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Kun RS, Salazar-Cerezo S, Peng M, Zhang Y, Savage E, Lipzen A, Ng V, Grigoriev IV, de Vries RP, Garrigues S. The Amylolytic Regulator AmyR of Aspergillus niger Is Involved in Sucrose and Inulin Utilization in a Culture-Condition-Dependent Manner. J Fungi (Basel) 2023; 9:jof9040438. [PMID: 37108893 PMCID: PMC10142829 DOI: 10.3390/jof9040438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Filamentous fungi degrade complex plant material to its monomeric building blocks, which have many biotechnological applications. Transcription factors play a key role in plant biomass degradation, but little is known about their interactions in the regulation of polysaccharide degradation. Here, we deepened the knowledge about the storage polysaccharide regulators AmyR and InuR in Aspergillus niger. AmyR controls starch degradation, while InuR is involved in sucrose and inulin utilization. In our study, the phenotypes of A. niger parental, ΔamyR, ΔinuR and ΔamyRΔinuR strains were assessed in both solid and liquid media containing sucrose or inulin as carbon source to evaluate the roles of AmyR and InuR and the effect of culture conditions on their functions. In correlation with previous studies, our data showed that AmyR has a minor contribution to sucrose and inulin utilization when InuR is active. In contrast, growth profiles and transcriptomic data showed that the deletion of amyR in the ΔinuR background strain resulted in more pronounced growth reduction on both substrates, mainly evidenced by data originating from solid cultures. Overall, our results show that submerged cultures do not always reflect the role of transcription factors in the natural growth condition, which is better represented on solid substrates. Importance: The type of growth has critical implications in enzyme production by filamentous fungi, a process that is controlled by transcription factors. Submerged cultures are the preferred setups in laboratory and industry and are often used for studying the physiology of fungi. In this study, we showed that the genetic response of A. niger to starch and inulin was highly affected by the culture condition, since the transcriptomic response obtained in a liquid environment did not fully match the behavior of the fungus in a solid environment. These results have direct implications in enzyme production and would help industry choose the best approaches to produce specific CAZymes for industrial purposes.
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Affiliation(s)
- Roland S Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Yu Zhang
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Emily Savage
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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A Suppressor Mutation in the β-Subunit Kis1 Restores Functionality of the SNF1 Complex in Candida albicans snf4Δ Mutants. mSphere 2021; 6:e0092921. [PMID: 34908458 PMCID: PMC8673253 DOI: 10.1128/msphere.00929-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The heterotrimeric protein kinase SNF1 is a key regulator of metabolic adaptation in the pathogenic yeast Candida albicans, and mutants with a defective SNF1 complex cannot grow on carbon sources other than glucose. We identified a novel type of suppressor mutation in the β-subunit Kis1 that rescued the growth defects of cells lacking the regulatory γ-subunit Snf4 of the SNF1 complex. Unlike wild-type Kis1, the mutated Kis1A396T could bind to the catalytic α-subunit Snf1 in the absence of Snf4. Binding of Kis1A396T did not enhance phosphorylation of Snf1 by the upstream activating kinase Sak1, which is impaired in snf4Δ mutants. Nevertheless, the mutated Kis1A396T reestablished SNF1-dependent gene expression, confirming that SNF1 functionality was restored. The repressor proteins Mig1 and Mig2 were phosphorylated even in the absence of Snf1, but their phosphorylation patterns were altered, indicating that SNF1 regulates Mig1 and Mig2 activity indirectly. In contrast to wild-type cells, mutants lacking Snf4 were unable to reduce the amounts of Mig1 and Mig2 when grown on alternative carbon sources, and this deficiency was also remediated by the mutated Kis1A396T. These results provide novel insights into the regulation of SNF1 and the repressors Mig1 and Mig2 in the metabolic adaptation of C. albicans. IMPORTANCE The highly conserved protein kinase SNF1 plays a key role in the metabolic adaptation of the pathogenic yeast Candida albicans, but it is not clear how it regulates its downstream targets in this fungus. We show that the repressor proteins Mig1 and Mig2 are phosphorylated also in cells lacking the catalytic α-subunit Snf1 of the SNF1 complex, but the amounts of both proteins were reduced in wild-type cells when glucose was replaced by alternative carbon sources, pointing to an indirect mechanism of regulation. Mutants lacking the regulatory γ-subunit Snf4 of the SNF1 complex, which cannot grow on alternative carbon sources, were unable to downregulate Mig1 and Mig2 levels. We identified a novel type of suppressor mutation, an amino acid substitution in the β-subunit Kis1, which enabled Kis1 to bind to Snf1 in the absence of Snf4, thereby restoring Mig1 and Mig2 downregulation, SNF1-dependent gene expression, and growth on alternative carbon sources. These results provide new insights into the SNF1 signaling pathway in C. albicans.
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Garcia-Gonzalez M, Minguet-Lobato M, Plou FJ, Fernandez-Lobato M. Molecular characterization and heterologous expression of two α-glucosidases from Metschnikowia spp, both producers of honey sugars. Microb Cell Fact 2020; 19:140. [PMID: 32652991 PMCID: PMC7353701 DOI: 10.1186/s12934-020-01397-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND α-Glucosidases are widely distributed enzymes with a varied substrate specificity that are traditionally used in biotechnological industries based on oligo- and polysaccharides as starting materials. According to amino acid sequence homology, α-glucosidases are included into two major families, GH13 and GH31. The members of family GH13 contain several α-glucosidases with confirmed hydrolytic activity on sucrose. Previously, a sucrose splitting activity from the nectar colonizing yeast Metschnikowia reukaufii which produced rare sugars with α-(1→1), α-(1→3) and α-(1→6) glycosidic linkages from sucrose was described. RESULTS In this study, genes codifying for α-glucosidases from the nectaries yeast M. gruessii and M. reukaufii were characterised and heterologously expressed in Escherichia coli for the first time. Recombinant proteins (Mg-αGlu and Mr-αGlu) were purified and biochemically analysed. Both enzymes mainly displayed hydrolytic activity towards sucrose, maltose and p-nitrophenyl-α-D-glucopyranoside. Structural analysis of these proteins allowed the identification of common features from the α-amylase family, in particular from glycoside hydrolases that belong to family GH13. The three acidic residues comprising the catalytic triad were identified and their relevance for the protein hydrolytic mechanism confirmed by site-directed mutagenesis. Recombinant enzymes produced oligosaccharides naturally present in honey employing sucrose as initial substrate and gave rise to mixtures with the same products profile (isomelezitose, trehalulose, erlose, melezitose, theanderose and esculose) previously obtained with M. reukaufii cell extracts. Furthermore, the same enzymatic activity was detected with its orthologous Mg-αGlu from M. gruessii. Interestingly, the isomelezitose amounts obtained in reactions mediated by the recombinant proteins, ~ 170 g/L, were the highest reported so far. CONCLUSIONS Mg/Mr-αGlu were heterologously overproduced and their biochemical and structural characteristics analysed. The recombinant α-glucosidases displayed excellent properties in terms of mild reaction conditions, in addition to pH and thermal stability. Besides, the enzymes produced a rare mixture of hetero-gluco-oligosaccharides by transglucosylation, mainly isomelezitose and trehalulose. These compounds are natural constituents of honey which purification from this natural source is quite unviable, what make these enzymes very interesting for the biotechnological industry. Finally, it should be remarked that these sugars have potential applications as food additives due to their suitable sweetness, viscosity and humectant capacity.
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Affiliation(s)
- Martin Garcia-Gonzalez
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid. C/Nicolás Cabrera, 1. Cantoblanco, 28049, Madrid, Spain
| | - Marina Minguet-Lobato
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid. C/Nicolás Cabrera, 1. Cantoblanco, 28049, Madrid, Spain
| | - Francisco J Plou
- Institute of Catalysis and Petrochemistry, CSIC, C/Marie Curie, 2. Cantoblanco, 28049, Madrid, Spain
| | - Maria Fernandez-Lobato
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid. C/Nicolás Cabrera, 1. Cantoblanco, 28049, Madrid, Spain.
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The ploidy determination of the biotechnologically important yeast Candida utilis. J Appl Genet 2020; 61:275-286. [PMID: 31965459 DOI: 10.1007/s13353-020-00544-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 10/25/2022]
Abstract
Yeast Candida utilis is considered to be a potentially advantageous expression system for production of recombinant proteins utilizable for industrial and pharmaceutical purposes. As the scientific literature is not consistent in the ploidy of this yeast, in this work, we focused on resolving the problem via several methods such as the copy number determination of maltase gene by multiplex PCR, measuring α-glucosidase activity, the characterization of maltase gene copy number in deletion mutants using qPCR and flow cytometry. In context with the published data and results obtained in this study about the copy number of the maltase gene on C. utilis genome, we attempted to hypothesise and made conclusion about the ploidy of C. utilis. The results of this work, besides the biotechnological aspect, contribute to the elementary knowledge of C. utilis. The exact information about the ploidy or more specifically about the copy number of appropriate gene is essential for expression cassette dosage determination integrated into the chromosome of the host. In this study, we come to the conclusion that the maltase gene is present in C. utilis genome in four alleles, and in combination with flow cytometry, published information and the published genome sequences, the observations support the theory about tetraploidy of C. utilis.
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Visnapuu T, Meldre A, Põšnograjeva K, Viigand K, Ernits K, Alamäe T. Characterization of a Maltase from an Early-Diverged Non-Conventional Yeast Blastobotrys adeninivorans. Int J Mol Sci 2019; 21:E297. [PMID: 31906253 PMCID: PMC6981392 DOI: 10.3390/ijms21010297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/20/2019] [Accepted: 12/30/2019] [Indexed: 11/17/2022] Open
Abstract
Genome of an early-diverged yeast Blastobotrys (Arxula) adeninivorans (Ba) encodes 88 glycoside hydrolases (GHs) including two α-glucosidases of GH13 family. One of those, the rna_ARAD1D20130g-encoded protein (BaAG2; 581 aa) was overexpressed in Escherichia coli, purified and characterized. We showed that maltose, other maltose-like substrates (maltulose, turanose, maltotriose, melezitose, malto-oligosaccharides of DP 4‒7) and sucrose were hydrolyzed by BaAG2, whereas isomaltose and isomaltose-like substrates (palatinose, α-methylglucoside) were not, confirming that BaAG2 is a maltase. BaAG2 was competitively inhibited by a diabetes drug acarbose (Ki = 0.8 µM) and Tris (Ki = 70.5 µM). BaAG2 was competitively inhibited also by isomaltose-like sugars and a hydrolysis product-glucose. At high maltose concentrations, BaAG2 exhibited transglycosylating ability producing potentially prebiotic di- and trisaccharides. Atypically for yeast maltases, a low but clearly recordable exo-hydrolytic activity on amylose, amylopectin and glycogen was detected. Saccharomyces cerevisiae maltase MAL62, studied for comparison, had only minimal ability to hydrolyze these polymers, and its transglycosylating activity was about three times lower compared to BaAG2. Sequence identity of BaAG2 with other maltases was only moderate being the highest (51%) with the maltase MalT of Aspergillus oryzae.
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Affiliation(s)
| | | | | | | | | | - Tiina Alamäe
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia; (T.V.); (A.M.); (K.P.); (K.V.); (K.E.)
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Burgain A, Pic É, Markey L, Tebbji F, Kumamoto CA, Sellam A. A novel genetic circuitry governing hypoxic metabolic flexibility, commensalism and virulence in the fungal pathogen Candida albicans. PLoS Pathog 2019; 15:e1007823. [PMID: 31809527 PMCID: PMC6919631 DOI: 10.1371/journal.ppat.1007823] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 12/18/2019] [Accepted: 10/18/2019] [Indexed: 01/04/2023] Open
Abstract
Inside the human host, the pathogenic yeast Candida albicans colonizes predominantly oxygen-poor niches such as the gastrointestinal and vaginal tracts, but also oxygen-rich environments such as cutaneous epithelial cells and oral mucosa. This suppleness requires an effective mechanism to reversibly reprogram the primary metabolism in response to oxygen variation. Here, we have uncovered that Snf5, a subunit of SWI/SNF chromatin remodeling complex, is a major transcriptional regulator that links oxygen status to the metabolic capacity of C. albicans. Snf5 and other subunits of SWI/SNF complex were required to activate genes of carbon utilization and other carbohydrates related process specifically under hypoxia. snf5 mutant exhibited an altered metabolome reflecting that SWI/SNF plays an essential role in maintaining metabolic homeostasis and carbon flux in C. albicans under hypoxia. Snf5 was necessary to activate the transcriptional program linked to both commensal and invasive growth. Accordingly, snf5 was unable to maintain its growth in the stomach, the cecum and the colon of mice. snf5 was also avirulent as it was unable to invade Galleria larvae or to cause damage to human enterocytes and murine macrophages. Among candidates of signaling pathways in which Snf5 might operate, phenotypic analysis revealed that mutants of Ras1-cAMP-PKA pathway, as well as mutants of Yak1 and Yck2 kinases exhibited a similar carbon flexibility phenotype as did snf5 under hypoxia. Genetic interaction analysis indicated that the adenylate cyclase Cyr1, a key component of the Ras1-cAMP pathway interacted genetically with Snf5. Our study yielded new insight into the oxygen-sensitive regulatory circuit that control metabolic flexibility, stress, commensalism and virulence in C. albicans. A critical aspect of eukaryotic cell fitness is the ability to sense and adapt to variations in oxygen level in their local environment. Hypoxia leads to a substantial remodeling of cell metabolism and energy homeostasis, and thus, organisms must develop an effective regulatory mechanism to cope with oxygen depletion. Candida albicans is an opportunistic yeast that is the most prevalent human fungal pathogens. This yeast colonizes diverse niches inside the human host with contrasting carbon sources and oxygen concentrations. While hypoxia is the predominant condition that C. albicans encounters inside most of the niches, the impact of this condition on metabolic flexibility, a major determinant of fungal virulence, was completely unexplored. Here, we uncovered that the chromatin remodelling complex SWI/SNF is a master regulator of the circuit that links oxygen status to a broad spectrum of carbon utilization routes. Snf5 was essential for the maintenance of C. albicans as a commensal and also for the expression of its virulence. The oxygen-sensitive regulators identified in this work provide a framework to comprehensively understand the virulence of human fungal pathogens and represent a therapeutic value to fight fungal infections.
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Affiliation(s)
- Anaïs Burgain
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, Quebec, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Émilie Pic
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, Quebec, Canada
| | - Laura Markey
- Program in Molecular Microbiology, Tufts University, Boston, Massachusetts, United States of America
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
| | - Faiza Tebbji
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, Quebec, Canada
| | - Carol A. Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
| | - Adnane Sellam
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, Quebec, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
- Big Data Research Centre (BDRC-UL), Université Laval, Faculty of Sciences and Engineering, Quebec City, Quebec, Canada
- * E-mail:
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Viigand K, Põšnograjeva K, Visnapuu T, Alamäe T. Genome Mining of Non-Conventional Yeasts: Search and Analysis of MAL Clusters and Proteins. Genes (Basel) 2018; 9:E354. [PMID: 30013016 PMCID: PMC6070925 DOI: 10.3390/genes9070354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022] Open
Abstract
Genomic clustering of functionally related genes is rare in yeasts and other eukaryotes with only few examples available. Here, we summarize our data on a nontelomeric MAL cluster of a non-conventional methylotrophic yeast Ogataea (Hansenula) polymorpha containing genes for α-glucosidase MAL1, α-glucoside permease MAL2 and two hypothetical transcriptional activators. Using genome mining, we detected MAL clusters of varied number, position and composition in many other maltose-assimilating non-conventional yeasts from different phylogenetic groups. The highest number of MAL clusters was detected in Lipomyces starkeyi while no MAL clusters were found in Schizosaccharomyces pombe and Blastobotrys adeninivorans. Phylograms of α-glucosidases and α-glucoside transporters of yeasts agreed with phylogenesis of the respective yeast species. Substrate specificity of unstudied α-glucosidases was predicted from protein sequence analysis. Specific activities of Scheffersomycesstipitis α-glucosidases MAL7, MAL8, and MAL9 heterologously expressed in Escherichia coli confirmed the correctness of the prediction-these proteins were verified promiscuous maltase-isomaltases. α-Glucosidases of earlier diverged yeasts L. starkeyi, B. adeninivorans and S. pombe showed sequence relatedness with α-glucosidases of filamentous fungi and bacilli.
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Affiliation(s)
- Katrin Viigand
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Kristina Põšnograjeva
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Triinu Visnapuu
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Tiina Alamäe
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
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de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, dos Santos RAC, Damásio ARDL, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AFJ, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JVDC, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 2017; 18:28. [PMID: 28196534 PMCID: PMC5307856 DOI: 10.1186/s13059-017-1151-0] [Citation(s) in RCA: 316] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
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Affiliation(s)
- Ronald P. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Robert Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ad Wiebenga
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Guillermo Aguilar-Osorio
- Department of Food Science and Biotechnology, Faculty of Chemistry, National University of Mexico, Ciudad Universitaria, D.F. C.P. 04510 Mexico
| | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Cristiane Akemi Uchima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Present address: VTT Brasil, Alameda Inajá, 123, CEP 06460-055 Barueri, São Paulo Brazil
| | - Gregor Anderluh
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Mojtaba Asadollahi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Marion Askin
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: CSIRO Publishing, Unipark, Building 1 Level 1, 195 Wellington Road, Clayton, VIC 3168 Australia
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Evy Battaglia
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Özgür Bayram
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Biology, Maynooth University, Maynooth, Co. Kildare Ireland
| | - Tiziano Benocci
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Susanna A. Braus-Stromeyer
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Max Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, CEP 13083-100 Campinas, Sao Paulo Brazil
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU) Vienna, Vienna, Austria
| | | | - Fusheng Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cindy Choi
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Renato Augusto Corrêa dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - André Ricardo de Lima Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, CEP 13083-862 Campinas, SP Brazil
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Tamás Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Susanne Freyberg
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Antonia Gallo
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), via Provinciale Lecce-Monteroni, 73100 Lecce, Italy
| | - Christos Gournas
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
- Present address: Université Libre de Bruxelles Institute of Molecular Biology and Medicine (IBMM), Brussels, Belgium
| | - Rob Habgood
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | | | - María Laura Harispe
- Institut Pasteur de Montevideo, Unidad Mixta INIA-IPMont, Mataojo 2020, CP11400 Montevideo, Uruguay
- Present address: Instituto de Profesores Artigas, Consejo de Formación en Educación, ANEP, CP 11800, Av. del Libertador 2025, Montevideo, Uruguay
| | - Bernard Henrissat
- CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kristiina S. Hildén
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ryan Hope
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Abeer Hossain
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Eugenia Karabika
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
- Present Address: Department of Chemistry, University of Ioannina, Ioannina, 45110 Greece
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsolt Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary
| | - Nada Kraševec
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Harald Kusch
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Medical Informatics, University Medical Centre, Robert-Koch-Str.40, 37075 Göttingen, Germany
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen, 37073 Germany
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ellen L. Lagendijk
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Alla Lapidus
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
- Present address: Center for Algorithmic Biotechnology, St.Petersburg State University, St. Petersburg, Russia
| | - Anthony Levasseur
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Andrew MacCabe
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Miia R. Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Petter Melin
- Uppsala BioCenter, Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, 750 07 Uppsala, Sweden
- Present address: Swedish Chemicals Agency, Box 2, 172 13 Sundbyberg, Sweden
| | - Vera Meyer
- Institute of Biotechnology, Department Applied and Molecular Microbiology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Natalia Mielnichuk
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Present address: Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 C1440FFX, Ciudad de Buenos Aires, Argentina
| | - Márton Miskei
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt.98., 4032 Debrecen, Hungary
| | - Ákos P. Molnár
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Giuseppina Mulé
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Margarita Orejas
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Erzsébet Orosz
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Jean Paul Ouedraogo
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Karin M. Overkamp
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 702-701 Republic of Korea
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Francois Piumi
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: INRA UMR1198 Biologie du Développement et de la Reproduction - Domaine de Vilvert, Jouy en Josas, 78352 Cedex France
| | - Peter J. Punt
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Arthur F. J. Ram
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Stefan Rauscher
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Eric Record
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Julian Röhrig
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Nadhira S. Salih
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Department of Biology, School of Science, University of Sulaimani, Al Sulaymaneyah, Iraq
| | - Rob A. Samson
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Tabea Schütze
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Department Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Kristina Sepčić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Ekaterina Shelest
- Systems Biology/Bioinformatics group, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305-5120 USA
| | - Vicky Sophianopoulou
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
| | - Fabio M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Hui Sun
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonia Susca
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Richard B. Todd
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Shiela E. Unkles
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
| | - Nathalie van de Wiele
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Diana van Rossen-Uffink
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, The Netherlands
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Tammi C. Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Jaap Visser
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jae-Hyuk Yu
- Departments of Bacteriology and Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706 USA
| | - Miaomiao Zhou
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mikael R. Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Scott E. Baker
- Fungal Biotechnology Team, Pacific Northwest National Laboratory, Richland, Washington, 99352 USA
| | - Isabelle Benoit
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present address: Centre of Functional and Structure Genomics Biology Department Concordia University, 7141 Sherbrooke St. W., Montreal, QC H4B 1R6 Canada
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz-Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI) and Institute for Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Reinhard Fischer
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903 Ribeirão Preto, São Paulo Brazil
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Berl Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045 USA
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, SW7 2AZ UK
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060 Vienna, Austria
| | - Patricia A. vanKuyk
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jennifer Wortman
- Broad Institute, 415 Main St, Cambridge, MA 02142 USA
- Present address: Seres Therapeutics, 200 Sidney St, Cambridge, MA 02139 USA
| | - Paul S. Dyer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
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Gientka I, Bzducha-Wróbel A, Stasiak-Różańska L, Bednarska AA, Błażejak S. The exopolysaccharides biosynthesis by Candida yeast depends on carbon sources. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.02.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Viigand K, Visnapuu T, Mardo K, Aasamets A, Alamäe T. Maltase protein of Ogataea (Hansenula) polymorpha is a counterpart to the resurrected ancestor protein ancMALS of yeast maltases and isomaltases. Yeast 2016; 33:415-32. [PMID: 26919272 PMCID: PMC5074314 DOI: 10.1002/yea.3157] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/05/2016] [Accepted: 02/15/2016] [Indexed: 01/11/2023] Open
Abstract
Saccharomyces cerevisiae maltases use maltose, maltulose, turanose and maltotriose as substrates, isomaltases use isomaltose, α‐methylglucoside and palatinose and both use sucrose. These enzymes are hypothesized to have evolved from a promiscuous α‐glucosidase ancMALS through duplication and mutation of the genes. We studied substrate specificity of the maltase protein MAL1 from an earlier diverged yeast, Ogataea polymorpha (Op), in the light of this hypothesis. MAL1 has extended substrate specificity and its properties are strikingly similar to those of resurrected ancMALS. Moreover, amino acids considered to determine selective substrate binding are highly conserved between Op MAL1 and ancMALS. Op MAL1 represents an α‐glucosidase in which both maltase and isomaltase activities are well optimized in a single enzyme. Substitution of Thr200 (corresponds to Val216 in S. cerevisiae isomaltase IMA1) with Val in MAL1 drastically reduced the hydrolysis of maltose‐like substrates (α‐1,4‐glucosides), confirming the requirement of Thr at the respective position for this function. Differential scanning fluorimetry (DSF) of the catalytically inactive mutant Asp199Ala of MAL1 in the presence of its substrates and selected monosaccharides suggested that the substrate‐binding pocket of MAL1 has three subsites (–1, +1 and +2) and that binding is strongest at the –1 subsite. The DSF assay results were in good accordance with affinity (Km) and inhibition (Ki) data of the enzyme for tested substrates, indicating the power of the method to predict substrate binding. Deletion of either the maltase (MAL1) or α‐glucoside permease (MAL2) gene in Op abolished the growth of yeast on MAL1 substrates, confirming the requirement of both proteins for usage of these sugars. © 2016 The Authors. Yeast published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Katrin Viigand
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Triinu Visnapuu
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Karin Mardo
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Anneli Aasamets
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Tiina Alamäe
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Estonia
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11
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Seddigh S, Darabi M. Structural and phylogenetic analysis of α-glucosidase protein in insects. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Nishimoto M, Mori H, Moteki T, Takamura Y, Iwai G, Miyaguchi Y, Okuyama M, Wongchawalit J, Surarit R, Svasti J, Kimura A, Chiba S. Molecular Cloning of cDNAs and Genes for Three α-Glucosidases from European Honeybees,Apis melliferaL., and Heterologous Production of Recombinant Enzymes inPichia pastoris. Biosci Biotechnol Biochem 2014; 71:1703-16. [PMID: 17617712 DOI: 10.1271/bbb.70125] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
cDNAs encoding three alpha-glucosidases (HBGases I, II, and III) from European honeybees, Apis mellifera, were cloned and sequenced, two of which were expressed in Pichia pastoris. The cDNAs for HBGases I, II, and III were 1,986, 1,910, and 1,915 bp in length, and included ORFs of 1,767, 1,743, and 1,704 bp encoding polypeptides comprised of 588, 580, and 567 amino acid residues, respectively. The deduced proteins of HBGases I, II, and III contained 18, 14, and 8 putative N-linked glycosylation sites, respectively, but at least 2 sites in HBGase II were unmodified by N-linked oligosaccharide. In spite of remarkable differences in the substrate specificities of the three HBGases, high homologies (38-44% identity) were found in the deduced amino acid sequences. In addition, three genomic DNAs, of 13,325, 2,759, and 27,643 bp, encoding HBGases I, II, and III, respectively, were isolated from honeybees, and the sequences were analyzed. The gene of HBGase I was found to be composed of 8 exons and 7 introns. The gene of HBGase II was not divided by intron. The gene of HBGase III was confirmed to be made up of 9 exons and 8 introns, and to be located in the region upstream the gene of HBGase I.
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Affiliation(s)
- Mamoru Nishimoto
- Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Comparison of Sucrose-Hydrolyzing Enzymes Produced byRhizopus oryzaeandAmylomyces rouxii. Biosci Biotechnol Biochem 2014; 72:3167-73. [DOI: 10.1271/bbb.80346] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Similarities and differences in the biochemical and enzymological properties of the four isomaltases from Saccharomyces cerevisiae. FEBS Open Bio 2014; 4:200-12. [PMID: 24649402 PMCID: PMC3953731 DOI: 10.1016/j.fob.2014.02.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/29/2014] [Accepted: 02/10/2014] [Indexed: 11/21/2022] Open
Abstract
Isomaltases (Imap) preferably cleave α-(1,6) bonds, yet show clear substrate ambiguity. With only 3 different aa, Ima3p activities and thermostability diverge from Ima2p. The most distant protein, Ima5p, is extremely sensitive to temperature. Ima5p nevertheless displays most of the same catalytic properties as Ima1p and Ima2p. Ima5p challenges previous conclusions about specific aa needs for the active site.
The yeast Saccharomyces cerevisiae IMA multigene family encodes four isomaltases sharing high sequence identity from 65% to 99%. Here, we explore their functional diversity, with exhaustive in-vitro characterization of their enzymological and biochemical properties. The four isoenzymes exhibited a preference for the α-(1,6) disaccharides isomaltose and palatinose, with Michaëlis–Menten kinetics and inhibition at high substrates concentration. They were also able to hydrolyze trisaccharides bearing an α-(1,6) linkage, but also α-(1,2), α-(1,3) and α-(1,5) disaccharides including sucrose, highlighting their substrate ambiguity. While Ima1p and Ima2p presented almost identical characteristics, our results nevertheless showed many singularities within this protein family. In particular, Ima3p presented lower activities and thermostability than Ima2p despite only three different amino acids between the sequences of these two isoforms. The Ima3p_R279Q variant recovered activity levels of Ima2p, while the Leu-to-Pro substitution at position 240 significantly increased the stability of Ima3p and supported the role of prolines in thermostability. The most distant protein, Ima5p, presented the lowest optimal temperature and was also extremely sensitive to temperature. Isomaltose hydrolysis by Ima5p challenged previous conclusions about the requirement of specific amino acids for determining the specificity for α-(1,6) substrates. We finally found a mixed inhibition by maltose for Ima5p while, contrary to a previous work, Ima1p inhibition by maltose was competitive at very low isomaltose concentrations and uncompetitive as the substrate concentration increased. Altogether, this work illustrates that a gene family encoding proteins with strong sequence similarities can lead to enzyme with notable differences in biochemical and enzymological properties.
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15
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Evolutionary History of Eukaryotic α-Glucosidases from the α-Amylase Family. J Mol Evol 2013; 76:129-45. [DOI: 10.1007/s00239-013-9545-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 01/25/2013] [Indexed: 11/26/2022]
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Yamamoto K, Miyake H, Kusunoki M, Osaki S. Steric hindrance by 2 amino acid residues determines the substrate specificity of isomaltase from Saccharomyces cerevisiae. J Biosci Bioeng 2011; 112:545-50. [DOI: 10.1016/j.jbiosc.2011.08.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 08/18/2011] [Indexed: 10/17/2022]
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17
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Klinke T, Guggenheim B, Klimm W, Thurnheer T. Dental caries in rats associated with Candida albicans. Caries Res 2011; 45:100-6. [PMID: 21412001 DOI: 10.1159/000324809] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 01/31/2011] [Indexed: 11/19/2022] Open
Abstract
In addition to occasional opportunistic colonization of the oral mucosa, Candida albicans is frequently found in carious dentin. The yeast's potential to induce dental caries as a consequence of its pronounced ability to produce and tolerate acids was investigated. Eighty caries-active Osborne-Mendel rats were raised on an ampicillin-supplemented diet and exposed to C. albicans and/or Streptococcus mutans, except for controls. Throughout the 28-day test period, the animals were offered the modified cariogenic diet 2000a, containing 40% various sugars. Subsequently, maxillary molars were scored for plaque extent. After dissection, the mandibular molars were evaluated for smooth surface and fissure caries. Test animals exposed to C. albicans displayed considerably more advanced fissure lesions (p < 0.001) than non-exposed controls. While S. mutans yielded similar results, a combined association of C. albicans and S. mutans had no effect on occlusal caries incidence. Substituting dietary sucrose by glucose did not modify caries induction by C. albicans. However, animals fed a diet containing 20% of both sugars showed no differences to non-infected controls. Smooth surface caries was not generated by the yeast. This study provides experimental evidence that C. albicans is capable of causing occlusal caries in rats at a high rate.
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Affiliation(s)
- T Klinke
- Restorative Dentistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Germany.
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Candida albicans Hap43 is a repressor induced under low-iron conditions and is essential for iron-responsive transcriptional regulation and virulence. EUKARYOTIC CELL 2010; 10:207-25. [PMID: 21131439 DOI: 10.1128/ec.00158-10] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Candida albicans is an opportunistic fungal pathogen that exists as normal flora in healthy human bodies but causes life-threatening infections in immunocompromised patients. In addition to innate and adaptive immunities, hosts also resist microbial infections by developing a mechanism of "natural resistance" that maintains a low level of free iron to restrict the growth of invading pathogens. C. albicans must overcome this iron-deprived environment to cause infections. There are three types of iron-responsive transcriptional regulators in fungi; Aft1/Aft2 activators in yeast, GATA-type repressors in many fungi, and HapX/Php4 in Schizosaccharomyces pombe and Aspergillus species. In this study, we characterized the iron-responsive regulator Hap43, which is the C. albicans homolog of HapX/Php4 and is repressed by the GATA-type repressor Sfu1 under iron-sufficient conditions. We provide evidence that Hap43 is essential for the growth of C. albicans under low-iron conditions and for C. albicans virulence in a mouse model of infection. Hap43 was not required for iron acquisition under low-iron conditions. Instead, it was responsible for repression of genes that encode iron-dependent proteins involved in mitochondrial respiration and iron-sulfur cluster assembly. We also demonstrated that Hap43 executes its function by becoming a transcriptional repressor and accumulating in the nucleus in response to iron deprivation. Finally, we found a connection between Hap43 and the global corepressor Tup1 in low-iron-induced flavinogenesis. Taken together, our data suggest a complex interplay among Hap43, Sfu1, and Tup1 to coordinately regulate iron acquisition, iron utilization, and other iron-responsive metabolic activities.
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Sorgo AG, Heilmann CJ, Dekker HL, Brul S, de Koster CG, Klis FM. Mass spectrometric analysis of the secretome of Candida albicans. Yeast 2010; 27:661-72. [DOI: 10.1002/yea.1775] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Characterization and expression analysis of a maltose-utilizing (MAL) cluster in Aspergillus oryzae. Fungal Genet Biol 2010; 47:1-9. [PMID: 19850146 DOI: 10.1016/j.fgb.2009.10.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2009] [Revised: 10/08/2009] [Accepted: 10/13/2009] [Indexed: 11/22/2022]
Abstract
Starch and maltooligosaccharides such as maltose and maltotriose induce the production of amylolytic enzymes including alpha-amylase in Aspergillus oryzae. A transcriptional activator gene amyR, required for maltose induction of amylolytic enzymes, has been cloned and characterized. The amyR gene deletion mutant showed significantly poor growth on starch medium but normal growth on maltose medium. This indicated the existence of another maltose-utilizing system, whose expression might not be controlled by amyR. We have identified a gene cluster homologous to the MAL cluster of Saccharomyces cerevisiae in the A. oryzae genome. The cluster consists of a MAL61 homolog (designated malP), a MAL62 homolog (designated malT), and a MAL63 homolog (designated malR). Overexpression of malT in A. oryzae resulted in a significant increase in intracellular alpha-glucosidase activity, and that of malP allowed S. cerevisiaemal61Delta to grow on maltose. The expression of both malP and malT genes was highly up-regulated in the presence of maltose, but malR expressed constitutively irrespective of carbon sources. Disruption of malR resulted in the loss of malP and malT expression and thus in restricted growth on maltose medium. In addition, a malP disruptant showed a significantly reduced expression of malT and malR and exhibited a growth defect on maltose similar to the malR disruptant. These results suggest that the MAL cluster of A. oryzae is responsible for the assimilation of maltose in A. oryzae.
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Barnett JA. A history of research on yeasts 13. Active transport and the uptake of various metabolites. Yeast 2008; 25:689-731. [PMID: 18951365 DOI: 10.1002/yea.1630] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- James A Barnett
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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Yuan XL, van der Kaaij RM, van den Hondel CAMJJ, Punt PJ, van der Maarel MJEC, Dijkhuizen L, Ram AFJ. Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles. Mol Genet Genomics 2008; 279:545-61. [PMID: 18320228 PMCID: PMC2413074 DOI: 10.1007/s00438-008-0332-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 02/14/2008] [Indexed: 11/25/2022]
Abstract
The filamentous ascomycete Aspergillus niger is well known for its ability to produce a large variety of enzymes for the degradation of plant polysaccharide material. A major carbon and energy source for this soil fungus is starch, which can be degraded by the concerted action of α-amylase, glucoamylase and α-glucosidase enzymes, members of the glycoside hydrolase (GH) families 13, 15 and 31, respectively. In this study we have combined analysis of the genome sequence of A. niger CBS 513.88 with microarray experiments to identify novel enzymes from these families and to predict their physiological functions. We have identified 17 previously unknown family GH13, 15 and 31 enzymes in the A. niger genome, all of which have orthologues in other aspergilli. Only two of the newly identified enzymes, a putative α-glucosidase (AgdB) and an α-amylase (AmyC), were predicted to play a role in starch degradation. The expression of the majority of the genes identified was not induced by maltose as carbon source, and not dependent on the presence of AmyR, the transcriptional regulator for starch degrading enzymes. The possible physiological functions of the other predicted family GH13, GH15 and GH31 enzymes, including intracellular enzymes and cell wall associated proteins, in alternative α-glucan modifying processes are discussed.
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Affiliation(s)
- Xiao-Lian Yuan
- Clusius Laboratory, Molecular Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biology Leiden, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
- Microarray Department, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Rachel M. van der Kaaij
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- Centre for Carbohydrate Bioprocessing, TNO, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | - Cees A. M. J. J. van den Hondel
- Clusius Laboratory, Molecular Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biology Leiden, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| | - Peter J. Punt
- TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Utrechtseweg 48, 3704 HE Zeist, The Netherlands
| | - Marc J. E. C. van der Maarel
- Centre for Carbohydrate Bioprocessing, TNO, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Rouaanstraat 27, 9723 CC Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- Centre for Carbohydrate Bioprocessing, TNO, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
| | - Arthur F. J. Ram
- Clusius Laboratory, Molecular Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biology Leiden, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
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Cloning and overexpression of a maltase gene from Schizosaccharomyces pombe in Escherichia coli and characterization of the recombinant maltase. ACTA ACUST UNITED AC 2008; 112:983-9. [PMID: 18556189 DOI: 10.1016/j.mycres.2008.01.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 12/26/2007] [Accepted: 01/24/2008] [Indexed: 11/22/2022]
Abstract
The Schizosaccharomyces pombe maltase structural gene (SPMAL1(+)) was amplified from genomic DNA of S. pombe by PCR. An open reading frame of 1740bp, encoding a putative 579 amino-acid protein with a calculated molecular mass of 67.7kDa was characterized in the genomic DNA insert of plasmid pQE30. The specific maltase activity in the induced transformants was 21 times higher than that in wild-type. However, the estimated molecular mass of the purified recombinant maltase was 44.3kDa by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). The optimal temperature and pH of the purified recombinant maltase were 40 degrees C and 6, respectively. The recombinant maltase was weakly activated by Mg(2+), Ca(2+), Na(+), and Ba(2+), but was strongly inhibited by Hg(2+), Ag(+) and Cu(2+), EDTA, and PMSF. The purified maltase could actively hydrolyse rho-nitrophenyl glucoside (PNPG), maltose, dextrin, and soluble starch. The results demonstrate that maltase from S. pombe was different from that from other yeasts, and might be usefully exploited in the future by the biotechnology industry or lead to the development of new molecular genetic tools.
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Yuan XL, Roubos JA, van den Hondel CAMJJ, Ram AFJ. Identification of InuR, a new Zn(II)2Cys6 transcriptional activator involved in the regulation of inulinolytic genes in Aspergillus niger. Mol Genet Genomics 2007; 279:11-26. [PMID: 17917744 PMCID: PMC2129107 DOI: 10.1007/s00438-007-0290-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 09/11/2007] [Indexed: 11/25/2022]
Abstract
The expression of inulinolytic genes in Aspergillus niger is co-regulated and induced by inulin and sucrose. We have identified a positive acting transcription factor InuR, which is required for the induced expression of inulinolytic genes. InuR is a member of the fungal specific class of transcription factors of the Zn(II)2Cys6 type. Involvement of InuR in inulin and sucrose metabolism was suspected because of the clustering of inuR gene with sucB, which encodes an intracellular invertase with transfructosylation activity and a putative sugar transporter encoding gene (An15g00310). Deletion of the inuR gene resulted in a strain displaying a severe reduction in growth on inulin and sucrose medium. Northern analysis revealed that expression of inulinolytic and sucrolytic genes, e.g., inuE, inuA, sucA, as well as the putative sugar transporter gene (An15g00310) is dependent on InuR. Genome-wide expression analysis revealed, three additional putative sugar transporters encoding genes (An15g04060, An15g03940 and An17g01710), which were strongly induced by sucrose in an InuR dependent way. In silico analysis of the promoter sequences of strongly InuR regulated genes suggests that InuR might bind as dimer to two CGG triplets, which are separated by eight nucleotides.
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Affiliation(s)
- Xiao-Lian Yuan
- Institute of Biology, Clusius Laboratory, Molecular Microbiology, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| | | | - Cees A. M. J. J. van den Hondel
- Institute of Biology, Clusius Laboratory, Molecular Microbiology, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
| | - Arthur F. J. Ram
- Institute of Biology, Clusius Laboratory, Molecular Microbiology, Leiden University, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands
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25
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Dmytruk KV, Sibirny AA. Molecular mechanisms of insertional mutagenesis in yeasts and mycelium fungi. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407080017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Marín D, Linde D, Fernández Lobato M. Purification and biochemical characterization of an alpha-glucosidase from Xanthophyllomyces dendrorhous. Yeast 2006; 23:117-25. [PMID: 16491468 DOI: 10.1002/yea.1345] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Xanthophyllomyces dendrorhous grown in different media shows amylolytic activity, consisting in an extracellular exo-acting enzyme able to hydrolysed alpha,1-4 glycosidic bonds from soluble starch, which also cleaves maltose and malto-oligosaccharides. The enzyme was purified, using basically a couple of chromatography process on DEAE-Sephacel. It is a glycoprotein with a molecular weight estimated to be 60.2 kDa based on its mobility in SDS-PAGE and 115 kDa based on gel filtration. N-linked carbohydrate accounts for 12% of the total mass. It exhibited optimum activity at pH 5.5 and 45 degrees C. Thermostability analysis indicated that it was stable to thermal treatment up to 50 degrees C; 50% of the activity was maintained after 3 h. The rate parameters measured for the hydrolysis of starch and various chain length malto-oligosaccharides shows high catalytic efficiency, calculated by the relationship V(cat)/K(m), for malto-oligosaccharides, such as maltotriose (873 mM(-1) min(-1)), or maltoheptose (698 mM(-1) min(-1)). The new enzyme hydrolysed soluble starch with nearly 3.5- and 1.4-fold lower efficiency than that for maltotriose and maltose, respectively. No activity was found on heterogeneous substrates, such as sucrose and aryl alpha-glucoside, or on isomalto-oligosaccharides. In accordance to substrate specificity profile, the new enzyme was classified as an alpha-glucosidase.
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Affiliation(s)
- Dolores Marín
- Centro de Biología Molecular Severo Ochoa, Departamento de Biología Molecular (CSIC-UAM), Universidad Autónoma Madrid, Cantoblanco, 28049 Madrid, Spain
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Yao S, Chi Z, He S. Studies on inositol-mediated expression of MAL gene encoding maltase and phospholipid biosynthesis in Schizosaccharomyces pombe. J Ind Microbiol Biotechnol 2006; 33:417-22. [PMID: 16496115 DOI: 10.1007/s10295-005-0069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2005] [Accepted: 12/03/2005] [Indexed: 10/25/2022]
Abstract
In this study, the effects of inositol addition on expression of the MAL gene encoding maltase and phosphatidylinositol (PI) biosynthesis in Schizosaccharomyces pombe (a naturally inositol-requiring strain) were examined. We found that specific maltase activity was at its maximum when the concentration of added inositol reached 6 microg ml(-1) in a synthetic medium containing 2.0% (w/v) glucose. When the concentration of added inositol was 1 microg ml(-1) in the medium, repression of MAL gene expression occurred at glucose concentration higher than 0.2% (w/v). However, when S. pombe was cultured in the synthetic medium containing 6 microg ml(-1), repression of maltase gene expression occurred only at initial glucose concentration above 1.0% (w/v). More mRNA encoding maltase was detected in the cells grown in the medium with 6 microg ml(-1) inositol than in those grown in the same medium with 1 microg ml(-1) inositol. These results demonstrate that higher inositol concentrations in the synthetic medium could derepress MAL gene expression in S. pombe. PI content of the yeast cells grown in the synthetic medium with 6 microg ml(-1) of inositol was higher than that of the yeast cells grown in the same medium with 1 microg ml(-1) of inositol. This means that PI may be involved in the derepression of MAL gene expression in S. pombe.
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Affiliation(s)
- Shumin Yao
- College of Marine Life Science, Ocean University of China, 266003, Shandong, Qingdao, China
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28
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Oh CS, Martin CE. Candida albicans Spt23p controls the expression of the Ole1p Delta9 fatty acid desaturase and regulates unsaturated fatty acid biosynthesis. J Biol Chem 2006; 281:7030-9. [PMID: 16415349 DOI: 10.1074/jbc.m510746200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Saccharomyces cerevisiae the endoplasmic reticulum membrane proteins scSpt23p and scMga2p control the formation of unsaturated fatty acids by a mechanism that involves their release from the membrane by ubiquitin-mediated proteolysis. The resulting soluble polypeptides act as transcription activators that specifically control the expression of scOLE1, a gene that encodes scOle1p, a Delta9 fatty acid desaturase that forms cis-monounsaturated fatty acids (9Z-16:1 and 9Z-18:1) from saturated fatty acyl-CoA precursors. ScOle1p is the only long chain fatty acid desaturase in Saccharomyces and its membrane and storage lipids contain only saturated fatty acids and the monounsaturated products of that enzyme. Most other fungi, however, express multiple endoplasmic reticulum desaturases, including enzymes that form both mono- and polyunsaturated fatty acids. These typically include Delta12 and Delta15 enzymes that form the polyunsaturated species, 9Z,12Z-18:2, and 9Z,12Z,15Z-18:3, which are the most abundant fatty acids in membrane and storage lipids. An analysis of genomic DNA sequences shows that Candida albicans has a single homologue of the Saccharomyces scSPT23 and scMGA2 genes that we designate here as caSPT23. This study describes the characterization of the caSPT23 gene product and shows that it can repair the unsaturated fatty acid auxotrophy when it is expressed in a Saccharomyces scspt23Delta;scmga2Delta strain. In addition we show caSPT23 is essential for the expression of one of the two Delta9 desaturase homologues in Candida and potentially other functions associated with fatty acid metabolism.
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Affiliation(s)
- Chan-Seok Oh
- Department of Cell Biology and Neuroscience, Nelson Laboratories, Rutgers University, 604 Allison Road, Piscataway, NJ 08854-8082, USA
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Yamamoto K, Nakayama A, Yamamoto Y, Tabata S. Val216 decides the substrate specificity of alpha-glucosidase in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2004; 271:3414-20. [PMID: 15291818 DOI: 10.1111/j.1432-1033.2004.04276.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Differences in the substrate specificity of alpha-glucosidases should be due to the differences in the substrate binding and the catalytic domains of the enzymes. To elucidate such differences of enzymes hydrolyzing alpha-1,4- and alpha-1,6-glucosidic linkages, two alpha-glucosidases, maltase and isomaltase, from Saccharomyces cerevisiae were cloned and analyzed. The cloned yeast isomaltase and maltase consisted of 589 and 584 amino acid residues, respectively. There was 72.1% sequence identity with 165 amino acid alterations between the two alpha-glucosidases. These two alpha-glucosidase genes were subcloned into the pKP1500 expression vector and expressed in Escherichia coli. The purified alpha-glucosidases showed the same substrate specificities as those of their parent native glucosidases. Chimeric enzymes constructed from isomaltase by exchanging with maltase fragments were characterized by their substrate specificities. When the consensus region II, which is one of the four regions conserved in family 13 (alpha-amylase family), is replaced with the maltase type, the chimeric enzymes alter to hydrolyze maltose. Three amino acid residues in consensus region II were different in the two alpha-glucosidases. Thus, we modified Val216, Gly217, and Ser218 of isomaltase to the maltase-type amino acids by site-directed mutagenesis. The Val216 mutant was altered to hydrolyze both maltose and isomaltose but neither the Gly217 nor the Ser218 mutant changed their substrate specificity, indicating that Val216 is an important residue discriminating the alpha-1,4- and 1,6-glucosidic linkages of substrates.
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Affiliation(s)
- Keizo Yamamoto
- Department of Chemistry, Nara Medical University, Japan.
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Alonso-Monge R, Navarro-García F, Román E, Eisman B, Nombela C, Pla J. Strategies for the identification of virulence determinants in human pathogenic fungi. Curr Genet 2003; 42:301-12. [PMID: 12612803 DOI: 10.1007/s00294-002-0364-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2002] [Revised: 12/05/2002] [Accepted: 12/05/2002] [Indexed: 10/26/2022]
Abstract
The incidence of fungal infections is increasing in different countries. The current available therapy of these infections does not satisfy all requirements in terms of specificity and therapeutic index, a fact that has stimulated the scientific community to identify fungal virulence determinants. Several pathogenic fungi are opportunistic and, therefore, identification of virulence genes is difficult, given their close relationship with host cells. In recent years, the development of genetic tools in several pathogenic fungi has enabled the development of genetic strategies for their identification. These include several strategies based on the phenotypic analysis of strains or environmental conditions in which the expression of the putative gene(s) is either altered or deleted; and this is accomplished through the development of in vitro or in vivo systems. In the near future, this research will produce a better picture of fungal pathogenesis and therefore define novel promising targets in antifungal therapy.
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Affiliation(s)
- R Alonso-Monge
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040, Madrid, Spain
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Berman J, Sudbery PE. Candida Albicans: a molecular revolution built on lessons from budding yeast. Nat Rev Genet 2002; 3:918-30. [PMID: 12459722 DOI: 10.1038/nrg948] [Citation(s) in RCA: 382] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Candida albicans is an opportunistic fungal pathogen that is found in the normal gastrointestinal flora of most healthy humans. However, in immunocompromised patients, blood-stream infections often cause death, despite the use of anti-fungal therapies. The recent completion of the C. albicans genome sequence, the availability of whole-genome microarrays and the development of tools for rapid molecular-genetic manipulations of the C. albicans genome are generating an explosion of information about the intriguing biology of this pathogen and about its mechanisms of virulence. They also reveal the extent of similarities and differences between C. albicans and its benign relative, Saccharomyces cerevisiae.
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Affiliation(s)
- Judith Berman
- Department of Genetics, Cell Biology and Development, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, Minnesota 55455, USA.
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Baev D, Li X, Edgerton M. Genetically engineered human salivary histatin genes are functional in Candida albicans: development of a new system for studying histatin candidacidal activity. MICROBIOLOGY (READING, ENGLAND) 2001; 147:3323-34. [PMID: 11739764 DOI: 10.1099/00221287-147-12-3323] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Histatins are a structurally related family of salivary proteins known as histidine-rich proteins that are produced and secreted by the human major salivary glands. In vitro, histatins are potent cytotoxic proteins with selectivity for pathogenic yeasts including Candida albicans. Studies that investigate the mechanism of action of histatin proteins upon this important human pathogen have used a candidacidal assay in which the histatin is applied extracellularly. In order to develop a model system to study the mechanism of histatin action independently from binding and translocation events, the authors constructed C. albicans strains that contain chromosomally encoded human salivary histatin genes under the control of a regulated promoter. Intracellular expression of either histatin 5 or histatin 3 induced cell killing and ATP release in parallel. Since histatin killing can be initiated solely from intracellular sites, extracellular binding and internalization are preceding transport events. Thus the mechanism of histatin-induced ATP release does not require extracellular binding, and intracellular targets alone can activate ATP release. By employing a codon-optimization strategy it was shown that expression of heterologous sequences in C. albicans can be a useful tool for functional studies.
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Affiliation(s)
- D Baev
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo Main Street Campus, 3435 Main Street, Buffalo, NY 14214, USA
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Aaron KE, Pierson CA, Lees ND, Bard M. The Candida albicans ERG26 gene encoding the C-3 sterol dehydrogenase (C-4 decarboxylase) is essential for growth. FEMS Yeast Res 2001; 1:93-101. [PMID: 12702354 DOI: 10.1111/j.1567-1364.2001.tb00020.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The Candida albicans ERG26 gene encoding the C-3 sterol dehydrogenase (C-4 decarboxylase) was cloned by complementing a Saccharomyces cerevisiae erg26 mutant with a C. albicans genomic library. Sequence analysis showed a 70% identity between the C. albicans and S. cerevisiae ERG26 genes at the amino acid level. Sequential disruption of both copies of the ERG26 gene in the presence of an integrated rescue cassette containing a third copy of the ERG26 gene under the control of the inducible pMAL2 promoter, resulted in cells capable of growing only in the presence of the inducer. The results establish that the ERG26 gene is essential for growth and that inhibitors of the Erg26p may represent a new and highly effective class of antifungal agents.
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Affiliation(s)
- K E Aaron
- Department of Biology, Indiana University Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN 46202-5132, USA
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Abstract
Through the discovery of Buchner, Biology was relieved of another fragment of mysticism. The splitting up of sugar into CO2 and alcohol is no more the effect of a "vital principle" than the splitting up of cane sugar by invertase. (Jacques Loeb 1906 [138] p.22.)
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Affiliation(s)
- J A Barnett
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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MacGregor EA, Janecek S, Svensson B. Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1546:1-20. [PMID: 11257505 DOI: 10.1016/s0167-4838(00)00302-2] [Citation(s) in RCA: 454] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The hydrolases and transferases that constitute the alpha-amylase family are multidomain proteins, but each has a catalytic domain in the form of a (beta/alpha)(8)-barrel, with the active site being at the C-terminal end of the barrel beta-strands. Although the enzymes are believed to share the same catalytic acids and a common mechanism of action, they have been assigned to three separate families - 13, 70 and 77 - in the classification scheme for glycoside hydrolases and transferases that is based on amino acid sequence similarities. Each enzyme has one glutamic acid and two aspartic acid residues necessary for activity, while most enzymes of the family also contain two histidine residues critical for transition state stabilisation. These five residues occur in four short sequences conserved throughout the family, and within such sequences some key amino acid residues are related to enzyme specificity. A table is given showing motifs distinctive for each specificity as extracted from 316 sequences, which should aid in identifying the enzyme from primary structure information. Where appropriate, existing problems with identification of some enzymes of the family are pointed out. For enzymes of known three-dimensional structure, action is discussed in terms of molecular architecture. The sequence-specificity and structure-specificity relationships described may provide useful pointers for rational protein engineering.
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Affiliation(s)
- E A MacGregor
- Department of Chemistry, University of Manitoba, Winnepeg, Manitoba R3T 2N2, Canada
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Abstract
The Hansenula polymorpha maltase structural gene (HPMAL1) was isolated from a genomic library by hybridization of the library clones with maltase-specific gene probe. An open reading frame of 1695 nt encoding a 564 amino-acid protein with calculated molecular weight of 65.3 kD was characterized in the genomic DNA insert of the plasmid p51. The protein sequence deduced from the HPMAL1 exhibited 58 and 47% identity with maltases from Candida albicans and Saccharomyces carlsbergesis encoded by CAMAL2 and MAL62, respectively, and 44% identity with oligo-alpha-1,6-glucosidase from Bacillus cereus. The recombinant Hansenula polymorpha maltase produced in Escherichia coli hydrolyzed p-nitrophenyl-alpha-D-glucopyranoside (PNPG), sucrose, maltose and alpha-methylglucoside and did not act on melibiose, cellobiose, trehalose and o-nitrophenyl-beta-D-galactopyranoside (ONPG). The affinity of the recombinant enzyme for its substrates increased in the order maltose <alpha-methylglucoside <sucrose <PNPG. Southern analysis revealed presence of a single maltase gene in H. polymorpha. This is the first report on the maltase gene sequence from a methylotrophic yeast.
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Affiliation(s)
- L Liiv
- Institute of Molecular and Cell Biology, Riia 23, University of Tartu, 51010, Tartu, Estonia
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Shanmugam V, Sriram S, Babu S, Nandakumar R, Raguchander T, Balasubramanian P, Samiyappan R. Purification and characterization of an extracellular alpha-glucosidase protein from Trichoderma viride which degrades a phytotoxin associated with sheath blight disease in rice. J Appl Microbiol 2001; 90:320-9. [PMID: 11298225 DOI: 10.1046/j.1365-2672.2001.01248.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To purify and characterize an extracellular alpha-glucosidase from Trichoderma viride capable of inactivating a host-specific phytotoxin, designated RS toxin, produced by the rice sheath blight pathogen, Rhizoctonia solani Kühn. METHODS AND RESULTS The host-specific RS toxin was purified from both culture filtrates (culture filtrate toxin, CFTox) and R. solani-inoculated rice sheaths (sheath blight toxin, SBTox). Sodium dodecyl sulphate-polyacrylamide gel electrophoresis analyses of extracellular proteins, purified from a biocontrol fungus T. viride (TvMNT7) grown on SBTox and CFTox separately, were carried out. The antifungal activity of the purified high molecular weight protein (110 kDa) was studied against RS toxin as well as on the sclerotial germination and mycelial growth of R. solani. Enzyme assay and Western blot analysis with the antirabbit TvMNT7 110-kDa protein indicated that the protein was an alpha-glucosidase. The 110-kDa protein was highly specific to RS toxin and its Michaelis-Menten constant value was 0.40 mmol l-1 when p-nitrophenyl alpha-D-glucopyranoside was used as the substrate. The isoelectric point of the protein was 5.2. N-terminal sequencing of the alpha-glucosidase protein showed that its amino acid sequence showed no homology with other known alpha-glucosidases. CONCLUSION This appears to be the first report of the purification and characterization of an alpha-glucosidase capable of inactivating a host-specific toxin of fungal origin. The alpha-glucosidase is specific to RS toxin and is different from the known alpha-glucosidases. SIGNIFICANCE AND IMPACT OF THE STUDY As RS toxin could be inactivated by the microbial alpha-glucosidase enzyme, isolation of the gene that codes for the enzyme from T. viride and transfer of the gene to rice plants would lead to enhanced resistance against sheath blight pathogen by inactivation of RS toxin.
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Affiliation(s)
- V Shanmugam
- Department of Plant Pathology and Centre for Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore, India
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Abstract
The frequency of opportunistic infections caused by the fungus Candida albicans is very high and is expected to continue to increase as the number of immunocompromised patients rises. Research initiatives to study the biology of this organism and elucidate its pathogenic determinants have therefore expanded significantly during the last 5-10 years. The past few years have also brought continuous improvement in the techniques to study gene function by gene inactivation and by regulated gene expression and to study gene expression and protein localization by using gene reporter systems. As steadily more genomic sequence information from this human fungal pathogen becomes available, we are entering a new era in antimicrobial research. However, many of the currently available molecular genetics tools are poorly adapted to a genome-wide functional analysis in C. albicans, and further development of these tools is hampered by the asexual and diploid nature of this organism. This review outlines recent advances in the development of molecular tools for functional analysis in C. albicans and summarizes current knowledge about the genomic and genetic variability of this important human fungal pathogen.
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Affiliation(s)
- M D De Backer
- Department of Advanced Bio-Technologies, Janssen Research Foundation, B-2340 Beerse, Belgium.
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Flores CL, Rodríguez C, Petit T, Gancedo C. Carbohydrate and energy-yielding metabolism in non-conventional yeasts. FEMS Microbiol Rev 2000; 24:507-29. [PMID: 10978549 DOI: 10.1111/j.1574-6976.2000.tb00553.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Sugars are excellent carbon sources for all yeasts. Since a vast amount of information is available on the components of the pathways of sugar utilization in Saccharomyces cerevisiae it has been tacitly assumed that other yeasts use sugars in the same way. However, although the pathways of sugar utilization follow the same theme in all yeasts, important biochemical and genetic variations on it exist. Basically, in most non-conventional yeasts, in contrast to S. cerevisiae, respiration in the presence of oxygen is prominent for the use of sugars. This review provides comparative information on the different steps of the fundamental pathways of sugar utilization in non-conventional yeasts: glycolysis, fermentation, tricarboxylic acid cycle, pentose phosphate pathway and respiration. We consider also gluconeogenesis and, briefly, catabolite repression. We have centered our attention in the genera Kluyveromyces, Candida, Pichia, Yarrowia and Schizosaccharomyces, although occasional reference to other genera is made. The review shows that basic knowledge is missing on many components of these pathways and also that studies on regulation of critical steps are scarce. Information on these points would be important to generate genetically engineered yeast strains for certain industrial uses.
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Affiliation(s)
- C L Flores
- Instituto de Investigaciones Biomédicas Alberto Sols C.S.I.C.-UAM, Unidad de Bioquímica y Genética de Levaduras, 28029, Madrid, Spain
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Backen AC, Broadbent ID, Fetherston RW, Rosamond JDC, Schnell NF, Stark MJR. Evaluation of theCaMAL2 promoter for regulated expression of genes inCandida albicans. Yeast 2000. [DOI: 10.1002/1097-0061(20000915)16:12%3c1121::aid-yea614%3e3.0.co;2-u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Backen AC, Broadbent ID, Fetherston RW, Rosamond JD, Schnell NF, Stark MJ. Evaluation of the CaMAL2 promoter for regulated expression of genes in Candida albicans. Yeast 2000; 16:1121-9. [PMID: 10953084 DOI: 10.1002/1097-0061(20000915)16:12<1121::aid-yea614>3.0.co;2-u] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An expression vector (CIp10-MAL2p) for use in Candida albicans has been constructed in which a gene of interest can be placed under the control of the CaMAL2 maltase promoter and stably integrated at the CaRP10 locus. Using this vector to express the Candida URA3 gene from the CaMAL2 promoter, we have demonstrated tight regulation of CaURA3 expression by carbon source. Thus under conditions when the CaMAL2 promoter is not induced, expression of Candida URA3 was unable either to complement a C. albicans ura3 mutation or to confer sensitivity to 5-fluoroorotic acid, a compound which is highly toxic to URA3 strains. Since Candida albicans is an obligate diploid organism, analysis of gene function requires manipulation of both copies of any gene of interest. Our expression vector provides a strategy by which the remaining copy of a gene of interest can be placed under CaMAL2 promoter control in a strain where the first copy has been deleted, permitting analysis of gene function by manipulation of carbon source. CIp10-MAL2p should therefore provide a useful means for functional analysis of genes in C. albicans. We have used this strategy with C. albicans DPB2 to demonstrate that the gene is essential and that loss of function leads cells to adopt a hypha-like morphology as they cease proliferation.
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Affiliation(s)
- A C Backen
- University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
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42
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Fekete‐Forgács K, Jeney A, Varga G, Lenkey B. Investigation of
α
‐glucosidase as a potential virulence factor of
Candida albicans. J Basic Microbiol 2000. [DOI: 10.1002/(sici)1521-4028(200005)40:2<105::aid-jobm105>3.0.co;2-#] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katalin Fekete‐Forgács
- Department of Microbiology and Biotechnology, Kossuth Lajos University, P.O. Box 63, H‐4010 Debrecen, Hungary
| | - Apor Jeney
- Department of Microbiology and Biotechnology, Kossuth Lajos University, P.O. Box 63, H‐4010 Debrecen, Hungary
| | - Gábor Varga
- Department of Microbiology and Biotechnology, Kossuth Lajos University, P.O. Box 63, H‐4010 Debrecen, Hungary
| | - Béla Lenkey
- Department of Microbiology and Biotechnology, Kossuth Lajos University, P.O. Box 63, H‐4010 Debrecen, Hungary
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Zaragoza O, Rodríguez C, Gancedo C. Isolation of the MIG1 gene from Candida albicans and effects of its disruption on catabolite repression. J Bacteriol 2000; 182:320-6. [PMID: 10629176 PMCID: PMC94279 DOI: 10.1128/jb.182.2.320-326.2000] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have cloned a Candida albicans gene (CaMIG1) that encodes a protein homologous to the DNA-binding protein Mig1 from Saccharomyces cerevisiae (ScMig1). The C. albicans Mig1 protein (CaMig1) differs from ScMig1, in that, among other things, it lacks a putative phosphorylation site for Snf1 and presents several long stretches rich in glutamine or in asparagine, serine, and threonine and has the effector domain located at some distance (50 amino acids) from the carboxy terminus. Expression of CaMIG1 was low and was similar in glucose-, sucrose-, or ethanol-containing media. Disruption of the two CaMIG1 genomic copies had no effect in filamentation or infectivity. Levels of a glucose-repressible alpha-glucosidase, implicated in both sucrose and maltose utilization, were similar in wild-type or mig1/mig1 cells. Disruption of CaMIG1 had also no effect on the expression of the glucose-repressed gene CaGAL1. CaMIG1 was functional in S. cerevisiae, as judged by its ability to suppress the phenotypes produced by mig1 or tps1 mutations. In addition, CaMig1 formed specific complexes with the URS1 region of the S. cerevisiae FBP1 gene. The existence of a possible functional analogue of CaMIG1 in C. albicans was suggested by the results of band shift experiments.
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Affiliation(s)
- O Zaragoza
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas-UAM, Unidad de Bioquímica y Genética de Levaduras, 28029 Madrid, Spain
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Brown DH, Giusani AD, Chen X, Kumamoto CA. Filamentous growth of Candida albicans in response to physical environmental cues and its regulation by the unique CZF1 gene. Mol Microbiol 1999; 34:651-62. [PMID: 10564506 DOI: 10.1046/j.1365-2958.1999.01619.x] [Citation(s) in RCA: 206] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hyphal growth in the opportunistic fungal pathogen Candida albicans is believed to contribute to the virulence of the organism by promoting penetration of fungal cells into host tissue. In this study, stimulation of hyphal growth by a feature of the physical environment was demonstrated. Specifically, growth of cells embedded within a matrix promoted the formation of hyphae. The CZF1 gene, encoding a putative transcription factor, was shown to be involved in the regulation of hyphal growth under certain conditions, including embedded conditions. Ectopic expression of CZF1 in embedded cells promoted the rapid formation of hyphae. Elimination of CZF1 and CPH1, encoding a homologue of the Saccharomyces cerevisiae Ste12p transcription factor, led to a pronounced defect in filamentous growth of embedded cells. Elimination of CZF1 alone led to a moderate defect in hyphal growth under some conditions, including embedded conditions. Hyphal morphogenesis in response to matrix embedding may occur in the opportunistic pathogen, C. albicans, to promote invasion of fungal cells into host tissue.
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Affiliation(s)
- D H Brown
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
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45
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Feng Q, Summers E, Guo B, Fink G. Ras signaling is required for serum-induced hyphal differentiation in Candida albicans. J Bacteriol 1999; 181:6339-46. [PMID: 10515923 PMCID: PMC103768 DOI: 10.1128/jb.181.20.6339-6346.1999] [Citation(s) in RCA: 283] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serum induces Candida albicans to make a rapid morphological change from the yeast cell form to hyphae. Contrary to the previous reports, we found that serum albumin does not play a critical role in this morphological change. Instead, a filtrate (molecular mass, <1 kDa) devoid of serum albumin induces hyphae. To study genes controlling this response, we have isolated the RAS1 gene from C. albicans by complementation. The Candida Ras1 protein, like Ras1 and Ras2 of Saccharomyces cerevisiae, has a long C-terminal extension. Although RAS1 appears to be the only RAS gene present in the C. albicans genome, strains homozygous for a deletion of RAS1 (ras1-2/ras1-3) are viable. The Candida ras1-2/ras1-3 mutant fails to form germ tubes and hyphae in response to serum or to a serum filtrate but does form pseudohyphae. Moreover, strains expressing the dominant active RAS1(V13) allele manifest enhanced hyphal growth, whereas those expressing a dominant negative RAS1(A16) allele show reduced hyphal growth. These data show that low-molecular-weight molecules in serum induce hyphal differentiation in C. albicans through a Ras-mediated signal transduction pathway.
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Affiliation(s)
- Q Feng
- Whitehead Institute for Biomedical Research/Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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46
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Pérez-Martín J, Uría JA, Johnson AD. Phenotypic switching in Candida albicans is controlled by a SIR2 gene. EMBO J 1999; 18:2580-92. [PMID: 10228170 PMCID: PMC1171338 DOI: 10.1093/emboj/18.9.2580] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report the cloning of a gene from the human fungal pathogen Candida albicans with sequence and functional similarity to the Saccharomyces cerevisiae SIR2 gene. Deletion of the gene in C. albicans produces a dramatic phenotype: variant colony morphologies arise at frequencies as high as 1 in 10. The morphologies resemble those described previously as part of a phenotypic switching system proposed to contribute to pathogenesis. Deletion of SIR2 also produces a high frequency of karyotypic changes. These and other results are consistent with a model whereby Sir2 controls phenotypic switching and chromosome stability in C.albicans by organizing chromatin structure.
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Affiliation(s)
- J Pérez-Martín
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143-0414, USA
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Schönert S, Buder T, Dahl MK. Properties of maltose-inducible alpha-glucosidase MalL (sucrase-isomaltase-maltase) in Bacillus subtilis: evidence for its contribution to maltodextrin utilization. Res Microbiol 1999; 150:167-77. [PMID: 10229946 DOI: 10.1016/s0923-2508(99)80033-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, we identified the maltose inducible alpha-glucosidase MalL of Bacillus subtilis. The malL gene encodes a 561-residue protein with amino acid identities to several alpha-glucosidases and is located in a nine-gene spanning gene cluster, which is presumably organized in an operon. MalL was overproduced, purified, and its enzymatic characteristics were described in more detail. This characterization of the enzyme showed a protein stable up to 37 degrees C after temperature treatment for 15 min and exhibiting an optimal reaction temperature of 42 degrees C. Various disaccharides such as sucrose, maltose, and isomaltose were hydrolyzed with different efficiencies. MalL also hydrolyzes longer maltodextrins from maltotriose up to maltohexaose, but not maltoheptaose, palatinose, isomaltotriose, or isomaltotetraose. MalL expression is subject to both maltose induction and carbon catabolite repression. In this article, we present data demonstrating that induction of MalL expression also occurs when starch, amylose, or glycogen are present in the growth medium. The hydrolysis of these substrates by alpha-amylase presumably leads to products which, when taken up into the cytoplasm, trigger the initiation of maltose operon transcription. Furthermore, MalL expression varies temporally, showing a second induction in the stationary growth phase.
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Affiliation(s)
- S Schönert
- Lehrstuhl für Mikrobiologie, Universität Erlangen-Nürnberg, Germany
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48
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Abstract
Glucose and related sugars repress the transcription of genes encoding enzymes required for the utilization of alternative carbon sources; some of these genes are also repressed by other sugars such as galactose, and the process is known as catabolite repression. The different sugars produce signals which modify the conformation of certain proteins that, in turn, directly or through a regulatory cascade affect the expression of the genes subject to catabolite repression. These genes are not all controlled by a single set of regulatory proteins, but there are different circuits of repression for different groups of genes. However, the protein kinase Snf1/Cat1 is shared by the various circuits and is therefore a central element in the regulatory process. Snf1 is not operative in the presence of glucose, and preliminary evidence suggests that Snf1 is in a dephosphorylated state under these conditions. However, the enzymes that phosphorylate and dephosphorylate Snf1 have not been identified, and it is not known how the presence of glucose may affect their activity. What has been established is that Snf1 remains active in mutants lacking either the proteins Grr1/Cat80 or Hxk2 or the Glc7 complex, which functions as a protein phosphatase. One of the main roles of Snf1 is to relieve repression by the Mig1 complex, but it is also required for the operation of transcription factors such as Adr1 and possibly other factors that are still unidentified. Although our knowledge of catabolite repression is still very incomplete, it is possible in certain cases to propose a partial model of the way in which the different elements involved in catabolite repression may be integrated.
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Affiliation(s)
- J M Gancedo
- Instituto de Investigaciones Biomédicas, Unidad de Bioquímica y Genética de Levaduras, CSIC, 28029 Madrid, Spain.
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Alamäe T, Liiv L. Glucose repression of maltase and methanol-oxidizing enzymes in the methylotrophic yeast Hansenula polymorpha: isolation and study of regulatory mutants. Folia Microbiol (Praha) 1998; 43:443-52. [PMID: 9821297 DOI: 10.1007/bf02820789] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Regulation of the synthesis of maltase and methanol-oxidizing enzymes by the carbon source has been analyzed in the methylotrophic yeast Hansenula polymorpha. Maltase was shown to be responsible for the growth of H. polymorpha not only on maltose, but also on sucrose. The affinity of maltase towards maltase substrates decreased in the order: 4-nitrophenyl glucoside (PNPG) < sucrose < maltose. Mutants with glucose repression-insensitive synthesis of alcohol oxidase and maltase were obtained from H. polymorpha by mutagenesis and subsequent selection on methanol medium in the presence of 2-deoxy-D-glucose. One of the isolated mutants, L63, was studied in more detail. Mutant L63 was recessive and monogenic and it was not deficient in hexokinase. Its analysis revealed that H. polymorpha most probably has a repressor protein that in the presence of glucose can down-regulate expression of both maltase and enzymes of methanol oxidation.
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Affiliation(s)
- T Alamäe
- Department of Genetics, University of Tartu, Estonia.
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