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Mazzoli R, Pescarolo S, Gilli G, Gilardi G, Valetti F. Hydrogen production pathways in Clostridia and their improvement by metabolic engineering. Biotechnol Adv 2024; 73:108379. [PMID: 38754796 DOI: 10.1016/j.biotechadv.2024.108379] [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: 12/04/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Biological production of hydrogen has a tremendous potential as an environmentally sustainable technology to generate a clean fuel. Among the different available methods to produce biohydrogen, dark fermentation features the highest productivity and can be used as a means to dispose of organic waste biomass. Within this approach, Clostridia have the highest theoretical H2 production yield. Nonetheless, most strains show actual yields far lower than the theoretical maximum: improving their efficiency becomes necessary for achieving cost-effective fermentation processes. This review aims at providing a survey of the metabolic network involved in H2 generation in Clostridia and strategies used to improve it through metabolic engineering. Together with current achievements, a number of future perspectives to implement these results will be illustrated.
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Affiliation(s)
- Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
| | - Simone Pescarolo
- Biology applied to the environment, Laboratories of microbiology and ecotoxicology, Ecobioqual, Environment Park. Via Livorno 60, 10144 Torino, Italy
| | - Giorgio Gilli
- Department of Sciences of Public Health and Pediatrics, School of Medicine, University of Torino, Via Santena 5 bis, 10126 Torino, Italy
| | - Gianfranco Gilardi
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Valetti
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
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2
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Chou KJ, Croft T, Hebdon SD, Magnusson LR, Xiong W, Reyes LH, Chen X, Miller EJ, Riley DM, Dupuis S, Laramore KA, Keller LM, Winkelman D, Maness PC. Engineering the cellulolytic bacterium, Clostridium thermocellum, to co-utilize hemicellulose. Metab Eng 2024; 83:193-205. [PMID: 38631458 DOI: 10.1016/j.ymben.2024.03.008] [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: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic biomass holds promise to realize economic production of second-generation biofuels/chemicals, and Clostridium thermocellum is a leading candidate for CBP due to it being one of the fastest degraders of crystalline cellulose and lignocellulosic biomass. However, CBP by C. thermocellum is approached with co-cultures, because C. thermocellum does not utilize hemicellulose. When compared with a single-species fermentation, the co-culture system introduces unnecessary process complexity that may compromise process robustness. In this study, we engineered C. thermocellum to co-utilize hemicellulose without the need for co-culture. By evolving our previously engineered xylose-utilizing strain in xylose, an evolved clonal isolate (KJC19-9) was obtained and showed improved specific growth rate on xylose by ∼3-fold and displayed comparable growth to a minimally engineered strain grown on the bacteria's naturally preferred substrate, cellobiose. To enable full xylan deconstruction to xylose, we recombinantly expressed three different β-xylosidase enzymes originating from Thermoanaerobacterium saccharolyticum into KJC19-9 and demonstrated growth on xylan with one of the enzymes. This recombinant strain was capable of co-utilizing cellulose and xylan simultaneously, and we integrated the β-xylosidase gene into the KJC19-9 genome, creating the KJCBXint strain. The strain, KJC19-9, consumed monomeric xylose but accumulated xylobiose when grown on pretreated corn stover, whereas the final KJCBXint strain showed significantly greater deconstruction of xylan and xylobiose. This is the first reported C. thermocellum strain capable of degrading and assimilating hemicellulose polysaccharide while retaining its cellulolytic capabilities, unlocking significant potential for CBP in advancing the bioeconomy.
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Affiliation(s)
- Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA.
| | - Trevor Croft
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Skyler D Hebdon
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lauren R Magnusson
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Wei Xiong
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Luis H Reyes
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA; Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Xiaowen Chen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Emily J Miller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Danielle M Riley
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Sunnyjoy Dupuis
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Kathrin A Laramore
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lisa M Keller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Dirk Winkelman
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
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3
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Uke A, Sornyotha S, Baramee S, Tachaapaikoon C, Pason P, Waeonukul R, Ratanakhanokchai K, Kosugi A. Genomic analysis of Paenibacillus macerans strain I6, which can effectively saccharify oil palm empty fruit bunches under nutrient-free conditions. J Biosci Bioeng 2023:S1389-1723(23)00111-1. [PMID: 37095007 DOI: 10.1016/j.jbiosc.2023.03.016] [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: 12/21/2022] [Revised: 03/17/2023] [Accepted: 03/30/2023] [Indexed: 04/26/2023]
Abstract
The improper disposal of palm oil industrial waste has led to serious environmental pollution. In this study, we isolated Paenibacillus macerans strain I6, which can degrade oil palm empty fruit bunches generated by the palm oil industry in nutrient-free water, from bovine manure biocompost and sequenced its genome on PacBio RSII and Illumina NovaSeq 6000 platforms. We obtained 7.11 Mbp of genomic sequences with 52.9% GC content from strain I6. Strain I6 was phylogenetically closely related to P. macerans strains DSM24746 and DSM24 and was positioned close to the head of the branch containing strains I6, DSM24746, and DSM24 in the phylogenetic tree. We used the RAST (rapid annotation using subsystem technology) server to annotate the strain I6 genome and discovered genes related to biological saccharification; 496 genes were related to carbohydrate metabolism and 306 genes were related to amino acids and derivatives. Among them were carbohydrate-active enzymes (CAZymes), including 212 glycoside hydrolases. Up to 23.6% of the oil palm empty fruit bunches was degraded by strain I6 under anaerobic and nutrient-free conditions. Evaluation of the enzymatic activity of extracellular fractions of strain I6 showed that amylase and xylanase activity was highest when xylan was the carbon source. The high enzyme activity and the diversity in the associated genes may contribute to the efficient degradation of oil palm empty fruit bunches by strain I6. Our results indicate the potential utility of P. macerans strain I6 for lignocellulosic biomass degradation.
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Affiliation(s)
- Ayaka Uke
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Somphit Sornyotha
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan; Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Chalongkrung Road, Ladkrabang, Bangkok 10520, Thailand
| | - Sirilak Baramee
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Khanok Ratanakhanokchai
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand; School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan.
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Deivayanai VC, Yaashikaa PR, Senthil Kumar P, Rangasamy G. A comprehensive review on the biological conversion of lignocellulosic biomass into hydrogen: Pretreatment strategy, technology advances and perspectives. BIORESOURCE TECHNOLOGY 2022; 365:128166. [PMID: 36283663 DOI: 10.1016/j.biortech.2022.128166] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 05/16/2023]
Abstract
The globe has dependent on energy generation and utilization for many years; conversely, ecological concerns constrained the world to view hydrogen as an alternative for economic development. Lignocellulosic biomass is broadly accessible as a low-cost renewable feedstock and nonreactive nature; it has received a lot of consideration as a global energy source and the most attractive alternative to replace fossil natural substances for energy production. Pretreatment of lignocellulosic biomass is essential to advance its fragmentation and lower the lignin content for sustainable energy generation. This review's goal is to provide the different pretreatment strategies for enlarging the solubility and surface area of lignocellulosic biomass. The biological conversion of lignocellulosic biomass to hydrogen was reviewed and operational conditions and enhancing methods were discussed. This review summarizes the working conditions, parameters, yield percentages, techno-economic analysis, challenges, and future recommendations on the direct conversion of biomass to hydrogen.
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Affiliation(s)
- V C Deivayanai
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai 602105, India
| | - P R Yaashikaa
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai 602105, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India; School of Engineering, Lebanese American University, Byblos, Lebanon.
| | - Gayathri Rangasamy
- University Centre for Research and Development & Department of Civil Engineering, Chandigarh University, Gharuan, Mohali, Punjab 140413, India
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Nanoscale characterization coupled to multi-parametric optimization of Hi5 cell transient gene expression. Appl Microbiol Biotechnol 2018; 102:10495-10510. [DOI: 10.1007/s00253-018-9423-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 01/08/2023]
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Singh N, Mathur AS, Gupta RP, Barrow CJ, Tuli D, Puri M. Enhanced cellulosic ethanol production via consolidated bioprocessing by Clostridium thermocellum ATCC 31924☆. BIORESOURCE TECHNOLOGY 2018; 250:860-867. [PMID: 30001594 DOI: 10.1016/j.biortech.2017.11.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 05/23/2023]
Abstract
The production of bioethanol was studied by the cultivation of Clostridium thermocellum ATCC 31924 in MTC medium including crystalline cellulose as the sole substrate. The effects of key operational parameters that affect bioethanol production from microcrystalline cellulose were optimized. Under optimum conditions (pH 8.0, temperature 55 °C, inoculum size 4% (v/v) and 0.5% (w/v) substrate concentration), a maximum ethanol yield of 0.30 g ethanol/g cellulose consumed and 95.32% cellulose conversion was obtained. An inclusion of modest acetate concentration in the medium showed that carbon flux shifted away from lactate accompanied by 20% increase in ethanol production. It suggests that strain ATCC 31924 differed in its cellulose conversion efficacy and optimum pH requirements compared to the other reported strains of Clostridium thermocellum. The purified cellulosome of strain ATCC 31924 found to be rich in both cellulase and xylanase enzymes emphasizing the importance of this strain for the degradation of lignocellulosic biomass.
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Affiliation(s)
- Nisha Singh
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Geelong, Victoria 3216, Australia; DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Anshu S Mathur
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Ravi P Gupta
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Geelong, Victoria 3216, Australia
| | - Deepak Tuli
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Munish Puri
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Geelong, Victoria 3216, Australia.
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Chen P, Yan L, Zhang S, Wu Z, Li S, Yan X, Wang N, Liang N, Li H. Optimizing bioconversion of ferulic acid to vanillin by Bacillus subtilis in the stirred packed reactor using Box-Behnken design and desirability function. Food Sci Biotechnol 2017; 26:143-152. [PMID: 30263521 DOI: 10.1007/s10068-017-0019-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/12/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022] Open
Abstract
A stirring bioreactor packed with a carbon fiber textiles (FT) biofilm formed by Bacillus subtilis was used to produce vanillin from ferulic acid. Biofilm formation was characterized by scanning electron microscopy. The interactive effects of three variables on vanillin molar yield (M) and conversion efficiency of ferulic acid (E) were evaluated by response surface methodology (RSM) with a Box-Behnken design (BBD). The optimal conversion conditions with a maximum overall desirability D of 0.983 were obtained by a desirability function. Considering the actual operation, the confirmation tests were performed using the slightly modified optimal conditions (initial ferulic acid concentration 1.55 g/L, temperature 35°C, stirring speed 220 rpm). The results showed that M and E were 57.42 and 93.53%, respectively. This was only 1.03% and 1.87%, respectively, different from the predicted values, confirming the validity of the predicted models. These revealed that the stirred packed reactor could be successfully used in vanillin bioconversion from ferulic acid.
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Affiliation(s)
- Peng Chen
- 1School of Pharmacy, Lanzhou University, Lanzhou, 730020 China
| | - Lei Yan
- 2College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319 China
| | - Shuang Zhang
- 2College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163319 China
| | - Zhengrong Wu
- 1School of Pharmacy, Lanzhou University, Lanzhou, 730020 China
| | - Suyue Li
- Gansu Institute of Business and Technology, Lanzhou, 730010 China
| | - Xiaojuan Yan
- Gansu Institute of Business and Technology, Lanzhou, 730010 China
| | - Ningbo Wang
- Gansu Institute of Business and Technology, Lanzhou, 730010 China
| | - Ning Liang
- Gansu Institute of Business and Technology, Lanzhou, 730010 China
| | - Hongyu Li
- 1School of Pharmacy, Lanzhou University, Lanzhou, 730020 China
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Lewis A, Waters JC, Stanton J, Hess J, Salas-de la Cruz D. Macromolecular Interactions Control Structural and Thermal Properties of Regenerated Tri-Component Blended Films. Int J Mol Sci 2016; 17:E1989. [PMID: 27916801 PMCID: PMC5187789 DOI: 10.3390/ijms17121989] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 11/16/2022] Open
Abstract
With a growing need for sustainable resources research has become highly interested in investigating the structure and physical properties of biomaterials composed of natural macromolecules. In this study, we assessed the structural, morphological, and thermal properties of blended, regenerated films comprised of cellulose, lignin, and hemicellulose (xylan) using the ionic liquid 1-allyl-3-methylimidazolium chloride (AMIMCl). Attenuated total reflectance Fourier transform infrared (ATR-FTIR) analysis, scanning electron microscopy (SEM), atomic force microscopy (AFM), X-ray scattering, and thermogravimetric analysis (TGA) were used to qualitatively and quantitatively measure bonding interactions, morphology, and thermal stability of the regenerated films. The results demonstrated that the regenerated films' structural, morphological, and thermal character changed as a function of lignin-xylan concentration. The decomposition temperature rose according to an increase in lignin content and the surface topography of the regenerated films changed from fibrous to spherical patterns. This suggests that lignin-xylan concentration alters the self-assembly of lignin and the cellulose microfibril development. X-ray scattering confirms the extent of the morphological and molecular changes. Our data reveals that the inter- and intra-molecular interactions with the cellulose crystalline domains, along with the amount of disorder in the system, control the microfibril dimensional characteristics, lignin self-assembly, and possibly the overall material's structural and thermal properties.
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Affiliation(s)
- Ashley Lewis
- Department of Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ 08102, USA.
| | - Joshua C Waters
- Department of Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ 08102, USA.
| | - John Stanton
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ 08102, USA.
| | - Joseph Hess
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ 08102, USA.
| | - David Salas-de la Cruz
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ 08102, USA.
- Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ 08102, USA.
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Zheng Z, Guo X, Zhu K, Peng W, Zhou H. The optimization of the fermentation process of wheat germ for flavonoids and two benzoquinones using EKF-ANN and NSGA-II. RSC Adv 2016. [DOI: 10.1039/c5ra27004a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bi-objective optimization of wheat germ fermentation using EKF-ANN combined with NSGA-II.
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Affiliation(s)
- Ziyi Zheng
- State Key Laboratory of Food Science and Technology
- Collaborative Innovation Center for Food Safety and Quality Control
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
| | - Xiaona Guo
- State Key Laboratory of Food Science and Technology
- Collaborative Innovation Center for Food Safety and Quality Control
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
| | - Kexue Zhu
- State Key Laboratory of Food Science and Technology
- Collaborative Innovation Center for Food Safety and Quality Control
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
| | - Wei Peng
- State Key Laboratory of Food Science and Technology
- Collaborative Innovation Center for Food Safety and Quality Control
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
| | - Huiming Zhou
- State Key Laboratory of Food Science and Technology
- Collaborative Innovation Center for Food Safety and Quality Control
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
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