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Baeza M, Sepulveda D, Cifuentes V, Alcaíno J. Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure. Front Microbiol 2024; 15:1414422. [PMID: 39040903 PMCID: PMC11260810 DOI: 10.3389/fmicb.2024.1414422] [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: 04/08/2024] [Accepted: 06/25/2024] [Indexed: 07/24/2024] Open
Abstract
Codon usage bias (CUB) has been described in viruses, prokaryotes, and eukaryotes and has been linked to several cellular and environmental factors, such as the organism's growth temperature, gene expression levels, and regulation of protein synthesis and folding. Most of the studies in this area have been conducted in bacteria and higher eukaryotes, in some cases with different results. In this study, a comparative analysis of CUB in yeasts isolated from cold and template environments was performed in order to evaluate the correlation of CUB with yeast optimal temperature of growth (OTG), gene expression levels, cellular function, and structure of encoded proteins. Among the main findings, highly expressed ORFs tend to have a more similar CUB within and between yeasts, and a direct correlation between codons ending in C and expression level was generally found. A low correspondence between CUB and OTG was observed, with an inverse correlation for some codons ending in C. The clustering of yeasts based on their CUB partially aligns with their OTG, being more consistent for yeasts with lower OTG. In most yeasts, the abundance of preferred codons was generally lower at the 5' end of ORFs, higher in segments encoding beta strand, lower in segments encoding extracellular and transmembrane regions, and higher in "translation" and "energy metabolism" pathways, especially in highly expressed ORFs. Based on our findings, it is suggested that the abundance and distribution of preferred and non-preferred codons along mRNAs contribute to proper protein folding and functionality by regulating protein synthesis rates, becoming a more important factor under conditions that require faster protein synthesis in yeasts.
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Affiliation(s)
- Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Venegas M, Durán A, Campusano S, Barahona S, Sepúlveda D, Baeza M, Cifuentes V, Alcaíno J. Identification of Potential New Genes Related to the SREBP Pathway in Xanthophyllomyces dendrorhous. Biomolecules 2024; 14:778. [PMID: 39062491 PMCID: PMC11274570 DOI: 10.3390/biom14070778] [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: 06/12/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
The sterol regulatory element-binding protein (SREBP) pathway is an integral cellular mechanism that regulates lipid homeostasis, in which transcriptional activator SREBPs regulate the expression of various genes. In the carotenogenic yeast Xanthophyllomyces dendrorhous, Sre1 (the yeast SREBP homolog) regulates lipid biosynthesis and carotenogenesis, among other processes. Despite the characterization of several components of the SREBP pathway across various eukaryotes, the specific elements of this pathway in X. dendrorhous remain largely unknown. This study aimed to explore the potential regulatory mechanisms of the SREBP pathway in X. dendrorhous using the strain CBS.cyp61- as a model, which is known to have Sre1 in its active state under standard culture conditions, resulting in a carotenoid-overproducing phenotype. This strain was subjected to random mutagenesis with N-methyl-N'-nitro-N-nitrosoguanidine (NTG), followed by a screening methodology that focused on identifying mutants with altered Sre1 activation phenotypes. Single-nucleotide polymorphism (SNP) analysis of 20 selected mutants detected 5439 single-nucleotide variants (SNVs), narrowing them down to 1327 SNPs of interest after a series of filters. Classification based on SNP impact identified 116 candidate genes, including 49 genes with high impact and 68 genes with deleterious moderate-impact mutations. BLAST, InterProScan, and gene ontology enrichment analyses highlighted 25 genes as potential participants in regulating Sre1 in X. dendrorhous. The key findings of this study include the identification of genes potentially encoding proteins involved in protein import/export to the nucleus, sterol biosynthesis, the ubiquitin-proteasome system, protein regulatory activities such as deacetylases, a subset of kinases and proteases, as well as transcription factors that could be influential in SREBP regulation. These findings are expected to significantly contribute to the current understanding of the intricate regulation of the transcription factor Sre1 in X. dendrorhous, providing valuable groundwork for future research and potential biotechnological applications.
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Affiliation(s)
- Maximiliano Venegas
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago 7800003, Chile; (M.V.)
| | - Alejandro Durán
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago 7800003, Chile; (M.V.)
| | - Sebastián Campusano
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago 7800003, Chile; (M.V.)
| | - Salvador Barahona
- Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago 7800003, Chile
| | - Dionisia Sepúlveda
- Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago 7800003, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago 7800003, Chile; (M.V.)
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago 7800003, Chile; (M.V.)
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago 7800003, Chile; (M.V.)
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Naz T, Ullah S, Nazir Y, Li S, Iqbal B, Liu Q, Mohamed H, Song Y. Industrially Important Fungal Carotenoids: Advancements in Biotechnological Production and Extraction. J Fungi (Basel) 2023; 9:jof9050578. [PMID: 37233289 DOI: 10.3390/jof9050578] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
Carotenoids are lipid-soluble compounds that are present in nature, including plants and microorganisms such as fungi, certain bacteria, and algae. In fungi, they are widely present in almost all taxonomic classifications. Fungal carotenoids have gained special attention due to their biochemistry and the genetics of their synthetic pathway. The antioxidant potential of carotenoids may help fungi survive longer in their natural environment. Carotenoids may be produced in greater quantities using biotechnological methods than by chemical synthesis or plant extraction. The initial focus of this review is on industrially important carotenoids in the most advanced fungal and yeast strains, with a brief description of their taxonomic classification. Biotechnology has long been regarded as the most suitable alternative way of producing natural pigment from microbes due to their immense capacity to accumulate these pigments. So, this review mainly presents the recent progress in the genetic modification of native and non-native producers to modify the carotenoid biosynthetic pathway for enhanced carotenoid production, as well as factors affecting carotenoid biosynthesis in fungal strains and yeast, and proposes various extraction methods to obtain high yields of carotenoids in an attempt to find suitable greener extraction methods. Finally, a brief description of the challenges regarding the commercialization of these fungal carotenoids and the solution is also given.
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Affiliation(s)
- Tahira Naz
- Colin Ratledge Center for Microbial Lipids, College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
| | - Samee Ullah
- Colin Ratledge Center for Microbial Lipids, College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
- Faculty of Allied Health Sciences, University Institute of Food Science and Technology, The University of Lahore, Lahore 54000, Pakistan
| | - Yusuf Nazir
- Colin Ratledge Center for Microbial Lipids, College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
- Innovation Centre for Confectionery Technology (MANIS), Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
| | - Shaoqi Li
- Colin Ratledge Center for Microbial Lipids, College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
| | - Bushra Iqbal
- Colin Ratledge Center for Microbial Lipids, College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
| | - Qing Liu
- Colin Ratledge Center for Microbial Lipids, College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
| | - Hassan Mohamed
- Colin Ratledge Center for Microbial Lipids, College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo 255000, China
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Sepúlveda D, Campusano S, Moliné M, Barahona S, Baeza M, Alcaíno J, Colabella F, Urzúa B, Libkind D, Cifuentes V. Unraveling the Molecular Basis of Mycosporine Biosynthesis in Fungi. Int J Mol Sci 2023; 24:ijms24065930. [PMID: 36983003 PMCID: PMC10057719 DOI: 10.3390/ijms24065930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/13/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
The Phaffia rhodozyma UCD 67-385 genome harbors a 7873 bp cluster containing DDGS, OMT, and ATPG, encoding 2-desmethy-4-deoxygadusol synthase, O-methyl transferase, and ATP-grasp ligase, respectively, of the mycosporine glutaminol (MG) biosynthesis pathway. Homozygous deletion mutants of the entire cluster, single-gene mutants, and the Δddgs-/-;Δomt-/- and Δomt-/-;Δatpg-/- double-gene mutants did not produce mycosporines. However, Δatpg-/- accumulated the intermediate 4-deoxygadusol. Heterologous expression of the DDGS and OMT or DDGS, OMT, and ATPG cDNAs in Saccharomyces cerevisiae led to 4-deoxygadusol or MG production, respectively. Genetic integration of the complete cluster into the genome of the non-mycosporine-producing CBS 6938 wild-type strain resulted in a transgenic strain (CBS 6938_MYC) that produced MG and mycosporine glutaminol glucoside. These results indicate the function of DDGS, OMT, and ATPG in the mycosporine biosynthesis pathway. The transcription factor gene mutants Δmig1-/-, Δcyc8-/-, and Δopi1-/- showed upregulation, Δrox1-/- and Δskn7-/- showed downregulation, and Δtup6-/- and Δyap6-/- showed no effect on mycosporinogenesis in glucose-containing medium. Finally, comparative analysis of the cluster sequences in several P. rhodozyma strains and the four newly described species of the genus showed the phylogenetic relationship of the P. rhodozyma strains and their differentiation from the other species of the genus Phaffia.
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Affiliation(s)
- Dionisia Sepúlveda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Sebastián Campusano
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Martín Moliné
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (Consejo Nacional de Investigaciones Científicas y Técnicas), CONICET-UNCo, Universidad Nacional del Comahue, Bariloche 8400, Rio Negro, Argentina
| | - Salvador Barahona
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | | | - Blanca Urzúa
- Instituto de Investigación en Ciencias Odontológicas, Facultad de Odontología, Universidad de Chile, Santiago 8380492, Chile
| | - Diego Libkind
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (Consejo Nacional de Investigaciones Científicas y Técnicas), CONICET-UNCo, Universidad Nacional del Comahue, Bariloche 8400, Rio Negro, Argentina
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
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Watcharawipas A, Runguphan W. Red yeasts and their carotenogenic enzymes for microbial carotenoid production. FEMS Yeast Res 2023; 23:6895548. [PMID: 36513367 DOI: 10.1093/femsyr/foac063] [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: 06/24/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Carotenoids are C40 isoprene-based compounds with significant commercial interests that harbor diverse bioactivities. Prominent examples of carotenoids are beta-carotene, a precursor to vitamin A essential for proper eye health, and lycopene and astaxanthin, powerful antioxidants implicated in preventing cancers and atherosclerosis. Due to their benefits to human health, the market value for carotenoids is rapidly increasing and is projected to reach USD 1.7 billion by 2025. However, their production now relies on chemical synthesis and extraction from plants that pose risks to food management and numerous biological safety issues. Thus, carotenoid production from microbes is considered a promising strategy for achieving a healthy society with more sustainability. Red yeast is a heterogeneous group of basidiomycetous fungi capable of producing carotenoids. It is a critical source of microbial carotenoids from low-cost substrates. Carotenogenic enzymes from red yeasts have also been highly efficient, invaluable biological resources for biotechnological applications. In this minireview, we focus on red yeast as a promising source for microbial carotenoids, strain engineering strategies for improving carotenoid production in red yeasts, and potential applications of carotenogenic enzymes from red yeasts in conventional and nonconventional yeasts.
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Affiliation(s)
- Akaraphol Watcharawipas
- Department of Microbiology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
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Rapid Gene Target Tracking for Enhancing β-Carotene Production Using Flow Cytometry-Based High-Throughput Screening in Yarrowia lipolytica. Appl Environ Microbiol 2022; 88:e0114922. [PMID: 36094200 PMCID: PMC9552598 DOI: 10.1128/aem.01149-22] [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: 11/20/2022] Open
Abstract
β-Carotene is a provitamin A precursor and an important antioxidant that is used widely in the aquaculture, food, cosmetic, and pharmaceutical industries. Oleaginous Yarrowia lipolytica has been demonstrated as a competitive producer microorganism for the production of hydrophobic β-carotene through rational engineering strategies. However, the limited understanding of the complexity of the metabolic network between carotenoid biosynthesis and other cellular processes has hampered further advancement. Genome-scale mutagenesis and high-throughput screening of mutagenesis libraries have been extensively employed in gene mining or in the identification of key targets associated with particular phenotypes. In this study, we developed a fluorescence-activated cell-sorting approach for the effective high-throughput screening of high-β-carotene-producing strains. Using this approach, millions of mutants were screened rapidly, and new gene targets involved in lipid metabolism, sterol metabolism, signal transduction, and stress response were identified. The disruption of the genes affecting fatty acid oxidation, lipid composition, and sterol transcriptional regulation (4CL-8, GCS, and YIsterTF) increased β-carotene significantly. By engineering these targets in a high-β-carotene production, a strain that produced 9.4 g/L β-carotene was constructed. Here, we used a flow cytometry approach to improve screening efficiency and eliminate the interference of intermediate metabolites. The targets obtained in this study can be used in studies focusing on metabolic engineering in the future for improving carotenoid production. IMPORTANCE β-Carotene is a high-value-added product that is widely used in the aquaculture, food, cosmetic, and pharmaceutical industries. In our previous study, Yarrowia lipolytica has been engineered extensively to produce β-carotene. To further improve its production, high-throughput screening and the identification of new beneficial gene targets are required. Herein, we developed a fluorescence-activated cell-sorting approach for the effective high-throughput screening of high-β-carotene-producing strains. Using this approach, millions of mutants were screened rapidly, and new gene targets involved in lipid metabolism, sterol metabolism, signal transduction, and stress response were identified. The disruption of the genes affecting fatty acid oxidation, lipid composition, and sterol transcriptional regulation (4CL-8, GCS, and YIsterTF) increased β-carotene significantly. By engineering these targets in a high-β-carotene production, a strain that produced 9.4 g/L β-carotene was constructed.
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Role of ROX1, SKN7, and YAP6 Stress Transcription Factors in the Production of Secondary Metabolites in Xanthophyllomyces dendrorhous. Int J Mol Sci 2022; 23:ijms23169282. [PMID: 36012547 PMCID: PMC9409151 DOI: 10.3390/ijms23169282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Xanthophyllomyces dendrorhous is a natural source of astaxanthin and mycosporines. This yeast has been isolated from high and cold mountainous regions around the world, and the production of these secondary metabolites may be a survival strategy against the stress conditions present in its environment. Biosynthesis of astaxanthin is regulated by catabolic repression through the interaction between MIG1 and corepressor CYC8–TUP1. To evaluate the role of the stress-associated transcription factors SKN7, ROX1, and YAP6, we employed an omic and phenotypic approach. Null mutants were constructed and grown in two fermentable carbon sources. The yeast proteome and transcriptome were quantified by iTRAQ and RNA-seq, respectively. The total carotenoid, sterol, and mycosporine contents were determined and compared to the wild-type strain. Each mutant strain showed significant metabolic changes compared to the wild type that were correlated to its phenotype. In a metabolic context, the principal pathways affected were glycolysis/gluconeogenesis, the pentose phosphate (PP) pathway, and the citrate (TCA) cycle. Additionally, fatty acid synthesis was affected. The absence of ROX1 generated a significant decline in carotenoid production. In contrast, a rise in mycosporine and sterol synthesis was shown in the absence of the transcription factors SKN7 and YAP6, respectively.
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Sandmann G. Generation of stable homozygous transformants of diploid yeasts such as Xanthophyllomyces dendrorhous. Appl Microbiol Biotechnol 2022; 106:4921-4927. [PMID: 35831455 PMCID: PMC9329418 DOI: 10.1007/s00253-022-12054-2] [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: 05/04/2022] [Revised: 06/22/2022] [Accepted: 06/26/2022] [Indexed: 11/24/2022]
Abstract
The nonconventional yeast Xanthophyllomyces dendrorhous is an established platform for genetic pathway modification. A genetic tool box is available and can be used extensively to select from for different engineering strategies. Due to the diploid nature of X. dendrorhous, genetic transformation typically results in heterozygous lines. They are genetically unstable and lose their phenotypes caused by mitotic recombination. In addition, targeted integration for inactivation of genes of the carotenoid pathway resulted in an intermediary phenotype of incomplete pathway disruption. This issue is the main scope of this review. It is illustrated by using genetic modification of the carotenoid pathway of X. dendrorhous as a model system with a focus on the demonstration of how to solve these problems by generation of homozygous lines. They can be selected from heterozygous transformants after spontaneous mitotic recombination and selection or after induced meiotic recombination. Corresponding methods of how to proceed including the initiation of a sexual cycle are described. The selected segregated lines are stable in fermenter cultures without the need of selection pressure. This is an essential requirement for any industrial application. KEY POINTS: • Genetic interventions of diploid yeasts result in heterozygous transformants that are unstable without selection pressure. • This is due to mitotic recombination leading to the elimination of inserted DNA. • Stable homozygous lines can be obtained and selected after either meiotic or mitotic recombination.
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Affiliation(s)
- Gerhard Sandmann
- Institute for Molecular Biosciences, Department of Bio Sciences, Goethe University Frankfurt, Frankfurt/M, Max von Laue Str. 9, 60438, Frankfurt, Germany.
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Park H, Lee D, Kim JE, Park S, Park JH, Ha CW, Baek M, Yoon SH, Park KH, Lee P, Hahn JS. Efficient production of retinol in Yarrowia lipolytica by increasing stability using antioxidant and detergent extraction. Metab Eng 2022; 73:26-37. [PMID: 35671979 DOI: 10.1016/j.ymben.2022.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022]
Abstract
The demand for bio-based retinol (vitamin A) is currently increasing, however its instability represents a major bottleneck in microbial production. Here, we developed an efficient method to selectively produce retinol in Yarrowia lipolytica. The β-carotene 15,15'-dioxygenase (BCO) cleaves β-carotene into retinal, which is reduced to retinol by retinol dehydrogenase (RDH). Therefore, to produce retinol, we first generated β-carotene-producing strain based on a high-lipid-producer via overexpressing genes including heterologous β-carotene biosynthetic genes, GGS1F43I mutant of endogenous geranylgeranyl pyrophosphate synthase isolated by directed evolution, and FAD1 encoding flavin adenine dinucleotide synthetase, while deleting several genes previously known to be beneficial for carotenoid production. To produce retinol, 11 copies of BCO gene from marine bacterium 66A03 (Mb.Blh) were integrated into the rDNA sites of the β-carotene overproducer. The resulting strain produced more retinol than retinal, suggesting strong endogenous promiscuous RDH activity in Y. lipolytica. The introduction of Mb.BCO led to a considerable reduction in β-carotene level, but less than 5% of the consumed β-carotene could be detected in the form of retinal or retinol, implying severe degradation of the produced retinoids. However, addition of the antioxidant butylated hydroxytoluene (BHT) led to a >20-fold increase in retinol production, suggesting oxidative damage is the main cause of intracellular retinol degradation. Overexpression of GSH2 encoding glutathione synthetase further improved retinol production. Raman imaging revealed co-localization of retinol with lipid droplets, and extraction of retinol using Tween 80 was effective in improving retinol production. By combining BHT treatment and extraction using Tween 80, the final strain CJ2104 produced 4.86 g/L retinol and 0.26 g/L retinal in fed-batch fermentation in a 5-L bioreactor, which is the highest retinol production titer ever reported. This study demonstrates that Y. lipolytica is a suitable host for the industrial production of bio-based retinol.
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Affiliation(s)
- Hyemin Park
- Bio Research Institutes, CJ CheilJedang, Suwon, 16495, South Korea
| | - Dongpil Lee
- Bio Research Institutes, CJ CheilJedang, Suwon, 16495, South Korea
| | - Jae-Eung Kim
- Bio Research Institutes, CJ CheilJedang, Suwon, 16495, South Korea
| | - Seonmi Park
- Bio Research Institutes, CJ CheilJedang, Suwon, 16495, South Korea
| | - Joo Hyun Park
- Bio Research Institutes, CJ CheilJedang, Suwon, 16495, South Korea
| | - Cheol Woong Ha
- Bio Research Institutes, CJ CheilJedang, Suwon, 16495, South Korea
| | - Minji Baek
- Bio Research Institutes, CJ CheilJedang, Suwon, 16495, South Korea
| | - Seok-Hwan Yoon
- Bio Research Institutes, CJ CheilJedang, Suwon, 16495, South Korea
| | - Kwang Hyun Park
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Peter Lee
- Bio Research Institutes, CJ CheilJedang, Suwon, 16495, South Korea.
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea.
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Basiony M, Ouyang L, Wang D, Yu J, Zhou L, Zhu M, Wang X, Feng J, Dai J, Shen Y, Zhang C, Hua Q, Yang X, Zhang L. Optimization of microbial cell factories for astaxanthin production: Biosynthesis and regulations, engineering strategies and fermentation optimization strategies. Synth Syst Biotechnol 2022; 7:689-704. [PMID: 35261927 PMCID: PMC8866108 DOI: 10.1016/j.synbio.2022.01.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/08/2021] [Accepted: 01/03/2022] [Indexed: 12/29/2022] Open
Abstract
The global market demand for natural astaxanthin is rapidly increasing owing to its safety, the potential health benefits, and the diverse applications in food and pharmaceutical industries. The major native producers of natural astaxanthin on industrial scale are the alga Haematococcus pluvialis and the yeast Xanthopyllomyces dendrorhous. However, the natural production via these native producers is facing challenges of limited yield and high cost of cultivation and extraction. Alternatively, astaxanthin production via metabolically engineered non-native microbial cell factories such as Escherichia coli, Saccharomyces cerevisiae and Yarrowia lipolytica is another promising strategy to overcome these limitations. In this review we summarize the recent scientific and biotechnological progresses on astaxanthin biosynthetic pathways, transcriptional regulations, the interrelation with lipid metabolism, engineering strategies as well as fermentation process control in major native and non-native astaxanthin producers. These progresses illuminate the prospects of producing astaxanthin by microbial cell factories on industrial scale.
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Affiliation(s)
- Mostafa Basiony
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Liming Ouyang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Danni Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiaming Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Liming Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Mohan Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xuyuan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jie Feng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jing Dai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yijie Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Chengguo Zhang
- Shandong Jincheng Bio-Pharmaceutical Co., Ltd., No. 117 Qixing River Road, Zibo, 255130, Shandong, China
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiuliang Yang
- Shandong Jincheng Bio-Pharmaceutical Co., Ltd., No. 117 Qixing River Road, Zibo, 255130, Shandong, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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González AM, Venegas M, Barahona S, Gómez M, Gutiérrez MS, Sepúlveda D, Baeza M, Cifuentes V, Alcaíno J. Damage response protein 1 (Dap1) functions in the synthesis of carotenoids and sterols in Xanthophyllomyces dendrorhous. J Lipid Res 2022; 63:100175. [PMID: 35120994 PMCID: PMC8953664 DOI: 10.1016/j.jlr.2022.100175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 11/25/2022] Open
Abstract
Cytochrome P450s (P450s) are heme-containing proteins involved in several cellular functions, including biosynthesis of steroidal hormones, detoxification of xenobiotic compounds, among others. Damage response protein 1 (Dap1) has been described as a positive regulator of P450s through protein-protein interactions in organisms such as Schizosaccharomyces pombe. Three P450s in the carotenogenic yeast Xanthophyllomyces dendrorhous have thus far been characterized: Cyp51 and Cyp61, which are involved in ergosterol biosynthesis, and CrtS (astaxanthin synthase), which is involved in biosynthesis of the carotenoid astaxanthin. In this work, we describe the X. dendrorhous DAP1 gene, deletion of which affected yeast pigmentation by decreasing the astaxanthin fraction and increasing the β-carotene (a substrate of CrtS) fraction, which is consistent with the known role of CrtS. We found that the proportion of ergosterol was also decreased in the Δdap1 mutant. However, even though the fractions of the end products of these two pathways (the synthesis of carotenoids and sterols) were decreased in the Δdap1 mutant, the transcript levels of genes from the P450 systems involved were higher than those in the wild-type strain. We demonstrate that Dap1 coimmunoprecipitates with these three P450s, suggesting that Dap1 interacts with these three proteins. We propose that Dap1 regulates the synthesis of astaxanthin and ergosterol in X. dendrorhous, probably by regulating the P450s involved in both biosynthetic pathways at the protein level. This work suggests a new role for Dap1 in the regulation of carotenoid biosynthesis in X. dendrorhous.
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Affiliation(s)
- Ana-María González
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Maximiliano Venegas
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Salvador Barahona
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Melissa Gómez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - María-Soledad Gutiérrez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dionisia Sepúlveda
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile; Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile; Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile; Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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12
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Li Z, Yang H, Zheng C, Du X, Ni H, He N, Yang L, You L, Zhu Y, Li L. Effectively Improve the Astaxanthin Production by Combined Additives Regulating Different Metabolic Nodes in Phaffia rhodozyma. Front Bioeng Biotechnol 2022; 9:812309. [PMID: 35111739 PMCID: PMC8801872 DOI: 10.3389/fbioe.2021.812309] [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: 11/10/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022] Open
Abstract
Astaxanthin is an important natural resource that is widely found in marine environments. Metabolic regulation is an effective method for improving astaxanthin production in Phaffia rhodozyma. Most studies have focused on single regulators, which have limited effects. In this study, 16 metabolic regulators were screened to improve astaxanthin production in high-yield and wild-type strains. Fluconazol and glutamic acid increased astaxanthin volumetric yield in MVP14 by 25.8 and 30.9%, respectively, while ethanol increased astaxanthin volumetric yield in DSM626, 29.3%. Furthermore, six additives that inhibit the competing pathways and promote the main pathway for astaxanthin synthesis were selected for combination treatment. We found that the optimal combination was penicillin, ethanol, triclosan, and fluconazol, which increased astaxanthin cell yield by 51%. Therefore, we suggest that simultaneously promoting the master pathways (mevalonate) and inhibiting competing pathways (fatty acid synthesis and ergosterol) is the best strategy to improve astaxanthin cell yield. Moreover, regulators of the biomass pathway should be avoided to improve cell yield. This study provides a technical basis for the utilisation of astaxanthin in P. rhodozyma.
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Affiliation(s)
- Zhipeng Li
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Haoyi Yang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Chenhua Zheng
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Xiping Du
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Hui Ni
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Liang Yang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Li You
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Yanbing Zhu
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Lijun Li
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Technology, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, Xiamen, China
- *Correspondence: Lijun Li,
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13
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Gómez M, Baeza M, Cifuentes V, Alcaíno J. The SREBP (Sterol Regulatory Element-Binding Protein) pathway: a regulatory bridge between carotenogenesis and sterol biosynthesis in the carotenogenic yeast Xanthophyllomyces dendrorhous. Biol Res 2021; 54:34. [PMID: 34702374 PMCID: PMC8549280 DOI: 10.1186/s40659-021-00359-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/16/2021] [Indexed: 11/22/2022] Open
Abstract
Xanthophyllomyces dendrorhous is a basidiomycete yeast that naturally produces the red–orange carotenoid astaxanthin, which has remarkable antioxidant properties. The biosynthesis of carotenoids and sterols share some common elements that have been studied in X. dendrorhous. For example, their synthesis requires metabolites derived from the mevalonate pathway and in both specific pathways, cytochrome P450 enzymes are involved that share a single cytochrome P450 reductase, CrtR, which is essential for astaxanthin biosynthesis, but is replaceable for ergosterol biosynthesis. Research on the regulation of carotenoid biosynthesis is still limited in X. dendrorhous; however, it is known that the Sterol Regulatory Element-Binding Protein (SREBP) pathway, which is a conserved regulatory pathway involved in the control of lipid metabolism, also regulates carotenoid production in X. dendrorhous. This review addresses the similarities and differences that have been observed between mammal and fungal SREBP pathways and what it is known about this pathway regarding the regulation of the production of carotenoids and sterols in X. dendrorhous.
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Affiliation(s)
- Melissa Gómez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile.,Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile.,Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile. .,Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile.
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14
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Liu XG, Lu X, Gao W, Li P, Yang H. Structure, synthesis, biosynthesis, and activity of the characteristic compounds from Ginkgo biloba L. Nat Prod Rep 2021; 39:474-511. [PMID: 34581387 DOI: 10.1039/d1np00026h] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: 1928-2021Ginkgo biloba L. is one of the most distinctive plants to have emerged on earth and has no close living relatives. Owing to its phylogenetic divergence from other plants, G. biloba contains many compounds with unique structures that have served to broaden the chemical diversity of herbal medicine. Examples of such compounds include terpene trilactones (ginkgolides), acylated flavonol glycosides (ginkgoghrelins), biflavones (ginkgetin), ginkgotides and ginkgolic acids. The extract of G. biloba leaf is used to prevent and/or treat cardiovascular diseases, while many ginkgo-derived compounds are currently at various stages of preclinical and clinical trials worldwide. The global annual sales of G. biloba products are estimated to total US$10 billion. However, the content and purity of the active compounds isolated by traditional methods are usually low and subject to varying environmental factors, making it difficult to meet the huge demand of the international market. This highlights the need to develop new strategies for the preparation of these characteristic compounds from G. biloba. In this review, we provide a detailed description of the structures and bioactivities of these compounds and summarize the recent research on the development of strategies for the synthesis, biosynthesis, and biotechnological production of the characteristic terpenoids, flavonoids, and alkylphenols/alkylphenolic acids of G. biloba. Our aim is to provide an important point of reference for all scientists who research ginkgo-related compounds for medicinal or other purposes.
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Affiliation(s)
- Xin-Guang Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, #24 Tong Jia Xiang, Nanjing 210009, China.
| | - Xu Lu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, #24 Tong Jia Xiang, Nanjing 210009, China.
| | - Wen Gao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, #24 Tong Jia Xiang, Nanjing 210009, China.
| | - Ping Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, #24 Tong Jia Xiang, Nanjing 210009, China.
| | - Hua Yang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, #24 Tong Jia Xiang, Nanjing 210009, China.
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15
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Torres-Haro A, Verdín J, Kirchmayr MR, Arellano-Plaza M. Metabolic engineering for high yield synthesis of astaxanthin in Xanthophyllomyces dendrorhous. Microb Cell Fact 2021; 20:175. [PMID: 34488760 PMCID: PMC8420053 DOI: 10.1186/s12934-021-01664-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
Astaxanthin is a carotenoid with a number of assets useful for the food, cosmetic and pharmaceutical industries. Nowadays, it is mainly produced by chemical synthesis. However, the process leads to an enantiomeric mixture where the biologically assimilable forms (3R, 3'R or 3S, 3'S) are a minority. Microbial production of (3R, 3'R) astaxanthin by Xanthophyllomyces dendrorhous is an appealing alternative due to its fast growth rate and easy large-scale production. In order to increase X. dendrorhous astaxanthin yields, random mutant strains able to produce from 6 to 10 mg/g dry mass have been generated; nevertheless, they often are unstable. On the other hand, site-directed mutant strains have also been obtained, but they increase only the yield of non-astaxanthin carotenoids. In this review, we insightfully analyze the metabolic carbon flow converging in astaxanthin biosynthesis and, by integrating the biological features of X. dendrorhous with available metabolic, genomic, transcriptomic, and proteomic data, as well as the knowledge gained with random and site-directed mutants that lead to increased carotenoids yield, we propose new metabolic engineering targets to increase astaxanthin biosynthesis.
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Affiliation(s)
- Alejandro Torres-Haro
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, Col. El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
| | - Jorge Verdín
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, Col. El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
| | - Manuel R Kirchmayr
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, Col. El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico
| | - Melchor Arellano-Plaza
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, Col. El Bajío del Arenal, 45019, Zapopan, Jalisco, Mexico.
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16
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Gómez M, Campusano S, Gutiérrez MS, Sepúlveda D, Barahona S, Baeza M, Cifuentes V, Alcaíno J. Sterol regulatory element-binding protein Sre1 regulates carotenogenesis in the red yeast Xanthophyllomyces dendrorhous. J Lipid Res 2020; 61:1658-1674. [PMID: 32933952 PMCID: PMC7707178 DOI: 10.1194/jlr.ra120000975] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Xanthophyllomyces dendrorhous is a basidiomycete yeast that produces carotenoids, mainly astaxanthin. Astaxanthin is an organic pigment of commercial interest due to its antioxidant and coloring properties. X. dendrorhous has a functional SREBP pathway, and the Sre1 protein is the SREBP homolog in this yeast. However, how sterol regulatory element (Sre)1 promotes the biosynthesis of sterols and carotenoids in X. dendrorhous is unknown. In this work, comparative RNA-sequencing analysis between modified X. dendrorhous strains that have an active Sre1 protein and the WT was performed to identify Sre1-dependent genes. In addition, Sre1 direct target genes were identified through ChIP combined with lambda exonuclease digestion (ChIP-exo) assays. SRE motifs were detected in the promoter regions of several Sre1 direct target genes and were consistent with the SREs described in other yeast species. Sre1 directly regulates genes related to ergosterol biosynthesis as well as genes related to the mevalonate (MVA) pathway, which synthesizes the building blocks of isoprenoids, including carotenoids. Two carotenogenic genes, crtE and crtR, were also identified as Sre1 direct target genes. Thus, carotenogenesis in X. dendrorhous is regulated by Sre1 through the regulation of the MVA pathway and the regulation of the crtE and crtR genes. As the crtR gene encodes a cytochrome P450 reductase, Sre1 regulates pathways that include cytochrome P450 enzymes, such as the biosynthesis of carotenoids and sterols. These results demonstrate that Sre1 is a sterol master regulator that is conserved in X. dendrorhous.
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Affiliation(s)
- Melissa Gómez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sebastián Campusano
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - María Soledad Gutiérrez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dionisia Sepúlveda
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Salvador Barahona
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile; Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile; Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile; Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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17
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David-Palma M, Libkind D, Brito PH, Silva M, Bellora N, Coelho MA, Heitman J, Gonçalves P, Sampaio JP. The Untapped Australasian Diversity of Astaxanthin-Producing Yeasts with Biotechnological Potential- Phaffia australis sp. nov. and Phaffia tasmanica sp. nov. Microorganisms 2020; 8:E1651. [PMID: 33114402 PMCID: PMC7692969 DOI: 10.3390/microorganisms8111651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 01/28/2023] Open
Abstract
Phaffia is an orange-colored basidiomycetous yeast genus of the order Cystofilobasidiales that contains a single species, P. rhodozyma. This species is the only fungus known to produce the economically relevant carotenoid astaxanthin. Although Phaffia was originally found in the Northern hemisphere, its diversity in the southern part of the globe has been shown to be much greater. Here we analyze the genomes of two Australasian lineages that are markedly distinct from P. rhodozyma. The two divergent lineages were investigated within a comprehensive phylogenomic study of representatives of the Cystofilobasidiales that supported the recognition of two novel Phaffia species, for which we propose the names of P. australis sp. nov. and P. tasmanica sp. nov. Comparative genomics and other analyses confirmed that the two new species have the typical Phaffia hallmark-the six genes necessary for the biosynthesis of astaxanthin could be retrieved from the draft genome sequences, and this carotenoid was detected in culture extracts. In addition, the organization of the mating-type (MAT) loci is similar to that of P. rhodozyma, with synteny throughout most regions. Moreover, cases of trans-specific polymorphism involving pheromone receptor genes and pheromone precursor proteins in the three Phaffia species, together with their shared homothallism, provide additional support for their classification in a single genus.
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Affiliation(s)
- Márcia David-Palma
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC)—CONICET/Universidad Nacional del Comahue, Bariloche, Rio Negro 8400, Argentina; (D.L.); (N.B.)
| | - Patrícia H. Brito
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
| | - Margarida Silva
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
| | - Nicolás Bellora
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC)—CONICET/Universidad Nacional del Comahue, Bariloche, Rio Negro 8400, Argentina; (D.L.); (N.B.)
| | - Marco A. Coelho
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Paula Gonçalves
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
| | - José Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (M.D.-P.); (P.H.B.); (M.S.); (M.A.C.); (P.G.)
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18
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Venegas M, Barahona S, González AM, Sepúlveda D, Zúñiga GE, Baeza M, Cifuentes V, Alcaíno J. Phenotypic Analysis of Mutants of Ergosterol Biosynthesis Genes ( ERG3 and ERG4) in the Red Yeast Xanthophyllomyces dendrorhous. Front Microbiol 2020; 11:1312. [PMID: 32612595 PMCID: PMC7309136 DOI: 10.3389/fmicb.2020.01312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/25/2020] [Indexed: 12/29/2022] Open
Abstract
Xanthophyllomyces dendrorhous synthesizes astaxanthin, a carotenoid used in aquaculture. Astaxanthin is synthesized from metabolites of the mevalonate pathway, which are also precursors for sterols biosynthesis. The interruption of the CYP61 gene, which is involved in the synthesis of ergosterol (mutant CBS.cyp61 -), resulted in a phenotype that overproduces carotenoids due to the activation of the SREBP pathway. In this work, we constructed other mutants of ergosterol biosynthesis in this yeast to evaluate whether they have the same phenotype as mutant CBS.cyp61 -. By bioinformatic analysis, the ERG3 and ERG4 genes of X. dendrorhous were identified, and each gene was deleted in the wild-type strain. Mutants CBS.Δerg3 and CBS.Δerg4 did not produce ergosterol; CBS.Δerg3 primarily accumulated episterol, and CBS.Δerg4 primarily accumulated ergosta-5,7,22,24(28)-tetraenol. The transcription levels of the HMGS gene of the mevalonate pathway were evaluated by RT-qPCR, which showed a slight increase in CBS.Δerg4, but the transcription levels were still 10-fold lower than in strain CBS.cyp61 -. Both CBS.Δerg3 and CBS.Δerg4 did not overproduce carotenoids, even though they do not produce ergosterol. Thus, the results of this study indicate that the absence of ergosterol does not activate the SREBP pathway in X. dendrorhous, but rather it depends on other alterations in sterol composition.
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Affiliation(s)
- Maximiliano Venegas
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Salvador Barahona
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ana María González
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dionisia Sepúlveda
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Gustavo E. Zúñiga
- Departamento de Biología, Facultad de Química y Biología, CEDENNA, Universidad de Santiago de Chile, Santiago, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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19
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Venil CK, Velmurugan P, Dufossé L, Renuka Devi P, Veera Ravi A. Fungal Pigments: Potential Coloring Compounds for Wide Ranging Applications in Textile Dyeing. J Fungi (Basel) 2020; 6:E68. [PMID: 32443916 PMCID: PMC7344934 DOI: 10.3390/jof6020068] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 12/25/2022] Open
Abstract
Synthetic pigments/non-renewable coloring sources used normally in the textile industry release toxic substances into the environment, causing perilous ecological challenges. To be safer from such challenges of synthetic colorants, academia and industries have explored the use of natural colorants such as microbial pigments. Such explorations have created a fervent interest among textile stakeholders to undertake the dyeing of textile fabrics, especially with fungal pigments. The biodegradable and sustainable production of natural colorants from fungal sources stand as being comparatively advantageous to synthetic dyes. The prospective scope of fungal pigments has emerged in the opening of many new avenues in textile colorants for wide ranging applications. Applying the biotechnological processes, fungal pigments like carotenoids, melanins, flavins, phenazines, quinones, monascins, violacein, indigo, etc. could be extracted on an industrial scale. This review appraises the studies and applications of various fungal pigments in dyeing textile fabrics and is furthermore shedding light on the importance of toxicity testing, genetic manipulations of fungal pigments, and their future perspectives under biotechnological approaches.
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Affiliation(s)
| | - Palanivel Velmurugan
- Department of Biotechnology, Alagappa University – Science Campus, Karaikudi 630003, Tamil Nadu, India; (P.V.); (A.V.R.)
| | - Laurent Dufossé
- CHEMBIOPRO Chimie et Biotechnologie des Produits Naturels, ESIROI Département agroalimentaire, Université de la Réunion, F-97490 Sainte-Clotilde, Ile de La Réunion, Indian Ocean, France
| | - Ponnuswamy Renuka Devi
- Department of Biotechnology, Anna University, Regional Campus – Coimbatore, Coimbatore 641046, Tamil Nadu, India;
| | - Arumugam Veera Ravi
- Department of Biotechnology, Alagappa University – Science Campus, Karaikudi 630003, Tamil Nadu, India; (P.V.); (A.V.R.)
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Gómez M, Gutiérrez MS, González AM, Gárate-Castro C, Sepúlveda D, Barahona S, Baeza M, Cifuentes V, Alcaíno J. Metallopeptidase Stp1 activates the transcription factor Sre1 in the carotenogenic yeast Xanthophyllomyces dendrorhous. J Lipid Res 2020; 61:229-243. [PMID: 31806730 PMCID: PMC6997601 DOI: 10.1194/jlr.ra119000431] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/07/2019] [Indexed: 01/10/2023] Open
Abstract
Xanthophyllomyces dendrorhous is a basidiomycete yeast known as a natural producer of astaxanthin, a carotenoid of commercial interest because of its antioxidant properties. Recent studies indicated that X. dendrorhous has a functional SREBP pathway involved in the regulation of isoprenoid compound biosynthesis, which includes ergosterol and carotenoids. SREBP is a major regulator of sterol metabolism and homeostasis in mammals; characterization in fungi also provides information about its role in the hypoxia adaptation response and virulence. SREBP protease processing is required to activate SREBP pathway functions in fungi. Here, we identified and described the STP1 gene, which encodes a metallopeptidase of the M50 family involved in the proteolytic activation of the transcription factor Sre1 of the SREBP pathway, in X. dendrorhous We assessed STP1 function in Δstp1 strains derived from the wild-type and a mutant of ergosterol biosynthesis that overproduces carotenoids and sterols. Bioinformatic analysis of the deduced protein predicted the presence of characteristic features identified in homologs from mammals and fungi. The Δstp1 mutation decreased yeast growth in the presence of azole drugs and reduced transcript levels of Sre1-dependent genes. This mutation also negatively affected the carotenoid- and sterol-overproducing phenotype. Western blot analysis demonstrated that Sre1 was activated in the yeast ergosterol biosynthesis mutant and that the Δstp1 mutation introduced in this strain prevented Sre1 proteolytic activation. Overall, our results demonstrate that STP1 encodes a metallopeptidase involved in proteolytic activation of Sre1 in X. dendrorhous, contributing to our understanding of fungal SREBP pathways.
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Affiliation(s)
- Melissa Gómez
- Departamento de Ciencias Ecológicas Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - María Soledad Gutiérrez
- Departamento de Ciencias Ecológicas Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ana María González
- Departamento de Ciencias Ecológicas Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Carla Gárate-Castro
- Departamento de Ciencias Ecológicas Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dionisia Sepúlveda
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Salvador Barahona
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Wang B, Pan X, Jia J, Xiong W, Manirafasha E, Ling X, Yinghua L. Strategy and regulatory mechanisms of glutamate feeding to enhance astaxanthin yield in Xanthophyllomyces dendrorhous. Enzyme Microb Technol 2019; 125:45-52. [DOI: 10.1016/j.enzmictec.2019.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 01/31/2019] [Accepted: 02/27/2019] [Indexed: 01/05/2023]
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22
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Gutiérrez MS, Campusano S, González AM, Gómez M, Barahona S, Sepúlveda D, Espenshade PJ, Fernández-Lobato M, Baeza M, Cifuentes V, Alcaíno J. Sterol Regulatory Element-Binding Protein (Sre1) Promotes the Synthesis of Carotenoids and Sterols in Xanthophyllomyces dendrorhous. Front Microbiol 2019; 10:586. [PMID: 30984134 PMCID: PMC6449425 DOI: 10.3389/fmicb.2019.00586] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/07/2019] [Indexed: 12/31/2022] Open
Abstract
Xanthophyllomyces dendrorhous is a basidiomycete yeast that synthesizes carotenoids, mainly astaxanthin, which are of great commercial interest. Currently, there are many unknown aspects related to regulatory mechanisms on the synthesis of carotenoids in this yeast. Our recent studies showed that changes in sterol levels and composition resulted in upregulation of genes in the mevalonate pathway required for the synthesis of carotenoid precursors, leading to increased production of these pigments. Sterol Regulatory Element-Binding Proteins (SREBP), called Sre1 in yeast, are conserved transcriptional regulators of sterol homeostasis and other cellular processes. Given the results linking sterols and carotenoids, we investigated the role of SREBP in sterol and carotenoid synthesis in X. dendrorhous. In this study, we present the identification and functional characterization of the X. dendrorhous SRE1 gene, which encodes the transcription factor Sre1. The deduced protein has the characteristic features of SREBP/Sre1 and binds to consensus DNA sequences in vitro. RNA-seq analysis and chromatin-immunoprecipitation experiments showed that genes of the mevalonate pathway and ergosterol biosynthesis are directly regulated by Sre1. The sre1- mutation reduced sterol and carotenoid production in X. dendrorhous, and expression of the Sre1 N-terminal domain (Sre1N) increased carotenoid production more than twofold compared to wild-type. Overall, our results indicate that in X. dendrorhous transcriptional regulation of genes in the mevalonate pathway control production of the isoprenoid derivatives, carotenoids and sterol. Our results provide new insights into the conserved regulatory functions of SREBP/Sre1 and identify pointing to the SREBP pathway as a potential target to enhance carotenoid production in X. dendrorhous.
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Affiliation(s)
- María Soledad Gutiérrez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sebastián Campusano
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ana María González
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Melissa Gómez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Salvador Barahona
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dionisia Sepúlveda
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Peter J. Espenshade
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - María Fernández-Lobato
- Centro de Biologiìa Molecular Severo Ochoa, Departamento de Biologiìa Molecular (UAM-CSIC), Universidad Autoìnoma de Madrid, Madrid, Spain
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Reyes-Cerpa S, Vallejos-Vidal E, Gonzalez-Bown MJ, Morales-Reyes J, Pérez-Stuardo D, Vargas D, Imarai M, Cifuentes V, Spencer E, Sandino AM, Reyes-López FE. Effect of yeast (Xanthophyllomyces dendrorhous) and plant (Saint John's wort, lemon balm, and rosemary) extract based functional diets on antioxidant and immune status of Atlantic salmon (Salmo salar) subjected to crowding stress. FISH & SHELLFISH IMMUNOLOGY 2018; 74:250-259. [PMID: 29305990 DOI: 10.1016/j.fsi.2017.12.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/18/2017] [Accepted: 12/31/2017] [Indexed: 06/07/2023]
Abstract
Salmon farming may face stress due to the intensive culture conditions with negative impacts on overall performance. In this aspect, functional feed improves not only the basic nutritional requirements but also the health status and fish growth. However, to date no studies have been carried out to evaluate the effect of functional diets in salmon subjected to crowding stress. Thus, the aim of this study was to evaluate the effect of yeast extract (Xanthophyllomyces dendrorhous; diet A) and the combination of plant extracts (common Saint John's wort, lemon balm, and rosemary; diet B) on the antioxidant and immune status of Atlantic salmon grown under normal cultured conditions and then subjected to crowding stress. Fish were fed with functional diets during 30 days (12 kg/m3) and then subjected to crowding stress (20 kg/m3) for 10 days. The lipid peroxidation in gut showed that both diets induced a marked decrease on oxidative damage when fish were subjected to crowding stress. The protein carbonylation in muscle displayed at day 30 a marked decrease in both functional diets that was more marked on the stress condition. The expression of immune markers (IFNγ, CD4, IL-10, TGF-β, IgMmb, IgMsec, T-Bet, and GATA-3) indicated the upregulation of those associated to humoral-like response (CD4, IL-10, GATA-3) when fish were subjected to crowding stress. These results were confirmed with the expression of secreted IgM. Altogether, these functional diets improved the antioxidant status and increased the expression of genes related to Th2-like response suggesting a protective role on fish subjected to crowding stress.
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Affiliation(s)
| | - Eva Vallejos-Vidal
- Department of Cell Biology, Physiology and Immunology, Faculty of Biosciences (Building C), Universitat Autonoma de Barcelona, 08193, Bellaterra, Spain
| | - María José Gonzalez-Bown
- Laboratorio de Virología, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Jonathan Morales-Reyes
- Laboratorio de Virología, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Diego Pérez-Stuardo
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Chile
| | - Deborah Vargas
- Laboratorio de Virología, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mónica Imarai
- Laboratorio de Inmunología, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Víctor Cifuentes
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Eugenio Spencer
- Laboratorio de Virología, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Ana María Sandino
- Laboratorio de Virología, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile; ActivaQ S.A. General del Canto 460, Providencia, Santiago, Chile.
| | - Felipe E Reyes-López
- Department of Cell Biology, Physiology and Immunology, Faculty of Biosciences (Building C), Universitat Autonoma de Barcelona, 08193, Bellaterra, Spain.
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Alcalde E, Fraser PD. Extending our tools and resources in the non-conventional industrial yeast Xanthophyllomyces dendrorhous through the application of metabolite profiling methodologies. Metabolomics 2018; 14:30. [PMID: 29479298 PMCID: PMC5809543 DOI: 10.1007/s11306-017-1313-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/22/2017] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Xanthophyllomyces dendrorhous is a non-conventional industrial yeast. It has the unique ability among yeasts to produce geranylgeranyl pyrophosphate derived terpenoids such as carotenoids and in particular the high value pigment astaxanthin. OBJECTIVE In order to fully exploit the industrial potential of Xanthophyllomyces using modern industrial biotechnology approaches the further development of "omic" resources in this organism are required to build on the now sequenced and annotated genome. To contribute to this goal, the present study has developed and implemented an efficient metabolite profiling system comprised of, quenching, extraction and associated GC-MS and UPLC analysis. METHOD Four quenching methods and five extraction methods compatible with GC-MS and UPLC profiling were tested and validated by analysing steady state metabolite changes of Xanthophyllomyces cultivated at laboratory scale in liquid shake culture at lag, exponential and early and late stationary phases. RESULTS A customised Automated Mass Spectral Deconvolution and Identification System (AMDIS) library has been created for Xanthophyllomyces, over 400 compounds are present in the library of which 78 are detected and quantified routinely in polar and non-polar derived extracts. A preliminary biochemical network has been constructed. Over a standardised laboratory growth cycle, changes in metabolite levels have been determined to create reference point for future strain improvement approaches and the initial biochemical network construction. Correlation analysis has illustrated that astaxanthin formation correlates positively with different sectors of intermediary metabolism (e.g. the TCA cycle intermediates and amino acid formation), "short" saturated fatty acids and β-carotene, while other metabolites are reduced in response to astaxanthin production. These sectors of intermediary metabolism offer potential future targets for the manipulation resulting in the generation of strains with improved titres of given terpenoids. DISCUSSION In summary a robust metabolite profiling system for Xanthophyllomyces is in place to further our understanding and potential exploitation of this underutilised industrial yeast.
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Affiliation(s)
- Eugenio Alcalde
- School Biological Sciences, Royal Holloway, University London, Egham Hill, Egham, Surrey TW20OEX UK
| | - Paul D. Fraser
- School Biological Sciences, Royal Holloway, University London, Egham Hill, Egham, Surrey TW20OEX UK
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Plotkin BJ, Konakieva MI. Attenuation of antimicrobial activity by the human steroid hormones. Steroids 2017; 128:120-127. [PMID: 28951169 DOI: 10.1016/j.steroids.2017.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/28/2017] [Accepted: 09/20/2017] [Indexed: 11/16/2022]
Abstract
Upon entering the human host, Staphylococcus aureus is exposed to endogenous steroid hormones. The interaction between S. aureus and dehydroepiandosterone (DHEA) results in an increased resistance to the host cationic defense peptide, β-1 defensin, as well as vancomycin and other antibiotics that have a positive charge. The increased resistance to vancomycin is phenotypic and appears to correlate with a DHEA-mediated alteration in cell surface architecture. DHEA-mediated cell surface changes include alterations in: cell surface charge, surface hydrophobicity, capsule production, and carotenoid production. In addition, exposure to DHEA results in decreased resistance to lysis by Triton X-100 and lysozyme, indicating activation of murien hydrolase activity. We propose that DHEA is an interspecies quorum-like signal that triggers innate phenotypic host survival strategies in S. aureus that include increased carotenoid production and increased vancomycin resistance. Furthermore, this DHEA-mediated survival system may share the cholesterol-squalene pathway shown to be statin sensitive thus, providing a potential pathway for drug targeting.
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Affiliation(s)
- Balbina J Plotkin
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, IL 60515, United States.
| | - Monika I Konakieva
- Department of Chemistry, American University, Washington, DC 20016, United States.
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Córdova P, Gonzalez AM, Nelson DR, Gutiérrez MS, Baeza M, Cifuentes V, Alcaíno J. Characterization of the cytochrome P450 monooxygenase genes (P450ome) from the carotenogenic yeast Xanthophyllomyces dendrorhous. BMC Genomics 2017; 18:540. [PMID: 28724407 PMCID: PMC5516332 DOI: 10.1186/s12864-017-3942-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/13/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases involved in the oxidative metabolism of an enormous diversity of substrates. These enzymes require electrons for their activity, and the electrons are supplied by NAD(P)H through a P450 electron donor system, which is generally a cytochrome P450 reductase (CPR). The yeast Xanthophyllomyces dendrorhous has evolved an exclusive P450-CPR system that specializes in the synthesis of astaxanthin, a carotenoid with commercial potential. For this reason, the aim of this work was to identify and characterize other potential P450 genes in the genome of this yeast using a bioinformatic approach. RESULTS Thirteen potential P450-encoding genes were identified, and the analysis of their deduced proteins allowed them to be classified in ten different families: CYP51, CYP61, CYP5139 (with three members), CYP549A, CYP5491, CYP5492 (with two members), CYP5493, CYP53, CYP5494 and CYP5495. Structural analyses of the X. dendrorhous P450 proteins showed that all of them have a predicted transmembrane region at their N-terminus and have the conserved domains characteristic of the P450s, including the heme-binding region (FxxGxRxCxG); the PER domain, with the characteristic signature for fungi (PxRW); the ExxR motif in the K-helix region and the oxygen-binding domain (OBD) (AGxDTT); also, the characteristic secondary structure elements of all the P450 proteins were identified. The possible functions of these P450s include primary, secondary and xenobiotic metabolism reactions such as sterol biosynthesis, carotenoid synthesis and aromatic compound degradation. CONCLUSIONS The carotenogenic yeast X. dendrorhous has thirteen P450-encoding genes having potential functions in primary, secondary and xenobiotic metabolism reactions, including some genes of great interest for fatty acid hydroxylation and aromatic compound degradation. These findings established a basis for future studies about the role of P450s in the carotenogenic yeast X. dendrorhous and their potential biotechnological applications.
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Affiliation(s)
- Pamela Córdova
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Ana-María Gonzalez
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - María-Soledad Gutiérrez
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile.
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Tian Y, Feng F, Zhang B, Li M, Wang F, Gu L, Chen A, Li Z, Shan W, Wang X, Chen X, Zhang Z. Transcriptome analysis reveals metabolic alteration due to consecutive monoculture and abiotic stress stimuli in Rehamannia glutinosa Libosch. PLANT CELL REPORTS 2017; 36:859-875. [PMID: 28275853 DOI: 10.1007/s00299-017-2115-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/07/2017] [Indexed: 06/06/2023]
Abstract
We deeply investigated the mechanism underlying metabolic regulation in response to consecutive monoculture (replanting disease) and different abiotic stresses that unfolded the response mechanism to consecutive monoculture problem through RNA-seq analysis. The consecutive monoculture problem (CMP) resulted of complex environmental stresses mediated by multiple factors. Previous studies have noted that multiple stress factors in consecutive monoculture soils or plants severely limited the interpretation of the critical molecular mechanism, and made a predict that the specifically responding factor was autotoxic allelochemicals. To identify the specifically responding genes, we compared transcriptome changes in roots of Rehamannia glutinosa Libosch using consecutive monoculture, salt, drought, and ferulic acid as stress factors. Comparing with normal growth, 2502, 2672, 2485, and 1956 genes were differentially expressed in R. glutinosa under consecutive monoculture practice, salt, drought, and ferulic acid stress, respectively. In addition, 510 genes were specifically expressed under consecutive monoculture, which were not present under the other stress conditions. Integrating the biological and enrichment analyses of the differentially expressed genes, the result demonstrated that the plants could alter enzyme genes expression to reconstruct the complicated metabolic pathways, which used to tolerate the CMP and abiotic stresses. Furthermore, most of the affected pathway genes were closely related to secondary metabolic processes, and the influence of consecutive monoculture practice on the transcriptome genes expression profile was very similar to the profile under salt stress and then to the profile under drought stress. The outlined schematic diagram unfolded the putative signal regulation mechanism in response to the CMP. Genes that differentially up- or down-regulated under consecutive monoculture practice may play important roles in the CMP or replanting disease in R. glutinosa.
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Affiliation(s)
- Yunhe Tian
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fajie Feng
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bao Zhang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingjie Li
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fengqing Wang
- Henan Agricultural University, Zhengzhou, 450002, China
| | - Li Gu
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Aiguo Chen
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhanjie Li
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenbo Shan
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoran Wang
- Henan Agricultural University, Zhengzhou, 450002, China
| | - Xinjian Chen
- Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhongyi Zhang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, China.
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Gmoser R, Ferreira JA, Lennartsson PR, Taherzadeh MJ. Filamentous ascomycetes fungi as a source of natural pigments. Fungal Biol Biotechnol 2017; 4:4. [PMID: 28955473 PMCID: PMC5611665 DOI: 10.1186/s40694-017-0033-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/25/2017] [Indexed: 01/14/2023] Open
Abstract
Filamentous fungi, including the ascomycetes Monascus, Fusarium, Penicillium and Neurospora, are being explored as novel sources of natural pigments with biological functionality for food, feed and cosmetic applications. Such edible fungi can be used in biorefineries for the production of ethanol, animal feed and pigments from waste sources. The present review gathers insights on fungal pigment production covering biosynthetic pathways and stimulatory factors (oxidative stress, light, pH, nitrogen and carbon sources, temperature, co-factors, surfactants, oxygen, tricarboxylic acid intermediates and morphology) in addition to pigment extraction, analysis and identification methods. Pigmentation is commonly regarded as the output of secondary protective mechanisms against oxidative stress and light. Although several studies have examined pigmentation in Monascus spp., research gaps exist in the investigation of interactions among factors as well as process development on larger scales under submerged and solid-state fermentation. Currently, research on pigmentation in Neurospora spp. is at its infancy, but the increasing interest for biorefineries shows potential for booming research in this area.
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Affiliation(s)
- Rebecca Gmoser
- Swedish Centre for Resource Recovery, University of Borås, 501 90 Borås, Sweden.,University of Borås, Allégatan 1, 503 32 Borås, Sweden
| | - Jorge A Ferreira
- Swedish Centre for Resource Recovery, University of Borås, 501 90 Borås, Sweden
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Lu X, Yang H, Liu X, Shen Q, Wang N, Qi LW, Li P. Combining Metabolic Profiling and Gene Expression Analysis to Reveal the Biosynthesis Site and Transport of Ginkgolides in Ginkgo biloba L. FRONTIERS IN PLANT SCIENCE 2017; 8:872. [PMID: 28603534 PMCID: PMC5445427 DOI: 10.3389/fpls.2017.00872] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 05/10/2017] [Indexed: 05/07/2023]
Abstract
The most unique components of Ginkgo biloba extracts are terpene trilactones (TTLs) including ginkgolides and bilobalide. Study of TTLs biosynthesis has been stagnant in recent years. Metabolic profiling of 40 compounds, including TTLs, flavonoids, and phenolic acids, were globally analyzed in leaf, fibrous root, main root, old stem and young stem extracts of G. biloba. Most of the flavonoids were mainly distributed in the leaf and old stem. Most of phenolic acids were generally distributed among various tissues. The total content of TTLs decreased in the order of the leaf, fibrous root, main root, old stem and young stem. The TTLs were further analyzed in different parts of the main root and old stem. The content of TTLs decreases in the order of the main root periderm, the main root cortex and phloem and the main root xylem. In old stems, the content of TTLs in the cortex and phloem was much higher than both the old stem periderm and xylem. The expression patterns of five key genes in the ginkgolide biosynthetic pathway were measured by real-time quantitative polymerase chain reaction (RT-Q-PCR). Combining metabolic profiling and RT-Q-PCR, the results showed that the fibrous root and main root periderm tissues were the important biosynthesis sites of ginkgolides. Based on the above results, a model of the ginkgolide biosynthesis site and transport pathway in G. biloba was proposed. In this putative model, ginkgolides are synthesized in the fibrous root and main root periderm, and these compounds are then transported through the old stem cortex and phloem to the leaves.
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Affiliation(s)
- Xu Lu
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjing, China
- *Correspondence: Xu Lu, Lian-wen Qi, Ping Li,
| | - Hua Yang
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjing, China
| | - Xinguang Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjing, China
| | - Qian Shen
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong UniversityShanghai, China
| | - Ning Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjing, China
| | - Lian-wen Qi
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjing, China
- *Correspondence: Xu Lu, Lian-wen Qi, Ping Li,
| | - Ping Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjing, China
- *Correspondence: Xu Lu, Lian-wen Qi, Ping Li,
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Werner N, Gómez M, Baeza M, Cifuentes V, Alcaíno J. Functional characterization of thiolase-encoding genes from Xanthophyllomyces dendrorhous and their effects on carotenoid synthesis. BMC Microbiol 2016; 16:278. [PMID: 27871246 PMCID: PMC5117609 DOI: 10.1186/s12866-016-0893-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/11/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The basidiomycetous yeast Xanthophyllomyces dendrorhous has been described as a potential biofactory for terpenoid-derived compounds due to its ability to synthesize astaxanthin. Functional knowledge of the genes involved in terpenoid synthesis would create opportunities to enhance carotenoid production. A thiolase enzyme catalyzes the first step in terpenoid synthesis. RESULTS Two potential thiolase-encoding genes were found in the yeast genome; bioinformatically, one was identified as an acetyl-CoA C-acetyltransferase (ERG10), and the other was identified as a 3-ketoacyl Co-A thiolase (POT1). Heterologous complementation assays in Saccharomyces cerevisiae showed that the ERG10 gene from X. dendrorhous could complement the lack of the endogenous ERG10 gene in S. cerevisiae, thereby allowing cellular growth and sterol synthesis. X. dendrorhous heterozygous mutants for each gene were created, and a homozygous POT1 mutant was also obtained. This mutant exhibited changes in pigment composition and higher ERG10 transcript levels than the wild type strain. CONCLUSIONS The results support the notion that the ERG10 gene in X. dendrorhous is a functional acetyl-CoA C-acetyltransferase essential for the synthesis of mevalonate in yeast. The POT1 gene would encode a functional 3-ketoacyl Co-A thiolase that is non-essential for cell growth, but its mutation indirectly affects pigment production.
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Affiliation(s)
- Nicole Werner
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
| | - Melissa Gómez
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
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Córdova P, Alcaíno J, Bravo N, Barahona S, Sepúlveda D, Fernández-Lobato M, Baeza M, Cifuentes V. Regulation of carotenogenesis in the red yeast Xanthophyllomyces dendrorhous: the role of the transcriptional co-repressor complex Cyc8-Tup1 involved in catabolic repression. Microb Cell Fact 2016; 15:193. [PMID: 27842591 PMCID: PMC5109733 DOI: 10.1186/s12934-016-0597-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/10/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The yeast Xanthophyllomyces dendrorhous produces carotenoids of commercial interest, including astaxanthin and β-carotene. Although carotenogenesis in this yeast and the expression profiles of the genes controlling this pathway are known, the mechanisms regulating this process remain poorly understood. Several studies have demonstrated that glucose represses carotenogenesis in X. dendrorhous, suggesting that this pathway could be regulated by catabolic repression. Catabolic repression is a highly conserved regulatory mechanism in eukaryotes and has been widely studied in Saccharomyces cerevisiae. Glucose-dependent repression is mainly observed at the transcriptional level and depends on the DNA-binding regulator Mig1, which recruits the co-repressor complex Cyc8-Tup1, which then represses the expression of target genes. In this work, we studied the regulation of carotenogenesis by catabolic repression in X. dendrorhous, focusing on the role of the co-repressor complex Cyc8-Tup1. RESULTS The X. dendrorhous CYC8 and TUP1 genes were identified, and their functions were demonstrated by heterologous complementation in S. cerevisiae. In addition, cyc8 - and tup1 - mutant strains of X. dendrorhous were obtained, and both mutations were shown to prevent the glucose-dependent repression of carotenogenesis in X. dendrorhous, increasing the carotenoid production in both mutant strains. Furthermore, the effects of glucose on the transcript levels of genes involved in carotenogenesis differed between the mutant strains and wild-type X. dendrorhous, particularly for genes involved in the synthesis of carotenoid precursors, such as HMGR, idi and FPS. Additionally, transcriptomic analyses showed that cyc8 - and tup1 - mutations affected the expression of over 250 genes in X. dendrorhous. CONCLUSIONS The CYC8 and TUP1 genes are functional in X. dendrorhous, and their gene products are involved in catabolic repression and carotenogenesis regulation. This study presents the first report involving the participation of Cyc8 and Tup1 in carotenogenesis regulation in yeast.
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Affiliation(s)
- Pamela Córdova
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
| | - Natalia Bravo
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
| | - Salvador Barahona
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
| | - Dionisia Sepúlveda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
| | - María Fernández-Lobato
- Centro de Biología Molecular Severo Ochoa, Departamento de Biología Molecular (UAM-CSIC), Universidad Autónoma Madrid, Campus de Cantoblanco, calle Nicolás Cabrera No 1, Cantoblanco, 28049 Madrid, Spain
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile
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Lu X, Tang K, Li P. Plant Metabolic Engineering Strategies for the Production of Pharmaceutical Terpenoids. FRONTIERS IN PLANT SCIENCE 2016; 7:1647. [PMID: 27877181 PMCID: PMC5099148 DOI: 10.3389/fpls.2016.01647] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/19/2016] [Indexed: 05/18/2023]
Abstract
Pharmaceutical terpenoids belong to the most diverse class of natural products. They have significant curative effects on a variety of diseases, such as cancer, cardiovascular diseases, malaria and Alzheimer's disease. Nowadays, elicitors, including biotic and abiotic elicitors, are often used to activate the pathway of secondary metabolism and enhance the production of target terpenoids. Based on Agrobacterium-mediated genetic transformation, several plant metabolic engineering strategies hold great promise to regulate the biosynthesis of pharmaceutical terpenoids. Overexpressing terpenoids biosynthesis pathway genes in homologous and ectopic plants is an effective strategy to enhance the yield of pharmaceutical terpenoids. Another strategy is to suppress the expression of competitive metabolic pathways. In addition, global regulation which includes regulating the relative transcription factors, endogenous phytohormones and primary metabolism could also markedly increase their yield. All these strategies offer great opportunities to enhance the supply of scarce terpenoids drugs, reduce the price of expensive drugs and improve people's standards of living.
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Affiliation(s)
- Xu Lu
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjing, China
| | - Kexuan Tang
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong UniversityShanghai, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical UniversityNanjing, China
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Yamamoto K, Hara KY, Morita T, Nishimura A, Sasaki D, Ishii J, Ogino C, Kizaki N, Kondo A. Enhancement of astaxanthin production in Xanthophyllomyces dendrorhous by efficient method for the complete deletion of genes. Microb Cell Fact 2016; 15:155. [PMID: 27624332 PMCID: PMC5022159 DOI: 10.1186/s12934-016-0556-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 09/07/2016] [Indexed: 12/24/2022] Open
Abstract
Background Red yeast, Xanthophyllomyces dendrorhous is the only yeast known to produce astaxanthin, an anti-oxidant isoprenoid (carotenoid) widely used in the aquaculture, food, pharmaceutical and cosmetic industries. The potential of this microorganism as a platform cell factory for isoprenoid production has been recognized because of high flux through its native terpene pathway. Recently, we developed a multiple gene expression system in X. dendrorhous and enhanced the mevalonate synthetic pathway to increase astaxanthin production. In contrast, the mevalonate synthetic pathway is suppressed by ergosterol through feedback inhibition. Therefore, releasing the mevalonate synthetic pathway from this inhibition through the deletion of genes involved in ergosterol synthesis is a promising strategy to improve isoprenoid production. An efficient method for deleting diploid genes in X. dendrorhous, however, has not yet been developed. Results Xanthophyllomyces dendrorhous was cultivated under gradually increasing concentrations of antibiotics following the introduction of antibiotic resistant genes to be replaced with target genes. Using this method, double CYP61 genes encoding C-22 sterol desaturases relating to ergosterol biosynthesis were deleted sequentially. This double CYP61 deleted strain showed decreased ergosterol biosynthesis compared with the parental strain and single CYP61 disrupted strain. Additionally, this double deletion of CYP61 genes showed increased astaxanthin production compared with the parental strain and the single CYP61 knockout strain. Finally, astaxanthin production was enhanced by 1.4-fold compared with the parental strain, although astaxanthin production was not affected in the single CYP61 knockout strain. Conclusions In this study, we developed a system to completely delete target diploid genes in X. dendrorhous. Using this method, we deleted diploid CYP61 genes involved in the synthesis of ergosterol that inhibits the pathway for mevalonate, which is a common substrate for isoprenoid biosynthesis. The resulting decrease in ergosterol biosynthesis increased astaxanthin production. The efficient method for deleting diploid genes developed in this study has the potential to improve industrial production of various isoprenoids in X. dendrorhous. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0556-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keisuke Yamamoto
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - Kiyotaka Y Hara
- Division of Environmental and Life Sciences, Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.,Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - Toshihiko Morita
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - Akira Nishimura
- Medical Device Development Laboratories, Kaneka Corporation, Takasago, Hyogo, Japan
| | - Daisuke Sasaki
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Jun Ishii
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - Noriyuki Kizaki
- Biotechnology Development Laboratories, Kaneka Corporation, Takasago, Hyogo, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan. .,Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
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Molecular characterization and heterologous expression of a Xanthophyllomyces dendrorhous α-glucosidase with potential for prebiotics production. Appl Microbiol Biotechnol 2015; 100:3125-35. [PMID: 26615395 DOI: 10.1007/s00253-015-7171-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 10/22/2022]
Abstract
Basidiomycetous yeast Xanthophyllomyces dendrorhous expresses an α-glucosidase with strong transglycosylation activity producing prebiotic sugars such as panose and an unusual tetrasaccharides mixture including α-(1-6) bonds as major products, which makes it of biotechnological interest. Initial analysis pointed to a homodimeric protein of 60 kDa subunit as responsible for this activity. In this study, the gene Xd-AlphaGlu was characterized. The 4131-bp-long gene is interrupted by 13 short introns and encodes a protein of 990 amino acids (Xd-AlphaGlu). The N-terminal sequence of the previously detected 60 kDa protein resides in this larger protein at residues 583-602. Functionality of the gene was proved in Saccharomyces cerevisiae, which produced a protein of about 130 kDa containing Xd-AlphaGlu sequences. All properties of the heterologously expressed protein, including thermal and pH profiles, activity on different substrates, and ability to produce prebiotic sugars were similar to that of the α-glucosidase produced in X. dendrorhous. No activity was detected in S. cerevisiae containing exclusively the 1256-bp from gene Xd-AlphaGlu that would encode synthesis of the 60 kDa protein previously detected. Data were compatible with an active monomeric α-glucosidase of 990 amino acids and an inactive hydrolysis product of 60 kDa. Protein Xd-AlphaGlu contained most of the elements characteristic of α-glucosidases included in the glycoside hydrolases family GH31 and its structural model based on the homologous human maltase-glucoamylase was obtained. Remarkably, the Xd-AlphaGlu C-terminal domain presents an unusually long 115-residue insertion that could be involved in this enzyme's activity against long-size substrates such as maltoheptaose and soluble starch.
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35
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Li L, Yu Y, Du X, Jiang Z, Chen F, Ni H. An improved high performance liquid chromatography method for the separation of carotenoids extracted from Phaffia rhodozyma. JOURNAL OF ANALYTICAL CHEMISTRY 2015. [DOI: 10.1134/s1061934815120102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Gutiérrez MS, Rojas MC, Sepúlveda D, Baeza M, Cifuentes V, Alcaíno J. Molecular Characterization and Functional Analysis of Cytochrome b5 Reductase (CBR) Encoding Genes from the Carotenogenic Yeast Xanthophyllomyces dendrorhous. PLoS One 2015; 10:e0140424. [PMID: 26466337 PMCID: PMC4605618 DOI: 10.1371/journal.pone.0140424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/25/2015] [Indexed: 12/21/2022] Open
Abstract
The eukaryotic microsomal cytochrome P450 systems consist of a cytochrome P450 enzyme (P450) and a cytochrome P450 redox partner, which generally is a cytochrome P450 reductase (CPR) that supplies electrons from NADPH. However, alternative electron donors may exist such as cytochrome b5 reductase and cytochrome b5 (CBR and CYB5, respectively) via, which is NADH-dependent and are also anchored to the endoplasmic reticulum. In the carotenogenic yeast Xanthophyllomyces dendrorhous, three P450-encoding genes have been described: crtS is involved in carotenogenesis and the CYP51 and CYP61 genes are both implicated in ergosterol biosynthesis. This yeast has a single CPR (encoded by the crtR gene), and a crtR- mutant does not produce astaxanthin. Considering that this mutant is viable, the existence of alternative cytochrome P450 electron donors like CBR and CYB5 could operate in this yeast. The aim of this work was to characterize the X. dendrorhous CBR encoding gene and to study its involvement in P450 reactions in ergosterol and carotenoid biosynthesis. Two CBRs genes were identified (CBR.1 and CBR.2), and deletion mutants were constructed. The two mutants and the wild-type strain showed similar sterol production, with ergosterol being the main sterol produced. The crtR- mutant strain produced a lower proportion of ergosterol than did the parental strain. These results indicate that even though one of the two CBR genes could be involved in ergosterol biosynthesis, crtR complements their absence in the cbr- mutant strains, at least for ergosterol production. The higher NADH-dependent cytochrome c reductase activity together with the higher transcript levels of CBR.1 and CYB5 in the crtR- mutant as well as the lower NADH-dependent activity in CBS-cbr.1- strongly suggest that CBR.1-CYB5 via participates as an alternative electron donor pathway for P450 enzymes involved in ergosterol biosynthesis in X. dendrorhous.
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Affiliation(s)
- María Soledad Gutiérrez
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - María Cecilia Rojas
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dionisia Sepúlveda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- * E-mail:
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Castelblanco-Matiz LM, Barbachano-Torres A, Ponce-Noyola T, Ramos-Valdivia AC, Cerda García-Rojas CM, Flores-Ortiz CM, Barahona-Crisóstomo SK, Baeza-Cancino ME, Alcaíno-Gorman J, Cifuentes-Guzmán VH. Carotenoid production and gene expression in an astaxanthin-overproducing Xanthophyllomyces dendrorhous mutant strain. Arch Microbiol 2015; 197:1129-39. [DOI: 10.1007/s00203-015-1153-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/07/2015] [Accepted: 09/11/2015] [Indexed: 12/25/2022]
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Derbyshire MC, Michaelson L, Parker J, Kelly S, Thacker U, Powers SJ, Bailey A, Hammond-Kosack K, Courbot M, Rudd J. Analysis of cytochrome b(5) reductase-mediated metabolism in the phytopathogenic fungus Zymoseptoria tritici reveals novel functionalities implicated in virulence. Fungal Genet Biol 2015; 82:69-84. [PMID: 26074495 PMCID: PMC4557397 DOI: 10.1016/j.fgb.2015.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 12/15/2022]
Abstract
Septoria tritici blotch (STB) caused by the Ascomycete fungus Zymoseptoria tritici is one of the most economically damaging diseases of wheat worldwide. Z. tritici is currently a major target for agricultural fungicides, especially in temperate regions where it is most prevalent. Many fungicides target electron transfer enzymes because these are often important for cell function. Therefore characterisation of genes encoding such enzymes may be important for the development of novel disease intervention strategies. Microsomal cytochrome b5 reductases (CBRs) are an important family of electron transfer proteins which in eukaryotes are involved in the biosynthesis of fatty acids and complex lipids including sphingolipids and sterols. Unlike the model yeast Saccharomyces cerevisiae which possesses only one microsomal CBR, the fully sequenced genome of Z. tritici bears three possible microsomal CBRs. RNA sequencing analysis revealed that ZtCBR1 is the most highly expressed of these genes under all in vitro and in planta conditions tested, therefore ΔZtCBR1 mutant strains were generated through targeted gene disruption. These strains exhibited delayed disease symptoms on wheat leaves and severely limited asexual sporulation. ΔZtCBR1 strains also exhibited aberrant spore morphology and hyphal growth in vitro. These defects coincided with alterations in fatty acid, sphingolipid and sterol biosynthesis observed through GC-MS and HPLC analyses. Data is presented which suggests that Z. tritici may use ZtCBR1 as an additional electron donor for key steps in ergosterol biosynthesis, one of which is targeted by azole fungicides. Our study reports the first functional characterisation of CBR gene family members in a plant pathogenic filamentous fungus. This also represents the first direct observation of CBR functional ablation impacting upon fungal sterol biosynthesis.
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Affiliation(s)
- Mark C Derbyshire
- Department of Plant Biology and Crop Science, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - Louise Michaelson
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Josie Parker
- Centre for Cytochrome P450 Diversity, Institute of Life Science, College of Medicine, Swansea University Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Steven Kelly
- Centre for Cytochrome P450 Diversity, Institute of Life Science, College of Medicine, Swansea University Singleton Park, Swansea SA2 8PP, Wales, UK
| | | | - Stephen J Powers
- Department of Computational and Systems Biology, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Andy Bailey
- Bristol University, Senate House, Tyndall Avenue, Bristol BS8 1TH, UK
| | - Kim Hammond-Kosack
- Department of Plant Biology and Crop Science, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Mikael Courbot
- Syngenta, Syngenta AG, Schaffhauserstrasse, CH-4332 Stein, Switzerland
| | - Jason Rudd
- Department of Plant Biology and Crop Science, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK.
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Chávez-Cabrera C, Marsch R, Bartolo-Aguilar Y, Flores-Bustamante ZR, Hidalgo-Lara ME, Martínez-Cárdenas A, Cancino-Díaz JC, Sánchez S, Flores-Cotera LB. Molecular cloning and characterization of the ATP citrate lyase from carotenogenic yeast Phaffia rhodozyma. FEMS Yeast Res 2015; 15:fov054. [PMID: 26122278 DOI: 10.1093/femsyr/fov054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2015] [Indexed: 12/31/2022] Open
Abstract
ATP citrate lyase (ACL), is a key cytosolic source of acetyl-CoA for fatty acid and sterol biosynthesis and appear to be involved in carotenoid biosynthesis in yeasts. Three homologous DNA sequences encoding ACLs in Phaffia rhodozyma were isolated i.e two genes and one cDNA. The two genes were multi-intronic, with 3450-bp-coding sequences and both genes, as the cDNA, encoded identical 120.1-kDa polypeptides. Full-length amino acid sequences of these ACLs showed the two multidomains, PLN02235 and PLN02522, which are necessary for activity. The ACLs showed 82-87% similarity to putative ACLs from other basidiomycetes and 71% similarity to human ACL. The acl cDNA was used to express the heterologous ACL 6XHis-tagged which was identified using MALDI-TOF-MS. The sequenced peptides with 42.2% coverage showed 100% identity to the amino acid sequence generated in silico. The recombinant ACL purified to homogeneity showed an activity of 2 U. This is the first study to characterize a recombinant ACL from a carotenogenic yeast. The present study provides a key foundation for future studies to assess (a) the possible occurrence of alternative splicing, (b) identify the promoter(s) sequence(s) and (c) the involvement of ACL in the differential regulation of fatty acid and carotenoid biosynthesis in yeasts.
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Affiliation(s)
- Cipriano Chávez-Cabrera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México D.F. 07360, México
| | - Rodolfo Marsch
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México D.F. 07360, México
| | - Yaneth Bartolo-Aguilar
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México D.F. 07360, México
| | - Zoila Rosa Flores-Bustamante
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México D.F. 07360, México
| | - María Eugenia Hidalgo-Lara
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México D.F. 07360, México
| | - Anahí Martínez-Cárdenas
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México D.F. 07360, México
| | - Juan Carlos Cancino-Díaz
- Department of Microbiology, National School of Biological Sciences -IPN, Prol. Carpio y Plan de Ayala S/N Col. Santo Tomás, México D.F. 11340, México
| | - Sergio Sánchez
- Department of Molecular Biology and Biotechnology, Biomedical Research Institute, National Autonomous University of Mexico (UNAM), México D.F. 04510, México
| | - Luis Bernardo Flores-Cotera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México D.F. 07360, México
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Study on the relationship between intracellular metabolites and astaxanthin accumulation during Phaffia rhodozyma fermentation. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2015.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Leiva K, Werner N, Sepúlveda D, Barahona S, Baeza M, Cifuentes V, Alcaíno J. Identification and functional characterization of the CYP51 gene from the yeast Xanthophyllomyces dendrorhous that is involved in ergosterol biosynthesis. BMC Microbiol 2015; 15:89. [PMID: 25906980 PMCID: PMC4415319 DOI: 10.1186/s12866-015-0428-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/17/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Xanthophyllomyces dendrorhous is a basidiomycetous yeast that synthesizes astaxanthin, a carotenoid with great biotechnological impact. The ergosterol and carotenoid synthetic pathways derive from the mevalonate pathway and involve cytochrome P450 enzymes. Among these enzymes, the CYP51 family, which is involved in ergosterol biosynthesis, is one of the most remarkable that has C14-demethylase activity. RESULTS In this study, the CYP51 gene from X. dendrorhous was isolated and its function was analyzed. The gene is composed of ten exons and encodes a predicted 550 amino acid polypeptide that exhibits conserved cytochrome P450 structural characteristics and shares significant identity with the sterol C14-demethylase from other fungi. The functionality of this gene was confirmed by heterologous complementation in S. cerevisiae. Furthermore, a CYP51 gene mutation in X. dendrorhous reduced sterol production by approximately 40% and enhanced total carotenoid production by approximately 90% compared to the wild-type strain after 48 and 120 h of culture, respectively. Additionally, the CYP51 gene mutation in X. dendrorhous increased HMGR (hydroxy-methylglutaryl-CoA reductase, involved in the mevalonate pathway) and crtR (cytochrome P450 reductase) transcript levels, which could be associated with reduced ergosterol production. CONCLUSIONS These results suggest that the CYP51 gene identified in X. dendrorhous encodes a functional sterol C14-demethylase that is involved in ergosterol biosynthesis.
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Affiliation(s)
- Kritsye Leiva
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile.
| | - Nicole Werner
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile.
| | - Dionisia Sepúlveda
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile.
| | - Salvador Barahona
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile.
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile.
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile.
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas y Centro de Biotecnología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago, Chile.
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Martinez-Moya P, Niehaus K, Alcaíno J, Baeza M, Cifuentes V. Proteomic and metabolomic analysis of the carotenogenic yeast Xanthophyllomyces dendrorhous using different carbon sources. BMC Genomics 2015; 16:289. [PMID: 25887121 PMCID: PMC4404605 DOI: 10.1186/s12864-015-1484-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/25/2015] [Indexed: 11/27/2022] Open
Abstract
Background Astaxanthin is a potent antioxidant with increasing biotechnological interest. In Xanthophyllomyces dendrorhous, a natural source of this pigment, carotenogenesis is a complex process regulated through several mechanisms, including the carbon source. X. dendrorhous produces more astaxanthin when grown on a non-fermentable carbon source, while decreased astaxanthin production is observed in the presence of high glucose concentrations. In the present study, we used a comparative proteomic and metabolomic analysis to characterize the yeast response when cultured in minimal medium supplemented with glucose (fermentable) or succinate (non-fermentable). Results A total of 329 proteins were identified from the proteomic profiles, and most of these proteins were associated with carotenogenesis, lipid and carbohydrate metabolism, and redox and stress responses. The metabolite profiles revealed 92 metabolites primarily associated with glycolysis, the tricarboxylic acid cycle, amino acids, organic acids, sugars and phosphates. We determined the abundance of proteins and metabolites of the central pathways of yeast metabolism and examined the influence of these molecules on carotenogenesis. Similar to previous proteomic-stress response studies, we observed modulation of abundance from several redox, stress response, carbohydrate and lipid enzymes. Additionally, the accumulation of trehalose, absence of key ROS response enzymes, an increased abundance of the metabolites of the pentose phosphate pathway and tricarboxylic acid cycle suggested an association between the accumulation of astaxanthin and oxidative stress in the yeast. Moreover, we observed the increased abundance of late carotenogenesis enzymes during astaxanthin accumulation under succinate growth conditions. Conclusions The use of succinate as a carbon source in X. dendrorhous cultures increases the availability of acetyl-CoA for the astaxanthin production compared with glucose, likely reflecting the positive regulation of metabolic enzymes of the tricarboxylic acid and glyoxylate cycles. The high metabolite level generated in this pathway could increase the cellular respiration rate, producing reactive oxygen species, which induces carotenogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1484-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pilar Martinez-Moya
- Departamento de Ciencias Ecológicas, Centro de Biotecnologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Karsten Niehaus
- Department of Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Centro de Biotecnologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Centro de Biotecnologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Centro de Biotecnologia, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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Sharma R, Gassel S, Steiger S, Xia X, Bauer R, Sandmann G, Thines M. The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina. BMC Genomics 2015; 16:233. [PMID: 25887949 PMCID: PMC4393869 DOI: 10.1186/s12864-015-1380-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/21/2015] [Indexed: 11/14/2022] Open
Abstract
Background Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the organization of its CoA-derived pathways and to use the genomic information of X. dendrorhous for a phylogenomic investigation of the Basidiomycota. Results The genome assembly of a haploid strain of Xanthophyllomyces dendrorhous revealed a genome of 19.50 Megabases with 6385 protein coding genes. Phylogenetic analyses were conducted including 48 fungal genomes. These revealed Ustilaginomycotina and Agaricomycotina as sister groups. In the latter a well-supported sister-group relationship of two major orders, Polyporales and Russulales, was inferred. Wallemia occupies a basal position within the Agaricomycotina and X. dendrorhous represents the basal lineage of the Tremellomycetes, highlighting that the typical tremelloid parenthesomes have either convergently evolved in Wallemia and the Tremellomycetes, or were lost in the Cystofilobasidiales lineage. A detailed characterization of the CoA-related pathways was done and all genes for fatty acid, sterol and carotenoid synthesis have been assigned. Conclusions The current study ascertains that Wallemia with tremelloid parenthesomes is the most basal agaricomycotinous lineage and that Cystofilobasidiales without tremelloid parenthesomes are deeply rooted within Tremellomycetes, suggesting that parenthesomes at septal pores might be the core synapomorphy for the Agaricomycotina. Apart from evolutionary insights the genome sequence of X. dendrorhous will facilitate genetic pathway engineering for optimized astaxanthin or oxidative alcohol production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1380-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany.
| | - Sören Gassel
- Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany.
| | - Sabine Steiger
- Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany.
| | - Xiaojuan Xia
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany.
| | - Robert Bauer
- Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
| | - Gerhard Sandmann
- Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany.
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany.
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Contreras G, Barahona S, Sepúlveda D, Baeza M, Cifuentes V, Alcaíno J. Identification and analysis of metabolite production with biotechnological potential in Xanthophyllomyces dendrorhous isolates. World J Microbiol Biotechnol 2015; 31:517-26. [PMID: 25643668 PMCID: PMC4333312 DOI: 10.1007/s11274-015-1808-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/23/2015] [Indexed: 12/31/2022]
Abstract
Antarctic microorganisms have developed different strategies to live in their environments, including modifications to their membrane components to regulate fluidity and the production of photoprotective metabolites such as carotenoids. Three yeast colonies (ANCH01, ANCH06 and ANCH08) were isolated from soil samples collected at King George Island, which according to their rDNA sequence analyses, were determined to be Xanthophyllomyces dendrorhous. This yeast is of biotechnological interest, because it can synthesize astaxanthin as its main carotenoid, which is a powerful antioxidant pigment used in aquaculture. Then, the aim of this work was to characterize the ANCH isolates at their molecular and phenotypic level. The isolates did not display any differences in their rDNA and COX1 gene nucleotide sequences. However, ANCH01 produces approximately sixfold more astaxanthin than other wild type strains. Moreover, even though ANCH06 and ANCH08 produce astaxanthin, their main carotenoid was β-carotene. In contrast to other X. dendrorhous strains, the ANCH isolates did not produce mycosporines. Finally, the ANCH isolates had a higher proportion of polyunsaturated fatty acids than other wild type strains. In conclusion, the reported X. dendrorhous isolates are phenotypically different from other wild type strains, including characteristics that could make them more resistant and better able to inhabit their original habitat, which may also have biotechnological potential.
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Affiliation(s)
- Gabriela Contreras
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
| | - Salvador Barahona
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
| | - Dionisia Sepúlveda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Ñuñoa, Santiago Chile
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Alcaíno J, Romero I, Niklitschek M, Sepúlveda D, Rojas MC, Baeza M, Cifuentes V. Functional characterization of the Xanthophyllomyces dendrorhous farnesyl pyrophosphate synthase and geranylgeranyl pyrophosphate synthase encoding genes that are involved in the synthesis of isoprenoid precursors. PLoS One 2014; 9:e96626. [PMID: 24796858 PMCID: PMC4010515 DOI: 10.1371/journal.pone.0096626] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/09/2014] [Indexed: 12/21/2022] Open
Abstract
The yeast Xanthophyllomyces dendrorhous synthesizes the carotenoid astaxanthin, which has applications in biotechnology because of its antioxidant and pigmentation properties. However, wild-type strains produce too low amounts of carotenoids to be industrially competitive. Considering this background, it is indispensable to understand how the synthesis of astaxanthin is controlled and regulated in this yeast. In this work, the steps leading to the synthesis of the carotenoid precursor geranylgeranyl pyrophosphate (GGPP, C20) in X. dendrorhous from isopentenyl pyrophosphate (IPP, C5) and dimethylallyl pyrophosphate (DMAPP, C5) was characterized. Two prenyl transferase encoding genes, FPS and crtE, were expressed in E. coli. The enzymatic assays using recombinant E. coli protein extracts demonstrated that FPS and crtE encode a farnesyl pyrophosphate (FPP, C15) synthase and a GGPP-synthase, respectively. X. dendrorhous FPP-synthase produces geranyl pyrophosphate (GPP, C10) from IPP and DMAPP and FPP from IPP and GPP, while the X. dendrorhous GGPP-synthase utilizes only FPP and IPP as substrates to produce GGPP. Additionally, the FPS and crtE genes were over-expressed in X. dendrorhous, resulting in an increase of the total carotenoid production. Because the parental strain is diploid, the deletion of one of the alleles of these genes did not affect the total carotenoid production, but the composition was significantly altered. These results suggest that the over-expression of these genes might provoke a higher carbon flux towards carotenogenesis, most likely involving an earlier formation of a carotenogenic enzyme complex. Conversely, the lower carbon flux towards carotenogenesis in the deletion mutants might delay or lead to a partial formation of a carotenogenic enzyme complex, which could explain the accumulation of astaxanthin carotenoid precursors in these mutants. In conclusion, the FPS and the crtE genes represent good candidates to manipulate to favor carotenoid biosynthesis in X. dendrorhous.
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Affiliation(s)
- Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ignacio Romero
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio Niklitschek
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Dionisia Sepúlveda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - María Cecilia Rojas
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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David-Palma M, Libkind D, Sampaio JP. Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe. Mol Ecol 2014; 23:921-32. [DOI: 10.1111/mec.12642] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 12/05/2013] [Accepted: 12/13/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Márcia David-Palma
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Centro de Recursos Microbiológicos (CREM); Universidade Nova de Lisboa; 2829-516 Caparica Portugal
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología; Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA); CONICET - UNComahue; Quintral 1250 (8400), Bariloche Argentina
| | - José Paulo Sampaio
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Centro de Recursos Microbiológicos (CREM); Universidade Nova de Lisboa; 2829-516 Caparica Portugal
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Contreras G, Barahona S, Rojas MC, Baeza M, Cifuentes V, Alcaíno J. Increase in the astaxanthin synthase gene (crtS) dose by in vivo DNA fragment assembly in Xanthophyllomyces dendrorhous. BMC Biotechnol 2013; 13:84. [PMID: 24103677 PMCID: PMC3852557 DOI: 10.1186/1472-6750-13-84] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/04/2013] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Xanthophyllomyces dendrorhous is a basidiomycetous yeast that is relevant to biotechnology, as it can synthesize the carotenoid astaxanthin. However, the astaxanthin levels produced by wild-type strains are low. Although different approaches for promoting increased astaxanthin production have been attempted, no commercially competitive results have been obtained thus far. A promising alternative to facilitate the production of carotenoids in this yeast involves the use of genetic modification. However, a major limitation is the few available molecular tools to manipulate X. dendrorhous. RESULTS In this work, the DNA assembler methodology that was previously described in Saccharomyces cerevisiae was successfully applied to assemble DNA fragments in vivo and integrate these fragments into the genome of X. dendrorhous by homologous recombination in only one transformation event. Using this method, the gene encoding astaxanthin synthase (crtS) was overexpressed in X. dendrorhous and a higher level of astaxanthin was produced. CONCLUSIONS This methodology could be used to easily and rapidly overexpress individual genes or combinations of genes simultaneously in X. dendrorhous, eliminating numerous steps involved in conventional cloning methods.
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Affiliation(s)
- Gabriela Contreras
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla, Santiago 653, Chile
| | - Salvador Barahona
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla, Santiago 653, Chile
| | - María Cecilia Rojas
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla, Santiago 653, Chile
| | - Marcelo Baeza
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla, Santiago 653, Chile
| | - Víctor Cifuentes
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla, Santiago 653, Chile
| | - Jennifer Alcaíno
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla, Santiago 653, Chile
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