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Ortiz-Sanchez M, Solarte-Toro JC, Inocencio-García PJ, Cardona Alzate CA. Sustainability analysis of orange peel biorefineries. Enzyme Microb Technol 2024; 172:110327. [PMID: 37804740 DOI: 10.1016/j.enzmictec.2023.110327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/02/2023] [Accepted: 09/18/2023] [Indexed: 10/09/2023]
Abstract
Biorefineries are constantly evolving since new technological advances in enzyme and microbial processes are boosting research for producing new bio-based products. Nevertheless, the step towards real process implementation must overcome a series of stages based on process sustainability in the early design stages. Orange peel (OP) has been profiled as a potential raw material for producing different products. Few studies have estimated the sustainability of OP-based biorefineries considering the upstream influence on the final process performance. This research aims to perform the sustainability assessment of several OP valorization pathways based on experimental data applying the biorefinery concept. Steam distillation and polyphenolic compound extraction prior to saccharification and anaerobic digestion increase the process performance. A glucose concentration and biogas yield of 21.43 g/L (0.44 g/g OP, db) and 415 mL/g SV were obtained, respectively. An essential oil extraction yield of 1.17 g/100 g OP (db) with a d-limonene content of 91.62% was produced. Moreover, hesperidin, apigenin, and naringenin yields of 7.88 mg/g, 0.475 mg/g, and 0.675 mg/g were obtained. An OP-based biorefinery addressed to produce essential oil, polyphenolic compounds, and biogas with a processing 25 tons/day (wb) has a sustainability index of 66.88%, higher than the values obtained with lesser upstream stages. In conclusion, an integral OP upgrading leads to better enzymatic and anaerobic digestion performances, as well as, a high process sustainability.
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Affiliation(s)
- Mariana Ortiz-Sanchez
- Universidad Nacional de Colombia sede Manizales, Instituto de Biotecnología y Agroindustria, Departamento de Ingeniería Química, Km 07 vía al Magdalena, Manizales, Colombia.
| | - Juan Camilo Solarte-Toro
- Universidad Nacional de Colombia sede Manizales, Instituto de Biotecnología y Agroindustria, Departamento de Ingeniería Química, Km 07 vía al Magdalena, Manizales, Colombia.
| | - Pablo José Inocencio-García
- Universidad Nacional de Colombia sede Manizales, Instituto de Biotecnología y Agroindustria, Departamento de Ingeniería Química, Km 07 vía al Magdalena, Manizales, Colombia.
| | - Carlos Ariel Cardona Alzate
- Universidad Nacional de Colombia sede Manizales, Instituto de Biotecnología y Agroindustria, Departamento de Ingeniería Química, Km 07 vía al Magdalena, Manizales, Colombia.
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Salazar-Cerezo S, de Vries RP, Garrigues S. Strategies for the Development of Industrial Fungal Producing Strains. J Fungi (Basel) 2023; 9:834. [PMID: 37623605 PMCID: PMC10455633 DOI: 10.3390/jof9080834] [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: 06/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed.
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Affiliation(s)
- Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, VLC, Spain
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D-Galacturonic acid reduction by S. cerevisiae for L-galactonate production from extracted sugar beet press pulp hydrolysate. Appl Microbiol Biotechnol 2021; 105:5795-5807. [PMID: 34268581 PMCID: PMC8390429 DOI: 10.1007/s00253-021-11433-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/03/2021] [Accepted: 06/25/2021] [Indexed: 11/06/2022]
Abstract
Abstract Pectin-rich residues are considered as promising feedstocks for sustainable production of platform chemicals. Enzymatic hydrolysis of extracted sugar beet press pulp (SBPP) releases the main constituent of pectin, d-galacturonic acid (d-GalA). Using engineered Saccharomyces cerevisiae, d-GalA is then reduced to l-galactonate (l-GalOA) with sorbitol as co-substrate. The current work addresses the combination of enzymatic hydrolysis of pectin in SBPP with a consecutive optimized biotransformation of the released d-GalA to l-GalOA in simple batch processes in stirred-tank bioreactors. Process conditions were first identified with synthetic media, where a product concentration of 9.9 g L-1 L-GalOA was obtained with a product selectivity of 99% (L-GalOA D-GalA-1) at pH 5 with 4% (w/v) sorbitol within 48 h. A very similar batch process performance with a product selectivity of 97% was achieved with potassium citrate buffered SBPP hydrolysate, demonstrating for the first time direct production of L-GalOA from hydrolyzed biomass using engineered S. cerevisiae. Combining the hydrolysis process of extracted SBPP and the biotransformation process with engineered S. cerevisiae paves the way towards repurposing pectin-rich residues as substrates for value-added chemicals. Key points • Efficient bioreduction of D-GalA with S. cerevisiae in stirred-tank reactors • Batch production of L-GalOA by engineered S. cerevisiae with high selectivity • Direct L-GalOA production from hydrolyzed sugar beet press pulp Graphical abstract Bioreduction of D-galacturonic acid to L-galactonate with recombinant Saccharomyces cerevisiae enables for the first time the valorization of hydrolysates from extracted sugar beet press pulp for the sustainable production of value-added chemicals. ![]()
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Suhaimi H, Dailin DJ, Malek RA, Hanapi SZ, Ambehabati KK, Keat HC, Prakasham S, Elsayed EA, Misson M, El Enshasy H. Fungal Pectinases: Production and Applications in Food Industries. Fungal Biol 2021. [DOI: 10.1007/978-3-030-64406-2_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Alvarez-Zúñiga MT, Castañeda García D, Aguilar Osorio G. Effect of different carbon sources on the growth and enzyme production of a toxigenic and a non-toxigenic strain of Aspergillus flavus. Prep Biochem Biotechnol 2020; 51:769-779. [DOI: 10.1080/10826068.2020.1858426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- María Teresa Alvarez-Zúñiga
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
| | - Diana Castañeda García
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
| | - Guillermo Aguilar Osorio
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
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Engineering cofactor supply and NADH-dependent D-galacturonic acid reductases for redox-balanced production of L-galactonate in Saccharomyces cerevisiae. Sci Rep 2020; 10:19021. [PMID: 33149263 PMCID: PMC7642425 DOI: 10.1038/s41598-020-75926-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022] Open
Abstract
D-Galacturonic acid (GalA) is the major constituent of pectin-rich biomass, an abundant and underutilized agricultural byproduct. By one reductive step catalyzed by GalA reductases, GalA is converted to the polyhydroxy acid L-galactonate (GalOA), the first intermediate of the fungal GalA catabolic pathway, which also has interesting properties for potential applications as an additive to nutrients and cosmetics. Previous attempts to establish the production of GalOA or the full GalA catabolic pathway in Saccharomyces cerevisiae proved challenging, presumably due to the inefficient supply of NADPH, the preferred cofactor of GalA reductases. Here, we tested this hypothesis by coupling the reduction of GalA to the oxidation of the sugar alcohol sorbitol that has a higher reduction state compared to glucose and thereby yields the necessary redox cofactors. By choosing a suitable sorbitol dehydrogenase, we designed yeast strains in which the sorbitol metabolism yields a "surplus" of either NADPH or NADH. By biotransformation experiments in controlled bioreactors, we demonstrate a nearly complete conversion of consumed GalA into GalOA and a highly efficient utilization of the co-substrate sorbitol in providing NADPH. Furthermore, we performed structure-guided mutagenesis of GalA reductases to change their cofactor preference from NADPH towards NADH and demonstrated their functionality by the production of GalOA in combination with the NADH-yielding sorbitol metabolism. Moreover, the engineered enzymes enabled a doubling of GalOA yields when glucose was used as a co-substrate. This significantly expands the possibilities for metabolic engineering of GalOA production and valorization of pectin-rich biomass in general.
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Chroumpi T, Mäkelä MR, de Vries RP. Engineering of primary carbon metabolism in filamentous fungi. Biotechnol Adv 2020; 43:107551. [DOI: 10.1016/j.biotechadv.2020.107551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 10/24/2022]
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Kuivanen J, Biz A, Richard P. Microbial hexuronate catabolism in biotechnology. AMB Express 2019; 9:16. [PMID: 30701402 PMCID: PMC6353982 DOI: 10.1186/s13568-019-0737-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
The most abundant hexuronate in plant biomass is D-galacturonate. D-Galacturonate is the main constituent of pectin. Pectin-rich biomass is abundantly available as sugar beet pulp or citrus processing waste and is currently mainly used as cattle feed. Other naturally occurring hexuronates are D-glucuronate, L-guluronate, D-mannuronate and L-iduronate. D-Glucuronate is a constituent of the plant cell wall polysaccharide glucuronoxylan and of the algal polysaccharide ulvan. Ulvan also contains L-iduronate. L-Guluronate and D-mannuronate are the monomers of alginate. These raw materials have the potential to be used as raw material in biotechnology-based production of fuels or chemicals. In this communication, we will review the microbial pathways related to these hexuronates and their potential use in biotechnology.
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Schmitz K, Protzko R, Zhang L, Benz JP. Spotlight on fungal pectin utilization-from phytopathogenicity to molecular recognition and industrial applications. Appl Microbiol Biotechnol 2019; 103:2507-2524. [PMID: 30694345 DOI: 10.1007/s00253-019-09622-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 11/29/2022]
Abstract
Pectin is a complex polysaccharide with D-galacturonic acid as its main component that predominantly accumulates in the middle lamella of the plant cell wall. Integrity and depolymerization of pectic structures have long been identified as relevant factors in fungal phytosymbiosis and phytopathogenicity in the context of tissue penetration and carbon source supply. While the pectic content of a plant cell wall can vary significantly, pectin was reported to account for up to 20-25% of the total dry weight in soft and non-woody tissues with non- or mildly lignified secondary cell walls, such as found in citrus peel, sugar beet pulp, and apple pomace. Due to their potential applications in various industrial sectors, pectic sugars from these and similar agricultural waste streams have been recognized as valuable targets for a diverse set of biotechnological fermentations.Recent advances in uncovering the molecular regulation mechanisms for pectinase expression in saprophytic fungi have led to a better understanding of fungal pectin sensing and utilization that could help to improve industrial, pectin-based fermentations. Related research in phytopathogenic fungi has furthermore added to our knowledge regarding the relevance of pectinases in plant cell wall penetration during onset of disease and is therefore highly relevant for agricultural sciences and the agricultural industry. This review therefore aims at summarizing (i) the role of pectinases in phytopathogenicity, (ii) the global regulation patterns for pectinase expression in saprophytic filamentous fungi as a highly specialized class of pectin degraders, and (iii) the current industrial applications in pectic sugar fermentations and transformations.
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Affiliation(s)
- Kevin Schmitz
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Ryan Protzko
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lisha Zhang
- Department of Plant Biochemistry, Centre for Plant Molecular Biology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - J Philipp Benz
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany.
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Engineering Saccharomyces cerevisiae for co-utilization of D-galacturonic acid and D-glucose from citrus peel waste. Nat Commun 2018; 9:5059. [PMID: 30498222 PMCID: PMC6265301 DOI: 10.1038/s41467-018-07589-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/19/2018] [Indexed: 11/08/2022] Open
Abstract
Pectin-rich biomasses, such as citrus peel and sugar beet pulp, hold promise as inexpensive feedstocks for microbial fermentations as enzymatic hydrolysis of their component polysaccharides can be accomplished inexpensively to yield high concentrations of fermentable sugars and D-galacturonic acid (D-galUA). In this study, we tackle a number of challenges associated with engineering a microbial strain to convert pectin-rich hydrolysates into commodity and specialty chemicals. First, we engineer D-galUA utilization into yeast, Saccharomyces cerevisiae. Second, we identify that the mechanism of D-galUA uptake into yeast is mediated by hexose transporters and that consumption of D-galUA is inhibited by D-glucose. Third, we enable co-utilization of D-galUA and D-glucose by identifying and expressing a heterologous transporter, GatA, from Aspergillus niger. Last, we demonstrate the use of this transporter for production of the platform chemical, meso-galactaric acid, directly from industrial Navel orange peel waste.
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11
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Zhou X, Hua X, Zhou X, Xu Y. Process for the successive production of calcium galactonate crystals by Gluconobacter oxydans. BIORESOURCE TECHNOLOGY 2018; 261:458-460. [PMID: 29685484 DOI: 10.1016/j.biortech.2018.04.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 05/04/2023]
Abstract
Galactonic acid and its salts can be potentially used in foodstuffs and as specialty chemicals. So far, the researches on microbial conversion of galactose to galactonate are still scarce. In this study, we initially used Gluconobacter oxydans strain NL 71 to convert galactose to galactonic acid via aerobic fermentation by fed-batch and product separation process in shaken flasks, finally 390 g/L galactonic acid could be obtained after 96 h fermentation. To harvest calcium galactonate product, an aeration-agitation bioreactor with product drain port was applied. The lower solubility of calcium galactonate aided its crystallization during fermentation and after 96 h fermentation, approximately 720 g calcium galactonate crystals were produced from 1 L broth. The results showed that successive production of calcium galactonate by a combination of fed-batch and natural crystallization in the process of fermentation was feasible.
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Affiliation(s)
- Xin Zhou
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, People's Republic of China; College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Xia Hua
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, People's Republic of China; College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Xuelian Zhou
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, People's Republic of China; College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yong Xu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, People's Republic of China; College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
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Kuivanen J, Richard P. NADPH-dependent 5-keto-D-gluconate reductase is a part of the fungal pathway for D-glucuronate catabolism. FEBS Lett 2017; 592:71-77. [PMID: 29265364 PMCID: PMC5814732 DOI: 10.1002/1873-3468.12946] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/28/2017] [Accepted: 12/09/2017] [Indexed: 11/18/2022]
Abstract
NADPH‐dependent 5‐keto‐D‐gluconate reductase was identified as a missing element in the pathway for D‐glucuronate catabolism in fungi. The disruption of the gene, gluF, by CRISPR/Cas9 in the filamentous fungus Aspergillus niger resulted in a strain unable to catabolise D‐glucuronate. The purified GluF protein was characterized and kcat and Km values of 23.7 ± 1.8 s−1 and 3.2 ± 0.1 mm for 5‐keto‐D‐gluconate, respectively, were determined. The enzyme is reversible and is active with NADP+ and D‐gluconate. We suggest a pathway for D‐glucuronate catabolism with the intermediates L‐gulonate, 2‐keto‐L‐gulonate, L‐idonate, 5‐keto‐D‐gluconate, D‐gluconate and D‐gluconate‐6‐phosphate which is a part of the pentose phosphate pathway. A fungal enzyme activity for the conversion of L‐gulonate to 2‐keto‐L‐gulonate remains to be identified.
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Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Peter Richard
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
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Alazi E, Khosravi C, Homan TG, du Pré S, Arentshorst M, Di Falco M, Pham TTM, Peng M, Aguilar-Pontes MV, Visser J, Tsang A, de Vries RP, Ram AFJ. The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger. FEBS Lett 2017; 591:1408-1418. [PMID: 28417461 PMCID: PMC5488244 DOI: 10.1002/1873-3468.12654] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/10/2017] [Indexed: 01/21/2023]
Abstract
In Aspergillus niger, the enzymes encoded by gaaA, gaaB, and gaaC catabolize d‐galacturonic acid (GA) consecutively into l‐galactonate, 2‐keto‐3‐deoxy‐l‐galactonate, pyruvate, and l‐glyceraldehyde, while GaaD converts l‐glyceraldehyde to glycerol. Deletion of gaaB or gaaC results in severely impaired growth on GA and accumulation of l‐galactonate and 2‐keto‐3‐deoxy‐l‐galactonate, respectively. Expression levels of GA‐responsive genes are specifically elevated in the ∆gaaC mutant on GA as compared to the reference strain and other GA catabolic pathway deletion mutants. This indicates that 2‐keto‐3‐deoxy‐l‐galactonate is the inducer of genes required for GA utilization.
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Affiliation(s)
- Ebru Alazi
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Claire Khosravi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht University, The Netherlands
| | - Tim G Homan
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Saskia du Pré
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Mark Arentshorst
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Thi T M Pham
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht University, The Netherlands
| | | | - Jaap Visser
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands.,Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht University, The Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht University, The Netherlands
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
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Byrne C, Cavalitto S, Voget C. Purification and characterization of two inducible exopolygalacturonases from Aspergillus kawachii. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Ibrahim E, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:52. [PMID: 28413443 PMCID: PMC5327597 DOI: 10.1186/s13068-017-0732-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/11/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The high crystallinity of cellulosic biomass myofibrils as well as the complexity of their intermolecular structure is a significant impediment for biofuel production. Cloning of celB-, celC-encoded cellulases (cel12B and cel8C) and peh-encoded polygalacturonase (peh28) from Pectobacterium carotovorum subsp. carotovorum (Pcc) was carried out in our previous study using Escherichia coli as a host vector. The current study partially characterizes the enzymes' molecular structures as well as their catalytic performance on different substrates which can be used to improve their potential for lignocellulosic biomass conversion. RESULTS β-Jelly roll topology, (α/α)6 antiparallel helices and right-handed β-helices were the folds identified for cel12B, cel8C, and peh28, respectively, in their corresponding protein model structures. Purifications of 17.4-, 6.2-, and 6.0-fold, compared to crude extract, were achieved for cel12B and cel8C, and peh28, respectively, using specific membrane ultrafiltrations and size-exclusion chromatography. Avicel and carboxymethyl cellulose (CMC) were substrates for cel12B, whereas for cel8C catalytic activity was only shown on CMC. The enzymes displayed significant synergy on CMC but not on Avicel when tested for 3 h at 45 °C. No observed β-glucosidase activities were identified for cel8C and cel12B when tested on p-nitrophenyl-β-d-glucopyranoside. Activity stimulation of 130% was observed when a recombinant β-glucosidase from Pcc was added to cel8C and cel12B as tested for 3 h at 45 °C. Optimum temperature and pH of 45 °C and 5.4, respectively, were identified for all three enzymes using various substrates. Catalytic efficiencies (kcat/Km) were calculated for cel12B and cel8C on CMC as 0.141 and 2.45 ml/mg/s respectively, at 45 °C and pH 5.0 and for peh28 on polygalacturonic acid as 4.87 ml/mg/s, at 40 °C and pH 5.0. Glucose and cellobiose were the end-products identified for cel8C, cel12B, and β-glucosidase acting together on Avicel or CMC, while galacturonic acid and other minor co-products were identified for peh28 action on pectin. CONCLUSIONS This study provides some insight into which parameters should be optimized when application of cel8C, cel12B, and peh28 to biomass conversion is the goal.
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Affiliation(s)
- Eman Ibrahim
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Kim D. Jones
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Keith E. Taylor
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4 Canada
| | - Ebtesam N. Hosseney
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Patrick L. Mills
- Department of Chemical Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Jean M. Escudero
- Department of Basic Science, St. Louis College of Pharmacy, St. Louis, MO 63110-1088 USA
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Matsubara T, Hamada S, Wakabayashi A, Kishida M. Fermentative production of l-galactonate by using recombinant Saccharomyces cerevisiae containing the endogenous galacturonate reductase gene from Cryptococcus diffluens. J Biosci Bioeng 2016; 122:639-644. [PMID: 27259388 DOI: 10.1016/j.jbiosc.2016.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/19/2016] [Accepted: 05/08/2016] [Indexed: 11/17/2022]
Abstract
The GAR1 gene, encoding d-galacturonate reductase in Cryptococcus diffluens, was isolated, and the GAR1-expression plasmid was constructed by insertion of GAR1 downstream of the yeast constitutive promoter in the yeast-integrating vector. Recombinant Saccharomyces cerevisiae expressing C. diffluensd-galacturonate reductase from a genome integrated copy of the gene was cultured for use the conversion of d-galacturonic acid to l-galactonic acid. The optimum conditions for l-galactonic acid production were determined in terms of the initial concentration of d-galacturonic acid, fermentation pH, and mixed sugars. The following conditions yielded high efficiency in the conversion of d-galacturonic acid to l-galactonic acid in large-scale cultures: 0.1% initial d-galacturonic acid concentration, pH 3.5, and glucose as additional sugar. The aerobic condition was necessary for the conversion of d-galacturonic acid. Subculture of that recombinant was not showing to decrease of the d-galacturonic acid conversion rate even though it was repeated in ten generations. Culturing in scale-up, the conversion rate of d-galacturonic acid to l-galactonic acid was increased.
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Affiliation(s)
- Takeo Matsubara
- Division of Applied Life Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Shohei Hamada
- Division of Applied Life Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Ayaka Wakabayashi
- Division of Applied Life Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Masao Kishida
- Division of Applied Life Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
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Alazi E, Niu J, Kowalczyk JE, Peng M, Aguilar Pontes MV, van Kan JAL, Visser J, de Vries RP, Ram AFJ. The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of d-galacturonic acid from pectin. FEBS Lett 2016; 590:1804-15. [PMID: 27174630 PMCID: PMC5111758 DOI: 10.1002/1873-3468.12211] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/04/2016] [Accepted: 05/05/2016] [Indexed: 01/15/2023]
Abstract
We identified the d-galacturonic acid (GA)-responsive transcriptional activator GaaR of the saprotrophic fungus, Aspergillus niger, which was found to be essential for growth on GA and polygalacturonic acid (PGA). Growth of the ΔgaaR strain was reduced on complex pectins. Genome-wide expression analysis showed that GaaR is required for the expression of genes necessary to release GA from PGA and more complex pectins, to transport GA into the cell, and to induce the GA catabolic pathway. Residual growth of ΔgaaR on complex pectins is likely due to the expression of pectinases acting on rhamnogalacturonan and subsequent metabolism of the monosaccharides other than GA.
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Affiliation(s)
- Ebru Alazi
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Jing Niu
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Joanna E Kowalczyk
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Mao Peng
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Maria Victoria Aguilar Pontes
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Jaap Visser
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands.,Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
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18
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Kuivanen J, Sugai-Guérios MH, Arvas M, Richard P. A novel pathway for fungal D-glucuronate catabolism contains an L-idonate forming 2-keto-L-gulonate reductase. Sci Rep 2016; 6:26329. [PMID: 27189775 PMCID: PMC4870679 DOI: 10.1038/srep26329] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/29/2016] [Indexed: 11/09/2022] Open
Abstract
For the catabolism of D-glucuronate, different pathways are used by different life forms. The pathways in bacteria and animals are established, however, a fungal pathway has not been described. In this communication, we describe an enzyme that is essential for D-glucuronate catabolism in the filamentous fungus Aspergillus niger. The enzyme has an NADH dependent 2-keto-L-gulonate reductase activity forming L-idonate. The deletion of the corresponding gene, the gluC, results in a phenotype of no growth on D-glucuronate. The open reading frame of the A. niger 2-keto-L-gulonate reductase was expressed as an active protein in the yeast Saccharomyces cerevisiae. A histidine tagged protein was purified and it was demonstrated that the enzyme converts 2-keto-L-gulonate to L-idonate and, in the reverse direction, L-idonate to 2-keto-L-gulonate using the NAD(H) as cofactors. Such an L-idonate forming 2-keto-L-gulonate dehydrogenase has not been described previously. In addition, the finding indicates that the catabolic D-glucuronate pathway in A. niger differs fundamentally from the other known D-glucuronate pathways.
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Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044-VTT, Finland
| | - Maura H Sugai-Guérios
- Departamento de Engenharia Química e Engenharia de Alimentos, Universidade Federal de Santa Catarina, Cx.P. 476 Centro Tecnológico, Florianópolis 88040-900, Santa Catarina, Brazil
| | - Mikko Arvas
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044-VTT, Finland
| | - Peter Richard
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, 02044-VTT, Finland
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19
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Zhang L, Lubbers RJM, Simon A, Stassen JHM, Vargas Ribera PR, Viaud M, van Kan JAL. A novel Zn2 Cys6 transcription factor BcGaaR regulates D-galacturonic acid utilization in Botrytis cinerea. Mol Microbiol 2016; 100:247-62. [PMID: 26691528 DOI: 10.1111/mmi.13314] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2015] [Indexed: 12/16/2023]
Abstract
D-galacturonic acid (GalA) is the most abundant monosaccharide component of pectin. Previous transcriptome analysis in the plant pathogenic fungus Botrytis cinerea identified eight GalA-inducible genes involved in pectin decomposition, GalA transport and utilization. Co-expression of these genes indicates that a specific regulatory mechanism occurs in B. cinerea. In this study, promoter regions of these genes were analysed and eight conserved sequence motifs identified. The Bclga1 promoter, containing all these motifs, was functionally analysed and the motif designated GalA Responsive Element (GARE) was identified as the crucial cis-regulatory element in regulation of GalA utilization in B. cinerea. Yeast one-hybrid screening with the GARE motif led to identification of a novel Zn2 Cys6 transcription factor (TF), designated BcGaaR. Targeted knockout analysis revealed that BcGaaR is required for induction of GalA-inducible genes and growth of B. cinerea on GalA. A BcGaaR-GFP fusion protein was predominantly localized in nuclei in mycelium grown in GalA. Fluorescence in nuclei was much stronger in mycelium grown in GalA, as compared to fructose and glucose. This study provides the first report of a GalA-specific TF in filamentous fungi. Orthologs of BcGaaR are present in other ascomycete fungi that are able to utilize GalA, including Aspergillus spp., Trichoderma reesei and Neurospora crassa.
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Affiliation(s)
- Lisha Zhang
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Ronnie J M Lubbers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Adeline Simon
- UMR1290 BIOGER, INRA-AgroParisTech, Avenue Lucien Brétignières, 78850, Thiverval-Grignon, France
| | - Joost H M Stassen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Pablo R Vargas Ribera
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Muriel Viaud
- UMR1290 BIOGER, INRA-AgroParisTech, Avenue Lucien Brétignières, 78850, Thiverval-Grignon, France
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
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20
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Zhang H, Li X, Su X, Ang EL, Zhang Y, Zhao H. Production of Adipic Acid from Sugar Beet Residue by Combined Biological and Chemical Catalysis. ChemCatChem 2016. [DOI: 10.1002/cctc.201600069] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Hongfang Zhang
- Metabolic Engineering Research Laboratory; Science and Engineering Institutes; 31 Biopolis Way The Nanos 138669 Singapore
| | - Xiukai Li
- Institute of Bioengineering and Nanotechnology; 31 Biopolis Way The Nanos 138669 Singapore
| | - Xiaoyun Su
- Metabolic Engineering Research Laboratory; Science and Engineering Institutes; 31 Biopolis Way The Nanos 138669 Singapore
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute; Chinese Academy of Agricultural Sciences; No. 12 South Zhongguancun Street Haidian District Beijing 100081 P.R. China
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory; Science and Engineering Institutes; 31 Biopolis Way The Nanos 138669 Singapore
| | - Yugen Zhang
- Institute of Bioengineering and Nanotechnology; 31 Biopolis Way The Nanos 138669 Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory; Science and Engineering Institutes; 31 Biopolis Way The Nanos 138669 Singapore
- Departments of Chemical and Biomolecular Engineering, Chemistry, Biochemistry and Bioengineering; Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana IL 61801 USA
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21
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Druzhinina IS, Kubicek CP. Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:69-147. [PMID: 27261782 DOI: 10.1016/bs.aambs.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.
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Affiliation(s)
- I S Druzhinina
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - C P Kubicek
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
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22
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The interaction of induction and repression mechanisms in the regulation of galacturonic acid-induced genes in Aspergillus niger. Fungal Genet Biol 2015; 82:32-42. [DOI: 10.1016/j.fgb.2015.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 02/05/2023]
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23
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Mehtiö T, Toivari M, Wiebe MG, Harlin A, Penttilä M, Koivula A. Production and applications of carbohydrate-derived sugar acids as generic biobased chemicals. Crit Rev Biotechnol 2015; 36:904-16. [DOI: 10.3109/07388551.2015.1060189] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Tuomas Mehtiö
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Mervi Toivari
- VTT Technical Research Centre of Finland, Espoo, Finland
| | | | - Ali Harlin
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland, Espoo, Finland
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24
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Abstract
Itaconic acid is an important building block for the chemical industry. Currently, Aspergillus terreus is the main organism used for itaconic acid production. Due to the enormous citric acid production capacity of Aspergillus niger, this host is investigated as a potential itaconic acid production host. Several strategies have been tried so far: fermentation optimization, expression of cis-aconitate decarboxylase (cadA) alone and in combination with aconitase targeted to the same compartment, chassis optimization, and the heterologous expression of two transporters flanking the cadA gene. We showed that the heterologous expression of these two transporters were key to improving itaconic acid production in an A. niger strain that was unable to produce oxalic acid and gluconic acid. The expression of transporters has increased the production levels of other industrially relevant processes as well, such as β-lactam antibiotics and bioethanol. Thus far, the role of transporters in production process optimization is a bit overlooked.
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Affiliation(s)
- Laura van der Straat
- a Microbial Systems and Synthetic Biology; Laboratory of Systems and Synthetic Biology; Wageningen University; Wageningen, the Netherlands
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25
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Kuivanen J, Penttilä M, Richard P. Metabolic engineering of the fungal D-galacturonate pathway for L-ascorbic acid production. Microb Cell Fact 2015; 14:2. [PMID: 25566698 PMCID: PMC4299797 DOI: 10.1186/s12934-014-0184-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 12/19/2014] [Indexed: 11/29/2022] Open
Abstract
Background Synthetic L-ascorbic acid (vitamin C) is widely used as a preservative and nutrient in food and pharmaceutical industries. In the current production method, D-glucose is converted to L-ascorbic acid via several biochemical and chemical steps. The main source of L-ascorbic acid in human nutrition is plants. Several alternative metabolic pathways for L-ascorbic acid biosynthesis are known in plants. In one of them, D-galacturonic acid is the precursor. D-Galacturonic acid is also the main monomer in pectin, a plant cell wall polysaccharide. Pectin is abundant in biomass and is readily available from several waste streams from fruit and sugar processing industries. Results In the present work, we engineered the filamentous fungus Aspergillus niger for the conversion of D-galacturonic acid to L-ascorbic acid. In the generated pathway, the native D-galacturonate reductase activity was utilized while the gene coding for the second enzyme in the fungal D-galacturonic acid pathway, an L-galactonate consuming dehydratase, was deleted. Two heterologous genes coding for enzymes from the plant L-ascorbic acid pathway – L-galactono-1,4-lactone lactonase from Euglena gracilis (EgALase) and L-galactono-1,4-lactone dehydrogenase from Malpighia glabra (MgGALDH) – were introduced into the A. niger strain. Alternatively, an unspecific L-gulono-1,4-lactone lactonase (smp30) from the animal L-ascorbic acid pathway was introduced in the fungal strain instead of the plant L-galactono-1,4-lactone lactonase. In addition, a strain with the production pathway inducible with D-galacturonic acid was generated by using a bidirectional and D-galacturonic acid inducible promoter from the fungus. Even though, the lactonase enzyme activity was not observed in the resulting strains, they were capable of producing L-ascorbic acid from pure D-galacturonic acid or pectin-rich biomass in a consolidated bioprocess. Product titers up to 170 mg/l were achieved. Conclusions In the current study, an L-ascorbic acid pathway using D-galacturonic acid as a precursor was introduced to a microorganism for the first time. This is also the first report on an engineered filamentous fungus for L-ascorbic acid production and a proof-of-concept of consolidated bioprocess for the production.
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Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland, PO Box 1000, 02044 VTT, Espoo, Finland.
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, PO Box 1000, 02044 VTT, Espoo, Finland.
| | - Peter Richard
- VTT Technical Research Centre of Finland, PO Box 1000, 02044 VTT, Espoo, Finland.
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26
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Khosravi C, Benocci T, Battaglia E, Benoit I, de Vries RP. Sugar catabolism in Aspergillus and other fungi related to the utilization of plant biomass. ADVANCES IN APPLIED MICROBIOLOGY 2015; 90:1-28. [PMID: 25596028 DOI: 10.1016/bs.aambs.2014.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are found in all natural and artificial biotopes and can use highly diverse carbon sources. They play a major role in the global carbon cycle by decomposing plant biomass and this biomass is the main carbon source for many fungi. Plant biomass is composed of cell wall polysaccharides (cellulose, hemicellulose, pectin) and lignin. To degrade cell wall polysaccharides to different monosaccharides, fungi produce a broad range of enzymes with a large variety in activities. Through a series of enzymatic reactions, sugar-specific and central metabolic pathways convert these monosaccharides into energy or metabolic precursors needed for the biosynthesis of biomolecules. This chapter describes the carbon catabolic pathways that are required to efficiently use plant biomass as a carbon source. It will give an overview of the known metabolic pathways in fungi, their interconnections, and the differences between fungal species.
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27
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Biochemical characterization of uronate dehydrogenases from three Pseudomonads, Chromohalobacter salixigens, and Polaromonas naphthalenivorans. Enzyme Microb Technol 2014; 69:62-8. [PMID: 25640726 DOI: 10.1016/j.enzmictec.2014.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 11/20/2022]
Abstract
Enzyme catalysts will be vital in the development of synthetic biology approaches for converting pectinic monosaccharides from citrus and beet processing waste streams to value-added materials. We describe here the biophysical and mechanistic characterization of uronate dehydrogenases from a wide variety of bacterial sources that convert galacturonic acid, the predominate building block of pectin from these plant sources, and glucuronic acid to their corresponding dicarboxylic acids galactarate and glucarate, the latter being a DOE top value biochemical from biomass. The enzymes from Pseudomonas syringae and Polaromonas naphthalenivorans were found to have the highest reported kcat(glucuronic acid) values, on the order of 220-270 s(-1). The thermal stability of this enzyme type is described for the first time here, where it was found that the Kt((0.5)) value range was >20 °C, and the enzyme from Chromohalobacter was moderately thermostable with Kt((0.5))=62.2 °C. The binding mechanism for these bi-substrate enzymes was also investigated in initial rate experiments, where a predominately steady-state ordered binding pattern was indicated.
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28
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Zhang L, Hua C, Stassen JHM, Chatterjee S, Cornelissen M, van Kan JAL. Genome-wide analysis of pectate-induced gene expression in Botrytis cinerea: identification and functional analysis of putative d-galacturonate transporters. Fungal Genet Biol 2014; 72:182-191. [PMID: 24140151 DOI: 10.1016/j.fgb.2013.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 10/03/2013] [Indexed: 11/22/2022]
Abstract
The fungal plant pathogen Botrytis cinerea produces a spectrum of cell wall degrading enzymes for the decomposition of host cell wall polysaccharides and the consumption of the monosaccharides that are released. Especially pectin is an abundant cell wall component, and the decomposition of pectin by B. cinerea has been extensively studied. An effective concerted action of the appropriate pectin depolymerising enzymes, monosaccharide transporters and catabolic enzymes is important for complete d-galacturonic acid utilization by B. cinerea. In this study, we performed RNA sequencing to compare genome-wide transcriptional profiles between B. cinerea cultures grown in media containing pectate or glucose as sole carbon source. Transcript levels of 32 genes that are induced by pectate were further examined in cultures grown on six different monosaccharides, by means of quantitative RT-PCR, leading to the identification of 8 genes that are exclusively induced by d-galacturonic acid. Among these, the hexose transporter encoding genes Bchxt15 and Bchxt19 were functionally characterised. The subcellular location was studied of BcHXT15-GFP and BcHXT19-GFP fusion proteins expressed under control of their native promoter, in a B. cinerea wild-type strain. Both genes are expressed during growth on d-galacturonic acid and the fusion proteins are localized in plasma membranes and intracellular vesicles. Target gene knockout analysis revealed that BcHXT15 contributes to d-galacturonic acid uptake at pH 5∼5.6. The virulence of all B. cinerea hexose transporter mutants tested was unaltered on tomato and Nicotiana benthamiana leaves.
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Affiliation(s)
- Lisha Zhang
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany.
| | - Chenlei Hua
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Joost H M Stassen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Sayantani Chatterjee
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maxim Cornelissen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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29
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Single cell and in vivo analyses elucidate the effect of xylC lactonase during production of D-xylonate in Saccharomyces cerevisiae. Metab Eng 2014; 25:238-47. [DOI: 10.1016/j.ymben.2014.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 06/15/2014] [Accepted: 07/17/2014] [Indexed: 11/21/2022]
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30
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Sloothaak J, Schilders M, Schaap PJ, de Graaff LH. Overexpression of the Aspergillus niger GatA transporter leads to preferential use of D-galacturonic acid over D-xylose. AMB Express 2014; 4:66. [PMID: 25177540 PMCID: PMC4143577 DOI: 10.1186/s13568-014-0066-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/08/2014] [Indexed: 11/10/2022] Open
Abstract
Pectin is a structural heteropolysaccharide of the primary cell walls of plants and as such is a significant fraction of agricultural waste residues that is currently insufficiently used. Its main component, D-galacturonic acid, is an attractive substrate for bioconversion. The complete metabolic pathway is present in the genome of Aspergillus niger, that is used in this study. The objective was to identify the D-galacturonic acid transporter in A. niger and to use this transporter to study D-galacturonic acid metabolism. We have functionally characterized the gene An14g04280 that encodes the D-galacturonic acid transporter in A. niger. In a mixed sugar fermentation it was found that the An14g04280 overexpression strain, in contrast to the parent control strain, has a preference for D-galacturonic acid over D-xylose as substrate. Overexpression of this transporter in A. niger resulted in a strong increase of D-galacturonic acid uptake and induction of the D-galacturonic acid reductase activity, suggesting a metabolite controlled regulation of the endogenous D-galacturonic acid catabolic pathway.
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31
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Valkonen M, Penttilä M, Benčina M. Intracellular pH responses in the industrially important fungus Trichoderma reesei. Fungal Genet Biol 2014; 70:86-93. [PMID: 25046860 DOI: 10.1016/j.fgb.2014.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 12/14/2022]
Abstract
Preserving an optimal intracellular pH is critical for cell fitness and productivity. The pH homeostasis of the industrially important filamentous fungus Trichoderma reesei (Hypocrea jecorina) is largely unexplored. We analyzed the impact of growth conditions on regulation of intracellular pH of the strain Rut-C30 and the strain M106 derived from the Rut-C30 that accumulates L-galactonic acid-from provided galacturonic acid-as a consequence of L-galactonate dehydratase deletion. For live-cell measurements of intracellular pH, we used the genetically encoded ratiometric pH-sensitive fluorescent protein RaVC. Glucose and lactose, used as carbon sources, had specific effects on intracellular pH of T. reesei. The growth in lactose-containing medium extensively acidified cytosol, while intracellular pH of hyphae cultured in a medium with glucose remained at a higher level. The strain M106 maintained higher intracellular pH in the presence of D-galacturonic acid than its parental strain Rut-C30. Acidic external pH caused significant acidification of cytosol. Altogether, the pH homeostasis of T. reesei Rut-C30 strain is sensitive to extracellular pH and the degree of acidification depends on carbon source.
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Affiliation(s)
- Mari Valkonen
- VTT Technical Research Centre of Finland, Espoo, Finland.
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Mojca Benčina
- Laboratory of Biotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia; Centre of Excellence EN-FIST, 1000 Ljubljana, Slovenia.
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Kuivanen J, Richard P. The yjjN of E. coli codes for an L-galactonate dehydrogenase and can be used for quantification of L-galactonate and L-gulonate. Appl Biochem Biotechnol 2014; 173:1829-35. [PMID: 24861318 DOI: 10.1007/s12010-014-0969-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 05/16/2014] [Indexed: 01/29/2023]
Abstract
Escherichia coli is able to utilize L-galactonate as a sole carbon source. A metabolic pathway for L-galactonate catabolism is described in E. coli, and it is known to be interconnected with D-galacturonate metabolism. The corresponding gene encoding the first enzyme in the L-galactonate pathway, L-galactonate-5-dehydrogenase, was suggested to be yjjN. However, L-galactonate dehydrogenase activity was never demonstrated with the yjjN gene product. Here, we show that YjjN is indeed an L-galactonate dehydrogenase having activity also for L-gulonate. The K m and k cat for L-galactonate were 19.5±0.6 mM and 0.51±0.03 s(-1), respectively. In addition, YjjN was applied for a quantitative detection of the both of these substances in a coupled assay. The detection limits for L-galactonate and L-gulonate were 1.65 and 10 μM, respectively.
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Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland,
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Liu H, Valdehuesa KNG, Ramos KRM, Nisola GM, Lee WK, Chung WJ. L-arabonate and D-galactonate production by expressing a versatile sugar dehydrogenase in metabolically engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2014; 159:455-459. [PMID: 24713235 DOI: 10.1016/j.biortech.2014.03.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/08/2014] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
The production of L-arabonate and D-galactonate employing a versatile l-arabinose dehydrogenase (AraDH) from Azospirillum brasilense is presented. The promiscuity of AraDH is manifested by its appreciable activity towards L-arabinose and D-galactose as substrates, and NAD(+) and NADP(+) as cofactors. The AraDH was introduced into an engineered Escherichia coli with inactive L-arabinose or D-galactose metabolism, resulting in strains EMA2 and EWG4, respectively. EMA2 produced 43.9 g L(-1)L-arabonate with a productivity of 1.22 g L(-1)h(-1) and 99.1% (mol/mol) yield. After methanol precipitation, 92.6% of L-arabonate potassium salt was recovered with a purity of 88.8%. Meanwhile, EWG4 produced 24.0 g L(-1)D-galactonate, which is 36% higher than that of the strain carrying the specific d-galactose dehydrogenase. Overall results reveal that the versatility of AraDH to efficiently catalyze the formation of L-arabonate and D-galactonate could be a useful tool in advancing industrial viability for sugar acids production.
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Affiliation(s)
- Huaiwei Liu
- Energy and Environment Fusion Technology Center (E(2)FTC), Department of Energy and Biotechnology (DEB), Myongji University, Yongin-si, Gyeonggi-do 449-728, Republic of Korea
| | - Kris Niño G Valdehuesa
- Energy and Environment Fusion Technology Center (E(2)FTC), Department of Energy and Biotechnology (DEB), Myongji University, Yongin-si, Gyeonggi-do 449-728, Republic of Korea
| | - Kristine Rose M Ramos
- Energy and Environment Fusion Technology Center (E(2)FTC), Department of Energy and Biotechnology (DEB), Myongji University, Yongin-si, Gyeonggi-do 449-728, Republic of Korea
| | - Grace M Nisola
- Energy and Environment Fusion Technology Center (E(2)FTC), Department of Energy and Biotechnology (DEB), Myongji University, Yongin-si, Gyeonggi-do 449-728, Republic of Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Yongin-si, Gyeonggi-do 449-728, Republic of Korea
| | - Wook-Jin Chung
- Energy and Environment Fusion Technology Center (E(2)FTC), Department of Energy and Biotechnology (DEB), Myongji University, Yongin-si, Gyeonggi-do 449-728, Republic of Korea.
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Alonso S, Rendueles M, Díaz M. Microbial production of specialty organic acids from renewable and waste materials. Crit Rev Biotechnol 2014; 35:497-513. [DOI: 10.3109/07388551.2014.904269] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Conversion of orange peel to L-galactonic acid in a consolidated process using engineered strains of Aspergillus niger. AMB Express 2014; 4:33. [PMID: 24949267 PMCID: PMC4052776 DOI: 10.1186/s13568-014-0033-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/02/2014] [Indexed: 11/10/2022] Open
Abstract
Citrus processing waste is a leftover from the citrus processing industry and is available in large amounts. Typically, this waste is dried to produce animal feed, but sometimes it is just dumped. Its main component is the peel, which consists mostly of pectin, with D-galacturonic acid as the main monomer. Aspergillus niger is a filamentous fungus that efficiently produces pectinases for the hydrolysis of pectin and uses the resulting D-galacturonic acid and most of the other components of citrus peel for growth. We used engineered A. niger strains that were not able to catabolise D-galacturonic acid, but instead converted it to L-galactonic acid. These strains also produced pectinases for the hydrolysis of pectin and were used for the conversion of pectin in orange peel to L-galactonic acid in a consolidated process. The D-galacturonic acid in the orange peel was converted to L-galactonic acid with a yield close to 90%. Submerged and solid-state fermentation processes were compared.
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Benz JP, Protzko RJ, Andrich JMS, Bauer S, Dueber JE, Somerville CR. Identification and characterization of a galacturonic acid transporter from Neurospora crassa and its application for Saccharomyces cerevisiae fermentation processes. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:20. [PMID: 24502254 PMCID: PMC3933009 DOI: 10.1186/1754-6834-7-20] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 01/15/2014] [Indexed: 05/15/2023]
Abstract
BACKGROUND Pectin-rich agricultural wastes potentially represent favorable feedstocks for the sustainable production of alternative energy and bio-products. Their efficient utilization requires the conversion of all major constituent sugars. The current inability of the popular fermentation host Saccharomyces cerevisiae to metabolize the major pectic monosaccharide D-galacturonic acid (D-GalA) significantly hampers these efforts. While it has been reasoned that the optimization of cellular D-GalA uptake will be critical for the engineering of D-GalA utilization in yeast, no dedicated eukaryotic transport protein has been biochemically described. Here we report for the first time such a eukaryotic D-GalA transporter and characterize its functionality in S. cerevisiae. RESULTS We identified and characterized the D-GalA transporter GAT-1 out of a group of candidate genes obtained from co-expression analysis in N. crassa. The N. crassa Δgat-1 deletion strain is substantially affected in growth on pectic substrates, unable to take up D-GalA, and impaired in D-GalA-mediated signaling events. Moreover, expression of a gat-1 construct in yeast conferred the ability for strong high-affinity D-GalA accumulation rates, providing evidence for GAT-1 being a bona fide D-GalA transport protein. By recombinantly co-expressing D-galacturonate reductase or uronate dehydrogenase in yeast we furthermore demonstrated a transporter-dependent conversion of D-GalA towards more reduced (L-galactonate) or oxidized (meso-galactaric acid) downstream products, respectively, over a broad concentration range. CONCLUSIONS By utilizing the novel D-GalA transporter GAT-1 in S. cerevisiae we successfully generated a transporter-dependent uptake and catalysis system for D-GalA into two products with high potential for utilization as platform chemicals. Our data thereby provide a considerable first step towards a more complete utilization of biomass for biofuel and value-added chemicals production.
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Affiliation(s)
- J Philipp Benz
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ryan J Protzko
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jonas MS Andrich
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA, USA
- present address: Institute of Environmental and Sustainable Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Bauer
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA, USA
| | - John E Dueber
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Chris R Somerville
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
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Categorisation of sugar acid dehydratases in Aspergillus niger. Fungal Genet Biol 2013; 64:67-72. [PMID: 24382357 DOI: 10.1016/j.fgb.2013.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 12/18/2013] [Accepted: 12/19/2013] [Indexed: 11/24/2022]
Abstract
In the genome of Aspergillus niger five genes were identified coding for proteins with homologies to sugar acid dehydratases. The open reading frames were expressed in Saccharomyces cerevisiae and the activities tested with a library of sugar acids. Four genes were identified to code for proteins with activities with sugar acids: an l-galactonate dehydratase (gaaB), two d-galactonate dehydratases (dgdA, dgdB) and an l-rhamnonate dehydratase (lraC). The specificities of the proteins were characterised. The l-galactonate dehydratase had highest activity with l-fuconate, however it is unclear whether the enzyme is involved in l-fuconate catabolism. None of the proteins showed activity with galactaric acid or galactarolactone.
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Metabolic engineering of Escherichia coli for biosynthesis of D-galactonate. Bioprocess Biosyst Eng 2013; 37:383-91. [PMID: 23820824 DOI: 10.1007/s00449-013-1003-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/13/2013] [Indexed: 10/26/2022]
Abstract
D-galactose is an attractive substrate for bioconversion. Herein, Escherichia coli was metabolically engineered to convert D-galactose into D-galactonate, a valuable compound in the polymer and cosmetic industries. D-galactonate productions by engineered E. coli strains were observed in shake flask cultivations containing 2 g L(-1) D-galactose. Engineered E. coli expressing gld coding for galactose dehydrogenase from Pseudomonas syringae was able to produce 0.17 g L(-1) D-galactonate. Inherent metabolic pathways for assimilating both D-galactose and D-galactonate were blocked to enhance the production of D-galactonate. This approach finally led to a 7.3-fold increase with D-galactonate concentration of 1.24 g L(-1) and yield of 62.0 %. Batch fermentation in 20 g L(-1) D-galactose of E. coli ∆galK∆dgoK mutant expressing the gld resulted in 17.6 g L(-1) of D-galactonate accumulation and highest yield of 88.1 %. Metabolic engineering strategy developed in this study could be useful for industrial production of D-galactonate.
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