum extorquens AM1 are subjected to evolutionary pressures to thrive under low methanol conditions. A mutation in the phosphoribosylpyrophosphate synthetase gene is identified, which converts it into a metabolic valve. This valve redirects limited C1-carbon resources towards the synthesis of biomass by up-regulating a non-essential phosphoketolase pathway. These newly acquired bacterial traits demonstrate superior colonization capabilities, even at low abundance, leading to increased growth of inoculated plants. This function is prevalent in Methylobacterium/Methylorubrum strains. In summary, our findings offer insights that could guide the selection of Methylobacterium/Methylorubrum strains for advantageous agricultural applications.
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Affiliation(s)
- Cong Zhang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Di-Fei Zhou
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Meng-Ying Wang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Ya-Zhen Song
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Chong Zhang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, PR China
| | - Ming-Ming Zhang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Jing Sun
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Lu Yao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong, PR China
| | - Xu-Hua Mo
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Zeng-Xin Ma
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Xiao-Jie Yuan
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Yi Shao
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Hao-Ran Wang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Si-Han Dong
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Kai Bao
- School of Life Sciences, Hubei University, Wuhan, Hubei, PR China
| | - Shu-Huan Lu
- CABIO Biotech (Wuhan) Co. Ltd., Wuhan, Hubei, PR China
| | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | | | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, PR China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, PR China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, PR China
| | - Song Yang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, PR China.
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4
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Banerjee D, Yunus IS, Wang X, Kim J, Srinivasan A, Menchavez R, Chen Y, Gin JW, Petzold CJ, Martin HG, Magnuson JK, Adams PD, Simmons BA, Mukhopadhyay A, Kim J, Lee TS. Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida. Metab Eng 2024; 82:157-170. [PMID: 38369052 DOI: 10.1016/j.ymben.2024.02.004] [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: 07/28/2023] [Revised: 01/10/2024] [Accepted: 02/10/2024] [Indexed: 02/20/2024]
Abstract
Sustainable aviation fuel (SAF) will significantly impact global warming in the aviation sector, and important SAF targets are emerging. Isoprenol is a precursor for a promising SAF compound DMCO (1,4-dimethylcyclooctane) and has been produced in several engineered microorganisms. Recently, Pseudomonas putida has gained interest as a future host for isoprenol bioproduction as it can utilize carbon sources from inexpensive plant biomass. Here, we engineer metabolically versatile host P. putida for isoprenol production. We employ two computational modeling approaches (Bilevel optimization and Constrained Minimal Cut Sets) to predict gene knockout targets and optimize the "IPP-bypass" pathway in P. putida to maximize isoprenol production. Altogether, the highest isoprenol production titer from P. putida was achieved at 3.5 g/L under fed-batch conditions. This combination of computational modeling and strain engineering on P. putida for an advanced biofuels production has vital significance in enabling a bioproduction process that can use renewable carbon streams.
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Affiliation(s)
- Deepanwita Banerjee
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ian S Yunus
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xi Wang
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jinho Kim
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Aparajitha Srinivasan
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Russel Menchavez
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer W Gin
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hector Garcia Martin
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jon K Magnuson
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Energy Processes & Materials Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Paul D Adams
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Energy Processes & Materials Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Taek Soon Lee
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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5
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Baruah N, Haajanen R, Rahman MT, Pirttilä AM, Koskimäki JJ. Biosynthesis of polyhydroxybutyrate by Methylorubrum extorquens DSM13060 is essential for intracellular colonization in plant endosymbiosis. FRONTIERS IN PLANT SCIENCE 2024; 15:1302705. [PMID: 38390299 PMCID: PMC10883064 DOI: 10.3389/fpls.2024.1302705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Methylorubrum extorquens DSM13060 is an endosymbiont that lives in the cells of shoot tip meristems. The bacterium is methylotrophic and consumes plant-derived methanol for the production of polyhydroxybutyrate (PHB). The PHB provides protection against oxidative stress for both host and endosymbiont cells through its fragments, methyl-esterified 3-hydroxybutyrate (ME-3HB) oligomers. We evaluated the role of the genes involved in the production of ME-3HB oligomers in the host colonization by the endosymbiont M. extorquens DSM13060 through targeted genetic mutations. The strains with deletions in PHB synthase (phaC), PHB depolymerase (phaZ1), and a transcription factor (phaR) showed altered PHB granule characteristics, as ΔphaC had a significantly low number of granules, ΔphaR had a significantly increased number of granules, and ΔphaZ1 had significantly large PHB granules in the bacterial cells. When the deletion strains were exposed to oxidative stress, the ΔphaC strain was sensitive to 10 mM HO· and 20 mM H2O2. The colonization of the host, Scots pine (Pinus sylvestris L.), by the deletion strains varied greatly. The deletion strain ΔphaR colonized the host mainly intercellularly, whereas the ΔphaZ1 strain was a slightly poorer colonizer than the control. The deletion strain ΔphaC lacked the colonization potential, living mainly on the surfaces of the epidermis of pine roots and shoots in contrast to the control, which intracellularly colonized all pine tissues within the study period. In earlier studies, deletions within the PHB metabolic pathway have had a minor effect on plant colonization by rhizobia. We have previously shown the association between ME-3HB oligomers, produced by PhaC and PhaZ1, and the ability to alleviate host-generated oxidative stress during plant infection by the endosymbiont M. extorquens DSM13060. Our current results show that the low capacity for PHB synthesis leads to poor tolerance of oxidative stress and loss of colonization potential by the endosymbiont. Altogether, our findings demonstrate that the metabolism of PHB in M. extorquens DSM13060 is an important trait in the non-rhizobial endosymbiosis.
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Affiliation(s)
- Namrata Baruah
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roosa Haajanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Mohammad Tanvir Rahman
- Disease Networks, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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6
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Ma ZX, Feng CX, Song YZ, Sun J, Shao Y, Song SZ, Wan B, Zhang C, Fan H, Bao K, Yang S. Engineering photo-methylotrophic Methylobacterium for enhanced 3-hydroxypropionic acid production during non-growth stage fermentation. BIORESOURCE TECHNOLOGY 2024; 393:130104. [PMID: 38008225 DOI: 10.1016/j.biortech.2023.130104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
This study explored the potential of methanol as a sustainable feedstock for biomanufacturing, focusing on Methylobacterium extorquens, a well-established representative of methylotrophic cell factories. Despite this bacterium's long history, its untapped photosynthetic capabilities for production enhancement have remained unreported. Using genome-scale flux balance analysis, it was hypothesized that introducing photon fluxes could boost the yield of 3-hydroxypropionic acid (3-HP), an energy- and reducing equivalent-consuming chemicals. To realize this, M. extorquens was genetically modified by eliminating the negative regulator of photosynthesis, leading to improved ATP levels and metabolic activity in non-growth cells during a two-stage fermentation process. This modification resulted in a remarkable 3.0-fold increase in 3-HP titer and a 2.1-fold increase in its yield during stage (II). Transcriptomics revealed that enhanced light-driven methanol oxidation, NADH transhydrogenation, ATP generation, and fatty acid degradation were key factors. This development of photo-methylotrophy as a platform technology introduced novel opportunities for future production enhancements.
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Affiliation(s)
- Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Chen-Xi Feng
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Ya-Zhen Song
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Jing Sun
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Yi Shao
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Shu-Zhen Song
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Bin Wan
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Cong Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China
| | - Huan Fan
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, People's Republic of China
| | - Kai Bao
- School of Life Sciences, Hubei University, Wuhan 430062, Hubei, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong, People's Republic of China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People's Republic of China.
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7
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Zhu L, Song Y, Ma S, Yang S. Heterologous production of 3-hydroxypropionic acid in Methylorubrum extorquens by introducing the mcr gene via a multi-round chromosomal integration system based on cre-lox71/lox66 and transposon. Microb Cell Fact 2024; 23:5. [PMID: 38172868 PMCID: PMC10763676 DOI: 10.1186/s12934-023-02275-z] [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: 04/12/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND AND AIM Reprogramming microorganisms to enhance the production of metabolites is a part of contemporary synthetic biology, which relies on the availability of genetic tools to successfully manipulate the bacteria. Methylorubrum extorquens AM1 is a platform microorganism used to convert C1 compounds into various value-added products. However, the repertoire of available plasmids to conveniently and quickly fine-tune the expression of multiple genes in this strain is extremely limited compared with other model microorganisms such as Escherichia coli. Thus, this study aimed to integrate existing technologies, such as transposon-mediated chromosomal integration and cre-lox-mediated recombination, to achieve the diversified expression of target genes through multiple chromosomal insertions in M. extorquens AM1. RESULTS A single plasmid toolkit, pSL-TP-cre-km, containing a miniHimar1 transposon and an inducible cre-lox71/lox66 system, was constructed and characterized for its multiple chromosomal integration capacity. A co-transcribed mcr-egfp cassette [for the production of 3-hydroxypropionic acid (3-HP) and a reporting green fluorescent protein] was added to construct pTP-cre-mcr-egfp for evaluating its utility in mediating the expression of heterologous genes, resulting in the production of 3-HP with a titer of 34.7-55.2 mg/L by two chromosomal integration copies. Furthermore, in association with the expression of plasmid-based mcr, 3-HP production increased to 65.5-92.4 mg/L. CONCLUSIONS This study used a multi-round chromosomal integration system based on cre-lox71/lox66 and a transposon to construct a single constructed vector. A heterologous mcr gene was introduced through this vector, and high expression of 3-hydroxypropionic acid was achieved in M. extorquens. This study provided an efficient genetic tool for manipulating M. extorquens, which not only help increase the expression of heterologous genes in M. extorquens but also provide a reference for strains lacking genetic manipulation vectors.
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Affiliation(s)
- Liping Zhu
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.
| | - Yazhen Song
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Shunan Ma
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Song Yang
- Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China.
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8
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Pfeilmeier S, Werz A, Ote M, Bortfeld-Miller M, Kirner P, Keppler A, Hemmerle L, Gäbelein CG, Petti GC, Wolf S, Pestalozzi CM, Vorholt JA. Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens. Nat Microbiol 2024; 9:136-149. [PMID: 38172620 PMCID: PMC10769872 DOI: 10.1038/s41564-023-01555-z] [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: 05/09/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
In healthy plants, the innate immune system contributes to maintenance of microbiota homoeostasis, while disease can be associated with microbiome perturbation or dysbiosis, and enrichment of opportunistic plant pathogens like Xanthomonas. It is currently unclear whether the microbiota change occurs independently of the opportunistic pathogens or is caused by the latter. Here we tested if protein export through the type-2 secretion system (T2SS) by Xanthomonas causes microbiome dysbiosis in Arabidopsis thaliana in immunocompromised plants. We found that Xanthomonas strains secrete a cocktail of plant cell wall-degrading enzymes that promote Xanthomonas growth during infection. Disease severity and leaf tissue degradation were increased in A. thaliana mutants lacking the NADPH oxidase RBOHD. Experiments with gnotobiotic plants, synthetic bacterial communities and wild-type or T2SS-mutant Xanthomonas revealed that virulence and leaf microbiome composition are controlled by the T2SS. Overall, a compromised immune system in plants can enrich opportunistic pathogens, which damage leaf tissues and ultimately cause microbiome dysbiosis by facilitating growth of specific commensal bacteria.
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Affiliation(s)
- Sebastian Pfeilmeier
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
- Molecular Plant Pathology, Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
| | - Anja Werz
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Marine Ote
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Pascal Kirner
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Lucas Hemmerle
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | | | - Sarah Wolf
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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9
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Martinson JNV, Chacón JM, Smith BA, Villarreal AR, Hunter RC, Harcombe WR. Mutualism reduces the severity of gene disruptions in predictable ways across microbial communities. THE ISME JOURNAL 2023; 17:2270-2278. [PMID: 37865718 PMCID: PMC10689784 DOI: 10.1038/s41396-023-01534-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/23/2023]
Abstract
Predicting evolution in microbial communities is critical for problems from human health to global nutrient cycling. Understanding how species interactions impact the distribution of fitness effects for a focal population would enhance our ability to predict evolution. Specifically, does the type of ecological interaction, such as mutualism or competition, change the average effect of a mutation (i.e., the mean of the distribution of fitness effects)? Furthermore, how often does increasing community complexity alter the impact of species interactions on mutant fitness? To address these questions, we created a transposon mutant library in Salmonella enterica and measured the fitness of loss of function mutations in 3,550 genes when grown alone versus competitive co-culture or mutualistic co-culture with Escherichia coli and Methylorubrum extorquens. We found that mutualism reduces the average impact of mutations, while competition had no effect. Additionally, mutant fitness in the 3-species communities can be predicted by averaging the fitness in each 2-species community. Finally, we discovered that in the mutualism S. enterica obtained vitamins and more amino acids than previously known. Our results suggest that species interactions can predictably impact fitness effect distributions, in turn suggesting that evolution may ultimately be predictable in multi-species communities.
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Affiliation(s)
- Jonathan N V Martinson
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Jeremy M Chacón
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
- Minnesota Super Computing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Brian A Smith
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Alex R Villarreal
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Ryan C Hunter
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN, USA
| | - William R Harcombe
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA.
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
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10
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Mo XH, Sun YM, Bi YX, Zhao Y, Yu GH, Tan LL, Yang S. Characterization of C 30 carotenoid and identification of its biosynthetic gene cluster in Methylobacterium extorquens AM1. Synth Syst Biotechnol 2023; 8:527-535. [PMID: 37637201 PMCID: PMC10448405 DOI: 10.1016/j.synbio.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023] Open
Abstract
Methylobacterium species, the representative bacteria distributed in phyllosphere region of plants, often synthesize carotenoids to resist harmful UV radiations. Methylobacterium extorquens is known to produce a carotenoid pigment and recent research revealed that this carotenoid has a C30 backbone. However, its exact structure remains unknown. In the present study, the carotenoid produced by M. extorquens AM1 was isolated and its structure was determined as 4-[2-O-11Z-octadecenoyl-β-glucopyranosyl]-4,4'-diapolycopenedioc acid (1), a glycosylated C30 carotenoid. Furthermore, the genes related to the C30 carotenoid synthesis were investigated. Squalene, the precursor of the C30 carotenoid, is synthesized by the co-occurrence of META1p1815, META1p1816 and META1p1817. Further overexpression of the genes related to squalene synthesis improved the titer of carotenoid 1. By using gene deletion and gene complementation experiments, the glycosyltransferase META1p3663 and acyltransferase META1p3664 were firstly confirmed to catalyze the tailoring steps from 4,4'-diapolycopene-4,4'-dioic acid to carotenoid 1. In conclusion, the structure and biosynthetic genes of carotenoid 1 produced by M. extorquens AM1 were firstly characterized in this work, which shed lights on engineering M. extorquens AM1 for producing carotenoid 1 in high yield.
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Affiliation(s)
- Xu-Hua Mo
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Yu-Man Sun
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Yu-Xing Bi
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Yan Zhao
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Gui-Hong Yu
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Ling-ling Tan
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Song Yang
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
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11
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He S, Wang W, Wang W, Hu H, Xu P, Tang H. Microbial production of cis,cis-muconic acid from aromatic compounds in engineered Pseudomonas. Synth Syst Biotechnol 2023; 8:536-545. [PMID: 37637202 PMCID: PMC10448021 DOI: 10.1016/j.synbio.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 08/29/2023] Open
Abstract
Industrial expansion has led to environmental pollution by xenobiotic compounds like polycyclic aromatic hydrocarbons and monoaromatic hydrocarbons. Pseudomonas spp. have broad metabolic potential for degrading aromatic compounds. The objective of this study was to develop a "biological funneling" strategy based on genetic modification to convert complex aromatic compounds into cis,cis-muconate (ccMA) using Pseudomonas putida B6-2 and P. brassicacearum MPDS as biocatalysts. The engineered strains B6-2 (B6-2ΔcatBΔsalC) and MPDS (MPDSΔsalC(pUCP18k-catA)) thrived with biphenyl or naphthalene as the sole carbon source and produced ccMA, attaining molar conversions of 95.3% (ccMA/biphenyl) and 100% (ccMA/naphthalene). Under mixed substrates, B6-2ΔcatBΔsalC grew on biphenyl as a carbon source and transformed ccMA from non-growth substrates benzoate or salicylate to obtain higher product concentration. Inserting exogenous clusters like bedDC1C2AB and xylCMAB allowed B6-2 recombinant strains to convert benzene and toluene to ccMA. In mixed substrates, constructed consortia of engineered strains B6-2 and MPDS specialized in catabolism of biphenyl and naphthalene; the highest molar conversion rate of ccMA from mixed substrates was 85.2% when B6-2ΔcatBΔsalC was added after 24 h of MPDSΔsalC(pUCP18k-catA) incubation with biphenyl and naphthalene. This study provides worthwhile insights into efficient production of ccMA from aromatic hydrocarbons by reusing complex pollutants.
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Affiliation(s)
- Siyang He
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Weidong Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
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12
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Martinson JNV, Chacón JM, Smith BA, Villarreal AR, Hunter RC, Harcombe WR. Mutualism reduces the severity of gene disruptions in predictable ways across microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539835. [PMID: 37214994 PMCID: PMC10197568 DOI: 10.1101/2023.05.08.539835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Predicting evolution in microbial communities is critical for problems from human health to global nutrient cycling. Understanding how species interactions impact the distribution of fitness effects for a focal population would enhance our ability to predict evolution. Specifically, it would be useful to know if the type of ecological interaction, such as mutualism or competition, changes the average effect of a mutation (i.e., the mean of the distribution of fitness effects). Furthermore, how often does increasing community complexity alter the impact of species interactions on mutant fitness? To address these questions, we created a transposon mutant library in Salmonella enterica and measured the fitness of loss of function mutations in 3,550 genes when grown alone versus competitive co-culture or mutualistic co-culture with Escherichia coli and Methylorubrum extorquens. We found that mutualism reduces the average impact of mutations, while competition had no effect. Additionally, mutant fitness in the 3-species communities can be predicted by averaging the fitness in each 2-species community. Finally, the fitness effects of several knockouts in the mutualistic communities were surprising. We discovered that S. enterica is obtaining a different source of carbon and more vitamins and amino acids than we had expected. Our results suggest that species interactions can predictably impact fitness effect distributions, in turn suggesting that evolution may ultimately be predictable in multi-species communities.
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Affiliation(s)
- Jonathan N V Martinson
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Jeremy M Chacón
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
- Current address: Minnesota Super Computing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Brian A Smith
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Alex R Villarreal
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Ryan C Hunter
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, MN, USA
| | - William R Harcombe
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
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13
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Wilkes RA, Waldbauer J, Carroll A, Nieto-Domínguez M, Parker DJ, Zhang L, Guss AM, Aristilde L. Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism. Nat Chem Biol 2023; 19:651-662. [PMID: 36747056 PMCID: PMC10154247 DOI: 10.1038/s41589-022-01237-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/29/2022] [Indexed: 02/08/2023]
Abstract
Critical to a sustainable energy future are microbial platforms that can process aromatic carbons from the largely untapped reservoir of lignin and plastic feedstocks. Comamonas species present promising bacterial candidates for such platforms because they can use a range of natural and xenobiotic aromatic compounds and often possess innate genetic constraints that avoid competition with sugars. However, the metabolic reactions of these species are underexplored, and the regulatory mechanisms are unknown. Here we identify multilevel regulation in the conversion of lignin-related natural aromatic compounds, 4-hydroxybenzoate and vanillate, and the plastics-related xenobiotic aromatic compound, terephthalate, in Comamonas testosteroni KF-1. Transcription-level regulation controls initial catabolism and cleavage, but metabolite-level thermodynamic regulation governs fluxes in central carbon metabolism. Quantitative 13C mapping of tricarboxylic acid cycle and cataplerotic reactions elucidates key carbon routing not evident from enzyme abundance changes. This scheme of transcriptional activation coupled with metabolic fine-tuning challenges outcome predictions during metabolic manipulations.
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Affiliation(s)
- Rebecca A Wilkes
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Austin Carroll
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Darren J Parker
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA.
- Northwestern Center for Synthetic Biology, Evanston, IL, USA.
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14
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Rumah B, Claxton Stevens BH, Yeboah JE, Stead CE, Harding EL, Minton NP, Zhang Y. In Vivo Genome Editing in Type I and II Methanotrophs Using a CRISPR/Cas9 System. ACS Synth Biol 2023; 12:544-554. [PMID: 36688528 PMCID: PMC9942187 DOI: 10.1021/acssynbio.2c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Methanotrophic bacteria are Gram-negative, aerobic organisms that use methane as their sole source of carbon and energy. In this study, we constructed and exemplified a CRISPR/Cas9 genome editing system and used it to successfully make gene deletions and insertions in the type I methanotroph Methylococcus capsulatus Bath and the type II methanotroph Methylocystis parvus OBBP. High frequencies of gene deletions and insertions were achieved in combination with homology-directed repair. In M. parvus OBBP, we also investigated the impact of several parameters on the CRISPR/Cas9 genome editing, where the ligD gene was targeted with various PAM sequences and guide RNA spacer sequences, homology arms of variable length, differences in the duration of mating during conjugation, and exploiting promoters of different strengths to control the expression of cas9 and sgRNA. Although not the first attempt to develop a CRISPR/Cas system in methanotrophs, this work demonstrated for the first time an efficient CRISPR/Cas9 system generating scarless clean gene deletions and insertions in methanotroph genomes.
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15
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Shin SM, Jha RK, Dale T. Tackling the Catch-22 Situation of Optimizing a Sensor and a Transporter System in a Whole-Cell Microbial Biosensor Design for an Anthropogenic Small Molecule. ACS Synth Biol 2022; 11:3996-4008. [PMID: 36472954 DOI: 10.1021/acssynbio.2c00364] [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: 12/12/2022]
Abstract
Whole-cell biosensors provide a convenient detection tool for the high-throughput screening of genetically engineered biocatalytic activity. But establishing a biosensor for an anthropogenic molecule requires both a custom transporter and a transcription factor. This results in an unavoidable "Catch-22" situation in which transporter activity cannot be easily confirmed without a biosensor and a biosensor cannot be established without a functional transporter in a host organism. We overcame this type of circular problem while developing an adipic acid (ADA) sensor. First, leveraging an established cis,cis-muconic acid (ccMA) sensor, an annotated ccMA transporter MucK, which is expected to be broadly responsive to dicarboxylates, was stably expressed in the genome of Pseudomonas putida to function as a transporter for ADA, and then a PcaR transcription factor (endogenous to the strain and naturally induced by β-ketoadipic acid, BKA) was diversified and selected to detect the ADA molecule. While MucK expression is otherwise very unstable in P. putida under strong promoter expression, our optimized mucK expression was functional for over 70 generations without loss of function, and we selected an ADA sensor that showed a specificity switch of over 35-fold from BKA at low concentrations (typically <0.1 mM of inducers). Our ADA and BKA biosensors show high sensitivity (low detection concentration <10 μM) and dynamic range (∼50-fold) in an industrially relevant organism and will open new avenues for high throughput discovery and optimization of enzymes and metabolic pathways for the biomanufacture of these molecules. In particular, the novel ADA sensor will aid the discovery and evolution of efficient biocatalysts for the biological recycling of ADA from the degradation of nylon-6,6 waste.
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Affiliation(s)
- Sang-Min Shin
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico87545, United States.,BOTTLE Consortium, Golden, Colorado80401, United States
| | - Ramesh K Jha
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico87545, United States.,BOTTLE Consortium, Golden, Colorado80401, United States.,Agile BioFoundry, Emeryville, California94608, United States
| | - Taraka Dale
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico87545, United States.,BOTTLE Consortium, Golden, Colorado80401, United States.,Agile BioFoundry, Emeryville, California94608, United States
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16
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Khmelenina VN, But SY, Rozova ON, Oshkin IY, Pimenov NV, Dedysh SN. Genome Editing in Methanotrophic Bacteria: Potential Targets and Available Tools. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722602196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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17
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Good NM, Lee HD, Hawker ER, Su MZ, Gilad AA, Martinez-Gomez NC. Hyperaccumulation of Gadolinium by Methylorubrum extorquens AM1 Reveals Impacts of Lanthanides on Cellular Processes Beyond Methylotrophy. Front Microbiol 2022; 13:820327. [PMID: 35369483 PMCID: PMC8969499 DOI: 10.3389/fmicb.2022.820327] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/19/2022] [Indexed: 11/20/2022] Open
Abstract
Lanthanides (Ln) are a new group of life metals, and many questions remain regarding how they are acquired and used in biology. Methylotrophic bacteria can acquire, transport, biomineralize, and use Ln as part of a cofactor complex with pyrroloquinoline quinone (PQQ) in alcohol dehydrogenases. For most methylotrophic bacteria use is restricted to the light Ln, which range from lanthanum to samarium (atomic numbers 57–62). Understanding how the cell differentiates between light and heavy Ln, and the impacts of these metals on the metabolic network, will advance the field of Ln biochemistry and give insights into enzyme catalysis, stress homeostasis, and metal biomineralization and compartmentalization. We report robust methanol growth with the heavy Ln gadolinium by a genetic variant of the model methylotrophic bacterium Methylorubrum extorquens AM1, named evo-HLn, for “evolved for Heavy Lanthanides.” A non-synonymous single nucleotide polymorphism in a cytosolic hybrid histidine kinase/response regulator allowed for sweeping transcriptional alterations to heavy metal stress response, methanol oxidation, and central metabolism. Increased expression of genes for Ln acquisition and uptake, production of the Ln-chelating lanthanophore, PQQ biosynthesis, and phosphate transport and metabolism resulted in gadolinium hyperaccumulation of 36-fold with a trade-off for light Ln accumulation. Gadolinium was hyperaccumulated in an enlarged acidocalcisome-like compartment. This is the first evidence of a bacterial intracellular Ln-containing compartment that we name the “lanthasome.” Carotenoid and toblerol biosynthesis were also upregulated. Due to its unique capabilities, evo-HLn can be used to further magnetic resonance imaging (MRI) and bioremediation technologies. In this regard, we show that gadolinium hyperaccumulation was sufficient to produce MRI contrast in whole cells, and that evo-HLn was able to readily acquire the metal from the MRI contrast agent gadopentetic acid. Finally, hyperaccumulation of gadolinium, differential uptake of light and heavy Ln, increased PQQ levels, and phosphate transport provide new insights into strategies for Ln recovery.
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Affiliation(s)
- Nathan M. Good
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Harvey D. Lee
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
- Division of Synthetic Biology, The Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, United States
| | - Emily R. Hawker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Morgan Z. Su
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Assaf A. Gilad
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
- Division of Synthetic Biology, The Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, United States
- Department of Radiology, Michigan State University, East Lansing, MI, United States
| | - N. Cecilia Martinez-Gomez
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: N. Cecilia Martinez-Gomez,
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18
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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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19
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Rizk S, Henke P, Santana-Molina C, Martens G, Gnädig M, Nguyen NA, Devos DP, Neumann-Schaal M, Saenz JP. Functional diversity of isoprenoid lipids in Methylobacterium extorquens PA1. Mol Microbiol 2021; 116:1064-1078. [PMID: 34387371 DOI: 10.1111/mmi.14794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/29/2021] [Accepted: 08/10/2021] [Indexed: 11/29/2022]
Abstract
Hopanoids and carotenoids are two of the major isoprenoid-derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as sterols. Methylobacterium extorquens contains hopanoids and carotenoids in their outer membrane, making them an ideal system to investigate the role of isoprenoid lipids in surface membrane function and cellular fitness. By genetically knocking out hpnE, and crtB we disrupted the production of squalene, and phytoene in Methylobacterium extorquens PA1, which are the presumed precursors for hopanoids and carotenoids, respectively. Deletion of hpnE revealed that carotenoid biosynthesis utilizes squalene as a precursor resulting in pigmentation with a C30 backbone, rather than the previously predicted canonical C40 phytoene-derived pathway. Phylogenetic analysis suggested that M. extorquens may have acquired the C30 pathway through lateral gene transfer from Planctomycetes. Surprisingly, disruption of carotenoid synthesis did not generate any major growth or membrane biophysical phenotypes, but slightly increased sensitivity to oxidative stress. We further demonstrated that hopanoids but not carotenoids are essential for growth at higher temperatures, membrane permeability and tolerance of low divalent cation concentrations. These observations show that hopanoids and carotenoids serve diverse roles in the outer membrane of M. extorquens PA1.
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Affiliation(s)
- Sandra Rizk
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Petra Henke
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Carlos Santana-Molina
- Centro Andaluz de Biologıa del Desarrollo (CABD)-CSIC, Junta de Andalucıa, Universidad Pablo de Olavide, Seville, Spain
| | - Gesa Martens
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Marén Gnädig
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | | | - Damien P Devos
- Centro Andaluz de Biologıa del Desarrollo (CABD)-CSIC, Junta de Andalucıa, Universidad Pablo de Olavide, Seville, Spain
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - James P Saenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
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20
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The RNA Chaperone Hfq Participates in Persistence to Multiple Antibiotics in the Fish Pathogen Yersinia ruckeri. Microorganisms 2021; 9:microorganisms9071404. [PMID: 34209738 PMCID: PMC8308036 DOI: 10.3390/microorganisms9071404] [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: 05/29/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Yersinia ruckeri causes outbreaks of enteric redmouth disease in salmon aquaculture all over the world. The transient antibiotic tolerance exhibited by bacterial persisters is commonly thought to be responsible for outbreaks; however, the molecular factors underlying this behavior have not been explored in Y. ruckeri. In this study, we investigated the participation of the RNA chaperone Hfq from Y. ruckeri in antibiotic persistence. Cultures of the hfq-knockout mutant (Δhfq) exhibited faster replication, increased ATP levels and a more reductive environment than the wild type. The growth curves of bacteria exposed to sublethal concentrations of ampicillin, oxolinic acid, ciprofloxacin and polymyxin B revealed a greater susceptibility for the Δhfq strain. The time-kill curves of bacteria treated with the antibiotics mentioned above and florfenicol, using inoculums from exponential, stationary and biofilm cultures, demonstrated that the Δhfq strain has significant defects in persister cells production. To shed more light on the role of Hfq in antibiotic persistence, we analyzed its dependence on the (p)ppGpp synthetase RelA by determining the persister cells production in the absence of the relA gene. The ΔrelA and ΔrelAΔhfq strains displayed similar defects in persister cells formation, but higher than Δhfq strain. Similarly, stationary cultures of the ΔrelA and ΔrelAΔhfq strains exhibited comparable levels of ATP but higher than that of the Δhfq strain, indicating that relA is epistatic over hfq. Taken together, our findings provide valuable information on antibiotic persistence in Y. ruckeri, shedding light on the participation of Hfq in the persistence phenomenon.
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21
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Bazurto JV, Nayak DD, Ticak T, Davlieva M, Lee JA, Hellenbrand CN, Lambert LB, Benski OJ, Quates CJ, Johnson JL, Patel JS, Ytreberg FM, Shamoo Y, Marx CJ. EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde. PLoS Biol 2021; 19:e3001208. [PMID: 34038406 PMCID: PMC8153426 DOI: 10.1371/journal.pbio.3001208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/25/2021] [Indexed: 01/07/2023] Open
Abstract
Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such as Methylorubrum extorquens face an acute challenge due to their production of formaldehyde as an obligate central intermediate of single-carbon metabolism. Mechanisms to sense and respond to formaldehyde were speculated to exist in methylotrophs for decades but had never been discovered. Here, we identify a member of the DUF336 domain family, named efgA for enhanced formaldehyde growth, that plays an important role in endogenous formaldehyde stress response in M. extorquens PA1 and is found almost exclusively in methylotrophic taxa. Our experimental analyses reveal that EfgA is a formaldehyde sensor that rapidly arrests growth in response to elevated levels of formaldehyde. Heterologous expression of EfgA in Escherichia coli increases formaldehyde resistance, indicating that its interaction partners are widespread and conserved. EfgA represents the first example of a formaldehyde stress response system that does not involve enzymatic detoxification. Thus, EfgA comprises a unique stress response mechanism in bacteria, whereby a single protein directly senses elevated levels of a toxic intracellular metabolite and safeguards cells from potential damage.
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Affiliation(s)
- Jannell V. Bazurto
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, Twin Cities, Minnesota, United States of America
- Biotechnology Institute, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail: (JVB); (CJM)
| | - Dipti D. Nayak
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Tomislav Ticak
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Milya Davlieva
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Jessica A. Lee
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, California, United States of America
| | - Chandler N. Hellenbrand
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota, United States of America
| | - Leah B. Lambert
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Olivia J. Benski
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Caleb J. Quates
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
| | - Jill L. Johnson
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Jagdish Suresh Patel
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
| | - F. Marty Ytreberg
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Physics, University of Idaho, Moscow, Idaho, United States of America
| | - Yousif Shamoo
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Christopher J. Marx
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (JVB); (CJM)
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22
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Bruger EL, Chubiz LM, Rojas Echenique JI, Renshaw CJ, Espericueta NV, Draghi JA, Marx CJ. Genetic Context Significantly Influences the Maintenance and Evolution of Degenerate Pathways. Genome Biol Evol 2021; 13:6245841. [PMID: 33885815 PMCID: PMC8214414 DOI: 10.1093/gbe/evab082] [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] [Accepted: 04/19/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding the evolution of novel physiological traits is highly relevant for expanding the characterization and manipulation of biological systems. Acquisition of new traits can be achieved through horizontal gene transfer (HGT). Here, we investigate drivers that promote or deter the maintenance of HGT-driven degeneracy, occurring when processes accomplish identical functions through nonidentical components. Subsequent evolution can optimize newly acquired functions; for example, beneficial alleles identified in an engineered Methylorubrum extorquens strain allowed it to utilize a “Foreign” formaldehyde oxidation pathway substituted for its Native pathway for methylotrophic growth. We examined the fitness consequences of interactions between these alleles when they were combined with the Native pathway or both (Dual) pathways. Unlike the Foreign pathway context where they evolved, these alleles were often neutral or deleterious when moved into these alternative genetic backgrounds. However, there were instances where combinations of multiple alleles resulted in higher fitness outcomes than individual allelic substitutions could provide. Importantly, the genetic context accompanying these allelic substitutions significantly altered the fitness landscape, shifting local fitness peaks and restricting the set of accessible evolutionary trajectories. These findings highlight how genetic context can negatively impact the probability of maintaining native and HGT-introduced functions together, making it difficult for degeneracy to evolve. However, in cases where the cost of maintaining degeneracy was mitigated by adding evolved alleles impacting the function of these pathways, we observed rare opportunities for pathway coevolution to occur. Together, our results highlight the importance of genetic context and resulting epistasis in retaining or losing HGT-acquired degenerate functions.
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Affiliation(s)
- Eric L Bruger
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.,Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, USA.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA.,The BEACON Center for the Study of Evolution in Action, University of Idaho, Moscow, Idaho, USA
| | - Lon M Chubiz
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Biology, University of Missouri, St. Louis, Missouri, USA
| | - José I Rojas Echenique
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Caleb J Renshaw
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.,Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, USA
| | - Nora Victoria Espericueta
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.,Department of Biological Sciences, California State University, Long Beach, California, USA
| | - Jeremy A Draghi
- Department of Biological Sciences, Virginia Institute of Technology, Blacksburg, Virginia, USA
| | - Christopher J Marx
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.,Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, USA.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA.,The BEACON Center for the Study of Evolution in Action, University of Idaho, Moscow, Idaho, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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23
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Elmore JR, Dexter GN, Salvachúa D, Martinez-Baird J, Hatmaker EA, Huenemann JD, Klingeman DM, Peabody GL, Peterson DJ, Singer C, Beckham GT, Guss AM. Production of itaconic acid from alkali pretreated lignin by dynamic two stage bioconversion. Nat Commun 2021; 12:2261. [PMID: 33859194 PMCID: PMC8050072 DOI: 10.1038/s41467-021-22556-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/17/2021] [Indexed: 02/02/2023] Open
Abstract
Expanding the portfolio of products that can be made from lignin will be critical to enabling a viable bio-based economy. Here, we engineer Pseudomonas putida for high-yield production of the tricarboxylic acid cycle-derived building block chemical, itaconic acid, from model aromatic compounds and aromatics derived from lignin. We develop a nitrogen starvation-detecting biosensor for dynamic two-stage bioproduction in which itaconic acid is produced during a non-growth associated production phase. Through the use of two distinct itaconic acid production pathways, the tuning of TCA cycle gene expression, deletion of competing pathways, and dynamic regulation, we achieve an overall maximum yield of 56% (mol/mol) and titer of 1.3 g/L from p-coumarate, and 1.4 g/L titer from monomeric aromatic compounds produced from alkali-treated lignin. This work illustrates a proof-of-principle that using dynamic metabolic control to reroute carbon after it enters central metabolism enables production of valuable chemicals from lignin at high yields by relieving the burden of constitutively expressing toxic heterologous pathways.
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Affiliation(s)
- Joshua R. Elmore
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA ,grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Gara N. Dexter
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Davinia Salvachúa
- grid.419357.d0000 0001 2199 3636National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Jessica Martinez-Baird
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - E. Anne Hatmaker
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Jay D. Huenemann
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA ,grid.411461.70000 0001 2315 1184Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN USA
| | - Dawn M. Klingeman
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - George L. Peabody
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Darren J. Peterson
- grid.419357.d0000 0001 2199 3636National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Christine Singer
- grid.419357.d0000 0001 2199 3636National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Gregg T. Beckham
- grid.419357.d0000 0001 2199 3636National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Adam M. Guss
- grid.135519.a0000 0004 0446 2659Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN USA ,grid.411461.70000 0001 2315 1184Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN USA
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24
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Formaldehyde-responsive proteins, TtmR and EfgA, reveal a tradeoff between formaldehyde resistance and efficient transition to methylotrophy in Methylorubrum extorquens. J Bacteriol 2021; 203:JB.00589-20. [PMID: 33619153 PMCID: PMC8092166 DOI: 10.1128/jb.00589-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
For bacteria to thrive they must be well-adapted to their environmental niche, which may involve specialized metabolism, timely adaptation to shifting environments, and/or the ability to mitigate numerous stressors. These attributes are highly dependent on cellular machinery that can sense both the external and intracellular environment. Methylorubrum extorquens is an extensively studied facultative methylotroph, an organism that can use single-carbon compounds as their sole source of carbon and energy. In methylotrophic metabolism, carbon flows through formaldehyde as a central metabolite; thus, formaldehyde is both an obligate metabolite and a metabolic stressor. Via the one-carbon dissimilation pathway, free formaldehyde is rapidly incorporated by formaldehyde activating enzyme (Fae), which is constitutively expressed at high levels. In the presence of elevated formaldehyde levels, a recently identified formaldehyde-sensing protein, EfgA, induces growth arrest. Herein, we describe TtmR, a formaldehyde-responsive transcription factor that, like EfgA, modulates formaldehyde resistance. TtmR is a member of the MarR family of transcription factors and impacts the expression of 75 genes distributed throughout the genome, many of which are transcription factors and/or involved in stress response, including efgA Notably, when M. extorquens is adapting its metabolic network during the transition to methylotrophy, efgA and ttmR mutants experience an imbalance in formaldehyde production and a notable growth delay. Although methylotrophy necessitates that M. extorquens maintain a relatively high level of formaldehyde tolerance, this work reveals a tradeoff between formaldehyde resistance and the efficient transition to methylotrophic growth and suggests that TtmR and EfgA play a pivotal role in maintaining this balance.Importance: All organisms produce formaldehyde as a byproduct of enzymatic reactions and as a degradation product of metabolites. The ubiquity of formaldehyde in cellular biology suggests all organisms have evolved mechanisms of mitigating formaldehyde toxicity. However, formaldehyde-sensing is poorly described and prevention of formaldehyde-induced damage is primarily understood in the context of detoxification. Here we use an organism that is regularly exposed to elevated intracellular formaldehyde concentrations through high-flux one-carbon utilization pathways to gain insight into the role of formaldehyde-responsive proteins that modulate formaldehyde resistance. Using a combination of genetic and transcriptomic analyses, we identify dozens of genes putatively involved in formaldehyde resistance, determined the relationship between two different formaldehyde response systems and identified an inherent tradeoff between formaldehyde resistance and optimal transition to methylotrophic metabolism.
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25
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Ma ZX, Zhang M, Zhang CT, Zhang H, Mo XH, Xing XH, Yang S. Metabolomic analysis improves bioconversion of methanol to isobutanol in Methylorubrum extorquens AM1. Biotechnol J 2021; 16:e2000413. [PMID: 33595188 DOI: 10.1002/biot.202000413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Methylorubrum extorquens AM1 can be engineered to convert methanol to value-added chemicals. Most of these chemicals derive from acetyl-CoA involved in the serine cycle. However, recent studies on methylotrophic metabolism have suggested that C3 pyruvate is a good potential precursor for broadening the types of synthesized products. METHODS AND RESULTS In the present study, we found that isobutanol was a model chemical that could be generated from pyruvate through a 2-keto acid pathway. Initially, the engineered M. extorquens AM1 could only produce a trace amount of isobutanol at 0.62 mgL-1 after introducing the heterologous 2-ketoisovalerate decarboxylase and alcohol dehydrogenase. Furthermore, the metabolomic analysis revealed that insufficient carbon fluxes through 2-ketoisovalerate and pyruvate were the key limitation steps for efficient biosynthesis of isobutanol. Based on this analysis, the titer of isobutanol was improved by over 20-fold after overexpressing alsS gene encoding acetolactate synthase and deleting ldhA gene for lactate dehydrogenase. Moreover, substituting the cell chassis with the isobutanol-tolerant strain isolated from adaptive evolution of M. extorquens AM1 further increased the production of isobutanol by 1.7-fold, resulting in the final titer of 19 mgL-1 in flask cultivation. CONCLUSION Our current findings provided promising insights into engineering methylotrophic cell factories capable of converting methanol to isobutanol or value-added chemicals using pyruvate as the precursor.
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Affiliation(s)
- Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Min Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Shandong Longkete Enzyme Co., Ltd., Linyi, Shandong, People's Republic of China
| | - Chang-Tai Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Hui Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, and Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
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26
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Yuan XJ, Chen WJ, Ma ZX, Yuan QQ, Zhang M, He L, Mo XH, Zhang C, Zhang CT, Wang MY, Xing XH, Yang S. Rewiring the native methanol assimilation metabolism by incorporating the heterologous ribulose monophosphate cycle into Methylorubrum extorquens. Metab Eng 2021; 64:95-110. [PMID: 33493644 DOI: 10.1016/j.ymben.2021.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/05/2021] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
Methanol is assimilated through the serine cycle to generate acetyl-CoA without carbon loss. However, a highly active serine cycle requires high consumption of reducing equivalents and ATP, thereby leading to the impaired efficiency of methanol conversion to reduced chemicals. In the present study, a genome-scale flux balance analysis (FBA) predicted that the introduction of the heterologous ribulose monophosphate (RuMP) cycle, a more energy-efficient pathway for methanol assimilation, could theoretically increase growth rate by 31.3% for the model alphaproteobacterial methylotroph Methylorubrum extorquens AM1. Based on this analysis, we constructed a novel synergistic assimilation pathway in vivo by incorporating the RuMP cycle into M. extroquens metabolism with the intrinsic serine cycle. We demonstrated that the operation of the synergistic pathway could increase cell growth rate by 16.5% and methanol consumption rate by 13.1%. This strategy rewired the central methylotrophic metabolism through adjusting core gene transcription, leading to a pool size increase of C2 to C5 central intermediates by 1.2- to 3.6-fold and an NADPH cofactor improvement by 1.3-fold. The titer of 3-hydroxypropionic acid (3-HP), a model product in the newly engineered chassis of M. extorquens AM1, was increased to 91.2 mg/L in shake-flask culture, representing a 3.1-fold increase compared with the control strain with only the serine cycle. The final titer of 3-HP was significantly improved to 0.857 g/L in the fed-batch bioreactor, which was more competitive compared with the other 3-HP producers using methane and CO2 as C1 sources. Collectively, our current study demonstrated that engineering the synergistic methanol assimilation pathway was a promising strategy to increase the carbon assimilation and the yields of reduced chemicals in diverse host strains for C1 microbial cell factories.
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Affiliation(s)
- Xiao-Jie Yuan
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China; Department of Molecular Biology, Qingdao Vland Biotech Inc., Qingdao, Shandong Province, People's Republic of China
| | - Wen-Jing Chen
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Qian-Qian Yuan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Min Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Lian He
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Chong Zhang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China
| | - Chang-Tai Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Meng-Ying Wang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, And Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China.
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Acuña LG, Barros MJ, Montt F, Peñaloza D, Núñez P, Valdés I, Gil F, Fuentes JA, Calderón IL. Participation of two sRNA RyhB homologs from the fish pathogen Yersinia ruckeri in bacterial physiology. Microbiol Res 2020; 242:126629. [PMID: 33153884 DOI: 10.1016/j.micres.2020.126629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 09/11/2020] [Accepted: 10/13/2020] [Indexed: 01/19/2023]
Abstract
Small noncoding RNAs (sRNAs) are important regulators of gene expression and physiology in bacteria. RyhB is an iron-responsive sRNA well characterized in Escherichia coli and conserved in other Enterobacteriaceae. In this study, we identified and characterized two RyhB homologs (named RyhB-1 and RyhB-2) in the fish pathogen Yersinia ruckeri. We found that, as in other Enterobacteriaceae, both RyhB-1 and RyhB-2 are induced under iron starvation, repressed by the Fur regulator, and depend on Hfq for stability. Despite these similarities in expression, the mutant strains of Y. ruckeri lacking RyhB-1 (ΔryhB-1) or RyhB-2 (ΔryhB-2) exhibited differential phenotypes. In comparison with the wild type, the ΔryhB-1 strain showed a hypermotile phenotype, reduced biofilm formation, increased replication rate, faster growth, and increased ATP levels in bacterial cultures. By contrast, in salmon cell cultures, the ΔryhB-1 strain exhibited an increased survival. On the other hand, the ΔryhB-2 strain was non-motile and showed augmented biofilm formation as compared to the wild type. The expression of a subset of RyhB conserved targets, selected from different bacterial species, was analyzed by quantitative RT-PCR in wild type, ΔryhB-1, ΔryhB-2, and ΔryhB-1 ΔryhB-2 strains cultured in iron-depleted media. RyhB-1 negatively affected the expression of most analyzed genes (sodB, acnA, sdhC, bfr, fliF, among others), whose functions are related to metabolism and motility, involving iron-containing proteins. Among the genes analyzed, only sdhC and bfr appeared as targets for RyhB-2. Taken together, these results indicate that Y. ruckeri RyhB homologs participate in the modulation of the bacterial physiology with non-redundant roles.
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Affiliation(s)
- Lillian G Acuña
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - M José Barros
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Fernanda Montt
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Diego Peñaloza
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Paula Núñez
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Iván Valdés
- Desarrollo de Biológicos, Veterquímica S.A., Santiago, Chile.
| | - Fernando Gil
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Iván L Calderón
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
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But SY, Dedysh SN, Popov VO, Pimenov NV, Khmelenina VN. Construction of a Type-I Metanotroph with Reduced Capacity for Glycogen and Sucrose Accumulation. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820050063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Roszczenko-Jasińska P, Vu HN, Subuyuj GA, Crisostomo RV, Cai J, Lien NF, Clippard EJ, Ayala EM, Ngo RT, Yarza F, Wingett JP, Raghuraman C, Hoeber CA, Martinez-Gomez NC, Skovran E. Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1. Sci Rep 2020; 10:12663. [PMID: 32728125 PMCID: PMC7391723 DOI: 10.1038/s41598-020-69401-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/09/2020] [Indexed: 11/08/2022] Open
Abstract
Lanthanide elements have been recently recognized as "new life metals" yet much remains unknown regarding lanthanide acquisition and homeostasis. In Methylorubrum extorquens AM1, the periplasmic lanthanide-dependent methanol dehydrogenase XoxF1 produces formaldehyde, which is lethal if allowed to accumulate. This property enabled a transposon mutagenesis study and growth studies to confirm novel gene products required for XoxF1 function. The identified genes encode an MxaD homolog, an ABC-type transporter, an aminopeptidase, a putative homospermidine synthase, and two genes of unknown function annotated as orf6 and orf7. Lanthanide transport and trafficking genes were also identified. Growth and lanthanide uptake were measured using strains lacking individual lanthanide transport cluster genes, and transmission electron microscopy was used to visualize lanthanide localization. We corroborated previous reports that a TonB-ABC transport system is required for lanthanide incorporation to the cytoplasm. However, cells were able to acclimate over time and bypass the requirement for the TonB outer membrane transporter to allow expression of xoxF1 and growth. Transcriptional reporter fusions show that excess lanthanides repress the gene encoding the TonB-receptor. Using growth studies along with energy dispersive X-ray spectroscopy and transmission electron microscopy, we demonstrate that lanthanides are stored as cytoplasmic inclusions that resemble polyphosphate granules.
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Affiliation(s)
- Paula Roszczenko-Jasińska
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, USA
- Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Huong N Vu
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Gabriel A Subuyuj
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Microbiology and Molecular Genetics, University of California At Davis, Davis, CA, USA
| | - Ralph Valentine Crisostomo
- Department of Biological Sciences, San José State University, San José, CA, USA
- Molecular Biology Institute, University of California At Los Angeles, Los Angeles, CA, USA
| | - James Cai
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Nicholas F Lien
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Erik J Clippard
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Elena M Ayala
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Richard T Ngo
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Fauna Yarza
- Department of Biological Sciences, San José State University, San José, CA, USA
- Department of Biochemistry and Biophysics, University of California At San Francisco, San Francisco, CA, USA
| | - Justin P Wingett
- Department of Biological Sciences, San José State University, San José, CA, USA
| | | | - Caitlin A Hoeber
- Department of Biological Sciences, San José State University, San José, CA, USA
| | - Norma C Martinez-Gomez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, USA.
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, California, USA.
| | - Elizabeth Skovran
- Department of Biological Sciences, San José State University, San José, CA, USA.
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Evaluation of chromosomal insertion loci in the Pseudomonas putida KT2440 genome for predictable biosystems design. Metab Eng Commun 2020; 11:e00139. [PMID: 32775199 PMCID: PMC7398981 DOI: 10.1016/j.mec.2020.e00139] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/02/2020] [Accepted: 07/15/2020] [Indexed: 01/27/2023] Open
Abstract
The development of Pseudomonas strains for industrial production of fuels and chemicals will require the integration of heterologous genes and pathways into the chromosome. Finding the most appropriate integration site to maximize strain performance is an essential part of the strain design process. We characterized seven chromosomal loci in Pseudomonas putida KT2440 for integration of a fluorescent protein expression construct. Insertion in five of the loci did not affect growth rate, but fluorescence varied by up to 27-fold. Three sites displaying a diversity of phenotypes with the fluorescent reporter were also chosen for the integration of a gene encoding a muconate importer. Depending on the integration locus, expression of the importer varied by approximately 3-fold and produced significant phenotypic differences. This work demonstrates the impact of the integration location on host viability, gene expression, and overall strain performance. Pseudomonas putida KT2440 chromosomal loci were characterized as potential insertion targets for heterologous genes. Integration location had a significant effect on heterologous protein expression and host phenotype. The identification of an appropriate chromosomal insertion location is essential to optimize genetic engineering design.
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O'Donnell MP, Fox BW, Chao PH, Schroeder FC, Sengupta P. A neurotransmitter produced by gut bacteria modulates host sensory behaviour. Nature 2020; 583:415-420. [PMID: 32555456 PMCID: PMC7853625 DOI: 10.1038/s41586-020-2395-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 03/27/2020] [Indexed: 12/18/2022]
Abstract
Animals coexist in commensal, pathogenic or mutualistic relationships with complex communities of diverse organisms, including microorganisms1. Some bacteria produce bioactive neurotransmitters that have previously been proposed to modulate nervous system activity and behaviours of their hosts2,3. However, the mechanistic basis of this microbiota-brain signalling and its physiological relevance are largely unknown. Here we show that in Caenorhabditis elegans, the neuromodulator tyramine produced by commensal Providencia bacteria, which colonize the gut, bypasses the requirement for host tyramine biosynthesis and manipulates a host sensory decision. Bacterially produced tyramine is probably converted to octopamine by the host tyramine β-hydroxylase enzyme. Octopamine, in turn, targets the OCTR-1 octopamine receptor on ASH nociceptive neurons to modulate an aversive olfactory response. We identify the genes that are required for tyramine biosynthesis in Providencia, and show that these genes are necessary for the modulation of host behaviour. We further find that C. elegans colonized by Providencia preferentially select these bacteria in food choice assays, and that this selection bias requires bacterially produced tyramine and host octopamine signalling. Our results demonstrate that a neurotransmitter produced by gut bacteria mimics the functions of the cognate host molecule to override host control of a sensory decision, and thereby promotes fitness of both the host and the microorganism.
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Affiliation(s)
| | - Bennett W Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Pin-Hao Chao
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA, USA.
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Mo XH, Zhang H, Wang TM, Zhang C, Zhang C, Xing XH, Yang S. Establishment of CRISPR interference in Methylorubrum extorquens and application of rapidly mining a new phytoene desaturase involved in carotenoid biosynthesis. Appl Microbiol Biotechnol 2020; 104:4515-4532. [PMID: 32215707 DOI: 10.1007/s00253-020-10543-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 02/04/2023]
Abstract
The methylotrophic bacterium Methylorubrum extorquens AM1 holds a great potential of a microbial cell factory in producing high value chemicals with methanol as the sole carbon and energy source. However, many gene functions remain unknown, hampering further rewiring of metabolic networks. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been demonstrated to be a robust tool for gene knockdown in diverse organisms. In this study, we developed an efficient CRISPRi system through optimizing the promoter strength of Streptococcus pyogenes-derived deactivated cas9 (dcas9). When the dcas9 and sgRNA were respectively controlled by medium PR/tetO and strong PmxaF-g promoters, dynamic repression efficacy of cell growth through disturbing a central metabolism gene glyA was achieved from 41.9 to 96.6% dependent on the sgRNA targeting sites. Furthermore, the optimized CRISPRi system was shown to effectively decrease the abundance of exogenous fluorescent protein gene mCherry over 50% and to reduce the expression of phytoene desaturase gene crtI by 97.7%. We then used CRISPRi technology combined with 26 sgRNAs pool to rapidly discover a new phytoene desaturase gene META1_3670 from 2470 recombinant mutants. The gene function was further verified through gene deletion and complementation as well as phylogenetic tree analysis. In addition, we applied CRISPRi to repress the transcriptional level of squalene-hopene cyclase gene shc involved in hopanoid biosynthesis by 64.9%, which resulted in enhancing 1.9-fold higher of carotenoid production without defective cell growth. Thus, the CRISPRi system developed here provides a useful tool in mining functional gene of M. extorquens as well as in biotechnology for producing high-valued chemicals from methanol. KEY POINTS: Developing an efficient CRISPRi to knockdown gene expression in C1-utilizing bacteria CRISPRi combined with sgRNAs pool to rapidly discover a new phytoene desaturase gene Improvement of carotenoid production by repressing a competitive pathway.
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Affiliation(s)
- Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Hui Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Tian-Min Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Chong Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Cong Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China.
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Gan HM, Wengert P, Barton HA, Hudson AO, Savka MA. Insight into the resistome and quorum sensing system of a divergent Acinetobacter pittii isolate from an untouched site of the Lechuguilla Cave. Access Microbiol 2020; 2:acmi000089. [PMID: 34568753 PMCID: PMC8459101 DOI: 10.1099/acmi.0.000089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/11/2019] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter are Gram-negative bacteria belonging to the sub-phyla Gammaproteobacteria, commonly associated with soils, animal feeds and water. Some members of the Acinetobacter have been implicated in hospital-acquired infections, with broad-spectrum antibiotic resistance. Here we report the whole-genome sequence of LC510, an Acinetobacter species isolated from deep within a pristine location of the Lechuguilla Cave. Pairwise nucleotide comparison to three type strains within the genus Acinetobacter assigned LC510 as an Acinetobacter pittii isolate. Scanning of the LC510 genome identified two genes coding for b-lactamase resistance, despite the fact that LC510 was isolated from a portion of the cave not previously visited by humans and protected from anthropogenic input. The ability to produce acyl-homoserine lactone (AHL) signal in culture medium, an observation that is consistent with the identification of the luxI and luxR homologues in its genome, suggests that cell-to-cell communication remains important in an isolated cave ecosystem.
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Affiliation(s)
- Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong 3220, Victoria, Australia.,Deakin Genomics Centre, Deakin University, Geelong 3220, Victoria, Australia.,School of Science, Monash University Malaysia, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia
| | - Peter Wengert
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Hazel A Barton
- Department of Biology, University of Akron, Akron, OH, USA
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Michael A Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
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Peabody GL, Elmore JR, Martinez-Baird J, Guss AM. Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:295. [PMID: 31890023 PMCID: PMC6927180 DOI: 10.1186/s13068-019-1627-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/04/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Efficient conversion of plant biomass to commodity chemicals is an important challenge that needs to be solved to enable a sustainable bioeconomy. Deconstruction of biomass to sugars and lignin yields a wide variety of low molecular weight carbon substrates that need to be funneled to product. Pseudomonas putida KT2440 has emerged as a potential platform for bioconversion of lignin and the other components of plant biomass. However, P. putida is unable to natively utilize several of the common sugars in hydrolysate streams, including galactose. RESULTS In this work, we integrated a De Ley-Doudoroff catabolic pathway for galactose catabolism into the chromosome of P. putida KT2440, using genes from several different organisms. We found that the galactonate catabolic pathway alone (DgoKAD) supported slow growth of P. putida on galactose. Further integration of genes to convert galactose to galactonate and to optimize the transporter expression level resulted in a growth rate of 0.371 h-1. Additionally, the best-performing strain was demonstrated to co-utilize galactose with glucose. CONCLUSIONS We have engineered P. putida to catabolize galactose, which will allow future engineered strains to convert more plant biomass carbon to products of interest. Further, by demonstrating co-utilization of glucose and galactose, continuous bioconversion processes for mixed sugar streams are now possible.
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Affiliation(s)
- George L. Peabody
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Joshua R. Elmore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Present Address: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | | | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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35
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Upadhyay P, Singh NK, Tupe R, Odenath A, Lali A. Biotransformation of corn bran derived ferulic acid to vanillic acid using engineered Pseudomonas putida KT2440. Prep Biochem Biotechnol 2019; 50:341-348. [PMID: 31809239 DOI: 10.1080/10826068.2019.1697935] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Ferulic acid is a fraction of the phenolics present in cereals such as rice and corn as a component of the bran. Substantial amounts of waste bran are generated by the grain processing industry and this can be valorized via extraction, purification and conversion of phenolics to value added chemical products. Alkaline alcohol based extracted and purified ferulic acid from corn bran was converted to vanillic acid using engineered Pseudomonas putida KT2440. The strain was engineered by rendering the vanAB gene nonfunctional and obtaining the mutant defective in vanillic acid metabolism. Biotransformation of ferulic acid using resting Pseudomonas putida KT2440 mutant cells resulted in more than 95 ± 1.4% molar yield from standard ferulic acid; while the corn bran derived ferulic acid gave 87 ± 0.38% molar yield. With fermentation time of less than 24 h the mutant becomes a promising candidate for the stable biosynthesis of vanillic acid at industrial scale.
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Affiliation(s)
- Priya Upadhyay
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Nitesh K Singh
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Rasika Tupe
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Annamma Odenath
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India
| | - Arvind Lali
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Mumbai, India.,Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, India
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36
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Draft Genome Sequences of Five Proteobacteria Isolated from Lechuguilla Cave, New Mexico, USA, and Insights into Taxonomy and Quorum Sensing. Microbiol Resour Announc 2019; 8:8/40/e00913-19. [PMID: 31582457 PMCID: PMC6776774 DOI: 10.1128/mra.00913-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Genomic resources remain scarce for bacteria isolated from oligotrophic caves. We sequenced the genomes of five Proteobacteria isolated from Lechuguilla Cave in New Mexico. Genome-based phylogeny indicates that each strain belongs to a distinct genus. Two Rhizobiaceae isolates possess genomic potential for the biosynthesis of acyl-homoserine lactone. Genomic resources remain scarce for bacteria isolated from oligotrophic caves. We sequenced the genomes of five Proteobacteria isolated from Lechuguilla Cave in New Mexico. Genome-based phylogeny indicates that each strain belongs to a distinct genus. Two Rhizobiaceae isolates possess genomic potential for the biosynthesis of acyl-homoserine lactone.
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37
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Salvachúa D, Rydzak T, Auwae R, De Capite A, Black BA, Bouvier JT, Cleveland NS, Elmore JR, Huenemann JD, Katahira R, Michener WE, Peterson DJ, Rohrer H, Vardon DR, Beckham GT, Guss AM. Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate production from lignin. Microb Biotechnol 2019; 13:290-298. [PMID: 31468725 PMCID: PMC6922519 DOI: 10.1111/1751-7915.13481] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/10/2019] [Indexed: 12/01/2022] Open
Abstract
Microbial conversion offers a promising strategy for overcoming the intrinsic heterogeneity of the plant biopolymer, lignin. Soil microbes that natively harbour aromatic‐catabolic pathways are natural choices for chassis strains, and Pseudomonas putida KT2440 has emerged as a viable whole‐cell biocatalyst for funnelling lignin‐derived compounds to value‐added products, including its native carbon storage product, medium‐chain‐length polyhydroxyalkanoates (mcl‐PHA). In this work, a series of metabolic engineering targets to improve mcl‐PHA production are combined in the P. putida chromosome and evaluated in strains growing in a model aromatic compound, p‐coumaric acid, and in lignin streams. Specifically, the PHA depolymerase gene phaZ was knocked out, and the genes involved in β‐oxidation (fadBA1 and fadBA2) were deleted. Additionally, to increase carbon flux into mcl‐PHA biosynthesis, phaG, alkK, phaC1 and phaC2 were overexpressed. The best performing strain – which contains all the genetic modifications detailed above – demonstrated a 53% and 200% increase in mcl‐PHA titre (g l−1) and a 20% and 100% increase in yield (g mcl‐PHA per g cell dry weight) from p‐coumaric acid and lignin, respectively, compared with the wild type strain. Overall, these results present a promising strain to be employed in further process development for enhancing mcl‐PHA production from aromatic compounds and lignin.
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Affiliation(s)
- Davinia Salvachúa
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Thomas Rydzak
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Raquel Auwae
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Annette De Capite
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Brenna A Black
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Jason T Bouvier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nicholas S Cleveland
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Joshua R Elmore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jay D Huenemann
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Rui Katahira
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - William E Michener
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Darren J Peterson
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Holly Rohrer
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Derek R Vardon
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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Nguyen LT, Lee EY. Biological conversion of methane to putrescine using genome-scale model-guided metabolic engineering of a methanotrophic bacterium Methylomicrobium alcaliphilum 20Z. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:147. [PMID: 31223337 PMCID: PMC6570963 DOI: 10.1186/s13068-019-1490-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/07/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Methane is the primary component of natural gas and biogas. The huge abundance of methane makes it a promising alternative carbon source for industrial biotechnology. Herein, we report diamine compound, putrescine, production from methane by an industrially promising methanotroph Methylomicrobium alcaliphilum 20Z. RESULTS We conducted adaptive evolution to improve putrescine tolerance of M. alcaliphilum 20Z because putrescine highly inhibits the cell growth. The evolved strain 20ZE was able to grow in the presence of 400 mM of putrescine dihydrochloride. The expression of linear pathway ornithine decarboxylase genes from Escherichia coli and Methylosinus trichosporium OB3b allowed the engineered strain to produce putrescine. A higher putrescine titer of 12.44 mg/L was obtained in the strain 20ZE-pACO with ornithine decarboxylase from M. trichosporium OB3b. For elimination of the putrescine utilization pathway, spermidine synthase (MEALZ_3408) was knocked out, resulting in no spermidine formation in the strain 20ZES1-pACO with a putrescine titer of 18.43 mg/L. Next, a genome-scale metabolic model was applied to identify gene knockout strategies. Acetate kinase (MEALZ_2853) and subsequently lactate dehydrogenase (MEALZ_0534) were selected as knockout targets, and the deletion of these genes resulted in an improvement of the putrescine titer to 26.69 mg/L. Furthermore, the putrescine titer was improved to 39.04 mg/L by overexpression of key genes in the ornithine biosynthesis pathway under control of the pTac promoter. Finally, suitable nitrogen sources for growth of M. alcaliphilum 20Z and putrescine production were optimized with the supplement of 2 mM ammonium chloride to nitrate mineral salt medium, and this led to the production of 98.08 mg/L putrescine, almost eightfold higher than that from the initial strain. Transcriptome analysis of the engineered strains showed upregulation of most genes involved in methane assimilation, citric acid cycle, and ammonia assimilation in ammonia nitrate mineral salt medium, compared to nitrate mineral salt medium. CONCLUSIONS The engineered M. alcaliphilum 20ZE4-pACO strain was able to produce putrescine up to 98.08 mg/L, almost eightfold higher than the initial strain. This study represents the bioconversion of methane to putrescine-a high value-added diamine compound.
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Affiliation(s)
- Linh Thanh Nguyen
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104 Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104 Republic of Korea
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Lim CK, Villada JC, Chalifour A, Duran MF, Lu H, Lee PKH. Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production. Front Microbiol 2019; 10:1027. [PMID: 31143170 PMCID: PMC6520949 DOI: 10.3389/fmicb.2019.01027] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/24/2019] [Indexed: 01/05/2023] Open
Abstract
Methylorubrum extorquens (formerly Methylobacterium extorquens) AM1 is a methylotrophic bacterium with a versatile lifestyle. Various carbon sources including acetate, succinate and methanol are utilized by M. extorquens AM1 with the latter being a promising inexpensive substrate for use in the biotechnology industry. Itaconic acid (ITA) is a high-value building block widely used in various industries. Given that no wildtype methylotrophic bacteria are able to utilize methanol to produce ITA, we tested the potential of M. extorquens AM1 as an engineered host for this purpose. In this study, we successfully engineered M. extorquens AM1 to express a heterologous codon-optimized gene encoding cis-aconitic acid decarboxylase. The engineered strain produced ITA using acetate, succinate and methanol as the carbon feedstock. The highest ITA titer in batch culture with methanol as the carbon source was 31.6 ± 5.5 mg/L, while the titer and productivity were 5.4 ± 0.2 mg/L and 0.056 ± 0.002 mg/L/h, respectively, in a scaled-up fed-batch bioreactor under 60% dissolved oxygen saturation. We attempted to enhance the carbon flux toward ITA production by impeding poly-β-hydroxybutyrate accumulation, which is used as carbon and energy storage, via mutation of the regulator gene phaR. Unexpectedly, ITA production by the phaR mutant strain was not higher even though poly-β-hydroxybutyrate concentration was lower. Genome-wide transcriptomic analysis revealed that phaR mutation in the ITA-producing strain led to complex rewiring of gene transcription, which might result in a reduced carbon flux toward ITA production. Besides poly-β-hydroxybutyrate metabolism, we found evidence that PhaR might regulate the transcription of many other genes including those encoding other regulatory proteins, methanol dehydrogenases, formate dehydrogenases, malate:quinone oxidoreductase, and those synthesizing pyrroloquinoline quinone and thiamine co-factors. Overall, M. extorquens AM1 was successfully engineered to produce ITA using acetate, succinate and methanol as feedstock, further supporting this bacterium as a feasible host for use in the biotechnology industry. This study showed that PhaR could have a broader regulatory role than previously anticipated, and increased our knowledge of this regulator and its influence on the physiology of M. extorquens AM1.
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Affiliation(s)
- Chee Kent Lim
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Juan C Villada
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Annie Chalifour
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Maria F Duran
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Hongyuan Lu
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
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40
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Jha RK, Narayanan N, Pandey N, Bingen JM, Kern TL, Johnson CW, Strauss CEM, Beckham GT, Hennelly SP, Dale T. Sensor-Enabled Alleviation of Product Inhibition in Chorismate Pyruvate-Lyase. ACS Synth Biol 2019; 8:775-786. [PMID: 30861344 DOI: 10.1021/acssynbio.8b00465] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Product inhibition is a frequent bottleneck in industrial enzymes, and testing mutations to alleviate product inhibition via traditional methods remains challenging as many variants need to be tested against multiple substrate and product concentrations. Further, traditional screening methods are conducted in vitro, and resulting enzyme variants may perform differently in vivo in the context of whole-cell metabolism and regulation. In this study, we address these two problems by establishing a high-throughput screening method to alleviate product inhibition in an industrially relevant enzyme, chorismate pyruvate-lyase (UbiC). First, we engineered a highly specific, genetically encoded biosensor for 4-hydroxybenzoate (4HB) in an industrially relevant host, Pseudomonas putida KT2440. We subsequently applied the biosensor to detect the activity of a heterologously expressed UbiC that converts chorismate into 4HB and pyruvate. By using benzoate as a product surrogate that inhibits UbiC without activating the biosensor, we were able to efficiently create and screen a diversified library for UbiC variants with reduced product inhibition. Introduction of the improved UbiC enzyme variant into an experimental production strain for the industrial precursor cis,cis-muconic acid (muconate), enabled a >2-fold yield improvement for glucose to muconate conversion when the new UbiC variant was expressed from a plasmid and a 60% yield increase when the same UbiC variant was genomically integrated into the strain. Overall, this work demonstrates that by coupling a library of enzyme variants to whole-cell catalysis and biosensing, variants with reduced product inhibition can be identified, and that this improved enzyme can result in increased titers of a downstream molecule of interest.
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Affiliation(s)
- Ramesh K. Jha
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Niju Narayanan
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Naresh Pandey
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jeremy M. Bingen
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Theresa L. Kern
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Christopher W. Johnson
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Charlie E. M. Strauss
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Scott P. Hennelly
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Taraka Dale
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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A Counterselectable Sucrose Sensitivity Marker Permits Efficient and Flexible Mutagenesis in Streptococcus agalactiae. Appl Environ Microbiol 2019; 85:AEM.03009-18. [PMID: 30658970 DOI: 10.1128/aem.03009-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/13/2019] [Indexed: 12/25/2022] Open
Abstract
Streptococcus agalactiae (group B Streptococcus [GBS]) is a cause of severe infections, particularly during the newborn period. While methods exist for generating chromosomal mutations in GBS, they are cumbersome and inefficient and present significant challenges if the goal is to study subtle mutations, such as single-base-pair polymorphisms. To address this problem, we have developed an efficient and flexible GBS mutagenesis protocol based on sucrose counterselection against levansucrase (SacB) expressed from a temperature-selective shuttle vector. GBS containing the SacB expression cassette demonstrates lethal sensitivity to supplemental sucrose whether the plasmid DNA is replicating outside of the chromosome or has been integrated during a crossover event. Transmission electron microscopy shows that SacB-mediated lethal sucrose sensitivity results from the accumulation of inclusion bodies that eventually lead to complete degradation of normal cellular architecture and subsequent lysis. We used this new mutagenesis technique to generate an in-frame, allelic exchange knockout of the GBS sortase gene srtA, demonstrating that >99% of colonies that emerge from our protocol had the expected knockout phenotype and that among a subset tested by sequencing, 100% had the correct genotype. We also generated barcoded nonsense mutations in the cylE gene in two GBS strains, showing that the approach can be used to make small, precise chromosomal mutations.IMPORTANCE The ability to generate chromosomal mutations is fundamental to microbiology. Historically, however, GBS pathogenesis research has been made challenging by the relative genetic intractability of the organism. Generating a single knockout in GBS using traditional techniques can take many months, with highly variable success rates. Furthermore, traditional methods do not offer a straightforward way to generate single-base-pair polymorphisms or other subtle changes, especially to noncoding regions of the chromosome. We have developed a new sucrose counterselection-based method that permits rapid, efficient, and flexible GBS mutagenesis. Our technique requires no additional equipment beyond what is needed for traditional approaches. We believe that it will catalyze rapid advances in GBS genetics research by significantly easing the path to generating mutants.
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42
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Ochsner AM, Hemmerle L, Vonderach T, Nüssli R, Bortfeld-Miller M, Hattendorf B, Vorholt JA. Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1. Mol Microbiol 2019; 111:1152-1166. [PMID: 30653750 PMCID: PMC6850437 DOI: 10.1111/mmi.14208] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2019] [Indexed: 01/03/2023]
Abstract
Until recently, rare‐earth elements (REEs) had been thought to be biologically inactive. This view changed with the discovery of the methanol dehydrogenase XoxF that strictly relies on REEs for its activity. Some methylotrophs only contain xoxF, while others, including the model phyllosphere colonizer Methylobacterium extorquens PA1, harbor this gene in addition to mxaFI encoding a Ca2+‐dependent enzyme. Here we found that REEs induce the expression of xoxF in M. extorquens PA1, while repressing mxaFI, suggesting that XoxF is the preferred methanol dehydrogenase in the presence of sufficient amounts of REE. Using reporter assays and a suppressor screen, we found that lanthanum (La3+) is sensed both in a XoxF‐dependent and independent manner. Furthermore, we investigated the role of REEs during Arabidopsisthaliana colonization. Element analysis of the phyllosphere revealed the presence of several REEs at concentrations up to 10 μg per g dry weight. Complementary proteome analyses of M. extorquens PA1 identified XoxF as a top induced protein in planta and a core set of La3+‐regulated proteins under defined artificial media conditions. Among these was a REE‐binding protein that is encoded next to a gene for a TonB‐dependent transporter. The latter was essential for REE‐dependent growth on methanol indicating chelator‐assisted uptake of REEs.
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Affiliation(s)
- Andrea M Ochsner
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Lucas Hemmerle
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Thomas Vonderach
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Ralph Nüssli
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Miriam Bortfeld-Miller
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Bodo Hattendorf
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
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43
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Adamowicz EM, Flynn J, Hunter RC, Harcombe WR. Cross-feeding modulates antibiotic tolerance in bacterial communities. ISME JOURNAL 2018; 12:2723-2735. [PMID: 29991761 PMCID: PMC6194032 DOI: 10.1038/s41396-018-0212-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/18/2018] [Accepted: 06/11/2018] [Indexed: 12/29/2022]
Abstract
Microbes frequently rely on metabolites excreted by other bacterial species, but little is known about how this cross-feeding influences the effect of antibiotics. We hypothesized that when species rely on each other for essential metabolites, the minimum inhibitory concentration (MIC) for all species will drop to that of the “weakest link”—the species least resistant in monoculture. We tested this hypothesis in an obligate cross-feeding system that was engineered between Escherichia coli, Salmonella enterica, and Methylobacterium extorquens. The effect of tetracycline and ampicillin were tested on both liquid and solid media. In all cases, resistant species were inhibited at significantly lower antibiotic concentrations in the cross-feeding community than in monoculture or a competitive community. However, deviation from the “weakest link” hypothesis was also observed in cross-feeding communities apparently as result of changes in the timing of growth and cross-protection. Comparable results were also observed in a clinically relevant system involving facultative cross-feeding between Pseudomonas aeruginosa and an anaerobic consortium found in the lungs of cystic fibrosis patients. P. aeruginosa was inhibited by lower concentrations of ampicillin when cross-feeding than when grown in isolation. These results suggest that cross-feeding significantly alters tolerance to antibiotics in a variety of systems.
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Affiliation(s)
- Elizabeth M Adamowicz
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA.,Department of Ecology and Evolutionary Biology, University of Minnesota, St. Paul, MN, USA
| | - Jeffrey Flynn
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Ryan C Hunter
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - William R Harcombe
- Department of Ecology and Evolutionary Biology, University of Minnesota, St. Paul, MN, USA. .,BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.
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44
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Freed E, Fenster J, Smolinski SL, Walker J, Henard CA, Gill R, Eckert CA. Building a genome engineering toolbox in nonmodel prokaryotic microbes. Biotechnol Bioeng 2018; 115:2120-2138. [PMID: 29750332 DOI: 10.1002/bit.26727] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/02/2018] [Accepted: 03/10/2018] [Indexed: 12/26/2022]
Abstract
The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop "design rules" for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.
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Affiliation(s)
- Emily Freed
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Jacob Fenster
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | | | - Julie Walker
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Calvin A Henard
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO
| | - Ryan Gill
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | - Carrie A Eckert
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
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45
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Schada von Borzyskowski L, Carrillo M, Leupold S, Glatter T, Kiefer P, Weishaupt R, Heinemann M, Erb TJ. An engineered Calvin-Benson-Bassham cycle for carbon dioxide fixation in Methylobacterium extorquens AM1. Metab Eng 2018; 47:423-433. [DOI: 10.1016/j.ymben.2018.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 03/21/2018] [Accepted: 04/02/2018] [Indexed: 10/17/2022]
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46
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A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution. Metab Eng Commun 2018; 6:33-38. [PMID: 29765865 PMCID: PMC5949891 DOI: 10.1016/j.meteno.2018.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/03/2018] [Accepted: 03/03/2018] [Indexed: 11/27/2022] Open
Abstract
Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. Here we demonstrate the optimization of an Escherichia coli-based biosensor in a robust microbial strain for the catabolism of aromatic compounds, Pseudomonas putida KT2440, through a generalizable approach of modulating interactions at the protein-DNA interface in the promoter and the protein-protein dimer interface. The high-throughput biosensor optimization approach demonstrated here is readily applicable towards other allosteric regulators. A biosensor optimized for a robust, industrially useful P. putida strain. Modulation of protein-DNA and protein-protein interactions pursued. Offers a generalized optimization protocol for transcription factor-based sensors. Intracellular metabolite production and detection made possible in P. putida. Functional biosensor in P. putida will allow high throughput strain evolution.
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47
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Schada von Borzyskowski L, Sonntag F, Pöschel L, Vorholt JA, Schrader J, Erb TJ, Buchhaupt M. Replacing the Ethylmalonyl-CoA Pathway with the Glyoxylate Shunt Provides Metabolic Flexibility in the Central Carbon Metabolism of Methylobacterium extorquens AM1. ACS Synth Biol 2018; 7:86-97. [PMID: 29216425 DOI: 10.1021/acssynbio.7b00229] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ethylmalonyl-CoA pathway (EMCP) is an anaplerotic reaction sequence in the central carbon metabolism of numerous Proteo- and Actinobacteria. The pathway features several CoA-bound mono- and dicarboxylic acids that are of interest as platform chemicals for the chemical industry. The EMCP, however, is essential for growth on C1 and C2 carbon substrates and therefore cannot be simply interrupted to drain these intermediates. In this study, we aimed at reengineering central carbon metabolism of the Alphaproteobacterium Methylobacterium extorquens AM1 for the specific production of EMCP derivatives in the supernatant. Establishing a heterologous glyoxylate shunt in M. extorquens AM1 restored wild type-like growth in several EMCP knockout strains on defined minimal medium with acetate as carbon source. We further engineered one of these strains that carried a deletion of the gene encoding crotonyl-CoA carboxylase/reductase to demonstrate in a proof-of-concept the specific production of crotonic acid in the supernatant on a defined minimal medium. Our experiments demonstrate that it is in principle possible to further exploit the EMCP by establishing an alternative central carbon metabolic pathway in M. extorquens AM1, opening many possibilities for the biotechnological production of EMCP-derived compounds in future.
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Affiliation(s)
| | - Frank Sonntag
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Laura Pöschel
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Julia A. Vorholt
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Jens Schrader
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Tobias J. Erb
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology, SYNMIKRO, 35043 Marburg, Germany
| | - Markus Buchhaupt
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
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Collins DA, Kalyuzhnaya MG. Navigating methane metabolism: Enzymes, compartments, and networks. Methods Enzymol 2018; 613:349-383. [DOI: 10.1016/bs.mie.2018.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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49
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Liang WF, Sun MY, Cui LY, Zhang C, Xing XH. Cre/loxP-Mediated Multicopy Integration of the Mevalonate Operon into the Genome of Methylobacterium extorquens AM1. Appl Biochem Biotechnol 2017; 185:565-577. [PMID: 29243041 DOI: 10.1007/s12010-017-2673-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/30/2017] [Indexed: 01/08/2023]
Abstract
Methylobacterium extorquens AM1 is the model strain for methylotrophic bacteria that metabolize methanol as the sole carbon and energy source. Genetically modified M. extorquens AM1 is used as a methylotrophic cell factory (MeCF) for high value-added chemical production. We tested the Cre-loxP recombination system for its ability to mediate multicopy gene integration of the mvt3 operon (mvt3) in M. extorquens AM1. mvt3 controls the expression of the first three enzymes of the mevalonate synthesis pathway. We assayed for Cre-mediated multigene integration by screening for multicopy mutants via their survival in culture with a high kanamycin concentration (600 μg/mL). We identified mutant strains in which the mevalonate titer was increased by up to 1.9-fold compared with M2 (M. extorquens AM1ΔcelABCΔattTn7::mvt3::loxP) and confirmed mvt3 integration at 2-3 copies per genome. This result demonstrates the feasibility of multicopy integration in M. extorquens AM1 mediated by Cre-loxP recombination and its potential for improving the output of M. extorquens AM1 metabolic pathways, e.g., optimization of terpenoid synthesis.
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Affiliation(s)
- Wei-Fan Liang
- Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Center for Synthetic and Systems Biology, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
- Guangdong Hainabiotech CO., LTD, Foshan, 511400, People's Republic of China
| | - Ming-Yang Sun
- Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Center for Synthetic and Systems Biology, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Lan-Yu Cui
- Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Center for Synthetic and Systems Biology, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Chong Zhang
- Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Center for Synthetic and Systems Biology, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China.
| | - Xin-Hui Xing
- Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Center for Synthetic and Systems Biology, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
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50
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Production of 3-hydroxypropionic acid in engineered Methylobacterium extorquens AM1 and its reassimilation through a reductive route. Microb Cell Fact 2017; 16:179. [PMID: 29084554 PMCID: PMC5663086 DOI: 10.1186/s12934-017-0798-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/24/2017] [Indexed: 12/01/2022] Open
Abstract
Background 3-Hydroxypropionic acid (3-HP) is an important platform chemical, serving as a precursor for a wide range of industrial applications such as the production of acrylic acid and 1,3-propanediol. Although Escherichia coli or Saccharomyces cerevisiae are the primary industrial microbes for the production of 3-HP, alternative engineered hosts have the potential to generate 3-HP from other carbon feedstocks. Methylobacterium extorquens AM1, a facultative methylotrophic α-proteobacterium, is a model system for assessing the possibility of generating 3-HP from one-carbon feedstock methanol. Results Here we constructed a malonyl-CoA pathway by heterologously overexpressing the mcr gene to convert methanol into 3-HP in M. extorquens AM1. The engineered strains demonstrated 3-HP production with initial titer of 6.8 mg/l in shake flask cultivation, which was further improved to 69.8 mg/l by increasing the strength of promoter and mcr gene copy number. In vivo metabolic analysis showed a significant decrease of the acetyl-CoA pool size in the strain with the highest 3-HP titer, suggesting the supply of acetyl-CoA is a potential bottleneck for further improvement. Notably, 3-HP was rapidly degraded after the transition from exponential phase to stationary phase. Metabolomics analysis showed the accumulation of intracellular 3-hydroxypropionyl-CoA at stationary phase with the addition of 3-HP into the cultured medium, indicating 3-HP was first converted to its CoA derivatives. In vitro enzymatic assay and β-alanine pathway dependent 13C-labeling further demonstrated that a reductive route sequentially converted 3-HP-CoA to acrylyl-CoA and propionyl-CoA, with the latter being reassimilated into the ethylmalonyl-CoA pathway. The deletion of the gene META1_4251 encoding a putative acrylyl-CoA reductase led to reduced degradation rate of 3-HP in late stationary phase. Conclusions We demonstrated the feasibility of constructing the malonyl-CoA pathway in M. extorquens AM1 to generate 3-HP. Furthermore, we showed that a reductive route coupled with the ethylmalonyl-CoA pathway was the major channel responsible for degradation of the 3-HP during the growth transition. Engineered M. extorquens AM1 represents a good platform for 3-HP production from methanol. Electronic supplementary material The online version of this article (10.1186/s12934-017-0798-2) contains supplementary material, which is available to authorized users.
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