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Mendonca C, Zhang L, Waldbauer JR, Aristilde L. Disproportionate Carbon Dioxide Efflux in Bacterial Metabolic Pathways for Different Organic Substrates Leads to Variable Contribution to Carbon-Use Efficiency. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11041-11052. [PMID: 38860668 PMCID: PMC11210201 DOI: 10.1021/acs.est.4c01328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024]
Abstract
Microbial organic matter turnover is an important contributor to the terrestrial carbon dioxide (CO2) budget. Partitioning of organic carbons into biomass relative to CO2 efflux, termed carbon-use efficiency (CUE), is widely used to characterize organic carbon cycling by soil microorganisms. Recent studies challenge proposals of CUE dependence on the oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variability in CUE. We performed a multiomics investigation of these mechanisms in Pseudomonas putida, a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our 13C-metabolomics data captured substrate carbons into different metabolic pathways: cellulose-derived sugar carbons in glycolytic and pentose-phosphate pathways; lignin-related aromatic carbons in the tricarboxylic acid cycle. Subsequent 13C-metabolic flux analysis revealed a 3-fold lower investment of sugar carbons in CO2 efflux compared to aromatic carbons, in agreement with reported substrate-dependent CUE. Proteomics analysis revealed enzyme-level regulation only for substrate uptake and initial catabolism, which dictated downstream fluxes through CO2-producing versus biomass-synthesizing reactions. Metabolic partitioning as shown here explained the substrate-dependent CUE calculated from reported metabolic flux analyses of other bacteria, further supporting a metabolism-guided perspective for predicting the microbial conversion of accessible organic matter to CO2 efflux.
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Affiliation(s)
- Caroll
M. Mendonca
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Lichun Zhang
- Department
of the Geophysical Sciences, University
of Chicago, Chicago, Illinois 60637, United States
| | - Jacob R. Waldbauer
- Department
of the Geophysical Sciences, University
of Chicago, Chicago, Illinois 60637, United States
| | - Ludmilla Aristilde
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
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2
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Dvořák P, Burýšková B, Popelářová B, Ebert BE, Botka T, Bujdoš D, Sánchez-Pascuala A, Schöttler H, Hayen H, de Lorenzo V, Blank LM, Benešík M. Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. Nat Commun 2024; 15:2666. [PMID: 38531855 DOI: 10.1038/s41467-024-46812-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
To broaden the substrate scope of microbial cell factories towards renewable substrates, rational genetic interventions are often combined with adaptive laboratory evolution (ALE). However, comprehensive studies enabling a holistic understanding of adaptation processes primed by rational metabolic engineering remain scarce. The industrial workhorse Pseudomonas putida was engineered to utilize the non-native sugar D-xylose, but its assimilation into the bacterial biochemical network via the exogenous xylose isomerase pathway remained unresolved. Here, we elucidate the xylose metabolism and establish a foundation for further engineering followed by ALE. First, native glycolysis is derepressed by deleting the local transcriptional regulator gene hexR. We then enhance the pentose phosphate pathway by implanting exogenous transketolase and transaldolase into two lag-shortened strains and allow ALE to finetune the rewired metabolism. Subsequent multilevel analysis and reverse engineering provide detailed insights into the parallel paths of bacterial adaptation to the non-native carbon source, highlighting the enhanced expression of transaldolase and xylose isomerase along with derepressed glycolysis as key events during the process.
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Affiliation(s)
- Pavel Dvořák
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic.
| | - Barbora Burýšková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Barbora Popelářová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Birgitta E Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Cnr College Rd & Cooper Rd, St Lucia, QLD, QLD 4072, Australia
| | - Tibor Botka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Dalimil Bujdoš
- APC Microbiome Ireland, University College Cork, College Rd, Cork, T12 YT20, Ireland
- School of Microbiology, University College Cork, College Rd, Cork, T12 Y337, Ireland
| | - Alberto Sánchez-Pascuala
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Hannah Schöttler
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, Darwin 3, 28049, Madrid, Spain
| | - Lars M Blank
- Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Martin Benešík
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
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Casas-Román A, Lorite MJ, Sanjuán J, Gallegos MT. Two glyceraldehyde-3-phosphate dehydrogenases with distinctive roles in Pseudomonas syringae pv. tomato DC3000. Microbiol Res 2024; 278:127530. [PMID: 37890268 DOI: 10.1016/j.micres.2023.127530] [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: 08/23/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH or Gap) is a ubiquitously distributed enzyme that plays an essential role in the glycolytic and gluconeogenic pathways. However, additional roles have been described unrelated to its enzymatic function in diverse organisms, often linked to its presence in the cell surface or as a secreted protein. Despite being a paradigm among multifunctional/moonlighting proteins, little is known about its possible roles in phytopathogenic bacteria. In the present work we have studied three putative gap paralogous genes identified in the genome of Pseudomonas syringae pv. tomato (Pto) DC3000, an important model in molecular plant pathology, with the aim of determining their physiological and possible non-canonical roles in this bacterium and in the plant infection process. We have established that the Gap1 protein has a predominantly glycolytic activity, whereas the NADPH-dependent Gap2 main activity is gluconeogenic. The third paralogue lacks GAPDH activity in Pto but is indispensable for vitamin B6 metabolism and displays erythrose-4-phosphate dehydrogenase activity, thus referred as epd. Both Gap enzymes exhibit distinct functional characteristics depending on the bacterium physiological state, with Gap1 presenting a substantial role in motility, biosurfactant production and biofilm formation. On the other hand, solely Gap2 appears to be essential for growth on tomato plant. Furthermore, Gap1 and Gap2 present a distinctive transcriptional regulation and both have been identified exported outside the cells with different definite media compositions. This serves as compelling evidence of additional roles beyond their central metabolic functions.
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Affiliation(s)
- Ariana Casas-Román
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - María-José Lorite
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Juan Sanjuán
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain.
| | - María-Trinidad Gallegos
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain.
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Lin H, Ning X, Wang D, Wang Q, Bai Y, Qu J. Quorum-sensing gene regulates hormetic effects induced by sulfonamides in Comamonadaceae. Appl Environ Microbiol 2023; 89:e0166223. [PMID: 38047646 PMCID: PMC10734536 DOI: 10.1128/aem.01662-23] [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: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE Antibiotics can induce dose-dependent hormetic effects on bacterial cell proliferation, i.e., low-dose stimulation and high-dose inhibition. However, the underlying molecular basis has yet to be clarified. Here, we showed that sulfonamides play dual roles as a weapon and signal against Comamonas testosteroni that can modulate cell physiology and phenotype. Subsequently, through investigating the hormesis mechanism, we proposed a comprehensive regulatory pathway for the hormetic effects of Comamonas testosteroni low-level sulfonamides and determined the generality of the observed regulatory model in the Comamonadaceae family. Considering the prevalence of Comamonadaceae in human guts and environmental ecosystems, we provide critical insights into the health and ecological effects of antibiotics.
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Affiliation(s)
- Hui Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Xue Ning
- MaREI Centre, Environmental Research Institute, School of Engineering, University College Cork, Cork, Ireland
| | - Donglin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qiaojuan Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Yaohui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jiuhui Qu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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Wilkes RA, Waldbauer J, Carroll A, Nieto-Domínguez M, Parker DJ, Zhang L, Guss AM, Aristilde L. Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism. Nat Chem Biol 2023; 19:651-662. [PMID: 36747056 PMCID: PMC10154247 DOI: 10.1038/s41589-022-01237-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/29/2022] [Indexed: 02/08/2023]
Abstract
Critical to a sustainable energy future are microbial platforms that can process aromatic carbons from the largely untapped reservoir of lignin and plastic feedstocks. Comamonas species present promising bacterial candidates for such platforms because they can use a range of natural and xenobiotic aromatic compounds and often possess innate genetic constraints that avoid competition with sugars. However, the metabolic reactions of these species are underexplored, and the regulatory mechanisms are unknown. Here we identify multilevel regulation in the conversion of lignin-related natural aromatic compounds, 4-hydroxybenzoate and vanillate, and the plastics-related xenobiotic aromatic compound, terephthalate, in Comamonas testosteroni KF-1. Transcription-level regulation controls initial catabolism and cleavage, but metabolite-level thermodynamic regulation governs fluxes in central carbon metabolism. Quantitative 13C mapping of tricarboxylic acid cycle and cataplerotic reactions elucidates key carbon routing not evident from enzyme abundance changes. This scheme of transcriptional activation coupled with metabolic fine-tuning challenges outcome predictions during metabolic manipulations.
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Affiliation(s)
- Rebecca A Wilkes
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Austin Carroll
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Darren J Parker
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA.
- Northwestern Center for Synthetic Biology, Evanston, IL, USA.
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Fan L, Hu J, Guo Z, Chen S, He Q. Shoot Nutrition and Flavor Variation in Two Phyllostachys Species: Does the Quality of Edible Bamboo Shoot Diaphragm and Flesh Differ? Foods 2023; 12:foods12061180. [PMID: 36981107 PMCID: PMC10048675 DOI: 10.3390/foods12061180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/24/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
For their quality evaluation, it is essential to determine both bamboo shoot nutrition and palatability, which will have a decisive effect on their economic value and market potential. However, differences in shoot nutrition and flavor variation among bamboo species, positions, and components have not been scientifically validated. This study assessed nutritional and flavor differences in two components (i.e., shoot flesh (BSF) and diaphragm (BSD)) of two Phyllostachys species (i.e., Phyllostachys edulis and Phyllostachys violascens) and analyzed any positional variation. Results showed that BSF protein, starch, fat, and vitamin C contents were comparatively higher. Nutrient compounds in the upper shoot segment of Ph. edulis were higher and contained less cellulose and lignin. However, both species’ BSD total acid, oxalic acid, and tannin contents were comparable. BSD soluble sugar and sugar:acid ratio were higher than upper BSD total amino acid, four key amino acids (i.e., essential amino acid, bitter amino acid, umami amino acid, and sweet amino acid flavor compounds), and associated ratios were all higher than BSF while also being rich in amino acids. The content and proportion of BSF essential and bitter amino acid flavor compounds in Ph. edulis were high relative to Ph. violascens. Conversely, the content and proportion of BSD umami and sweet amino acid flavor compounds were comparable to that of Ph. edulis. Our results showed that bamboo shoot quality was affected by flavor compound differences and that interspecific and shoot components interact. This study offers a new perspective to determine the formative mechanisms involved in bamboo shoot quality while providing a basis for their different usages.
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Affiliation(s)
- Lili Fan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Junjing Hu
- Hangzhou Academy of Forestry, Hangzhou 310005, China
| | - Ziwu Guo
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Correspondence:
| | - Shuanglin Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Qijiang He
- Hangzhou Academy of Forestry, Hangzhou 310005, China
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7
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Izrael Živković L, Hüttmann N, Susevski V, Medić A, Beškoski V, Berezovski MV, Minić Z, Živković L, Karadžić I. A comprehensive proteomics analysis of the response of Pseudomonas aeruginosa to nanoceria cytotoxicity. Nanotoxicology 2023; 17:20-41. [PMID: 36861958 DOI: 10.1080/17435390.2023.2180451] [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: 03/03/2023]
Abstract
The increased commercial use and spread of nanoceria raises concerns about the risks associated with its effects on living organisms. Although Pseudomonas aeruginosa may be ubiquitous in nature, it is largely found in locations closely linked with human activity. P. aeruginosa san ai was used as a model organism for a deeper understanding of the interaction between biomolecules of the bacteria with this intriguing nanomaterial. A comprehensive proteomics approach along with analysis of altered respiration and production of targeted/specific secondary metabolites was conducted to study the response of P. aeruginosa san ai to nanoceria. Quantitative proteomics found that proteins associated with redox homeostasis, biosynthesis of amino acids, and lipid catabolism were upregulated. Proteins from outer cellular structures were downregulated, including transporters responsible for peptides, sugars, amino acids and polyamines, and the crucial TolB protein of the Tol-Pal system, required for the structural formation of the outer membrane layer. In accordance with the altered redox homeostasis proteins, an increased amount of pyocyanin, a key redox shuttle, and the upregulation of the siderophore, pyoverdine, responsible for iron homeostasis, were found. Production of extracellular molecules, e.g. pyocyanin, pyoverdine, exopolysaccharides, lipase, and alkaline protease, was significantly increased in P. aeruginosa san ai exposed to nanoceria. Overall, nanoceria at sublethal concentrations induces profound metabolic changes in P. aeruginosa san ai and provokes increased secretion of extracellular virulence factors, revealing the powerful influence this nanomaterial has on the vital functions of the microorganism.
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Affiliation(s)
| | - Nico Hüttmann
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Vanessa Susevski
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Ana Medić
- Department of Chemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vladimir Beškoski
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Maxim V Berezovski
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Zoran Minić
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Ljiljana Živković
- The Vinča Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Ivanka Karadžić
- Department of Chemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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Bano A, Waqar A, Khan A, Tariq H. Phytostimulants in sustainable agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.801788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The consistent use of synthetic fertilizers and chemicals in traditional agriculture has not only compromised the fragile agroecosystems but has also adversely affected human, aquatic, and terrestrial life. The use of phytostimulants is an alternative eco-friendly approach that eliminates ecosystem disruption while maintaining agricultural productivity. Phytostimulants include living entities and materials, such as microorganisms and nanomaterials, which when applied to plants or to the rhizosphere, stimulate plant growth and induce tolerance to plants against biotic and abiotic stresses. In this review, we focus on plant growth-promoting rhizobacteria (PGPR), beneficial fungi, such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting fungi (PGPF), actinomycetes, cyanobacteria, azolla, and lichens, and their potential benefits in the crop improvement, and mitigation of abiotic and biotic stresses either alone or in combination. PGPR, AMF, and PGPF are plant beneficial microbes that can release phytohormones, such as indole acetic acid (IAA), gibberellic acid (GA), and cytokinins, promoting plant growth and improving soil health, and in addition, they also produce many secondary metabolites, antibiotics, and antioxidant compounds and help to combat biotic and abiotic stresses. Their ability to act as phytostimulator and a supplement of inorganic fertilizers is considered promising in practicing sustainable agriculture and organic farming. Glomalin is a proteinaceous product, produced by AMF, involved in soil aggregation and elevation of soil water holding capacity under stressed and unstressed conditions. The negative effects of continuous cropping can be mitigated by AMF biofertilization. The synergistic effects of PGPR and PGPF may be more effective. The mechanisms of control exercised by PGPF either direct or indirect to suppress plant diseases viz. by competing for space and nutrients, mycoparasitism, antibiosis, mycovirus-mediated cross-protection, and induced systemic resistance (ISR) have been discussed. The emerging role of cyanobacterial metabolites and the implication of nanofertilizers have been highlighted in sustainable agriculture.
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