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Bernard A, Rossignol T, Park YK. Biotechnological approaches for producing natural pigments in yeasts. Trends Biotechnol 2024:S0167-7799(24)00175-6. [PMID: 39019677 DOI: 10.1016/j.tibtech.2024.06.012] [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: 05/07/2024] [Revised: 06/13/2024] [Accepted: 06/25/2024] [Indexed: 07/19/2024]
Abstract
Pigments are widely used in the food, cosmetic, textile, pharmaceutical, and materials industries. Demand for natural pigments has been increasing due to concerns regarding potential health problems and environmental pollution from synthetic pigments. Microbial production of natural pigments is a promising alternative to chemical synthesis or extraction from natural sources. Here, we discuss yeasts as promising chassis for producing natural pigments with their advantageous traits such as genetic amenability, safety, rapid growth, metabolic diversity, and tolerance. Metabolic engineering strategies and optimizing strategies in downstream process to enhance production of natural pigments are thoroughly reviewed. We discuss the challenges, including expanding the range of natural pigments and improving their feasibility of industrial scale-up, as well as the potential strategies for future development.
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Affiliation(s)
- Armand Bernard
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Tristan Rossignol
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Young-Kyoung Park
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
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Dzanaeva LS, Wojdyła D, Fedorovych DV, Ruchala J, Dmytruk KV, Sibirny AA. Riboflavin overproduction on lignocellulose hydrolysate by the engineered yeast Candida famata. FEMS Yeast Res 2024; 24:foae020. [PMID: 39009031 PMCID: PMC11283204 DOI: 10.1093/femsyr/foae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/01/2024] [Accepted: 07/11/2024] [Indexed: 07/17/2024] Open
Abstract
Lignocellulose (dry plant biomass) is an abundant cheap inedible residue of agriculture and wood industry with great potential as a feedstock for biotechnological processes. Lignocellulosic substrates can serve as valuable resources in fermentation processes, allowing the production of a wide array of chemicals, fuels, and food additives. The main obstacle for cost-effective conversion of lignocellulosic hydrolysates to target products is poor metabolism of the major pentoses, xylose and L-arabinose, which are the second and third most abundant sugars of lignocellulose after glucose. We study the oversynthesis of riboflavin in the flavinogenic yeast Candida famata and found that all major lignocellulosic sugars, including xylose and L-arabinose, support robust growth and riboflavin synthesis in the available strains of C. famata. To further increase riboflavin production from xylose and lignocellulose hydrolysate, genes XYL1 and XYL2 coding for xylose reductase and xylitol dehydrogenase were overexpressed. The resulting strains exhibited increased riboflavin production in both shake flasks and bioreactors using diluted hydrolysate, reaching 1.5 g L-1.
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Affiliation(s)
- Ljubov S Dzanaeva
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St., 14/16, 79005 Lviv, Ukraine
| | - Dominik Wojdyła
- Institute of Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601 Rzeszow, Poland
| | - Dariya V Fedorovych
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St., 14/16, 79005 Lviv, Ukraine
| | - Justyna Ruchala
- Institute of Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601 Rzeszow, Poland
| | - Kostyantyn V Dmytruk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St., 14/16, 79005 Lviv, Ukraine
| | - Andriy A Sibirny
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St., 14/16, 79005 Lviv, Ukraine
- Institute of Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601 Rzeszow, Poland
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Mengucci C, Rampelli S, Picone G, Lucchi A, Litta G, Biagi E, Candela M, Manfreda G, Brigidi P, Capozzi F, De Cesare A. Application of multi-omic features clustering and pathway enrichment to clarify the impact of vitamin B2 supplementation on broiler caeca microbiome. Front Microbiol 2023; 14:1264361. [PMID: 37840729 PMCID: PMC10568133 DOI: 10.3389/fmicb.2023.1264361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Background The results of omic methodologies are often reported as separate datasets. In this study we applied for the first time multi-omic features clustering and pathway enrichment to clarify the biological impact of vitamin B2 supplementation on broiler caeca microbiome. Methods The caeca contents of broilers fed +50 and +100 mg/kg vitamin B2 were analyzed by shotgun metagenomic and metabolomic. Latent variables extracted from NMR spectra, as well as taxonomic and functional features profiled from metagenomes, were integrated to characterize the effect of vitamin B2 in modulating caeca microbiome. A pathway-based network was obtained by mapping the observed input genes and compounds, highlighting connected strands of metabolic ways through pathway-enrichment analysis. Results At day 14, the taxonomic, functional and metabolomic features in the caeca of tested broilers showed some degree of separation between control and treated groups, becoming fully clear at 28 days and persisting up to 42 days. In the caeca of birds belonging to the control group Alistipes spp. was the signature species, while the signature species in the caeca of broilers fed +50 and +100 mg/kg vitamin B2 were Bacteroides fragilis and Lactobacillus crispatus, Lactobacillus reuteri, Ruminococcus torques, Subdoligranum spp., respectively. The pathway enrichment analysis highlighted that the specific biochemical pathways enhanced by the supplementations of vitamin B2 were N-Formyl-L-aspartate amidohydrolase, producing Aspartate and Formate; L-Alanine:2-oxoglutarate amino transferase, supporting the conversion of L-Alanine and 2-Oxoglutarate in Pyruvate and L-Glutamate; 1D-myo-inositol 1/4 phosphate phosphohydrolase, converting Inositol 1/4-phosphate and water in myo-Inositol and Orthophosphate. The results of this study demonstrated that the caeca of birds fed +50 and + 100 mg/kg were those characterized by taxonomic groups more beneficial to the host and with a higher concentration of myo-inositol, formic acid, amino acids and pyruvate involved in glycolysis and amino acid biosynthesis. Conclusion In this study we demonstrated how to perform multi-omic features integration to describe the biochemical mechanisms enhanced by the supplementation of different concentrations of vitamin B2 in the poultry diet. The relationship between vitamin B2 supplementation and myo-inositol production was highlighted in our study for the first time.
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Affiliation(s)
- Carlo Mengucci
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Gianfranco Picone
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | | | - Elena Biagi
- Department of Civil, Chemical, Environmental, and Materials Engineering, University of Bologna, Bologna, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Francesco Capozzi
- Department of Agricultural and Food Sciences, University of Bologna, Cesena, Italy
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia (BO), Italy
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Dmytruk KV, Ruchala J, Fayura LR, Chrzanowski G, Dmytruk OV, Tsyrulnyk AO, Andreieva YA, Fedorovych DV, Motyka OI, Mattanovich D, Marx H, Sibirny AA. Efficient production of bacterial antibiotics aminoriboflavin and roseoflavin in eukaryotic microorganisms, yeasts. Microb Cell Fact 2023; 22:132. [PMID: 37474952 PMCID: PMC10357625 DOI: 10.1186/s12934-023-02129-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Actinomycetes Streptomyces davaonensis and Streptomyces cinnabarinus synthesize a promising broad-spectrum antibiotic roseoflavin, with its synthesis starting from flavin mononucleotide and proceeding through an immediate precursor, aminoriboflavin, that also has antibiotic properties. Roseoflavin accumulation by the natural producers is rather low, whereas aminoriboflavin accumulation is negligible. Yeasts have many advantages as biotechnological producers relative to bacteria, however, no recombinant producers of bacterial antibiotics in yeasts are known. RESULTS Roseoflavin biosynthesis genes have been expressed in riboflavin- or FMN-overproducing yeast strains of Candida famata and Komagataella phaffii. Both these strains accumulated aminoriboflavin, whereas only the latter produced roseoflavin. Aminoriboflavin isolated from the culture liquid of C. famata strain inhibited the growth of Staphylococcus aureus (including MRSA) and Listeria monocytogenes. Maximal accumulation of aminoriboflavin in shake-flasks reached 1.5 mg L- 1 (C. famata), and that of roseoflavin was 5 mg L- 1 (K. phaffii). Accumulation of aminoriboflavin and roseoflavin by K. phaffii recombinant strain in a bioreactor reached 22 and 130 mg L- 1, respectively. For comparison, recombinant strains of the native bacterial producer S. davaonensis accumulated near one-order less of roseoflavin while no recombinant producers of aminoriboflavin was reported at all. CONCLUSIONS Yeast recombinant producers of bacterial antibiotics aminoriboflavin and roseoflavin were constructed and evaluated.
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Affiliation(s)
- Kostyantyn V Dmytruk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Justyna Ruchala
- University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland
| | - Liubov R Fayura
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | | | - Olena V Dmytruk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Andriy O Tsyrulnyk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Yuliia A Andreieva
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Daria V Fedorovych
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Olena I Motyka
- Research Institute of Epidemiology and Hygiene of the Danylo Halytsky Lviv National Medical University, Zelena St, 12, Lviv, 79005, Ukraine
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Vienna, 1190, Austria
| | - Hans Marx
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Vienna, 1190, Austria
| | - Andriy A Sibirny
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine.
- University of Rzeszow, Zelwerowicza 4, Rzeszow, 35-601, Poland.
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Duan XY, Liu HH, Song LP, Wang C, Yang H, Lu XY, Ji XJ, Tian Y. Efficient production of cordycepin by engineered Yarrowia lipolytica from agro-industrial residues. BIORESOURCE TECHNOLOGY 2023; 377:128964. [PMID: 36972806 DOI: 10.1016/j.biortech.2023.128964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 06/18/2023]
Abstract
Cordycepin, a nucleoside compound with a variety of biological activities, has been extensively applied in the nutraceutical and pharmaceutical industries. The advancement of microbial cell factories using agro-industrial residues provides a sustainable pathway for cordycepin biosynthesis. Herein, the cordycepin production was enhanced by the modification of glycolysis and pentose phosphate pathway in engineered Yarrowia lipolytica. Then, cordycepin production based on economical and renewable substrates (sugarcane molasses, waste spent yeast, and diammonium hydrogen phosphate) was analyzed. Furthermore, the effects of C/N molar ratio and initial pH on cordycepin production were evaluated. Results indicated that the maximum cordycepin productivity of 656.27 mg/L/d (72 h) and cordycepin titer was 2286.04 mg/L (120 h) by engineered Y. lipolytica in the optimized medium, respectively. The cordycepin productivity in the optimized medium was increased by 28.81% compared with the original medium. This research establishes a promising way for efficient cordycepin production from agro-industrial residues.
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Affiliation(s)
- Xi-Yu Duan
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Hu-Hu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Li-Ping Song
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Chong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Hui Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Xiang-Yang Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China.
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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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7
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Ruchala J, Andreieva YA, Tsyrulnyk AO, Sobchuk SM, Najdecka A, Wen L, Kang Y, Dmytruk OV, Dmytruk KV, Fedorovych DV, Sibirny AA. Cheese whey supports high riboflavin synthesis by the engineered strains of the flavinogenic yeast Candida famata. Microb Cell Fact 2022; 21:161. [PMID: 35964025 PMCID: PMC9375410 DOI: 10.1186/s12934-022-01888-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
Background Riboflavin is a precursor of FMN and FAD which act as coenzymes of numerous enzymes. Riboflavin is an important biotechnological commodity with annual market sales exceeding nine billion US dollars. It is used primarily as a component of feed premixes, a food colorant, a component of multivitamin mixtures and medicines. Currently, industrial riboflavin production uses the bacterium, Bacillus subtilis, and the filamentous fungus, Ashbya gossypii, and utilizes glucose and/or oils as carbon substrates. Results We studied riboflavin biosynthesis in the flavinogenic yeast Candida famata that is a genetically stable riboflavin overproducer. Here it was found that the wild type C. famata is characterized by robust growth on lactose and cheese whey and the engineered strains also overproduce riboflavin on whey. The riboflavin synthesis on whey was close to that obtained on glucose. To further enhance riboflavin production on whey, the gene of the transcription activator SEF1 was expressed under control of the lactose-induced promoter of the native β-galactosidase gene LAC4. These transformants produced elevated amounts of riboflavin on lactose and especially on whey. The strain with additional overexpression of gene RIB6 involved in conversion of ribulose-5-phosphate to riboflavin precursor had the highest titer of accumulated riboflavin in flasks during cultivation on whey. Activation of riboflavin synthesis was also obtained after overexpression of the GND1 gene that is involved in the synthesis of the riboflavin precursor ribulose-5-phosphate. The best engineered strains accumulated 2.5 g of riboflavin/L on whey supplemented only with (NH4)2SO4 during batch cultivation in bioreactor with high yield (more than 300 mg/g dry cell weight). The use of concentrated whey inhibited growth of wild-type and engineered strains of C. famata, so the mutants tolerant to concentrated whey were isolated. Conclusions Our data show that the waste of dairy industry is a promising substrate for riboflavin production by C. famata. Possibilities for using the engineered strains of C. famata to produce high-value commodity (riboflavin) from whey are discussed. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01888-0.
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Affiliation(s)
- Justyna Ruchala
- Institute of Cell Biology, NAS of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine.,University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Yuliia A Andreieva
- Institute of Cell Biology, NAS of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine.,University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Andriy O Tsyrulnyk
- Institute of Cell Biology, NAS of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Svitlana M Sobchuk
- Institute of Cell Biology, NAS of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Alicja Najdecka
- University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Liu Wen
- Institute of Cell Biology, NAS of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine.,Guizhou Medical University, Guiyang, 550025, Guizhou, China
| | - Yingqian Kang
- Guizhou Medical University, Guiyang, 550025, Guizhou, China
| | - Olena V Dmytruk
- Institute of Cell Biology, NAS of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine.,University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Kostyantyn V Dmytruk
- Institute of Cell Biology, NAS of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine
| | - Dariya V Fedorovych
- Institute of Cell Biology, NAS of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine.,University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Andriy A Sibirny
- Institute of Cell Biology, NAS of Ukraine, Drahomanov St, 14/16, Lviv, 79005, Ukraine. .,University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland.
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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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You J, Pan X, Yang C, Du Y, Osire T, Yang T, Zhang X, Xu M, Xu G, Rao Z. Microbial production of riboflavin: Biotechnological advances and perspectives. Metab Eng 2021; 68:46-58. [PMID: 34481976 DOI: 10.1016/j.ymben.2021.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/19/2021] [Accepted: 08/31/2021] [Indexed: 10/24/2022]
Abstract
Riboflavin is an essential nutrient for humans and animals, and its derivatives flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are cofactors in the cells. Therefore, riboflavin and its derivatives are widely used in the food, pharmaceutical, nutraceutical and cosmetic industries. Advances in biotechnology have led to a complete shift in the commercial production of riboflavin from chemical synthesis to microbial fermentation. In this review, we provide a comprehensive review of biotechnologies that enhance riboflavin production in microorganisms, as well as representative examples. Firstly, the synthesis pathways and metabolic regulatory processes of riboflavin in microorganisms; and the current strategies and methods of metabolic engineering for riboflavin production are systematically summarized and compared. Secondly, the using of systematic metabolic engineering strategies to enhance riboflavin production is discussed, including laboratory evolution, histological analysis and high-throughput screening. Finally, the challenges for efficient microbial production of riboflavin and the strategies to overcome these challenges are prospected.
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Affiliation(s)
- Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Chen Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yuxuan Du
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Tolbert Osire
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guoqiang Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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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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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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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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Building Communities—The 8th Congress of European Microbiologists. Biotechnol J 2020; 15:e2000222. [DOI: 10.1002/biot.202000222] [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]
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