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Sibirny AA. Metabolic engineering of non-conventional yeasts for construction of the advanced producers of biofuels and high-value chemicals. BBA ADVANCES 2022; 3:100071. [PMID: 37082251 PMCID: PMC10074886 DOI: 10.1016/j.bbadva.2022.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Non-conventional yeasts, i.e. yeasts different from Saccharomyces cerevisiae, represent heterogenous group of unicellular fungi consisting of near 1500 species. Some of these species have interesting and sometimes unique properties like ability to grow on methanol, n-alkanes, ferment pentose sugars xylose and l-arabinose, grow at high temperatures (50°С and more), overproduce riboflavin (vitamin B2) and others. These unique properties are important for development of basic science; moreover, some of them possess also significant applied interest for elaboration of new biotechnologies. Current paper represents review of the recent own results and of those of other authors in the field of non-conventional yeast study for construction of the advanced producers of biofuels (ethanol, isobutanol) from lignocellulosic sugars glucose and xylose or crude glycerol (Ogataea polymorpha, Magnusiomyces magnusii) and vitamin B2 (riboflavin) from glucose and cheese whey (Candida famata).
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Affiliation(s)
- Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, Lviv 79005 Ukraine
- University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601 Poland
- Corresponding author at: Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, Lviv 79005 Ukraine.
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Co-Overexpression of RIB1 and RIB6 Increases Riboflavin Production in the Yeast Candida famata. FERMENTATION 2022. [DOI: 10.3390/fermentation8040141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Riboflavin or vitamin B2 is a water-soluble vitamin and a precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which play a key role as enzyme cofactors in energy metabolism. Candida famata yeast is a promising producer of riboflavin, as it belongs to the group of so-called flavinogenic yeasts, capable of riboflavin oversynthesis under conditions of iron starvation. The role of the particular structural genes in the limitation of riboflavin oversynthesis is not known. To study the impact of overexpression of the structural genes of riboflavin synthesis on riboflavin production, a set of plasmids containing genes RIB1, RIB6, and RIB7 in different combinations was constructed. The transformants of the wild-type strain of C. famata, as well as riboflavin overproducer, were obtained, and the synthesis of riboflavin was studied. It was found that overexpression of RIB1 and RIB6 genes coding for enzymes GTP cyclohydrolase II and 3,4-dihydroxy-2-butanone-4-phosphate synthase, which catalase the initial steps of riboflavin synthesis, elevated riboflavin production by 13–28% relative to the parental riboflavin-overproducing strains.
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Palma M, Mondo S, Pereira M, Vieira É, Grigoriev IV, Sá-Correia I. Genome Sequence and Analysis of the Flavinogenic Yeast Candida membranifaciens IST 626. J Fungi (Basel) 2022; 8:jof8030254. [PMID: 35330255 PMCID: PMC8955749 DOI: 10.3390/jof8030254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 02/04/2023] Open
Abstract
The ascomycetous yeast Candida membranifaciens has been isolated from diverse habitats, including humans, insects, and environmental sources, exhibiting a remarkable ability to use different carbon sources that include pentoses, melibiose, and inulin. In this study, we isolated four C. membranifaciens strains from soil and investigated their potential to overproduce riboflavin. C. membranifaciens IST 626 was found to produce the highest concentrations of riboflavin. The volumetric production of this vitamin was higher when C. membranifaciens IST 626 cells were cultured in a commercial medium without iron and when xylose was the available carbon source compared to the same basal medium with glucose. Supplementation of the growth medium with 2 g/L glycine favored the metabolization of xylose, leading to biomass increase and consequent enhancement of riboflavin volumetric production that reached 120 mg/L after 216 h of cultivation. To gain new insights into the molecular basis of riboflavin production and carbon source utilization in this species, the first annotated genome sequence of C. membranifaciens is reported in this article, as well as the result of a comparative genomic analysis with other relevant yeast species. A total of 5619 genes were predicted to be present in C. membranifaciens IST 626 genome sequence (11.5 Mbp). Among them are genes involved in riboflavin biosynthesis, iron homeostasis, and sugar uptake and metabolism. This work put forward C. membranifaciens IST 626 as a riboflavin overproducer and provides valuable molecular data for future development of superior producing strains capable of using the wide range of carbon sources, which is a characteristic trait of the species.
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Affiliation(s)
- Margarida Palma
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (M.P.); (É.V.); (I.S.-C.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Correspondence:
| | - Stephen Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.M.); (I.V.G.)
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Mariana Pereira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (M.P.); (É.V.); (I.S.-C.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Érica Vieira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (M.P.); (É.V.); (I.S.-C.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.M.); (I.V.G.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (M.P.); (É.V.); (I.S.-C.)
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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Fedorovych DV, Dmytruk KV, Sibirny AA. Recent Advances in Construction of the Efficient Producers of Riboflavin and Flavin Nucleotides (FMN, FAD) in the Yeast Candida famata. Methods Mol Biol 2021; 2280:15-30. [PMID: 33751426 DOI: 10.1007/978-1-0716-1286-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The approaches used by the authors to design the Candida famata strains capable to overproduce riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) are described. The metabolic engineering approaches include overexpression of SEF1 gene encoding positive regulator of riboflavin biosynthesis, IMH3 (coding for IMP dehydrogenase) orthologs from another species of flavinogenic yeast Debaryomyces hansenii, and the homologous genes RIB1 and RIB7 encoding GTP cyclohydrolase II and riboflavin synthase, the first and the last enzymes of riboflavin biosynthesis pathway, respectively. Overexpression of the above mentioned genes in the genetically stable riboflavin overproducer AF-4 obtained by classical selection resulted in fourfold increase of riboflavin production in shake flask experiments.Overexpression of engineered enzymes phosphoribosyl pyrophosphate synthetase and phosphoribosyl pyrophosphate amidotransferase catalyzing the initial steps of purine nucleotide biosynthesis enhances riboflavin synthesis in the flavinogenic yeast C. famata even more.Recombinant strains of C. famata containing FMN1 gene from D. hansenii encoding riboflavin kinase under control of the strong constitutive TEF1 promoter were constructed. Overexpression of the FMN1 gene in the riboflavin-producing mutant led to the 30-fold increase of the riboflavin kinase activity and 400-fold increase of FMN production in the resulting recombinant strains which reached maximally 318.2 mg/L.FAD overproducing strains of C. famata were also constructed. This was achieved by overexpression of FAD1 gene from D. hansenii in C. famata FMN overproducing strain. The 7- to 15-fold increase in FAD synthetase activity as compared to the wild-type strain and FAD accumulation into cultural medium were observed. The maximal FAD titer 451.5 mg/L was achieved.
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Affiliation(s)
- Dariya V Fedorovych
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Lviv, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Lviv, Ukraine
| | - Andriy A Sibirny
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Lviv, Ukraine.
- Department of Microbiology and Biotechnology, University of Rzeszow, Rzeszow, Poland.
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Overexpression of Riboflavin Excretase Enhances Riboflavin Production in the Yeast Candida famata. Methods Mol Biol 2021. [PMID: 33751427 DOI: 10.1007/978-1-0716-1286-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Many microorganisms are capable of riboflavin oversynthesis and accumulation in a medium, suggesting that they efficiently excrete riboflavin. The mechanisms of riboflavin efflux in microorganisms remain elusive. Candida famata are representatives of a group of so-called flavinogenic yeast species that overproduce riboflavin (vitamin B2) in response to iron limitation. The riboflavin overproducers of this yeast species have been obtained by classical mutagenesis and metabolic engineering. Overproduced riboflavin accumulates in the cultural medium rather than in the cells suggesting existence of the special mechanisms involved in riboflavin excretion. The appropriate protein and gene have not been identified in yeasts till recently. At the same time, the gene BCRP (breast cancer resistance protein) has been identified in mammal mammary glands. Several homologs of the mammal BCRP gene encoding putative riboflavin efflux protein (excretase) were identified in the flavinogenic yeasts Debaryomyces hansenii and C. famata. Here we evaluate the yeast homologs of BCRP with respect to improvement of a riboflavin production by C. famata. The closest homologs from D. hansenii or C. famata were expressed under the control of TEF1 promoter of these yeasts in the wild-type and riboflavin-overproducing strains of C. famata. Resulted transformants overexpressed the corresponding genes (designated as DhRFE and CfRFE) and produced 1.4- to 6-fold more riboflavin as compared to the corresponding parental strains. They also were characterized by overexpression of RIB1 and RIB6 genes which encode the first and the last structural enzymes of riboflavin synthesis and exhibited elevated specific activity of GTP cyclohydrolase II. Thus, overexpression of yeast homolog of mammal gene BCRP may be useful to increase the riboflavin yield in a riboflavin production process using a recombinant overproducing C. famata strain or other flavinogenic microorganisms.
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Fedorovych D, Boretsky V, Pynyaha Y, Bohovych I, Boretsky Y, Sibirny A. Cloning of Genes Sef1 and Tup1 Encoding Transcriptional Activator and Global Repressor in the Flavinogenic Yeast Meyerozyma (Candida, Pichia) guilliermondii. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720050072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Petrovska Y, Lyzak O, Dmytruk K, Sibirny A. Effect of Gene SFU1 on Riboflavin Synthesis in Flavinogenic Yeast Candida famata. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720050060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Andreieva Y, Lyzak O, Liu W, Kang Y, Dmytruk K, Sibirny A. SEF1 and VMA1 Genes Regulate Riboflavin Biosynthesis in the Flavinogenic Yeast Candida Famata. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720050023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Molecular Elucidation of Riboflavin Production and Regulation in Candida albicans, toward a Novel Antifungal Drug Target. mSphere 2020; 5:5/4/e00714-20. [PMID: 32759338 PMCID: PMC7407072 DOI: 10.1128/msphere.00714-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Candida albicans is an important fungal pathogen causing common superficial infections as well as invasive diseases with an extremely high morbidity and mortality. Antifungal therapies are limited in efficiency and availability. In this research, we describe the regulation of riboflavin production in C. albicans. Since riboflavin biosynthesis is essential to this organism, we can appreciate that targeting it would be a promising new strategy to combat these fungal infections. We provide evidence that one particular enzyme in the production process, CaRib1, would be most promising as an antifungal drug target, as it plays a central role in regulation and proves to be essential in a mouse model of systemic infection. Candida albicans is a major cause of fungal infections, both superficial and invasive. The economic costs as well as consequences for patient welfare are substantial. Only a few treatment options are available due to the high resemblance between fungal targets and host molecules, as both are eukaryotes. Riboflavin is a yellow pigment, also termed vitamin B2. Unlike animals, fungi can synthesize this essential component themselves, thereby leading us to appreciate that targeting riboflavin production is a promising novel strategy against fungal infections. Here, we report that the GTP cyclohydrolase encoded by C. albicansRIB1 (CaRIB1) is essential and rate-limiting for production of riboflavin in the fungal pathogen. We confirm the high potential of CaRib1 as an antifungal drug target, as its deletion completely impairs in vivo infectibility by C. albicans in model systems. Furthermore, the stimulating effect of iron deprivation and PKA activation on riboflavin production seems to involve CaRib1 and the upstream transcription factor CaSef1. Gathering insights in the synthesis mechanism of riboflavin in pathogenic fungi, like C. albicans, will allow us to design a novel strategy and specifically target this process to combat fungal infections. IMPORTANCECandida albicans is an important fungal pathogen causing common superficial infections as well as invasive diseases with an extremely high morbidity and mortality. Antifungal therapies are limited in efficiency and availability. In this research, we describe the regulation of riboflavin production in C. albicans. Since riboflavin biosynthesis is essential to this organism, we can appreciate that targeting it would be a promising new strategy to combat these fungal infections. We provide evidence that one particular enzyme in the production process, CaRib1, would be most promising as an antifungal drug target, as it plays a central role in regulation and proves to be essential in a mouse model of systemic infection.
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10
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Tsyrulnyk AO, Andreieva YA, Ruchala J, Fayura LR, Dmytruk KV, Fedorovych DV, Sibirny AA. Expression of yeast homolog of the mammalBCRPgene coding for riboflavin efflux protein activates vitamin B2production in the flavinogenic yeastCandida famata. Yeast 2020; 37:467-473. [DOI: 10.1002/yea.3470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/13/2020] [Accepted: 05/05/2020] [Indexed: 01/07/2023] Open
Affiliation(s)
- Andriy O. Tsyrulnyk
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology NAS of Ukraine Lviv Ukraine
| | - Yuliia A. Andreieva
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology NAS of Ukraine Lviv Ukraine
| | - Justyna Ruchala
- Department of Microbiology and Biotechnology University of Rzeszow Rzeszow Poland
| | - Lyubov R. Fayura
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology NAS of Ukraine Lviv Ukraine
| | - Kostyantyn V. Dmytruk
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology NAS of Ukraine Lviv Ukraine
| | - Daria V. Fedorovych
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology NAS of Ukraine Lviv Ukraine
| | - Andriy A. Sibirny
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology NAS of Ukraine Lviv Ukraine
- Department of Microbiology and Biotechnology University of Rzeszow Rzeszow Poland
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11
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Andreieva Y, Petrovska Y, Lyzak O, Liu W, Kang Y, Dmytruk K, Sibirny A. Role of the regulatory genes SEF1, VMA1 and SFU1 in riboflavin synthesis in the flavinogenic yeast Candida famata (Candida flareri). Yeast 2020; 37:497-504. [PMID: 32529692 DOI: 10.1002/yea.3503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/05/2020] [Accepted: 06/07/2020] [Indexed: 11/11/2022] Open
Abstract
Riboflavin or vitamin B2 is an essential dietary component for humans and animals that is the precursor of flavin coenzymes flavin mononucleotide and flavin adenine dinucleotide involved in numerous enzymatic reactions. The flavinogenic yeast Candida famata overproduces riboflavin under iron starvation; however, regulation of this process is poorly understood. Regulatory gene SEF1 encoding transcription activator has been identified. Its deletion blocks yeast ability to overproduce riboflavin under iron starvation. It was shown here that the SEF1 promoters from other flavinogenic (Candida albicans) and non-flavinogenic (Candida tropicalis) yeasts fused with the open reading frame (ORF) of SEF1 gene from C. famata are able to restore riboflavin oversynthesis in sef1Δ mutants. It is known that in the pathogenic flavinogenic yeast C. albicans, Sfu1 (GATA-type transcription factor) represses SEF1. Here, we found that deletion of SFU1 gene in wild-type C. famata leads to riboflavin oversynthesis. Moreover, it was shown that disruption of VMA1 gene (coding for vacuolar ATPase subunit A) also results in riboflavin oversynthesis in C. famata.
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Affiliation(s)
- Yuliia Andreieva
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine
| | - Yana Petrovska
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine
| | - Oleksii Lyzak
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wen Liu
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine.,Key Laboratory of Medical Microbiology and Parasitology of Education Department of Guizhou, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Yingqian Kang
- Key Laboratory of Medical Microbiology and Parasitology of Education Department of Guizhou, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou & Guizhou Talent Base for Microbiology and Human Health, Guiyang, China
| | - Kostyantyn Dmytruk
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine
| | - Andriy Sibirny
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine.,Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow, Poland
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Dmytruk KV, Ruchala J, Fedorovych DV, Ostapiv RD, Sibirny AA. Modulation of the Purine Pathway for Riboflavin Production in Flavinogenic Recombinant Strain of the Yeast Candida famata. Biotechnol J 2020; 15:e1900468. [PMID: 32087089 DOI: 10.1002/biot.201900468] [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: 10/12/2019] [Revised: 02/10/2020] [Indexed: 11/10/2022]
Abstract
Riboflavin (vitamin B2 ) is an indispensable nutrient for humans and animals, since it is the precursor of the essential coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), involved in variety of metabolic reactions. Riboflavin is produced on commercial scale and is used for feed and food fortification purposes, and in medicine. Until recently, the mutant strains of the flavinogenic yeast Candida famata were used in industry for riboflavin production. Guanosine triphosphate is the immediate precursor of riboflavin synthesis. Therefore, the activation of metabolic flux toward purine nucleotide biosynthesis is a promising approach to improve riboflavin production. The phosphoribosyl pyrophosphate synthetase and phosphoribosyl pyrophosphate amidotransferase are the rate limiting enzymes in purine biosynthesis. Corresponding genes PRS3 and ADE4 from yeast Debaryomyces hansenii are modified to avoid feedback inhibition and cooverexpressed on the background of a previously constructed riboflavin overproducing strain of C. famata. Constructed strain accumulates twofold more riboflavin when compared to the parental strain.
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Affiliation(s)
- Kostyantyn V Dmytruk
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Justyna Ruchala
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza, 4, Rzeszow, 35-601, Poland
| | - Daria V Fedorovych
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Roman D Ostapiv
- Laboratory of high-performance liquid chromatography, State Scientific-Research Control Institute of Veterinary Medicinal Products and Feed Additives, Donetska Street, 11, Lviv, 79019, Ukraine
| | - Andriy A Sibirny
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine.,Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza, 4, Rzeszow, 35-601, Poland
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13
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Berezka K, Semkiv M, Borbuliak M, Blomqvist J, Linder T, Ruchała J, Dmytruk K, Passoth V, Sibirny A. Insertional tagging of the Scheffersomyces stipitis gene HEM25 involved in regulation of glucose and xylose alcoholic fermentation. Cell Biol Int 2020; 45:507-517. [PMID: 31829471 DOI: 10.1002/cbin.11284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/10/2019] [Indexed: 11/10/2022]
Abstract
Amid known microbial bioethanol producers, the yeast Scheffersomyces (Pichia) stipitis is particularly promising in terms of alcoholic fermentation of both glucose and xylose, the main constituents of lignocellulosic biomass hydrolysates. However, the ethanol yield and productivity, especially from xylose, are still insufficient to meet the requirements of a feasible industrial technology; therefore, the construction of more efficient S. stipitis ethanol producers is of great significance. The aim of this study was to isolate the insertional mutants of S. stipitis with altered ethanol production from glucose and xylose and to identify the disrupted gene(s). Mutants obtained by random insertional mutagenesis were screened for their growth abilities on solid media with different sugars and for resistance to 3-bromopyruvate. Of more than 1,300 screened mutants, 17 were identified to have significantly changed ethanol yields during the fermentation. In one of the best fermenting strains (strain 4.6), insertion was found to occur within the ORF of a homolog to the Saccharomyces cerevisiae gene HEM25 (YDL119C), encoding a mitochondrial glycine transporter required for heme synthesis. The role of HEM25 in heme accumulation, respiration, and alcoholic fermentation in the yeast S. stipitis was studied using strain 4.6, the complementation strain Comp-a derivative from the 4.6 strain with expression of the WT HEM25 allele and the deletion strain hem25Δ. As hem25Δ produced lower amounts of ethanol than strain 4.6, we assume that the phenotype of strain 4.6 may be caused not only by HEM25 disruption but additionally by some point mutation.
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Affiliation(s)
- Krzysztof Berezka
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland
| | - Marta Semkiv
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Str.14/16, Lviv, 79005, Ukraine
| | - Mariia Borbuliak
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Str.14/16, Lviv, 79005, Ukraine
| | - Johanna Blomqvist
- Department Molecular Sciences, Swedish University of Agricultural Sciences, BioCentre, Almas allé 5, Uppsala, 750-07, Sweden
| | - Tomas Linder
- Department Molecular Sciences, Swedish University of Agricultural Sciences, BioCentre, Almas allé 5, Uppsala, 750-07, Sweden
| | - Justyna Ruchała
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland
| | - Kostyantyn Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Str.14/16, Lviv, 79005, Ukraine
| | - Volkmar Passoth
- Department Molecular Sciences, Swedish University of Agricultural Sciences, BioCentre, Almas allé 5, Uppsala, 750-07, Sweden
| | - Andriy Sibirny
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Str.14/16, Lviv, 79005, Ukraine
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14
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Navarrete C, L. Martínez J. Non-conventional yeasts as superior production platforms for sustainable fermentation based bio-manufacturing processes. AIMS BIOENGINEERING 2020. [DOI: 10.3934/bioeng.2020024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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15
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Novel endogenous promoters for genetic engineering of the marine microalga Nannochloropsis gaditana CCMP526. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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16
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Wang Q, Chen L, Fang C, Wang H, Shi Y, Zhao Y. The overexpression of one single cbh gene making Trichoderma asperellum T-1 a better cellulase producer. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01458-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Fraczek MG, Naseeb S, Delneri D. History of genome editing in yeast. Yeast 2018; 35:361-368. [PMID: 29345746 PMCID: PMC5969250 DOI: 10.1002/yea.3308] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 12/27/2022] Open
Abstract
For thousands of years humans have used the budding yeast Saccharomyces cerevisiae for the production of bread and alcohol; however, in the last 30-40 years our understanding of the yeast biology has dramatically increased, enabling us to modify its genome. Although S. cerevisiae has been the main focus of many research groups, other non-conventional yeasts have also been studied and exploited for biotechnological purposes. Our experiments and knowledge have evolved from recombination to high-throughput PCR-based transformations to highly accurate CRISPR methods in order to alter yeast traits for either research or industrial purposes. Since the release of the genome sequence of S. cerevisiae in 1996, the precise and targeted genome editing has increased significantly. In this 'Budding topic' we discuss the significant developments of genome editing in yeast, mainly focusing on Cre-loxP mediated recombination, delitto perfetto and CRISPR/Cas.
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Affiliation(s)
- Marcin G. Fraczek
- The University of Manchester, Faculty of Biology, Medicine and HealthManchester Institute of BiotechnologyManchesterM1 7DNUK
| | - Samina Naseeb
- The University of Manchester, Faculty of Biology, Medicine and HealthManchester Institute of BiotechnologyManchesterM1 7DNUK
| | - Daniela Delneri
- The University of Manchester, Faculty of Biology, Medicine and HealthManchester Institute of BiotechnologyManchesterM1 7DNUK
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Dmytruk KV, Ruchala J, Grabek-Lejko D, Puchalski C, Bulbotka NV, Sibirny AA. Autophagy-related gene ATG13 is involved in control of xylose alcoholic fermentation in the thermotolerant methylotrophic yeast Ogataea polymorpha. FEMS Yeast Res 2018; 18:4847886. [DOI: 10.1093/femsyr/foy010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/08/2018] [Indexed: 01/16/2023] Open
Affiliation(s)
- Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, Drahomanov Str., 14/16, Lviv 79005 Ukraine
| | - Justyna Ruchala
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow 35–601 Poland
| | - Dorota Grabek-Lejko
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow 35–601 Poland
| | - Czeslaw Puchalski
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow 35–601 Poland
| | - Nina V Bulbotka
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, Drahomanov Str., 14/16, Lviv 79005 Ukraine
| | - Andriy A Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, Drahomanov Str., 14/16, Lviv 79005 Ukraine
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow 35–601 Poland
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Yaguchi A, Rives D, Blenner M. New kids on the block: emerging oleaginous yeast of biotechnological importance. AIMS Microbiol 2017; 3:227-247. [PMID: 31294158 PMCID: PMC6605006 DOI: 10.3934/microbiol.2017.2.227] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 03/23/2017] [Indexed: 12/24/2022] Open
Abstract
There is growing interest in using oleaginous yeast for the production of a variety of fatty acids and fatty acid-derived oleochemicals. This is motivated by natural propensity for high flux through lipid biosynthesis that has naturally evolved, making them a logical starting point for additional genetic engineering to improve titers and productivities. Much of the academic and industrial focus has centered on yeast that have significant genetic engineering tool capabilities, such as Yarrowia lipolytica, and those that have naturally high lipid accumulation, such as Rhodosporidium toruloides and Lipomyces starkeyi; however, there are oleaginous yeast with phenotypes better aligned with typically inhibitory process conditions, such as high salt concentrations and lignocellulosic derived inhibitors. This review addresses the foundational work in characterizing two emerging oleaginous yeast of interest: Debaryomyces hansenii and Trichosporon oleaginosus. We focus on the physiological and metabolic properties of these yeast that make each attractive for bioprocessing of lignocellulose to fuels and chemicals, discuss their respective genetic engineering tools and highlight the critical barriers facing the broader implementation of these oleaginous yeast.
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Affiliation(s)
- Allison Yaguchi
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC 29634, USA
| | - Dyllan Rives
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC 29634, USA
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC 29634, USA
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20
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Defosse TA, Mélin C, Clastre M, Besseau S, Lanoue A, Glévarec G, Oudin A, Dugé de Bernonville T, Vandeputte P, Linder T, Bouchara JP, Courdavault V, Giglioli-Guivarc'h N, Papon N. An additionalMeyerozyma guilliermondii IMH3gene confers mycophenolic acid resistance in fungal CTG clade species. FEMS Yeast Res 2016; 16:fow078. [DOI: 10.1093/femsyr/fow078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2016] [Indexed: 01/11/2023] Open
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Fedorovych D, Boretsky Y, Bobak Y, Prokopiv T, Sybirny A. Putative ferroxidases in the Flavinogenic yeast Pichia guilliermondii are regulated by iron acquisition. CYTOL GENET+ 2015. [DOI: 10.3103/s0095452715050035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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23
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Insertional Mutagenesis of the Flavinogenic Yeast Candida famata (Candida flareri). Fungal Biol 2015. [DOI: 10.1007/978-3-319-10142-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Metabolic and bioprocess engineering of the yeast Candida famata for FAD production. J Ind Microbiol Biotechnol 2014; 41:823-35. [PMID: 24595668 DOI: 10.1007/s10295-014-1422-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
Abstract
Flavins in the form of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) play an important role in metabolism as cofactors for oxidoreductases and other enzymes. Flavin nucleotides have applications in the food industry and medicine; FAD supplements have been efficiently used for treatment of some inheritable diseases. FAD is produced biotechnologically; however, this compound is much more expensive than riboflavin. Flavinogenic yeast Candida famata synthesizes FAD from FMN and ATP in the reaction catalyzed by FAD synthetase, a product of the FAD1 gene. Expression of FAD1 from the strong constitutive promoter TEF1 resulted in 7- to 15-fold increase in FAD synthetase activity, FAD overproduction, and secretion to the culture medium. The effectiveness of FAD production under different growth conditions by one of these recombinant strains, C. famata T-FD-FM 27, was evaluated. First, the two-level Plackett-Burman design was performed to screen medium components that significantly influence FAD production. Second, central composite design was adopted to investigate the optimum value of the selected factors for achieving maximum FAD yield. FAD production varied most significantly in response to concentrations of adenine, KH2PO4, glycine, and (NH4)2SO4. Implementation of these optimization strategies resulted in 65-fold increase in FAD production when compared to the non-optimized control conditions. Recombinant strain that has been cultivated for 40 h under optimized conditions achieved a FAD accumulation of 451 mg/l. So, for the first time yeast strains overproducing FAD were obtained, and the growth media composition for maximum production of this nucleotide was designed.
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Dmytruk K, Lyzak O, Yatsyshyn V, Kluz M, Sibirny V, Puchalski C, Sibirny A. Construction and fed-batch cultivation of Candida famata with enhanced riboflavin production. J Biotechnol 2013; 172:11-7. [PMID: 24361297 DOI: 10.1016/j.jbiotec.2013.12.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 12/04/2013] [Accepted: 12/09/2013] [Indexed: 11/26/2022]
Abstract
Riboflavin (vitamin B2) is an essential nutrition component serving as a precursor of coenzymes FMN and FAD that are involved mostly in reactions of oxidative metabolism. Riboflavin is produced in commercial scale and is used in feed and food industries, and in medicine. The yeast Candida famata (Candida flareri) belongs to the group of so called "flavinogenic yeasts" which overproduce riboflavin under iron limitation. Three genes SEF1, RIB1 and RIB7 coding for a putative transcription factor, GTP cyclohydrolase II and riboflavin synthase, respectively were simultaneously overexpressed in the background of a non-reverting riboflavin producing mutant AF-4, obtained earlier in our laboratory using methods of classical selection (Dmytruk et al. (2011), Metabolic Engineering 13, 82-88). Cultivation conditions of the constructed strain were optimized for shake-flasks and bioreactor cultivations. The constructed strain accumulated up to 16.4g/L of riboflavin in optimized medium in a 7L laboratory bioreactor during fed-batch fermentation.
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Affiliation(s)
- Kostyantyn Dmytruk
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Oleksy Lyzak
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Valentyna Yatsyshyn
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Maciej Kluz
- University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland
| | | | | | - Andriy Sibirny
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine; University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.
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26
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Yarimizu T, Nonklang S, Nakamura J, Tokuda S, Nakagawa T, Lorreungsil S, Sutthikhumpha S, Pukahuta C, Kitagawa T, Nakamura M, Cha-aim K, Limtong S, Hoshida H, Akada R. Identification of auxotrophic mutants of the yeastKluyveromyces marxianusby non-homologous end joining-mediated integrative transformation with genes fromSaccharomyces cerevisiae. Yeast 2013; 30:485-500. [DOI: 10.1002/yea.2985] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 12/23/2022] Open
Affiliation(s)
- Tohru Yarimizu
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai Ube Japan
| | - Sanom Nonklang
- Department of Biological Science, Faculty of Science; Ubonratchathani University; Warinchumrap Ubonratchathani Thailand
| | - Junpei Nakamura
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai Ube Japan
| | - Shuya Tokuda
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai Ube Japan
| | - Takaaki Nakagawa
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai Ube Japan
| | - Sasithorn Lorreungsil
- Department of Biological Science, Faculty of Science; Ubonratchathani University; Warinchumrap Ubonratchathani Thailand
| | - Surasit Sutthikhumpha
- Department of Biological Science, Faculty of Science; Ubonratchathani University; Warinchumrap Ubonratchathani Thailand
| | - Charida Pukahuta
- Department of Biological Science, Faculty of Science; Ubonratchathani University; Warinchumrap Ubonratchathani Thailand
| | - Takao Kitagawa
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai Ube Japan
| | - Mikiko Nakamura
- Innovation Center; Yamaguchi University; Tokiwadai Ube Japan
| | - Kamonchai Cha-aim
- Faculty of Agricultural Product Innovation and Technology; Srinakharinwirot University; Wattana Bangkok Thailand
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science; Kasetsart University; Bangkok Thailand
| | - Hisashi Hoshida
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai Ube Japan
| | - Rinji Akada
- Department of Applied Molecular Bioscience, Graduate School of Medicine; Yamaguchi University; Tokiwadai Ube Japan
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27
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Foureau E, Courdavault V, Simkin AJ, Sibirny AA, Crèche J, Giglioli-Guivarc'h N, Clastre M, Papon N. Transformation ofCandida guilliermondiiwild-type strains using theStaphylococcus aureusMRSA 252blegene as a phleomycin-resistant marker. FEMS Yeast Res 2013; 13:354-8. [DOI: 10.1111/1567-1364.12034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/30/2013] [Accepted: 01/30/2013] [Indexed: 12/01/2022] Open
Affiliation(s)
- Emilien Foureau
- EA2106, Biomolécules et Biotechnologies Végétales; Faculté de Pharmacie; Université François-Rabelais de Tours; Tours; France
| | - Vincent Courdavault
- EA2106, Biomolécules et Biotechnologies Végétales; Faculté des Sciences et Techniques; Université François-Rabelais de Tours; Tours; France
| | - Andrew J. Simkin
- School of Biological Sciences; University of Essex; Colchester; UK
| | | | - Joël Crèche
- EA2106, Biomolécules et Biotechnologies Végétales; Faculté de Pharmacie; Université François-Rabelais de Tours; Tours; France
| | - Nathalie Giglioli-Guivarc'h
- EA2106, Biomolécules et Biotechnologies Végétales; Faculté des Sciences et Techniques; Université François-Rabelais de Tours; Tours; France
| | - Marc Clastre
- EA2106, Biomolécules et Biotechnologies Végétales; Faculté de Pharmacie; Université François-Rabelais de Tours; Tours; France
| | - Nicolas Papon
- EA2106, Biomolécules et Biotechnologies Végétales; Faculté de Pharmacie; Université François-Rabelais de Tours; Tours; France
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28
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Dmytruk KV, Sibirny AA. Candida famata (Candida flareri). Yeast 2012; 29:453-8. [DOI: 10.1002/yea.2929] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 09/21/2012] [Accepted: 09/25/2012] [Indexed: 11/10/2022] Open
Affiliation(s)
- Kostyantyn V. Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology; National Academy of Sciences (NAS); Lviv; Ukraine
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29
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Papon N, Courdavault V, Clastre M, Simkin AJ, Crèche J, Giglioli-Guivarc’h N. Deus ex Candida genetics: overcoming the hurdles for the development of a molecular toolbox in the CTG clade. Microbiology (Reading) 2012; 158:585-600. [DOI: 10.1099/mic.0.055244-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Nicolas Papon
- EA2106, Biomolécules et Biotechnologies Végétales, Université François-Rabelais de Tours, France
| | - Vincent Courdavault
- EA2106, Biomolécules et Biotechnologies Végétales, Université François-Rabelais de Tours, France
| | - Marc Clastre
- EA2106, Biomolécules et Biotechnologies Végétales, Université François-Rabelais de Tours, France
| | - Andrew J. Simkin
- EA2106, Biomolécules et Biotechnologies Végétales, Université François-Rabelais de Tours, France
| | - Joël Crèche
- EA2106, Biomolécules et Biotechnologies Végétales, Université François-Rabelais de Tours, France
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Identification of yeast associated with the planthopper, Perkinsiella saccharicida: potential applications for Fiji leaf gall control. Curr Microbiol 2011; 63:392-401. [PMID: 21850475 DOI: 10.1007/s00284-011-9990-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/27/2011] [Indexed: 10/17/2022]
Abstract
Yeasts associate with numerous insects, and they can assist the metabolic processes within their hosts. Two distinct yeasts were identified by PCR within the planthopper Perkinsiella saccharicida, the vector of Fiji disease virus to sugarcane. The utility of both microbes for potential paratransgenic approaches to control Fiji leaf gall (FLG) was assessed. Phylogenetic analysis showed one of the microbes is related to yeast-like symbionts from the planthoppers: Laodelphax striatellus, Nilaparvata lugens, and Sogetella furcifera. The second yeast was a member of the Candida genus, a group that has been identified in beetles and recently described in planthoppers. Microscopy revealed the presence of yeast in the fat body of P. saccharicida. The Candida yeast was cultured, and transformation was accomplished by electroporation of Candida albicans codon optimized plasmids, designed to integrate into the genome via homologous recombination. Transgenic lines conferred resistance to the antibiotic nourseothricin and expression of green fluorescent protein was observed in a proportion of the yeast cells. Stably transformed yeast lines could not be isolated as the integrative plasmids presumably replicated within the yeast without integration into the genome. If stable transformation can be achieved, then this yeast may be useful as an agent for a paratransgenic control of FLG.
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31
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Abbas CA, Sibirny AA. Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev 2011; 75:321-60. [PMID: 21646432 PMCID: PMC3122625 DOI: 10.1128/mmbr.00030-10] [Citation(s) in RCA: 243] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Riboflavin [7,8-dimethyl-10-(1'-d-ribityl)isoalloxazine, vitamin B₂] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.
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Affiliation(s)
| | - Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Lviv 79005, Ukraine
- University of Rzeszow, Rzeszow 35-601, Poland
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32
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Millerioux Y, Clastre M, Simkin AJ, Courdavault V, Marais E, Sibirny AA, Noël T, Crèche J, Giglioli-Guivarc'h N, Papon N. Drug-resistant cassettes for the efficient transformation of Candida guilliermondii wild-type strains. FEMS Yeast Res 2011; 11:457-63. [DOI: 10.1111/j.1567-1364.2011.00731.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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33
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Boretsky YR, Pynyaha YV, Boretsky VY, Fedorovych DV, Fayura LR, Protchenko O, Philpott CC, Sibirny AA. Identification of the genes affecting the regulation of riboflavin synthesis in the flavinogenic yeast Pichia guilliermondii using insertion mutagenesis. FEMS Yeast Res 2011; 11:307-14. [PMID: 21261808 DOI: 10.1111/j.1567-1364.2011.00720.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Pichia guilliermondii is a representative of a group of so-called flavinogenic yeast species that overproduce riboflavin (vitamin B(2)) in response to iron limitation. Using insertion mutagenesis, we isolated P. guilliermondii mutants overproducing riboflavin. Analysis of nucleotide sequence of recombination sites revealed that insertion cassettes integrated into the genome disrupting P. guilliermondii genes similar to the VMA1 gene of Ashbya gossypii and Saccharomyces cerevisiae and FES1 and FRA1 genes of S. cerevisiae. The constructed P. guilliermondiiΔvma1-17 mutant possessed five- to sevenfold elevated riboflavin production and twofold decreased iron cell content as compared with the parental strain. Pichia guilliermondiiΔfra1-45 mutant accumulated 1.8-2.2-fold more iron in the cells and produced five- to sevenfold more riboflavin as compared with the parental strain. Both Δvma1-17 and Δfes1-77 knockout strains could not grow at 37 °C in contrast to the wild-type strain and the Δfra1-45 mutant. Increased riboflavin production by the wild-type strain was observed at 37 °C. Although the Δfes1-77 mutant did not overproduce riboflavin, it showed partial complementation when crossed with previously isolated P. guilliermondii riboflavin-overproducing mutant rib80-22. Complementation analysis revealed that Δvma1-17 and Δfra1-45 mutants are distinct from previously reported riboflavin-producing mutants hit1-1, rib80-22 and rib81-31 of this yeast.
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Affiliation(s)
- Yuriy R Boretsky
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine
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34
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Dmytruk KV, Yatsyshyn VY, Sybirna NO, Fedorovych DV, Sibirny AA. Metabolic engineering and classic selection of the yeast Candida famata (Candida flareri) for construction of strains with enhanced riboflavin production. Metab Eng 2010; 13:82-8. [PMID: 21040798 DOI: 10.1016/j.ymben.2010.10.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 10/21/2010] [Accepted: 10/21/2010] [Indexed: 02/08/2023]
Abstract
Currently, the mutant of the flavinogenic yeast Candida famata dep8 isolated by classic mutagenesis and selection is used for industrial riboflavin production. Here we report on construction of a riboflavin overproducing strain of C. famata using a combination of random mutagenesis based on the selection of mutants resistant to different antimetabolites as well as rational approaches of metabolic engineering. The conventional mutagenesis involved consecutive selection for resistance to riboflavin structural analog 7-methyl-8-trifluoromethyl-10-(1'-d-ribityl)isoalloxazine), 8-azaguanine, 6-azauracil, 2-diazo-5-oxo-L-norleucine and guanosine as well as screening for yellow colonies at high pH. The metabolic engineering approaches involved introduction of additional copies of transcription factor SEF1 and IMH3 (coding for IMP dehydrogenase) orthologs from Debaryomyces hansenii, and the homologous genes RIB1 and RIB7, encoding GTP cyclohydrolase II and riboflavin synthetase, the first and the last enzymes of riboflavin biosynthesis pathway, respectively. Overexpression of the aforementioned genes in riboflavin overproducer AF-4 obtained by classical selection resulted in a 4.1-fold increase in riboflavin production in shake-flask experiments. D. hansenii IMH3 and modified ARO4 genes conferring resistance to mycophenolic acid and fluorophenylalanine, respectively, were successfully used as new dominant selection markers for C. famata.
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Affiliation(s)
- Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, Lviv 79005, Ukraine
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35
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Abdel-Banat BMA, Nonklang S, Hoshida H, Akada R. Random and targeted gene integrations through the control of non-homologous end joining in the yeast Kluyveromyces marxianus. Yeast 2010; 27:29-39. [PMID: 19894210 DOI: 10.1002/yea.1729] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Kluyveromyces marxianus DMKU3-1042 is a thermotolerant yeast strain suitable for high-temperature ethanol fermentation and genetic engineering with linear DNA. We have developed a highly efficient random gene integration method with a frequency that exceeds 2.5 x 10(6) transformants/microg linear DNA, a figure comparable to what is observed with autonomously replicating plasmid transformation in Saccharomyces cerevisiae. To establish the mechanism of random integration in DMKU3-1042, we identified and deleted the K. marxianus KU70 gene, which is known to be involved in the non-homologous end-joining (NHEJ) pathway. In yeast lacking KU70, high-frequency non-homologous gene integration was abolished and the Kmku70 mutants showed 82-95% homologous gene targeting efficiencies using homologous sequences of 40-1000 bp. These results indicate that the highly efficient NHEJ pathway can be utilized with random gene disruption techniques such as transposon mutagenesis and plasmid-free gene manipulations in K. marxianus.
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Affiliation(s)
- Babiker M A Abdel-Banat
- Department of Applied Molecular Bioscience, Yamaguchi University Graduate School of Medicine, Tokiwadai, Ube 755-8611, Japan
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Pynyaha YV, Boretsky YR, Fedorovych DV, Fayura LR, Levkiv AI, Ubiyvovk VM, Protchenko OV, Philpott CC, Sibirny AA. Deficiency in frataxin homologue YFH1 in the yeast Pichia guilliermondii leads to missregulation of iron acquisition and riboflavin biosynthesis and affects sulfate assimilation. Biometals 2009; 22:1051-61. [PMID: 19649569 PMCID: PMC3428027 DOI: 10.1007/s10534-009-9256-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 07/19/2009] [Indexed: 11/28/2022]
Abstract
Pichia guilliermondii is a representative of yeast species that overproduce riboflavin (vitamin B2) in response to iron deprivation. P. guilliermondii YFH1 gene coding for frataxin homologue, eukaryotic mitochondrial protein involved in iron trafficking and storage, was identified and deleted. Constructed P. guilliermondii Δyfh1 mutant grew very poorly in a sucrose-containing synthetic medium supplemented with sulfate or sulfite as a sole sulfur source. Addition of sodium sulfide, glutathione, cysteine, methionine, N-acetyl-L-cysteine partially restored growth rate of the mutant suggesting that it is impaired in sulfate assimilation. Cellular iron content in Δyfh1 mutant was ~3-3.5 times higher as compared to the parental strain. It produced 50-70 times more riboflavin in iron sufficient synthetic media relative to the parental wildtype strain. Biomass yield of the mutant in the synthetic glutathione containing medium supplemented with glycerol as a sole carbon source was 1.4- and 2.6-fold increased as compared to sucrose and succinate containing media, respectively. Oxygen uptake of the Δyfh1 mutant on sucrose, glycerol or succinate, when compared to the parental strain, was decreased 5.5-, 1.7- and 1.5-fold, respectively. Substitution of sucrose or glycerol in the synthetic iron sufficient medium with succinate completely abolished riboflavin overproduction by the mutants. Deletion of the YFH1 gene caused hypersensitivity to hydrogen peroxide and exogenously added riboflavin and led to alterations in superoxide dismutase activities. Thus, deletion of the gene coding for yeast frataxin homologue has pleiotropic effect on metabolism in P. guilliermondii.
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Affiliation(s)
- Yuriy V. Pynyaha
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Yuriy R. Boretsky
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Daria V. Fedorovych
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Lubov R. Fayura
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Andriy I. Levkiv
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Vira M. Ubiyvovk
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Olha V. Protchenko
- Liver Diseases Branch, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Building 10, Room 9B-16, 10 Center Drive, Bethesda, MD 20892-1800, USA
| | - Caroline C. Philpott
- Liver Diseases Branch, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Building 10, Room 9B-16, 10 Center Drive, Bethesda, MD 20892-1800, USA
| | - Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine. Rzeszów University, Ćwiklińskiej 2, 35-601 Rzeszów, Poland
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Yatsyshyn VY, Ishchuk OP, Voronovsky AY, Fedorovych DV, Sibirny AA. Production of flavin mononucleotide by metabolically engineered yeast Candida famata. Metab Eng 2009; 11:163-7. [PMID: 19558965 DOI: 10.1016/j.ymben.2009.01.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Revised: 12/31/2008] [Accepted: 01/20/2009] [Indexed: 11/15/2022]
Abstract
Recombinant strains of the flavinogenic yeast Candida famata able to overproduce flavin mononucleotide (FMN) that contain FMN1 gene encoding riboflavin (RF) kinase driven by the strong constitutive promoter TEF1 (translation elongation factor 1alpha) were constructed. Transformation of these strains with the additional plasmid containing the FMN1 gene under the TEF1 promoter resulted in the 200-fold increase in the riboflavin kinase activity and 100-fold increase in FMN production as compared to the wild-type strain (last feature was found only in iron-deficient medium). Overexpression of the FMN1 gene in the mutant that has deregulated riboflavin biosynthesis pathway and high level of riboflavin production in iron-sufficient medium led to the 30-fold increase in the riboflavin kinase activity and 400-fold increase in FMN production of the resulted transformants. The obtained C. famata recombinant strains can be used for the further construction of improved FMN overproducers.
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Affiliation(s)
- Valentyna Y Yatsyshyn
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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Maassen N, Freese S, Schruff B, Passoth V, Klinner U. Nonhomologous end joining and homologous recombination DNA repair pathways in integration mutagenesis in the xylose-fermenting yeastPichia stipitis. FEMS Yeast Res 2008; 8:735-43. [DOI: 10.1111/j.1567-1364.2008.00383.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Seda-Miró JM, Arroyo-González N, Pérez-Matos A, Govind NS. Impairment of cobalt-induced riboflavin biosynthesis in a Debaryomyces hansenii mutant. Can J Microbiol 2008; 53:1272-7. [PMID: 18026221 DOI: 10.1139/w07-098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Flavinogenic yeasts such as Debaryomyces hansenii overproduce riboflavin (RF) in the presence of heavy metals. Growth and RF production were compared between wild-type D. hansenii and a RF production-impaired metal-tolerant ura3 mutant in the presence of sublethal cobalt(II) concentrations. Debaryomyces hansenii (wild type) exhibits an extended lag phase with an increase in RF synthesis. Supplementation of exogenous uracil shortened the lag phase at the highest concentration of cobalt(II) used, suggesting that uracil has a possible role in metal acclimation. The D. hansenii ura3 mutant isolated by chemical mutagenesis exhibited a higher level of metal tolerance, no extended lag phase, and no marked increase in RF synthesis. Transformation of the mutant with the URA3 gene isolated from Saccharyomyces cerevisiae or D. hansenii did not restore wild-type characteristics, suggesting a second mutation that impairs RF oversynthesis. Our results demonstrate that growth, metal sensitivity, and RF biosynthesis are linked.
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Affiliation(s)
- Jasmine M Seda-Miró
- Department of Marine Sciences, University of Puerto Rico-Mayaguez, P.O. Box 908, Lajas, PR 00667, Puerto Rico
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Ishchuk OP, Dmytruk KV, Rohulya OV, Voronovsky AY, Abbas CA, Sibirny AA. Development of a promoter assay system for the flavinogenic yeast Candida famata based on the Kluyveromyces lactis β-galactosidase LAC4 reporter gene. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2007.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Dmytruk KV, Sibirny AA. Molecular mechanisms of insertional mutagenesis in yeasts and mycelium fungi. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407080017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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42
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Sasano Y, Yurimoto H, Sakai Y. Gene-tagging mutagenesis in the methylotrophic yeast Candida boidinii. J Biosci Bioeng 2007; 104:86-9. [PMID: 17697989 DOI: 10.1263/jbb.104.86] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 04/13/2007] [Indexed: 11/17/2022]
Abstract
A gene-tagging mutagenesis method by random integration of linear DNA fragments was developed and used in the methylotrophic yeast Candida boidinii to isolate mutants defective in methanol-inducible gene expression. A large number of mutants were obtained, indicating that this method is a powerful tool for random mutagenesis in C. boidinii.
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Affiliation(s)
- Yu Sasano
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Kyoto, Japan
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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