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Adamczyk PA, Coradetti ST, Gladden JM. Non-canonical D-xylose and L-arabinose metabolism via D-arabitol in the oleaginous yeast Rhodosporidium toruloides. Microb Cell Fact 2023; 22:145. [PMID: 37537595 PMCID: PMC10398940 DOI: 10.1186/s12934-023-02126-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/17/2023] [Indexed: 08/05/2023] Open
Abstract
R. toruloides is an oleaginous yeast, with diverse metabolic capacities and high tolerance for inhibitory compounds abundant in plant biomass hydrolysates. While R. toruloides grows on several pentose sugars and alcohols, further engineering of the native pathway is required for efficient conversion of biomass-derived sugars to higher value bioproducts. A previous high-throughput study inferred that R. toruloides possesses a non-canonical L-arabinose and D-xylose metabolism proceeding through D-arabitol and D-ribulose. In this study, we present a combination of genetic and metabolite data that refine and extend that model. Chiral separations definitively illustrate that D-arabitol is the enantiomer that accumulates under pentose metabolism. Deletion of putative D-arabitol-2-dehydrogenase (RTO4_9990) results in > 75% conversion of D-xylose to D-arabitol, and is growth-complemented on pentoses by heterologous xylulose kinase expression. Deletion of putative D-ribulose kinase (RTO4_14368) arrests all growth on any pentose tested. Analysis of several pentose dehydrogenase mutants elucidates a complex pathway with multiple enzymes mediating multiple different reactions in differing combinations, from which we also inferred a putative L-ribulose utilization pathway. Our results suggest that we have identified enzymes responsible for the majority of pathway flux, with additional unknown enzymes providing accessory activity at multiple steps. Further biochemical characterization of the enzymes described here will enable a more complete and quantitative understanding of R. toruloides pentose metabolism. These findings add to a growing understanding of the diversity and complexity of microbial pentose metabolism.
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Affiliation(s)
- Paul A Adamczyk
- Agile Biofoundry, Emeryville, CA, USA
- Sandia National Laboratories, Livermore, CA, USA
| | - Samuel T Coradetti
- Agile Biofoundry, Emeryville, CA, USA
- Sandia National Laboratories, Livermore, CA, USA
- United States Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA
| | - John M Gladden
- Agile Biofoundry, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, DOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
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Influence of glucose on xylose metabolization by Spathaspora passalidarum. Fungal Genet Biol 2021; 157:103624. [PMID: 34536506 DOI: 10.1016/j.fgb.2021.103624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/31/2021] [Accepted: 09/10/2021] [Indexed: 11/22/2022]
Abstract
The yeast Spathaspora passalidarum is able to produce ethanol from D-xylose and D-glucose. However, it is not clear how xylose metabolism is affected by D-glucose when both sugars are available in the culture medium. The aims of this work were to evaluate the influence of D-glucose on D-xylose consumption, ethanol production, gene expression, and the activity of key xylose-metabolism enzymes under both aerobic and oxygen-limited conditions. Ethanol yields and productivities were increased in culture media containing D-xylose as the sole carbon source or a mixture of D-xylose and D-glucose. S. passalidarum preferentially consumed D-glucose in the co-fermentations, which is consistent with the reduction in expression of genes encoding the key xylose-metabolism enzymes. In the presence of D-glucose, the specific activities of xylose reductase (XR), xylitol dehydrogenase (XDH), and xylulokinase (XK) were lower. Interestingly, in accordance with other studies, the presence of 2-deoxyglucose (2DG) did not inhibit the growth of S. passalidarum in culture medium containing D-xylose as the sole carbon source. This indicates that a non-canonical repression pathway is acting in S. passalidarum. In conclusion, the results suggest that D-glucose inhibits D-xylose consumption and prevents the D-xylose-mediated induction of the genes encoding XR, XDH, and XK.
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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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Abstract
Nowadays, the transport sector is one of the main sources of greenhouse gas (GHG) emissions and air pollution in cities. The use of renewable energies is therefore imperative to improve the environmental sustainability of this sector. In this regard, biofuels play an important role as they can be blended directly with fossil fuels and used in traditional vehicles’ engines. Bioethanol is the most used biofuel worldwide and can replace gasoline or form different gasoline-ethanol blends. Additionally, it is an important building block to obtain different high added-value compounds (e.g., acetaldehyde, ethylene, 1,3-butadiene, ethyl acetate). Today, bioethanol is mainly produced from food crops (first-generation (1G) biofuels), and a transition to the production of the so-called advanced ethanol (obtained from lignocellulosic feedstocks, non-food crops, or industrial waste and residue streams) is needed to meet sustainability criteria and to have a better GHG balance. This work gives an overview of the current production, use, and regulation rules of bioethanol as a fuel, as well as the advanced processes and the co-products that can be produced together with bioethanol in a biorefinery context. Special attention is given to the opportunities for making a sustainable transition from bioethanol 1G to advanced bioethanol.
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Moriwaki-Takano M, Iwakura R, Hoshino K. Dimorphic Mechanism on cAMP Mediated Signal Pathway in Mucor circinelloides. Appl Biochem Biotechnol 2020; 193:1252-1265. [PMID: 32424738 DOI: 10.1007/s12010-020-03342-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/23/2020] [Indexed: 11/27/2022]
Abstract
Mucor circinelloides is a dimorphic fungus that is a non-pathogen strain belonging to zygomycetes. In this research, a part of hypothetical mechanism on yeast-like cell induction of M. circinelloides in CO2 atmosphere was reported from the viewpoint of gene expression. To explain the relation between the change and the expressions of some genes involved in morphological changes of the strain, these were analyzed on the filamentous and yeast cell by real-time qPCR. The compared genes were Nce103, Ras3, Cyr1, Pde, and Efg1 encoding carbonic anhydrase, GTPase, adenylate cyclase, phosphodiesterase, and elongation factor G1, respectively. In anaerobic grown yeast cell with 70%N2 + 30%CO2, the Nce103 and Ras3 gene expressions decreased to 24 h whereas that of the filamentous cell increased. However, a downstream gene of Cyr1 expression level in the yeast cell was higher than that of filamentous cell. A lower level of Pde in the yeast cell than that of the filamentous cell indicated intracellular cAMP accumulation. The actual cAMP in the yeast cell remained whereas that of the filamentous cell decreased with cultivation. The Efg1 expression level controlling hyphal elongation was suppressed in the yeast cell. The intracellular cAMP accumulation and Efg1 expression regulate hyphal elongation or yeast forming.
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Affiliation(s)
- Maki Moriwaki-Takano
- Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Ryo Iwakura
- Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Kazuhiro Hoshino
- Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.
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Hardt N, Kind S, Schoenenberger B, Eggert T, Obkircher M, Wohlgemuth R. Facile synthesis of D-xylulose-5-phosphate and L-xylulose-5-phosphate by xylulokinase-catalyzed phosphorylation. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1630385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | | | | | | | | | - Roland Wohlgemuth
- Sigma-Aldrich/Merck KGaA, Buchs, Switzerland
- Institute of Technical Biochemistry, Technical University Lodz, Lodz, Poland
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Zhang Y, Zhao C, Ni Z, Shao M, Han M, Huang D, Liu F. Heterologous expression and biochemical characterization of a thermostable xylulose kinase from Bacillus coagulans IPE22. J Basic Microbiol 2019; 59:542-551. [PMID: 30747439 DOI: 10.1002/jobm.201800482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/02/2019] [Accepted: 01/13/2019] [Indexed: 12/28/2022]
Abstract
Xylulose kinase is an important enzyme involved in xylose metabolism, which is considered as essential biocatalyst for sustainable lignocellulosic-derived pentose utilization. Bacillus coagulans IPE22 is an ideal bacterium for refinery due to its strong ability to ferment xylose at high temperature. However, the B. coagulans xylose utilization mechanism remains unclear and the related promising enzymes need to be developed. In the present study, the gene coding for xylulose kinase from B. coagulans IPE22 (Bc-XK) was expressed in Escherichia coli BL21 (DE3). Bc-XK has a 1536 bp open reading frame, encoding a protein of 511 amino acids (56.15 kDa). Multiple sequence alignments were performed and a phylogenetic tree was built to evaluate differences among Bc-XK and other bacteria homologs. Bc-XK showed a broad adaptability to high temperature and the enzyme displayed its best performance at pH 8.0 and 60 °C. Bc-XK was activated by Mg2+ , Mn2+ , and Co2+ . Meanwhile, the enzyme could keep activity at 60 °C for at least 180 min. KM values of Bc-XK for xylulose and ATP were 1.29 mM and 0.76 mM, respectively. The high temperature stability of Bc-XK implied that it was an attractive candidate for industrial application.
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Affiliation(s)
- Yuming Zhang
- College of Life Sciences, Hebei University, Baoding, China
| | | | - Zhihua Ni
- College of Life Sciences, Hebei University, Baoding, China
| | - Menghua Shao
- College of Life Sciences, Hebei University, Baoding, China
| | - Mengying Han
- College of Life Sciences, Hebei University, Baoding, China
| | - Dawei Huang
- College of Life Sciences, Hebei University, Baoding, China
| | - Fengsong Liu
- College of Life Sciences, Hebei University, Baoding, China
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Takano M, Hoshino K. Bioethanol production from rice straw by simultaneous saccharification and fermentation with statistical optimized cellulase cocktail and fermenting fungus. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0203-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Moreno AD, Alvira P, Ibarra D, Tomás-Pejó E. Production of Ethanol from Lignocellulosic Biomass. PRODUCTION OF PLATFORM CHEMICALS FROM SUSTAINABLE RESOURCES 2017. [DOI: 10.1007/978-981-10-4172-3_12] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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Chu L, Zan X, Tang X, Zhao L, Chen H, Chen YQ, Chen W, Song Y. The role of a xylose isomerase pathway in the conversion of xylose to lipid in Mucor circinelloides. RSC Adv 2016. [DOI: 10.1039/c6ra12379a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The xylose isomerase (XI) pathway, which converts xylose in lignocellulosic materials into intermediate metabolites, is characterized for the first time in M. circinelloides.
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Affiliation(s)
- Linfang Chu
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi
- P. R. China
| | - Xinyi Zan
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi
- P. R. China
| | - Xin Tang
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi
- P. R. China
| | - Lina Zhao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi
- P. R. China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi
- P. R. China
| | - Yong Q. Chen
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi
- P. R. China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi
- P. R. China
| | - Yuanda Song
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi
- P. R. China
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