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Zhao M, Ma J, Zhang L, Qi H. Engineering strategies for enhanced heterologous protein production by Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:32. [PMID: 38247006 PMCID: PMC10801990 DOI: 10.1186/s12934-024-02299-z] [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: 05/12/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Microbial proteins are promising substitutes for animal- and plant-based proteins. S. cerevisiae, a generally recognized as safe (GRAS) microorganism, has been frequently employed to generate heterologous proteins. However, constructing a universal yeast chassis for efficient protein production is still a challenge due to the varying properties of different proteins. With progress in synthetic biology, a multitude of molecular biology tools and metabolic engineering strategies have been employed to alleviate these issues. This review first analyses the advantages of protein production by S. cerevisiae. The most recent advances in improving heterologous protein yield are summarized and discussed in terms of protein hyperexpression systems, protein secretion engineering, glycosylation pathway engineering and systems metabolic engineering. Furthermore, the prospects for efficient and sustainable heterologous protein production by S. cerevisiae are also provided.
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Affiliation(s)
- Meirong Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Jianfan Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Lei Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Haishan Qi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China.
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Méndez-Líter JA, de Eugenio LI, Nieto-Domínguez M, Prieto A, Martínez MJ. Expression and Characterization of Two α-l-Arabinofuranosidases from Talaromyces amestolkiae: Role of These Enzymes in Biomass Valorization. Int J Mol Sci 2023; 24:11997. [PMID: 37569374 PMCID: PMC10418624 DOI: 10.3390/ijms241511997] [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: 06/30/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
α-l-arabinofuranosidases are glycosyl hydrolases that catalyze the break between α-l-arabinofuranosyl substituents or between α-l-arabinofuranosides and xylose from xylan or xylooligosaccharide backbones. While they belong to several glycosyl hydrolase (GH) families, there are only 24 characterized GH62 arabinofuranosidases, making them a small and underrepresented group, with many of their features remaining unknown. Aside from their applications in the food industry, arabinofuranosidases can also aid in the processing of complex lignocellulosic materials, where cellulose, hemicelluloses, and lignin are closely linked. These materials can be fully converted into sugar monomers to produce secondary products like second-generation bioethanol. Alternatively, they can be partially hydrolyzed to release xylooligosaccharides, which have prebiotic properties. While endoxylanases and β-xylosidases are also necessary to fully break down the xylose backbone from xylan, these enzymes are limited when it comes to branched polysaccharides. In this article, two new GH62 α-l-arabinofuranosidases from Talaromyces amestolkiae (named ARA1 and ARA-2) have been heterologously expressed and characterized. ARA-1 is more sensitive to changes in pH and temperature, whereas ARA-2 is a robust enzyme with wide pH and temperature tolerance. Both enzymes preferentially act on arabinoxylan over arabinan, although ARA-1 has twice the catalytic efficiency of ARA-2 on this substrate. The production of xylooligosaccharides from arabinoxylan catalyzed by a T. amestolkiae endoxylanase was significantly increased upon pretreatment of the polysaccharide with ARA-1 or ARA-2, with the highest synergism values reported to date. Finally, both enzymes (ARA-1 or ARA-2 and endoxylanase) were successfully applied to enhance saccharification by combining them with a β-xylosidase already characterized from the same fungus.
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Affiliation(s)
- Juan A. Méndez-Líter
- Department of Microbial & Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), C/Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (L.I.d.E.)
| | - Laura I. de Eugenio
- Department of Microbial & Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), C/Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (L.I.d.E.)
| | - Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Alicia Prieto
- Department of Microbial & Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), C/Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (L.I.d.E.)
| | - María Jesús Martínez
- Department of Microbial & Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), C/Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (L.I.d.E.)
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Osiebe O, Adewale IO, Omafuvbe BO. Intracellular invertase hyperproducing strain of Saccharomyces cerevisiae isolated from Abagboro palm wine. Sci Rep 2023; 13:4937. [PMID: 36973340 PMCID: PMC10043029 DOI: 10.1038/s41598-023-32289-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/25/2023] [Indexed: 03/29/2023] Open
Abstract
There is an ever-increasing demand for industrial enzyme, necessitating a constant search for its efficient producers. The isolation and characterization of invertase producer yeasts from natural palm wine is reported in this study. Yeasts were isolated from fresh palm wine obtained from Abagboro community Ile-Ife, Nigeria following standard methods. A total of six yeast strains were isolated from the palm wine. The strains were screened for their ability to produce invertase and the most efficient invertase producer was characterized and identified using phenotypic and molecular methods. Isolate C showed the highest invertase activity (34.15 µmole/ml/min), followed by isolate B (18.070 µmole/ml/min) and isolate A (14.385 µmole/ml/min). The identity of isolate C was confirmed by genotypic methods to be Saccharomyces cerevisiae (OL629078.1 accession number on NCBI database). The Saccharomyces cerevisiae strain fermented galactose, arabinose, maltose, glucose, sucrose and raffinose, grew in 50% and 60% glucose and at 25-35 °C. The newly isolated Saccharomyces cerevisiae strain is an efficient producer of invertase and can be exploited for commercial biosynthesis of the enzyme for use in biotechnological applications.
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Affiliation(s)
- Oghenesivwe Osiebe
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife, Nigeria.
| | - Isaac Olusanjo Adewale
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife, Nigeria
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Tomioka S, Seki N, Sugiura Y, Akiyama M, Uchiyama J, Yamaguchi G, Yakabe K, Ejima R, Hattori K, Kimizuka T, Fujimura Y, Sato H, Gondo M, Ozaki S, Honme Y, Suematsu M, Kimura I, Inohara N, Núñez G, Hase K, Kim YG. Cooperative action of gut-microbiota-accessible carbohydrates improves host metabolic function. Cell Rep 2022; 40:111087. [PMID: 35858544 DOI: 10.1016/j.celrep.2022.111087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/17/2022] [Accepted: 06/22/2022] [Indexed: 12/31/2022] Open
Abstract
Microbiota-accessible carbohydrates (MACs) exert health-promoting effects, but how each MAC impacts gut microbiota and regulates host physiology remains unclear. Here, we show that l-arabinose and sucrose cooperatively act on gut microbiota and exert anti-obesogenic effects. Specifically, l-arabinose, a monosaccharide that is poorly absorbed in the gut and inhibits intestinal sucrase, suppresses diet-induced obesity in mice in the presence of sucrose. Additionally, the suppressive effect of l-arabinose on adiposity is abrogated in mice lacking the short-chain fatty acid (SCFA) receptors GPR43 and GPR41. Mechanistically, l-arabinose increases the relative abundance of acetate and propionate producers (e.g., Bacteroides), while sucrose enhances SCFA production. Furthermore, l-arabinose and sucrose activate the glycolytic and pentose phosphate pathways of Bacteroides, respectively, indicating that they synergistically promote acetate production through distinct pathways. These findings suggest that each MAC has a unique property and thus may serve as a precision gut-microbiota modulator to promote host homeostasis.
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Affiliation(s)
- Sawako Tomioka
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Natsumi Seki
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masahiro Akiyama
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Jun Uchiyama
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Genki Yamaguchi
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Kyosuke Yakabe
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Ryuta Ejima
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Kouya Hattori
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Tatsuki Kimizuka
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Yumiko Fujimura
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Hiroki Sato
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Monica Gondo
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan; Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Satoru Ozaki
- Co-Creation Center, Meiji Holdings Co., Ltd., Tokyo 192-0919, Japan
| | - Yoshiko Honme
- Co-Creation Center, Meiji Holdings Co., Ltd., Tokyo 192-0919, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ikuo Kimura
- Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naohiro Inohara
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gabriel Núñez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Koji Hase
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Yun-Gi Kim
- Research Center for Drug Discovery and Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan.
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Arrey G, Li G, Murphy R, Guimaraes L, Alizadeh S, Poulsen M, Regenberg B. Isolation, characterization, and genome assembly of Barnettozyma botsteinii sp. nov. and novel strains of Kurtzmaniella quercitrusa isolated from the intestinal tract of the termite Macrotermes bellicosus. G3 (BETHESDA, MD.) 2021; 11:jkab342. [PMID: 34586397 PMCID: PMC8664483 DOI: 10.1093/g3journal/jkab342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/17/2021] [Indexed: 11/12/2022]
Abstract
Bioconversion of hemicelluloses into simpler sugars leads to the production of a significant amount of pentose sugars, such as d-xylose. However, efficient utilization of pentoses by conventional yeast production strains remains challenging. Wild yeast strains can provide new industrially relevant characteristics and efficiently utilize pentose sugars. To explore this strategy, we isolated gut-residing yeasts from the termite Macrotermes bellicosus collected in Comoé National Park, Côte d'Ivoire. The yeasts were classified through their Internal Transcribed Spacer/Large Subunit sequence, and their genomes were sequenced and annotated. We identified a novel yeast species, which we name Barnettozyma botsteinii sp. nov. 1118T (MycoBank: 833563, CBS 16679T and IBT 710) and two new strains of Kurtzmaniella quercitrusa: var. comoensis (CBS 16678, IBT 709) and var. filamentosus (CBS 16680, IBT 711). The two K. quercitrusa strains grow 15% faster on synthetic glucose medium than Saccharomyces cerevisiae CEN.PKT in acidic conditions (pH = 3.2) and both strains grow on d-xylose as the sole carbon source at a rate of 0.35 h-1. At neutral pH, the yeast form of K. quercitrusa var. filamentosus, but not var. comoensis, switched to filamentous growth in a carbon source-dependent manner. Their genomes are 11.0-13.2 Mb in size and contain between 4888 and 5475 predicted genes. Together with closely related species, we did not find any relationship between gene content and ability to grow on xylose. Besides its metabolism, K. quercitrusa var. filamentosus has a large potential as a production organism, because of its capacity to grow at low pH and to undergo a dimorphic shift.
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Affiliation(s)
- Gerard Arrey
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 1165, Denmark
| | - Guangshuo Li
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 1165, Denmark
| | - Robert Murphy
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 1165, Denmark
| | - Leandro Guimaraes
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 1165, Denmark
| | - Sefa Alizadeh
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 1165, Denmark
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 1165, Denmark
| | - Birgitte Regenberg
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 1165, Denmark
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Varaprasad D, Narasimham D, Paramesh K, Sudha NR, Himabindu Y, Keerthi Kumari M, Nazaneen Parveen S, Chandrasekhar T. Improvement of ethanol production using green alga Chlorococcum minutum. ENVIRONMENTAL TECHNOLOGY 2021; 42:1383-1391. [PMID: 31526318 DOI: 10.1080/09593330.2019.1669719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Incessant depletion of fossil fuels urges the governments and non-governmental organizations to invest more on renewable energy sectors including generation of biofuels such as bioethanol. Production of ethanol from algal feedstock has been an interesting area of research in recent times. In the present investigation, feedstock of a green alga Chlorococcum minutum was selected for ethanol production and compared with feedstock of model alga Chlamydomonas reinhardtii. Both the species were grown under in vitro conditions using universal tris-acetate-phosphate (TAP) medium with various concentrations and combinations of vitamins such as thiamin, biotin and cobalamin (B1, B7 and B12) to enhance the biomass in turn reducing sugars in both the algal cultures. Later, these algal feedstocks were used for the production of ethanol under fermentation conditions using yeast. Reducing sugars were more in both the algal cultures grown in Cr3 or Cm3 media (TAP with 0.8 g/L of B1, 0.004 g/L of B7 & 0.004 g/L of B12) and also in Cr2 or Cm2 media (TAP with 0.4 g/L of B1, 0.002 g/L of B7 & 0.002 g/L of B12). In extent, the enhancement of ethanol production was noticed in C. reinhardtii (33.57 g/L) and C. minutum (46.97 g/L) from the feedstocks grown in Cr3 or Cm3 media when compared with feedstocks grown in other vitamin combinations or without vitamin assistance. Specifically, feedstock of C. minutum generated more output at 48 h when compared with model alga. The present work may be useful for the production of ethanol at a commercial level.
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Affiliation(s)
- Duddela Varaprasad
- Department of Environmental Science, Yogi Vemana University, Kadapa, India
| | - Dokka Narasimham
- Department of Environmental Science, Yogi Vemana University, Kadapa, India
| | - Kurva Paramesh
- Department of Environmental Science, Yogi Vemana University, Kadapa, India
| | | | - Yeduguri Himabindu
- Department of Environmental Science, Yogi Vemana University, Kadapa, India
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Armstrong H, Mander I, Zhang Z, Armstrong D, Wine E. Not All Fibers Are Born Equal; Variable Response to Dietary Fiber Subtypes in IBD. Front Pediatr 2021; 8:620189. [PMID: 33520902 PMCID: PMC7844368 DOI: 10.3389/fped.2020.620189] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022] Open
Abstract
Diet provides a safe and attractive alternative to available treatment options in a variety of diseases; however, research has only just begun to elucidate the role of diet in chronic diseases, such as the inflammatory bowel diseases (IBD). The chronic and highly debilitating IBDs, Crohn disease and ulcerative colitis, are hallmarked by intestinal inflammation, immune dysregulation, and dysbiosis; and evidence supports a role for genetics, microbiota, and the environment, including diet, in disease pathogenesis. This is true especially in children with IBD, where diet-based treatments have shown excellent results. One interesting group of dietary factors that readily links microbiota to gut health is dietary fibers. Fibers are not digested by human cells, but rather fermented by the gut microbes within the bowel. Evidence has been mounting over the last decade in support of the importance of dietary fibers in the maintenance of gut health and in IBD; however, more recent studies highlight the complexity of this interaction and importance of understanding the role of each individual dietary fiber subtype, especially during disease. There are roughly ten subtypes of dietary fibers described to date, categorized as soluble or insoluble, with varying chemical structures, and large differences in their fermentation profiles. Many studies to date have described the benefits of the byproducts of fermentation in healthy individuals and the potential health benefits in select disease models. However, there remains a void in our understanding of how each of these individual fibers affect human health in dysbiotic settings where appropriate fermentation may not be achieved. This review highlights the possibilities for better defining the role of individual dietary fibers for use in regulating inflammation in IBD.
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Affiliation(s)
- Heather Armstrong
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Inderdeep Mander
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB, Canada
| | - Zhengxiao Zhang
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - David Armstrong
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Eytan Wine
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
- Department of Physiology, University of Alberta, Edmonton, AB, Canada
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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Sun L, Jin YS. Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae. Biotechnol J 2020; 16:e2000142. [PMID: 33135317 DOI: 10.1002/biot.202000142] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 10/15/2020] [Indexed: 11/09/2022]
Abstract
Microbial conversion of plant biomass into fuels and chemicals offers a practical solution to global concerns over limited natural resources, environmental pollution, and climate change. Pursuant to these goals, researchers have put tremendous efforts and resources toward engineering the yeast Saccharomyces cerevisiae to efficiently convert xylose, the second most abundant sugar in lignocellulosic biomass, into various fuels and chemicals. Here, recent advances in metabolic engineering of yeast is summarized to address bottlenecks on xylose assimilation and to enable simultaneous co-utilization of xylose and other substrates in lignocellulosic hydrolysates. Distinct characteristics of xylose metabolism that can be harnessed to produce advanced biofuels and chemicals are also highlighted. Although many challenges remain, recent research investments have facilitated the efficient fermentation of xylose and simultaneous co-consumption of xylose and glucose. In particular, understanding xylose-induced metabolic rewiring in engineered yeast has encouraged the use of xylose as a carbon source for producing various non-ethanol bioproducts. To boost the lignocellulosic biomass-based bioeconomy, much attention is expected to promote xylose-utilizing efficiency via reprogramming cellular regulatory networks, to attain robust co-fermentation of xylose and other cellulosic carbon sources under industrial conditions, and to exploit the advantageous traits of yeast xylose metabolism for producing diverse fuels and chemicals.
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Affiliation(s)
- Liang Sun
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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10
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Cascaded valorization of seaweed using microbial cell factories. Curr Opin Biotechnol 2020; 65:102-113. [DOI: 10.1016/j.copbio.2020.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 11/17/2022]
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Martins LC, Monteiro CC, Semedo PM, Sá-Correia I. Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges. Appl Microbiol Biotechnol 2020; 104:6527-6547. [PMID: 32474799 PMCID: PMC7347521 DOI: 10.1007/s00253-020-10697-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/08/2020] [Accepted: 05/19/2020] [Indexed: 01/29/2023]
Abstract
Pectin-rich agro-industrial residues are feedstocks with potential for sustainable biorefineries. They are generated in high amounts worldwide from the industrial processing of fruits and vegetables. The challenges posed to the industrial implementation of efficient bioprocesses are however manyfold and thoroughly discussed in this review paper, mainly at the biological level. The most important yeast cell factory platform for advanced biorefineries is currently Saccharomyces cerevisiae, but this yeast species cannot naturally catabolise the main sugars present in pectin-rich agro-industrial residues hydrolysates, in particular D-galacturonic acid and L-arabinose. However, there are non-Saccharomyces species (non-conventional yeasts) considered advantageous alternatives whenever they can express highly interesting metabolic pathways, natively assimilate a wider range of carbon sources or exhibit higher tolerance to relevant bioprocess-related stresses. For this reason, the interest in non-conventional yeasts for biomass-based biorefineries is gaining momentum. This review paper focuses on the valorisation of pectin-rich residues by exploring the potential of yeasts that exhibit vast metabolic versatility for the efficient use of the carbon substrates present in their hydrolysates and high robustness to cope with the multiple stresses encountered. The major challenges and the progresses made related with the isolation, selection, sugar catabolism, metabolic engineering and use of non-conventional yeasts and S. cerevisiae-derived strains for the bioconversion of pectin-rich residue hydrolysates are discussed. The reported examples of value-added products synthesised by different yeasts using pectin-rich residues are reviewed. Key Points • Review of the challenges and progresses made on the bioconversion of pectin-rich residues by yeasts. • Catabolic pathways for the main carbon sources present in pectin-rich residues hydrolysates. • Multiple stresses with potential to affect bioconversion productivity. • Yeast metabolic engineering to improve pectin-rich residues bioconversion. Graphical abstract.
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Affiliation(s)
- Luís C Martins
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Catarina C Monteiro
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Paula M Semedo
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
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12
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Milessi TS, Perez CL, Zangirolami TC, Corradini FAS, Sandri JP, Foulquié-Moreno MR, Giordano RC, Thevelein JM, Giordano RLC. Repeated batches as a strategy for high 2G ethanol production from undetoxified hemicellulose hydrolysate using immobilized cells of recombinant Saccharomyces cerevisiae in a fixed-bed reactor. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:85. [PMID: 32426034 PMCID: PMC7216711 DOI: 10.1186/s13068-020-01722-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The search for sustainable energy sources has become a worldwide issue, making the development of efficient biofuel production processes a priority. Immobilization of second-generation (2G) xylose-fermenting Saccharomyces cerevisiae strains is a promising approach to achieve economic viability of 2G bioethanol production from undetoxified hydrolysates through operation at high cell load and mitigation of inhibitor toxicity. In addition, the use of a fixed-bed reactor can contribute to establish an efficient process because of its distinct advantages, such as high conversion rate per weight of biocatalyst and reuse of biocatalyst. RESULTS This work assessed the influence of alginate entrapment on the tolerance of recombinant S. cerevisiae to acetic acid. Encapsulated GSE16-T18SI.1 (T18) yeast showed an outstanding performance in repeated batch fermentations with cell recycling in YPX medium supplemented with 8 g/L acetic acid (pH 5.2), achieving 10 cycles without significant loss of productivity. In the fixed-bed bioreactor, a high xylose fermentation rate with ethanol yield and productivity values of 0.38 gethanol/gsugars and 5.7 g/L/h, respectively were achieved in fermentations using undetoxified sugarcane bagasse hemicellulose hydrolysate, with and without medium recirculation. CONCLUSIONS The performance of recombinant strains developed for 2G ethanol production can be boosted strongly by cell immobilization in alginate gels. Yeast encapsulation allows conducting fermentations in repeated batch mode in fixed-bed bioreactors with high xylose assimilation rate and high ethanol productivity using undetoxified hemicellulose hydrolysate.
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Affiliation(s)
- Thais S. Milessi
- Department of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
- Institute of Natural Resources, Federal University of Itajubá, Av. Benedito Pereira dos Santos, 1303, 37500-903 Itajubá, MG Brazil
| | - Caroline L. Perez
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
| | - Teresa C. Zangirolami
- Department of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
| | - Felipe A. S. Corradini
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
| | - Juliana P. Sandri
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
| | - Roberto C. Giordano
- Department of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
| | - Raquel L. C. Giordano
- Department of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
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Arumugam N, Boobalan T, Saravanan S, Jothi Basu M, Arun A, Suganya Devi T, Kavitha T. In silico and in vitro comparison of nicotinamide adenine dinucleotide phosphate dependent xylose reductase rossmaan fold in Debaryomycetaceae yeast family. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Nijland JG, Driessen AJM. Engineering of Pentose Transport in Saccharomyces cerevisiae for Biotechnological Applications. Front Bioeng Biotechnol 2020; 7:464. [PMID: 32064252 PMCID: PMC7000353 DOI: 10.3389/fbioe.2019.00464] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
Lignocellulosic biomass yields after hydrolysis, besides the hexose D-glucose, D-xylose, and L-arabinose as main pentose sugars. In second generation bioethanol production utilizing the yeast Saccharomyces cerevisiae, it is critical that all three sugars are co-consumed to obtain an economically feasible and robust process. Since S. cerevisiae is unable to metabolize pentose sugars, metabolic pathway engineering has been employed to introduce the respective pathways for D-xylose and L-arabinose metabolism. However, S. cerevisiae lacks specific pentose transporters, and these sugars enter the cell with low affinity via glucose transporters of the Hxt family. Therefore, in the presence of D-glucose, utilization of D-xylose and L-arabinose is poor as the Hxt transporters prefer D-glucose. To solve this problem, heterologous expression of pentose transporters has been attempted but often with limited success due to poor expression and stability, and/or low turnover. A more successful approach is the engineering of the endogenous Hxt transporter family and evolutionary selection for D-glucose insensitive growth on pentose sugars. This has led to the identification of a critical and conserved asparagine residue in Hxt transporters that, when mutated, reduces the D-glucose affinity while leaving the D-xylose affinity mostly unaltered. Likewise, mutant Gal2 transporter have been selected supporting specific uptake of L-arabinose. In fermentation experiments, the transporter mutants support efficient uptake and consumption of pentose sugars, and even co-consumption of D-xylose and D-glucose when used at industrial concentrations. Further improvements are obtained by interfering with the post-translational inactivation of Hxt transporters at high or low D-glucose concentrations. Transporter engineering solved major limitations in pentose transport in yeast, now allowing for co-consumption of sugars that is limited only by the rates of primary metabolism. This paves the way for a more economical second-generation biofuels production process.
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Affiliation(s)
- Jeroen G Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, Netherlands
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15
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Ruchala J, Kurylenko OO, Dmytruk KV, Sibirny AA. Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha). J Ind Microbiol Biotechnol 2019; 47:109-132. [PMID: 31637550 PMCID: PMC6970964 DOI: 10.1007/s10295-019-02242-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
This review summarizes progress in the construction of efficient yeast ethanol producers from glucose/sucrose and lignocellulose. Saccharomyces cerevisiae is the major industrial producer of first-generation ethanol. The different approaches to increase ethanol yield and productivity from glucose in S. cerevisiae are described. Construction of the producers of second-generation ethanol is described for S. cerevisiae, one of the best natural xylose fermenters, Scheffersomyces stipitis and the most thermotolerant yeast known Ogataea polymorpha. Each of these organisms has some advantages and drawbacks. S. cerevisiae is the primary industrial ethanol producer and is the most ethanol tolerant natural yeast known and, however, cannot metabolize xylose. S. stipitis can effectively ferment both glucose and xylose and, however, has low ethanol tolerance and requires oxygen for growth. O. polymorpha grows and ferments at high temperatures and, however, produces very low amounts of ethanol from xylose. Review describes how the mentioned drawbacks could be overcome.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Olena O Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland.
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16
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Tsoi R, Dai Z, You L. Emerging strategies for engineering microbial communities. Biotechnol Adv 2019; 37:107372. [PMID: 30880142 DOI: 10.1016/j.biotechadv.2019.03.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022]
Abstract
From biosynthesis to bioremediation, microbes have been engineered to address a variety of biotechnological applications. A promising direction in these endeavors is harnessing the power of designer microbial consortia that consist of multiple populations with well-defined interactions. Consortia can accomplish tasks that are difficult or potentially impossible to achieve using monocultures. Despite their potential, the rules underlying microbial community maintenance and function (i.e. the task the consortium is engineered to carry out) are not well defined, though rapid progress is being made. This limited understanding is in part due to the greater challenges associated with increased complexity when dealing with multi-population interactions. Here, we review key features and design strategies that emerge from the analysis of both natural and engineered microbial communities. These strategies can provide new insights into natural consortia and expand the toolbox available to engineers working to develop novel synthetic consortia.
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Affiliation(s)
- Ryan Tsoi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Zhuojun Dai
- Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA.
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17
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Li X, Chen Y, Nielsen J. Harnessing xylose pathways for biofuels production. Curr Opin Biotechnol 2019; 57:56-65. [PMID: 30785001 DOI: 10.1016/j.copbio.2019.01.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/04/2019] [Accepted: 01/15/2019] [Indexed: 01/02/2023]
Abstract
Energy security, environmental pollution, and economic development drive the development of alternatives to fossil fuels as an urgent global priority. Lignocellulosic biomass has the potential to contribute to meeting the demand for biofuel production via hydrolysis and fermentation of released sugars, such as glucose, xylose, and arabinose. Construction of robust cell factories requires introducing and rewiring of their metabolism to efficiently use all these sugars. Here, we review recent advances in re-constructing pathways for metabolism of pentoses, with special focus on xylose metabolism in the most widely used cell factories Saccharomyces cerevisiae and Escherichia coli. We also highlight engineering advanced biofuels-synthesis pathways and describes progress toward overcoming the challenges facing adoption of large-scale biofuel production.
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Affiliation(s)
- Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark; Wallenberg Center for Protein Research, Chalmers University of Technology, Gothenburg, Sweden.
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18
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Dasgupta D, Junghare V, Nautiyal AK, Jana A, Hazra S, Ghosh D. Xylitol Production from Lignocellulosic Pentosans: A Rational Strain Engineering Approach toward a Multiproduct Biorefinery. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1173-1186. [PMID: 30618252 DOI: 10.1021/acs.jafc.8b05509] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Kluyveromyces marxianus IIPE453 can utilize biomass-derived fermentable sugars for xylitol and ethanol fermentation. In this study, the xylitol production in the native strain was improved by overexpression of endogenous d-xylose reductase gene. A suitable expression cassette harboring the gene of interest was constructed and incorporated in the native yeast. qPCR analysis demonstrated the 2.1-fold enhancement in d-xylose reductase transcript levels in the modified strain with 1.62-fold enhancement in overall xylitol yield without affecting its ethanol fermenting capacity. Material balance analysis on 2 kg of sugar cane bagasse-derived fermentable sugars illustrated an excess of 58.62 ± 0.15 g of xylitol production by transformed strain in comparison to the wild variety with similar ethanol yield. The modified strain can be suitably used as a single biocatalyst for multiproduct biorefinery application.
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Affiliation(s)
- Diptarka Dasgupta
- Biotechnology Conversion Area, Bio Fuels Division , CSIR-Indian Institute of Petroleum , Dehradun , Uttarakhand 248005 , India
| | | | - Abhilek K Nautiyal
- Biotechnology Conversion Area, Bio Fuels Division , CSIR-Indian Institute of Petroleum , Dehradun , Uttarakhand 248005 , India
| | - Arijit Jana
- Biotechnology Conversion Area, Bio Fuels Division , CSIR-Indian Institute of Petroleum , Dehradun , Uttarakhand 248005 , India
| | | | - Debashish Ghosh
- Biotechnology Conversion Area, Bio Fuels Division , CSIR-Indian Institute of Petroleum , Dehradun , Uttarakhand 248005 , India
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19
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Gao M, Ploessl D, Shao Z. Enhancing the Co-utilization of Biomass-Derived Mixed Sugars by Yeasts. Front Microbiol 2019; 9:3264. [PMID: 30723464 PMCID: PMC6349770 DOI: 10.3389/fmicb.2018.03264] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/14/2018] [Indexed: 12/11/2022] Open
Abstract
Plant biomass is a promising carbon source for producing value-added chemicals, including transportation biofuels, polymer precursors, and various additives. Most engineered microbial hosts and a select group of wild-type species can metabolize mixed sugars including oligosaccharides, hexoses, and pentoses that are hydrolyzed from plant biomass. However, most of these microorganisms consume glucose preferentially to non-glucose sugars through mechanisms generally defined as carbon catabolite repression. The current lack of simultaneous mixed-sugar utilization limits achievable titers, yields, and productivities. Therefore, the development of microbial platforms capable of fermenting mixed sugars simultaneously from biomass hydrolysates is essential for economical industry-scale production, particularly for compounds with marginal profits. This review aims to summarize recent discoveries and breakthroughs in the engineering of yeast cell factories for improved mixed-sugar co-utilization based on various metabolic engineering approaches. Emphasis is placed on enhanced non-glucose utilization, discovery of novel sugar transporters free from glucose repression, native xylose-utilizing microbes, consolidated bioprocessing (CBP), improved cellulase secretion, and creation of microbial consortia for improving mixed-sugar utilization. Perspectives on the future development of biorenewables industry are provided in the end.
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Affiliation(s)
- Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States
| | - Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States.,The Ames Laboratory, Iowa State University, Ames, IA, United States.,The Interdisciplinary Microbiology Program, Biorenewables Research Laboratory, Iowa State University, Ames, IA, United States
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20
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Ahangangoda Arachchige MS, Mizutani O, Toyama H. Yeast strains from coconut toddy in Sri Lanka show high tolerance to inhibitors derived from the hydrolysis of lignocellulosic materials. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1676167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
| | - Osamu Mizutani
- United Graduate School of Agricultural Science, Kagoshima University, Kagoshima, Japan
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Hirohide Toyama
- United Graduate School of Agricultural Science, Kagoshima University, Kagoshima, Japan
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
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21
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Endalur Gopinarayanan V, Nair NU. Pentose Metabolism in Saccharomyces cerevisiae: The Need to Engineer Global Regulatory Systems. Biotechnol J 2019; 14:e1800364. [PMID: 30171750 PMCID: PMC6452637 DOI: 10.1002/biot.201800364] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/27/2018] [Indexed: 12/13/2022]
Abstract
Extending the host substrate range of industrially relevant microbes, such as Saccharomyces cerevisiae, has been a highly-active area of research since the conception of metabolic engineering. Yet, rational strategies that enable non-native substrate utilization in this yeast without the need for combinatorial and/or evolutionary techniques are underdeveloped. Herein, this review focuses on pentose metabolism in S. cerevisiae as a case study to highlight the challenges in this field. In the last three decades, work has focused on expressing exogenous pentose metabolizing enzymes as well as endogenous enzymes for effective pentose assimilation, growth, and biofuel production. The engineering strategies that are employed for pentose assimilation in this yeast are reviewed, and compared with metabolism and regulation of native sugar, galactose. In the case of galactose metabolism, multiple signals regulate and aid growth in the presence of the sugar. However, for pentoses that are non-native, it is unclear if similar growth and regulatory signals are activated. Such a comparative analysis aids in identifying missing links in xylose and arabinose utilization. While research on pentose metabolism have mostly concentrated on pathway level optimization, recent transcriptomics analyses highlight the need to consider more global regulatory, structural, and signaling components.
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Affiliation(s)
| | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, U.S.A
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22
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Verhoeven MD, de Valk SC, Daran JMG, van Maris AJA, Pronk JT. Fermentation of glucose-xylose-arabinose mixtures by a synthetic consortium of single-sugar-fermenting Saccharomyces cerevisiae strains. FEMS Yeast Res 2018; 18:5054444. [DOI: 10.1093/femsyr/foy075] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/13/2018] [Indexed: 11/15/2022] Open
Affiliation(s)
- Maarten D Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sophie C de Valk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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23
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Lane S, Dong J, Jin YS. Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2018; 260:380-394. [PMID: 29655899 DOI: 10.1016/j.biortech.2018.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 05/26/2023]
Abstract
The substantial research efforts into lignocellulosic biofuels have generated an abundance of valuable knowledge and technologies for metabolic engineering. In particular, these investments have led to a vast growth in proficiency of engineering the yeast Saccharomyces cerevisiae for consuming lignocellulosic sugars, enabling the simultaneous assimilation of multiple carbon sources, and producing a large variety of value-added products by introduction of heterologous metabolic pathways. While microbial conversion of cellulosic sugars into large-volume low-value biofuels is not currently economically feasible, there may still be opportunities to produce other value-added chemicals as regulation of cellulosic sugar metabolism is quite different from glucose metabolism. This review summarizes these recent advances with an emphasis on employing engineered yeast for the bioconversion of lignocellulosic sugars into a variety of non-ethanol value-added products.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jia Dong
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Diwan B, Parkhey P, Gupta P. From agro-industrial wastes to single cell oils: a step towards prospective biorefinery. Folia Microbiol (Praha) 2018; 63:547-568. [DOI: 10.1007/s12223-018-0602-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
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25
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Turner TL, Kim H, Kong II, Liu JJ, Zhang GC, Jin YS. Engineering and Evolution of Saccharomyces cerevisiae to Produce Biofuels and Chemicals. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:175-215. [PMID: 27913828 DOI: 10.1007/10_2016_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To mitigate global climate change caused partly by the use of fossil fuels, the production of fuels and chemicals from renewable biomass has been attempted. The conversion of various sugars from renewable biomass into biofuels by engineered baker's yeast (Saccharomyces cerevisiae) is one major direction which has grown dramatically in recent years. As well as shifting away from fossil fuels, the production of commodity chemicals by engineered S. cerevisiae has also increased significantly. The traditional approaches of biochemical and metabolic engineering to develop economic bioconversion processes in laboratory and industrial settings have been accelerated by rapid advancements in the areas of yeast genomics, synthetic biology, and systems biology. Together, these innovations have resulted in rapid and efficient manipulation of S. cerevisiae to expand fermentable substrates and diversify value-added products. Here, we discuss recent and major advances in rational (relying on prior experimentally-derived knowledge) and combinatorial (relying on high-throughput screening and genomics) approaches to engineer S. cerevisiae for producing ethanol, butanol, 2,3-butanediol, fatty acid ethyl esters, isoprenoids, organic acids, rare sugars, antioxidants, and sugar alcohols from glucose, xylose, cellobiose, galactose, acetate, alginate, mannitol, arabinose, and lactose.
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Affiliation(s)
- Timothy L Turner
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Heejin Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - In Iok Kong
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jing-Jing Liu
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Guo-Chang Zhang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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A semi-synthetic regulon enables rapid growth of yeast on xylose. Nat Commun 2018; 9:1233. [PMID: 29581426 PMCID: PMC5964326 DOI: 10.1038/s41467-018-03645-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 03/01/2018] [Indexed: 01/27/2023] Open
Abstract
Nutrient assimilation is the first step that allows biological systems to proliferate and produce value-added products. Yet, implementation of heterologous catabolic pathways has so far relied on constitutive gene expression without consideration for global regulatory systems that may enhance nutrient assimilation and cell growth. In contrast, natural systems prefer nutrient-responsive gene regulation (called regulons) that control multiple cellular functions necessary for cell survival and growth. Here, in Saccharomyces cerevisiae, by partially- and fully uncoupling galactose (GAL)-responsive regulation and metabolism, we demonstrate the significant growth benefits conferred by the GAL regulon. Next, by adapting the various aspects of the GAL regulon for a non-native nutrient, xylose, we build a semi-synthetic regulon that exhibits higher growth rate, better nutrient consumption, and improved growth fitness compared to the traditional and ubiquitous constitutive expression strategy. This work provides an elegant paradigm to integrate non-native nutrient catabolism with native, global cellular responses to support fast growth. Efficient assimilation of nutrients is essential for the production of value-added products in microbial fermentation. Here the authors design a semi-synthetic xylose regulon to improve growth characteristics of Saccharomyces cerevisiae on this non-native sugar.
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27
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Radek A, Tenhaef N, Müller MF, Brüsseler C, Wiechert W, Marienhagen J, Polen T, Noack S. Miniaturized and automated adaptive laboratory evolution: Evolving Corynebacterium glutamicum towards an improved d-xylose utilization. BIORESOURCE TECHNOLOGY 2017; 245:1377-1385. [PMID: 28552568 DOI: 10.1016/j.biortech.2017.05.055] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 05/22/2023]
Abstract
Adaptive Laboratory Evolution (ALE) is increasingly being used as a technique for untargeted strain optimization. This work aimed at developing an automated and miniaturized ALE approach based on repetitive batch cultivations in microtiter plates. The new method is applied to the recently published strain Corynebacterium glutamicum pEKEx3-xylXABCDCc, which is capable of utilizing d-xylose via the Weimberg (WMB) pathway. As a result, the significantly improved strain WMB2evo was obtained, showing a specific growth rate of 0.26h-1 on d-xylose as sole carbon and energy source. WMB2evo grows stable during lab-scale bioreactor operation, demonstrating the high potential of this strain for future biorefinery applications. Genome sequencing of cell samples from two different ALE processes revealed potential key mutations, e.g. in the gene cg0196 (encoding for the transcriptional regulator IolR of the myo-inositol metabolism). These findings open up new perspectives for the rational engineering of C. glutamicum towards improved d-xylose utilization.
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Affiliation(s)
- Andreas Radek
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Moritz Fabian Müller
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Christian Brüsseler
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany.
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28
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Maleki N, Safari M, Eiteman MA. Conversion of glucose-xylose mixtures to pyruvate using a consortium of metabolically engineered Escherichia coli. Eng Life Sci 2017; 18:40-47. [PMID: 32624859 DOI: 10.1002/elsc.201700109] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/11/2017] [Accepted: 09/06/2017] [Indexed: 11/12/2022] Open
Abstract
Two strains of Escherichia coli were engineered to accumulate pyruvic acid from two sugars found in lignocellulosic hydrolysates by knockouts in the aceE, ppsA, poxB, and ldhA genes. Additionally, since glucose and xylose are typically consumed sequentially due to carbon catabolite repression in E. coli, one strain (MEC590) was engineered to grow only on glucose while a second strain (MEC589) grew only on xylose. On a single substrate, each strain generated pyruvate at a yield of about 0.60 g/g in both continuous culture and batch culture. In a glucose-xylose mixture under continuous culture, a consortium of both strains maintained a pyruvate yield greater than 0.60 g/g when three different concentrations of glucose and xylose were sequentially fed into the system. In a fed-batch process, both sugars in a glucose-xylose mixture were consumed simultaneously to accumulate 39 g/L pyruvate in less than 24 h at a yield of 0.59 g/g.
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Affiliation(s)
- Neda Maleki
- Department of Food Science Engineering and Technology University of Tehran Karaj Iran.,School of Chemical, Materials and Biomedical Engineering University of Georgia Athens GA USA
| | - Mohammad Safari
- Department of Food Science Engineering and Technology University of Tehran Karaj Iran
| | - Mark A Eiteman
- School of Chemical, Materials and Biomedical Engineering University of Georgia Athens GA USA
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29
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Growth and lovastatin production by Aspergillus terreus under different carbohyrates as carbon sources. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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30
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Caballero A, Ramos JL. Enhancing ethanol yields through d-xylose and l-arabinose co-fermentation after construction of a novel high efficient l-arabinose-fermenting Saccharomyces cerevisiae strain. Microbiology (Reading) 2017; 163:442-452. [DOI: 10.1099/mic.0.000437] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Antonio Caballero
- Abengoa Research, Department of Biotechnology, Campus de Palmas Altas, c/Energia Solar number 1, 41004 Sevilla, Spain
- BacMine, C/de Santiago Grisolía 28760 Tres Cantos, Spain
| | - Juan Luis Ramos
- Abengoa Research, Department of Biotechnology, Campus de Palmas Altas, c/Energia Solar number 1, 41004 Sevilla, Spain
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31
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Challenges and prospects of xylitol production with whole cell bio-catalysis: A review. Microbiol Res 2017; 197:9-21. [DOI: 10.1016/j.micres.2016.12.012] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/09/2016] [Accepted: 12/30/2016] [Indexed: 11/19/2022]
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32
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Coutilization of D-Glucose, D-Xylose, and L-Arabinose in Saccharomyces cerevisiae by Coexpressing the Metabolic Pathways and Evolutionary Engineering. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5318232. [PMID: 28459063 PMCID: PMC5385224 DOI: 10.1155/2017/5318232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/04/2017] [Accepted: 03/20/2017] [Indexed: 11/23/2022]
Abstract
Efficient and cost-effective fuel ethanol production from lignocellulosic materials requires simultaneous cofermentation of all hydrolyzed sugars, mainly including D-glucose, D-xylose, and L-arabinose. Saccharomyces cerevisiae is a traditional D-glucose fermenting strain and could utilize D-xylose and L-arabinose after introducing the initial metabolic pathways. The efficiency and simultaneous coutilization of the two pentoses and D-glucose for ethanol production in S. cerevisiae still need to be optimized. Previously, we constructed an L-arabinose-utilizing S. cerevisiae BSW3AP. In this study, we further introduced the XI and XR-XDH metabolic pathways of D-xylose into BSW3AP to obtain D-glucose, D-xylose, and L-arabinose cofermenting strain. Benefits of evolutionary engineering: the resulting strain BSW4XA3 displayed a simultaneous coutilization of D-xylose and L-arabinose with similar consumption rates, and the D-glucose metabolic capacity was not decreased. After 120 h of fermentation on mixed D-glucose, D-xylose, and L-arabinose, BSW4XA3 consumed 24% more amounts of pentoses and the ethanol yield of mixed sugars was increased by 30% than that of BSW3AP. The resulting strain BSW4XA3 was a useful chassis for further enhancing the coutilization efficiency of mixed sugars for bioethanol production.
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33
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Sukpipat W, Komeda H, Prasertsan P, Asano Y. Purification and characterization of xylitol dehydrogenase with l-arabitol dehydrogenase activity from the newly isolated pentose-fermenting yeast Meyerozyma caribbica 5XY2. J Biosci Bioeng 2017; 123:20-27. [DOI: 10.1016/j.jbiosc.2016.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/05/2016] [Accepted: 07/18/2016] [Indexed: 11/26/2022]
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34
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Chatellard L, Trably E, Carrère H. The type of carbohydrates specifically selects microbial community structures and fermentation patterns. BIORESOURCE TECHNOLOGY 2016; 221:541-549. [PMID: 27686722 DOI: 10.1016/j.biortech.2016.09.084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/16/2016] [Accepted: 09/17/2016] [Indexed: 05/24/2023]
Abstract
The impact on dark fermentation of seven carbohydrates as model substrates of lignocellulosic fractions (glucose, cellobiose, microcrystalline cellulose, arabinose, xylose, xylan and wheat straw) was investigated. Metabolic patterns and bacterial communities were characterized at the end of batch tests inoculated with manure digestate. It was found that hydrogen production was linked to the sugar type (pentose or hexose) and the degree of polymerisation. Hexoses produced less hydrogen, with a specific selection of lactate-producing bacterial community structures. Maximal hydrogen production was five times higher on pentose-based substrates, with specific bacterial community structures producing acetate and butyrate as main metabolites. Low hydrogen amounts accumulated from complex sugars (cellulose, xylan and wheat straw). A relatively high proportion of the reads was affiliated to Ruminococcaceae suggesting an efficient hydrolytic activity. Knowing that the bacterial community structure is very specific to a particular substrate offers new possibilities to design more efficient H2-producing biological systems.
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Affiliation(s)
| | - Eric Trably
- LBE, INRA, 102 avenue des Etangs, 11100 Narbonne, France.
| | - Hélène Carrère
- LBE, INRA, 102 avenue des Etangs, 11100 Narbonne, France
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35
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Lang C, Yang R, Yang Y, Gao B, Zhao L, Wei W, Wang H, Matsukawa S, Xie J, Wei D. An Acid-Adapted Endo-α-1,5-L-arabinanase for Pectin Releasing. Appl Biochem Biotechnol 2016; 180:900-916. [PMID: 27246002 DOI: 10.1007/s12010-016-2141-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
Abstract
An arabinanase gene was cloned by overlap-PCR from Penicillium sp. Y702 and expressed in Pichia pastoris. The recombinant enzyme was named AbnC702 with 20 U/mg of endo-arabinanase activity toward linear α-1,5-L-arabinan. The optimal pH and temperature of AbnC702 were 5.0 and 50 °C, respectively. The recombinant AbnC702 was highly stable at pH 5.0-7.0 and 50 °C. It could retain about 72.3 % of maximum specific activity at pH 5.0 after incubation for 2.5 h, which indicated AbnC702 was an acid-adapted enzyme. The K m and V max values were 24.8 ± 4.7 mg/ml and 88.5 ± 5.6 U/mg, respectively. A three-dimensional structure of AbnC702 was made by homology modeling, and the counting of acidic/basic amino residues within the region of 10 Å around the active site, as well the hydrogen bonds within the area of 5 Å around the active site, might theoretically interpret the acid adaptability of AbnC702. Analysis of hydrolysis products by thin layer chromatography (TLC) combined with high-performance liquid chromatography (HPLC) verified that the recombinant AbnC702 was an endo-1,5-α-L-arabinanase, which yielded arabinobiose and arabinotriose as major products. AbnC702 was applied in pectin extraction from apple pomace with synergistic action of α-L-arabinofuranosidase.
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Affiliation(s)
- Chong Lang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Rujian Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Ying Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Li Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Shingo Matsukawa
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan
| | - Jingli Xie
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China. .,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China. .,Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, People's Republic of China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, People's Republic of China
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36
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Simultaneous Saccharification and Fermentation of Sugar Beet Pulp for Efficient Bioethanol Production. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3154929. [PMID: 27722169 PMCID: PMC5046097 DOI: 10.1155/2016/3154929] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/16/2016] [Indexed: 11/17/2022]
Abstract
Sugar beet pulp, a byproduct of sugar beet processing, can be used as a feedstock in second-generation ethanol production. The objective of this study was to investigate the effects of pretreatment, of the dosage of cellulase and hemicellulase enzyme preparations used, and of aeration on the release of fermentable sugars and ethanol yield during simultaneous saccharification and fermentation (SSF) of sugar beet pulp-based worts. Pressure-thermal pretreatment was applied to sugar beet pulp suspended in 2% w/w sulphuric acid solution at a ratio providing 12% dry matter. Enzymatic hydrolysis was conducted using Viscozyme and Ultraflo Max (Novozymes) enzyme preparations (0.015-0.02 mL/g dry matter). Two yeast strains were used for fermentation: Ethanol Red (S. cerevisiae) (1 g/L) and Pichia stipitis (0.5 g/L), applied sequentially. The results show that efficient simultaneous saccharification and fermentation of sugar beet pulp was achieved. A 6 h interval for enzymatic activation between the application of enzyme preparations and inoculation with Ethanol Red further improved the fermentation performance, with the highest ethanol concentration reaching 26.9 ± 1.2 g/L and 86.5 ± 2.1% fermentation efficiency relative to the theoretical yield.
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37
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Liu JJ, Zhang GC, Oh EJ, Pathanibul P, Turner TL, Jin YS. Lactose fermentation by engineered Saccharomyces cerevisiae capable of fermenting cellobiose. J Biotechnol 2016; 234:99-104. [DOI: 10.1016/j.jbiotec.2016.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 11/26/2022]
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38
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Rahman MM, Andberg M, Koivula A, Rouvinen J, Hakulinen N. Crystallization and X-ray diffraction analysis of an L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:604-8. [PMID: 27487924 PMCID: PMC4973301 DOI: 10.1107/s2053230x16010311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/25/2016] [Indexed: 11/28/2022]
Abstract
l-Arabinonate dehydratase and d-xylonate dehydratase from the IlvD/EDD family were crystallized by the vapour-diffusion method. Diffraction data sets were collected to resolutions of 2.40 and 2.66 Å from crystals of l-arabinonate dehydratase and d-xylonate dehydratase, respectively. l-Arabinonate dehydratase (EC 4.2.1.25) and d-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. l-Arabinonate dehydratase converts l-arabinonate into 2-dehydro-3-deoxy-l-arabinonate, and d-xylonate dehydratase catalyzes the dehydration of d-xylonate to 2-dehydro-3-deoxy-d-xylonate. l-Arabinonate and d-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any l-arabinonate or d-xylonate dehydratase is available in the PDB. In this study, recombinant l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and d-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P21, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 Å, β = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a VM value of 3.2 Å3 Da−1 and a solvent content of 62%. Crystals of CcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space group C2, with unit-cell parameters a = 270.42, b = 236.13, c = 65.17 Å, β = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a VM value of 4.0 Å3 Da−1 and a solvent content of 69%.
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Affiliation(s)
- Mohammad Mubinur Rahman
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT Espoo, Finland
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland
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Anasontzis GE, Kourtoglou E, Villas-Boâs SG, Hatzinikolaou DG, Christakopoulos P. Metabolic Engineering of Fusarium oxysporum to Improve Its Ethanol-Producing Capability. Front Microbiol 2016; 7:632. [PMID: 27199958 PMCID: PMC4854878 DOI: 10.3389/fmicb.2016.00632] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/18/2016] [Indexed: 12/13/2022] Open
Abstract
Fusarium oxysporum is one of the few filamentous fungi capable of fermenting ethanol directly from plant cell wall biomass. It has the enzymatic toolbox necessary to break down biomass to its monosaccharides and, under anaerobic and microaerobic conditions, ferments them to ethanol. Although these traits could enable its use in consolidated processes and thus bypass some of the bottlenecks encountered in ethanol production from lignocellulosic material when Saccharomyces cerevisiae is used—namely its inability to degrade lignocellulose and to consume pentoses—two major disadvantages of F. oxysporum compared to the yeast—its low growth rate and low ethanol productivity—hinder the further development of this process. We had previously identified phosphoglucomutase and transaldolase, two major enzymes of glucose catabolism and the pentose phosphate pathway, as possible bottlenecks in the metabolism of the fungus and we had reported the effect of their constitutive production on the growth characteristics of the fungus. In this study, we investigated the effect of their constitutive production on ethanol productivity under anaerobic conditions. We report an increase in ethanol yield and a concomitant decrease in acetic acid production. Metabolomics analysis revealed that the genetic modifications applied did not simply accelerate the metabolic rate of the microorganism; they also affected the relative concentrations of the various metabolites suggesting an increased channeling toward the chorismate pathway, an activation of the γ-aminobutyric acid shunt, and an excess in NADPH regeneration.
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Affiliation(s)
- George E Anasontzis
- Microbial Biotechnology Unit, Sector of Botany, Department of Biology, National and Kapodistrian University of Athens Zografou, Greece
| | - Elisavet Kourtoglou
- BIOtechMASS Unit, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens Zografou, Greece
| | - Silas G Villas-Boâs
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland Auckland, New Zealand
| | - Dimitris G Hatzinikolaou
- Microbial Biotechnology Unit, Sector of Botany, Department of Biology, National and Kapodistrian University of Athens Zografou, Greece
| | - Paul Christakopoulos
- Biochemical and Chemical Process Engineering, Division of Sustainable Process Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology Luleå, Sweden
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40
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Combining C6 and C5 sugar metabolism for enhancing microbial bioconversion. Curr Opin Chem Biol 2015; 29:49-57. [DOI: 10.1016/j.cbpa.2015.09.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/09/2015] [Accepted: 09/15/2015] [Indexed: 11/18/2022]
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41
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Knoshaug EP, Vidgren V, Magalhães F, Jarvis EE, Franden MA, Zhang M, Singh A. Novel transporters from
Kluyveromyces marxianus
and
Pichia guilliermondii
expressed in
Saccharomyces cerevisiae
enable growth on
l
‐arabinose and
d
‐xylose. Yeast 2015; 32:615-28. [DOI: 10.1002/yea.3084] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 05/11/2015] [Accepted: 06/23/2015] [Indexed: 11/08/2022] Open
Affiliation(s)
- Eric P. Knoshaug
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Virve Vidgren
- VTT Technical Research Centre of Finland PO Box 1000 FI‐02044 VTT Finland
| | | | - Eric E. Jarvis
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Mary Ann Franden
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Min Zhang
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Arjun Singh
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
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42
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Wang M, Li S, Zhao H. Design and engineering of intracellular-metabolite-sensing/regulation gene circuits inSaccharomyces cerevisiae. Biotechnol Bioeng 2015; 113:206-15. [DOI: 10.1002/bit.25676] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/27/2015] [Accepted: 06/01/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
- Energy Biosciences Institute, Institute for Genomic Biology; Urbana Illinois 61801
| | - Sijin Li
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
- Energy Biosciences Institute, Institute for Genomic Biology; Urbana Illinois 61801
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
- Energy Biosciences Institute, Institute for Genomic Biology; Urbana Illinois 61801
- Departments of Chemistry, Biochemistry, and Bioengineering; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
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43
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Organic acids from lignocellulose: Candida lignohabitans as a new microbial cell factory. ACTA ACUST UNITED AC 2015; 42:681-91. [DOI: 10.1007/s10295-015-1590-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/24/2015] [Indexed: 11/27/2022]
Abstract
Abstract
Biorefinery applications require microbial cell factories for the conversion of various sugars derived from lignocellulosic material into value-added chemicals. Here, the capabilities of the yeast Candida lignohabitans to utilize a range of such sugars is characterized. Substrates efficiently converted by this yeast include the pentoses xylose and arabinose. Genetic engineering of C. lignohabitans with the isolated endogenous GAP promoter and GAP terminator was successful. GFP expression was used as a proof of functionality for the isolated transcription elements. Expression of lactate dehydrogenase and cis-aconitate decarboxylase resulted in stable and reproducible production of lactic acid and itaconic acid, respectively. The desired organic acids were accumulated converting pure sugars as well as lignocellulosic hydrolysates. C. lignohabitans proved therefore to be a promising reliable microbial host for production of organic acids from lignocellulosic material.
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44
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Kordowska-Wiater M. Production of arabitol by yeasts: current status and future prospects. J Appl Microbiol 2015; 119:303-14. [PMID: 25809659 DOI: 10.1111/jam.12807] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/28/2015] [Accepted: 03/12/2015] [Indexed: 11/30/2022]
Abstract
Arabitol belongs to the pentitol family and is used in the food industry as a sweetener and in the production of human therapeutics as an anticariogenic agent and an adipose tissue reducer. It can also be utilized as a substrate for chemical products such as arabinoic and xylonic acids, propylene, ethylene glycol, xylitol and others. It is included on the list of 12 building block C3-C6 compounds, designated for further biotechnological research. This polyol can be produced by yeasts in the processes of bioconversion or biotransformation of waste materials from agriculture, the forest industry (l-arabinose, glucose) and the biodiesel industry (glycerol). The present review discusses research on native yeasts from the genera Candida, Pichia, Debaryomyces and Zygosaccharomyces as well as genetically modified strains of Saccharomyces cerevisiae which are able to utilize biomass hydrolysates to effectively produce L- or D-arabitol. The metabolic pathways of these yeasts leading from sugars and glycerol to arabitol are presented. Although the number of reports concerning microbial production of arabitol is rather limited, the research on this topic has been growing for the last several years, with researchers looking for new micro-organisms, substrates and technologies.
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Affiliation(s)
- M Kordowska-Wiater
- Department of Biotechnology, Human Nutrition and Science of Food Commodities, University of Life Sciences in Lublin, Lublin, Poland
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45
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Challenges for the production of bioethanol from biomass using recombinant yeasts. ADVANCES IN APPLIED MICROBIOLOGY 2015; 92:89-125. [PMID: 26003934 DOI: 10.1016/bs.aambs.2015.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lignocellulose biomass, one of the most abundant renewable resources on the planet, is an alternative sustainable energy source for the production of second-generation biofuels. Energy in the form of simple or complex carbohydrates can be extracted from lignocellulose biomass and fermented by microorganisms to produce bioethanol. Despite 40 years of active and cutting-edge research invested into the development of technologies to produce bioethanol from lignocellulosic biomass, the process remains commercially unviable. This review describes the achievements that have been made in generating microorganisms capable of utilizing both simple and complex sugars from lignocellulose biomass and the fermentation of these sugars into ethanol. We also provide a discussion on the current "roadblocks" standing in the way of making second-generation bioethanol a commercially viable alternative to fossil fuels.
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46
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Jung Y, Kim S, Lee S, Ha KS, Lee J. Effect of heterologous expression of genes involved in the elongation cycle of fatty acid synthesis on fatty acid production in Saccharomyces cerevisiae. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0484-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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47
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Shin HY, Nijland JG, de Waal PP, de Jong RM, Klaassen P, Driessen AJM. An engineered cryptic Hxt11 sugar transporter facilitates glucose-xylose co-consumption in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:176. [PMID: 26535057 PMCID: PMC4630928 DOI: 10.1186/s13068-015-0360-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/22/2015] [Indexed: 05/15/2023]
Abstract
BACKGROUND The yeast Saccharomyces cerevisiae is unable to ferment pentose sugars like d-xylose. Through the introduction of the respective metabolic pathway, S. cerevisiae is able to ferment xylose but first utilizes d-glucose before the d-xylose can be transported and metabolized. Low affinity d-xylose uptake occurs through the endogenous hexose (Hxt) transporters. For a more robust sugar fermentation, co-consumption of d-glucose and d-xylose is desired as d-xylose fermentation is in particular prone to inhibition by compounds present in pretreated lignocellulosic feedstocks. RESULTS Evolutionary engineering of a d-xylose-fermenting S. cerevisiae strain lacking the major transporter HXT1-7 and GAL2 genes yielded a derivative that shows improved growth on xylose because of the expression of a normally cryptic HXT11 gene. Hxt11 also supported improved growth on d-xylose by the wild-type strain. Further selection for glucose-insensitive growth on d-xylose employing a quadruple hexokinase deletion yielded mutations at N366 of Hxt11 that reversed the transporter specificity for d-glucose into d-xylose while maintaining high d-xylose transport rates. The Hxt11 mutant enabled the efficient co-fermentation of xylose and glucose at industrially relevant sugar concentrations when expressed in a strain lacking the HXT1-7 and GAL2 genes. CONCLUSIONS Hxt11 is a cryptic sugar transporter of S. cerevisiae that previously has not been associated with effective d-xylose transport. Mutagenesis of Hxt11 yielded transporters that show a better affinity for d-xylose as compared to d-glucose while maintaining high transport rates. d-glucose and d-xylose co-consumption is due to a redistribution of the sugar transport flux while maintaining the total sugar conversion rate into ethanol. This method provides a single transporter solution for effective fermentation on lignocellulosic feedstocks.
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Affiliation(s)
- Hyun Yong Shin
- />Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jeroen G. Nijland
- />Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paul P. de Waal
- />DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - René M. de Jong
- />DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Paul Klaassen
- />DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Arnold J. M. Driessen
- />Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Centre for Genomics of Industrial Fermentation, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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48
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Production of Industrially Relevant Isoprenoid Compounds in Engineered Microbes. MICROORGANISMS IN BIOREFINERIES 2015. [DOI: 10.1007/978-3-662-45209-7_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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49
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French CE, Horsfall L, Barnard DK, Duedu K, Fletcher E, Joshi N, Kane SD, Lakhundi SS, Liu CK, Oltmanns J, Radford D, Salinas A, White J, Elfick A. Beyond Genetic Engineering: Technical Capabilities in the Application Fields of Biocatalysis and Biosensors. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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50
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Harcus D, Dignard D, Lépine G, Askew C, Raymond M, Whiteway M, Wu C. Comparative xylose metabolism among the Ascomycetes C. albicans, S. stipitis and S. cerevisiae. PLoS One 2013; 8:e80733. [PMID: 24236198 PMCID: PMC3827475 DOI: 10.1371/journal.pone.0080733] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 10/07/2013] [Indexed: 11/19/2022] Open
Abstract
The ascomycetes Candida albicans, Saccharomyces cerevisiae and Scheffersomyces stipitis metabolize the pentose sugar xylose very differently. S. cerevisiae fails to grow on xylose, while C. albicans can grow, and S. stipitis can both grow and ferment xylose to ethanol. However, all three species contain highly similar genes that encode potential xylose reductases and xylitol dehydrogenases required to convert xylose to xylulose, and xylulose supports the growth of all three fungi. We have created C. albicans strains deleted for the xylose reductase gene GRE3, the xylitol dehydrogenase gene XYL2, as well as the gre3 xyl2 double mutant. As expected, all the mutant strains cannot grow on xylose, while the single gre3 mutant can grow on xylitol. The gre3 and xyl2 mutants are efficiently complemented by the XYL1 and XYL2 from S. stipitis. Intriguingly, the S. cerevisiae GRE3 gene can complement the Cagre3 mutant, while the ScSOR1 gene can complement the Caxyl2 mutant, showing that S. cerevisiae contains the enzymatic capacity for converting xylose to xylulose. In addition, the gre3 xyl2 double mutant of C. albicans is effectively rescued by the xylose isomerase (XI) gene of either Piromyces or Orpinomyces, suggesting that the XI provides an alternative to the missing oxido-reductase functions in the mutant required for the xylose-xylulose conversion. Overall this work suggests that C. albicans strains engineered to lack essential steps for xylose metabolism can provide a platform for the analysis of xylose metabolism enzymes from a variety of species, and confirms that S. cerevisiae has the genetic potential to convert xylose to xylulose, although non-engineered strains cannot proliferate on xylose as the sole carbon source.
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Affiliation(s)
- Doreen Harcus
- Biotechnology Research Institute, National Research Council, Montréal, Quebec, Canada
| | - Daniel Dignard
- Biotechnology Research Institute, National Research Council, Montréal, Quebec, Canada
| | | | - Chris Askew
- Department of Biology, McGill University, Montréal, Quebec, Canada
| | - Martine Raymond
- Institut de Recherche en Immunologie et en Cancérologie (IRIC), Université de Montréal, Montréal, Quebec, Canada
| | - Malcolm Whiteway
- Biotechnology Research Institute, National Research Council, Montréal, Quebec, Canada
- Department of Biology, McGill University, Montréal, Quebec, Canada
- Department of Biology, Concordia University, Montréal, Quebec, Canada
- * E-mail: (MW); (CW)
| | - Cunle Wu
- Biotechnology Research Institute, National Research Council, Montréal, Quebec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Quebec, Canada
- * E-mail: (MW); (CW)
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