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Adamczyk PA, Coradetti ST, Gladden JM. Non-canonical D-xylose and L-arabinose metabolism via D-arabitol in the oleaginous yeast Rhodosporidium toruloides. Microb Cell Fact 2023; 22:145. [PMID: 37537595 PMCID: PMC10398940 DOI: 10.1186/s12934-023-02126-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/17/2023] [Indexed: 08/05/2023] Open
Abstract
R. toruloides is an oleaginous yeast, with diverse metabolic capacities and high tolerance for inhibitory compounds abundant in plant biomass hydrolysates. While R. toruloides grows on several pentose sugars and alcohols, further engineering of the native pathway is required for efficient conversion of biomass-derived sugars to higher value bioproducts. A previous high-throughput study inferred that R. toruloides possesses a non-canonical L-arabinose and D-xylose metabolism proceeding through D-arabitol and D-ribulose. In this study, we present a combination of genetic and metabolite data that refine and extend that model. Chiral separations definitively illustrate that D-arabitol is the enantiomer that accumulates under pentose metabolism. Deletion of putative D-arabitol-2-dehydrogenase (RTO4_9990) results in > 75% conversion of D-xylose to D-arabitol, and is growth-complemented on pentoses by heterologous xylulose kinase expression. Deletion of putative D-ribulose kinase (RTO4_14368) arrests all growth on any pentose tested. Analysis of several pentose dehydrogenase mutants elucidates a complex pathway with multiple enzymes mediating multiple different reactions in differing combinations, from which we also inferred a putative L-ribulose utilization pathway. Our results suggest that we have identified enzymes responsible for the majority of pathway flux, with additional unknown enzymes providing accessory activity at multiple steps. Further biochemical characterization of the enzymes described here will enable a more complete and quantitative understanding of R. toruloides pentose metabolism. These findings add to a growing understanding of the diversity and complexity of microbial pentose metabolism.
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Affiliation(s)
- Paul A Adamczyk
- Agile Biofoundry, Emeryville, CA, USA
- Sandia National Laboratories, Livermore, CA, USA
| | - Samuel T Coradetti
- Agile Biofoundry, Emeryville, CA, USA
- Sandia National Laboratories, Livermore, CA, USA
- United States Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA
| | - John M Gladden
- Agile Biofoundry, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, DOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
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Sanya DRA, Onésime D, Passoth V, Maiti MK, Chattopadhyay A, Khot MB. Yeasts of the Blastobotrys genus are promising platform for lipid-based fuels and oleochemicals production. Appl Microbiol Biotechnol 2021; 105:4879-4897. [PMID: 34110474 DOI: 10.1007/s00253-021-11354-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/29/2021] [Accepted: 05/16/2021] [Indexed: 12/31/2022]
Abstract
Strains of the yeast genus Blastobotrys (subphylum Saccharomycotina) represent a valuable biotechnological resource for basic biochemistry research, single-cell protein, and heterologous protein production processes. Species of this genus are dimorphic, non-pathogenic, thermotolerant, and can assimilate a variety of hydrophilic and hydrophobic substrates. These can constitute a single-cell oil platform in an emerging bio-based economy as oleaginous traits have been discovered recently. However, the regulatory network of lipogenesis in these yeasts is poorly understood. To keep pace with the growing market demands for lipid-derived products, it is critical to understand the lipid biosynthesis in these unconventional yeasts to pinpoint what governs the preferential channelling of carbon flux into lipids instead of the competing pathways. This review summarizes information relevant to the regulation of lipid metabolic pathways and prospects of metabolic engineering in Blastobotrys yeasts for their application in food, feed, and beyond, particularly for fatty acid-based fuels and oleochemicals. KEY POINTS: • The production of biolipids by heterotrophic yeasts is reviewed. • Summary of information concerning lipid metabolism regulation is highlighted. • Special focus on the importance of diacylglycerol acyltransferases encoding genes in improving lipid production is made.
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Affiliation(s)
- Daniel Ruben Akiola Sanya
- Université Paris-Saclay, Institut Micalis, Diversité génomique et fonctionnelle des levures, domaine de Vilvert, 78350, Jouy-en-Josas, France.
| | - Djamila Onésime
- Université Paris-Saclay, Institut Micalis, Diversité génomique et fonctionnelle des levures, domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Volkmar Passoth
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden
| | - Mrinal K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Atrayee Chattopadhyay
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Mahesh B Khot
- Laboratorio de Recursos Renovables, Centro de Biotecnologia, Universidad de Concepcion, Barrio Universitario s/n, Concepcion, Chile
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Li M, Zhu W, Meng Q, Miao M, Zhang T. Characterization of xylitol 4-dehydrogenase from Erwinia aphidicola and its co-expression with NADH oxidase in Bacillus subtilis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Gündüz Ergün B, Hüccetoğulları D, Öztürk S, Çelik E, Çalık P. Established and Upcoming Yeast Expression Systems. Methods Mol Biol 2019; 1923:1-74. [PMID: 30737734 DOI: 10.1007/978-1-4939-9024-5_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.
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Affiliation(s)
- Burcu Gündüz Ergün
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Damla Hüccetoğulları
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Sibel Öztürk
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Eda Çelik
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey
- Bioengineering Division, Institute of Science, Hacettepe University, Ankara, Turkey
| | - Pınar Çalık
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey.
- Industrial Biotechnology and Metabolic Engineering Laboratory, Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara, Turkey.
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Malak A, Baronian K, Kunze G. Blastobotrys (Arxula) adeninivorans: a promising alternative yeast for biotechnology and basic research. Yeast 2016; 33:535-547. [PMID: 27372304 DOI: 10.1002/yea.3180] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 01/31/2023] Open
Abstract
Blastobotrys adeninivorans (syn. Arxula adeninivorans) is a non-conventional, non-pathogenic, imperfect, haploid yeast, belonging to the subphylum Saccharomycotina, which has to date received comparatively little attention from researchers. It possesses unusual properties such as thermo- and osmotolerance, and a broad substrate spectrum. Depending on the cultivation temperature B. (A.) adeninivorans exhibits different morphological forms and various post-translational modifications and protein expression properties that are strongly correlated with the morphology. The genome has been completely sequenced and, in addition, there is a well-developed transformation/expression platform, which makes rapid, simple gene manipulations possible. This yeast species is a very good host for homologous and heterologous gene expression and is also a useful gene donor. Blastobotrys (A.) adeninivorans is able to use a very wide range of substrates as carbon and/or nitrogen sources and is an interesting organism owing to the presence of many metabolic pathways, for example degradation of n-butanol, purines and tannin. In addition, its unusual properties and robustness make it a useful bio-component for whole cell biosensors. There are currently a number of products on the market produced by B. (A.) adeninivorans and further investigation may contribute further innovative solutions for current challenges that exist in the biotechnology industry. Additionally it may become a useful alternative to existing commercial yeast strains and as a model organism in research. In this review we present information relevant to the exploitation of B. (A.) adeninivorans in research and industrial settings. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Anna Malak
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Kim Baronian
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany.
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Ledesma-Amaro R, Lazar Z, Rakicka M, Guo Z, Fouchard F, Coq AMCL, Nicaud JM. Metabolic engineering of Yarrowia lipolytica to produce chemicals and fuels from xylose. Metab Eng 2016; 38:115-124. [PMID: 27396355 DOI: 10.1016/j.ymben.2016.07.001] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/17/2016] [Accepted: 07/05/2016] [Indexed: 11/29/2022]
Abstract
Yarrowia lipolytica is a biotechnological chassis for the production of a range of products, such as microbial oils and organic acids. However, it is unable to consume xylose, the major pentose in lignocellulosic hydrolysates, which are considered a preferred carbon source for bioprocesses due to their low cost, wide abundance and high sugar content. Here, we engineered Y. lipolytica to metabolize xylose to produce lipids or citric acid. The overexpression of xylose reductase and xylitol dehydrogenase from Scheffersomyces stipitis were necessary but not sufficient to permit growth. The additional overexpression of the endogenous xylulokinase enabled identical growth as the wild type strain in glucose. This mutant was able to produce up to 80g/L of citric acid from xylose. Transferring these modifications to a lipid-overproducing strain boosted the production of lipids from xylose. This is the first step towards a consolidated bioprocess to produce chemicals and fuels from lignocellulosic materials.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Zbigniew Lazar
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego Str. 37/41, 51-630 Wrocław, Poland
| | - Magdalena Rakicka
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego Str. 37/41, 51-630 Wrocław, Poland
| | - Zhongpeng Guo
- LISBP-Biocatalysis Group, INSA/INRA, Université de Toulouse, 135 Avenue de Rangueil, 31077 Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France; CNRS, UMR5504, 31400 Toulouse, France
| | - Florian Fouchard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Yamasaki-Yashiki S, Komeda H, Hoshino K, Asano Y. Molecular analysis of NAD⁺-dependent xylitol dehydrogenase from the zygomycetous fungus Rhizomucor pusillus and reversal of the coenzyme preference. Biosci Biotechnol Biochem 2014; 78:1943-53. [PMID: 25082263 DOI: 10.1080/09168451.2014.943646] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The zygomycetous fungus Rhizomucor pusillus NBRC 4578 is able to ferment not only d-glucose but also d-xylose into ethanol. Xylitol dehydrogenase from R. pusillus NBRC 4578 (RpXDH), which catalyzes the second step of d-xylose metabolism, was purified, and its enzymatic properties were characterized. The purified RpXDH preferred NAD(+) as its coenzyme and showed substrate specificity for xylitol, d-sorbitol, and ribitol. cDNA cloning of xyl2 gene encoding RpXDH revealed that the gene included a coding sequence of 1,092 bp with a molecular mass of 39,185 kDa. Expression of the xyl2 in R. pusillus NBRC 4578 was induced by d-xylose, and the expression levels were increased with accumulation of xylitol. The xyl2 gene was expressed in Escherichia coli, and coenzyme preference of the recombinant RpXDH was reversed from NAD(+) to NADP(+) in the double mutant D205A/I206R by site-directed mutagenesis.
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8
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Gruber C, Krahulec S, Nidetzky B, Kratzer R. Harnessing Candida tenuis and Pichia stipitis in whole-cell bioreductions of o-chloroacetophenone: stereoselectivity, cell activity, in situ substrate supply and product removal. Biotechnol J 2013; 8:699-708. [PMID: 23589466 DOI: 10.1002/biot.201200322] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 03/15/2013] [Accepted: 04/10/2013] [Indexed: 11/10/2022]
Abstract
Generally, recombinant and native microorganisms can be employed as whole-cell catalysts. The application of native hosts, however, shortens the process development time by avoiding multiple steps of strain construction. Herein, we studied the NAD(P)H-dependent reduction of o-chloroacetophenone by isolated xylose reductases and their native hosts Candida tenuis and Pichia stipitis. The natural hosts were benchmarked against Escherichia coli strains co-expressing xylose reductase and a dehydrogenase for co-enzyme recycling. Xylose-grown cells of C. tenuis and P. stipitis displayed specific o-chloroacetophenone reductase activities of 366 and 90 U gCDW (-1) , respectively, in the cell-free extracts. Fresh biomass was employed in batch reductions of 100 mM o-chloroacetophenone using glucose as co-substrate. Reaction stops at a product concentration of about 15 mM, which suggests sensitivity of the catalyst towards the formed product. In situ substrate supply and product removal by the addition of 40% hexane increased catalyst stability. Optimisation of the aqueous phase led to a (S)-1-(2-chlorophenyl)ethanol concentration of 71 mM (ee > 99.9%) obtained with 44 gCDW L(-1) of C. tenuis. The final difference in productivities between native C. tenuis and recombinant E. coli was < 1.7-fold. The optically pure product is a required key intermediate in the synthesis of a new class of chemotherapeutic substances (polo-like kinase 1 inhibitors).
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Affiliation(s)
- Christoph Gruber
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology TUG, A-8010 Graz, Austria
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Sędzielewska KA, Böer E, Bellebna C, Wartmann T, Bode R, Melzer M, Baronian K, Kunze G. Role of the AFRD1-encoded fumarate reductase in hypoxia and osmotolerance in Arxula adeninivorans. FEMS Yeast Res 2012; 12:924-37. [PMID: 22900669 DOI: 10.1111/j.1567-1364.2012.00842.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 07/16/2012] [Accepted: 08/07/2012] [Indexed: 11/30/2022] Open
Abstract
Fumarate reductase is an enzyme involved in maintaining redox balance through regeneration of reduced cofactors during oxygen deficiency conditions. This work reports the identification and characterization of the gene and its promoter and terminator elements that encodes cytosolic fumarate reductase enzyme in the nonconventional yeast, Arxula adeninivorans. The gene harbours an ORF of 1446 bp, encoding a 482-amino acid protein. The deduced amino acid sequence is similar to those of fumarate reductases from other yeast and fungi, such as the two fumarate reductases of Saccharomyces cerevisiae, Frd1p (44%) and Osm1p (41%). This enzyme is located in the cytosol and has a pH optimum of ca. 7.5 and a Michaelis constant (K(M)) of 2.9 mM with fumarate as the substrate. Expression of AFRD1 is regulated by the cultivation conditions. A shift from NaCl-free to NaCl-supplemented media and aerobic to hypoxic growth conditions leads to reduced AFRD1 transcription levels, but not to alteration in the concentration of Afrd1p. The functional analyses of Afrd1p were performed in A. adeninivorans and S. cerevisiae disruption mutants. The A. adeninivorans fumarate reductase is capable of functional complementation of the missing S. cerevisiae genes during anoxia; however, it is not involved in yeast growth under osmotic stress.
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Affiliation(s)
- Kinga A Sędzielewska
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
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Production of recombinant proteins by yeast cells. Biotechnol Adv 2012; 30:1108-18. [DOI: 10.1016/j.biotechadv.2011.09.011] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/12/2011] [Accepted: 09/17/2011] [Indexed: 01/14/2023]
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Molecular cloning, characterization, and engineering of xylitol dehydrogenase from Debaryomyces hansenii. Appl Microbiol Biotechnol 2012; 97:1613-23. [DOI: 10.1007/s00253-012-4020-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 03/11/2012] [Accepted: 03/12/2012] [Indexed: 01/28/2023]
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Cloning and characterization of thermotolerant xylitol dehydrogenases from yeast Pichia angusta. Appl Microbiol Biotechnol 2010; 88:1311-20. [DOI: 10.1007/s00253-010-2818-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Revised: 07/27/2010] [Accepted: 08/02/2010] [Indexed: 10/19/2022]
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Tiwari MK, Moon HJ, Jeya M, Lee JK. Cloning and characterization of a thermostable xylitol dehydrogenase from Rhizobium etli CFN42. Appl Microbiol Biotechnol 2010; 87:571-81. [PMID: 20177886 DOI: 10.1007/s00253-010-2478-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 01/26/2010] [Accepted: 01/27/2010] [Indexed: 11/29/2022]
Abstract
An NAD(+)-dependent xylitol dehydrogenase from Rhizobium etli CFN42 (ReXDH) was cloned and overexpressed in Escherichia coli. The DNA sequence analysis revealed an open reading frame of 1,044 bp, capable of encoding a polypeptide of 347 amino acid residues with a calculated molecular mass of 35,858 Da. The ReXDH protein was purified as an active soluble form using GST affinity chromatography. The molecular mass of the purified enzyme was estimated to be approximately 34 kDa by sodium dodecyl sulfate-polyacrylamide gel and approximately 135 kDa with gel filtration chromatography, suggesting that the enzyme is a homotetramer. Among various polyols, xylitol was the preferred substrate of ReXDH with a K (m) = 17.9 mM and k(cat) /K (m) = 0.5 mM(-1) s(-1) for xylitol. The enzyme had an optimal pH and temperature of 9.5 and 70 degrees C, respectively. Heat inactivation studies revealed a half life of the ReXDH at 40 degrees C of 120 min and a half denaturation temperature (T (1/2)) of 53.1 degrees C. ReXDH showed the highest optimum temperature and thermal stability among the known XDHs. Homology modeling and sequence analysis of ReXDH shed light on the factors contributing to the high thermostability of ReXDH. Although XDHs have been characterized from several other sources, ReXDH is distinguished from other XDHs by its high thermostability.
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Affiliation(s)
- Manish Kumar Tiwari
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 143-701, Korea
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Cloning, overexpression, purification, and site-directed mutagenesis of xylitol-2-dehydrogenase from Candida albicans. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2009.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Böer E, Bode R, Mock HP, Piontek M, Kunze G. Atan1p-an extracellular tannase from the dimorphic yeast Arxula adeninivorans: molecular cloning of the ATAN1 gene and characterization of the recombinant enzyme. Yeast 2009; 26:323-37. [PMID: 19387973 DOI: 10.1002/yea.1669] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The tannase-encoding Arxula adeninivorans gene ATAN1 was isolated from genomic DNA by PCR, using as primers oligonucleotide sequences derived from peptides obtained after tryptic digestion of the purified tannase protein. The gene harbours an ORF of 1764 bp, encoding a 587-amino acid protein, preceded by an N-terminal secretion sequence comprising 28 residues. The deduced amino acid sequence was similar to those of tannases from Aspergillus oryzae (50% identity), A. niger (48%) and putative tannases from A. fumigatus (52%) and A. nidulans (50%). The sequence contains the consensus pentapeptide motif (-Gly-X-Ser-X-Gly-) which forms part of the catalytic centre of serine hydrolases. Expression of ATAN1 is regulated by the carbon source. Supplementation with tannic acid or gallic acid leads to induction of ATAN1, and accumulation of the native tannase enzyme in the medium. The enzymes recovered from both wild-type and recombinant strains were essentially indistinguishable. A molecular mass of approximately 320 kDa was determined, indicating that the native, glycosylated tannase consists of four identical subunits. The enzyme has a temperature optimum at 35-40 degrees C and a pH optimum at approximately 6.0. The enzyme is able to remove gallic acid from both condensed and hydrolysable tannins. The wild-type strain LS3 secreted amounts of tannase equivalent to 100 U/l under inducing conditions, while the transformant strain, which overexpresses the ATAN1 gene from the strong, constitutively active A. adeninivorans TEF1 promoter, produced levels of up to 400 U/l when grown in glucose medium in shake flasks.
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Affiliation(s)
- Erik Böer
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
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Böer E, Schröter A, Bode R, Piontek M, Kunze G. Characterization and expression analysis of a gene cluster for nitrate assimilation from the yeast Arxula adeninivorans. Yeast 2009; 26:83-93. [PMID: 19191338 DOI: 10.1002/yea.1653] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In Arxula adeninivorans nitrate assimilation is mediated by the combined actions of a nitrate transporter, a nitrate reductase and a nitrite reductase. Single-copy genes for these activities (AYNT1, AYNR1, AYNI1, respectively) form a 9103 bp gene cluster localized on chromosome 2. The 3210 bp AYNI1 ORF codes for a protein of 1070 amino acids, which exhibits a high degree of identity to nitrite reductases from the yeasts Pichia anomala (58%), Hansenula polymorpha (58%) and Dekkera bruxellensis (54%). The second ORF (AYNR1, 2535 bp) encodes a nitrate reductase of 845 residues that shows significant (51%) identity to nitrate reductases of P. anomala and H. polymorpha. The third ORF in the cluster (AYNT1, 1518 bp) specifies a nitrate transporter with 506 amino acids, which is 46% identical to that of H. polymorpha. The three genes are independently expressed upon induction with NaNO(3). We quantitatively analysed the promoter activities by qRT-PCR and after fusing individual promoter fragments to the phytase (phyK) gene from Klebsiella sp. ASR1. The AYNI1 promoter was found to exhibit the highest activity, followed by the AYNT1 and AYNR1 elements. Direct measurements of nitrate and nitrite reductase activities performed after induction with NaNO(3) are compatible with these results. Both enzymes show optimal activity at around 42 degrees C and near-neutral pH, and require FAD as a co-factor and NADPH as electron donor.
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Affiliation(s)
- Erik Böer
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
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Metabolic engineering of the initial stages of xylose catabolism in yeast for the purpose of constructing efficient producers of ethanol from lignocellulosics. CYTOL GENET+ 2008. [DOI: 10.1007/s11956-008-2011-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Steinborn G, Gellissen G, Kunze G. A novel vector element providing multicopy vector integration in Arxula adeninivorans. FEMS Yeast Res 2007; 7:1197-205. [PMID: 17655689 DOI: 10.1111/j.1567-1364.2007.00280.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
An Arxula adeninivorans vector element has been identified that provides multicopy integration in an atrp1 host strain. The element consists of the ATRP1 selection marker fused to a newly generated truncated ALEU2 promoter of 53 bp. In the described example eight copies of an amyA expression vector encoding heterologous alpha-amylase from Bacillus amyloliquefaciens are integrated in the genome of the recombinant strain instead of a single copy observed when using the ATRP1 element with the complete promoter. The high copy number results in strains of superior productivity for a secreted recombinant alpha-amylase. The vector design enables the integration of a small vector fragment that consists of yeast DNA only providing high transformation frequencies and a high mitotic stability.
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Affiliation(s)
- Gerhard Steinborn
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
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Fiki AE, Metabteb GE, Bellebna C, Wartmann T, Bode R, Gellissen G, Kunze G. The Arxula adeninivorans ATAL gene encoding transaldolase-gene characterization and biotechnological exploitation. Appl Microbiol Biotechnol 2007; 74:1292-9. [PMID: 17221198 DOI: 10.1007/s00253-006-0785-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 11/28/2006] [Accepted: 11/28/2006] [Indexed: 11/28/2022]
Abstract
The yeast Arxula adeninivorans provides an attractive expression platform and can be exploited as gene source for biotechnologically interesting proteins. In the following study, a striking example for the combination of both aspects is presented. The transaldolase-encoding A. adeninivorans ATAL gene, including its promoter and terminator elements, was isolated and characterized. The gene includes a coding sequence of 963 bp encoding a putative 321 amino acid protein of 35.0 kDa. The enzyme characteristics analyzed from isolates of native strains and recombinant strains overexpressing the ATAL gene revealed a molecular mass of ca. 140 kDa corresponding to a tetrameric structure, a pH optimum of ca. 5.5, and a temperature optimum of 20 degrees C. The preferred substrates for the enzyme include D-erythrose-4-phosphate and D-fructose-6-phosphate, whereas D-glyceraldehyde is not converted. The ATAL expression level under salt-free conditions was observed to increase in media supplemented with 5% NaCl rendering the ATAL promoter attractive for moderate heterologous gene expression under high-salt conditions. Its suitability was assessed for the expression of a human serum albumin (HSA) reporter gene.
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Affiliation(s)
- Ayman El Fiki
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstr. 3, 06466 Gatersleben, Germany
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Steinborn G, Böer E, Scholz A, Tag K, Kunze G, Gellissen G. Application of a wide-range yeast vector (CoMed) system to recombinant protein production in dimorphic Arxula adeninivorans, methylotrophic Hansenula polymorpha and other yeasts. Microb Cell Fact 2006; 5:33. [PMID: 17105649 PMCID: PMC1654170 DOI: 10.1186/1475-2859-5-33] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 11/14/2006] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Yeasts provide attractive expression platforms in combining ease of genetic manipulation and fermentation of a microbial organism with the capability to secrete and to modify proteins according to a general eukaryotic scheme. However, early restriction to a single yeast platform can result in costly and time-consuming failures. It is therefore advisable to assess several selected systems in parallel for the capability to produce a particular protein in desired amounts and quality. A suitable vector must contain a targeting sequence, a promoter element and a selection marker that function in all selected organisms. These criteria are fulfilled by a wide-range integrative yeast expression vector (CoMed) system based on A. adeninivorans- and H. polymorpha-derived elements that can be introduced in a modular way. RESULTS The vector system and a selection of modular elements for vector design are presented. Individual single vector constructs were used to transform a range of yeast species. Various successful examples are described. A vector with a combination of an rDNA sequence for genomic targeting, the E. coli-derived hph gene for selection and the A. adeninivorans-derived TEF1 promoter for expression control of a GFP (green fluorescent protein) gene was employed in a first example to transform eight different species including Hansenula polymorpha, Arxula adeninivorans and others. In a second example, a vector for the secretion of IL-6 was constructed, now using an A. adeninivorans-derived LEU2 gene for selection of recombinants in a range of auxotrophic hosts. In this example, differences in precursor processing were observed: only in A. adeninivorans processing of a MFalpha1/IL-6 fusion was performed in a faithful way. CONCLUSION rDNA targeting provides a tool to co-integrate up to 3 different expression plasmids by a single transformation step. Thus, a versatile system is at hand that allows a comparative assessment of newly introduced metabolic pathways in several organisms or a comparative co-expression of bottleneck genes in cases where production or secretion of a certain product is impaired.
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Affiliation(s)
- Gerhard Steinborn
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstr. 3, 06466 Gatersleben, Germany
| | - Erik Böer
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstr. 3, 06466 Gatersleben, Germany
| | - Anja Scholz
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstr. 3, 06466 Gatersleben, Germany
| | - Kristina Tag
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstr. 3, 06466 Gatersleben, Germany
| | - Gotthard Kunze
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstr. 3, 06466 Gatersleben, Germany
| | - Gerd Gellissen
- PharmedArtis GmbH, Forckenbeckstr. 6, D-52074 Aachen, Germany
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Kaur P, Lingner A, Singh B, Böer E, Polajeva J, Steinborn G, Bode R, Gellissen G, Satyanarayana T, Kunze G. APHO1 from the yeast Arxula adeninivorans encodes an acid phosphatase of broad substrate specificity. Antonie van Leeuwenhoek 2006; 91:45-55. [PMID: 17016743 DOI: 10.1007/s10482-006-9094-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Accepted: 05/18/2006] [Indexed: 10/24/2022]
Abstract
The extracellular acid phosphatase-encoding Arxula adeninivorans APHO1 gene was isolated using degenerated specific oligonucleotide primers in a PCR screening approach. The gene harbours an ORF of 1449 bp encoding a protein of 483 amino acids with a calculated molecular mass of 52.4 kDa. The sequence includes an N-terminal secretion sequence of 17 amino acids. The deduced amino acid sequence exhibits 54% identity to phytases from Aspergillus awamori, Asp. niger and Asp. ficuum and a more distant relationship to phytases of the yeasts Candida albicans and Debaryomyces hansenii (36-39% identity). The sequence contains the phosphohistidine signature and the conserved active site sequence of acid phosphatases. APHO1 expression is induced under conditions of phosphate limitation. Enzyme isolates from wild and recombinant strains with the APHO1 gene expressed under control of the strong A. adeninivorans-derived TEF1 promoter were characterized. For both proteins, a molecular mass of approx. 350 kDa, corresponding to a hexameric structure, a pH optimum of pH 4.8 and a temperature optimum of 60 degrees C were determined. The preferred substrates include p-nitrophenyl-phosphate, pyridoxal-5-phosphate, 3-indoxyl-phosphate, 1-naphthylphosphate, ADP, glucose-6-phosphate, sodium-pyrophosphate, and phytic acid. Thus the enzyme is a secretory acid phosphatase with phytase activity and not a phytase as suggested by strong homology to such enzymes.
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Affiliation(s)
- Parvinder Kaur
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India
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Lima LHA, Pinheiro CGDA, de Moraes LMP, de Freitas SM, Torres FAG. Xylitol dehydrogenase from Candida tropicalis: molecular cloning of the gene and structural analysis of the protein. Appl Microbiol Biotechnol 2006; 73:631-9. [PMID: 16896602 DOI: 10.1007/s00253-006-0525-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 05/30/2006] [Accepted: 06/01/2006] [Indexed: 11/30/2022]
Abstract
Yeasts can metabolize xylose by the action of two key enzymes: xylose reductase and xylitol dehydrogenase. In this work, we present data concerning the cloning of the XYL2 gene encoding xylitol dehydrogenase from the yeast Candida tropicalis. The gene is present as a single copy in the genome and is controlled at the transcriptional level by the presence of the inducer xylose. XYL2 was functionally tested by heterologous expression in Saccharomyces cerevisiae to develop a yeast strain capable of producing ethanol from xylose. Structural analysis of C. tropicalis xylitol dehydrogenase, Xyl2, suggests that it is a member of the medium-chain dehydrogenase (MDR) family. This is supported by the presence of the amino acid signature [GHE]xx[G]xxxxx[G]xx[V] in its primary sequence and a typical alcohol dehydrogenase Rossmann fold pattern composed by NAD(+) and zinc ion binding domains.
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Steinborn G, Wartmann T, Gellissen G, Kunze G. Construction of an Arxula adeninivorans host-vector system based on trp1 complementation. J Biotechnol 2006; 127:392-401. [PMID: 16934902 DOI: 10.1016/j.jbiotec.2006.07.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 07/12/2006] [Accepted: 07/25/2006] [Indexed: 11/19/2022]
Abstract
A host/vector expression system based on an Arxula adeninivorans Delta atrp1 gene disruption mutant has been constructed. For this purpose the ATRP1 gene encoding a phosphoribosyl anthranilate isomerase was isolated from the yeast A. adeninivorans and its genome locus was characterized. The Delta atrp1 mutant was generated applying an amplified DNA fragment containing the ALEU2m gene flanked by ATRP1 gene sequences of some 750 bp. The generated auxotrophic host strain was transformed with the plasmid pAL-ATRP1-amyA, which contains the ATRP1 gene as selection marker and the 25S rDNA for targeting. For expression assessment, the plasmid was equipped with an expression cassette consisting of the Bacillus amyloliquefaciens-derived amyA gene fused to the constitutive A. adeninivorans-derived TEF1 promoter and Saccharomyces cerevisiae-derived PHO5 terminator. Transformants contained a single chromosomal copy of the heterologous DNA and were found to be mitotically stable. In initial fermentation trials on a 200 ml shake flask scale maximal alpha-amylase product levels of ca. 300 nkat ml(-1) were observed after 72 h of cultivation with more than 95% of the recombinant alpha-amylase accumulated in the culture medium.
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Affiliation(s)
- Gerhard Steinborn
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstr. 3, D-06466 Gatersleben, Germany
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Ko BS, Jung HC, Kim JH. Molecular Cloning and Characterization of NAD+-Dependent Xylitol Dehydrogenase fromCandida tropicalisATCC 20913. Biotechnol Prog 2006. [DOI: 10.1002/bp060263i] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Steinborn G, Gellissen G, Kunze G. Assessment of Hansenula polymorpha and Arxula adeninivorans-derived rDNA-targeting elements for the design of Arxula adeninivorans expression vectors. FEMS Yeast Res 2005; 5:1047-54. [PMID: 16144776 DOI: 10.1016/j.femsyr.2005.07.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Revised: 06/18/2005] [Accepted: 07/11/2005] [Indexed: 12/16/2022] Open
Abstract
Different targeting sequences derived from the Arxula adeninivorans and Hansenula polymorpha rDNA clusters were tested in A. adeninivorans integration/expression vectors. For element identification, the rDNA unit of A. adeninivorans (accession number ) was first isolated and characterized in addition to the known H. polymorpha unit. The rDNA is a cluster of some forty 7653-bp units without the 5S rDNA gene. The selected elements were integrated into a set of A. adeninivorans expression/integration vectors harbouring a TEF1 promoter - amyA ORF - PHO5 terminator sequence as reporter gene. No differences in mitotic stability, copy number and transformation frequency were observed. All transformants harboured a single copy integrated into the rDNA by a homologous recombination. In contrast, the choice of the rDNA targeting sequence was found to be of impact on productivity. Use of ETS-18S-5.8S fragments from both organisms resulted in a more than 50% increase in comparison to the use of other elements, independent of the orientation within the vector.
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Affiliation(s)
- Gerhard Steinborn
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstr. 3, D-06466 Gatersleben, Germany
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Gellissen G, Kunze G, Gaillardin C, Cregg JM, Berardi E, Veenhuis M, van der Klei I. New yeast expression platforms based on methylotrophic Hansenula polymorpha and Pichia pastoris and on dimorphic Arxula adeninivorans and Yarrowia lipolytica - a comparison. FEMS Yeast Res 2005; 5:1079-96. [PMID: 16144775 DOI: 10.1016/j.femsyr.2005.06.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Revised: 06/09/2005] [Accepted: 06/09/2005] [Indexed: 11/29/2022] Open
Abstract
Yeasts combine the ease of genetic manipulation and fermentation of a microbial organism with the capability to secrete and to modify proteins according to a general eukaryotic scheme. Yeasts thus provide attractive platforms for the production of recombinant proteins. Here, four important species are presented and compared: the methylotrophic Hansenula polymorpha and Pichia pastoris, distinguished by an increasingly large track record as industrial platforms, and the dimorphic species Arxula adeninivorans and Yarrrowia lipolytica, not yet established as industrial platforms, but demonstrating promising technological potential, as discussed in this article.
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Affiliation(s)
- Gerd Gellissen
- PharmedArtis GmbH, Forckenbeckstr. 6, 52074 Aachen, Germany
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Böer E, Mock HP, Bode R, Gellissen G, Kunze G. An extracellular lipase from the dimorphic yeastArxula adeninivorans: molecular cloning of theALIP1 gene and characterization of the purified recombinant enzyme. Yeast 2005; 22:523-35. [PMID: 15942926 DOI: 10.1002/yea.1230] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The lipase-encoding Arxula adeninivorans ALIP1 gene was isolated using fragments of lipase isolates obtained by trypsin digestion for the definition of oligonucleotide primers in a PCR screening approach. The gene harbours an ORF of 1347 bp encoding a 420 amino acid protein of some 50 kDa preceded by an N-terminal 28 prepro-secretion sequence. The deduced amino acid sequence was found to be similar to the lipases from Candida albicans and C. parapsilosis (34-38% identity) and more distantly related to other lipases. The sequence contains the consensus pentapeptide motif (-Gly-X-Ser-X-Gly-) that forms a part of the interfacial lipid recognition site in lipases. The expression of the gene is regulated by carbon source. In media supplemented with Tween 20, induction of the ALIP1 gene and accumulation of the encoded lipase in the medium is observed, thus demonstrating gene regulation by lipophilic compounds. The enzyme characteristics are analysed from isolates of native strains as well as from those of recombinant strains expressing the ALIP1 gene under control of the strong A. adeninivorans-derived TEF1 promoter. For both proteins a molecular mass of 100 kDa was determined, indicating a dimeric structure, a pH optimum at pH 7.5 and a temperature optimum at 30 degrees C. The enzyme hydrolyses all ester bonds in all triglyceride substrates tested. Middle-sized chain fatty acids are more efficiently hydrolysed than short- and long-chain fatty acids, with the highest activity on C8/C10 fatty acid esters pNP-caprylate, pNP-caprate and tricaprylin.
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Affiliation(s)
- Erik Böer
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse 3, D-06466 Gatersleben, Germany
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