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Malfoy T, Alkim C, Barthe M, Fredonnet J, François JM. Enzymatic promiscuity and underground reactions accounted for the capability of Escherichia coli to use the non-natural chemical synthon 2,4-dihydroxybutyric acid as a carbon source for growth. Microbiol Res 2024; 288:127888. [PMID: 39236473 DOI: 10.1016/j.micres.2024.127888] [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: 07/18/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/07/2024]
Abstract
2,4-dihydroxybutyric acid (DHB) and 2-keto-4-hydroxybutyrate (OHB) are non-natural molecules obtained through synthetic pathways from renewable carbon source. As they are structurally similar to lactate and pyruvate respectively, they could possibly interfere with the metabolic network of Escherichia coli. In fact, we showed that DHB can be easily oxidized by the membrane associated L and D-lactate dehydrogenases encoded by lldD, dld and ykgF into OHB, and the latter being cleaved into pyruvate and formaldehyde by several pyruvate-dependent aldolases, with YagE being the most effective. While formaldehyde was readily detoxified into formate, Escherichia coli K12 MG1655 strain failed to grow on DHB despite of the production of pyruvate. To find out the reason for this failure, we constructed a mutant strain whose growth was rendered dependent on DHB and subjected this strain to adaptive evolution. Genome sequencing of the adapted strain revealed an essential role for ygbI encoding a transcriptional repressor of the threonate operon in this DHB-dependent growth. This critical function was attributed to the derepression of ygbN encoding a putative threonate transporter, which was found to exclusively transport the D form of DHB. A subsequent laboratory evolution was carried out with E. coli K12 MG1655 deleted for ΔygbI to adapt for growth on DHB as sole carbon source. Remarkably, only two additional mutations were disclosed in the adapted strain, which were demonstrated by reverse engineering to be necessary and sufficient for robust growth on DHB. One mutation was in nanR encoding the transcription repressor of sialic acid metabolic genes, causing 140-fold increase in expression of nanA encoding N-acetyl neuraminic acid lyase, a pyruvate-dependent aldolase, and the other was in the promoter of dld leading to 14-fold increase in D-lactate dehydrogenase activity on DHB. Taken together, this work illustrates the importance of promiscuous enzymes in underground metabolism and moreover, in the frame of synthetic pathways aiming at producing non-natural products, these underground reactions could potentially penalize yield and title of these bio-based products.
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Affiliation(s)
- Thibault Malfoy
- Toulouse Biotechnology Institute, UMR INSA -CNRS5504 and UMR INSA-INRAE 792, 135 avenue de Rangueil, Toulouse 31077, France.
| | - Ceren Alkim
- Toulouse Biotechnology Institute, UMR INSA -CNRS5504 and UMR INSA-INRAE 792, 135 avenue de Rangueil, Toulouse 31077, France; Toulouse White Biotechnology, UMS INRAE-INSA-CNRS, 135 Avenue de Rangueil, Toulouse 31077, France.
| | - Manon Barthe
- Toulouse Biotechnology Institute, UMR INSA -CNRS5504 and UMR INSA-INRAE 792, 135 avenue de Rangueil, Toulouse 31077, France.
| | - Julie Fredonnet
- Toulouse White Biotechnology, UMS INRAE-INSA-CNRS, 135 Avenue de Rangueil, Toulouse 31077, France.
| | - Jean Marie François
- Toulouse Biotechnology Institute, UMR INSA -CNRS5504 and UMR INSA-INRAE 792, 135 avenue de Rangueil, Toulouse 31077, France; Toulouse White Biotechnology, UMS INRAE-INSA-CNRS, 135 Avenue de Rangueil, Toulouse 31077, France.
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Florek LC, Lin X, Lin YC, Lin MH, Chakraborty A, Price-Whelan A, Tong L, Rahme L, Dietrich LEP. The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection. mBio 2024; 15:e0085224. [PMID: 39162563 PMCID: PMC11389411 DOI: 10.1128/mbio.00852-24] [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: 03/20/2024] [Accepted: 07/09/2024] [Indexed: 08/21/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it can serve as a carbon source for P. aeruginosa in the diverse settings that it inhabits. In this study, we evaluate the production and use of two redundant P. aeruginosa L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and ɑ-hydroxybutyrate, which, like lactate, are ɑ-hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays reveal that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosa's success as a resident of contaminated environments and animal hosts.IMPORTANCEPseudomonas aeruginosa is a major cause of lung infections in people with cystic fibrosis, of hospital-acquired infections, and of wound infections. It consumes L-lactate, which is found at substantial levels in human blood and tissues. In this study, we investigated the spatial regulation of two redundant enzymes, called LldD and LldA, which enable L-lactate metabolism in P. aeruginosa biofilms. We uncovered mechanisms and identified compounds that control the preference of P. aeruginosa for LldD versus LldA. We also showed that both enzymes contribute to its ability to survive within macrophages, a behavior that is thought to augment the chronicity and recalcitrance of infections. Our findings shed light on a key metabolic strategy used by P. aeruginosa and have the potential to inform the development of therapies targeting bacterial metabolism during infection.
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Affiliation(s)
- Lindsey C Florek
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Xi Lin
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Yu-Cheng Lin
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Arijit Chakraborty
- Department of Surgery, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Shriners Hospitals for Children Boston, Boston, Massachusetts, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Laurence Rahme
- Department of Surgery, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Shriners Hospitals for Children Boston, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, New York, USA
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3
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Li F, Yu H, Zhang B, Hu C, Lan F, Wang Y, You Z, Liu Q, Tang R, Zhang J, Li C, Shi L, Li WW, Nealson KH, Liu Z, Song H. Engineered Cell Elongation Promotes Extracellular Electron Transfer of Shewanella Oneidensis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403067. [PMID: 39234800 DOI: 10.1002/advs.202403067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 08/12/2024] [Indexed: 09/06/2024]
Abstract
To investigate how cell elongation impacts extracellular electron transfer (EET) of electroactive microorganisms (EAMs), the division of model EAM Shewanella oneidensis (S. oneidensis) MR-1 is engineered by reducing the formation of cell divisome. Specially, by blocking the translation of division proteins via anti-sense RNAs or expressing division inhibitors, the cellular length and output power density are all increased. Electrophysiological and transcriptomic results synergistically reveal that the programmed cell elongation reinforces EET by enhancing NADH oxidation, inner-membrane quinone pool, and abundance of c-type cytochromes. Moreover, cell elongation enhances hydrophobicity due to decreased cell-surface polysaccharide, thus facilitates the initial surface adhesion stage during biofilm formation. The output current and power density all increase in positive correction with cellular length. However, inhibition of cell division reduces cell growth, which is then restored by quorum sensing-based dynamic regulation of cell growth and elongation phases. The QS-regulated elongated strain thus enables a cell length of 143.6 ± 40.3 µm (72.6-fold of that of S. oneidensis MR-1), which results in an output power density of 248.0 ± 10.6 mW m-2 (3.41-fold of that of S. oneidensis MR-1) and exhibits superior potential for pollutant treatment. Engineering cellular length paves an innovate avenue for enhancing the EET of EAMs.
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Affiliation(s)
- Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Huan Yu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Baocai Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Chaoning Hu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Fei Lan
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yuxuan Wang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zixuan You
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Rui Tang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Chao Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geoscience in Wuhan, Wuhan, Hubei, 430074, China
| | - Wen-Wei Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, 230026, China
| | - Kenneth H Nealson
- Departments of Earth Science & Biological Sciences, University of Southern California, 4953 Harriman Ave., South Pasadena, CA, 91030, USA
| | - ZhanYing Liu
- Center for Energy Conservation and Emission Reduction in Fermentation Industry in Inner Mongolia, Engineering Research Center of Inner Mongolia for Green Manufacturing in Bio-fermentation Industry, and School of Chemical Engineering, Inner Mongolia University of Technology, Inner Mongolia, Hohhot, 010051, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
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4
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Hou L, Zheng B, Jiang Z, Hu Y, Shi L, Dong Y, Jiang Y. The dmsEFABGH operon encodes an essential and modular electron transfer pathway for extracellular iodate reduction by Shewanella oneidensis MR-1. Microbiol Spectr 2024; 12:e0051224. [PMID: 38916364 PMCID: PMC11302344 DOI: 10.1128/spectrum.00512-24] [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: 02/27/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Extracellular iodate reduction by Shewanella spp. contributes to iodide generation in the biogeochemical cycling of iodine. However, there is a disagreement on whether Shewanella spp. use different extracellular electron transfer pathways with dependence on electron donors in iodate reduction. In this study, a series of gene deletion mutants of Shewanella oneidensis MR-1 were created to investigate the roles of dmsEFABGH, mtrCAB, and so4357-so4362 operons in iodate reduction. The iodate-reducing activity of the mutants was tested with lactate, formate, and H2 as the sole electron donors, respectively. In the absence of single-dms gene, iodate reduction efficiency of the mutants was only 12.9%-84.0% with lactate at 24 hours, 22.1%-85.9% with formate at 20 hours, and 19.6%-57.7% with H2 at 42 hours in comparison to complete reduction by the wild type. Progressive inhibition of iodate reduction was observed when the dms homolog from the so4357-so4362 operon was deleted in the single-dms gene mutants. This result revealed complementation of dmsEFABGH by so4357-so4362 at the single-gene level, indicating modularity of the extracellular electron transfer pathway encoded by dmsEFABGH operon. Under the conditions of all electron donors, significant inhibition of iodate reduction and accumulation of H2O2 were detected for ΔmtrCAB. Collectively, these results demonstrated that the dmsEFABGH operon encodes an essential and modular iodate-reducing pathway without electron donor dependence in S. oneidensis MR-1. The mtrCAB operon was involved in H2O2 elimination with all electron donors. The findings in this study improved the understanding of molecular mechanisms underlying extracellular iodate reduction.IMPORTANCEIodine is an essential trace element for human and animals. Recent studies revealed the contribution of microbial extracellular reduction of iodate in biogeochemical cycling of iodine. Multiple reduced substances can be utilized by microorganisms as energy source for iodate reduction. However, varied electron transfer pathways were proposed for iodate reduction with different electron donors in the model strain Shewanella oneidensis MR-1. Here, through a series of gene deletion and iodate reduction experiments, we discovered that the dmsEFABGH operon was essential for iodate reduction with at least three electron donors, including lactate, formate, and H2. The so4357-so4362 operon was first demonstrated to be capable of complementing the function of dmsEFABGH at single-gene level.
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Affiliation(s)
- Lingyu Hou
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Beiling Zheng
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Zhou Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Yidan Hu
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Yiran Dong
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Yongguang Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- Hubei Key Laboratory of Wetland Evolution & Eco-Restoration, Wuhan, Hubei, China
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Kim G, Covian R, Edwards L, He Y, Balaban RS, Levine RL. Lactate oxidation in Paracoccus denitrificans. Arch Biochem Biophys 2024; 756:109988. [PMID: 38631502 PMCID: PMC11096779 DOI: 10.1016/j.abb.2024.109988] [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: 02/15/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
Paracoccus denitrificans has a classical cytochrome-dependent electron transport chain and two alternative oxidases. The classical transport chain is very similar to that in eukaryotic mitochondria. Thus, P. denitrificans can serve as a model of the mammalian mitochondrion that may be more tractable in elucidating mechanisms of regulation of energy production than are mitochondria. In a previous publication we reported detailed studies on respiration in P. denitrificans grown aerobically on glucose or malate. We noted that P. denitrificans has large stores of lactate under various growth conditions. This is surprising because P. denitrificans lacks an NAD+-dependent lactate dehydrogenase. The aim of this study was to investigate the mechanisms of lactate oxidation in P. denitrificans. We found that the bacterium grows well on either d-lactate or l-lactate. Growth on lactate supported a rate of maximum respiration that was equal to that of cells grown on glucose or malate. We report proteomic, metabolomic, and biochemical studies that establish that the metabolism of lactate by P. denitrificans is mediated by two non-NAD+-dependent lactate dehydrogenases. One prefers d-lactate over l-lactate (D-iLDH) and the other prefers l-lactate (L-iLDH). We cloned and produced the D-iLDH and characterized it. The Km for d-lactate was 34 μM, and for l-lactate it was 3.7 mM. Pyruvate was not a substrate, rendering the reaction unidirectional with lactate being converted to pyruvate for entry into the TCA cycle. The intracellular lactate was ∼14 mM such that both isomers could be metabolized by the enzyme. The enzyme has 1 FAD per molecule and utilizes a quinone rather than NAD + as an electron acceptor. D-iLDH provides a direct entry of lactate reducing equivalents into the cytochrome chain, potentially explaining the high respiratory capacity of P. denitrificans in the presence of lactate.
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Affiliation(s)
- Geumsoo Kim
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raul Covian
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lanelle Edwards
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yi He
- Fermentation Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert S Balaban
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rodney L Levine
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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Zhou Y, Li Q, Wu Y, Zhang W, Ding L, Ji C, Li P, Chen T, Feng L, Tang BZ, Huang X. Synergistic Brilliance: Engineered Bacteria and Nanomedicine Unite in Cancer Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2313953. [PMID: 38400833 DOI: 10.1002/adma.202313953] [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: 12/20/2023] [Revised: 02/21/2024] [Indexed: 02/26/2024]
Abstract
Engineered bacteria are widely used in cancer treatment because live facultative/obligate anaerobes can selectively proliferate at tumor sites and reach hypoxic regions, thereby causing nutritional competition, enhancing immune responses, and producing anticancer microbial agents in situ to suppress tumor growth. Despite the unique advantages of bacteria-based cancer biotherapy, the insufficient treatment efficiency limits its application in the complete ablation of malignant tumors. The combination of nanomedicine and engineered bacteria has attracted increasing attention owing to their striking synergistic effects in cancer treatment. Engineered bacteria that function as natural vehicles can effectively deliver nanomedicines to tumor sites. Moreover, bacteria provide an opportunity to enhance nanomedicines by modulating the TME and producing substrates to support nanomedicine-mediated anticancer reactions. Nanomedicine exhibits excellent optical, magnetic, acoustic, and catalytic properties, and plays an important role in promoting bacteria-mediated biotherapies. The synergistic anticancer effects of engineered bacteria and nanomedicines in cancer therapy are comprehensively summarized in this review. Attention is paid not only to the fabrication of nanobiohybrid composites, but also to the interpromotion mechanism between engineered bacteria and nanomedicine in cancer therapy. Additionally, recent advances in engineered bacteria-synergized multimodal cancer therapies are highlighted.
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Affiliation(s)
- Yaofeng Zhou
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang, 330047, P. R. China
| | - Qianying Li
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang, 330047, P. R. China
| | - Yuhao Wu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang, 330047, P. R. China
| | - Wan Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, P. R. China
| | - Lu Ding
- Department of Cardiology, Jiangxi Hypertension Research Institute, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, P. R. China
| | - Chenlin Ji
- School of Engineering, Westlake University, Hangzhou, 310030, P. R. China
| | - Ping Li
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang, 330047, P. R. China
| | - Tingtao Chen
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, 330036, P. R. China
| | - Lili Feng
- Key Laboratory of Superlight Materials and Surface Technology Ministry of Education, College of Material Sciences and Chemical Engineering, Harbin Engineering University, Harbin, 150001, P. R. China
| | - Ben Zhong Tang
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong, 518172, P. R. China
| | - Xiaolin Huang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Nanchang University, Nanchang, 330047, P. R. China
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Florek LC, Lin X, Lin YC, Lin MH, Chakraborty A, Price-Whelan A, Tong L, Rahme L, Dietrich LE. The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586142. [PMID: 38562866 PMCID: PMC10983889 DOI: 10.1101/2024.03.21.586142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it is available to serve as a carbon source for P. aeruginosa in the diverse settings it inhabits. Here, we evaluate P. aeruginosa's production and use of its redundant L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and - hydroxybutyrate, which, like lactate, are -hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays revealed that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosa's success as a resident of contaminated environments and animal hosts.
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Affiliation(s)
- Lindsey C. Florek
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Xi Lin
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Yu-Cheng Lin
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan 112
| | - Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Arijit Chakraborty
- Department of Surgery, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Shriners Hospitals for Children Boston, Boston, Massachusetts, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Laurence Rahme
- Department of Surgery, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Shriners Hospitals for Children Boston, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lars E.P. Dietrich
- Department of Biological Sciences, Columbia University, New York, NY 10027
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8
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Zhang J, Li F, Liu D, Liu Q, Song H. Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production. Chem Soc Rev 2024; 53:1375-1446. [PMID: 38117181 DOI: 10.1039/d3cs00537b] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.
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Affiliation(s)
- Junqi Zhang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Feng Li
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Dingyuan Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Qijing Liu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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Zhao C, Duan X, Liu C, Huang H, Wu M, Zhang X, Chen Y. Metabolite Cross-Feeding Promoting NADH Production and Electron Transfer during Efficient SMX Biodegradation by a Denitrifier and S. oneidensis MR-1 in the Presence of Nitrate. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:18306-18316. [PMID: 37043541 DOI: 10.1021/acs.est.2c09341] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Antibiotics often coexist with other pollutants (e.g., nitrate) in an aquatic environment, and their simultaneous biological removal has attracted widespread interest. We have found that sulfamethoxazole (SMX) and nitrate can be efficiently removed by the coculture of a model denitrifier (Paracoccus denitrificans, Pd) and Shewanella oneidensis MR-1 (So), and SMX degradation is affected by NADH production and electron transfer. In this paper, the mechanism of a coculture promoting NADH production and electron transfer was investigated by proteomic analysis and intermediate experiments. The results showed that glutamine and lactate produced by Pd were captured by So to synthesize thiamine and heme, and the released thiamine was taken up by Pd as a cofactor of pyruvate and ketoglutarate dehydrogenase, which were related to NADH generation. Additionally, Pd acquired heme, which facilitated electron transfer as heme, was the important composition of complex III and cytochrome c and the iron source of iron sulfur clusters, the key component of complex I in the electron transfer chain. Further investigation revealed that lactate and glutamine generated by Pd prompted So chemotactic moving toward Pd, which helped the two bacteria effectively obtain their required substances. Obviously, metabolite cross-feeding promoted NADH production and electron transfer, resulting in efficient SMX biodegradation by Pd and So in the presence of nitrate. Its feasibility was finally verified by the coculture of an activated sludge denitrifier and So.
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Affiliation(s)
- Chunxia Zhao
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xu Duan
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Chao Liu
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Meirou Wu
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xuemeng Zhang
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and ReSource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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10
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Saruuljavkhlan B, Alfaray RI, Oyuntsetseg K, Gantuya B, Khangai A, Renchinsengee N, Matsumoto T, Akada J, Azzaya D, Davaadorj D, Yamaoka Y. Study of Helicobacter pylori Isolated from a High-Gastric-Cancer-Risk Population: Unveiling the Comprehensive Analysis of Virulence-Associated Genes including Secretion Systems, and Genome-Wide Association Study. Cancers (Basel) 2023; 15:4528. [PMID: 37760497 PMCID: PMC10526929 DOI: 10.3390/cancers15184528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The prevalence of gastric cancer in Mongolia, in East Asia, remains the highest in the world. However, most Helicobacter pylori strains in Mongolia have a less virulent Western-type CagA. We aimed to determine how H. pylori genomic variation affected gastric diseases, especially gastric cancer, based on comprehensive genome analysis. METHODS We identified a set of 274 virulence-associated genes in H. pylori, including virulence factor and outer membrane protein (OMP) genes, the type four secretion system gene cluster, and 13 well-known virulence gene genotypes in 223 H. pylori strains and their associations with gastric cancer and other gastric diseases. We conducted a genome-wide association study on 158 H. pylori strains (15 gastric cancer and 143 non-gastric cancer strains). RESULTS Out of 274 genes, we found 13 genes were variable depending on disease outcome, especially iron regulating OMP genes. H. pylori strains from Mongolia were divided into two main subgroups: subgroup (Sg1) with high risk and Sg2 with low risk for gastric cancer. The general characteristics of Sg1 strains are that they possess more virulence genotype genes. We found nine non-synonymous single nucleotide polymorphisms in seven genes that are linked with gastric cancer strains. CONCLUSIONS Highly virulent H. pylori strains may adapt through host-influenced genomic variations, potentially impacting gastric carcinogenesis.
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Grants
- 18KK0266, 19H03473, 21H00346, 22H02871, 17K09353, 21K07898, 18K16182, 21K08010 Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 2021B13 Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University
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Affiliation(s)
- Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, East Java, Indonesia
| | - Khasag Oyuntsetseg
- Endoscopy Center, Mongolia Japan Hospital, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (K.O.); (B.G.)
| | - Boldbaatar Gantuya
- Endoscopy Center, Mongolia Japan Hospital, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (K.O.); (B.G.)
- Department of Gastroenterology and Hepatology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (D.A.); (D.D.)
| | - Ayush Khangai
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
| | - Namsrai Renchinsengee
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
| | - Dashdorj Azzaya
- Department of Gastroenterology and Hepatology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (D.A.); (D.D.)
| | - Duger Davaadorj
- Department of Gastroenterology and Hepatology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia; (D.A.); (D.D.)
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan; (B.S.); (R.I.A.); (A.K.); (N.R.); (T.M.); (J.A.)
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, East Java, Indonesia
- The Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu 870-1192, Oita, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA
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11
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Lu Z, Kong L, Ren S, Aschenbach JR, Shen H. Acid tolerance of lactate-utilizing bacteria of the order Bacteroidales contributes to prevention of ruminal acidosis in goats adapted to a high-concentrate diet. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2023; 14:130-140. [PMID: 37397354 PMCID: PMC10314236 DOI: 10.1016/j.aninu.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/07/2023] [Accepted: 05/11/2023] [Indexed: 07/04/2023]
Abstract
The rapid accumulation of organic acids, particularly lactate, has been suggested as the main cause of ruminal acidosis (RA) for ruminants fed high-concentrate diets. Previous research has shown that a gradual shift from low-to high-concentrate diets within 4 to 5 weeks effectively reduces the risk for RA. However, the mechanisms remain unknown. In this study, 20 goats were randomly allocated into four groups (n = 5) and fed with a diet containing a weekly increasing concentrate portion of 20%, 40%, 60%, and 80% over 28 d. At d 7, 14, 21, and 28, one group (named C20, C40, C60, and C80 according to the last concentrate level that they received) was killed and the ruminal microbiome was collected. Ruminal acidosis was not detected in any of the goats during the experiment. Nonetheless, ruminal pH dropped sharply from 6.2 to 5.7 (P < 0.05) when dietary concentrate increased from 40% to 60%. A combined metagenome and metatranscriptome sequencing approach identified that this was linked to a sharp decrease in the abundance and expression of genes encoding nicotinamide adenine dinucleotide (NAD)-dependent lactate dehydrogenase (nLDH), catalyzing the enzymatic conversion of pyruvate to lactate (P < 0.01), whereas the expression of two genes encoding NAD-independent lactate dehydrogenase (iLDH), catalyzing lactate oxidation to pyruvate, showed no significant concomitant change. Abundance and expression alterations for nLDH- and iLDH-encoding genes were attributable to bacteria from Clostridiales and Bacteroidales, respectively. By analyzing the gene profiles of 9 metagenome bins (MAG) with nLDH-encoding genes and 5 MAG with iLDH-encoding genes, we identified primary and secondary active transporters as being the major types of sugar transporter for lactate-producing bacteria (LPB) and lactate-utilizing bacteria (LUB), respectively. Furthermore, more adenosine triphosphate was required for the phosphorylation of sugars to initiate their catabolic pathways in LPB compared to LUB. Thus, the low dependence of sugar transport systems and catabolic pathways on primary energy sources supports the acid tolerance of LUB from Bacteroidales. It favors ruminal lactate utilization during the adaptation of goats to a high-concentrate diet. This finding has valuable implications for the development of measures to prevent RA.
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Affiliation(s)
- Zhongyan Lu
- Key Lab of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Lingmeng Kong
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Shenhao Ren
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jörg R. Aschenbach
- Institute of Veterinary Physiology, Freie Universität Berlin, Berlin, Germany
| | - Hong Shen
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu, China
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12
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Mayo-Pérez S, Gama-Martínez Y, Dávila S, Rivera N, Hernández-Lucas I. LysR-type transcriptional regulators: state of the art. Crit Rev Microbiol 2023:1-33. [PMID: 37635411 DOI: 10.1080/1040841x.2023.2247477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023]
Abstract
The LysR-type transcriptional regulators (LTTRs) are DNA-binding proteins present in bacteria, archaea, and in algae. Knowledge about their distribution, abundance, evolution, structural organization, transcriptional regulation, fundamental roles in free life, pathogenesis, and bacteria-plant interaction has been generated. This review focuses on these aspects and provides a current picture of LTTR biology.
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Affiliation(s)
- S Mayo-Pérez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Y Gama-Martínez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - S Dávila
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - N Rivera
- IPN: CICATA, Unidad Morelos del Instituto Politécnico Nacional, Atlacholoaya, Mexico
| | - I Hernández-Lucas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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13
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Ikeda S, Tomita K, Nakagawa G, Kouzuma A, Watanabe K. Supplementation with Amino Acid Sources Facilitates Fermentative Growth of Shewanella oneidensis MR-1 in Defined Media. Appl Environ Microbiol 2023; 89:e0086823. [PMID: 37367298 PMCID: PMC10370299 DOI: 10.1128/aem.00868-23] [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: 05/23/2023] [Accepted: 06/04/2023] [Indexed: 06/28/2023] Open
Abstract
Shewanella oneidensis MR-1 is a facultative anaerobe that grows by respiration using a variety of electron acceptors. This organism serves as a model to study how bacteria thrive in redox-stratified environments. A glucose-utilizing engineered derivative of MR-1 has been reported to be unable to grow in glucose minimal medium (GMM) in the absence of electron acceptors, despite this strain having a complete set of genes for reconstructing glucose to lactate fermentative pathways. To gain insights into why MR-1 is incapable of fermentative growth, this study examined a hypothesis that this strain is programmed to repress the expression of some carbon metabolic genes in the absence of electron acceptors. Comparative transcriptomic analyses of the MR-1 derivative were conducted in the presence and absence of fumarate as an electron acceptor, and these found that the expression of many genes involved in carbon metabolism required for cell growth, including several tricarboxylic acid (TCA) cycle genes, was significantly downregulated in the absence of fumarate. This finding suggests a possibility that MR-1 is unable to grow fermentatively on glucose in minimal media owing to the shortage of nutrients essential for cell growth, such as amino acids. This idea was demonstrated in subsequent experiments that showed that the MR-1 derivative fermentatively grows in GMM containing tryptone or a defined mixture of amino acids. We suggest that gene regulatory circuits in MR-1 are tuned to minimize energy consumption under electron acceptor-depleted conditions, and that this results in defective fermentative growth in minimal media. IMPORTANCE It is an enigma why S. oneidensis MR-1 is incapable of fermentative growth despite having complete sets of genes for reconstructing fermentative pathways. Understanding the molecular mechanisms behind this defect will facilitate the development of novel fermentation technologies for the production of value-added chemicals from biomass feedstocks, such as electro-fermentation. The information provided in this study will also improve our understanding of the ecological strategies of bacteria living in redox-stratified environments.
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Affiliation(s)
- Sota Ikeda
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Keisuke Tomita
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Gen Nakagawa
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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14
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Yangyanqiu W, Jian C, Yuqing Y, Zhanbo Q, Shuwen H. Gut microbes involvement in gastrointestinal cancers through redox regulation. Gut Pathog 2023; 15:35. [PMID: 37443096 DOI: 10.1186/s13099-023-00562-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Gastrointestinal (GI) cancers are among the most common and lethal cancers worldwide. GI microbes play an important role in the occurrence and development of GI cancers. The common mechanisms by which GI microbes may lead to the occurrence and development of cancer include the instability of the microbial internal environment, secretion of cancer-related metabolites, and destabilization of the GI mucosal barrier. In recent years, many studies have found that the relationship between GI microbes and the development of cancer is closely associated with the GI redox level. Redox instability associated with GI microbes may induce oxidative stress, DNA damage, cumulative gene mutation, protein dysfunction and abnormal lipid metabolism in GI cells. Redox-related metabolites of GI microbes, such as short-chain fatty acids, hydrogen sulfide and nitric oxide, which are involved in cancer, may also influence GI redox levels. This paper reviews the redox reactions of GI cells regulated by microorganisms and their metabolites, as well as redox reactions in the cancer-related GI microbes themselves. This study provides a new perspective for the prevention and treatment of GI cancers.
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Affiliation(s)
- Wang Yangyanqiu
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China
- Graduate School of Medical College, Zhejiang University, No. 268 Kaixuan Road, Jianggan District, Hangzhou, 310029, Zhejiang Province, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, Republic of China
| | - Chu Jian
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China
- Zhejiang Chinese Medical University, No. 548 Binwen Road, Binjiang District, Hangzhou, 310053, Zhejiang Province, Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, Republic of China
| | - Yang Yuqing
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, Republic of China
| | - Qu Zhanbo
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China
- Zhejiang Chinese Medical University, No. 548 Binwen Road, Binjiang District, Hangzhou, 310053, Zhejiang Province, Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, Republic of China
| | - Han Shuwen
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, China.
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, No. 1558, Sanhuan North Road, Wuxing District, Huzhou, 313000, Zhejiang Province, Republic of China.
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15
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Fukuda D, Aso Y, Nolasco-Hipólito C. Genome and fermentation analyses of Enterococcus faecalis DB-5 isolated from Japanese Mandarin orange: An assessment of potential application in lactic acid production. J Biosci Bioeng 2023:S1389-1723(23)00114-7. [PMID: 37221113 DOI: 10.1016/j.jbiosc.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/02/2023] [Accepted: 04/16/2023] [Indexed: 05/25/2023]
Abstract
Enterococcus faecalis strain DB-5 is a lactic acid bacterium newly isolated from the Japanese mandarin orange (mikan). The DB-5 strain produces organic acid from various carbohydrate sources including glycerol and starch. To gain deeper insights into its potential application in lactic acid fermentation (LAF), the genome and fermentation analyses of E. faecalis DB-5 were performed. Whole genome sequencing was carried out using the DNBSEQ platform. After trimming and assembly, the total size of the assembled genome was revealed to be 3,048,630 bp, distributed into 63 contigs with an N50 value of 203,673. The genome has 37.2% GC content, 2928 coding DNA sequences, and 54 putative RNA genes. The DB-5 strain harbored two l-lactate dehydrogenases (L-LDHs), both of which conserved the catalytic domain sequences. The optical purity measurement showed that strain DB-5 is homofermentative and produced only l-lactic acid (LA), which correlated with genome-based pathway analysis. To confirm its LA productivity at high temperatures, open repeated batch fermentation was performed at 45 °C using sucrose as a carbon source. The volumetric LA productivity of DB-5 was averaged at 3.66 g L-1 h-1 for 24 h during the 3rd to 11th fermentation cycles. E. faecalis DB-5 could efficiently convert around 94% of sucrose to LA throughout the fermentation cycles at 45 °C. These genomic characteristics and fermentation properties of E. faecalis DB-5 provide beneficial information for a deeper understanding of the functional properties of future high-temperature LAFs from biomass resources.
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Affiliation(s)
- Daisuke Fukuda
- Medical Affairs and Development, GlaxoSmithKline K.K., 1-8-1 Akasaka, Minato-ku, Tokyo 107-0052, Japan.
| | - Yuji Aso
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hachigami-cho, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Cirilo Nolasco-Hipólito
- Centro de Investigaciones Científicas, Universidad Del Papaloapan Campus Tuxtepec, Circuito Central Nº 200, Col. Parque Industrial, C.P. 68301, Tuxtepec, Oaxaca, Mexico.
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16
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Edwards EH, Jelušić J, Kosko RM, McClelland KP, Ngarnim SS, Chiang W, Lampa-Pastirk S, Krauss TD, Bren KL. Shewanella oneidensis MR-1 respires CdSe quantum dots for photocatalytic hydrogen evolution. Proc Natl Acad Sci U S A 2023; 120:e2206975120. [PMID: 37068259 PMCID: PMC10151509 DOI: 10.1073/pnas.2206975120] [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: 04/21/2022] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Abstract
Living bio-nano systems for artificial photosynthesis are of growing interest. Typically, these systems use photoinduced charge transfer to provide electrons for microbial metabolic processes, yielding a biosynthetic solar fuel. Here, we demonstrate an entirely different approach to constructing a living bio-nano system, in which electrogenic bacteria respire semiconductor nanoparticles to support nanoparticle photocatalysis. Semiconductor nanocrystals are highly active and robust photocatalysts for hydrogen (H2) evolution, but their use is hindered by the oxidative side of the reaction. In this system, Shewanella oneidensis MR-1 provides electrons to a CdSe nanocrystalline photocatalyst, enabling visible light-driven H2 production. Unlike microbial electrolysis cells, this system requires no external potential. Illuminating this system at 530 nm yields continuous H2 generation for 168 h, which can be lengthened further by replenishing bacterial nutrients.
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Affiliation(s)
- Emily H. Edwards
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Jana Jelušić
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Ryan M. Kosko
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | | | - Soraya S. Ngarnim
- Department of Chemistry, University of Rochester, Rochester, NY14627
| | - Wesley Chiang
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY14627
| | | | - Todd D. Krauss
- Department of Chemistry, University of Rochester, Rochester, NY14627
- Department of Optics, University of Rochester, Rochester, NY14627
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, NY14627
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17
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Hu S, Ottemann KM. Helicobacter pylori initiates successful gastric colonization by utilizing L-lactate to promote complement resistance. Nat Commun 2023; 14:1695. [PMID: 36973281 PMCID: PMC10042806 DOI: 10.1038/s41467-023-37160-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
The complement system has long been appreciated for its role in bloodborne infections, but its activities in other places, including the gastrointestinal tract, remain elusive. Here, we report that complement restricts gastric infection by the pathogen Helicobacter pylori. This bacterium colonized complement-deficient mice to higher levels than wild-type counterparts, particularly in the gastric corpus region. H. pylori uses uptake of the host molecule L-lactate to create a complement-resistant state that relies on blocking the deposition of the active complement C4b component on H. pylori's surface. H. pylori mutants unable to achieve this complement-resistant state have a significant mouse colonization defect that is largely corrected by mutational removal of complement. This work highlights a previously unknown role for complement in the stomach, and has revealed an unrecognized mechanism for microbial-derived complement resistance.
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Affiliation(s)
- Shuai Hu
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
| | - Karen M Ottemann
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA.
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18
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Willemin MS, Hamelin R, Armand F, Holliger C, Maillard J. Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms. Front Microbiol 2023; 14:1058127. [PMID: 36733918 PMCID: PMC9888536 DOI: 10.3389/fmicb.2023.1058127] [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: 09/30/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023] Open
Abstract
Introduction Desulfitobacterium hafniense was isolated for its ability to use organohalogens as terminal electron acceptors via organohalide respiration (OHR). In contrast to obligate OHR bacteria, Desulfitobacterium spp. show a highly versatile energy metabolism with the capacity to use different electron donors and acceptors and to grow fermentatively. Desulfitobacterium genomes display numerous and apparently redundant members of redox enzyme families which confirm their metabolic potential. Nonetheless, the enzymes responsible for many metabolic traits are not yet identified. Methods In the present work, we conducted an extended proteomic study by comparing the proteomes of Desulfitobacterium hafniense strain DCB-2 cultivated in combinations of electron donors and acceptors, triggering five alternative respiratory metabolisms that include OHR, as well as fermentation. Tandem Mass Tag labelling proteomics allowed us to identify and quantify almost 60% of the predicted proteome of strain DCB-2 (2,796 proteins) in all six growth conditions. Raw data are available via ProteomeXchange with identifier PXD030393. Results and discussion This dataset was analyzed in order to highlight the proteins that were significantly up-regulated in one or a subset of growth conditions and to identify possible key players in the different energy metabolisms. The addition of sodium sulfide as reducing agent in the medium - a very widespread practice in the cultivation of strictly anaerobic bacteria - triggered the expression of the dissimilatory sulfite reduction pathway in relatively less favorable conditions such as fermentative growth on pyruvate, respiration with H2 as electron donor and OHR conditions. The presence of H2, CO2 and acetate in the medium induced several metabolic pathways involved in carbon metabolism including the Wood-Ljungdahl pathway and two pathways related to the fermentation of butyrate that rely on electron-bifurcating enzymes. While the predicted fumarate reductase appears to be constitutively expressed, a new lactate dehydrogenase and lactate transporters were identified. Finally, the OHR metabolism with 3-chloro-4-hydroxyphenylacetate as electron acceptor strongly induced proteins encoded in several reductive dehalogenase gene clusters, as well as four new proteins related to corrinoid metabolism. We believe that this extended proteomic database represents a new landmark in understanding the metabolic versatility of Desulfitobacterium spp. and provides a solid basis for addressing future research questions.
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Affiliation(s)
- Mathilde Stéphanie Willemin
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Romain Hamelin
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Armand
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland,*Correspondence: Julien Maillard, ✉
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19
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Zhang J, Wu D, Zhao Y, Liu D, Guo X, Chen Y, Zhang C, Sun X, Guo J, Yuan D, Xiao D, Li F, Song H. Engineering Shewanella oneidensis to efficiently harvest electricity power by co-utilizing glucose and lactate in thin stillage of liquor industry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:158696. [PMID: 36108833 DOI: 10.1016/j.scitotenv.2022.158696] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Thin stillage, rich in glucose and lactate, can seriously pollute water resources when directly discharged into the natural environment. Microbial fuel cells (MFC), as a green and sustainable technology, could utilize exoelectrogens to break down organics in wastewater and harvest electricity. Nevertheless, Shewanella oneidensis MR-1, cannot utilize thin stillage for efficient power generation. Here, to enable S. oneidensis to co-utilize glucose and lactate from thin stillage, an engineered S. oneidensis G7∆RSL1 was first created by constructing glucose metabolism pathway, promoting glucose and lactate co-utilization, and enhancing biofilm formation. Then, to enhance biofilm conductivity, we constructed a 3D self-assembled G7∆RSL1-rGO/CNT biohybrid with maximum power density of 560.4 mW m-2 and 373.7 mW m-2 in artificial and actual thin stillage, respectively, the highest among the reported genetically engineered S. oneidensis with thin stillage as carbon source. This study provides a new strategy to facilitate practical applications of MFC in wastewater remediation and efficient power recovery.
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Affiliation(s)
- Junqi Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, PR China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China; Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Yakun Zhao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Qingdao Institute of Ocean Engineering, Tianjin University, Qingdao 266200, Shandong, China
| | - Dingyuan Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, PR China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xuewu Guo
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Yefu Chen
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Cuiying Zhang
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Xi Sun
- College of Biological Engineering, Tianjin Agricultural University, Tianjin, PR China
| | - Ju Guo
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Dezhi Yuan
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Box 08, No. 29, 13ST. TEDA, Tianjin 300457, PR China
| | - Feng Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, PR China; Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Qingdao Institute of Ocean Engineering, Tianjin University, Qingdao 266200, Shandong, China.
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20
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Tseng YC, Xue C, Ng IS. Symbiosis culture of probiotic Escherichia coli Nissle 1917 and Lactobacillus rhamnosus GG using lactate utilization protein YkgG. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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21
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Bannikova S, Khlebodarova T, Vasilieva A, Mescheryakova I, Bryanskaya A, Shedko E, Popik V, Goryachkovskaya T, Peltek S. Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation. Int J Mol Sci 2022; 23:ijms232315216. [PMID: 36499542 PMCID: PMC9735757 DOI: 10.3390/ijms232315216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Studying the effects of terahertz (THz) radiation on the proteome of temperature-sensitive organisms is limited by a number of significant technical difficulties, one of which is maintaining an optimal temperature range to avoid thermal shock as much as possible. In the case of extremophilic species with an increased temperature tolerance, it is easier to isolate the effects of THz radiation directly. We studied the proteomic response to terahertz radiation of the thermophilic Geobacillus icigianus, persisting under wide temperature fluctuations with a 60 °C optimum. The experiments were performed with a terahertz free-electron laser (FEL) from the Siberian Center for Synchrotron and Terahertz Radiation, designed and employed by the Institute of Nuclear Physics of the SB of the RAS. A G. icigianus culture in LB medium was THz-irradiated for 15 min with 0.23 W/cm2 and 130 μm, using a specially designed cuvette. The life cycle of this bacterium proceeds under conditions of wide temperature and osmotic fluctuations, which makes its enzyme systems stress-resistant. The expression of several proteins was shown to change immediately after fifteen minutes of irradiation and after ten minutes of incubation at the end of exposure. The metabolic systems of electron transport, regulation of transcription and translation, cell growth and chemotaxis, synthesis of peptidoglycan, riboflavin, NADH, FAD and pyridoxal phosphate cofactors, Krebs cycle, ATP synthesis, chaperone and protease activity, and DNA repair, including methylated DNA, take part in the fast response to THz radiation. When the response developed after incubation, the systems of the cell's anti-stress defense, chemotaxis, and, partially, cell growth were restored, but the respiration and energy metabolism, biosynthesis of riboflavin, cofactors, peptidoglycan, and translation system components remained affected and the amino acid metabolism system was involved.
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Affiliation(s)
- Svetlana Bannikova
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Correspondence:
| | - Tamara Khlebodarova
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Asya Vasilieva
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Irina Mescheryakova
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Alla Bryanskaya
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Elizaveta Shedko
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Vasily Popik
- Budker Institute of Nuclear Physics, Siberian Branch Russian Academy of Sciences (SB RAS), 11 Acad. Lavrentieva Pr., 630090 Novosibirsk, Russia
| | - Tatiana Goryachkovskaya
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Sergey Peltek
- Federal Research Center Institute of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
- Kurchatov Genomic Center of Cytology and Genetics (ICG), Siberian Branch of Russian Academy of Sciences (SB RAS), 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
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22
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Taylor SJ, Winter MG, Gillis CC, Silva LAD, Dobbins AL, Muramatsu MK, Jimenez AG, Chanin RB, Spiga L, Llano EM, Rojas VK, Kim J, Santos RL, Zhu W, Winter SE. Colonocyte-derived lactate promotes E. coli fitness in the context of inflammation-associated gut microbiota dysbiosis. MICROBIOME 2022; 10:200. [PMID: 36434690 PMCID: PMC9701030 DOI: 10.1186/s40168-022-01389-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/12/2022] [Indexed: 05/09/2023]
Abstract
BACKGROUND Intestinal inflammation disrupts the microbiota composition leading to an expansion of Enterobacteriaceae family members (dysbiosis). Associated with this shift in microbiota composition is a profound change in the metabolic landscape of the intestine. It is unclear how changes in metabolite availability during gut inflammation impact microbial and host physiology. RESULTS We investigated microbial and host lactate metabolism in murine models of infectious and non-infectious colitis. During inflammation-associated dysbiosis, lactate levels in the gut lumen increased. The disease-associated spike in lactate availability was significantly reduced in mice lacking the lactate dehydrogenase A subunit in intestinal epithelial cells. Commensal E. coli and pathogenic Salmonella, representative Enterobacteriaceae family members, utilized lactate via the respiratory L-lactate dehydrogenase LldD to increase fitness. Furthermore, mice lacking the lactate dehydrogenase A subunit in intestinal epithelial cells exhibited lower levels of inflammation in a model of non-infectious colitis. CONCLUSIONS The release of lactate by intestinal epithelial cells during gut inflammation impacts the metabolism of gut-associated microbial communities. These findings suggest that during intestinal inflammation and dysbiosis, changes in metabolite availability can perpetuate colitis-associated disturbances of microbiota composition. Video Abstract.
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Affiliation(s)
- Savannah J Taylor
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Present Address: Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Davis, CA, 95616, USA
| | - Caroline C Gillis
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Present Address: Novome Biotechnologies, South San Francisco, CA, 94080, USA
| | - Laice Alves da Silva
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270, Brazil
| | - Amanda L Dobbins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Matthew K Muramatsu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Present Address: Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Davis, CA, 95616, USA
| | - Angel G Jimenez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Present Address: Infectious Diseases, Genentech, South San Francisco, CA, 94080, USA
| | - Rachael B Chanin
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Present Address: Department of Medicine, Hematology, Blood and Marrow Transplantation, Stanford University, Stanford, CA, USA
| | - Luisella Spiga
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, USA
| | - Ernesto M Llano
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vivian K Rojas
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Present Address: Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Davis, CA, 95616, USA
| | - Jiwoong Kim
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Renato L Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270, Brazil
| | - Wenhan Zhu
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, USA
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Present Address: Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Davis, CA, 95616, USA.
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23
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Revealing the Characteristics of Glucose- and Lactate-Based Chain Elongation for Caproate Production by Caproicibacterium lactatifermentans through Transcriptomic, Bioenergetic, and Regulatory Analyses. mSystems 2022; 7:e0053422. [PMID: 36073803 PMCID: PMC9600882 DOI: 10.1128/msystems.00534-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Caproate, an important medium-chain fatty acid, can only be synthesized by limited bacterial species by using ethanol, lactate, or certain saccharides. Caproicibacterium lactatifermentans is a promising caproate producer due to its glucose and lactate utilization capabilities. However, the global cellular responses of this bacterium to different carbon sources were not well understood. Here, C. lactatifermentans showed robust growth on glucose but more active caproate synthesis on lactate. Comparative transcriptome revealed that the genes involved in reverse β-oxidation for caproate synthesis and V-type ATPase-dependent ATP generation were upregulated under lactate condition, while several genes responsible for biomass synthesis were upregulated under glucose condition. Based on metabolic pathway reconstructions and bioenergetics analysis, the biomass accumulation on glucose condition may be supported by sufficient supplies of ATP and metabolite intermediates via glycolysis. In contrast, the ATP yield per glucose equivalent from lactate conversion into caproate was only 20% of that from glucose. Thus, the upregulation of the reverse β-oxidation genes may be essential for cell survival under lactate conditions. Furthermore, the remarkably decreased lactate utilization was observed after glucose acclimatization, indicating the negative modulation of lactate utilization by glucose metabolism. Based on the cotranscription of the lactate utilization repressor gene lldR with sugar-specific PTS genes and the opposite expression patterns of lldR and lactate utilization genes, a novel regulatory mechanism of glucose-repressed lactate utilization mediated via lldR was proposed. The results of this study suggested the molecular mechanism underlying differential physiologic and metabolic characteristics of C. lactatifermentans grown on glucose and lactate. IMPORTANCE Caproicibacterium lactatifermentans is a unique and robust caproate-producing bacterium in the family Oscillospiraceae due to its lactate utilization capability, whereas its close relatives such as Caproicibacterium amylolyticum, Caproiciproducens galactitolivorans, and Caproicibacter fermentans cannot utilize lactate but produce lactate as the main fermentation end product. Moreover, C. lactatifermentans can also utilize several saccharides such as glucose and maltose. Although the metabolic versatility of the bacterium makes it to be a promising industrial caproate producer, the cellular responses of C. lactatifermentans to different carbon sources were unknown. Here, the molecular mechanisms of biomass synthesis supported by glucose utilization and the cell survival supported by lactate utilization were revealed. A novel insight into the regulatory machinery in which glucose negatively regulates lactate utilization was proposed. This study provides a valuable basis to control and optimize caproate production, which will contribute to achieving a circular economy and environmental sustainability.
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24
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Ford K, Kaste JAM, Shachar-Hill Y, TerAvest MA. Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a Conditionally Essential Gene in Shewanella oneidensis MR-1. ACS Synth Biol 2022; 11:3405-3413. [PMID: 36219726 PMCID: PMC9595118 DOI: 10.1021/acssynbio.2c00323] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Indexed: 01/24/2023]
Abstract
Carbon-neutral production of valuable bioproducts is critical to sustainable development but remains limited by the slow engineering of photosynthetic organisms. Improving existing synthetic biology tools to engineer model organisms to fix carbon dioxide is one route to overcoming the limitations of photosynthetic organisms. In this work, we describe a pipeline that enabled the deletion of a conditionally essential gene from the Shewanella oneidensis MR-1 genome. S. oneidensis is a simple bacterial host that could be used for electricity-driven conversion of carbon dioxide in the future with further genetic engineering. We used Flux Balance Analysis (FBA) to model carbon and energy flows in central metabolism and assess the effects of single and double gene deletions. We modeled the growth of deletion strains under several alternative conditions to identify substrates that restore viability to an otherwise lethal gene knockout. These predictions were tested in vivo using a Mobile-CRISPRi gene knockdown system. The information learned from FBA and knockdown experiments informed our strategy for gene deletion, allowing us to successfully delete an "expected essential" gene, gpmA. FBA predicted, knockdown experiments supported, and deletion confirmed that the "essential" gene gpmA is not needed for survival, dependent on the medium used. Removal of gpmA is a first step toward driving electrode-powered CO2 fixation via RuBisCO. This work demonstrates the potential for broadening the scope of genetic engineering in S. oneidensis as a synthetic biology chassis. By combining computational analysis with a CRISPRi knockdown system in this way, one can systematically assess the impact of conditionally essential genes and use this knowledge to generate mutations previously thought unachievable.
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Affiliation(s)
- Kathryne
C. Ford
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
- Department
of Microbiology and Molecular Genetics, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Joshua A. M. Kaste
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
- Department
of Plant Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yair Shachar-Hill
- Department
of Plant Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Michaela A. TerAvest
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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25
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Cao FT, Ma XL, Zhou XT, Han JC, Xiao X. Performance and mechanisms exploration of nano zinc oxide (nZnO) on anaerobic decolorization by Shewanella oneidensis MR-1. CHEMOSPHERE 2022; 305:135510. [PMID: 35772516 DOI: 10.1016/j.chemosphere.2022.135510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
Although the ecological safety of nanomaterials is of widespread concern, their current ambient concentrations are not yet sufficient to cause serious toxic effects. Thus, the nontoxic bioimpact of nanomaterials in wastewater treatment has attracted increasing attention. In this study, the effect of nano zinc oxide (nZnO), one of the most widely used nanomaterials, on the anaerobic biodegradation of methyl orange (MO) by Shewanella oneidensis MR-1 was comprehensively investigated. High-dosage nZnO (>0.5 mg/L) caused severe toxic stress on S. oneidensis MR-1, resulting in the decrease in decolorization efficiency. However, nZnO at ambient concentrations could act as nanostimulants and promote the anaerobic removal of MO by S. oneidensis MR-1, which should be attributed to the improvement of decolorization efficiency rather than cell proliferation. The dissolved Zn2+ was found to contribute to the bioeffect of nZnO on MO decolorization. Further investigation revealed that low-dosage nZnO could promote the cell viability, membrane permeability, anaerobic metabolism, as well as related gene expression, indicating that nZnO facilitated rather than inhibited the anaerobic wastewater treatment under ambient conditions. Thus, this work provides a new insight into the bioeffect of nZnO in actual environment and facilitates the practical application of nanomaterials as nanostimulants in biological process.
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Affiliation(s)
- Feng-Ting Cao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China
| | - Xiao-Lin Ma
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiang-Tong Zhou
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Jun-Cheng Han
- Department of Civil and Environmental Engineering, School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211, China
| | - Xiang Xiao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
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26
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Suarez C, Dalcin Martins P, Jetten MS, Karačić S, Wilén BM, Modin O, Hagelia P, Hermansson M, Persson F. Metagenomic evidence of a novel family of anammox bacteria in a subsea environment. Environ Microbiol 2022; 24:2348-2360. [PMID: 35415863 PMCID: PMC9325076 DOI: 10.1111/1462-2920.16006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/07/2022] [Indexed: 12/02/2022]
Abstract
Bacteria in the order 'Candidatus Brocadiales' within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome-assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK-like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss.
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Affiliation(s)
- Carolina Suarez
- Division of Water Resources Engineering, Faculty of Engineering LTHLund UniversityLundSweden
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Paula Dalcin Martins
- Department of Microbiology, RIBES, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Mike S.M. Jetten
- Department of Microbiology, RIBES, Radboud Institute for Biological and Environmental SciencesRadboud UniversityNijmegenThe Netherlands
| | - Sabina Karačić
- Division of Water Environment Technology, Department of Architecture and Civil EngineeringChalmers University of TechnologyGothenburgSweden
| | - Britt Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil EngineeringChalmers University of TechnologyGothenburgSweden
| | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil EngineeringChalmers University of TechnologyGothenburgSweden
| | - Per Hagelia
- Construction DivisionThe Norwegian Public Roads AdministrationOsloNorway
| | - Malte Hermansson
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil EngineeringChalmers University of TechnologyGothenburgSweden
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27
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Han HX, Tian LJ, Liu DF, Yu HQ, Sheng GP, Xiong Y. Reversing Electron Transfer Chain for Light-Driven Hydrogen Production in Biotic-Abiotic Hybrid Systems. J Am Chem Soc 2022; 144:6434-6441. [PMID: 35377628 DOI: 10.1021/jacs.2c00934] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biotic-abiotic photosynthetic system integrating inorganic light absorbers with whole-cell biocatalysts innovates the way for sustainable solar-driven chemical transformation. Fundamentally, the electron transfer at the biotic-abiotic interface, which may induce biological response to photoexcited electron stimuli, plays an essential role in solar energy conversion. Herein, we selected an electro-active bacterium Shewanella oneidensis MR-1 as a model, which constitutes a hybrid photosynthetic system with a self-assembled CdS semiconductor, to demonstrate unique biotic-abiotic interfacial behavior. The photoexcited electrons from CdS nanoparticles can reverse the extracellular electron transfer (EET) chain within S. oneidensis MR-1, realizing the activation of a bacterial catalytic network with light illumination. As compared with bare S. oneidensis MR-1, a significant upregulation of hydrogen yield (711-fold), ATP, and reducing equivalent (NADH/NAD+) was achieved in the S. oneidensis MR-1-CdS under visible light. This work sheds light on the fundamental mechanism and provides design guidelines for biotic-abiotic photosynthetic systems.
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Affiliation(s)
- He-Xing Han
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Li-Jiao Tian
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Guo-Ping Sheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yujie Xiong
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
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28
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Solchaga JI, Busalmen JP, Nercessian D. Unraveling Anaerobic Metabolisms in a Hypersaline Sediment. Front Microbiol 2022; 13:811432. [PMID: 35369499 PMCID: PMC8966722 DOI: 10.3389/fmicb.2022.811432] [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: 11/08/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The knowledge on the microbial diversity inhabiting hypersaline sediments is still limited. In particular, existing data about anaerobic hypersaline archaea and bacteria are scarce and refer to a limited number of genera. The approach to obtain existing information has been almost exclusively attempting to grow every organism in axenic culture on the selected electron acceptor with a variety of electron donors. Here, a different approach has been used to interrogate the microbial community of submerged hypersaline sediment of Salitral Negro, Argentina, aiming at enriching consortia performing anaerobic respiration of different electron acceptor compounds, in which ecological associations can maximize the possibilities of successful growth. Growth of consortia was demonstrated on all offered electron acceptors, including fumarate, nitrate, sulfate, thiosulfate, dimethyl sulfoxide, and a polarized electrode. Halorubrum and Haloarcula representatives are here shown for the first time growing on lactate, using fumarate or a polarized electrode as the electron acceptor; in addition, they are shown also growing in sulfate-reducing consortia. Halorubrum representatives are for the first time shown to be growing in nitrate-reducing consortia, probably thanks to reduction of N2O produced by other consortium members. Fumarate respiration is indeed shown for the first time supporting growth of Halanaeroarchaeum and Halorhabdus belonging to the archaea, as well as growth of Halanaerobium, Halanaerobaculum, Sporohalobacter, and Acetohalobium belonging to the bacteria. Finally, evidence is presented suggesting growth of nanohaloarchaea in anaerobic conditions.
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Affiliation(s)
- Juan Ignacio Solchaga
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
| | - Juan Pablo Busalmen
- Laboratorio de Bioelectroquímica, INTEMA - CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
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29
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Investigation and Alteration of Organic Acid Synthesis Pathways in the Mammalian Gut Symbiont Bacteroides thetaiotaomicron. Microbiol Spectr 2022; 10:e0231221. [PMID: 35196806 PMCID: PMC8865466 DOI: 10.1128/spectrum.02312-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Members of the gut-dwelling Bacteroides genus have remarkable abilities in degrading a diverse set of fiber polysaccharide structures, most of which are found in the mammalian diet. As part of their metabolism, they convert these fibers to organic acids that can in turn provide energy to their host. While many studies have identified and characterized the genes and corresponding proteins involved in polysaccharide degradation, relatively little is known about Bacteroides genes involved in downstream metabolic pathways. Bacteroides thetaiotaomicron is one of the most studied species from the genus and is representative of this group in producing multiple organic acids as part of its metabolism. We focused here on several organic acid synthesis pathways in B. thetaiotaomicron, including those involved in formate, lactate, propionate, and acetate production. We identified potential genes involved in each pathway and characterized these through gene deletions coupled to growth assays and organic acid quantification. In addition, we developed and employed a Golden Gate-compatible plasmid system to simplify alteration of native gene expression levels. Our work both validates and contradicts previous bioinformatic gene annotations, and we develop a model on which to base future efforts. A clearer understanding of Bacteroides metabolic pathways can inform and facilitate efforts to employ these bacteria for improved human health or other utilization strategies. IMPORTANCE Both humans and animals host a large community of bacteria and other microorganisms in their gastrointestinal tracts. This community breaks down dietary fiber and produces organic acids that are used as an energy source by the body and can also help the host resist infection by various pathogens. While the Bacteroides genus is one of the most common in the gut microbiota, it is only distantly related to bacteria with well-characterized metabolic pathways and it is therefore unclear whether research insights on organic acid production in those species can also be directly applied to the Bacteroides. By investigating multiple genetic pathways for organic acid production in Bacteroides thetaiotaomicron, we provide a basis for deeper understanding of these pathways. The work further enables greater understanding of Bacteroides–host relationships, as well as inter-species relationships in the microbiota, which are of importance for both human and animal gut health.
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30
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Thakur N, Sharma AN, Hade MD, Chhaya A, Kumar A, Jolly RS, Dikshit KL. New Insights Into the Function of Flavohemoglobin in Mycobacterium tuberculosis: Role as a NADPH-Dependent Disulfide Reductase and D-Lactate-Dependent Mycothione Reductase. Front Cell Infect Microbiol 2022; 11:796727. [PMID: 35237528 PMCID: PMC8883573 DOI: 10.3389/fcimb.2021.796727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) produces an unconventional flavohemoglobin (MtbFHb) that carries a FAD-binding site similar to D-lactate dehydrogenases (D-LDH) and oxidizes D-lactate into pyruvate. The molecular mechanism by which MtbFHb functions in Mtb remains unknown. We discovered that the D-LDH-type FAD-binding site in MtbFHb overlaps with another FAD-binding motif similar to thioredoxin reductases and reduces DTNB in the presence of NADPH similar to trxB of Mtb. These results suggested that MtbFHb is functioning as a disulfide oxidoreductase. Interestingly, D-lactate created a conformational change in MtbFHb and attenuated its ability to oxidize NADPH. Mass spectroscopy demonstrated that MtbFHb reduces des-myo-inositol mycothiol in the presence of D-lactate unlike NADPH, indicating that D-lactate changes the specificity of MtbFHb from di-thiol to di-mycothiol. When M. smegmatis carrying deletion in the fhbII gene (encoding a homolog of MtbFHb) was complemented with the fhb gene of Mtb, it exhibited four- to fivefold reductions in lipid peroxidation and significant enhancement in the cell survival under oxidative stress. These results were corroborated by reduced lipid peroxidation and enhanced cell survival of wild-type M. smegmatis after overexpression of the fhb gene of Mtb. Since D-lactate is a by-product of lipid peroxidation and MtbFHb is a membrane-associated protein, D-lactate-mediated reduction of mycothiol disulfide by MtbFHb may uniquely equip Mtb to relieve the toxicity of D-lactate accumulation and protect the cell from oxidative damage, simultaneously balancing the redox environment under oxidative stress that may be vital for the pathogenesis of Mtb.
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Affiliation(s)
- Naveen Thakur
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | | | - Ajay Chhaya
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Ashwani Kumar
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Kanak L. Dikshit
- CSIR-Institute of Microbial Technology, Chandigarh, India
- Department of Biotechnology, Panjab University, Chandigarh, India
- *Correspondence: Kanak L. Dikshit,
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31
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Augustiniene E, Malys N. Identification and characterization of L- and D-lactate-inducible systems from Escherichia coli MG1655, Cupriavidus necator H16 and Pseudomonas species. Sci Rep 2022; 12:2123. [PMID: 35136142 PMCID: PMC8827060 DOI: 10.1038/s41598-022-06028-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/17/2022] [Indexed: 12/22/2022] Open
Abstract
Lactic acid is an important platform chemical used for the production of various compounds including polylactic acid (PLA). Optically pure L- and D-lactic acids are required to obtain high quality PLA. To advance the development and selection of microbial strains for improved production of lactic acid enantiomers, a high-throughput screening, dynamic pathway control, or real-time monitoring are often applied. Inducible gene expression systems and their application in the genetically encoded biosensors contribute to the development of these techniques and are important devices for the advancement of lactic acid biotechnology. Here, we identify and characterize eleven lactate-inducible systems from Escherichia coli, Cupriavidus necator, and Pseudomonas spp. The specificity and dynamics of these systems in response to L- and D-lactate, or structurally similar compounds are investigated. We demonstrate that the inducible systems EcLldR/PlldP and CnGntR/PH16_RS19190 respond only to the L-lactate, exhibiting approximately 19- and 24-fold induction, respectively. Despite neither of the examined bacteria possess the D-lactate-specific inducible system, the PaPdhR/PlldP and PfPdhR/PlldP are induced approximately 37- and 366-fold, respectively, by D-lactate and can be used for developing biosensor with improved specificity. The findings of this study provide an insight into understanding of L- and D-lactate-inducible systems that can be employed as sensing and tuneable devices in synthetic biology.
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Affiliation(s)
- Ernesta Augustiniene
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas, LT-50254, Lithuania
| | - Naglis Malys
- Bioprocess Research Centre, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas, LT-50254, Lithuania. .,Department of Organic Chemistry, Faculty of Chemical Technology, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas, LT-50254, Lithuania.
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32
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Sheridan PO, Louis P, Tsompanidou E, Shaw S, Harmsen HJ, Duncan SH, Flint HJ, Walker AW. Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria. Microb Genom 2022; 8. [PMID: 35077342 PMCID: PMC8914356 DOI: 10.1099/mgen.0.000739] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lactate accumulation in the human gut is linked to a range of deleterious health impacts. However, lactate is consumed and converted to the beneficial short-chain fatty acids butyrate and propionate by indigenous lactate-utilizing bacteria. To better understand the underlying genetic basis for lactate utilization, transcriptomic analyses were performed for two prominent lactate-utilizing species from the human gut, Anaerobutyricum soehngenii and Coprococcus catus, during growth on lactate, hexose sugar or hexose plus lactate. In A. soehngenii L2-7 six genes of the lactate utilization (lct) cluster, including NAD-independent d-lactate dehydrogenase (d-iLDH), were co-ordinately upregulated during growth on equimolar d- and l-lactate (dl-lactate). Upregulated genes included an acyl-CoA dehydrogenase related to butyryl-CoA dehydrogenase, which may play a role in transferring reducing equivalents between reduction of crotonyl-CoA and oxidation of lactate. Genes upregulated in C. catus GD/7 included a six-gene cluster (lap) encoding propionyl CoA-transferase, a putative lactoyl-CoA epimerase, lactoyl-CoA dehydratase and lactate permease, and two unlinked acyl-CoA dehydrogenase genes that are candidates for acryloyl-CoA reductase. A d-iLDH homologue in C. catus is encoded by a separate, partial lct, gene cluster, but not upregulated on lactate. While C. catus converts three mols of dl-lactate via the acrylate pathway to two mols propionate and one mol acetate, some of the acetate can be re-used with additional lactate to produce butyrate. A key regulatory difference is that while glucose partially repressed lct cluster expression in A. soehngenii, there was no repression of lactate-utilization genes by fructose in the non-glucose utilizer C. catus. This suggests that these species could occupy different ecological niches for lactate utilization in the gut, which may be important factors to consider when developing lactate-utilizing bacteria as novel candidate probiotics.
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Affiliation(s)
- Paul O Sheridan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Petra Louis
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Eleni Tsompanidou
- Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Sophie Shaw
- Centre for Genome-Enabled Biology and Medicine, 23 St. Machar Drive, AB24 3RY Aberdeen, UK
| | - Hermie J Harmsen
- Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Sylvia H Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Harry J Flint
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Alan W Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
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33
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Ding DW, Sun X. Relating Translation Efficiency to Protein Networks Provides Evolutionary Insights in Shewanella and Its Implications for Extracellular Electron Transfer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:605-613. [PMID: 32750850 DOI: 10.1109/tcbb.2020.2996295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Shewanella species are well-known for their extracellular electron transfer (EET) capacity, by which these microorganisms can transfer the electrons from intracellular environment to extracellular space for the reduction of the extracellular insoluble electron acceptors. Using a time-stamped data for the paired protein-mRNA, we investigate the impact of differential translation on the EET process of Shewanella oneidensis MR-1. Firstly, differentially translated proteins when O2 levels are switched from high-O2 to low-O2 are identified by using a soft clustering method, 629 up-regulated translated proteins and 767 down-regulated translated proteins are considered to reflect the changes from inactivated to activated EET process. Then, we showed that the degrees of connectivity of differentially translated proteins were significantly larger than those of non-differentially translated proteins, and thereby these differentially translated proteins will be more important in the protein networks. After that, we networked these differentially translated proteins to construct the differentially translated sub-networks, and discussed the most important proteins that are involved in the EET process with the help of centralization analysis of these differentially translated networks. Furthermore, we also studied the differentially translated operonic genes. Taking together, this work searches the key proteins that potentially activated the EET process from a translational efficiency viewpoint.
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34
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Genomic Insights into the Ecological Role and Evolution of a Novel Thermoplasmata Order, " Candidatus Sysuiplasmatales". Appl Environ Microbiol 2021; 87:e0106521. [PMID: 34524897 DOI: 10.1128/aem.01065-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent omics studies have provided invaluable insights into the metabolic potential, adaptation, and evolution of novel archaeal lineages from a variety of extreme environments. We utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order ("Candidatus Sysuiplasmatales") in the class Thermoplasmata from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene-based analyses revealed a narrow habitat range for these uncultured archaea limited to AMD and hot spring-related environments. Metabolic reconstruction indicated a facultatively anaerobic heterotrophic lifestyle. This may allow the archaea to adapt to oxygen fluctuations and is thus in marked contrast to the majority of lineages in the domain Archaea, which typically show obligately anaerobic metabolisms. Notably, "Ca. Sysuiplasmatales" could conserve energy through degradation of fatty acids, amino acid metabolism, and oxidation of reduced inorganic sulfur compounds (RISCs), suggesting that they may contribute to acid generation in the extreme mine environments. Unlike the closely related orders Methanomassiliicoccales and "Candidatus Gimiplasmatales," "Ca. Sysuiplasmatales" lacks the capacity to perform methanogenesis and carbon fixation. Ancestral state reconstruction indicated that "Ca. Sysuiplasmatales," the closely related orders Methanomassiliicoccales and "Ca. Gimiplasmatales," and the orders SG8-5 and RBG-16-68-12 originated from a facultatively anaerobic ancestor capable of carbon fixation via the bacterial-type H4F Wood-Ljungdahl pathway (WLP). Their metabolic divergence might be attributed to different evolutionary paths. IMPORTANCE A wide array of archaea populate Earth's extreme environments; therefore, they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited, since the majority of the archaeal diversity is uncultured. For instance, most order-level lineages except Thermoplasmatales, Aciduliprofundales, and Methanomassiliicoccales within Thermoplasmata do not have cultured representatives. Here, we report the discovery and genomic characterization of a novel order, "Ca. Sysuiplasmatales," within Thermoplasmata in extremely acidic mine environments. "Ca. Sysuiplasmatales" are inferred to be facultatively anaerobic heterotrophs and likely contribute to acid generation through the oxidation of RISCs. The physiological divergence between "Ca. Sysuiplasmatales" and closely related Thermoplasmata lineages may be attributed to different evolutionary paths. These results expand our knowledge of archaea in the extreme mine ecosystem.
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35
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Cao B, Zhao Z, Peng L, Shiu HY, Ding M, Song F, Guan X, Lee CK, Huang J, Zhu D, Fu X, Wong GCL, Liu C, Nealson K, Weiss PS, Duan X, Huang Y. Silver nanoparticles boost charge-extraction efficiency in Shewanella microbial fuel cells. Science 2021; 373:1336-1340. [PMID: 34529487 DOI: 10.1126/science.abf3427] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Bocheng Cao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zipeng Zhao
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lele Peng
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hui-Ying Shiu
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mengning Ding
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Frank Song
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xun Guan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Calvin K Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jin Huang
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dan Zhu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaoyang Fu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chong Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kenneth Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Paul S Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiangfeng Duan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yu Huang
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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36
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Detman A, Laubitz D, Chojnacka A, Kiela PR, Salamon A, Barberán A, Chen Y, Yang F, Błaszczyk MK, Sikora A. Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production. MICROBIOME 2021; 9:158. [PMID: 34261525 PMCID: PMC8281708 DOI: 10.1186/s40168-021-01105-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 05/28/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND This study focuses on the processes occurring during the acidogenic step of anaerobic digestion, especially resulting from nutritional interactions between dark fermentation (DF) bacteria and lactic acid bacteria (LAB). Previously, we have confirmed that DF microbial communities (MCs) that fed on molasses are able to convert lactate and acetate to butyrate. The aims of the study were to recognize the biodiversity of DF-MCs able and unable to convert lactate and acetate to butyrate and to define the conditions for the transformation. RESULTS MCs sampled from a DF bioreactor were grown anaerobically in mesophilic conditions on different media containing molasses or sucrose and/or lactate and acetate in five independent static batch experiments. The taxonomic composition (based on 16S_rRNA profiling) of each experimental MC was analysed in reference to its metabolites and pH of the digestive liquids. In the samples where the fermented media contained carbohydrates, the two main tendencies were observed: (i) a low pH (pH ≤ 4), lactate and ethanol as the main fermentation products, MCs dominated with Lactobacillus, Bifidobacterium, Leuconostoc and Fructobacillus was characterized by low biodiversity; (ii) pH in the range 5.0-6.0, butyrate dominated among the fermentation products, the MCs composed mainly of Clostridium (especially Clostridium_sensu_stricto_12), Lactobacillus, Bifidobacterium and Prevotella. The biodiversity increased with the ability to convert acetate and lactate to butyrate. The MC processing exclusively lactate and acetate showed the highest biodiversity and was dominated by Clostridium (especially Clostridium_sensu_stricto_12). LAB were reduced; other genera such as Terrisporobacter, Lachnoclostridium, Paraclostridium or Sutterella were found. Butyrate was the main metabolite and pH was 7. Shotgun metagenomic analysis of the selected butyrate-producing MCs independently on the substrate revealed C.tyrobutyricum as the dominant Clostridium species. Functional analysis confirmed the presence of genes encoding key enzymes of the fermentation routes. CONCLUSIONS Batch tests revealed the dynamics of metabolic activity and composition of DF-MCs dependent on fermentation conditions. The balance between LAB and the butyrate producers and the pH values were shown to be the most relevant for the process of lactate and acetate conversion to butyrate. To close the knowledge gaps is to find signalling factors responsible for the metabolic shift of the DF-MCs towards lactate fermentation. Video Abstract.
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Affiliation(s)
- Anna Detman
- Institute of Biochemistry and Biophysics – Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Daniel Laubitz
- Department of Pediatrics at Steel Children’s Research Center College of Medicine, University of Arizona, 1501 N. Campbell Avenue, Room 3301, PO Box 245073, Tucson, Arizona 85724-5073 USA
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics – Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
- Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Pawel R. Kiela
- Department of Pediatrics at Steel Children’s Research Center College of Medicine, University of Arizona, 1501 N. Campbell Avenue, Room 3301, PO Box 245073, Tucson, Arizona 85724-5073 USA
| | - Agnieszka Salamon
- Institute of Agricultural and Food Biotechnology, Rakowiecka 36, 02-532 Warsaw, Poland
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, 1177 E. 4th Street, P.O. Box 210038, Tucson, Arizona 85721-0038 USA
| | - Yongjian Chen
- Department of Environmental Science, University of Arizona, 1177 E. 4th Street, P.O. Box 210038, Tucson, Arizona 85721-0038 USA
| | - Fei Yang
- Department of Environmental Science, University of Arizona, 1177 E. 4th Street, P.O. Box 210038, Tucson, Arizona 85721-0038 USA
| | - Mieczysław K. Błaszczyk
- Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Anna Sikora
- Institute of Biochemistry and Biophysics – Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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37
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Rodionov DA, Rodionova IA, Rodionov VA, Arzamasov AA, Zhang K, Rubinstein GM, Tanwee TNN, Bing RG, Crosby JR, Nookaew I, Basen M, Brown SD, Wilson CM, Klingeman DM, Poole FL, Zhang Y, Kelly RM, Adams MWW. Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii. mSystems 2021; 6:e0134520. [PMID: 34060910 PMCID: PMC8579813 DOI: 10.1128/msystems.01345-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/04/2021] [Indexed: 11/20/2022] Open
Abstract
Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade polysaccharide components of plant cell walls and subsequently utilize the constituting mono- and oligosaccharides. Through metabolic engineering, ethanol and other industrially important end products can be produced. Previous experimental studies identified a variety of carbohydrate-active enzymes in model species Caldicellulosiruptor saccharolyticus and Caldicellulosiruptor bescii, while prior transcriptomic experiments identified their putative carbohydrate uptake transporters. We investigated the mechanisms of transcriptional regulation of carbohydrate utilization genes using a comparative genomics approach applied to 14 Caldicellulosiruptor species. The reconstruction of carbohydrate utilization regulatory network includes the predicted binding sites for 34 mostly local regulators and point to the regulatory mechanisms controlling expression of genes involved in degradation of plant biomass. The Rex and CggR regulons control the central glycolytic and primary redox reactions. The identified transcription factor binding sites and regulons were validated with transcriptomic and transcription start site experimental data for C. bescii grown on cellulose, cellobiose, glucose, xylan, and xylose. The XylR and XynR regulons control xylan-induced transcriptional response of genes involved in degradation of xylan and xylose utilization. The reconstructed regulons informed the carbohydrate utilization reconstruction analysis and improved functional annotations of 51 transporters and 11 catabolic enzymes. Using gene deletion, we confirmed that the shared ATPase component MsmK is essential for growth on oligo- and polysaccharides but not for the utilization of monosaccharides. By elucidating the carbohydrate utilization framework in C. bescii, strategies for metabolic engineering can be pursued to optimize yields of bio-based fuels and chemicals from lignocellulose. IMPORTANCE To develop functional metabolic engineering platforms for nonmodel microorganisms, a comprehensive understanding of the physiological and metabolic characteristics is critical. Caldicellulosiruptor bescii and other species in this genus have untapped potential for conversion of unpretreated plant biomass into industrial fuels and chemicals. The highly interactive and complex machinery used by C. bescii to acquire and process complex carbohydrates contained in lignocellulose was elucidated here to complement related efforts to develop a metabolic engineering platform with this bacterium. Guided by the findings here, a clearer picture of how C. bescii natively drives carbohydrate utilization is provided and strategies to engineer this bacterium for optimal conversion of lignocellulose to commercial products emerge.
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Affiliation(s)
- Dmitry A. Rodionov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Irina A. Rodionova
- Department of Bioengineering, University of California—San Diego, La Jolla, California, USA
| | - Vladimir A. Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandr A. Arzamasov
- Sanford-Burnhams-Prebys Medical Discovery Institute, La Jolla, California, USA
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Ke Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Gabriel M. Rubinstein
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Tania N. N. Tanwee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - James R. Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mirko Basen
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Biowissenschaften, Mikrobiologie, Universität Rostock, Rostock, Germany
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Charlotte M. Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- University of Otago, Dunedin, New Zealand
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Farris L. Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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Dank A, van Mastrigt O, Boeren S, Lillevang SK, Abee T, Smid EJ. Propionibacterium freudenreichii thrives in microaerobic conditions by complete oxidation of lactate to CO 2. Environ Microbiol 2021; 23:3116-3129. [PMID: 33955639 PMCID: PMC8360058 DOI: 10.1111/1462-2920.15532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 04/13/2021] [Indexed: 11/28/2022]
Abstract
In this study we show increased biomass formation for four species of food-grade propionic acid bacteria (Acidipropionibacterium acidipropionici, Acidipropionibacterium jensenii, Acidipropionibacterium thoenii and Propionibacterium freudenreichii) when exposed to oxygen, implicating functional respiratory systems. Using an optimal microaerobic condition, P. freudenreichii DSM 20271 consumed lactate to produce propionate and acetate initially. When lactate was depleted propionate was oxidized to acetate. We propose to name the switch from propionate production to consumption in microaerobic conditions the 'propionate switch'. When propionate was depleted the 'acetate switch' occurred, resulting in complete consumption of acetate. Both growth rate on lactate (0.100 versus 0.078 h-1 ) and biomass yield (20.5 versus 8.6 g* mol-1 lactate) increased compared to anaerobic conditions. Proteome analysis revealed that the abundance of proteins involved in the aerobic and anaerobic electron transport chains and major metabolic pathways did not significantly differ between anaerobic and microaerobic conditions. This implicates that P. freudenreichii is prepared for utilizing O2 when it comes available in anaerobic conditions. The ecological niche of propionic acid bacteria can conceivably be extended to environments with oxygen gradients from oxic to anoxic, so-called microoxic environments, as found in the rumen, gut and soils, where they can thrive by utilizing low concentrations of oxygen.
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Affiliation(s)
- Alexander Dank
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
| | - Oscar van Mastrigt
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
| | - Sjef Boeren
- Laboratory of BiochemistryWageningen University & ResearchWageningenThe Netherlands
| | - Søren K. Lillevang
- Arla Innovation Centre, Arla Foods, Agro Food Park 19Aarhus N8200Denmark
| | - Tjakko Abee
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
| | - Eddy J. Smid
- Laboratory of Food MicrobiologyWageningen University & Research, P.O. Box 17Wageningen6700AAThe Netherlands
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Kouzuma A. Molecular mechanisms regulating the catabolic and electrochemical activities of Shewanella oneidensis MR-1. Biosci Biotechnol Biochem 2021; 85:1572-1581. [PMID: 33998649 DOI: 10.1093/bbb/zbab088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/17/2021] [Indexed: 11/14/2022]
Abstract
Electrochemically active bacteria (EAB) interact electrochemically with electrodes via extracellular electron transfer (EET) pathways. These bacteria have attracted significant attention due to their utility in environmental-friendly bioelectrochemical systems (BESs), including microbial fuel cells and electrofermentation systems. The electrochemical activity of EAB is dependent on their carbon catabolism and respiration; thus, understanding how these processes are regulated will provide insights into the development of a more efficient BES. The process of biofilm formation by EAB on BES electrodes is also important for electric current generation because it facilitates physical and electrochemical interactions between EAB cells and electrodes. This article summarizes the current knowledge on EET-related metabolic and cellular functions of a model EAB, Shewanella oneidensis MR-1, focusing specifically on regulatory systems for carbon catabolism, EET pathways, and biofilm formation. Based on recent developments, the author also discusses potential uses of engineered S. oneidensis strains for various biotechnological applications.
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Affiliation(s)
- Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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Novel Mode Engineering for β-Alanine Production in Escherichia coli with the Guide of Adaptive Laboratory Evolution. Microorganisms 2021; 9:microorganisms9030600. [PMID: 33803992 PMCID: PMC8000549 DOI: 10.3390/microorganisms9030600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 01/03/2023] Open
Abstract
The strategy of anaerobic biosynthesis of β-alanine by Escherichia coli (E. coli) has been reported. However, the low energy production under anaerobic condition limited cell growth and then affected the production efficiency of β-alanine. Here, the adaptive laboratory evolution was carried out to improve energy production of E. coli lacking phosphoenolpyruvate carboxylase under anaerobic condition. Five mutants were isolated and analyzed. Sequence analysis showed that most of the consistent genetic mutations among the mutants were related with pyruvate accumulation, indicating that pyruvate accumulation enabled the growth of the lethal parent. It is possible that the accumulated pyruvate provides sufficient precursors for energy generation and CO2 fixing reaction catalyzed by phosphoenolpyruvate carboxykinase. B0016-100BB (B0016-090BB, recE::FRT, mhpF::FRT, ykgF::FRT, mhpB:: mhpB *, mhpD:: mhpD *, rcsA:: rcsA *) was engineered based on the analysis of the genetic mutations among the mutants for the biosynthesis of β-alanine. Along with the recruitment of glycerol as the sole carbon source, 1.07 g/L β-alanine was generated by B0016-200BB (B0016-100BB, aspA::FRT) harboring pET24a-panD-AspDH, which was used for overexpression of two key enzymes in β-alanine fermentation process. Compared with the starting strain, which can hardly generate β-alanine under anaerobic condition, the production efficiency of β-alanine of the engineered cell factory was significantly improved.
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Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens. Appl Environ Microbiol 2021; 87:AEM.01968-20. [PMID: 33158892 DOI: 10.1128/aem.01968-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/22/2020] [Indexed: 11/20/2022] Open
Abstract
Growth of Geobacter sulfurreducens PCA on lactate was enhanced by laboratory adaptive evolution. The enhanced growth was considered to be attributed to increased expression of the sucCD genes, encoding a succinyl-coenzyme A (CoA) synthetase. To further investigate the function of the succinyl-CoA synthetase, the sucCD genes were deleted from G. sulfurreducens The mutant showed defective growth on lactate but not on acetate. Introduction of the sucCD genes into the mutant restored the full potential to grow on lactate. These results verify the importance of the succinyl-CoA synthetase in growth on lactate. Genome analysis of Geobacter species identified candidate genes, GSU1623, GSU1624, and GSU1620, for lactate dehydrogenase. Deletion mutants of the identified genes for d-lactate dehydrogenase (ΔGSU1623 ΔGSU1624 mutant) or l-lactate dehydrogenase (ΔGSU1620 mutant) could not grow on d-lactate or l-lactate but could grow on acetate and l- or d-lactate, respectively. Introduction of the respective genes into the mutants allowed growth on the corresponding lactate stereoisomer. These results suggest that the identified genes were essential for d- or l-lactate utilization. The lacZ reporter assay demonstrated that the putative promoter regions were more active during growth on lactate than during growth on acetate, indicating that the genes for the lactate dehydrogenases were expressed more during growth on lactate than during growth on acetate. The gene deletion phenotypes and the expression profiles indicate that there are metabolic switches between lactate and acetate. This study advances the understanding of anaerobic lactate utilization in G. sulfurreducens IMPORTANCE Lactate is a microbial fermentation product as well as a source of carbon and electrons for microorganisms in the environment. Furthermore, lactate is a common amendment for stimulation of microbial growth in environmental biotechnology applications. However, anaerobic metabolism of lactate has been poorly studied for environmentally relevant microorganisms. Geobacter species are found in various environments and environmental biotechnology applications. By employing genomic and genetic approaches, succinyl-CoA synthetase and lactate dehydrogenase were identified as key enzymes in anaerobic metabolism of lactate in Geobacter sulfurreducens, a representative Geobacter species. Differential gene expression during growth on lactate and acetate was observed, demonstrating that G. sulfurreducens could metabolically switch to adapt to available substrates in the environment. The findings provide new insights into basic physiology in lactate metabolism as well as cellular responses to growth conditions in the environment and can be informative for the application of lactate in environmental biotechnology.
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42
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Xiao X, Yu HQ. Molecular mechanisms of microbial transmembrane electron transfer of electrochemically active bacteria. Curr Opin Chem Biol 2020; 59:104-110. [DOI: 10.1016/j.cbpa.2020.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 10/23/2022]
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A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity. Genes (Basel) 2020; 11:genes11101115. [PMID: 32977700 PMCID: PMC7650540 DOI: 10.3390/genes11101115] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 01/19/2023] Open
Abstract
Propionibacteria have been studied extensively since the early 1930s due to their relevance to industry and importance as human pathogens. Still, their unique metabolism is far from fully understood. This is partly due to their signature high GC content, which has previously hampered the acquisition of quality sequence data, the accurate annotation of the available genomes, and the functional characterization of genes. The recent completion of the genome sequences for several species has led researchers to reassess the taxonomical classification of the genus Propionibacterium, which has been divided into several new genres. Such data also enable a comparative genomic approach to annotation and provide a new opportunity to revisit our understanding of their metabolism. Using pan-genome analysis combined with the reconstruction of the first high-quality Propionibacterium genome-scale metabolic model and a pan-metabolic model of current and former members of the genus Propionibacterium, we demonstrate that despite sharing unique metabolic traits, these organisms have an unexpected diversity in central carbon metabolism and a hidden layer of metabolic complexity. This combined approach gave us new insights into the evolution of Propionibacterium metabolism and led us to propose a novel, putative ferredoxin-linked energy conservation strategy. The pan-genomic approach highlighted key differences in Propionibacterium metabolism that reflect adaptation to their environment. Results were mathematically captured in genome-scale metabolic reconstructions that can be used to further explore metabolism using metabolic modeling techniques. Overall, the data provide a platform to explore Propionibacterium metabolism and a tool for the rational design of strains.
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Developing a population-state decision system for intelligently reprogramming extracellular electron transfer in Shewanella oneidensis. Proc Natl Acad Sci U S A 2020; 117:23001-23010. [PMID: 32855303 PMCID: PMC7502708 DOI: 10.1073/pnas.2006534117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The unique extracellular electron transfer (EET) ability has positioned electroactive bacteria (EAB) as a major class of cellular chassis for genetic engineering aimed at favorable environmental, energy, and geoscience applications. However, previous efforts to genetically enhance EET ability have often impaired the basal metabolism and cellular growth due to the competition for the limited cellular resource. Here, we design a quorum sensing-based population-state decision (PSD) system for intelligently reprogramming the EET regulation system, which allows the rebalanced allocation of the cellular resource upon the bacterial growth state. We demonstrate that the electron output from Shewanella oneidensis MR-1 could be greatly enhanced by the PSD system via shifting the dominant metabolic flux from initial bacterial growth to subsequent EET enhancement (i.e., after reaching a certain population-state threshold). The strain engineered with this system achieved up to 4.8-fold EET enhancement and exhibited a substantially improved pollutant reduction ability, increasing the reduction efficiencies of methyl orange and hexavalent chromium by 18.8- and 5.5-fold, respectively. Moreover, the PSD system outcompeted the constant expression system in managing EET enhancement, resulting in considerably enhanced electron output and pollutant bioreduction capability. The PSD system provides a powerful tool for intelligently managing extracellular electron transfer and may inspire the development of new-generation smart bioelectrical devices for various applications.
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45
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Cheng L, Min D, He R, Cheng Z, Liu D, Yu H. Developing a base‐editing system to expand the carbon source utilization spectra of
Shewanella oneidensis
MR‐1 for enhanced pollutant degradation. Biotechnol Bioeng 2020; 117:2389-2400. [DOI: 10.1002/bit.27368] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Lei Cheng
- School of Life Sciences, University of Science and Technology of China Hefei China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and EngineeringUniversity of Science and Technology of China Hefei China
| | - Ru‐Li He
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and EngineeringUniversity of Science and Technology of China Hefei China
| | - Zhou‐Hua Cheng
- School of Life Sciences, University of Science and Technology of China Hefei China
| | - Dong‐Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and EngineeringUniversity of Science and Technology of China Hefei China
| | - Han‐Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and EngineeringUniversity of Science and Technology of China Hefei China
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Alex A, Antunes A. Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses. Microorganisms 2019; 7:microorganisms7120635. [PMID: 31801294 PMCID: PMC6955870 DOI: 10.3390/microorganisms7120635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/19/2019] [Accepted: 11/27/2019] [Indexed: 11/29/2022] Open
Abstract
The most recently described bacterial members of the genus Endozoicomonas have been found in association with a wide variety of marine invertebrates. Despite their ubiquity in the host holobiont, limited information is available on the molecular genomic signatures of the symbiotic association of Endozoicomonas with marine sponges. Here, we generated a draft genome of Endozoicomonas sp. OPT23 isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative genomics analyses. Genome-specific analysis and metabolic pathway comparison of the members of the genus Endozoicomonas revealed the presence of gene clusters encoding for unique metabolic features, such as the utilization of carbon sources through lactate, L-rhamnose metabolism, and a phenylacetic acid degradation pathway in Endozoicomonas sp. OPT23. Moreover, the genome harbors genes encoding for eukaryotic-like proteins, such as ankyrin repeats, tetratricopeptide repeats, and Sel1 repeats, which likely facilitate sponge-bacterium attachment. The genome also encodes major secretion systems and homologs of effector molecules that seem to enable the sponge-associated bacterium to interact with the sponge and deliver the virulence factors for successful colonization. In conclusion, the genome analysis of Endozoicomonas sp. OPT23 revealed the presence of adaptive genomic signatures that might favor their symbiotic lifestyle within the sponge host.
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Affiliation(s)
- Anoop Alex
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (A.Al.); (A.An.); Tel.: +351-22-340-1813 (A.Al.); +351-22-340-1813 (A.An.)
| | - Agostino Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (A.Al.); (A.An.); Tel.: +351-22-340-1813 (A.Al.); +351-22-340-1813 (A.An.)
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Hirose A, Kouzuma A, Watanabe K. Towards development of electrogenetics using electrochemically active bacteria. Biotechnol Adv 2019; 37:107351. [DOI: 10.1016/j.biotechadv.2019.02.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/09/2019] [Accepted: 02/15/2019] [Indexed: 12/20/2022]
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Electrons selective uptake of a metal-reducing bacterium Shewanella oneidensis MR-1 from ferrocyanide. Biosens Bioelectron 2019; 142:111571. [DOI: 10.1016/j.bios.2019.111571] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/01/2019] [Accepted: 08/03/2019] [Indexed: 12/24/2022]
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Development of a longevous two-species biophotovoltaics with constrained electron flow. Nat Commun 2019; 10:4282. [PMID: 31537786 PMCID: PMC6753107 DOI: 10.1038/s41467-019-12190-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/27/2019] [Indexed: 01/07/2023] Open
Abstract
Microbial biophotovoltaics (BPV) offers a biological solution for renewable energy production by using photosynthetic microorganisms as light absorbers. Although abiotic engineering approaches, e.g., electrode modification and device optimization, can enhance the electrochemical communication between living cells and electrodes, the power densities of BPV are still low due to the weak exoelectrogenic activity of photosynthetic microorganisms. Here, we develop a BPV based on a D-lactate mediated microbial consortium consisting of photosynthetic cyanobacteria and exoelectrogenic Shewanella. By directing solar energy from photons to D-lactate, then to electricity, this BPV generates a power density of over 150 mW·m-2 in a temporal separation setup. Furthermore, a spatial-temporal separation setup with medium replenishment enables stable operation for over 40 days with an average power density of 135 mW·m-2. These results demonstrate the electron flow constrained microbial consortium can facilitate electron export from photosynthetic cells and achieve an efficient and durable power output.
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50
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Singh K, Ainala SK, Kim Y, Park S. A novel D(-)-lactic acid-inducible promoter regulated by the GntR-family protein D-LldR of Pseudomonas fluorescens. Synth Syst Biotechnol 2019; 4:157-164. [PMID: 31517075 PMCID: PMC6731338 DOI: 10.1016/j.synbio.2019.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 11/26/2022] Open
Abstract
Lactic acid has two stereoisomers of D(-)- and L(+)-forms, both of which are important monomers of biodegradable plastic, poly-lactic acid. In this study, a novel d-lactate inducible system was identified in Pseudomonas fluorescens A506, partially characterized and tested as biosensor. The d-lactate catabolic operon (lldP-dld-II) was negatively regulated through the inversely transcribed D-lldR (encoding a GntR-type regulator), where the repression is relieved by addition of d-lactate. The derepression was specific to d-lactate and marginally affected by l-lactate. The D-LldR-responsive operator, showing dyad symmetry and separated by one base, was located between +11 and + 27 from the transcription start site of the lldP-dld-II operon. By site-directed mutagenesis, a motif with a dyad symmetry (AATTGGTAtTACCAATT), present in the upstream region of lldP, was identified as essential for the binding of LldR. d-lactate biosensors were developed by connecting the upregulation by d-lactate to a green fluorescent readout. About ~6.0-fold induction by 100 mM d-lactate was observed compared to l-lactate.
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Affiliation(s)
- Kalpana Singh
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Satish Kumar Ainala
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Yeonhee Kim
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, UNIST, Ulsan, 44919, Republic of Korea
- School of Chemical and Biomolecular Engineering, Pusan National University, Busan, 46241, Republic of Korea
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