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Yang Z, Leero DD, Yin C, Yang L, Zhu L, Zhu Z, Jiang L. Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks. BIORESOURCE TECHNOLOGY 2022; 361:127656. [PMID: 35872277 DOI: 10.1016/j.biortech.2022.127656] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.
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Affiliation(s)
- Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Donald Delano Leero
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Chengtai Yin
- College of Overseas Education, Nanjing Tech University, Nanjing 211816, China
| | - Lei Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
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Ramos-Vivas J, Tapia O, Elexpuru-Zabaleta M, Pifarre KT, Armas Diaz Y, Battino M, Giampieri F. The Molecular Weaponry Produced by the Bacterium Hafnia alvei in Foods. Molecules 2022; 27:molecules27175585. [PMID: 36080356 PMCID: PMC9457839 DOI: 10.3390/molecules27175585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Hafnia alvei is receiving increasing attention from both a medical and veterinary point of view, but the diversity of molecules it produces has made the interest in this bacterium extend to the field of probiotics, the microbiota, and above all, to its presence and action on consumer foods. The production of Acyl Homoserine Lactones (AHLs), a type of quorum-sensing (QS) signaling molecule, is the most often-studied chemical signaling molecule in Gram-negative bacteria. H. alvei can use this communication mechanism to promote the expression of certain enzymatic activities in fermented foods, where this bacterium is frequently present. H. alvei also produces a series of molecules involved in the modification of the organoleptic properties of different products, especially cheeses, where it shares space with other microorganisms. Although some strains of this species are implicated in infections in humans, many produce antibacterial compounds, such as bacteriocins, that inhibit the growth of true pathogens, so the characterization of these molecules could be very interesting from the point of view of clinical medicine and the food industry. Lastly, in some cases, H. alvei is responsible for the production of biogenic amines or other compounds of special interest in food health. In this article, we will review the most interesting molecules that produce the H. alvei strains and will discuss some of their properties, both from the point of view of their biological activity on other microorganisms and the properties of different food matrices in which this bacterium usually thrives.
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Affiliation(s)
- José Ramos-Vivas
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Internacional Iberoamericana, Campeche 24560, Mexico
- CIBER of Infectious Diseases—CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (J.R.-V.); (M.B.)
| | - Olga Tapia
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain
| | - María Elexpuru-Zabaleta
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain
| | - Kilian Tutusaus Pifarre
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Internacional Iberoamericana, Campeche 24560, Mexico
| | - Yasmany Armas Diaz
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Maurizio Battino
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
- International Joint Research Laboratory of Intelligent Agriculture and Agri-Products Processing, Jiangsu University, Zhenjiang 212013, China
- Correspondence: (J.R.-V.); (M.B.)
| | - Francesca Giampieri
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 80200, Saudi Arabia
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Designing overall stoichiometric conversions and intervening metabolic reactions. Sci Rep 2015; 5:16009. [PMID: 26530953 PMCID: PMC4632160 DOI: 10.1038/srep16009] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/07/2015] [Indexed: 02/07/2023] Open
Abstract
Existing computational tools for de novo metabolic pathway assembly, either based on mixed integer linear programming techniques or graph-search applications, generally only find linear pathways connecting the source to the target metabolite. The overall stoichiometry of conversion along with alternate co-reactant (or co-product) combinations is not part of the pathway design. Therefore, global carbon and energy efficiency is in essence fixed with no opportunities to identify more efficient routes for recycling carbon flux closer to the thermodynamic limit. Here, we introduce a two-stage computational procedure that both identifies the optimum overall stoichiometry (i.e., optStoic) and selects for (non-)native reactions (i.e., minRxn/minFlux) that maximize carbon, energy or price efficiency while satisfying thermodynamic feasibility requirements. Implementation for recent pathway design studies identified non-intuitive designs with improved efficiencies. Specifically, multiple alternatives for non-oxidative glycolysis are generated and non-intuitive ways of co-utilizing carbon dioxide with methanol are revealed for the production of C2+ metabolites with higher carbon efficiency.
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