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Nagraj AK, Shukla M, Kulkarni M, Patil P, Borgave M, Banerjee SK. Reversal of carbapenem resistance in Pseudomonas aeruginosa by camelid single domain antibody fragment (VHH) against the C4-dicarboxylate transporter. J Antibiot (Tokyo) 2024; 77:612-626. [PMID: 38886486 DOI: 10.1038/s41429-024-00748-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 05/06/2024] [Accepted: 05/18/2024] [Indexed: 06/20/2024]
Abstract
Antimicrobial resistance is emerging as the new healthcare crisis necessitating the development of newer classes of drugs using non-traditional approaches. Pseudomonas aeruginosa, one of the most common pathogens involved in nosocomial infections, is extremely difficult to treat even with the last resort frontline drug, the carbapenems. As the pathogen has the ability to acquire resistance to new small-molecule antibiotics, being deployed, a novel biological approach has been tried using antibody fragments in combination with carbapenems and β-lactams as adjunct therapy for an enduring solution to the problem. In this study, we developed a camelid antibody fragment (VHH) library against P. aeruginosa and isolated a highly potent hit, PsC23. Mass spectrometry identified the target to be a component of the C4-dicarboxylate transporter that feeds metabolites to the glyoxylate shunt particularly under conditions of oxidative stress. PsC23 is bacteriostatic at a concentration of 1.66 µM (25 µg ml-1) and shows a synergistic effect with both the classes of drugs at an effective concentration of 100-200 nM (1.5-3.0 µg ml-1) when co administered with them. In combination with meropenem the VHH completely cleared the infection from a neutropenic mouse with a carbapenem-resistant P. aeruginosa systemic infection. Blocking the glyoxylate shunt by PsC23 resulted in disruption of energy transduction due to a respiratory shift to the oxygen-depleted TCA cycle causing inhibition of efflux and increased free radical generation from carbapenems and β-lactams exerting a strong bactericidal effect that reversed the resistance to multiple unrelated drugs.
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Affiliation(s)
| | | | | | - Pratik Patil
- AbGenics Life Sciences Pvt. Ltd, Pune, 411045, India
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2
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Meng B, Yang X, Luo S, Shen C, Qi J, Zhang H, Li Y, Xue Y, Zhao J, Qu P, Liu E. Significant alteration of protein profiles in a mouse model of polycystic ovary syndrome. Mol Reprod Dev 2024; 91:e23720. [PMID: 38054257 DOI: 10.1002/mrd.23720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Polycystic ovary syndrome (PCOS) is an endocrine disorder, affecting women of child-bearing age, and the incidence rate is growing and assuming epidemic proportions. The etiology of PCOS remains unknown and there is no cure. Some animal models for PCOS have been established which have enhanced our understanding of the underlying mechanisms, but omics data for revealing PCOS pathogenesis and for drug discovery are still lacking. In the present study, proteomics analysis was used to construct a protein profile of the ovaries in a PCOS mouse model. The result showed a clear difference in protein profile between the PCOS and control group, with 495 upregulated proteins and 404 downregulated proteins in the PCOS group. The GO term and KEGG pathway analyses of differentially expressed proteins mainly showed involvement in lipid metabolism, oxidative stress, and immune response, which are consistent with pathological characteristics of PCOS in terms of abnormal metabolism, endocrine disorders, chronic inflammation and imbalance between oxidant and antioxidant levels. Also, we found that inflammatory responses were activated in the PCOS ovarium, while lipid biosynthetic process peroxisome, and bile secretion were inhibited. In addition, we found some alteration in unexpected pathways, such as glyoxylate and dicarboxylate metabolism, which should be investigated. The present study makes an important contribution to the current lack of PCOS ovarian proteomic data and provides an important reference for research and development of effective drugs and treatments for PCOS.
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Affiliation(s)
- Bin Meng
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
- Center for Reproductive Medicine, Xi'an Angel Women's & Children's Hospital, Xi'an, China
| | - Xiaoning Yang
- Medical Imaging Department, Yangling Demonstration Area Hospital, Yangling, China
| | - Shiwei Luo
- State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, China
| | - Chong Shen
- Department of Orthopedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jia Qi
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
| | - Haifeng Zhang
- Department of Pathology, Xi'an International Medical Center Hospital, Xi'an, Shaanxi, China
| | - Yandong Li
- Department of Pathology, Xi'an International Medical Center Hospital, Xi'an, Shaanxi, China
| | - Ying Xue
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
| | - Juan Zhao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Pengxiang Qu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
| | - Enqi Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Centre, Xi'an, Shaanxi, China
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3
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Sui Q, Di F, Zhong H, Chen M, Wei Y. Molecular insight into the allocation of organic carbon to heterotrophic bacteria: Carbon metabolism and the involvement in nitrogen and phosphorus removal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173302. [PMID: 38759923 DOI: 10.1016/j.scitotenv.2024.173302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Carbon metabolism and nutrient removal are crucial for biological wastewater treatment. This study focuses on analyzing carbon allocation and utilization by heterotrophic bacteria in response to increasing COD concentration in the influent. The study also assesses the effect of denitrification and biological phosphorus removal, particularly in combination with anaerobic ammonia oxidation (anammox). The experiment was conducted in a SBR operating under anaerobic/anoxic/oxic conditions. As COD concentration in the influent increased from 100 to 275 mg/L, intracellular COD accounted for 95.72 % of the COD removed. By regulating the NO3- concentration in the anoxic stage from 10 to 30 mg/L, the nitrite accumulation rate reached 69.46 %, which could serve as an electron acceptor for anammox. Most genes related to the tricarboxylic acid (TCA) cycle declined, while the genes involved in the glyoxylate cycle, gluconeogenesis, PHA synthesis increased. This suggests that glycogen accumulation and carbon storage, rather than direct carbon oxidation, was the dominant pathway for carbon metabolism. However, the genes responsible for the reduction of NO2--N (nirK) and NO (nosB) decreased, contributing to NO2- accumulation. The study also employed metagenomic analysis to reveal microbial interactions. The enrichment of specific bacterial species, including Dechloromonas sp. (D2.bin.10), Ca. Competibacteraceae bacterium (D9.bin.8), Ca. Desulfobacillus denitrificans (D6.bin.17), and Ignavibacteriae bacterium (D3.bin.9), played a collaborative role in facilitating nutrient removal and promoting the combination with anammox.
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Affiliation(s)
- Qianwen Sui
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Fei Di
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hui Zhong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Meixue Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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4
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Ye D, Wang P, Chen LL, Guan KL, Xiong Y. Itaconate in host inflammation and defense. Trends Endocrinol Metab 2024; 35:586-606. [PMID: 38448252 DOI: 10.1016/j.tem.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 03/08/2024]
Abstract
Immune cells undergo rapid and extensive metabolic changes during inflammation. In addition to contributing to energetic and biosynthetic demands, metabolites can also function as signaling molecules. Itaconate (ITA) rapidly accumulates to high levels in myeloid cells under infectious and sterile inflammatory conditions. This metabolite binds to and regulates the function of diverse proteins intracellularly to influence metabolism, oxidative response, epigenetic modification, and gene expression and to signal extracellularly through binding the G protein-coupled receptor (GPCR). Administration of ITA protects against inflammatory diseases and blockade of ITA production enhances antitumor immunity in preclinical models. In this article, we review ITA metabolism and its regulation, discuss its target proteins and mechanisms, and conjecture a rationale for developing ITA-based therapeutics to treat inflammatory diseases and cancer.
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Affiliation(s)
- Dan Ye
- Molecular and Cell Biology Laboratory, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
| | - Pu Wang
- Molecular and Cell Biology Laboratory, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Lei-Lei Chen
- Molecular and Cell Biology Laboratory, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Kun-Liang Guan
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Yue Xiong
- Cullgen Inc., 12730 High Bluff Drive, San Diego, CA 92130, USA.
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5
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Kreimendahl S, Pernas L. Metabolic immunity against microbes. Trends Cell Biol 2024; 34:496-508. [PMID: 38030541 DOI: 10.1016/j.tcb.2023.10.013] [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: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023]
Abstract
Pathogens, including viruses, bacteria, fungi, and parasites, remodel the metabolism of their host to acquire the nutrients they need to proliferate. Thus, host cells are often perceived as mere exploitable nutrient pools during infection. Mounting reports challenge this perception and instead suggest that host cells can actively reprogram their metabolism to the detriment of the microbial invader. In this review, we present metabolic mechanisms that host cells use to defend against pathogens. We highlight the contribution of domesticated microbes to host defenses and discuss examples of host-pathogen arms races that are derived from metabolic conflict.
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Affiliation(s)
| | - Lena Pernas
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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6
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Rajacharya GH, Sharma A, Yazdani SS. Proteomics and metabolic burden analysis to understand the impact of recombinant protein production in E. coli. Sci Rep 2024; 14:12271. [PMID: 38806637 PMCID: PMC11133349 DOI: 10.1038/s41598-024-63148-y] [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: 03/12/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
The impact of recombinant protein production (RPP) on host cells and the metabolic burden associated with it undermine the efficiency of the production system. This study utilized proteomics to investigate the dynamics of parent and recombinant cells induced at different time points for RPP. The results revealed significant changes in both transcriptional and translational machinery that may have impacted the metabolic burden, growth rate of the culture and the RPP. The timing of protein synthesis induction also played a critical role in the fate of the recombinant protein within the host cell, affecting protein and product yield. The study identified significant differences in the expression of proteins involved in fatty acid and lipid biosynthesis pathways between two E. coli host strains (M15 and DH5⍺), with the E. coli M15 strain demonstrating superior expression characteristics for the recombinant protein. Overall, these findings contribute to the knowledge base for rational strain engineering for optimized recombinant protein production.
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Affiliation(s)
- Girish H Rajacharya
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- School of Interdisciplinary Research (SIRe), Indian Institute of Technology, New Delhi, India
| | - Ashima Sharma
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Life Sciences, J.C. Bose University of Science and Technology, YMCA, Faridabad, Haryana, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- DBT-ICGEB Centre for Advanced Bio-Energy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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7
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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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Borchert AJ, Bleem AC, Lim HG, Rychel K, Dooley KD, Kellermyer ZA, Hodges TL, Palsson BO, Beckham GT. Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440. mSystems 2024; 9:e0094223. [PMID: 38323821 PMCID: PMC10949508 DOI: 10.1128/msystems.00942-23] [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: 09/14/2023] [Accepted: 01/07/2024] [Indexed: 02/08/2024] Open
Abstract
There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules ("functional modules"), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida. Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.
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Affiliation(s)
- Andrew J. Borchert
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alissa C. Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Biological Engineering, Inha University, Incheon, Korea
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Keven D. Dooley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Zoe A. Kellermyer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Tracy L. Hodges
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Agile BioFoundry, Emeryville, California, USA
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9
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Barbe V, Jacquin J, Bouzon M, Wolinski A, Derippe G, Cheng J, Cruaud C, Roche D, Fouteau S, Petit JL, Conan P, Pujo-Pay M, Bruzaud S, Ghiglione JF. Bioplastic degradation and assimilation processes by a novel bacterium isolated from the marine plastisphere. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133573. [PMID: 38306834 DOI: 10.1016/j.jhazmat.2024.133573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/23/2023] [Accepted: 01/17/2024] [Indexed: 02/04/2024]
Abstract
Biosourced and biodegradable plastics offer a promising solution to reduce environmental impacts of plastics for specific applications. Here, we report a novel bacterium named Alteromonas plasticoclasticus MED1 isolated from the marine plastisphere that forms biofilms on foils of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). Experiments of degradation halo, plastic matrix weight loss, bacterial oxygen consumption and heterotrophic biosynthetic activity showed that the bacterial isolate MED1 is able to degrade PHBV and to use it as carbon and energy source. The likely entire metabolic pathway specifically expressed by this bacterium grown on PHBV matrices was shown by further genomic and transcriptomic analysis. In addition to a gene coding for a probable secreted depolymerase, a gene cluster was located that encodes characteristic enzymes involved in the complete depolymerization of PHBV, the transport of oligomers, and in the conversion of the monomers into intermediates of central carbon metabolism. The transcriptomic experiments showed the activation of the glyoxylate shunt during PHBV degradation, setting the isocitrate dehydrogenase activity as regulated branching point of the carbon flow entering the tricarboxylic acid cycle. Our study also shows the potential of exploring the natural plastisphere to discover new bacteria with promising metabolic capabilities.
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Affiliation(s)
- Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Justine Jacquin
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France
| | - Madeleine Bouzon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Adèle Wolinski
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France
| | - Gabrielle Derippe
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France; Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne-Sud, UMR CNRS 6027, Rue Saint Maudé, Lorient, France
| | - Jingguang Cheng
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Stéphanie Fouteau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Pascal Conan
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France
| | - Mireille Pujo-Pay
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France
| | - Stéphane Bruzaud
- Institut de Recherche Dupuy de Lôme (IRDL), Université de Bretagne-Sud, UMR CNRS 6027, Rue Saint Maudé, Lorient, France
| | - Jean-François Ghiglione
- CNRS, Sorbonne Université, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, France.
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10
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Woo H, Kim Y, Kim D, Yoon SH. Machine learning identifies key metabolic reactions in bacterial growth on different carbon sources. Mol Syst Biol 2024; 20:170-186. [PMID: 38291231 PMCID: PMC10912204 DOI: 10.1038/s44320-024-00017-w] [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: 08/16/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 02/01/2024] Open
Abstract
Carbon source-dependent control of bacterial growth is fundamental to bacterial physiology and survival. However, pinpointing the metabolic steps important for cell growth is challenging due to the complexity of cellular networks. Here, the elastic net model and multilayer perception model that integrated genome-wide gene-deletion data and simulated flux distributions were constructed to identify metabolic reactions beneficial or detrimental to Escherichia coli grown on 30 different carbon sources. Both models outperformed traditional in silico methods by identifying not just essential reactions but also nonessential ones that promote growth. They successfully predicted metabolic reactions beneficial to cell growth, with high convergence between the models. The models revealed that biosynthetic pathways generally promote growth across various carbon sources, whereas the impact of energy-generating pathways varies with the carbon source. Intriguing predictions were experimentally validated for findings beyond experimental training data and the impact of various carbon sources on the glyoxylate shunt, pyruvate dehydrogenase reaction, and redundant purine biosynthesis reactions. These highlight the practical significance and predictive power of the models for understanding and engineering microbial metabolism.
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Affiliation(s)
- Hyunjae Woo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Youngshin Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dohyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Sung Ho Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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11
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Gu P, Li F, Huang Z, Gao J. Application of Acetate as a Substrate for the Production of Value-Added Chemicals in Escherichia coli. Microorganisms 2024; 12:309. [PMID: 38399713 PMCID: PMC10891810 DOI: 10.3390/microorganisms12020309] [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: 01/08/2024] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
At present, the production of the majority of valuable chemicals is dependent on the microbial fermentation of carbohydrate substrates. However, direct competition is a potential problem for microbial feedstocks that are also used within the food/feed industries. The use of alternative carbon sources, such as acetate, has therefore become a research focus. As a common organic acid, acetate can be generated from lignocellulosic biomass and C1 gases, as well as being a major byproduct in microbial fermentation, especially in the presence of an excess carbon source. As a model microorganism, Escherichia coli has been widely applied in the production of valuable chemicals using different carbon sources. Recently, several valuable chemicals (e.g., succinic acid, itaconic acid, isobutanol, and mevalonic acid) have been investigated for synthesis in E. coli using acetate as the sole carbon source. In this review, we summarize the acetate metabolic pathway in E. coli and recent research into the microbial production of chemical compounds in E. coli using acetate as the carbon source. Although microbial synthetic pathways for different compounds have been developed in E. coli, the production titer and yield are insufficient for commercial applications. Finally, we discuss the development prospects and challenges of using acetate for microbial fermentation.
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Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
| | - Fangfang Li
- Yantai Food and Drug Control and Test Center, Yantai 264003, China;
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
| | - Juan Gao
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
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12
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François JM. Progress advances in the production of bio-sourced methionine and its hydroxyl analogues. Biotechnol Adv 2023; 69:108259. [PMID: 37734648 DOI: 10.1016/j.biotechadv.2023.108259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/11/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023]
Abstract
The essential sulphur-containing amino acid, methionine, is becoming a mass-commodity product with an annual production that exceeded 1,500,000 tons in 2018. This amino acid is today almost exclusively produced by chemical process from fossil resources. The environmental problems caused by this industrial process, and the expected scarcity of oil resources in the coming years, have recently accelerated the development of bioprocesses for producing methionine from renewable carbon feedstock. After a brief description of the chemical process and the techno-economic context that still justify the production of methionine by petrochemical processes, this review will present the current state of the art of biobased alternatives aiming at a sustainable production of this amino acid and its hydroxyl analogues from renewable carbon feedstock. In particular, this review will focus on three bio-based processes, namely a purely fermentative process based on the metabolic engineering of the natural methionine pathway, a mixed process combining the production of the O-acetyl/O-succinyl homoserine intermediate of this pathway by fermentation followed by an enzyme-based conversion of this intermediate into L-methionine and lately, a hybrid process in which the non-natural chemical synthon, 2,4-dihydroxybutyric acid, obtained by fermentation of sugars is converted by chemo-catalysis into hydroxyl methionine analogues. The industrial potential of these three bioprocesses, as well as the major technical and economic obstacles that remain to be overcome to reach industrial maturity are discussed. This review concludes by bringing up the assets of these bioprocesses to meet the challenge of the "green transition", with the accomplishment of the objective "zero carbon" by 2050 and how they can be part of a model of Bioeconomy enhancing local resources.
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Affiliation(s)
- Jean Marie François
- Toulouse Biotechnology Institute, UMR INSA -CNRS5504 and UMR INSA-INRAE 792, 135 avenue de Rangueil, 31077 Toulouse, France; Toulouse White Biotechnology, UMS INRAE-INSA-CNRS, 135 Avenue de Rangueil, 31077 Toulouse, France.
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13
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Zhang H, Hu W, Liu R, Bartlam M, Wang Y. Low and high nucleic acid content bacteria play discrepant roles in response to various carbon supply modes. Environ Microbiol 2023; 25:3703-3718. [PMID: 37964717 DOI: 10.1111/1462-2920.16539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
Planktonic bacteria can be grouped into 'high nucleic acid content (HNA) bacteria' and 'low nucleic acid content (LNA) bacteria.' Nutrient input modes vary in environments, causing nutrient availability heterogeneity. We incubated them with equal amounts of total glucose added in a continuous/pulsed mode. The pulse-treated LNA bacteria exhibited twice the cell abundance and four times the viability of the continuous-treated LNA, while HNA did not show an adaptation to pulsed treatment. In structural equation modelling, LNA bacteria had higher path coefficients than HNA, between growth and carbon-saving metabolic pathways, intracellular ATP and the inorganic energy storage polymer, polyphosphate, indicating their low-cost growth, and flexible energy storage and utilisation. After incubation, the pulse-treated LNA bacteria contained more proteins and polysaccharides (0.00064, 0.0012 ng cell-1 ) than the continuous-treated LNA (0.00014, 0.00014 ng cell-1 ), conferring endurance and rapid response to pulses. Compared to LNA, HNA keystone taxa had stronger correlations with the primary glucose metabolism step, glycolysis, and occupied leading positions to explain the random forest model. They are essential to introduce glucose into the element cycling of the whole community under both treatments. Our work outlines a systematic bacterial response to carbon input.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Wei Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Ruidan Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Mark Bartlam
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
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14
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Wang G, Laranjeiro R, LeValley S, Van Raamsdonk JM, Driscoll M. The glyoxylate shunt protein ICL-1 protects from mitochondrial superoxide stress through activation of the mitochondrial unfolded protein response. Free Radic Biol Med 2023; 208:771-779. [PMID: 37758122 DOI: 10.1016/j.freeradbiomed.2023.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/05/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
Disrupting mitochondrial superoxide dismutase (SOD) causes neonatal lethality in mice and death of flies within 24 h after eclosion. Deletion of mitochondrial sod genes in C. elegans impairs fertility as well, but surprisingly is not detrimental to survival of progeny generated. The comparison of metabolic pathways among mouse, flies and nematodes reveals that mice and flies lack the glyoxylate shunt, a shortcut that bypasses part of the tricarboxylic acid (TCA) cycle. Here we show that ICL-1, the sole protein that catalyzes the glyoxylate shunt, is critical for protection against embryonic lethality resulting from elevated levels of mitochondrial superoxide. In exploring the mechanism by which ICL-1 protects against ROS-mediated embryonic lethality, we find that ICL-1 is required for the efficient activation of mitochondrial unfolded protein response (UPRmt) and that ATFS-1, a key UPRmt transcription factor and an activator of icl-1 gene expression, is essential to limit embryonic/neonatal lethality in animals lacking mitochondrial SOD. In sum, we identify a biochemical pathway that highlights a molecular strategy for combating toxic mitochondrial superoxide consequences in cells.
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Affiliation(s)
- Guoqiang Wang
- Department of Molecular Biology and Biochemistry, School of Arts and Sciences, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Ricardo Laranjeiro
- Department of Molecular Biology and Biochemistry, School of Arts and Sciences, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Stephanie LeValley
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Jeremy M Van Raamsdonk
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA; Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Metabolic Disorders and Complications Program, and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, School of Arts and Sciences, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
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15
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Díaz-Pérez AL, Díaz-Pérez C, Gaona-García RY, Hernández-Santoyo A, Lázaro-Mixteco PE, Reyes-De La Cruz H, Campos-García J. Study of peripheral domains in structure-function of isocitrate lyase (ICL) from Pseudomonas aeruginosa. World J Microbiol Biotechnol 2023; 39:339. [PMID: 37821748 DOI: 10.1007/s11274-023-03768-0] [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: 05/04/2023] [Accepted: 09/15/2023] [Indexed: 10/13/2023]
Abstract
The capacity of Pseudomonas aeruginosa to assimilate nutrients is essential for niche colonization and contributes to its pathogenicity. Isocitrate lyase (ICL), the first enzyme of the glyoxylate cycle, redirects isocitrate from the tricarboxylic acid cycle to render glyoxylate and succinate. P. aeruginosa ICL (PaICL) is regarded as a virulence factor due to its role in carbon assimilation during infection. The AceA/ICL protein family shares the catalytic domain I, triosephosphate isomerase barrel (TIM-barrel). The carboxyl terminus of domain I is essential for Escherichia coli ICL (EcICL) of subfamily 1. PaICL, which belongs to subfamily 3, has domain II inserted at the periphery of domain I, which is believed to participate in enzyme oligomerization. In addition, PaICL has the α13-loop-α14 (extended motif), which protrudes from the enzyme core, being of unknown function. This study investigates the role of domain II, the extended motif, and the carboxyl-terminus (C-ICL) and amino-terminus (N-ICL) regions in the function of the PaICL enzyme, also as their involvement in the virulence of P. aeruginosa PAO1. Deletion of domain II and the extended motif results in enzyme inactivation and structural instability of the enzyme. The His6-tag fusion at the C-ICL protein produced a less efficient enzyme than fusion at the N-ICL, but without affecting the acetate assimilation or virulence. The PaICL homotetrameric structure of the enzyme was more stable in the N-His6-ICL than in the C-His6-ICL, suggesting that the C-terminus is critical for the ICL quaternary conformation. The ICL-mutant A39 complemented with the recombinant proteins N-His6-ICL or C-His6-ICL were more virulent than the WT PAO1 strain. The findings indicate that the domain II and the extended motif are essential for the ICL structure/function, and the C-terminus is involved in its quaternary structure conformation, confirming that in P. aeruginosa, the ICL is essential for acetate assimilation and virulence.
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Affiliation(s)
- Alma Laura Díaz-Pérez
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - César Díaz-Pérez
- Facultad de Agrobiologia, Campus Celaya-Salvatierra, Universiad de Guanajuato, Guanajuato, Gto., Mexico
| | - Roxana Yughadi Gaona-García
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - Alejandra Hernández-Santoyo
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Pedro E Lázaro-Mixteco
- Facultad de Ingeniería Química, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich., Mexico
| | - Homero Reyes-De La Cruz
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico
| | - Jesús Campos-García
- Lab. de Biotecnología Microbiana, Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. U-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico.
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16
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Rivier AJ, Myers KS, Garcia AK, Sobol MS, Kaçar B. Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii. Microbiol Spectr 2023; 11:e0281523. [PMID: 37702481 PMCID: PMC10581106 DOI: 10.1128/spectrum.02815-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/20/2023] [Indexed: 09/14/2023] Open
Abstract
Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs. IMPORTANCE Azotobacter vinelandii is a key model bacterium for the study of biological nitrogen fixation, an important metabolic process catalyzed by nitrogenase enzymes. Here, we demonstrate that compatibilities between engineered A. vinelandii strains and nitrogenase variants can be modulated at the regulatory level. The engineered strain studied here responds by adjusting the expression of proteins involved in cellular processes adjacent to nitrogen fixation, rather than that of nitrogenase proteins themselves. These insights can inform future strategies to transfer nitrogenase variants to non-native hosts.
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Affiliation(s)
- Alex J. Rivier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin S. Myers
- Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amanda K. Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Morgan S. Sobol
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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17
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Hyun JC, Palsson BO. Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome. Genome Biol 2023; 24:183. [PMID: 37553643 PMCID: PMC10411014 DOI: 10.1186/s13059-023-03028-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Cumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of organisms for which this is achievable, similar analyses for ancestral species are feasible through the integration of pangenomics and phylogenetics, promising deeper insights into the nature of ancient life. RESULTS We construct pangenomes for 183 bacterial species from 54,085 genomes and identify their core genomes using a novel statistical model to estimate genome-specific error rates and underlying gene frequencies. The core genomes are then integrated into a phylogenetic tree to reconstruct the core genome of the last bacterial common ancestor (LBCA), yielding three main results: First, the gene content of modern and ancestral core genomes are diverse at the level of individual genes but are similarly distributed by functional category and share several poorly characterized genes. Second, the LBCA core genome is distinct from any individual modern core genome but has many fundamental biological systems intact, especially those involving translation machinery and biosynthetic pathways to all major nucleotides and amino acids. Third, despite this metabolic versatility, the LBCA core genome likely requires additional non-core genes for viability, based on comparisons with the minimal organism, JCVI-Syn3A. CONCLUSIONS These results suggest that many cellular systems commonly conserved in modern bacteria were not just present in ancient bacteria but were nearly immutable with respect to short-term intraspecies variation. Extending this analysis to other domains of life will likely provide similar insights into more distant ancestral species.
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Affiliation(s)
- Jason C Hyun
- Bioinformatics and Systems Biology Program, University of California, La Jolla, San Diego, CA, USA
| | - Bernhard O Palsson
- Bioinformatics and Systems Biology Program, University of California, La Jolla, San Diego, CA, USA.
- Department of Bioengineering, University of California, La Jolla, San Diego, CA, USA.
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18
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Wang Y, Ferrinho S, Connaris H, Goss RJM. The Impact of Viral Infection on the Chemistries of the Earth's Most Abundant Photosynthesizes: Metabolically Talented Aquatic Cyanobacteria. Biomolecules 2023; 13:1218. [PMID: 37627283 PMCID: PMC10452541 DOI: 10.3390/biom13081218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Cyanobacteria are the most abundant photosynthesizers on earth, and as such, they play a central role in marine metabolite generation, ocean nutrient cycling, and the control of planetary oxygen generation. Cyanobacteriophage infection exerts control on all of these critical processes of the planet, with the phage-ported homologs of genes linked to photosynthesis, catabolism, and secondary metabolism (marine metabolite generation). Here, we analyze the 153 fully sequenced cyanophages from the National Center for Biotechnology Information (NCBI) database and the 45 auxiliary metabolic genes (AMGs) that they deliver into their hosts. Most of these AMGs are homologs of those found within cyanobacteria and play a key role in cyanobacterial metabolism-encoding proteins involved in photosynthesis, central carbon metabolism, phosphate metabolism, methylation, and cellular regulation. A greater understanding of cyanobacteriophage infection will pave the way to a better understanding of carbon fixation and nutrient cycling, as well as provide new tools for synthetic biology and alternative approaches for the use of cyanobacteria in biotechnology and sustainable manufacturing.
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Affiliation(s)
- Yunpeng Wang
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Scarlet Ferrinho
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Helen Connaris
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9AJ, UK; (S.F.); (H.C.)
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9SX, UK
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19
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Kremer K, Meier D, Theis L, Miller S, Rost-Nasshan A, Naing YT, Zarzycki J, Paczia N, Serrania J, Blumenkamp P, Goesmann A, Becker A, Thanbichler M, Hochberg GKA, Carter MS, Erb TJ. Functional Degeneracy in Paracoccus denitrificans Pd1222 Is Coordinated via RamB, Which Links Expression of the Glyoxylate Cycle to Activity of the Ethylmalonyl-CoA Pathway. Appl Environ Microbiol 2023:e0023823. [PMID: 37318336 PMCID: PMC10370305 DOI: 10.1128/aem.00238-23] [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: 02/14/2023] [Accepted: 04/26/2023] [Indexed: 06/16/2023] Open
Abstract
Metabolic degeneracy describes the phenomenon that cells can use one substrate through different metabolic routes, while metabolic plasticity, refers to the ability of an organism to dynamically rewire its metabolism in response to changing physiological needs. A prime example for both phenomena is the dynamic switch between two alternative and seemingly degenerate acetyl-CoA assimilation routes in the alphaproteobacterium Paracoccus denitrificans Pd1222: the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). The EMCP and the GC each tightly control the balance between catabolism and anabolism by shifting flux away from the oxidation of acetyl-CoA in the tricarboxylic acid (TCA) cycle toward biomass formation. However, the simultaneous presence of both the EMCP and GC in P. denitrificans Pd1222 raises the question of how this apparent functional degeneracy is globally coordinated during growth. Here, we show that RamB, a transcription factor of the ScfR family, controls expression of the GC in P. denitrificans Pd1222. Combining genetic, molecular biological and biochemical approaches, we identify the binding motif of RamB and demonstrate that CoA-thioester intermediates of the EMCP directly bind to the protein. Overall, our study shows that the EMCP and the GC are metabolically and genetically linked with each other, demonstrating a thus far undescribed bacterial strategy to achieve metabolic plasticity, in which one seemingly degenerate metabolic pathway directly drives expression of the other. IMPORTANCE Carbon metabolism provides organisms with energy and building blocks for cellular functions and growth. The tight regulation between degradation and assimilation of carbon substrates is central for optimal growth. Understanding the underlying mechanisms of metabolic control in bacteria is of importance for applications in health (e.g., targeting of metabolic pathways with new antibiotics, development of resistances) and biotechnology (e.g., metabolic engineering, introduction of new-to-nature pathways). In this study, we use the alphaproteobacterium P. denitrificans as model organism to study functional degeneracy, a well-known phenomenon of bacteria to use the same carbon source through two different (competing) metabolic routes. We demonstrate that two seemingly degenerate central carbon metabolic pathways are metabolically and genetically linked with each other, which allows the organism to control the switch between them in a coordinated manner during growth. Our study elucidates the molecular basis of metabolic plasticity in central carbon metabolism, which improves our understanding of how bacterial metabolism is able to partition fluxes between anabolism and catabolism.
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Affiliation(s)
- Katharina Kremer
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Doreen Meier
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Lisa Theis
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Stephanie Miller
- Department of Biological Sciences, Salisbury University, Maryland, USA
| | | | - Yadanar T Naing
- Department of Biological Sciences, Salisbury University, Maryland, USA
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for terrestrial Microbiology, Marburg, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Patrick Blumenkamp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anke Becker
- Department of Biology, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg K A Hochberg
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, University of Marburg, Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael S Carter
- Department of Biological Sciences, Salisbury University, Maryland, USA
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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20
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Diankristanti PA, Ng IS. Microbial itaconic acid bioproduction towards sustainable development: Insights, challenges, and prospects. BIORESOURCE TECHNOLOGY 2023:129280. [PMID: 37290713 DOI: 10.1016/j.biortech.2023.129280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Microbial biomanufacturing is a promising approach to produce high-value compounds with low-carbon footprint and significant economic benefits. Among twelve "Top Value-Added Chemicals from Biomass", itaconic acid (IA) stands out as a versatile platform chemical with numerous applications. IA is naturally produced by Aspergillus and Ustilago species through a cascade enzymatic reaction between aconitase (EC 4.2.1.3) and cis-aconitic acid decarboxylase (EC 4.1.1.6). Recently, non-native hosts such as Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Yarrowia lipolytica have been genetically engineered to produce IA through the introduction of key enzymes. This review provides an up-to-date summary of the progress made in IA bioproduction, from native to engineered hosts, covers in vivo and in vitro approaches, and highlights the prospects of combination tactics. Current challenges and recent endeavors are also addressed to envision comprehensive strategies for renewable IA production in the future towards sustainable development goals (SDGs).
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
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21
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Dulermo T, Lejeune C, Aybeke E, Abreu S, Bleton J, David M, Deniset-Besseau A, Chaminade P, Thibessard A, Leblond P, Virolle MJ. Genome Analysis of a Variant of Streptomyces coelicolor M145 with High Lipid Content and Poor Ability to Synthetize Antibiotics. Microorganisms 2023; 11:1470. [PMID: 37374972 DOI: 10.3390/microorganisms11061470] [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: 04/27/2023] [Revised: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Streptomyces coelicolor M145 is a model strain extensively studied to elucidate the regulation of antibiotic biosynthesis in Streptomyces species. This strain abundantly produces the blue polyketide antibiotic, actinorhodin (ACT), and has a low lipid content. In a process designed to delete the gene encoding the isocitrate lyase (sco0982) of the glyoxylate cycle, an unexpected variant of S. coelicolor was obtained besides bona fide sco0982 deletion mutants. This variant produces 7- to 15-fold less ACT and has a 3-fold higher triacylglycerol and phosphatidylethanolamine content than the original strain. The genome of this variant was sequenced and revealed that 704 genes were deleted (9% of total number of genes) through deletions of various sizes accompanied by the massive loss of mobile genetic elements. Some deletions include genes whose absence could be related to the high total lipid content of this variant such as those encoding enzymes of the TCA and glyoxylate cycles, enzymes involved in nitrogen assimilation as well as enzymes belonging to some polyketide and possibly trehalose biosynthetic pathways. The characteristics of this deleted variant of S. coelicolor are consistent with the existence of the previously reported negative correlation existing between lipid content and antibiotic production in Streptomyces species.
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Affiliation(s)
- Thierry Dulermo
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group "Energetic Metabolism of Streptomyces", 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Clara Lejeune
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group "Energetic Metabolism of Streptomyces", 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Ece Aybeke
- Université Paris-Saclay, CNRS, CEA, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
| | - Sonia Abreu
- Université Paris-Saclay, CNRS, CEA, Lip(Sys)2 (Lipides Systèmes Analytiques et Biologiques), UFR Pharmacie-Bâtiment Henri Moissan, 17 Avenue des Sciences, 91400 Orsay, France
| | - Jean Bleton
- Université Paris-Saclay, CNRS, CEA, Lip(Sys)2 (Lipides Systèmes Analytiques et Biologiques), UFR Pharmacie-Bâtiment Henri Moissan, 17 Avenue des Sciences, 91400 Orsay, France
| | - Michelle David
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group "Energetic Metabolism of Streptomyces", 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Ariane Deniset-Besseau
- Université Paris-Saclay, CNRS, CEA, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
| | - Pierre Chaminade
- Université Paris-Saclay, CNRS, CEA, Lip(Sys)2 (Lipides Systèmes Analytiques et Biologiques), UFR Pharmacie-Bâtiment Henri Moissan, 17 Avenue des Sciences, 91400 Orsay, France
| | | | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Marie-Joelle Virolle
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group "Energetic Metabolism of Streptomyces", 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
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22
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Waldrop MP, Chabot CL, Liebner S, Holm S, Snyder MW, Dillon M, Dudgeon SR, Douglas TA, Leewis MC, Walter Anthony KM, McFarland JW, Arp CD, Bondurant AC, Taş N, Mackelprang R. Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients. THE ISME JOURNAL 2023:10.1038/s41396-023-01429-6. [PMID: 37217592 DOI: 10.1038/s41396-023-01429-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/24/2023]
Abstract
Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25-50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.
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Affiliation(s)
- Mark P Waldrop
- Geology, Minerals, Energy, and Geophysics Science Center, United States Geological Survey, Menlo Park, CA, 94025, USA.
| | - Christopher L Chabot
- California State University Northridge, 18111 Nordhoff St., Northridge, CA, 91330, USA
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
- University of Potsdam, Institute of Biochemistry and Biology, 14476, Potsdam, Germany
| | - Stine Holm
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473, Potsdam, Germany
| | - Michael W Snyder
- California State University Northridge, 18111 Nordhoff St., Northridge, CA, 91330, USA
| | - Megan Dillon
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven R Dudgeon
- California State University Northridge, 18111 Nordhoff St., Northridge, CA, 91330, USA
| | - Thomas A Douglas
- U.S. Army Cold Regions Research and Engineering Laboratory 9th Avenue, Building 4070 Fort, Wainwright, AK, 99703, USA
| | - Mary-Cathrine Leewis
- Agriculture and Agri-Food Canada, 2560 Boulevard Hochelaga, Québec, QC, G1V 2J3, Canada
| | - Katey M Walter Anthony
- Water and Environmental Research Center, University Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Jack W McFarland
- Geology, Minerals, Energy, and Geophysics Science Center, United States Geological Survey, Menlo Park, CA, 94025, USA
| | - Christopher D Arp
- Water and Environmental Research Center, University Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Allen C Bondurant
- Water and Environmental Research Center, University Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Neslihan Taş
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rachel Mackelprang
- California State University Northridge, 18111 Nordhoff St., Northridge, CA, 91330, USA.
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23
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Dedman CJ, Barton S, Fournier M, Rickaby REM. The cellular response to ocean warming in Emiliania huxleyi. Front Microbiol 2023; 14:1177349. [PMID: 37256052 PMCID: PMC10225680 DOI: 10.3389/fmicb.2023.1177349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/12/2023] [Indexed: 06/01/2023] Open
Abstract
Marine phytoplankton contribute substantially to the global flux of carbon from the atmosphere to the deep ocean. Sea surface temperatures will inevitably increase in line with global climate change, altering the performance of marine phytoplankton. Differing sensitivities of photosynthesis and respiration to temperature, will likely shift the strength of the future oceanic carbon sink. To further clarify the molecular mechanisms driving these alterations in phytoplankton function, shotgun proteomic analysis was carried out on the globally-occurring coccolithophore Emiliania huxleyi exposed to moderate- (23°C) and elevated- (28°C) warming. Compared to the control (17°C), growth of E. huxleyi increased under elevated temperatures, with higher rates recorded under moderate- relative to elevated- warming. Proteomic analysis revealed a significant modification of the E. huxleyi cellular proteome as temperatures increased: at lower temperature, ribosomal proteins and photosynthetic machinery appeared abundant, as rates of protein translation and photosynthetic performance are restricted by low temperatures. As temperatures increased, evidence of heat stress was observed in the photosystem, characterized by a relative down-regulation of the Photosystem II oxygen evolving complex and ATP synthase. Acclimation to elevated warming (28°C) revealed a substantial alteration to carbon metabolism. Here, E. huxleyi made use of the glyoxylate cycle and succinate metabolism to optimize carbon use, maintain growth and maximize ATP production in heat-damaged mitochondria, enabling cultures to maintain growth at levels significantly higher than those recorded in the control (17°C). Based on the metabolic changes observed, we can predict that warming may benefit photosynthetic carbon fixation by E. huxleyi in the sub-optimal to optimal thermal range. Past the thermal optima, increasing rates of respiration and costs of repair will likely constrain growth, causing a possible decline in the contribution of this species to the oceanic carbon sink depending on the evolvability of these temperature thresholds.
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Affiliation(s)
- Craig J. Dedman
- Department of Earth Sciences, University of Oxford, Oxford, United Kingdom
| | - Samuel Barton
- Department of Earth Sciences, University of Oxford, Oxford, United Kingdom
| | - Marjorie Fournier
- Advanced Proteomics Facility, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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24
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Sharko A, Spitzbarth B, Hermans TM, Eelkema R. Redox-Controlled Shunts in a Synthetic Chemical Reaction Cycle. J Am Chem Soc 2023; 145:9672-9678. [PMID: 37092741 PMCID: PMC10161229 DOI: 10.1021/jacs.3c00985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Shunts, alternative pathways in chemical reaction networks (CRNs), are ubiquitous in nature, enabling adaptability to external and internal stimuli. We introduce a CRN in which the recovery of Michael-accepting species is driven by oxidation chemistry. Using weak oxidants can enable access to two shunts within this CRN with different kinetics and a reduced number of side reactions compared to the main cycle that is driven by strong oxidants. Furthermore, we introduce a strategy to recycle one of the main products under flow conditions to partially reverse the CRN and control product speciation throughout time. These findings introduce new levels of control over artificial CRNs, driven by redox chemistry, narrowing the gap between synthetic and natural systems.
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Affiliation(s)
| | - Benjamin Spitzbarth
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Thomas M Hermans
- University of Strasbourg & CNRS, UMR7140, 67083 Strasbourg, France
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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25
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Tejeda C, Villegas M, Steuer P, Ulloa F, Iranzo EC, Reyes-Jara A, Salgado M. Experimental evidence of the anti-bacterial activity pathway of copper ion treatment on Mycobacterium avium subsp. paratuberculosis. Braz J Microbiol 2023; 54:407-413. [PMID: 36572823 PMCID: PMC9943822 DOI: 10.1007/s42770-022-00897-w] [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: 09/06/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022] Open
Abstract
Copper causes significant damage to the integrity of many bacteria, mainly at the DNA level, through its redox states, as well as its reactive oxygen species (ROS) generating capacity at the cellular level. But whether these mechanisms also apply to Mycobacterium avium subsp. paratuberculosis (MAP) is unknown. In the present study, we have evaluated whether copper ions produce damage at the DNA level of MAP, either through their redox states or through ROS production. MAP-spiked PBS was first supplemented with different copper chelators (2) and ROS antioxidants (3), followed by treatment with copper ions at 942 ppm. MAP DNA integrity (qPCR, magnetic phage separation) was then evaluated. We found that bathocuproine (BCS), as a chelator, and D-mannitol, as an antioxidant of hydroxyl radicals, had a significant protective effect (P < 0.05) on DNA molecules, and that EDTA, as a chelator, and D-mannitol, as an antioxidant had a significant positive effect (P < 0.05) on the viability of this pathogen in contrast to the control and other chelators and anti-oxidants used. In light of the reported findings, it may be concluded that copper ions within MAP cells are directly related to MAP DNA damage.
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Affiliation(s)
- Carlos Tejeda
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Escuela de Graduados, Valdivia, Chile
| | - Marcela Villegas
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Pamela Steuer
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Fernando Ulloa
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Escuela de Graduados, Valdivia, Chile
| | - Esperanza C Iranzo
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Angelica Reyes-Jara
- Laboratorio de Microbiología Y Probióticos, Instituto de Nutrición Y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Miguel Salgado
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile.
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26
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Adaptation to Overflow Metabolism by Mutations That Impair tRNA Modification in Experimentally Evolved Bacteria. mBio 2023; 14:e0028723. [PMID: 36853041 PMCID: PMC10128029 DOI: 10.1128/mbio.00287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
When microbes grow in foreign nutritional environments, selection may enrich mutations in unexpected pathways connecting growth and homeostasis. An evolution experiment designed to identify beneficial mutations in Burkholderia cenocepacia captured six independent nonsynonymous substitutions in the essential gene tilS, which modifies tRNAIle2 by adding a lysine to the anticodon for faithful AUA recognition. Further, five additional mutants acquired mutations in tRNAIle2, which strongly suggests that disrupting the TilS-tRNAIle2 interaction was subject to strong positive selection. Mutated TilS incurred greatly reduced enzymatic function but retained capacity for tRNAIle2 binding. However, both mutant sets outcompeted the wild type by decreasing the lag phase duration by ~3.5 h. We hypothesized that lysine demand could underlie fitness in the experimental conditions. As predicted, supplemental lysine complemented the ancestral fitness deficit, but so did the additions of several other amino acids. Mutant fitness advantages were also specific to rapid growth on galactose using oxidative overflow metabolism that generates redox imbalance, not resources favoring more balanced metabolism. Remarkably, 13 tilS mutations also evolved in the long-term evolution experiment with Escherichia coli, including four fixed mutations. These results suggest that TilS or unknown binding partners contribute to improved growth under conditions of rapid sugar oxidation at the predicted expense of translational accuracy. IMPORTANCE There is growing evidence that the fundamental components of protein translation can play multiple roles in maintaining cellular homeostasis. Enzymes that interact with transfer RNAs not only ensure faithful decoding of the genetic code but also help signal the metabolic state by reacting to imbalances in essential building blocks like free amino acids and cofactors. Here, we present evidence of a secondary function for the essential enzyme TilS, whose only prior known function is to modify tRNAIle(CAU) to ensure accurate translation. Multiple nonsynonymous substitutions in tilS, as well as its cognate tRNA, were selected in evolution experiments favoring rapid, redox-imbalanced growth. These mutations alone decreased lag phase and created a competitive advantage, but at the expense of most primary enzyme function. These results imply that TilS interacts with other factors related to the timing of exponential growth and that tRNA-modifying enzymes may serve multiple roles in monitoring metabolic health.
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27
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Zhu M, Dai X. Stringent response ensures the timely adaptation of bacterial growth to nutrient downshift. Nat Commun 2023; 14:467. [PMID: 36709335 PMCID: PMC9884231 DOI: 10.1038/s41467-023-36254-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/20/2023] [Indexed: 01/30/2023] Open
Abstract
Timely adaptation to nutrient downshift is crucial for bacteria to maintain fitness during feast and famine cycle in the natural niche. However, the molecular mechanism that ensures the timely adaption of bacterial growth to nutrient downshift remains poorly understood. Here, we quantitatively investigated the adaptation of Escherichia coli to various kinds of nutrient downshift. We found that relA deficient strain, which is devoid of stringent response, exhibits a significantly longer growth lag than wild type strain during adapting to both amino acid downshift and carbon downshift. Quantitative proteomics show that increased (p)ppGpp level promotes the growth adaption of bacteria to amino acid downshift via triggering the proteome resource re-allocation from ribosome synthesis to amino acid biosynthesis. Such type of proteome re-allocation is significantly delayed in the relA-deficient strain, which underlies its longer lag than wild type strain during amino acid downshift. During carbon downshift, a lack of stringent response in relA deficient strain leads to disruption of the transcription-translation coordination, thus compromising the transcription processivity and further the timely expression of related catabolic operons for utilizing secondary carbon sources. Our studies shed light on the fundamental strategy of bacteria to maintain fitness under nutrient-fluctuating environments.
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Affiliation(s)
- Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China.
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China.
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28
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Cheng JH, Zou S, Ma J, Sun DW. Toxic reactive oxygen species stresses for reconfiguring central carbon metabolic fluxes in foodborne bacteria: Sources, mechanisms and pathways. Crit Rev Food Sci Nutr 2023; 63:1806-1821. [PMID: 36688292 DOI: 10.1080/10408398.2023.2169245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The toxic reactive oxygen species (toxROS) is the reactive oxygen species (ROS) beyond the normal concentration of cells, which has inactivation and disinfection effects on foodborne bacteria. However, foodborne bacteria can adapt and survive by physicochemical regulation of antioxidant systems, especially through central carbon metabolism (CCM), which is a significant concern for food safety. It is thus necessary to study the antioxidant regulation mechanisms of CCM in foodborne bacteria under toxROS stresses. Therefore, the purpose of this review is to provide an update and comprehensive overview of the reconfiguration of CCM fluxes in foodborne bacteria that respond to different toxROS stresses. In this review, two key types of toxROS including exogenous toxROS (exo-toxROS) and endogenous toxROS (endo-toxROS) are introduced. Exo-toxROS are produced by disinfectants, such as H2O2 and HOCl, or during food non-thermal processing such as ultraviolet (UV/UVA), cold plasma (CP), ozone (O3), electrolyzed water (EW), pulsed electric field (PEF), pulsed light (PL), and electron beam (EB) processing. Endo-toxROS are generated by bioreagents such as antibiotics (aminoglycosides, quinolones, and β-lactams). Three main pathways for CCM in foodborne bacteria under the toxROS stress are also highlighted, which are glycolysis (EMP), pentose phosphate pathway (PPP), and tricarboxylic acid cycle (TCA). In addition, energy metabolisms throughout these pathways are discussed. Finally, challenges and future work in this area are suggested. It is hoped that this review should be beneficial in providing insights for future research on bacterial antioxidant CCM defence under both exo-toxROS stresses and endo-toxROS stresses.
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Affiliation(s)
- Jun-Hu Cheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Sang Zou
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Ji Ma
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Dublin 4, Ireland
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29
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Targeted Metabolomics and High-Throughput RNA Sequencing-Based Transcriptomics Reveal Massive Changes in the Streptomyces venezuelae NRRL B-65442 Metabolism Caused by Ethanol Shock. Microbiol Spectr 2022; 10:e0367222. [PMID: 36314940 PMCID: PMC9769785 DOI: 10.1128/spectrum.03672-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The species Streptomyces venezuelae is represented by several distinct strains with variable abilities to biosynthesize structurally diverse secondary metabolites. In this work, we examined the effect of ethanol shock on the transcriptome and metabolome of Streptomyces venezuelae NRRL B-65442 using high-throughput RNA sequencing (RNA-seq) and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). Ethanol shock caused massive changes in the gene expression profile, differentially affecting genes for secondary metabolite biosynthesis and central metabolic pathways. Most of the data from the transcriptome analysis correlated well with the metabolome changes, including the overproduction of jadomycin congeners and a downshift in the production of desferrioxamines, legonoxamine, foroxymithin, and a small cryptic ribosomally synthesized peptide. Some of the metabolome changes, such as the overproduction of chloramphenicol, could not be explained by overexpression of the cognate biosynthetic genes but correlated with the expression profiles of genes for precursor biosynthesis. Changes in the transcriptome were also observed for several genes known to play a role in stress response in other bacteria and included at least 10 extracytoplasmic function σ factors. This study provides important new insights into the stress response in antibiotic-producing bacteria and will help to understand the complex mechanisms behind the environmental factor-induced regulation of secondary metabolite biosynthesis. IMPORTANCE Streptomyces spp. are filamentous Gram-positive bacteria known as versatile producers of secondary metabolites, of which some have been developed into human medicines against infections and cancer. The genomes of these bacteria harbor dozens of gene clusters governing the biosynthesis of secondary metabolites (BGCs), of which most are not expressed under laboratory conditions. Detailed knowledge of the complex regulation of BGC expression is still lacking, although certain growth conditions are known to trigger the production of previously undetected secondary metabolites. In this work, we investigated the effect of ethanol shock on the production of secondary metabolites by Streptomyces venezuelae and correlated these findings with the expression of cognate BGCs and primary metabolic pathways involved in the generation of cofactors and precursors. The findings of this study set the stage for the rational manipulation of bacterial genomes aimed at enhanced production of industrially important bioactive natural products.
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30
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Harten T, Nimzyk R, Gawlick VEA, Reinhold-Hurek B. Elucidation of Essential Genes and Mutant Fitness during Adaptation toward Nitrogen Fixation Conditions in the Endophyte Azoarcus olearius BH72 Revealed by Tn-Seq. Microbiol Spectr 2022; 10:e0216222. [PMID: 36416558 PMCID: PMC9769520 DOI: 10.1128/spectrum.02162-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/05/2022] [Indexed: 11/24/2022] Open
Abstract
Azoarcus olearius BH72 is a diazotrophic model endophyte that contributes fixed nitrogen to its host plant, Kallar grass, and expresses nitrogenase genes endophytically. Despite extensive studies on biological nitrogen fixation (BNF) of diazotrophic endophytes, little is known about global genetic players involved in survival under respective physiological conditions. Here, we report a global genomic screen for putatively essential genes of A. olearius employing Tn5 transposon mutagenesis with a modified transposon combined with high-throughput sequencing (Tn-Seq). A large Tn5 master library of ~6 × 105 insertion mutants of strain BH72 was obtained. Next-generation sequencing identified 183,437 unique insertion sites into the 4,376,040-bp genome, displaying one insertion every 24 bp on average. Applying stringent criteria, we describe 616 genes as putatively essential for growth on rich medium. COG (Clusters of Orthologous Groups) assignment of the 564 identified protein-coding genes revealed enrichment of genes related to core cellular functions and cell viability. To mimic gradual adaptations toward BNF conditions, the Tn5 mutant library was grown aerobically in synthetic medium or microaerobically on either combined or atmospheric nitrogen. Enrichment and depletion analysis of Tn5 mutants not only demonstrated the role of BNF- and metabolism-related proteins but also revealed that, strikingly, many genes relevant for plant-microbe interactions decrease bacterial competitiveness in pure culture, such type IV pilus- and bacterial envelope-associated genes. IMPORTANCE A constantly growing world population and the daunting challenge of climate change demand new strategies in agricultural crop production. Intensive usage of chemical fertilizers, overloading the world's fields with organic input, threaten terrestrial and marine ecosystems as well as human health. Long overlooked, the beneficial interaction of endophytic bacteria and grasses has attracted ever-growing interest in research in the last decade. Capable of biological nitrogen fixation, diazotrophic endophytes not only provide a valuable source of combined nitrogen but also are known for diverse plant growth-promoting effects, thereby contributing to plant productivity. Elucidation of an essential gene set for a prominent model endophyte such as A. olearius BH72 provides us with powerful insights into its basic lifestyle. Knowledge about genes detrimental or advantageous under defined physiological conditions may point out a way of manipulating key steps in the bacterium's lifestyle and plant interaction toward a more sustainable agriculture.
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Affiliation(s)
- Theresa Harten
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
| | - Rolf Nimzyk
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Nucleic Acid Analysis Facility (NAA), Bremen, Germany
| | - Vivian E. A. Gawlick
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
| | - Barbara Reinhold-Hurek
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
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Yang P, Liu W, Chen Y, Gong AD. Engineering the glyoxylate cycle for chemical bioproduction. Front Bioeng Biotechnol 2022; 10:1066651. [PMID: 36532595 PMCID: PMC9755347 DOI: 10.3389/fbioe.2022.1066651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 07/24/2023] Open
Abstract
With growing concerns about environmental issues and sustainable economy, bioproduction of chemicals utilizing microbial cell factories provides an eco-friendly alternative to current petro-based processes. Creating high-performance strains (with high titer, yield, and productivity) through metabolic engineering strategies is critical for cost-competitive production. Commonly, it is inevitable to fine-tuning or rewire the endogenous or heterologous pathways in such processes. As an important pathway involved in the synthesis of many kinds of chemicals, the potential of the glyoxylate cycle in metabolic engineering has been studied extensively these years. Here, we review the metabolic regulation of the glyoxylate cycle and summarize recent achievements in microbial production of chemicals through tuning of the glyoxylate cycle, with a focus on studies implemented in model microorganisms. Also, future prospects for bioproduction of glyoxylate cycle-related chemicals are discussed.
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Mutyala S, Kim JR. Recent advances and challenges in the bioconversion of acetate to value-added chemicals. BIORESOURCE TECHNOLOGY 2022; 364:128064. [PMID: 36195215 DOI: 10.1016/j.biortech.2022.128064] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Acetate is a major byproduct of the bioconversion of the greenhouse gas carbon dioxide, pretreatment of lignocellulose biomass, and microbial fermentation. The utilization and valorization of acetate have been emphasized in transforming waste to clean energy and value-added platform chemicals, contributing to the development of a closed carbon loop toward a low-carbon circular bio-economy. Acetate has been used to produce several platform chemicals, including succinate, 3-hydroxypropionate, and itaconic acid, highlighting the potential of acetate to synthesize many biochemicals and biofuels. On the other hand, the yields and titers have not reached the theoretical maximum. Recently, recombinant strain development and pathway regulation have been suggested to overcome this limitation. This review provides insights into the important constraints limiting the yields and titers of the biochemical and metabolic pathways of bacteria capable of metabolizing acetate for acetate bioconversion. The current developments in recombinant strain engineering are also discussed.
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Affiliation(s)
- Sakuntala Mutyala
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
| | - Jung Rae Kim
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea.
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Andrés CMC, Pérez de la Lastra JM, Juan CA, Plou FJ, Pérez-Lebeña E. The Role of Reactive Species on Innate Immunity. Vaccines (Basel) 2022; 10:vaccines10101735. [PMID: 36298601 PMCID: PMC9609844 DOI: 10.3390/vaccines10101735] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
This review examines the role of reactive species RS (of oxygen ROS, nitrogen RNS and halogen RHS) on innate immunity. The importance of these species in innate immunity was first recognized in phagocytes that underwent a “respiratory burst” after activation. The anion superoxide •O2− and hydrogen peroxide H2O2 are detrimental to the microbial population. NADPH oxidase NOx, as an •O2− producer is essential for microbial destruction, and patients lacking this functional oxidase are more susceptible to microbial infections. Reactive nitrogen species RNS (the most important are nitric oxide radical -•NO, peroxynitrite ONOO— and its derivatives), are also harmful to microorganisms, including bacteria, viruses, and parasites. Hypochlorous acid HOCl and hypothiocyanous acid HOSCN synthesized through the enzyme myeloperoxidase MPO, which catalyzes the reaction between H2O2 and Cl− or SCN−, are important inorganic bactericidal molecules, effective against a wide range of microbes. This review also discusses the role of antimicrobial peptides AMPs and their induction of ROS. In summary, reactive species RS are the heart of the innate immune system, and they are necessary for microbial lysis in infections that can affect mammals throughout their lives.
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Affiliation(s)
| | - José Manuel Pérez de la Lastra
- Institute of Natural Products and Agrobiology, CSIC-Spanish Research Council, Avda. Astrofísico Fco. Sánchez 3, 38206 La Laguna, Spain
- Correspondence:
| | - Celia Andrés Juan
- Cinquima Institute and Department of Organic Chemistry, Faculty of Sciences, Valladolid University, Paseo de Belén 7, 47011 Valladolid, Spain
| | - Francisco J. Plou
- Institute of Catalysis and Petrochemistry, CSIC-Spanish Research Council, 28049 Madrid, Spain
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Jugder BE, Batista JH, Gibson JA, Cunningham PM, Asara JM, Watnick PI. Vibrio cholerae high cell density quorum sensing activates the host intestinal innate immune response. Cell Rep 2022; 40:111368. [PMID: 36130487 PMCID: PMC9534793 DOI: 10.1016/j.celrep.2022.111368] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/17/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Quorum sensing fundamentally alters the interaction of Vibrio cholerae with aquatic environments, environmental hosts, and the human intestine. At high cell density, the quorum-sensing regulator HapR represses not only expression of cholera toxin and the toxin co-regulated pilus, virulence factors essential in human infection, but also synthesis of the Vibrio polysaccharide (VPS) exopolysaccharide-based matrix required for abiotic and biotic surface attachment. Here, we describe a feature of V. cholerae quorum sensing that shifts the host-pathogen interaction toward commensalism. By repressing pathogen consumptive anabolic metabolism and, in particular, tryptophan uptake, V. cholerae HapR stimulates host intestinal serotonin production. This, in turn, activates host intestinal innate immune signaling to promote host survival.
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Affiliation(s)
- Bat-Erdene Jugder
- Division of Infectious Diseases, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA
| | - Juliana H Batista
- Division of Infectious Diseases, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA
| | - Jacob A Gibson
- Division of Infectious Diseases, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Biological and Biomedical Sciences Program, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA
| | - Paul M Cunningham
- Division of Infectious Diseases, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Blackfan Circle, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Paula I Watnick
- Division of Infectious Diseases, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA.
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35
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Zhang S, An X, Gong J, Xu Z, Wang L, Xia X, Zhang Q. Molecular response of Anoxybacillus sp. PDR2 under azo dye stress: An integrated analysis of proteomics and metabolomics. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129500. [PMID: 35792431 DOI: 10.1016/j.jhazmat.2022.129500] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Treating azo dye wastewater using thermophilic bacteria is considered a more efficient bioremediation strategy. In this study, a thermophilic bacterial strain, Anoxybacillus sp. PDR2, was regarded as the research target. This strain was characterized at different stages of azo dye degradation by using TMT quantitative proteomic and non-targeted metabolome technology. A total of 165 differentially expressed proteins (DEPs) and 439 differentially metabolites (DMs) were detected in comparisons between bacteria with and without azo dye. It was found that Anoxybacillus sp. PDR2 can degrade azo dye Direct Black G (DBG) through extracellular electron transfer with glucose serving as electron donors. Most proteins related to carbohydrate metabolism, including acetoacetate synthase, and malate synthase G, were overexpressed to provide energy. The bacterium can also self-synthesize riboflavin as a redox mediator of in vitro electron transport. These results lay a theoretical basis for industrial bioremediation of azo dye wastewater.
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Affiliation(s)
- Shulin Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Xuejiao An
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Jiaming Gong
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Zihang Xu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Liuwei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Xiang Xia
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Qinghua Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, PR China.
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36
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Zeng N, Zhang N, Ma X, Wang Y, Zhang Y, Wang D, Pu F, Li B. Transcriptomics Integrated with Metabolomics: Assessing the Central Metabolism of Different Cells after Cell Differentiation in Aureobasidium pullulans NG. J Fungi (Basel) 2022; 8:jof8080882. [PMID: 36012870 PMCID: PMC9410427 DOI: 10.3390/jof8080882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
When organisms are stimulated by external stresses, oxidative stress is induced, resulting in the production of large amounts of reactive oxygen species (ROS) that inhibit cell growth and accelerate cellular aging until death. Understanding the molecular mechanisms of abiotic stress is important to enhance cellular resistance, and Aureobasidium pullulans, a highly resistant yeast-like fungus, can use cellular differentiation to resist environmental stress. Here, swollen cells (SCs) from two different differentiation periods in Aureobasidium pullulans NG showed significantly higher antioxidant capacity and stress defense capacity than yeast-like cells (YL). The transcriptome and the metabolome of both cells were analyzed, and the results showed that amino acid metabolism, carbohydrate metabolism, and lipid metabolism were significantly enriched in SCs. Glyoxylate metabolism was significantly upregulated in carbohydrate metabolism, replacing the metabolic hub of the citric acid (TCA) cycle, helping to coordinate multiple metabolic pathways and playing an important role in the resistance of Aureobasidium pullulans NG to environmental stress. Finally, we obtained 10 key genes and two key metabolites in SCs, which provide valuable clues for subsequent validation. In conclusion, these results provide valuable information for assessing central metabolism-mediating oxidative stress in Aureobasidium pullulans NG, and also provide new ideas for exploring the pathways of eukaryotic resistance to abiotic stress.
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Affiliation(s)
- Nan Zeng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Ning Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (N.Z.); (B.L.)
| | - Xin Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yunjiao Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yating Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Dandan Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Fangxiong Pu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Bingxue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (N.Z.); (B.L.)
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37
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Fung V, Xiao Y, Tan ZJD, Ma X, Zhou JFJ, Panda S, Yan N, Zhou K. Producing aromatic amino acid from corn husk by using polyols as intermediates. Biomaterials 2022; 287:121661. [PMID: 35842981 DOI: 10.1016/j.biomaterials.2022.121661] [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: 02/11/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/22/2022]
Abstract
Agricultural biomass remains as one of the commonly found waste on Earth. Although valorisation of these wastes has been studied in detail, the fermentation-based processes still need improvement due to the high cost of hydrolysing enzymes, and the presence of growth inhibitors which constrains the fermentation to produce high-value products. To address these challenges, we developed an integrated process in this study combining abiotic- and bio-catalysis to produce l-tyrosine from corn husk. The first step involved a one-pot hydrolytic hydrogenation tandem reaction without the use of the expensive enzymes, which yielded a mixture of polyols and sugars. Without any purification, these crude hydrolysates can be almost completely utilized by an engineered Escherichia coli strain, which did not exhibit any growth inhibition. The strain produced 0.44 g/L l-tyrosine from 10 g/L crude corn husk hydrolysates, demonstrating the feasibility of converting agricultural biomass into a valuable aromatic amino acid via an integrated process.
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Affiliation(s)
- Vincent Fung
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Yiying Xiao
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore; Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou, 350207, China
| | - Zhi Jun Daniel Tan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Xiaoqiang Ma
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Jie Fu J Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Smaranika Panda
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Ning Yan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore.
| | - Kang Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore.
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38
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Degradation of Exogenous Fatty Acids in Escherichia coli. Biomolecules 2022; 12:biom12081019. [PMID: 35892328 PMCID: PMC9329746 DOI: 10.3390/biom12081019] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/10/2022] Open
Abstract
Many bacteria possess all the machineries required to grow on fatty acids (FA) as a unique source of carbon and energy. FA degradation proceeds through the β-oxidation cycle that produces acetyl-CoA and reduced NADH and FADH cofactors. In addition to all the enzymes required for β-oxidation, FA degradation also depends on sophisticated systems for its genetic regulation and for FA transport. The fact that these machineries are conserved in bacteria suggests a crucial role in environmental conditions, especially for enterobacteria. Bacteria also possess specific enzymes required for the degradation of FAs from their environment, again showing the importance of this metabolism for bacterial adaptation. In this review, we mainly describe FA degradation in the Escherichia coli model, and along the way, we highlight and discuss important aspects of this metabolism that are still unclear. We do not detail exhaustively the diversity of the machineries found in other bacteria, but we mention them if they bring additional information or enlightenment on specific aspects.
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39
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Liu Y, Fang D, Yang K, Xu T, Su C, Li R, Xiao X, Wang Z. Sodium dehydroacetate confers broad antibiotic tolerance by remodeling bacterial metabolism. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128645. [PMID: 35299107 DOI: 10.1016/j.jhazmat.2022.128645] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic tolerance has been a growing crisis that is seriously threatening global public health. However, little is known about the exogenous factors capable of triggering the development of antibiotic tolerance, particularly in vivo. Here we uncovered that an previously approved food additive termed sodium dehydroacetate (DHA-S) supplementation remarkably impaired the activity of bactericidal antibiotics against various bacterial pathogens. Mechanistic studies indicated that DHA-S induced glyoxylate shunt and reduced bacterial cellular respiration by inhibiting the enzymatic activity of α-ketoglutarate dehydrogenase (α-KGDH). Furthermore, DHA-S mitigated oxidative stress imposed by bactericidal antibiotics and enhanced the function of multidrug efflux pumps. These actions worked together to induce bacterial tolerance to antibiotic killing. Interestingly, the addition of five exogenous amino acids, particularly cysteine and proline, effectively reversed antibiotic tolerance elicited by DHA-S both in vitro and in mouse models of infection. Taken together, these findings advance our understanding of the potential risks of DHA-S in the treatment of bacterial infections, and shed new insights into the relationships between antibiotic tolerance and bacterial metabolism.
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Affiliation(s)
- Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China.
| | - Dan Fang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Kangni Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Tianqi Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Chengrui Su
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xia Xiao
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
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40
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Cao M, Tran VG, Qin J, Olson A, Mishra S, Schultz JC, Huang C, Xie D, Zhao H. Metabolic engineering of oleaginous yeast Rhodotorula toruloides for overproduction of triacetic acid lactone. Biotechnol Bioeng 2022; 119:2529-2540. [PMID: 35701887 PMCID: PMC9540541 DOI: 10.1002/bit.28159] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/16/2022] [Accepted: 06/12/2022] [Indexed: 12/19/2022]
Abstract
The plant‐sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2‐pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl‐CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP‐citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl‐CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12‐ACL1‐ACC1 using fed‐batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl‐CoA‐derived polyketides from low‐cost carbon sources.
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Affiliation(s)
- Mingfeng Cao
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Vinh G Tran
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Andrew Olson
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Shekhar Mishra
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John C Schultz
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Chunshuai Huang
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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41
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Jindal S, Iyer MS, Jyoti P, Masakapalli SK, Venkatesh KV. Mutants lacking global regulators, fis and arcA, in Escherichia coli enhanced growth fitness under acetate metabolism by pathway reprogramming. Appl Microbiol Biotechnol 2022; 106:3231-3243. [PMID: 35416487 DOI: 10.1007/s00253-022-11890-6] [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: 08/13/2021] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 11/25/2022]
Abstract
Global regulatory transcription factors play a significant role in controlling microbial metabolism under genetic and environmental perturbations. A system-level effect of carbon sources such as acetate on microbial metabolism under disrupted global regulators has not been well established. Acetate is one of the major substrates available in various nutrient niches such as the mammalian gut and a keto diet. A substantial amount of acetate gets secreted in aerobic metabolism. Therefore, investigating the study on acetate metabolism is highly significant. It is known that the global regulators fis and arcA regulate acetate uptake genes in E. coli under glucose conditions. This study deciphered the growth and flux distribution of E. coli transcription regulatory knockouts Δfis, ΔarcA and double deletion mutant, ΔarcAΔfis under acetate using 13C-metabolic flux analysis (MFA), which has not been investigated before. We observed that the mutants exhibited an expeditious growth rate (~ 1.2-1.6-fold) with a proportionate increase in acetate uptake rates compared to the wild type. 13C-MFA displayed the distinct metabolic reprogramming of intracellular fluxes via the TCA cycle, anaplerotic pathway and gluconeogenesis, which conferred an advantage of a faster growth rate with better carbon usage in all the mutants. This resulted in higher metabolic fluxes through the TCA cycle (~ 18-90%), lower gluconeogenesis (~ 15-35%) and higher CO2 and ATP production with the proportional increase in growth rate. The study reveals a novel insight by stating the sub-optimality of the wild-type strain grown under acetate substrate aerobically. These mutant strains efficiently oxidize acetate, thus acting as potential candidates for the biosynthesis of isoprenoids, biofuels, vitamins and various pharmaceutical products.Key Points• Mutants exhibited a better balance between energy and precursor synthesis than WT.• Leveraged in the unravelling of regulatory control under various nutrient shifts.• Metabolic readjustment resulted in optimal biomass requirement and faster growth.
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Affiliation(s)
- Shikha Jindal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Mahesh S Iyer
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Poonam Jyoti
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, 175075, India
| | - Shyam Kumar Masakapalli
- BioX Center, School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, 175075, India.
| | - K V Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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42
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Rosenberg G, Riquelme S, Prince A, Avraham R. Immunometabolic crosstalk during bacterial infection. Nat Microbiol 2022; 7:497-507. [PMID: 35365784 DOI: 10.1038/s41564-022-01080-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/03/2022] [Indexed: 01/22/2023]
Abstract
Following detection of bacteria, macrophages switch their metabolism from oxidative respiration through the tricarboxylic acid cycle to high-rate aerobic glycolysis. This immunometabolic shift enables pro-inflammatory and antimicrobial responses and is facilitated by the accumulation of fatty acids, tricarboxylic acid-derived metabolites and catabolism of amino acids. Recent studies have shown that these immunometabolites are co-opted by pathogens as environmental cues for expression of virulence genes. We review mechanisms by which host immunometabolites regulate bacterial pathogenicity and discuss opportunities for the development of therapeutics targeting metabolic host-pathogen crosstalk.
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Affiliation(s)
- Gili Rosenberg
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Alice Prince
- Columbia University Medical Center, New York, NY, USA.
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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43
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Hartline CJ, Zhang R, Zhang F. Transient Antibiotic Tolerance Triggered by Nutrient Shifts From Gluconeogenic Carbon Sources to Fatty Acid. Front Microbiol 2022; 13:854272. [PMID: 35359720 PMCID: PMC8963472 DOI: 10.3389/fmicb.2022.854272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/22/2022] [Indexed: 12/04/2022] Open
Abstract
Nutrient shifts from glycolytic-to-gluconeogenic carbon sources can create large sub-populations of extremely antibiotic tolerant bacteria, called persisters. Positive feedback in Escherichia coli central metabolism was believed to play a key role in the formation of persister cells. To examine whether positive feedback in nutrient transport can also support high persistence to β-lactams, we performed nutrient shifts for E. coli from gluconeogenic carbon sources to fatty acid (FA). We observed tri-phasic antibiotic killing kinetics characterized by a transient period of high antibiotic tolerance, followed by rapid killing then a slower persister-killing phase. The duration of transient tolerance (3-44 h) varies with pre-shift carbon source and correlates strongly with the time needed to accumulate the FA degradation enzyme FadD after the shift. Additionally, FadD accumulation time and thus transient tolerance time can be reduced by induction of the glyoxylate bypass prior to switching, highlighting that two interacting feedback loops simultaneously control the length of transient tolerance. Our results demonstrate that nutrient switches along with positive feedback are not sufficient to trigger persistence in a majority of the population but instead triggers only a temporary tolerance. Additionally, our results demonstrate that the pre-shift metabolic state determines the duration of transient tolerance and that supplying glyoxylate can facilitate antibiotic killing of bacteria.
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Affiliation(s)
- Christopher J. Hartline
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, United States
| | - Ruixue Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, United States
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, United States
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO, United States
- Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, MO, United States
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Li H, Xie R, Xu X, Liao X, Guo J, Fang Y, Fang Z, Huang J. Static Magnetic Field Inhibits Growth of Escherichia coli Colonies via Restriction of Carbon Source Utilization. Cells 2022; 11:cells11050827. [PMID: 35269449 PMCID: PMC8909705 DOI: 10.3390/cells11050827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Magnetobiological effects on growth and virulence have been widely reported in Escherichia coli (E. coli). However, published results are quite varied and sometimes conflicting because the underlying mechanism remains unknown. Here, we reported that the application of 250 mT static magnetic field (SMF) significantly reduces the diameter of E. coli colony-forming units (CFUs) but has no impact on the number of CFUs. Transcriptomic analysis revealed that the inhibitory effect of SMF is attributed to differentially expressed genes (DEGs) primarily involved in carbon source utilization. Consistently, the addition of glycolate or glyoxylate to the culture media successfully restores the bacterial phenotype in SMF, and knockout mutants lacking glycolate oxidase are no longer sensitive to SMF. These results suggest that SMF treatment results in a decrease in glycolate oxidase activity. In addition, metabolomic assay showed that long-chain fatty acids (LCFA) accumulate while phosphatidylglycerol and middle-chain fatty acids decrease in the SMF-treated bacteria, suggesting that SMF inhibits LCFA degradation. Based on the published evidence together with ours derived from this study, we propose a model showing that free radicals generated by LCFA degradation are the primary target of SMF action, which triggers the bacterial oxidative stress response and ultimately leads to growth inhibition.
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Affiliation(s)
- Haodong Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Runnan Xie
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Xiang Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Xingru Liao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Jiaxin Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
| | - Yanwen Fang
- Heye Health Industrial Research Institute, Zhejiang Heye Health Technology, Anji, Huzhou 313300, China; (Y.F.); (Z.F.)
| | - Zhicai Fang
- Heye Health Industrial Research Institute, Zhejiang Heye Health Technology, Anji, Huzhou 313300, China; (Y.F.); (Z.F.)
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China; (H.L.); (R.X.); (X.X.); (X.L.); (J.G.)
- Correspondence:
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Cyanide as a primordial reductant enables a protometabolic reductive glyoxylate pathway. Nat Chem 2022; 14:170-178. [PMID: 35115655 DOI: 10.1038/s41557-021-00878-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022]
Abstract
Investigation of prebiotic metabolic pathways is predominantly based on abiotically replicating the reductive citric acid cycle. While attractive from a parsimony point of view, attempts using metal/mineral-mediated reductions have produced complex mixtures with inefficient and uncontrolled reactions. Here we show that cyanide acts as a mild and efficient reducing agent mediating abiotic transformations of tricarboxylic acid intermediates and derivatives. The hydrolysis of the cyanide adducts followed by their decarboxylation enables the reduction of oxaloacetate to malate and of fumarate to succinate, whereas pyruvate and α-ketoglutarate themselves are not reduced. In the presence of glyoxylate, malonate and malononitrile, alternative pathways emerge that bypass the challenging reductive carboxylation steps to produce metabolic intermediates and compounds found in meteorites. These results suggest a simpler prebiotic forerunner of today's metabolism, involving a reductive glyoxylate pathway without oxaloacetate and α-ketoglutarate-implying that the extant metabolic reductive carboxylation chemistries are an evolutionary invention mediated by complex metalloproteins.
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46
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Duncan D, Auclair K. Itaconate: an antimicrobial metabolite of macrophages. CAN J CHEM 2022. [DOI: 10.1139/cjc-2021-0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Itaconate is a conjugated 1,4-dicarboxylate produced by macrophages. This small molecule has recently received increasing attention due to its role in modulating the immune response of macrophages upon exposure to pathogens. Itaconate has also been proposed to play an antimicrobial function; however, this has not been explored as intensively. Consistent with the latter, itaconate is known to show antibacterial activity in vitro and was reported to inhibit isocitrate lyase, an enzyme required for survival of bacterial pathogens in mammalian systems. Recent studies have revealed bacterial growth inhibition under biologically relevant conditions. In addition, an antimicrobial role for itaconate is substantiated by the high concentration of itaconate found in bacteria-containing vacuoles, and by the production of itaconate-degrading enzymes in pathogens such as Salmonella enterica ser. Typhimurium, Pseudomonas aeruginosa, and Yersinia pestis. This review describes the current state of literature in understanding the role of itaconate as an antimicrobial agent in host–pathogen interactions.
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Affiliation(s)
- Dustin Duncan
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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Christensen M, Jablonski P, Altermark B, Irgum K, Hansen H. High natural PHA production from acetate in Cobetia sp. MC34 and Cobetia marina DSM 4741 T and in silico analyses of the genus specific PhaC 2 polymerase variant. Microb Cell Fact 2021; 20:225. [PMID: 34930259 PMCID: PMC8686332 DOI: 10.1186/s12934-021-01713-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/28/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Several members of the bacterial Halomonadacea family are natural producers of polyhydroxyalkanoates (PHA), which are promising materials for use as biodegradable bioplastics. Type-strain species of Cobetia are designated PHA positive, and recent studies have demonstrated relatively high PHA production for a few strains within this genus. Industrially relevant PHA producers may therefore be present among uncharacterized or less explored members. In this study, we characterized PHA production in two marine Cobetia strains. We further analyzed their genomes to elucidate pha genes and metabolic pathways which may facilitate future optimization of PHA production in these strains. RESULTS Cobetia sp. MC34 and Cobetia marina DSM 4741T were mesophilic, halotolerant, and produced PHA from four pure substrates. Sodium acetate with- and without co-supplementation of sodium valerate resulted in high PHA production titers, with production of up to 2.5 g poly(3-hydroxybutyrate) (PHB)/L and 2.1 g poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)/L in Cobetia sp. MC34, while C. marina DSM 4741T produced 2.4 g PHB/L and 3.7 g PHBV/L. Cobetia marina DSM 4741T also showed production of 2.5 g PHB/L from glycerol. The genome of Cobetia sp. MC34 was sequenced and phylogenetic analyses revealed closest relationship to Cobetia amphilecti. PHA biosynthesis genes were located at separate loci similar to the arrangement in other Halomonadacea. Further genome analyses revealed some differences in acetate- and propanoate metabolism genes between the two strains. Interestingly, only a single PHA polymerase gene (phaC2) was found in Cobetia sp. MC34, in contrast to two copies (phaC1 and phaC2) in C. marina DSM 4741T. In silico analyses based on phaC genes show that the PhaC2 variant is conserved in Cobetia and contains an extended C-terminus with a high isoelectric point and putative DNA-binding domains. CONCLUSIONS Cobetia sp. MC34 and C. marina DSM 4741T are natural producers of PHB and PHBV from industrially relevant pure substrates including acetate. However, further scale up, optimization of growth conditions, or use of metabolic engineering is required to obtain industrially relevant PHA production titers. The putative role of the Cobetia PhaC2 variant in DNA-binding and the potential implications remains to be addressed by in vitro- or in vivo methods.
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Affiliation(s)
- Mikkel Christensen
- Department of Chemistry, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Piotr Jablonski
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Bjørn Altermark
- Department of Chemistry, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Knut Irgum
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Hilde Hansen
- Department of Chemistry, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
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48
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Chang JD, Vaughan EE, Liu CG, Jelinski JW, Terwilliger AL, Maresso AW. Metabolic profiling reveals nutrient preferences during carbon utilization in Bacillus species. Sci Rep 2021; 11:23917. [PMID: 34903830 PMCID: PMC8669014 DOI: 10.1038/s41598-021-03420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/29/2021] [Indexed: 11/18/2022] Open
Abstract
The genus Bacillus includes species with diverse natural histories, including free-living nonpathogenic heterotrophs such as B. subtilis and host-dependent pathogens such as B. anthracis (the etiological agent of the disease anthrax) and B. cereus, a cause of food poisoning. Although highly similar genotypically, the ecological niches of these three species are mutually exclusive, which raises the untested hypothesis that their metabolism has speciated along a nutritional tract. Here, we developed a pipeline for quantitative total assessment of the use of diverse sources of carbon for general metabolism to better appreciate the "culinary preferences" of three distinct Bacillus species, as well as related Staphylococcus aureus. We show that each species has widely varying metabolic ability to utilize diverse sources of carbon that correlated to their ecological niches. This approach was applied to the growth and survival of B. anthracis in a blood-like environment and find metabolism shifts from sugar to amino acids as the preferred source of energy. Finally, various nutrients in broth and host-like environments are identified that may promote or interfere with bacterial metabolism during infection.
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Affiliation(s)
- James D Chang
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Ellen E Vaughan
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Carmen Gu Liu
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph W Jelinski
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Austen L Terwilliger
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony W Maresso
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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49
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Brinkman FSL, Winsor GL, Done RE, Filloux A, Francis VI, Goldberg JB, Greenberg EP, Han K, Hancock REW, Haney CH, Häußler S, Klockgether J, Lamont IL, Levesque RC, Lory S, Nikel PI, Porter SL, Scurlock MW, Schweizer HP, Tümmler B, Wang M, Welch M. The Pseudomonas aeruginosa whole genome sequence: A 20th anniversary celebration. Adv Microb Physiol 2021; 79:25-88. [PMID: 34836612 DOI: 10.1016/bs.ampbs.2021.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Toward the end of August 2000, the 6.3 Mbp whole genome sequence of Pseudomonas aeruginosa strain PAO1 was published. With 5570 open reading frames (ORFs), PAO1 had the largest microbial genome sequenced up to that point in time-including a large proportion of metabolic, transport and antimicrobial resistance genes supporting its ability to colonize diverse environments. A remarkable 9% of its ORFs were predicted to encode proteins with regulatory functions, providing new insight into bacterial network complexity as a function of network size. In this celebratory article, we fast forward 20 years, and examine how access to this resource has transformed our understanding of P. aeruginosa. What follows is more than a simple review or commentary; we have specifically asked some of the leaders in the field to provide personal reflections on how the PAO1 genome sequence, along with the Pseudomonas Community Annotation Project (PseudoCAP) and Pseudomonas Genome Database (pseudomonas.com), have contributed to the many exciting discoveries in this field. In addition to bringing us all up to date with the latest developments, we also ask our contributors to speculate on how the next 20 years of Pseudomonas research might pan out.
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Affiliation(s)
- Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Rachel E Done
- Department of Pediatrics, Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Emory Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, United States
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Vanessa I Francis
- Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Emory Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, United States
| | - E Peter Greenberg
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Kook Han
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | | | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Susanne Häußler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jens Klockgether
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Pavillon Charles-Eugène Marchand, Faculté of Médicine, Université Laval, Québec City, QC, Canada
| | - Stephen Lory
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Steven L Porter
- Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | | | - Herbert P Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Burkhard Tümmler
- Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Meng Wang
- Department of Biochemistry (Hopkins Building), University of Cambridge, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry (Hopkins Building), University of Cambridge, Cambridge, United Kingdom.
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50
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Regulation of the icl1 Gene Encoding the Major Isocitrate Lyase in Mycobacterium smegmatis. J Bacteriol 2021; 203:e0040221. [PMID: 34516281 DOI: 10.1128/jb.00402-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium smegmatis has two isocitrate lyase (ICL) isozymes (MSMEG_0911 and MSMEG_3706). We demonstrated that ICL1 (MSMEG_0911) is the predominantly expressed ICL in M. smegmatis and plays a major role in growth on acetate or fatty acid as the sole carbon and energy source. Expression of the icl1 gene in M. smegmatis was demonstrated to be strongly upregulated during growth on acetate relative to that in M. smegmatis grown on glucose. Expression of icl1 was shown to be positively regulated by the RamB activator, and three RamB-binding sites (RamBS1, RamBS2, and RamBS3) were identified in the upstream region of icl1 using DNase I footprinting analysis. Succinyl coenzyme A (succinyl-CoA) was shown to increase the affinity of binding of RamB to its binding sites and enable RamB to bind to RamBS2, which is the most important site for RamB-mediated induction of icl1 expression. These results suggest that succinyl-CoA serves as a coinducer molecule for RamB. Our study also showed that cAMP receptor protein (Crp1; MSMEG_6189) represses icl1 expression in M. smegmatis grown in the presence of glucose. Therefore, the strong induction of icl1 expression during growth on acetate as the sole carbon source relative to the weak expression of icl1 during growth on glucose is likely to result from combined effects of RamB-mediated induction of icl1 in the presence of acetate and Crp-mediated repression of icl1 in the presence of glucose. IMPORTANCE Carbon flux through the glyoxylate shunt has been suggested to affect virulence, persistence, and antibiotic resistance of Mycobacterium tuberculosis. Therefore, it is important to understand the precise mechanism underlying the regulation of the icl gene encoding the key enzyme of the glyoxylate shunt. Using Mycobacterium smegmatis, this study revealed the regulation mechanism underlying induction of icl1 expression in M. smegmatis when the glyoxylate shunt is required. The conservation of the cis- and trans-acting regulatory elements related to icl1 regulation in both M. smegmatis and M. tuberculosis implies that a similar regulatory mechanism operates for the regulation of icl1 expression in M. tuberculosis.
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