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Omar MN, Minggu MM, Nor Muhammad NA, Abdul PM, Zhang Y, Ramzi AB. Towards consolidated bioprocessing of biomass and plastic substrates for semi-synthetic production of bio-poly(ethylene furanoate) (PEF) polymer using omics-guided construction of artificial microbial consortia. Enzyme Microb Technol 2024; 177:110429. [PMID: 38537325 DOI: 10.1016/j.enzmictec.2024.110429] [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: 11/28/2023] [Revised: 02/20/2024] [Accepted: 03/14/2024] [Indexed: 04/29/2024]
Abstract
Poly(ethylene furanoate) (PEF) plastic is a 100% renewable polyester that is currently being pursued for commercialization as the next-generation bio-based plastic. This is in line with growing demand for circular bioeconomy and new plastics economy that is aimed at minimizing plastic waste mismanagement and lowering carbon footprint of plastics. However, the current catalytic route for the synthesis of PEF is impeded with technical challenges including high cost of pretreatment and catalyst refurbishment. On the other hand, the semi-biosynthetic route of PEF plastic production is of increased biotechnological interest. In particular, the PEF monomers (Furan dicarboxylic acid and ethylene glycol) can be synthesized via microbial-based biorefinery and purified for subsequent catalyst-mediated polycondensation into PEF. Several bioengineering and bioprocessing issues such as efficient substrate utilization and pathway optimization need to be addressed prior to establishing industrial-scale production of the monomers. This review highlights current advances in semi-biosynthetic production of PEF monomers using consolidated waste biorefinery strategies, with an emphasis on the employment of omics-driven systems biology approaches in enzyme discovery and pathway construction. The roles of microbial protein transporters will be discussed, especially in terms of improving substrate uptake and utilization from lignocellulosic biomass, as well as from depolymerized plastic waste as potential bio-feedstock. The employment of artificial bioengineered microbial consortia will also be highlighted to provide streamlined systems and synthetic biology strategies for bio-based PEF monomer production using both plant biomass and plastic-derived substrates, which are important for circular and new plastics economy advances.
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Affiliation(s)
- Mohd Norfikri Omar
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), UKM, Bangi, Selangor 43600, Malaysia
| | - Matthlessa Matthew Minggu
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), UKM, Bangi, Selangor 43600, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), UKM, Bangi, Selangor 43600, Malaysia
| | - Peer Mohamed Abdul
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia; Centre for Sustainable Process Technology (CESPRO), Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia
| | - Ying Zhang
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Ahmad Bazli Ramzi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), UKM, Bangi, Selangor 43600, Malaysia.
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Liu J, Liu D, Sun T, Fan TP, Cai Y. Construction and characterization of a promoter library with varying strengths to enhance acetoin production from xylose in Serratia marcescens. Biotechnol Appl Biochem 2024; 71:553-564. [PMID: 38225826 DOI: 10.1002/bab.2558] [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: 08/18/2023] [Accepted: 12/30/2023] [Indexed: 01/17/2024]
Abstract
Serratia marcescens is utilized as a significant enterobacteria in the production of various high-value secondary metabolites. Acetoin serves as a crucial foundational compound of development and finds application in a broad range of fields. Furthermore, S. marcescens HBQA-7 is capable of utilizing xylose as its exclusive carbon source for acetoin production. The objective of this study was to utilize a constitutive promoter screening strategy to enhance both xylose utilization and acetoin production in S. marcescens HBQA-7. By utilizing RNA-seq, we identified the endogenous constitutive promoter P6 that is the most robust, which facilitated the overexpression of the sugar transporter protein GlfL445I, α-acetyl lactate synthase, and α-acetyl lactate decarboxylase, respectively. The resultant recombinant strains exhibited enhanced xylose utilization rates and acetoin yields. Subsequently, a recombinant plasmid, denoted as pBBR1MCS-P6-glfL445IalsSalsD, was constructed, simultaneously expressing the aforementioned three genes. The resulting recombinant strain, designated as S3, demonstrated a 1.89-fold boost in xylose consumption rate compared with the original strain during shake flask fermentation. resulting in the accumulation of 7.14 g/L acetoin in the final fermentation medium. Subsequently, in a 5 L fermenter setup, the acetoin yield reached 48.75 g/L, corresponding to a xylose-to-acetoin conversion yield of 0.375 g/g.
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Affiliation(s)
- Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Di Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Tingting Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Smoktunowicz M, Wawrzyniak R, Jonca J, Waleron M, Waleron K. Untargeted metabolomics coupled with genomics in the study of sucrose and xylose metabolism in Pectobacterium betavasculorum. Front Microbiol 2024; 15:1323765. [PMID: 38812674 PMCID: PMC11133636 DOI: 10.3389/fmicb.2024.1323765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction Pectobacterium betavasculorum is a member of the Pectobacerium genus that inhabits a variety of niches and is found in all climates. Bacteria from the Pectobacterium genus can cause soft rot disease on various plants due to the secretion of plant cell wall degrading enzymes (PCWDEs). The species P. betavasculorum is responsible for the vascular necrosis of sugar beet and soft rot of many vegetables. It also infects sunflowers and artichokes. The main sugar present in sugar beet is sucrose while xylose is one of the main sugars in artichoke and sunflower. Methods In our work, we applied metabolomic studies coupled with genomics to investigate the metabolism of P. betavasculorum in the presence of xylose and sucrose as the only carbon source. The ability of the strains to use various sugars as the only carbon source were confirmed by the polypyridyl complex of Ru(II) method in 96-well plates. Results Our studies provided information on the metabolic pathways active during the degradation of those substrates. It was observed that different metabolic pathways are upregulated in the presence of xylose in comparison to sucrose. Discussion The presence of xylose enhances extracellular metabolism of sugars and glycerol as well as stimulates EPS and IPS synthesis. In contrast, in the presence of sucrose the intensive extracellular metabolism of amines and amino acids is promoted.
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Affiliation(s)
- Magdalena Smoktunowicz
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Renata Wawrzyniak
- Department of Biopharmaceutics and Pharmacodynamics, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Joanna Jonca
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Poland
| | - Małgorzata Waleron
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Poland
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
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Das S, Chandukishore T, Ulaganathan N, Dhodduraj K, Gorantla SS, Chandna T, Gupta LK, Sahoo A, Atheena PV, Raval R, Anjana PA, DasuVeeranki V, Prabhu AA. Sustainable biorefinery approach by utilizing xylose fraction of lignocellulosic biomass. Int J Biol Macromol 2024; 266:131290. [PMID: 38569993 DOI: 10.1016/j.ijbiomac.2024.131290] [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: 11/03/2023] [Revised: 03/20/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
Lignocellulosic biomass (LCB) has been a lucrative feedstock for developing biochemical products due to its rich organic content, low carbon footprint and abundant accessibility. The recalcitrant nature of this feedstock is a foremost bottleneck. It needs suitable pretreatment techniques to achieve a high yield of sugar fractions such as glucose and xylose with low inhibitory components. Cellulosic sugars are commonly used for the bio-manufacturing process, and the xylose sugar, which is predominant in the hemicellulosic fraction, is rejected as most cell factories lack the five‑carbon metabolic pathways. In the present review, more emphasis was placed on the efficient pretreatment techniques developed for disintegrating LCB and enhancing xylose sugars. Further, the transformation of the xylose to value-added products through chemo-catalytic routes was highlighted. In addition, the review also recapitulates the sustainable production of biochemicals by native xylose assimilating microbes and engineering the metabolic pathway to ameliorate biomanufacturing using xylose as the sole carbon source. Overall, this review will give an edge on the bioprocessing of microbial metabolism for the efficient utilization of xylose in the LCB.
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Affiliation(s)
- Satwika Das
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - T Chandukishore
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Nivedhitha Ulaganathan
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Kawinharsun Dhodduraj
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Sai Susmita Gorantla
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Teena Chandna
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Laxmi Kumari Gupta
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Ansuman Sahoo
- Biochemical Engineering Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - P V Atheena
- Department of Biotechnology, Manipal Institute of Technology, Manipal 576104, Karnataka, India
| | - Ritu Raval
- Department of Biotechnology, Manipal Institute of Technology, Manipal 576104, Karnataka, India
| | - P A Anjana
- Department of Chemical Engineering, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Venkata DasuVeeranki
- Biochemical Engineering Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ashish A Prabhu
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India.
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Barros KO, Mader M, Krause DJ, Pangilinan J, Andreopoulos B, Lipzen A, Mondo SJ, Grigoriev IV, Rosa CA, Sato TK, Hittinger CT. Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:20. [PMID: 38321504 PMCID: PMC10848558 DOI: 10.1186/s13068-024-02467-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/28/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Cost-effective production of biofuels from lignocellulose requires the fermentation of D-xylose. Many yeast species within and closely related to the genera Spathaspora and Scheffersomyces (both of the order Serinales) natively assimilate and ferment xylose. Other species consume xylose inefficiently, leading to extracellular accumulation of xylitol. Xylitol excretion is thought to be due to the different cofactor requirements of the first two steps of xylose metabolism. Xylose reductase (XR) generally uses NADPH to reduce xylose to xylitol, while xylitol dehydrogenase (XDH) generally uses NAD+ to oxidize xylitol to xylulose, creating an imbalanced redox pathway. This imbalance is thought to be particularly consequential in hypoxic or anoxic environments. RESULTS We screened the growth of xylose-fermenting yeast species in high and moderate aeration and identified both ethanol producers and xylitol producers. Selected species were further characterized for their XR and XDH cofactor preferences by enzyme assays and gene expression patterns by RNA-Seq. Our data revealed that xylose metabolism is more redox balanced in some species, but it is strongly affected by oxygen levels. Under high aeration, most species switched from ethanol production to xylitol accumulation, despite the availability of ample oxygen to accept electrons from NADH. This switch was followed by decreases in enzyme activity and the expression of genes related to xylose metabolism, suggesting that bottlenecks in xylose fermentation are not always due to cofactor preferences. Finally, we expressed XYL genes from multiple Scheffersomyces species in a strain of Saccharomyces cerevisiae. Recombinant S. cerevisiae expressing XYL1 from Scheffersomyces xylosifermentans, which encodes an XR without a cofactor preference, showed improved anaerobic growth on xylose as the primary carbon source compared to S. cerevisiae strain expressing XYL genes from Scheffersomyces stipitis. CONCLUSION Collectively, our data do not support the hypothesis that xylitol accumulation occurs primarily due to differences in cofactor preferences between xylose reductase and xylitol dehydrogenase; instead, gene expression plays a major role in response to oxygen levels. We have also identified the yeast Sc. xylosifermentans as a potential source for genes that can be engineered into S. cerevisiae to improve xylose fermentation and biofuel production.
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Affiliation(s)
- Katharina O Barros
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Megan Mader
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Krause
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bill Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Computer Science, San Jose State University, One Washington Square, San Jose, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen J Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Plant and Microbial Department, University of California Berkeley, Berkeley, CA, USA
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
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Fiamenghi MB, Prodonoff JS, Borelli G, Carazzolle MF, Pereira GAG, José J. Comparative genomics reveals probable adaptations for xylose use in Thermoanaerobacterium saccharolyticum. Extremophiles 2024; 28:9. [PMID: 38190047 DOI: 10.1007/s00792-023-01327-x] [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: 06/06/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024]
Abstract
Second-generation ethanol, a promising biofuel for reducing greenhouse gas emissions, faces challenges due to the inefficient metabolism of xylose, a pentose sugar. Overcoming this hurdle requires exploration of genes, pathways, and organisms capable of fermenting xylose. Thermoanaerobacterium saccharolyticum is an organism capable of naturally fermenting compounds of industrial interest, such as xylose, and understanding evolutionary adaptations may help to bring novel genes and information that can be used for industrial yeast, increasing production of current bio-platforms. This study presents a deep evolutionary study of members of the firmicutes clade, focusing on adaptations in Thermoanaerobacterium saccharolyticum that may be related to overall fermentation metabolism, especially for xylose fermentation. One highlight is the finding of positive selection on a xylose-binding protein of the xylFGH operon, close to the annotated sugar binding site, with this protein already being found to be expressed in xylose fermenting conditions in a previous study. Results from this study can serve as basis for searching for candidate genes to use in industrial strains or to improve Thermoanaerobacterium saccharolyticum as a new microbial cell factory, which may help to solve current problems found in the biofuels' industry.
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Affiliation(s)
- Mateus Bernabe Fiamenghi
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Juliana Silveira Prodonoff
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Guilherme Borelli
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Gonçalo Amarante Guimaraes Pereira
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil.
| | - Juliana José
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
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Yin Y, Wang P, Wang X, Wen J. Construction of Bacillus subtilis for efficient production of fengycin from xylose through CRISPR-Cas9. Front Microbiol 2024; 14:1342199. [PMID: 38249479 PMCID: PMC10797001 DOI: 10.3389/fmicb.2023.1342199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
Fengycin is a multifunctional peptide antibiotic produced mainly by Bacillus species and the purpose of this research was to construct a Bacillus subtilis strain that can produce fengycin with the xylose as the substrate with CRSIPR-Cas9. Hence, at the beginning of this study, functional sfp and degQ were expressed in B. subtilis 168 strain to give the strain the ability to produce the fengycin with the titer of 71.21 mg/L. Subsequently, the native promoter PppsA of the cluster responsible for the fengycin synthesis was replaced by the Pveg promoter, resulting in a further 5.22-fold increase in fengycin titer. To confer xylose utilization capacity to B. subtilis, deletion of araR and constitutive overexpression of araE were performed, and the xylose consumption rate of the engineered strain BSUY06 reached 0.29 g/L/h, which is about 6.25-fold higher than that of the parent strain BSUY04-1. In the final phase of this study, the fermentation characteristics were observed and the initial xylose concentration was optimized. In this study, 40 g/L xylose was proved to be the most suitable initial concentration for growth and fengycin fermentation, which leading to a fengycin titer of 430.86 mg/L. This study demonstrated that lignocellulose, the clean and sustainable substrate with xylose as the second largest sugar, is a potential substrate for the production of fengycin.
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Affiliation(s)
- Ying Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Pan Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Xin Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
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Franco DG, de Almeida AP, Galeano RMS, Vargas IP, Masui DC, Giannesi GC, Ruller R, Zanoelo FF. Exploring the potential of a new thermotolerant xylanase from Rasamsonia composticola (XylRc): production using agro-residues, biochemical studies, and application to sugarcane bagasse saccharification. 3 Biotech 2024; 14:3. [PMID: 38058364 PMCID: PMC10695910 DOI: 10.1007/s13205-023-03844-0] [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: 08/18/2023] [Accepted: 11/04/2023] [Indexed: 12/08/2023] Open
Abstract
Xylanases from thermophilic fungi have a wide range of commercial applications in the bioconversion of lignocellulosic materials and biobleaching in the pulp and paper industry. In this study, an endoxylanase from the thermophilic fungus Rasamsonia composticola (XylRc) was produced using waste wheat bran and pretreated sugarcane bagasse (PSB) in solid-state fermentation. The enzyme was purified, biochemically characterized, and used for the saccharification of sugarcane bagasse. XylRc was purified 30.6-fold with a 22% yield. The analysis using sodium dodecyl sulphate-polyacrylamide gel electrophoresis revealed a molecular weight of 53 kDa, with optimal temperature and pH values of 80 °C and 5.5, respectively. Thin-layer chromatography suggests that the enzyme is an endoxylanase and belongs to the glycoside hydrolase 10 family. The enzyme was stimulated by the presence of K+, Ca2+, Mg2+, and Co2+ and remained stable in the presence of the surfactant Triton X-100. XylRc was also stimulated by organic solvents butanol (113%), ethanol (175%), isopropanol (176%), and acetone (185%). The Km and Vmax values for oat spelt and birchwood xylan were 6.7 ± 0.7 mg/mL, 2.3 ± 0.59 mg/mL, 446.7 ± 12.7 µmol/min/mg, and 173.7 ± 6.5 µmol/min/mg, respectively. XylRc was unaffected by different phenolic compounds: ferulic, tannic, cinnamic, benzoic, and coumaric acids at concentrations of 2.5-10 mg/mL. The results of saccharification of PSB showed that supplementation of a commercial enzymatic cocktail (Cellic® CTec2) with XylRc (1:1 w/v) led to an increase in the degree of synergism (DS) in total reducing sugar (1.28) and glucose released (1.05) compared to the control (Cellic® HTec2). In summary, XylRc demonstrated significant potential for applications in lignocellulosic biomass hydrolysis, making it an attractive alternative for producing xylooligosaccharides and xylose, which can serve as precursors for biofuel production.
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Affiliation(s)
- Daniel Guerra Franco
- Programa Multicêntrico de Pós-Graduação em Bioquímica e Biologia Molecular, Sociedade Brasileira de Bioquímica e Biologia Molecular (SBBq), Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
- Laboratório de Bioquímica Geral e Microrganismos, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
| | - Aline Pereira de Almeida
- Laboratório de Microbiologia, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto-Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Rodrigo Mattos Silva Galeano
- Programa Multicêntrico de Pós-Graduação em Bioquímica e Biologia Molecular, Sociedade Brasileira de Bioquímica e Biologia Molecular (SBBq), Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
- Laboratório de Bioquímica Geral e Microrganismos, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
| | - Isabela Pavão Vargas
- Programa Multicêntrico de Pós-Graduação em Bioquímica e Biologia Molecular, Sociedade Brasileira de Bioquímica e Biologia Molecular (SBBq), Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
- Laboratório de Bioquímica Geral e Microrganismos, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
| | - Douglas Chodi Masui
- Programa Multicêntrico de Pós-Graduação em Bioquímica e Biologia Molecular, Sociedade Brasileira de Bioquímica e Biologia Molecular (SBBq), Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
- Laboratório de Bioquímica Geral e Microrganismos, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
| | - Giovana Cristina Giannesi
- Programa Multicêntrico de Pós-Graduação em Bioquímica e Biologia Molecular, Sociedade Brasileira de Bioquímica e Biologia Molecular (SBBq), Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
- Laboratório de Bioquímica Geral e Microrganismos, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
| | - Roberto Ruller
- Laboratório de Microbiologia, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto-Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Fabiana Fonseca Zanoelo
- Programa Multicêntrico de Pós-Graduação em Bioquímica e Biologia Molecular, Sociedade Brasileira de Bioquímica e Biologia Molecular (SBBq), Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
- Laboratório de Bioquímica Geral e Microrganismos, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS Brazil
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Song X, Ju Y, Chen L, Zhang W. Construction of Xylose-Utilizing Cyanobacterial Chassis for Bioproduction Under Photomixotrophic Conditions. Methods Mol Biol 2024; 2760:57-75. [PMID: 38468082 DOI: 10.1007/978-1-0716-3658-9_4] [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] [Indexed: 03/13/2024]
Abstract
Xylose is a major component of lignocellulose and the second most abundant sugar present in nature after glucose; it, therefore, has been considered to be a promising renewable resource for the production of biofuels and chemicals. However, no natural cyanobacterial strain is known capable of utilizing xylose. Here, we take the fast-growing cyanobacteria Synechococcus elongatus UTEX 2973 as an example to develop the synthetic biology-based methodology of constructing a new xylose-utilizing cyanobacterial chassis with increased acetyl-CoA for bioproduction.
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Affiliation(s)
- Xinyu Song
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, People's Republic of China
- Key Laboratory of Systems Bioengineering and Frontier Science Center of Synthetic Biology, The Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, People's Republic of China
| | - Yue Ju
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, People's Republic of China
- Key Laboratory of Systems Bioengineering and Frontier Science Center of Synthetic Biology, The Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, People's Republic of China
- Key Laboratory of Systems Bioengineering and Frontier Science Center of Synthetic Biology, The Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, People's Republic of China.
- Key Laboratory of Systems Bioengineering and Frontier Science Center of Synthetic Biology, The Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China.
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, People's Republic of China.
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10
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Asemoloye MD, Bello TS, Oladoye PO, Remilekun Gbadamosi M, Babarinde SO, Ebenezer Adebami G, Olowe OM, Temporiti MEE, Wanek W, Marchisio MA. Engineered yeasts and lignocellulosic biomaterials: shaping a new dimension for biorefinery and global bioeconomy. Bioengineered 2023; 14:2269328. [PMID: 37850721 PMCID: PMC10586088 DOI: 10.1080/21655979.2023.2269328] [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: 06/24/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023] Open
Abstract
The next milestone of synthetic biology research relies on the development of customized microbes for specific industrial purposes. Metabolic pathways of an organism, for example, depict its chemical repertoire and its genetic makeup. If genes controlling such pathways can be identified, scientists can decide to enhance or rewrite them for different purposes depending on the organism and the desired metabolites. The lignocellulosic biorefinery has achieved good progress over the past few years with potential impact on global bioeconomy. This principle aims to produce different bio-based products like biochemical(s) or biofuel(s) from plant biomass under microbial actions. Meanwhile, yeasts have proven very useful for different biotechnological applications. Hence, their potentials in genetic/metabolic engineering can be fully explored for lignocellulosic biorefineries. For instance, the secretion of enzymes above the natural limit (aided by genetic engineering) would speed-up the down-line processes in lignocellulosic biorefineries and the cost. Thus, the next milestone would greatly require the development of synthetic yeasts with much more efficient metabolic capacities to achieve basic requirements for particular biorefinery. This review gave comprehensive overview of lignocellulosic biomaterials and their importance in bioeconomy. Many researchers have demonstrated the engineering of several ligninolytic enzymes in heterologous yeast hosts. However, there are still many factors needing to be well understood like the secretion time, titter value, thermal stability, pH tolerance, and reactivity of the recombinant enzymes. Here, we give a detailed account of the potentials of engineered yeasts being discussed, as well as the constraints associated with their development and applications.
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Affiliation(s)
- Michael Dare Asemoloye
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, Nankai District, China
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Tunde Sheriffdeen Bello
- Department of Plant Biology, School of Life Sciences, Federal University of Technology Minna, Minna Niger State, Nigeria
| | | | | | - Segun Oladiran Babarinde
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
| | | | - Olumayowa Mary Olowe
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag, Mmabatho, South Africa
| | | | - Wolfgang Wanek
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, Nankai District, China
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11
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Saxena A, Hussain A, Parveen F, Ashfaque M. Current status of metabolic engineering of microorganisms for bioethanol production by effective utilization of pentose sugars of lignocellulosic biomass. Microbiol Res 2023; 276:127478. [PMID: 37625339 DOI: 10.1016/j.micres.2023.127478] [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: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Lignocellulosic biomass, consisting of homo- and heteropolymeric sugars, acts as a substrate for the generation of valuable biochemicals and biomaterials. The readily available hexoses are easily utilized by microbes due to the presence of transporters and native metabolic pathways. But, utilization of pentose sugar viz., xylose and arabinose are still challenging due to several reasons including (i) the absence of the particular native pathways and transporters, (ii) the presence of inhibitors, and (iii) lower uptake of pentose sugars. These challenges can be overcome by manipulating metabolic pathways/glycosidic enzymes cascade by using genetic engineering tools involving inverse-metabolic engineering, ex-vivo isomerization, Adaptive Laboratory Evolution, Directed Metabolic Engineering, etc. Metabolic engineering of bacteria and fungi for the utilization of pentose sugars for bioethanol production is the focus area of research in the current decade. This review outlines current approaches to biofuel development and strategies involved in the metabolic engineering of different microbes that can uptake pentose for bioethanol production.
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Affiliation(s)
- Ayush Saxena
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Akhtar Hussain
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Fouziya Parveen
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Mohammad Ashfaque
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
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12
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Long L, Liu Z, Wang Y, Lin Q, Ding S, Li C, Deng C. High-level production of cordycepin by the xylose-utilising Cordyceps militaris strain 147 in an optimised medium. BIORESOURCE TECHNOLOGY 2023; 388:129742. [PMID: 37734485 DOI: 10.1016/j.biortech.2023.129742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023]
Abstract
Cordycepin is an important active metabolite of Cordyceps militaris. Xylose, an attractive feedstock for producing chemicals through microbial fermentation, cannot be effectively utilised by many reported C. militaris strains. Herein, a xylose-utilising C. militaris strain 147 produced the highest level of cordycepin (3.03 g/L) in xylose culture. Xylose, alanine, and ammonium citrate were determined as the main affecting factors on the cordycepin production using a Plackett-Burman design. The combination of these factors was optimised using response surface methodology, and the maximal 6.54 g/L of cordycepin was produced by the fungus in the optimal medium. Transcriptome analysis revealed that xylose utilisation upregulated the transcriptional levels of genes participating in purine and energy metabolisms in the fungus, which may facilitate the formation of precursors for cordycepin biosynthesis. This investigation provides new insights into the efficient production of cordycepin and is conducive to the valorisation of biomass rich in xylose.
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Affiliation(s)
- Liangkun Long
- Jiangsu Co-Innovation Centre for Efficient Processing and Utilisation of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab for the Chemistry & Utilisation of Agricultural and Forest Biomass, Nanjing 210037, China
| | - Zhen Liu
- Jiangsu Co-Innovation Centre for Efficient Processing and Utilisation of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yizhou Wang
- Jiangsu Co-Innovation Centre for Efficient Processing and Utilisation of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Qunying Lin
- Nanjing Institute for the Comprehensive Utilisation of Wild Plants, Nanjing, 211111, China.
| | - Shaojun Ding
- Jiangsu Co-Innovation Centre for Efficient Processing and Utilisation of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab for the Chemistry & Utilisation of Agricultural and Forest Biomass, Nanjing 210037, China
| | - Chuanhua Li
- Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, National Engineering Research Centre of Edible Fungi; Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Chunying Deng
- Guizhou Institute of Biology, Guizhou Academy of Sciences, Guiyang 550009, China.
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13
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Gu P, Li F, Huang Z. Engineering Escherichia coli for Isobutanol Production from Xylose or Glucose-Xylose Mixture. Microorganisms 2023; 11:2573. [PMID: 37894231 PMCID: PMC10609591 DOI: 10.3390/microorganisms11102573] [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: 09/19/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Aiming to overcome the depletion of fossil fuels and serious environmental pollution, biofuels such as isobutanol have garnered increased attention. Among different synthesis methods, the microbial fermentation of isobutanol from raw substrate is a promising strategy due to its low cost and environmentally friendly and optically pure products. As an important component of lignocellulosics and the second most common sugar in nature, xylose has become a promising renewable resource for microbial production. However, bottlenecks in xylose utilization limit its wide application as substrates. In this work, an isobutanol synthetic pathway from xylose was first constructed in E. coli MG1655 through the combination of the Ehrlich and Dahms pathways. The engineering of xylose transport and electron transport chain complexes further improved xylose assimilation and isobutanol production. By optimizing xylose supplement concentration, the recombinant E. coli strain BWL4 could produce 485.35 mg/L isobutanol from 20 g/L of xylose. To our knowledge, this is the first report related to isobutanol production using xylose as a sole carbon source in E. coli. Additionally, a glucose-xylose mixture was utilized as the carbon source. The Entner-Doudorof pathway was used to assimilate glucose, and the Ehrlich pathway was applied for isobutanol production. After carefully engineering the recombinant E. coli, strain BWL9 could produce 528.72 mg/L isobutanol from a mixture of 20 g/L glucose and 10 g/L xylose. The engineering strategies applied in this work provide a useful reference for the microbial production of isobutanol from xylose or glucose-xylose mixture.
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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;
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14
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Bakratsas G, Polydera A, Nilson O, Chatzikonstantinou AV, Xiros C, Katapodis P, Stamatis H. Mycoprotein Production by Submerged Fermentation of the Edible Mushroom Pleurotus ostreatus in a Batch Stirred Tank Bioreactor Using Agro-Industrial Hydrolysate. Foods 2023; 12:2295. [PMID: 37372506 DOI: 10.3390/foods12122295] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
The demand for cheap, healthy, and sustainable alternative protein sources has turned research interest into microbial proteins. Mycoproteins prevail due to their quite balanced amino acid profile, low carbon footprint and high sustainability potential. The goal of this research was to investigate the capability of Pleurotus ostreatus to metabolize the main sugars of agro-industrial side streams, such as aspen wood chips hydrolysate, to produce high-value protein with low cost. Our results indicate that P. ostreatus LGAM 1123 could be cultivated both in a C-6 (glucose)- and C-5(xylose)-sugar-containing medium for mycoprotein production. A mixture of glucose and xylose was found to be ideal for biomass production with high protein content and rich amino acid profile. P. ostreatus LGAM 1123 cultivation in a 4 L stirred-tank bioreactor using aspen hydrolysate was achieved with 25.0 ± 3.4 g L-1 biomass production, 1.8 ± 0.4 d-1 specific growth rate and a protein yield of 54.5 ± 0.5% (g/100 g sugars). PCA analysis of the amino acids revealed a strong correlation between the amino acid composition of the protein produced and the ratios of glucose and xylose in the culture medium. The production of high-nutrient mycoprotein by submerged fermentation of the edible fungus P. ostreatus using agro-industrial hydrolysates is a promising bioprocess in the food and feed industry.
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Affiliation(s)
- Georgios Bakratsas
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece
| | - Angeliki Polydera
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece
| | - Oskar Nilson
- RISE Processum AB, SE-89122 Örnsköldsvik, Sweden
| | - Alexandra V Chatzikonstantinou
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece
| | | | - Petros Katapodis
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece
| | - Haralambos Stamatis
- Biotechnology Laboratory, Department of Biological Applications and Technologies, University of Ioannina, 45110 Ioannina, Greece
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15
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Fu J, Wang Z, Miao H, Yu C, Zheng Z, Ouyang J. Rapid adaptive evolution of Bacillus coagulans to undetoxified corncob hydrolysates for lactic acid production and new insights into its high phenolic degradation. BIORESOURCE TECHNOLOGY 2023; 383:129246. [PMID: 37247791 DOI: 10.1016/j.biortech.2023.129246] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Here, an adapted Bacillus coagulans (Weizmannia coagulans) strain CC17B-1 was developed for lignocellulosic lactic acid production through a short and rapid adaptive laboratory evolution technique. Without any detoxification, two actual corn cob hydrolysates from the factory were effectively fermented to lactic acid within 60 h. Strain CC17B-1 is capable of degrading all nine determined phenolic compounds in the hydrolysate, with the only exception being vanillic acid. Notably, its tolerances for ferulic acid and p-coumaric acid are the highest doses reported in anaerobic microbes. A proposed degradation pathway showed that strain CC17B-1 could convert phenolic aldehydes to phenolic alcohol and then further degrade them completely. This work provides new ideas for the microbe phenolic degradation pathway and paves the way for industrial lactic acid production from lignocellulosic biomass.
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Affiliation(s)
- Jiaming Fu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Zijie Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Hongcheng Miao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Chang Yu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Zhaojuan Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Jia Ouyang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
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16
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Barreto MQ, Garbelotti CV, de Moura Soares J, Grandis A, Buckeridge MS, Leone FA, Ward RJ. Xylose isomerase from Piromyces sp. E2 is a promiscuous enzyme with epimerase activity. Enzyme Microb Technol 2023; 166:110230. [PMID: 36966679 DOI: 10.1016/j.enzmictec.2023.110230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/15/2023] [Accepted: 03/18/2023] [Indexed: 04/03/2023]
Abstract
Xylose isomerase catalyzes the isomerization of D-xylose to D-xylulose with promiscuous activity for other saccharides including D-glucose, D-allose, and L-arabinose. The xylose isomerase from the fungus Piromyces sp. E2 (PirE2_XI) is used to engineer xylose usage by the fermenting yeast Saccharomyces cerevisiae, but its biochemical characterization is poorly understood with divergent catalytic parameters reported. We have measured the kinetic parameters of the PirE2_XI and analyzed its thermostability and pH-dependence towards different substrates. The PirE2_XI shows promiscuous activity towards D-xylose, D-glucose, D-ribose and L-arabinose with variable effects depending on different divalent ions and epimerizes D-xylose at C3 to produce D-ribulose in a substrate/product dependent ratio. The enzyme follows Michaelis-Menten kinetics for the substrates used and although KM values for D-xylose are comparable at 30 and 60 °C, the kcat/KM is three-fold greater at 60 °C. The purified PirE2_XI shows maximal activity at 65 °C in the pH range of 6.5-7.5 and is a thermostable enzyme, maintaining full activity over 48 h at 30 °C or 12 h at 60 °C. This is the first report demonstrating epimerase activity of the PirE2_XI and its ability to isomerize D-ribose and L-arabinose, and provides a comprehensive in vitro study of substrate specificity, effect of metal ions and temperature on enzyme activity and these findings advance the knowledge of the mechanism of action of this enzyme.
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17
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Willers VP, Beer B, Sieber V. Integrating Carbohydrate and C1 Utilization for Chemicals Production. CHEMSUSCHEM 2023; 16:e202202122. [PMID: 36520644 DOI: 10.1002/cssc.202202122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/14/2022] [Indexed: 06/17/2023]
Abstract
In the face of increasing mobility and energy demand, as well as the mitigation of climate change, the development of sustainable and environmentally friendly alternatives to fossil fuels will be one of the most important tasks facing humankind in the coming years. In order to initiate the transition from a petroleum-based economy to a new, greener future, biofuels and synthetic fuels have great potential as they can be adapted to already common processes. Thereby, especially synthetic fuels from CO2 and renewable energies are seen as the next big step for a sustainable and ecological life. In our study, we directly address the sustainable production of the most common biofuel, ethanol, and the highly interesting next-generation biofuel, isobutanol, from methanol and xylose, which are directly derivable from CO2 and lignocellulosic waste streams, respectively, such integrating synthetic fuel and biofuel production. After enzyme and reaction optimization, we succeeded in producing either 3 g L-1 ethanol or 2 g L-1 isobutanol from 7.5 g L-1 xylose and 1.6 g L-1 methanol. In our cell-free enzyme system, C1-compounds are efficiently combined and fixed by the key enzyme transketolase and converted to the intermediate pyruvate. This opens the way for a hybrid production of biofuels, platform chemicals and fine chemicals from CO2 and lignocellulosic waste streams as alternative to conventional routes depending solely either on CO2 or sugars.
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Affiliation(s)
- Vivian Pascal Willers
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
| | - Barbara Beer
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
- Current address: CASCAT GmbH, 94315, Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
- Technical University of Munich, 94315, Straubing, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, 4072, Australia
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18
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Huang T, Ma Y. Advances in biosynthesis of higher alcohols in Escherichia coli. World J Microbiol Biotechnol 2023; 39:125. [PMID: 36941474 DOI: 10.1007/s11274-023-03580-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/13/2023] [Indexed: 03/23/2023]
Abstract
In recent years, the development of green energy to replace fossil fuels has been the focus of research. Higher alcohols are important biofuels and chemicals. The production of higher alcohols in microbes has gained attention due to its environmentally friendly character. Higher alcohols have been synthesized in model microorganism Escherichia coli, and the production has reached the gram level through enhancement of metabolic flow, the balance of reducing power and the optimization of fermentation processes. Sustainable bio-higher alcohols production is expected to replace fossil fuels as a green and renewable energy source. Therefore, this review summarizes the latest developments in producing higher alcohols (C3-C6) by E. coli, elucidate the main bottlenecks limiting the biosynthesis of higher alcohols, and proposes potential engineering strategies of improving the production of biological higher alcohols. This review would provide a theoretical basis for further research on higher alcohols production by E. coli.
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Affiliation(s)
- Tong Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Yuanyuan Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- School of Marin Science and Technology, Tianjin University, Tianjin, 300072, China.
- R&D Center for Petrochemical Technology, Tianjin University, Tianjin, 300072, China.
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19
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Ye JW, Lin YN, Yi XQ, Yu ZX, Liu X, Chen GQ. Synthetic biology of extremophiles: a new wave of biomanufacturing. Trends Biotechnol 2023; 41:342-357. [PMID: 36535816 DOI: 10.1016/j.tibtech.2022.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/12/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Microbial biomanufacturing, powered by the advances of synthetic biology, has attracted growing interest for the production of diverse products. In contrast to conventional microbes, extremophiles have shown better performance for low-cost production owing to their outstanding growth and synthesis capacity under stress conditions, allowing unsterilized fermentation processes. We review increasing numbers of products already manufactured utilizing extremophiles in recent years. In addition, genetic parts, molecular tools, and manipulation approaches for extremophile engineering are also summarized, and challenges and opportunities are predicted for non-conventional chassis. Next-generation industrial biotechnology (NGIB) based on engineered extremophiles promises to simplify biomanufacturing processes and achieve open and continuous fermentation, without sterilization, and utilizing low-cost substrates, making NGIB an attractive green process for sustainable manufacturing.
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Affiliation(s)
- Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yi-Na Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xue-Qing Yi
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuo-Xuan Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xu Liu
- PhaBuilder Biotech Company, Shunyi District, Zhaoquan Ying, Beijing 101309, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; Ministry of Education (MOE) Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
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20
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Gao R, Zhang H, Xiong L, Li H, Chen X, Wang M, Chen X. Fermentation performance of oleaginous yeasts on Eucommia ulmoides Oliver hydrolysate: Impacts of the mixed strains fermentation. J Biotechnol 2023; 366:10-18. [PMID: 36868409 DOI: 10.1016/j.jbiotec.2023.02.009] [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: 11/01/2022] [Revised: 01/15/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023]
Abstract
This present study mainly focused on the investigation and optimization of the fermentation performance of oleaginous yeasts on Eucommia ulmoides Oliver hydrolysate (EUOH), which contains abundant and diverse sugars. More importantly, the impacts of the mixed strains fermentation compared with the single strain fermentation were analyzed and evaluated, through systematic investigations of substrate metabolism, cell growth, polysaccharide and lipid production, COD and ammonia-nitrogen removals. It was found that the mixed strains fermentation could effectively promote a more comprehensive and thorough utilization of the various sugars in EUOH, greatly improve COD removal effect, biomass and yeast polysaccharide production, but could not significantly improve the overall lipid content and ammonia nitrogen removal effect. In this study, when the two strains with the highest lipid content (i.e. L. starkeyi and R. toruloides) were mixed-cultured, the maximum lipid yield of 3.82 g/L was achieved, and the yeast polysaccharide yield, COD and ammonia-nitrogen removal rates of the fermentation (LS+RT) were 1.64 g/L, 67.4% and 74.9% respectively. When the strain with the highest polysaccharide content (i.e. R. toruloides) was mixed-cultured with the strains with strong growth activity (i.e. T. cutaneum and T. dermatis), a large amount of yeast polysaccharides could be obtained, which were 2.33 g/L (RT+TC) and 2.38 g/L (RT+TD) respectively. And the lipid yield, COD and ammonia-nitrogen removal rates of the fermentation (RT+TC), (RT+TD) were 3.09 g/L, 77.7%, 81.4% and 2.54 g/L, 74.9%, 80.4%, respectively.
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Affiliation(s)
- Ruiling Gao
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Hairong Zhang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Lian Xiong
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Hailong Li
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Xuefang Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Mengkun Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Xinde Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China.
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21
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Qiu Y, Qiu Z, Xia J, Liu X, Zhang H, Yang Y, Hou W, Li X, He J. Co-expression of Xylose Transporter and Fructose-Bisphosphate Aldolase Enhances the Utilization of Xylose by Lactococcus lactis IO-1. Appl Biochem Biotechnol 2023; 195:816-831. [PMID: 36205844 DOI: 10.1007/s12010-022-04168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
The raw material cost of lactic acid fermentation accounts for the main part of the production cost, and this necessitates the exploration of the efficient use of cheap raw materials in lactic acid production. We compared the outcomes of the homologous expressions of xylose transporters (xylFGH, xylE, araE, and xylT), 6-phosphofructokinase (pfkA), fructose-bisphosphate aldolase (fbaA), and their co-expression in Lactococcus lactis IO-1 on lactic acid production using xylose as the raw material. We found that the production rate of lactic acid on xylose fermentation by L. lactis IO-1 overexpressing fbaA was the highest (14.42%). Among the xylose transporters investigated, XylT had the strongest xylose transport capacity in L. lactis IO-1, with an increase in the lactic acid production rate by 10.38%. The genes near the overexpression of fbaA or xylT in the metabolic pathway were more upregulated than the distant genes. The co-expression of fbaA and xylT increased the production rate of lactic acid by 27.84% on xylose fermentation by L. lactis IO-1. This work presents a novel strategy for the simultaneous enhancement of the expression of important genes at the beginning and midway of the xylose metabolic pathway of L. lactis IO-1, which could greatly improve the target production.
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Affiliation(s)
- Yejuan Qiu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Zhongyang Qiu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Jun Xia
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Xiaoyan Liu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Hanwen Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Yuxiang Yang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Wenyi Hou
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Xiangqian Li
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China.
| | - Jianlong He
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China.
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22
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Ali N, Aiman A, Shamsi A, Hassan I, Shahid M, Gaur NA, Islam A. Identification of Thermostable Xylose Reductase from Thermothelomyces thermophilus: A Biochemical Characterization Approach to Meet Biofuel Challenges. ACS OMEGA 2022; 7:44241-44250. [PMID: 36506193 PMCID: PMC9730754 DOI: 10.1021/acsomega.2c05690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
The constant rise in energy demands, costs, and concerns about global warming has created a demand for new renewable alternative fuels that can be produced sustainably. Lignocellulose biomass can act as an excellent energy source and various value-added compounds like xylitol. In this research study, we have explored the xylose reductase that was obtained from the genome of a thermophilic fungus Thermothelomyces thermophilus while searching for an enzyme to convert xylose to xylitol at higher temperatures. The recombinant thermostable TtXR histidine-tagged fusion protein was expressed in Escherichia coli and successfully purified for the first time. Further, it was characterized for its function and novel structure at varying temperatures and pH. The enzyme showed maximal activity at 7.0 pH and favored d-xylose over other pentoses and hexoses. Biophysical approaches such as ultraviolet-visible (UV-visible), fluorescence spectrometry, and far-UV circular dichroism (CD) spectroscopy were used to investigate the structural integrity of pure TtXR. This research highlights the potential application of uncharacterized xylose reductase as an alternate source for the effective utilization of lignocellulose in fermentation industries at elevated temperatures. Moreover, this research would give environment-friendly and long-term value-added products, like xylitol, from lignocellulosic feedstock for both scientific and commercial purposes.
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Affiliation(s)
- Nabeel Ali
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi110025, India
| | - Ayesha Aiman
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi110025, India
| | - Anas Shamsi
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi110025, India
| | - Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi110025, India
| | - Mohammad Shahid
- Department
of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, P.O. Box: 173, Al Kharj11942, Kingdom of Saudi Arabia
| | - Naseem A. Gaur
- International
Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi110067, India
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi110025, India
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23
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Fiamenghi MB, Bueno JGR, Camargo AP, Borelli G, Carazzolle MF, Pereira GAG, dos Santos LV, José J. Machine learning and comparative genomics approaches for the discovery of xylose transporters in yeast. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:57. [PMID: 35596177 PMCID: PMC9123741 DOI: 10.1186/s13068-022-02153-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/05/2022] [Indexed: 11/15/2022]
Abstract
Background The need to mitigate and substitute the use of fossil fuels as the main energy matrix has led to the study and development of biofuels as an alternative. Second-generation (2G) ethanol arises as one biofuel with great potential, due to not only maintaining food security, but also as a product from economically interesting crops such as energy-cane. One of the main challenges of 2G ethanol is the inefficient uptake of pentose sugars by industrial yeast Saccharomyces cerevisiae, the main organism used for ethanol production. Understanding the main drivers for xylose assimilation and identify novel and efficient transporters is a key step to make the 2G process economically viable. Results By implementing a strategy of searching for present motifs that may be responsible for xylose transport and past adaptations of sugar transporters in xylose fermenting species, we obtained a classifying model which was successfully used to select four different candidate transporters for evaluation in the S. cerevisiae hxt-null strain, EBY.VW4000, harbouring the xylose consumption pathway. Yeast cells expressing the transporters SpX, SpH and SpG showed a superior uptake performance in xylose compared to traditional literature control Gxf1. Conclusions Modelling xylose transport with the small data available for yeast and bacteria proved a challenge that was overcome through different statistical strategies. Through this strategy, we present four novel xylose transporters which expands the repertoire of candidates targeting yeast genetic engineering for industrial fermentation. The repeated use of the model for characterizing new transporters will be useful both into finding the best candidates for industrial utilization and to increase the model’s predictive capabilities. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02153-7.
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24
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Tan B, Zheng Y, Yan H, Liu Y, Li ZJ. Metabolic engineering of Halomonas bluephagenesis to metabolize xylose for poly-3-hydroxybutyrate production. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Han X, Liu J, Tian S, Tao F, Xu P. Microbial cell factories for bio-based biodegradable plastics production. iScience 2022; 25:105462. [DOI: 10.1016/j.isci.2022.105462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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Zhang J, Xu T, Wang X, Jing X, Zhang J, Hong J, Xu J, Wang J. Lignocellulosic xylitol production from corncob using engineered Kluyveromycesmarxianus. Front Bioeng Biotechnol 2022; 10:1029203. [PMID: 36338133 PMCID: PMC9633946 DOI: 10.3389/fbioe.2022.1029203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/07/2022] [Indexed: 11/21/2022] Open
Abstract
Xylitol production from lignocellulose hydrolysate is a sustainable and environment-friendly process. In this study, a systematic process of converting corncob waste into xylitol is described. First, the corncobs are hydrolyzed with acid to a hydrolysate. Second, Kluyveromyces marxianus YZJQ016 derived from K. marxianus YZJ074, constructed by overexpressing ScGAL2-N376F from Saccharomyces cerevisiae, CtXYL1 from Candida tropicalis, and KmZWF1 from K. marxianus, produces xylitol from the hydrolysate. A total of ten xylose reductase genes were evaluated, and CtXYL1 proved best by showing the highest catalytic activity under the control of the KmGAPDH promoter. A 5 L fermenter at 42°C produced 105.22 g/L xylitol using K. marxianus YZJQ016—the highest production reported to date from corncob hydrolysate. Finally, for crystallization of the xylitol, the best conditions were 50% (v/v) methanol as an antisolvent, at 25°C, with purity and yield of 99%–100% and 74%, respectively—the highest yield reported to date.
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Affiliation(s)
- Jia Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Teng Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohang Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jichao Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Jichao Wang,
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27
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Geng B, Jia X, Peng X, Han Y. Biosynthesis of value-added bioproducts from hemicellulose of biomass through microbial metabolic engineering. Metab Eng Commun 2022; 15:e00211. [PMID: 36311477 PMCID: PMC9597109 DOI: 10.1016/j.mec.2022.e00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Hemicellulose is the second most abundant carbohydrate in lignocellulosic biomass and has extensive applications. In conventional biomass refinery, hemicellulose is easily converted to unwanted by-products in pretreatment and therefore can't be fully utilized. The present study aims to summarize the most recent development of lignocellulosic polysaccharide degradation and fully convert it to value-added bioproducts through microbial and enzymatic catalysis. Firstly, bioprocess and microbial metabolic engineering for enhanced utilization of lignocellulosic carbohydrates were discussed. The bioprocess for degradation and conversion of natural lignocellulose to monosaccharides and organic acids using anaerobic thermophilic bacteria and thermostable glycoside hydrolases were summarized. Xylose transmembrane transporting systems in natural microorganisms and the latest strategies for promoting the transporting capacity by metabolic engineering were summarized. The carbon catabolite repression effect restricting xylose utilization in microorganisms, and metabolic engineering strategies developed for co-utilization of glucose and xylose were discussed. Secondly, the metabolic pathways of xylose catabolism in microorganisms were comparatively analyzed. Microbial metabolic engineering for converting xylose to value-added bioproducts based on redox pathways, non-redox pathways, pentose phosphate pathway, and improving inhibitors resistance were summarized. Thirdly, strategies for degrading lignocellulosic polysaccharides and fully converting hemicellulose to value-added bioproducts through microbial metabolic engineering were proposed. Hemicellulose is the main carbohydrate of biomass and has valuable applications. Hemicellulose is underutilized in conventional biomass refinery and pretreatment. Microbial and enzymatic catalysis were applied for hemicellulose utilization. Xylose is converted to value-added bioproducts by metabolic engineering.
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Affiliation(s)
- Biao Geng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China,Corresponding author. National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
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28
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Cheng C, Wang WB, Sun ML, Tang RQ, Bai L, Alper HS, Zhao XQ. Deletion of NGG1 in a recombinant Saccharomyces cerevisiae improved xylose utilization and affected transcription of genes related to amino acid metabolism. Front Microbiol 2022; 13:960114. [PMID: 36160216 PMCID: PMC9493327 DOI: 10.3389/fmicb.2022.960114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Production of biofuels and biochemicals from xylose using yeast cell factory is of great interest for lignocellulosic biorefinery. Our previous studies revealed that a natural yeast isolate Saccharomyces cerevisiae YB-2625 has superior xylose-fermenting ability. Through integrative omics analysis, NGG1, which encodes a transcription regulator as well as a subunit of chromatin modifying histone acetyltransferase complexes was revealed to regulate xylose metabolism. Deletion of NGG1 in S. cerevisiae YRH396h, which is the haploid version of the recombinant yeast using S. cerevisiae YB-2625 as the host strain, improved xylose consumption by 28.6%. Comparative transcriptome analysis revealed that NGG1 deletion down-regulated genes related to mitochondrial function, TCA cycle, ATP biosynthesis, respiration, as well as NADH generation. In addition, the NGG1 deletion mutant also showed transcriptional changes in amino acid biosynthesis genes. Further analysis of intracellular amino acid content confirmed the effect of NGG1 on amino acid accumulation during xylose utilization. Our results indicated that NGG1 is one of the core nodes for coordinated regulation of carbon and nitrogen metabolism in the recombinant S. cerevisiae. This work reveals novel function of Ngg1p in yeast metabolism and provides basis for developing robust yeast strains to produce ethanol and biochemicals using lignocellulosic biomass.
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Affiliation(s)
- Cheng Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meng-Lin Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Long Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Xin-Qing Zhao,
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29
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Antoniêto ACC, Nogueira KMV, Mendes V, Maués DB, Oshiquiri LH, Zenaide-Neto H, de Paula RG, Gaffey J, Tabatabaei M, Gupta VK, Silva RN. Use of carbohydrate-directed enzymes for the potential exploitation of sugarcane bagasse to obtain value-added biotechnological products. Int J Biol Macromol 2022; 221:456-471. [PMID: 36070819 DOI: 10.1016/j.ijbiomac.2022.08.186] [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: 04/12/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022]
Abstract
Microorganisms, such as fungi and bacteria, are crucial players in the production of enzymatic cocktails for biomass hydrolysis or the bioconversion of plant biomass into products with industrial relevance. The biotechnology industry can exploit lignocellulosic biomass for the production of high-value chemicals. The generation of biotechnological products from lignocellulosic feedstock presents several bottlenecks, including low efficiency of enzymatic hydrolysis, high cost of enzymes, and limitations on microbe metabolic performance. Genetic engineering offers a route for developing improved microbial strains for biotechnological applications in high-value product biosynthesis. Sugarcane bagasse, for example, is an agro-industrial waste that is abundantly produced in sugar and first-generation processing plants. Here, we review the potential conversion of its feedstock into relevant industrial products via microbial production and discuss the advances that have been made in improving strains for biotechnological applications.
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Affiliation(s)
- Amanda Cristina Campos Antoniêto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Karoline Maria Vieira Nogueira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Vanessa Mendes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - David Batista Maués
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Letícia Harumi Oshiquiri
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Hermano Zenaide-Neto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Renato Graciano de Paula
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitória, ES 29047-105, Brazil
| | - James Gaffey
- Circular Bioeconomy Research Group, Shannon Applied Biotechnology Centre, Munster Technological University, Kerry, Ireland; BiOrbic, Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Meisam Tabatabaei
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Center for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil.
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30
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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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31
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Sugarcane Bagasse-Based Ethanol Production and Utilization of Its Vinasse for Xylitol Production as an Approach in Integrated Biorefinery. FERMENTATION 2022. [DOI: 10.3390/fermentation8070340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Biorefinery of sugarcane bagasse into ethanol and xylitol was investigated in this study. Ethanol fermentation of sugarcane bagasse hydrolysate was carried out by Saccharomyces cerevisiae. After ethanol distillation, the vinasse containing xylose was used to produce xylitol through fermentation by Candida guilliermondii TISTR 5068. During the ethanol fermentation, it was not necessary to supplement a nitrogen source to the hydrolysate. Approximately 50 g/L of bioethanol was produced after 36 h of fermentation. The vinasse was successfully used to produce xylitol. Supplementing the vinasse with 1 g/L of yeast extract improved xylitol production 1.4-fold. Cultivating the yeast with 10% controlled dissolved oxygen resulted in the best xylitol production and yields of 10.2 ± 1.12 g/L and 0.74 ± 0.04 g/g after 60 h fermentation. Supplementing the vinasse with low fraction of molasses to improve xylitol production did not yield a positive result. The supplementation caused decreases of up to 34% in xylitol production rate, 24% in concentration, and 24% in yield.
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Fermentation performance of a Mexican native Clavispora lusitaniae strain for xylitol and ethanol production from xylose, glucose and cellobiose. Enzyme Microb Technol 2022; 160:110094. [PMID: 35810624 DOI: 10.1016/j.enzmictec.2022.110094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 11/21/2022]
Abstract
Lignocellulose hydrolysates are rich in fermentable sugars such as xylose, cellobiose and glucose, with high potential in the biotechnology industry to obtain bioproducts of higher economic value. Thus, it is important to search for and study new yeast strains that co-consume these sugars to achieve better yields and productivity in the processes. The yeast Clavispora lusitaniae CDBB-L-2031, a native strain isolated from mezcal must, was studied under various culture conditions to potentially produce ethanol and xylitol due to its ability to assimilate xylose, cellobiose and glucose. This yeast produced ethanol under microaerobic conditions with yields of 0.451 gethanol/gglucose and 0.344 gethanol/gcellobiose, when grown on 1% glucose or cellobiose, respectively. In mixtures (0.5% each) of glucose:xylose and glucose:xylose:cellobiose the yields were 0.367 gethanol/gGX and 0. 380 gethanol/gGXC, respectively. Likewise, in identical conditions, C. lusitaniae produced xylitol from xylose with a yield of 0.421 gxylitol/gxylose. In 5% glucose or xylose, this yeast had better ethanol and xylitol titers and yields, respectively. However, glucose negatively affected xylitol production in the mixture of both sugars (3% each), producing only ethanol. Xylose reductase (XR) and xylitol dehydrogenase (XDH) activities were evaluated in cultures growing on xylose or glucose, obtaining the highest values in cultures on xylose at 8 h (25.9 and 6.22 mU/mg, respectively). While in glucose cultures, XR and XDH activities were detected once this substrate was consumed (4.06 and 3.32 mU/mg, respectively). Finally, the XYL1 and XYL2 genes encoding xylose reductase and xylitol dehydrogenase, respectively, were up-regulated by xylose, whereas glucose down-regulated their expression.
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Pereira de Almeida A, Vargas IP, Marciano CL, Zanoelo FF, Giannesi GC, Moraes Polizeli MDLTD, Jorge JA, Furriel RDPM, Ruller R, Masui DC. Investigation of biochemical and biotechnological potential of a thermo-halo-alkali-tolerant endo-xylanase (GH11) from Humicola brevis var. thermoidea for lignocellulosic valorization of sugarcane biomass. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Chaput G, Ford J, DeDiego L, Narayanan A, Tam WY, Whalen M, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O’Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Glavina del Rio T, DeAngelis KM. Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium. Microbiol Spectr 2022; 10:e0234621. [PMID: 35579457 PMCID: PMC9241852 DOI: 10.1128/spectrum.02346-21] [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: 12/05/2021] [Accepted: 04/19/2022] [Indexed: 11/20/2022] Open
Abstract
Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae. Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni. We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications.
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Affiliation(s)
- Gina Chaput
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Jacob Ford
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Lani DeDiego
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Achala Narayanan
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Wing Yin Tam
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Meghan Whalen
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
| | - Marcel Huntemann
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alicia Clum
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alex Spunde
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Manoj Pillay
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Neha Varghese
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Mikhailova
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - I-Min Chen
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Dimitrios Stamatis
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - T. B. K Reddy
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Ronan O’Malley
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nicole Shapiro
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Ivanova
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nikos C. Kyrpides
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Tanja Woyke
- United States Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts–Amherst, Amherst, Massachusetts, USA
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Rhizopus oryzae for Fumaric Acid Production: Optimising the Use of a Synthetic Lignocellulosic Hydrolysate. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The hydrolysis of lignocellulosic biomass opens an array of bioconversion possibilities for producing fuels and chemicals. Microbial fermentation is particularly suited to the conversion of sugar-rich hydrolysates into biochemicals. Rhizopus oryzae ATCC 20344 was employed to produce fumaric acid from glucose, xylose, and a synthetic lignocellulosic hydrolysate (glucose–xylose mixture) in batch and continuous fermentations. A novel immobilised biomass reactor was used to investigate the co-fermentation of xylose and glucose. Ideal medium conditions and a substrate feed strategy were then employed to optimise the production of fumaric acid. The batch fermentation of the synthetic hydrolysate at optimal conditions (urea feed rate 0.625mgL−1h−1 and pH 4) produced a fumaric acid yield of 0.439gg−1. A specific substrate feed rate (0.164gL−1h−1) that negated ethanol production and selected for fumaric acid was determined. Using this feed rate in a continuous fermentation, a fumaric acid yield of 0.735gg−1 was achieved; this was a 67.4% improvement. A metabolic analysis helped to determine a continuous synthetic lignocellulosic hydrolysate feed rate that selected for fumaric acid production while achieving the co-fermentation of glucose and xylose, thus avoiding the undesirable carbon catabolite repression. This work demonstrates the viability of fumaric acid production from lignocellulosic hydrolysate; the process developments discovered will pave the way for an industrially viable process.
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Growth and phycocyanin production with Galdieria sulphuraria UTEX 2919 using xylose, glucose, and corn stover hydrolysates under heterotrophy and mixotrophy. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Heistinger L, Dohm JC, Paes BG, Koizar D, Troyer C, Ata Ö, Steininger-Mairinger T, Mattanovich D. Genotypic and phenotypic diversity among Komagataella species reveals a hidden pathway for xylose utilization. Microb Cell Fact 2022; 21:70. [PMID: 35468837 PMCID: PMC9036795 DOI: 10.1186/s12934-022-01796-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The yeast genus Komagataella currently consists of seven methylotrophic species isolated from tree environments. Well-characterized strains of K. phaffii and K. pastoris are important hosts for biotechnological applications, but the potential of other species from the genus remains largely unexplored. In this study, we characterized 25 natural isolates from all seven described Komagataella species to identify interesting traits and provide a comprehensive overview of the genotypic and phenotypic diversity available within this genus. RESULTS Growth tests on different carbon sources and in the presence of stressors at two different temperatures allowed us to identify strains with differences in tolerance to high pH, high temperature, and growth on xylose. As Komagataella species are generally not considered xylose-utilizing yeasts, xylose assimilation was characterized in detail. Growth assays, enzyme activity measurements and 13C labeling confirmed the ability of K. phaffii to utilize D-xylose via the oxidoreductase pathway. In addition, we performed long-read whole-genome sequencing to generate genome assemblies of all Komagataella species type strains and additional K. phaffii and K. pastoris isolates for comparative analysis. All sequenced genomes have a similar size and share 83-99% average sequence identity. Genome structure analysis showed that K. pastoris and K. ulmi share the same rearrangements in difference to K. phaffii, while the genome structure of K. kurtzmanii is similar to K. phaffii. The genomes of the other, more distant species showed a larger number of structural differences. Moreover, we used the newly assembled genomes to identify putative orthologs of important xylose-related genes in the different Komagataella species. CONCLUSIONS By characterizing the phenotypes of 25 natural Komagataella isolates, we could identify strains with improved growth on different relevant carbon sources and stress conditions. Our data on the phenotypic and genotypic diversity will provide the basis for the use of so-far neglected Komagataella strains with interesting characteristics and the elucidation of the genetic determinants of improved growth and stress tolerance for targeted strain improvement.
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Affiliation(s)
- Lina Heistinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria.
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland.
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Barbara G Paes
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia (UnB), Brasilia, Brazil
| | - Daniel Koizar
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Özge Ata
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (Acib GmbH), 1190, Vienna, Austria
| | - Teresa Steininger-Mairinger
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (Acib GmbH), 1190, Vienna, Austria
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Gao W, Yin Y, Wang P, Tan W, He M, Wen J. Production of fengycin from D-xylose through the expression and metabolic regulation of the Dahms pathway. Appl Microbiol Biotechnol 2022; 106:2557-2567. [PMID: 35362719 DOI: 10.1007/s00253-022-11871-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 02/14/2022] [Accepted: 03/05/2022] [Indexed: 12/01/2022]
Abstract
D-Xylose is a key component of lignocellulosic biomass and the second-most abundant carbohydrate on the planet. As one of the most powerful cyclo-lipopeptide antibiotics, fengycin displays strong wide-spectrum antifungal and antiviral, as well as potential anti-cancer activity. Pyruvate is a key metabolite linking the biosynthesis of fatty acids and amino acids, the precursors for fengycin. In this study, the genes encoding the Dahms xylose-utilization pathway were integrated into the amyE site of Bacillus subtilis 168, and based on the metabolic characteristics of the Dahms pathway, the acetate kinase (ackA) and lactate dehydrogenase (ldh) genes were knocked out. Then, the metabolic control module II was designed to convert glycolaldehyde, another intermediate of the Dahms pathway, in addition to pathways for the conversion of acetaldehyde into malic acid and oxaloacetic acid, resulting in strain BSU03. In the presence of module II, the content of acetic and lactic acid decreased significantly, and the xylose uptake efficiency increased. At the same time, the yield of fengycin increased by 87% compared to the original strain. Additionally, the underlying factors for the increase of fengycin titer were revealed through metabonomic analysis. This study therefore demonstrates that this regulation approach can not only optimize the intracellular fluxes for the Dahms pathway, but is also conducive to the synthesis of secondary metabolites similar to fengycin. KEY POINTS: • The expression and effect of the Dahms pathway on the synthesis of fengycin in Bacillus subtilis 168. • The expression of regulatory module II can promote the metabolic rate of the Dahms pathway and increase the synthesis of the fengycin.
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Affiliation(s)
- Wenting Gao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Ying Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Pan Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Wei Tan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Mingliang He
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China. .,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China.
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de Souza Colombo G, Mendes IV, de Morais Souto B, Barreto CC, Serra LA, Noronha EF, Parachin NS, de Almeida JRM, Quirino BF. Identification and functional expression of a new xylose isomerase from the goat rumen microbiome in Saccharomyces cerevisiae. Lett Appl Microbiol 2022; 74:941-948. [PMID: 35239207 DOI: 10.1111/lam.13689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/01/2022]
Abstract
The current climate crisis demands replacement of fossil energy sources with sustainable alternatives. In this scenario, second-generation bioethanol, a product of lignocellulosic biomass fermentation, represents a more sustainable alternative. However, Saccharomyces cerevisiae cannot metabolize pentoses, such as xylose, present as a major component of lignocellulosic biomass. Xylose isomerase (XI) is an enzyme that allows xylose consumption by yeasts, since it converts xylose into xylulose, which is further converted to ethanol by the pentose-phosphate pathway. Only a few XI were successfully expressed in S. cerevisiae strains. This work presents a new bacterial xylose isomerase, named GR-XI 1, obtained from a Brazilian goat rumen metagenomic library. Phylogenetic analysis confirmed the bacterial origin of the gene, which is related to Firmicutes xylose isomerases. After codon optimization, this enzyme, renamed XySC1, was functionally expressed in S. cerevisiae, allowing growth in media with xylose as sole carbon source. Overexpression of XySC1 in S. cerevisiae allowed the recombinant strain to efficiently consume and metabolize xylose under aerobic conditions.
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Affiliation(s)
- Gabriel de Souza Colombo
- Genetics and Biotechnology Laboratory, Embrapa-Agroenergy, Brasília, DF, Brazil, 70770-901.,Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasília, DF, Brazil, 70790-160
| | - Isis Viana Mendes
- Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasília, DF, Brazil, 70790-160
| | | | - Cristine Chaves Barreto
- Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasília, DF, Brazil, 70790-160
| | - Luana Assis Serra
- Genetics and Biotechnology Laboratory, Embrapa-Agroenergy, Brasília, DF, Brazil, 70770-901
| | | | - Nádia Skorupa Parachin
- Departmentof Cellular Biology, Universidade de Brasília, Brasília, DF, Brazil, 70910-900
| | | | - Betania Ferraz Quirino
- Genetics and Biotechnology Laboratory, Embrapa-Agroenergy, Brasília, DF, Brazil, 70770-901
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Yao J, Wang J, Ju Y, Dong Z, Song X, Chen L, Zhang W. Engineering a Xylose-Utilizing Synechococcus elongatus UTEX 2973 Chassis for 3-Hydroxypropionic Acid Biosynthesis under Photomixotrophic Conditions. ACS Synth Biol 2022; 11:678-688. [PMID: 35119824 DOI: 10.1021/acssynbio.1c00364] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Photomixotrophic cultivation of cyanobacteria is considered a promising strategy to achieve both high cell density and product accumulation, since cyanobacteria can obtain carbon and energy sources from organic matter in addition to those obtained from CO2 and sunlight. Acetyl coenzyme A (acetyl-CoA) is a key precursor used for the biosynthesis of a wide variety of important value-added chemicals. However, the acetyl-CoA content in cyanobacteria is typically low under photomixotrophic conditions, which limits the productivity of the derived chemicals. In this study, a xylose utilization pathway from Escherichia coli was first engineered into fast-growing Synechococcus elongatus UTEX 2973 (hereafter Synechococcus 2973), enabling the xylose based photomixotrophy. Metabolomics analysis of the engineered strain showed that the utilization of xylose enhanced the carbon flow to the oxidative pentose phosphate (OPP) pathway, along with an increase in the intracellular abundance of metabolites such as fructose-6-phosphate (F6P), fructose-1,6-bisphosphate (FBP), ribose-5-phosphate (R5P), erythrose-4-phosphate (E4P), and glyceraldehyde-3-phosphate (G3P). Then, the native glycolytic pathway was rewired via heterologous phosphoketolase (Pkt) gene expression, combined with phosphofructokinase (Pfk) gene knockout and fructose-1,6-bisphosphatase (Fbp) gene overexpression, to drive more carbon flux from xylose to acetyl-CoA. Finally, a heterologous 3-hydroxypropionic acid (3-HP) biosynthetic pathway was introduced. The results showed that 3-HP biosynthesis was improved by up to approximately 4.1-fold (from 22.5 mg/L to 91.3 mg/L) compared with the engineered strain without a rewired metabolism under photomixotrophic conditions and up to approximately 14-fold compared with the strain under photoautotrophic conditions. Using 3-HP as a "proof-of-molecule", our results demonstrated that this strategy could be applied to improve the intracellular pool of acetyl-CoA for the photomixotrophic production of value-added chemicals that require acetyl-CoA as a precursor in a cyanobacterial chassis.
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Affiliation(s)
- Jiaqi Yao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Jin Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Yue Ju
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Zhengxin Dong
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Xinyu Song
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, PR China
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Lekshmi Sundar MS, Madhavan Nampoothiri K. An overview of the metabolically engineered strains and innovative processes used for the value addition of biomass derived xylose to xylitol and xylonic acid. BIORESOURCE TECHNOLOGY 2022; 345:126548. [PMID: 34906704 DOI: 10.1016/j.biortech.2021.126548] [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: 10/27/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Xylose, the most abundant pentose sugar of the hemicellulosic fraction of lignocellulosic biomass, has to be utilized rationally for the commercial viability of biorefineries. An effective pre-treatment strategy for the release of xylose from the biomass and an appropriate microbe of the status of an Industrial strain for the utilization of this pentose sugar are key challenges which need special attention for the economic success of the biomass value addition to chemicals. Xylitol and xylonic acid, the alcohol and acid derivatives of xylose are highly demanded commodity chemicals globally with plenty of applications in the food and pharma industries. This review emphasis on the natural and metabolically engineered strains utilizing xylose and the progressive and innovative fermentation strategies for the production and subsequent recovery of the above said chemicals from pre-treated biomass medium.
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Affiliation(s)
- M S Lekshmi Sundar
- Microbial Processes and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDG Campus, Ghaziabad, Uttar Pradesh 201002, India
| | - K Madhavan Nampoothiri
- Microbial Processes and Technology Division, CSIR - National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram 695019, Kerala, India.
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Bazzone A, Tesmer L, Kurt D, Kaback HR, Fendler K, Madej MG. Investigation of sugar binding kinetics of the E. coli sugar/H + symporter XylE using solid supported membrane-based electrophysiology. J Biol Chem 2021; 298:101505. [PMID: 34929170 PMCID: PMC8784342 DOI: 10.1016/j.jbc.2021.101505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 12/19/2022] Open
Abstract
Bacterial transporters are difficult to study using conventional electrophysiology because of their low transport rates and the small size of bacterial cells. Here, we applied solid-supported membrane–based electrophysiology to derive kinetic parameters of sugar translocation by the Escherichia coli xylose permease (XylE), including functionally relevant mutants. Many aspects of the fucose permease (FucP) and lactose permease (LacY) have also been investigated, which allow for more comprehensive conclusions regarding the mechanism of sugar translocation by transporters of the major facilitator superfamily. In all three of these symporters, we observed sugar binding and transport in real time to determine KM, Vmax, KD, and kobs values for different sugar substrates. KD and kobs values were attainable because of a conserved sugar-induced electrogenic conformational transition within these transporters. We also analyzed interactions between the residues in the available X-ray sugar/H+ symporter structures obtained with different bound sugars. We found that different sugars induce different conformational states, possibly correlating with different charge displacements in the electrophysiological assay upon sugar binding. Finally, we found that mutations in XylE altered the kinetics of glucose binding and transport, as Q175 and L297 are necessary for uncoupling H+ and d-glucose translocation. Based on the rates for the electrogenic conformational transition upon sugar binding (>300 s−1) and for sugar translocation (2 s−1 − 30 s−1 for different substrates), we propose a multiple-step mechanism and postulate an energy profile for sugar translocation. We also suggest a mechanism by which d-glucose can act as an inhibitor for XylE.
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Affiliation(s)
- Andre Bazzone
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - Laura Tesmer
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - Derya Kurt
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - H Ronald Kaback
- University of California, Department of Physiology and Department of Microbiology, Immunology, Molecular Genetics, Molecular Biology Institute in Los Angeles CA, USA
| | - Klaus Fendler
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - M Gregor Madej
- Institute of Biophysics and Biophysical Chemistry, Department of Structural Biology, University of Regensburg, Universitätsstr. 31, 95053 Regensburg, Germany; Institute of Biophysics, Department of Structural Biology, Saarland University, Center of Human and Molecular Biology, Building 60, 66421 Homburg, Germany
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43
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Kuschmierz L, Shen L, Bräsen C, Snoep J, Siebers B. Workflows for optimization of enzyme cascades and whole cell catalysis based on enzyme kinetic characterization and pathway modelling. Curr Opin Biotechnol 2021; 74:55-60. [PMID: 34794111 DOI: 10.1016/j.copbio.2021.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/21/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
To move towards a circular bioeconomy, sustainable strategies for the utilization of renewable, non-food biomass wastes such as lignocellulose, are needed. To this end, an efficient bioconversion of d-xylose - after d-glucose the most abundant sugar in lignocellulose - is highly desirable. Most standard organisms used in biotechnology are limited in metabolising d-xylose, and also in vitro enzymatic strategies for its conversion have not been very successful. We herein discuss that bioconversion of d-xylose is mostly hampered by missing knowledge on the kinetic properties of the enzymes involved in its metabolism. We propose a combination of classical enzyme characterizations and mathematical modelling approaches as a workflow for rational, model-based design to optimize enzyme cascades and/or whole cell biocatalysts for efficient d-xylose metabolism.
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Affiliation(s)
- Laura Kuschmierz
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - Lu Shen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - Jacky Snoep
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa; Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany.
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44
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Transporter engineering promotes the co-utilization of glucose and xylose by Candida glycerinogenes for d-xylonate production. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Miyamoto RY, de Melo RR, de Mesquita Sampaio IL, de Sousa AS, Morais ER, Sargo CR, Zanphorlin LM. Paradigm shift in xylose isomerase usage: a novel scenario with distinct applications. Crit Rev Biotechnol 2021; 42:693-712. [PMID: 34641740 DOI: 10.1080/07388551.2021.1962241] [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: 10/20/2022]
Abstract
Isomerases are enzymes that induce physical changes in a molecule without affecting the original molecular formula. Among this class of enzymes, xylose isomerases (XIs) are the most studied to date, partly due to their extensive application in industrial processes to produce high-fructose corn sirups. In recent years, the need for sustainable initiatives has triggered efforts to improve the biobased economy through the use of renewable raw materials. In this context, D-xylose usage is crucial as it is the second-most abundant sugar in nature. The application of XIs in biotransforming xylose, enabling downstream metabolism in several microorganisms, is a smart strategy for ensuring a low-carbon footprint and producing several value-added biochemicals with broad industrial applications such as in the food, cosmetics, pharmaceutical, and polymer industries. Considering recent advancements that have expanded the range of applications of XIs, this review provides a comprehensive and concise overview of XIs, from their primary sources to the biochemical and structural features that influence their mechanisms of action. This comprehensive review may help address the challenges involved in XI applications in different industries and facilitate the exploitation of xylose bioprocesses.
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Affiliation(s)
- Renan Yuji Miyamoto
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Pharmaceutical Sciences (FCF), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Ricardo Rodrigues de Melo
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Isabelle Lobo de Mesquita Sampaio
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Food Engineering (FEA), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Amanda Silva de Sousa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Edvaldo Rodrigo Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Food Engineering (FEA), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Cintia Regina Sargo
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Leticia Maria Zanphorlin
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
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Yin W, Cao Y, Jin M, Xian M, Liu W. Metabolic Engineering of E. coli for Xylose Production from Glucose as the Sole Carbon Source. ACS Synth Biol 2021; 10:2266-2275. [PMID: 34412469 DOI: 10.1021/acssynbio.1c00184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Xylose is the raw material for the synthesis of many important platform compounds. At present, xylose is commercially produced by chemical extraction. However, there are still some bottlenecks in the extraction of xylose, including complicated operation processes and the chemical substances introduced, leading to the high cost of xylose and of synthesizing the downstream compounds of xylose. The current market price of xylose is 8× that of glucose, so using low-cost glucose as the substrate to produce the downstream compounds of xylose can theoretically reduce the cost by 70%. Here, we designed a pathway for the biosynthesis of xylose from glucose in Escherichia coli. This biosynthetic pathway was achieved by overexpressing five genes, namely, zwf, pgl, gnd, rpe, and xylA, while replacing the native xylulose kinase gene xylB with araL from B. subtilis, which displays phosphatase activity toward d-xylulose 5-phosphate. The yield of xylose was increased to 3.3 g/L by optimizing the metabolic pathway. Furthermore, xylitol was successfully synthesized by introducing the xyl1 gene, which suggested that the biosynthetic pathway of xylose from glucose is universally applicable for the synthesis of xylose downstream compounds. This is the first study to synthesize xylose and its downstream compounds by using glucose as a substrate, which not only reduces the cost of raw materials, but also alleviates carbon catabolite repression (CCR), providing a new idea for the synthesis of downstream compounds of xylose.
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Affiliation(s)
- Wencheng Yin
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yujin Cao
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Miaomiao Jin
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Mo Xian
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Wei Liu
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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Malán AK, Tuleski T, Catalán AI, de Souza EM, Batista S. Herbaspirillum seropedicae expresses non-phosphorylative pathways for D-xylose catabolism. Appl Microbiol Biotechnol 2021; 105:7339-7352. [PMID: 34499201 DOI: 10.1007/s00253-021-11507-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 07/15/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
Herbaspirillum seropedicae is a β-proteobacterium that establishes as an endophyte in various plants. These bacteria can consume diverse carbon sources, including hexoses and pentoses like D-xylose. D-xylose catabolic pathways have been described in some microorganisms, but databases of genes involved in these routes are limited. This is of special interest in biotechnology, considering that D-xylose is the second most abundant sugar in nature and some microorganisms, including H. seropedicae, are able to accumulate poly-3-hydroxybutyrate when consuming this pentose as a carbon source. In this work, we present a study of D-xylose catabolic pathways in H. seropedicae strain Z69 using RNA-seq analysis and subsequent analysis of phenotypes determined in targeted mutants in corresponding identified genes. G5B88_22805 gene, designated xylB, encodes a NAD+-dependent D-xylose dehydrogenase. Mutant Z69∆xylB was still able to grow on D-xylose, although at a reduced rate. This appears to be due to the expression of an L-arabinose dehydrogenase, encoded by the araB gene (G5B88_05250), that can use D-xylose as a substrate. According to our results, H. seropedicae Z69 uses non-phosphorylative pathways to catabolize D-xylose. The lower portion of metabolism involves co-expression of two routes: the Weimberg pathway that produces α-ketoglutarate and a novel pathway recently described that synthesizes pyruvate and glycolate. This novel pathway appears to contribute to D-xylose metabolism, since a mutant in the last step, Z69∆mhpD, was able to grow on this pentose only after an extended lag phase (40-50 h). KEY POINTS: • xylB gene (G5B88_22805) encodes a NAD+-dependent D-xylose dehydrogenase. • araB gene (G5B88_05250) encodes a L-arabinose dehydrogenase able to recognize D-xylose. • A novel route involving mhpD gene is preferred for D-xylose catabolism.
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Affiliation(s)
- Ana Karen Malán
- Laboratorio Microbiología Molecular- Depto. BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay.
| | - Thalita Tuleski
- Department of Biochemistry and Molecular Biology, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Ana Inés Catalán
- Laboratorio Microbiología Molecular- Depto. BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Silvia Batista
- Laboratorio Microbiología Molecular- Depto. BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
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Xylose Metabolism in Bacteria—Opportunities and Challenges towards Efficient Lignocellulosic Biomass-Based Biorefineries. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11178112] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In a sustainable society based on circular economy, the use of waste lignocellulosic biomass (LB) as feedstock for biorefineries is a promising solution, since LB is the world’s most abundant renewable and non-edible raw material. LB is available as a by-product from agricultural and forestry processes, and its main components are cellulose, hemicellulose, and lignin. Following suitable physical, enzymatic, and chemical steps, the different fractions can be processed and/or converted to value-added products such as fuels and biochemicals used in several branches of industry through the implementation of the biorefinery concept. Upon hydrolysis, the carbohydrate-rich fraction may comprise several simple sugars (e.g., glucose, xylose, arabinose, and mannose) that can then be fed to fermentation units. Unlike pentoses, glucose and other hexoses are readily processed by microorganisms. Some wild-type and genetically modified bacteria can metabolize xylose through three different main pathways of metabolism: xylose isomerase pathway, oxidoreductase pathway, and non-phosphorylative pathway (including Weimberg and Dahms pathways). Two of the commercially interesting intermediates of these pathways are xylitol and xylonic acid, which can accumulate in the medium either through manipulation of the culture conditions or through genetic modification of the bacteria. This paper provides a state-of-the art perspective regarding the current knowledge on xylose transport and metabolism in bacteria as well as envisaged strategies to further increase xylose conversion into valuable products.
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49
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Bai X, Lin T, Liang N, Li BZ, Song H, Yuan YJ. Engineering synthetic microbial consortium for efficient conversion of lactate from glucose and xylose to generate electricity. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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50
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Zan X, Sun J, Chu L, Cui F, Huo S, Song Y, Koffas MAG. Improved glucose and xylose co-utilization by overexpression of xylose isomerase and/or xylulokinase genes in oleaginous fungus Mucor circinelloides. Appl Microbiol Biotechnol 2021; 105:5565-5575. [PMID: 34215904 DOI: 10.1007/s00253-021-11392-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/28/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022]
Abstract
Most of the oleaginous microorganisms cannot assimilate xylose in the presence of glucose, which is the major bottleneck in the bioconversion of lignocellulose to biodiesel. Our present study revealed that overexpression of xylose isomerase (XI) gene xylA or xylulokinase (XK) gene xks1 increased the xylose consumption by 25 to 37% and enhanced the lipid content by 8 to 28% during co-fermentation of glucose and xylose. In xylA overexpressing strain Mc-XI, the activity of XI was 1.8-fold higher and the mRNA level of xylA at 24 h and 48 h was 11- and 13-fold higher than that of the control, respectively. In xks1 overexpressing strain Mc-XK, the mRNA level of xks1 was 4- to 11-fold of that of the control strain and the highest XK activity of 950 nmol min-1 mg-1 at 72 h which was 2-fold higher than that of the control. Additionally, expression of a translational fusion of xylA and xks1 further enhanced the xylose utilization rate by 45%. Our results indicated that overexpression of xylA and/or xks1 is a promising strategy to improve the xylose and glucose co-utilization, alleviate the glucose repression, and produce lipid from lignocellulosic biomass in the oleaginous fungus M. circinelloides. KEY POINTS: • Overexpressing xylA or xks1 increased the xylose consumption and the lipid content. • The xylose isomerase activity and the xylA mRNA level were enhanced in strain Mc-XI. • Co-expression of xylA and xks1 further enhanced the xylose utilization rate by 45%.
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Affiliation(s)
- Xinyi Zan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Jianing Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Linfang Chu
- School of Food Science and Technology, Jiang University, Wuxi, 214000, People's Republic of China
| | - Fengjie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Shuhao Huo
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255049, People's Republic of China.
| | - Mattheos A G Koffas
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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