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Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, De Vries RP. Expression-based clustering of CAZyme-encoding genes of Aspergillus niger. BMC Genomics 2017; 18:900. [PMID: 29169319 PMCID: PMC5701360 DOI: 10.1186/s12864-017-4164-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 10/05/2017] [Indexed: 11/29/2022] Open
Abstract
Background The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX that were grown on their specific inducing compounds. Results The cluster analysis of the expression data revealed several groups of co-regulated genes, which goes beyond the traditionally described co-regulated gene sets. Additional putative target genes of the selected regulators were identified, based on their expression profile. Notably, in several cases the expression profile puts questions on the function assignment of uncharacterized genes that was based on homology searches, highlighting the need for more extensive biochemical studies into the substrate specificity of enzymes encoded by these non-characterized genes. The data also revealed sets of genes that were upregulated in the regulatory mutants, suggesting interaction between the regulatory systems and a therefore even more complex overall regulatory network than has been reported so far. Conclusions Expression profiling on a large number of substrates provides better insight in the complex regulatory systems that drive the conversion of plant biomass by fungi. In addition, the data provides additional evidence in favor of and against the similarity-based functions assigned to uncharacterized genes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4164-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Birgit S Gruben
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Joanna E Kowalczyk
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Current affiliation: ATGM, Avans University of Applied Sciences, Lovensdijkstraat 61-63, 4818, AJ, Breda, The Netherlands
| | - Isabelle Benoit-Gelber
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Current affiliation: Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
| | - Ronald P De Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. .,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands. .,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
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2
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The minimal regulatory region necessary for the expression of the Penicillium griseoroseum plg1 gene. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-014-0873-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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3
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Argôlo Santos Carvalho H, de Andrade Silva EM, Carvalho Santos S, Micheli F. Polygalacturonases from Moniliophthora perniciosa are regulated by fermentable carbon sources and possible post-translational modifications. Fungal Genet Biol 2013; 60:110-21. [DOI: 10.1016/j.fgb.2013.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 09/30/2013] [Accepted: 10/06/2013] [Indexed: 11/30/2022]
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4
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Andersen MR, Giese M, de Vries RP, Nielsen J. Mapping the polysaccharide degradation potential of Aspergillus niger. BMC Genomics 2012; 13:313. [PMID: 22799883 PMCID: PMC3542576 DOI: 10.1186/1471-2164-13-313] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 06/08/2012] [Indexed: 11/10/2022] Open
Abstract
Background The degradation of plant materials by enzymes is an industry of increasing importance. For sustainable production of second generation biofuels and other products of industrial biotechnology, efficient degradation of non-edible plant polysaccharides such as hemicellulose is required. For each type of hemicellulose, a complex mixture of enzymes is required for complete conversion to fermentable monosaccharides. In plant-biomass degrading fungi, these enzymes are regulated and released by complex regulatory structures. In this study, we present a methodology for evaluating the potential of a given fungus for polysaccharide degradation. Results Through the compilation of information from 203 articles, we have systematized knowledge on the structure and degradation of 16 major types of plant polysaccharides to form a graphical overview. As a case example, we have combined this with a list of 188 genes coding for carbohydrate-active enzymes from Aspergillus niger, thus forming an analysis framework, which can be queried. Combination of this information network with gene expression analysis on mono- and polysaccharide substrates has allowed elucidation of concerted gene expression from this organism. One such example is the identification of a full set of extracellular polysaccharide-acting genes for the degradation of oat spelt xylan. Conclusions The mapping of plant polysaccharide structures along with the corresponding enzymatic activities is a powerful framework for expression analysis of carbohydrate-active enzymes. Applying this network-based approach, we provide the first genome-scale characterization of all genes coding for carbohydrate-active enzymes identified in A. niger.
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Affiliation(s)
- Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
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5
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Fungal enzyme sets for plant polysaccharide degradation. Appl Microbiol Biotechnol 2011; 91:1477-92. [PMID: 21785931 PMCID: PMC3160556 DOI: 10.1007/s00253-011-3473-2] [Citation(s) in RCA: 355] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/27/2011] [Accepted: 07/10/2011] [Indexed: 02/01/2023]
Abstract
Enzymatic degradation of plant polysaccharides has many industrial applications, such as within the paper, food, and feed industry and for sustainable production of fuels and chemicals. Cellulose, hemicelluloses, and pectins are the main components of plant cell wall polysaccharides. These polysaccharides are often tightly packed, contain many different sugar residues, and are branched with a diversity of structures. To enable efficient degradation of these polysaccharides, fungi produce an extensive set of carbohydrate-active enzymes. The variety of the enzyme set differs between fungi and often corresponds to the requirements of its habitat. Carbohydrate-active enzymes can be organized in different families based on the amino acid sequence of the structurally related catalytic modules. Fungal enzymes involved in plant polysaccharide degradation are assigned to at least 35 glycoside hydrolase families, three carbohydrate esterase families and six polysaccharide lyase families. This mini-review will discuss the enzymes needed for complete degradation of plant polysaccharides and will give an overview of the latest developments concerning fungal carbohydrate-active enzymes and their corresponding families.
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SUZUKI S, FUKUOKA M, TADA S, MATSUSHITA-MORITA M, HATTORI R, KITAMOTO N, KUSUMOTO KI. Production of Polygalacturonase by Recombinant Aspergillus oryzae in Solid-State Fermentation Using Potato Pulp. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2010. [DOI: 10.3136/fstr.16.517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Mertens JA, Burdick RC, Rooney AP. Identification, biochemical characterization, and evolution of the Rhizopus oryzae 99–880 polygalacturonase gene family. Fungal Genet Biol 2008; 45:1616-24. [DOI: 10.1016/j.fgb.2008.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Revised: 09/22/2008] [Accepted: 09/30/2008] [Indexed: 11/25/2022]
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9
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Yoshida S, Suzuki F, Tsukiboshi T, Shinohara H. Cloning and characterization of a gene rpg1 encoding polygalacturonase of Rhizopus oryzae. ACTA ACUST UNITED AC 2004; 108:1407-14. [PMID: 15757176 DOI: 10.1017/s0953756204001571] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The polygalacturonase (PG)-encoding gene (rpg1) of Rhizopus oryzae, the causal pathogen of rhizopus rot of mulberry, was cloned and sequenced. PGs were partially purified from incubation mixture of 2% pectin medium and their N-terminal amino acid sequences were determined by a gas-phase protein sequencer. RT-PCR was performed using degenerate primers designed from the amino acid sequences, which resulted in part of a PG-encoding gene being obtained. By 3'-RACE and TAIL-PCR analyses, the entire region of the PG-encoding gene was cloned and sequenced. The structural gene comprised 1199 bp coding for 383 amino acids with a putative signal peptide of 26 amino acids, and the open reading frame was interrupted by single intron of 47 bp. Phylogenetic analysis using the deduced amino acid sequence revealed that R. oryzae RPG1 belonged to a clade consisting of exo-PGs of ascomycete fungi.
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Affiliation(s)
- Shigenobu Yoshida
- Natural Resources Inventory Center, National Institute for Agro-Environmental Sciences, 3-1-3, Kan-nondai, Tsukuba, Ibaraki 305-8604, Japan.
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de Vries RP, Jansen J, Aguilar G, Parenicová L, Joosten V, Wülfert F, Benen JAE, Visser J. Expression profiling of pectinolytic genes from Aspergillus niger. FEBS Lett 2002; 530:41-7. [PMID: 12387863 DOI: 10.1016/s0014-5793(02)03391-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The expression of 26 pectinolytic genes from Aspergillus niger was studied in a wild type strain and a CreA derepressed strain, under 16 different growth conditions, to obtain an expression profile for each gene. These expression profiles were then submitted to cluster analysis to identify subsets of genes with similar expression profiles. With the exception of the feruloyl esterase encoding genes, all genes were expressed in the presence of D-galacturonic acid, polygalacturonate, and/or sugar beet pectin. Despite this general observation five distinct groups of genes were identified. The major group consisted of 12 genes of which the corresponding enzymes act on the pectin backbone and for which the expression, in general, is higher after 8 and 24 h of incubation, than after 2 or 4 h. Two other groups of genes encoding pectin main chain acting enzymes were detected. Two additional groups contained genes encoding L-arabinose and D-galactose releasing enzymes, and ferulic acid releasing enzymes, respectively. The genes encoding beta-galactosidase and the L-arabinose releasing enzymes were not only expressed in the presence of D-galacturonic acid, but also in the presence of L-arabinose, suggesting that they are under the control of two regulatory systems. Similarly, the rhamnogalacturonan acetylesterase encoding gene was not only expressed in the presence of D-galacturonic acid, polygalacturonate and sugar beet pectin, but also in the presence of L-rhamnose. The data presented provides indications for a general pectinolytic regulatory system responding to D-galacturonic acid or a metabolite derived from it. In addition, subsets of pectinolytic genes are expressed in response to the presence of L-arabinose, L-rhamnose or ferulic acid.
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Affiliation(s)
- Ronald P de Vries
- Molecular Genetics of Industrial Microorganisms, Wageningen University, The Netherlands.
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Williams HL, Tang Y, Hintz WE. Endopolygalacturonase is encoded by a multigene family in the basidiomycete Chondrostereum purpureum. Fungal Genet Biol 2002; 36:71-83. [PMID: 12051896 DOI: 10.1016/s1087-1845(02)00005-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The basidiomycete Chondrostereum purpureum produces several plant cell wall-degrading enzymes, including endopolygalacturonase (endoPG). Degenerate oligonucleotide primers were designed according to conserved regions of endoPG genes from various fungi, plants, and bacteria and used to amplify members of this gene family from C. purpureum. Four different amplification products showed significant similarity to known endoPGs and were used as hybridization probes to screen a library of genomic DNA sequences and to retrieve five full-length endoPG genes (epgA, epgB1, epgB2, epgC, and epgD). The identities between the deduced polypeptides for epgA, epgB1, epgC, and epgD ranged from 61.8 to 80.0%, while the deduced polypeptides for epgB1 and epgB2 shared 97.1% identity. Phylogenetic analysis suggested that the duplication of existing endoPG genes occurred after the divergence of the ascomycetes and basidiomycetes. C. purpureum is the first basidiomycete fungus for which the endoPG gene family has been described.
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Affiliation(s)
- Holly L Williams
- Department of Biology, University of Victoria, P.O. Box 3020, Victoria, BC, Canada V8W 3N5
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12
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Ribon AOB, Queiroz MV, Araújo EFD. Structural organization of polygalacturonase-encoding genes from Penicillium griseoroseum. Genet Mol Biol 2002. [DOI: 10.1590/s1415-47572002000400020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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13
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de Vries RP, Visser J. Aspergillus enzymes involved in degradation of plant cell wall polysaccharides. Microbiol Mol Biol Rev 2001; 65:497-522, table of contents. [PMID: 11729262 PMCID: PMC99039 DOI: 10.1128/mmbr.65.4.497-522.2001] [Citation(s) in RCA: 542] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Degradation of plant cell wall polysaccharides is of major importance in the food and feed, beverage, textile, and paper and pulp industries, as well as in several other industrial production processes. Enzymatic degradation of these polymers has received attention for many years and is becoming a more and more attractive alternative to chemical and mechanical processes. Over the past 15 years, much progress has been made in elucidating the structural characteristics of these polysaccharides and in characterizing the enzymes involved in their degradation and the genes of biotechnologically relevant microorganisms encoding these enzymes. The members of the fungal genus Aspergillus are commonly used for the production of polysaccharide-degrading enzymes. This genus produces a wide spectrum of cell wall-degrading enzymes, allowing not only complete degradation of the polysaccharides but also tailored modifications by using specific enzymes purified from these fungi. This review summarizes our current knowledge of the cell wall polysaccharide-degrading enzymes from aspergilli and the genes by which they are encoded.
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Affiliation(s)
- R P de Vries
- Molecular Genetics of Industrial Microorganisms, Wageningen University, 6703 HA Wageningen, The Netherlands.
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14
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Pages S, Kester HC, Visser J, Benen JA. Changing a single amino acid residue switches processive and non-processive behavior of Aspergillus niger endopolygalacturonase I and II. J Biol Chem 2001; 276:33652-6. [PMID: 11445590 DOI: 10.1074/jbc.m105770200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Processivity, also known as multiple attack on a single chain, is a feature commonly encountered only in enzymes in which the substrate binds in a tunnel. However, of the seven Aspergillus niger endopolygalacturonases, which have an open substrate binding cleft, four enzymes show processive behavior, whereas the other endopolygalacturonases are randomly acting enzymes. In a previous study (Benen, J.A.E., Kester, H.C.M., and Visser, J. (1999) Eur. J. Biochem. 259, 577-585) we proposed that the high affinity for the substrate of subsite -5 of processive endopolygalacturonase I constitutes the origin of the multiple attack behavior. Based on primary sequence alignments of A. niger endopolygalacturonases and three-dimensional structure analysis of endopolygalacturonase II, an arginine residue was identified in the processive enzymes at a position commensurate with subsite -5, whereas a serine residue was present at this position in the non-processive enzymes. In endopolygalacturonase I mutation R95S was introduced, and in endopolygalacturonase II mutation S91R was introduced. Product progression analysis on polymer substrate and bond cleavage frequency studies using oligogalacturonides of defined chain length for the mutant enzymes revealed that processive/non-processive behavior is indeed interchangeable by one single amino acid substitution at subsite -5, Arg-->Ser or Ser-->Arg.
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Affiliation(s)
- S Pages
- Section Molecular Genetics of Industrial Microorganisms, Wageningen University, Dreyenlaan 2, 6703 HA Wageningen, The Netherlands
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15
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García-Maceira FI, Di Pietro A, Huertas-González MD, Ruiz-Roldán MC, Roncero MI. Molecular characterization of an endopolygalacturonase from Fusarium oxysporum expressed during early stages of infection. Appl Environ Microbiol 2001; 67:2191-6. [PMID: 11319099 PMCID: PMC92854 DOI: 10.1128/aem.67.5.2191-2196.2001] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2000] [Accepted: 02/28/2001] [Indexed: 11/20/2022] Open
Abstract
The tomato vascular wilt pathogen Fusarium oxysporum f. sp. lycopersici produces an array of pectinolytic enzymes that may contribute to penetration and colonization of the host plant. Here we report the isolation of pg5, encoding a novel extracellular endopolygalacturonase (endoPG) that is highly conserved among different formae speciales of F. oxysporum. The putative mature pg5 product has a calculated molecular mass of 35 kDa and a pI of 8.3 and is more closely related to endoPGs from other fungal plant pathogens than to PG1, the major endoPG of F. oxysporum. Overexpression of pg5 in a bacterial heterologous system produced a 35-kDa protein with endoPG activity. Accumulation of pg5 transcript is induced by citrus pectin and D-galacturonic acid and repressed by glucose. As shown by reverse transcription-PCR, pg5 is expressed by F. oxysporum in tomato roots during the initial stages of infection. Targeted inactivation of pg5 has no detectable effect on virulence toward tomato plants.
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Affiliation(s)
- F I García-Maceira
- Departamento de Genética, Facultad de Ciencias, Universidad de Córdoba, Avda. San Alberto Magno s/n, 14071 Córdoba, Spain
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Pagès S, Heijne WH, Kester HC, Visser J, Benen JA. Subsite mapping of Aspergillus niger endopolygalacturonase II by site-directed mutagenesis. J Biol Chem 2000; 275:29348-53. [PMID: 10893426 DOI: 10.1074/jbc.m910112199] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To assess the subsites involved in substrate binding in Aspergillus niger endopolygalacturonase II, residues located in the potential substrate binding cleft stretching along the enzyme from the N to the C terminus were subjected to site-directed mutagenesis. Mutant enzymes were characterized with respect to their kinetic parameters using polygalacturonate as a substrate and with respect to their mode of action using oligogalacturonates of defined length (n = 3-6). In addition, the effect of the mutations on the hydrolysis of pectins with various degrees of esterification was studied. Based on the results obtained with enzymes N186E and D282K it was established that the substrate binds with the nonreducing end toward the N terminus of the enzyme. Asn(186) is located at subsite -4, and Asp(282) is located at subsite +2. The mutations D183N and M150Q, both located at subsite -2, affected catalysis, probably mediated via the sugar residue bound at subsite -1. Tyr(291), located at subsite +1 and strictly conserved among endopolygalacturonases appeared indispensable for effective catalysis. The mutations E252A and Q288E, both located at subsite +2, showed only slight effects on catalysis and mode of action. Tyr(326) is probably located at the imaginary subsite +3. The mutation Y326L affected the stability of the enzyme. For mutant E252A, an increased affinity for partially methylesterified substrates was recorded. Enzyme N186E displayed the opposite behavior; the specificity for completely demethylesterified regions of substrate, already high for the native enzyme, was increased. The origin of the effects of the mutations is discussed.
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Affiliation(s)
- S Pagès
- Section of Molecular Genetics of Industrial Micro-Organisms, Wageningen University, Dreyenlaan 2, 6703 HA Wageningen, The Netherlands
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Prade RA, Zhan D, Ayoubi P, Mort AJ. Pectins, pectinases and plant-microbe interactions. Biotechnol Genet Eng Rev 2000; 16:361-91. [PMID: 10819085 DOI: 10.1080/02648725.1999.10647984] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- R A Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater 74078, USA
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Parenicová L, Kester HC, Benen JA, Visser J. Characterization of a novel endopolygalacturonase from Aspergillus niger with unique kinetic properties. FEBS Lett 2000; 467:333-6. [PMID: 10675564 DOI: 10.1016/s0014-5793(00)01173-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We isolated and characterized a new type of endopolygalacturonase (PG)-encoding gene, pgaD, from Aspergillus niger. The primary structure of PGD differs from that of other A. niger PGs by a 136 amino acid residues long N-terminal extension. Biochemical analysis demonstrated extreme processive behavior of the enzyme on oligomers longer than five galacturonate units. Furthermore, PGD is the only A. niger PG capable of hydrolyzing di-galacturonate. It is tentatively concluded that the enzyme is composed of four subsites. The physiological role of PGD is discussed.
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Affiliation(s)
- L Parenicová
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, Dreyenlaan 2, 6703 HA, Wageningen, The Netherlands
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van der Vlugt-Bergmans CJ, Meeuwsen PJ, Voragen AG, van Ooyen AJ. Endo-xylogalacturonan hydrolase, a novel pectinolytic enzyme. Appl Environ Microbiol 2000; 66:36-41. [PMID: 10618200 PMCID: PMC91782 DOI: 10.1128/aem.66.1.36-41.2000] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/1999] [Accepted: 10/01/1999] [Indexed: 11/20/2022] Open
Abstract
We screened an Aspergillus tubingensis expression library constructed in the yeast Kluyveromyces lactis for xylogalacturonan-hydrolyzing activity in microwell plates by using a bicinchoninic acid assay. This assay detects reducing carbohydrate groups when they are released from a carbohydrate by enzymatic activity. Two K. lactis recombinants exhibiting xylogalacturonan-hydrolyzing activity were found among the 3,400 colonies tested. The cDNA insert of these recombinants encoded a 406-amino-acid protein, designated XghA, which was encoded by a single-copy gene, xghA. A multiple-sequence alignment revealed that XghA was similar to both polygalacturonases (PGs) and rhamnogalacturonases. A detailed examination of conserved regions in the sequences of these enzymes revealed that XghA resembled PGs more. High-performance liquid chromatography and matrix-assisted laser desorption ionization-time of flight mass spectrometry of the products of degradation of xylogalacturonan and saponified modified hairy regions of apple pectin by XghA demonstrated that this enzyme uses an endo type of mechanism. XghA activity appeared to be specific for a xylose-substituted galacturonic acid backbone.
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Affiliation(s)
- C J van der Vlugt-Bergmans
- Industrial Microbiology Group, Department of Food Technology and Nutritional Sciences, Wageningen Agricultural University, NL-6700 EV Wageningen, The Netherlands.
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Jalving R, van de Vondervoort PJ, Visser J, Schaap PJ. Characterization of the kexin-like maturase of Aspergillus niger. Appl Environ Microbiol 2000; 66:363-8. [PMID: 10618249 PMCID: PMC91831 DOI: 10.1128/aem.66.1.363-368.2000] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Secreted yields of foreign proteins may be enhanced in filamentous fungi through the use of translational fusions in which the target protein is fused to an endogenous secreted carrier protein. The fused proteins are usually separated in vivo by cleavage of an engineered Kex2 endoprotease recognition site at the fusion junction. We have cloned the kexin-encoding gene of Aspergillus niger (kexB). We constructed strains that either overexpressed KexB or lacked a functional kexB gene. Kexin-specific activity doubled in membrane-protein fractions of the strain overexpressing KexB. In contrast, no kexin-specific activity was detected in the similar protein fractions of the kexB disruptant. Expression in this loss-of-function strain of a glucoamylase human interleukin-6 fusion protein with an engineered Kex2 dibasic cleavage site at the fusion junction resulted in secretion of unprocessed fusion protein. The results show that KexB is the endoproteolytic proprotein processing enzyme responsible for the processing of (engineered) dibasic cleavage sites in target proteins that are transported through the secretion pathway of A. niger.
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Affiliation(s)
- R Jalving
- Section Molecular Genetics of Industrial Microorganisms, Wageningen University, Wageningen, The Netherlands
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Kester HC, Magaud D, Roy C, Anker D, Doutheau A, Shevchik V, Hugouvieux-Cotte-Pattat N, Benen JA, Visser J. Performance of selected microbial pectinases on synthetic monomethyl-esterified di- and trigalacturonates. J Biol Chem 1999; 274:37053-9. [PMID: 10601263 DOI: 10.1074/jbc.274.52.37053] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two monomethyl esters of alpha-(1-4)-linked D-galacturonic dimers and three monomethyl esters of alpha-(1-4)-linked D-galacturonic acid trimers were synthesized chemically and further used as substrates in order to establish the substrate specificity of six different endopolygalacturonases from Aspergillus niger, one exopolygalacturonase from Aspergillus tubingensis, and four selected Erwinia chrysanthemi pectinases; exopolygalacturonan hydrolase X (PehX), exopolygalacturonate lyase X (PelX), exopectate lyase W (PelW), and oligogalacturonan lyase (Ogl). All A. niger endopolygalacturonases (PGs) were unable to hydrolyze the two monomethyldigalacturonates and 2-methyltrigalacturonate, whereas 1-methyltrigalacturonate was only cleaved by PGI, PGII, and PGB albeit at an extremely low rate. The hydrolysis of 3-methyltrigalacturonate into 2-methyldigalacturonate and galacturonate by all endopolygalacturonases demonstrates that these enzymes can accommodate a methylgalacturonate at subsite -2. The A. tubingensis exopolygalacturonase hydrolyzed the monomethyl-esterified digalacturonates and trigalacturonates although at lower rates than for the corresponding oligogalacturonates. 1-Methyltrigalacturonate was hydrolyzed at the same rate as trigalacturonate which demonstrates that the presence of a methyl ester at the third galacturonic acid from the nonreducing end does not have any effect on the performance of exopolygalacturonase. Of the four E. chrysanthemi pectinases, Ogl was the only enzyme able to cleave digalacturonate, whereas all four enzymes cleaved trigalacturonate. Ogl does not cleave monomethyl-esterified digalacturonate and trigalacturonate in case the second galacturonic acid residue from the reducing end is methyl-esterified. PehX did not hydrolyze any of the monomethyl-esterified trigalacturonates. The two lyases, PelX and PelW, were both only able to cleave 1-methyltrigalacturonate into Delta4,5-unsaturated 1-methyldigalacturonate and galacturonate.
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Affiliation(s)
- H C Kester
- Section of Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
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22
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Wubben JP, Mulder W, ten Have A, van Kan JA, Visser J. Cloning and partial characterization of endopolygalacturonase genes from Botrytis cinerea. Appl Environ Microbiol 1999; 65:1596-602. [PMID: 10103256 PMCID: PMC91226 DOI: 10.1128/aem.65.4.1596-1602.1999] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Botrytis cinerea is a plant-pathogenic fungus infecting over 200 different plant species. We use a molecular genetic approach to study the process of pectin degradation by the fungus. Recently, we described the cloning and characterization of an endopolygalacturonase (endoPG) gene from B. cinerea (Bcpg1) which is required for full virulence. Here we describe the cloning and characterization of five additional endoPG-encoding genes from B. cinerea SAS56. The identity at the amino acid level between the six endoPGs of B. cinerea varied from 34 to 73%. Phylogenetic analysis, by using a group of 35 related fungal endoPGs and as an outgroup one plant PG, resulted in the identification of five monophyletic groups of closely related proteins. The endoPG proteins from B. cinerea SAS56 could be assigned to three different monophyletic groups. DNA blot analysis revealed the presence of the complete endoPG gene family in other strains of B. cinerea, as well as in other Botrytis species. Differential gene expression of the gene family members was found in mycelium grown in liquid culture with either glucose or polygalacturonic acid as the carbon source.
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Affiliation(s)
- J P Wubben
- Section of Molecular Genetics of Industrial Micro-organisms, Wageningen Agricultural University, 6703 HA Wageningen, The Netherlands
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23
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Siekstele R, Bartkeviciute D, Sasnauskas K. Cloning, targeted disruption and heterologous expression of the Kluyveromyces marxianus endopolygalacturonase gene (EPG1). Yeast 1999; 15:311-22. [PMID: 10206190 DOI: 10.1002/(sici)1097-0061(19990315)15:4<311::aid-yea379>3.0.co;2-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The yeast Kluyveromyces marxianus strain BKM Y-719 produces an efficient pectin-degrading endopolygalacturonase (EPG) that cleaves the internal alpha-1,4-D-glycosidic linkages to yield oligomers of varying sizes. The EPG1 gene encoding this industrially important EPG was cloned by using the polymerase chain reaction (PCR) technique and degenerate primers to generate a 135 bp DNA fragment with which a genomic library was screened. The cloned fragment contained an open reading frame (ORF) of 1083 bp, encoding a 361 amino acid polypeptide. The predicted amino acid (aa) sequence of EPG showed similarity with polygalacturonases (PGs) of fungi. Analysis of the aa sequence indicated that the first 25 aa constitute a signal sequence and a motif (C218XGGHGXSIGSVG230) that is usually associated with a PG active site. Pulsed-field gel electrophoresis resolved chromosomal bands for K. marxianus BKM Y-719 and using chromoblotting it seems that EPG1 is present as only a single copy in the genome.
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Affiliation(s)
- R Siekstele
- Institute of Biotechnology, Vilnius, Lithuania.
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24
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Kojima Y, Sakamoto T, Kishida M, Sakai T, Kawasaki H. Acidic condition-inducible polygalacturonase of Aspergillus kawachii. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1381-1177(98)00120-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Benen JA, Kester HC, Visser J. Kinetic characterization of Aspergillus niger N400 endopolygalacturonases I, II and C. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 259:577-85. [PMID: 10092840 DOI: 10.1046/j.1432-1327.1999.00080.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Endopolygalacturonases I, II and C isolated from recombinant Aspergillus niger strains were characterized with respect to pH optimum, activity on polygalacturonic acid and mode of action and kinetics on oligogalacturonates of different chain length (n = 3-7). Apparent Vmax values using polygalacturonate as a substrate at the pH optimum, pH 4.1, were calculated as 13.8 mukat.mg-1, 36.5 mukat.mg-1 and 415 nkat.mg-1 for endopolygalacturonases I, II and C, respectively. K(m) values were < 0.15 mg.mL-1 for all three enzymes. Product progression analysis using polygalacturonate as a substrate revealed a random cleavage pattern for all three enzymes and suggested processive behavior for endopolygalacturonases I and C. This result was confirmed by analysis of the mode of action using oligogalacturonates. Processivity was observed when the degree of polymerization of the substrate exceeded 5 or 6 for endopolygalacturonase I and endopolygalacturonase C, respectively. The bond-cleavage frequencies obtained for the hydrolysis of the oligogalacturonates were used to assess subsite maps. The maps indicate that the minimum number of subsites is seven for all three enzymes. Using pectins of various degrees of esterification, it was shown that endopolygalacturonase II is the most sensitive to the presence of methyl esters. Like endopolygalacturonase II, endopolygalacturonases I, C and E, which was also included in this part of the study, preferred the non-esterified pectate. Additional differences in substrate specificity were revealed by analysis of the reaction products of hydrolysis of a mixture of pectate lyase-generated delta 4,5-unsaturated oligogalacturonates of degree of polymerization 4-8. Whereas endopolygalacturonase I showed a strong preference for generating the delta 4,5-unsaturated dimer, with endopolygalacturonase II the delta 4,5-unsaturated trimer accumulated, indicating further differences in substrate specificity. For endopolygalacturonases C and E both the delta 4,5-unsaturated dimer and trimer were observed, although in different ratios.
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Affiliation(s)
- J A Benen
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, The Netherlands.
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26
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Van Dross RT, Rao KV, Eisenberg E, Sanders MM. Cloning and characterization of the Aspergillus nidulans DNA topoisomerase I gene. Gene 1997; 203:169-74. [PMID: 9426247 DOI: 10.1016/s0378-1119(97)00508-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The topoisomerase I (TOP1) gene was cloned and sequenced from Aspergillus nidulans using the polymerase chain reaction (PCR). Genomic DNA was used as a template to obtain a 2987-bp gene containing five small introns. PCR from a cDNA library yielded a 2613-bp sequence which codes for an 871 amino acid protein. Comparison of the deduced amino acid sequence with other DNA topoisomerase I (topo I) protein sequences shows a somewhat higher degree of identity with other fungal amino acid sequences than with the human enzyme. Topo I is a ubiquitous enzyme which can be converted to a cytotoxic molecule in the presence of drugs that function as topo I poisons. The Aspergillus TOP1 cDNA will be used in an effort to identify novel cytotoxic antifungals which target this enzyme.
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Affiliation(s)
- R T Van Dross
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway 08855, USA
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27
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Doostdar H, McCollum T, Mayer RT. Purification and Characterization of an endo-Polygalacturonase from the Gut of West Indies Sugarcane Rootstalk Borer Weevil (Diaprepes abbreviatus L.) Larvae*. Comp Biochem Physiol B Biochem Mol Biol 1997. [DOI: 10.1016/s0305-0491(97)00285-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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28
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Patiño B, Posada ML, González-Jaén MT, Martínez del Pozo A, Vázquez C. Control of polygalacturonase synthesis in Fusarium oxysporum f.sp. radicis lycopersici. Can J Microbiol 1997; 43:1084-90. [PMID: 9436311 DOI: 10.1139/m97-155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Genetic control of polygalacturonase (PG) activity from Fusarium oxysporum f.sp. radicis lycopersici was analyzed on pectin and glucose cultures. One exopolygalacturonase from F. oxysporum f.sp. radicis lycopersici was strongly induced, in stationary culture, when the fungus was grown on apple pectin, while on glucose no extracellular PG activity could be detected. Although SDS-PAGE detected the presence of a putative PG band (66 kDa) in both conditions, specific antibodies obtained against the purified PG only detected it in PG-inducing conditions, that is to say, when apple pectin was used as the carbon source. Northern blot analysis of RNA of two isolates of F. oxysporum f.sp. radicis lycopersici (r6 and r2) confirmed that this regulation of PG synthesis was exerted at the transcriptional level. Only one single mRNA species of around 1400 nucleotides was detected on the cultures containing pectin and was absent in glucose-grown cultures. Southern blot analysis of genomic DNA indicated that pg gene seems to be present in a single copy in the genomes of F. oxysporum f.sp. radicis lycopersici r6 and r2 and Fusarium oxysporum f.sp. lycopersici, showing similar hybridization patterns in all species. The partial sequence of this pg gene from F. oxysporum f.sp. radicis lycopersici r6, which is also reported, showed high similarity to diverse PGs already reported. Exopolygalacturonase of F. oxysporum f.sp. radicis lycopersici r6 is heavily glycosylated; its deglycosylated form had a molecular mass of 50 kDa.
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Affiliation(s)
- B Patiño
- Departamento de Microbiología III, Facultad de Biología, Universidad Complutense de Madrid, Spain
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29
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Sakai T, Sirasaka N, Hirano H, Kishida M, Kawasaki H. Isolation and expression of the gene which encodes a novel enzyme with polymethoxygalacturonate-degrading activity in Trichosporon penicillatum. FEBS Lett 1997; 414:439-43. [PMID: 9315736 DOI: 10.1016/s0014-5793(97)01032-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The novel gene named PSX1, encoding a new protopectinase with the polymethoxygalacturonase activity, was isolated from Trichosporon penicillatum. Nucleotide sequencing revealed that the PSX1 gene is composed of 1080 bases (360 amino acids, 38,747 Da). The N-terminal amino acid sequences of the open reading frame correspond to a signal peptide and propeptide processed by a Kex2-like proteinase. Mature PPase SX1 was composed of 334 amino acids (36,121 Da). PPase SX1 produced by a S. cerevisiae transformant harboring the PSX1 gene degraded methoxylated polygalacturonic acid as a substrate, but not degraded unmethoxylated polygalacturonic acid.
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Affiliation(s)
- T Sakai
- Department of Applied Biochemistry, College of Agriculture, Osaka Prefecture University, Sakai, Japan
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30
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Shieh MT, Brown RL, Whitehead MP, Cary JW, Cotty PJ, Cleveland TE, Dean RA. Molecular genetic evidence for the involvement of a specific polygalacturonase, P2c, in the invasion and spread of Aspergillus flavus in cotton bolls. Appl Environ Microbiol 1997; 63:3548-52. [PMID: 9293005 PMCID: PMC168660 DOI: 10.1128/aem.63.9.3548-3552.1997] [Citation(s) in RCA: 149] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Isolates of Aspergillus flavus can be differentiated based on production of the polygalacturonase P2c. One group of isolates produces P2c, whereas the other group does not. In general, the group that produces P2c causes more damage and spreads to a greater extent in cotton bolls than those isolates that do not produce P2c. To determine whether P2c contributes to disease, the expression of pecA, the gene previously determined to encode P2c, was genetically altered. Adding the pecA gene to a strain previously lacking the gene resulted in the ability to cause significantly more damage to the intercarpellary membrane and the ability spread to a greater extent within the adjacent locule compared to the abilities of a control transformant. Conversely, eliminating the expression of pecA by targeted disruption caused a significant reduction in aggressiveness compared to that of a nondisrupted control transformant. These results provide direct evidence that P2c contributes to the invasion and spread of A. flavus during infection of cotton bolls. However, other factors not evaluated in this study also contribute to aggressiveness.
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Affiliation(s)
- M T Shieh
- Department of Plant Pathology and Physiology, Clemson University, South Carolina 29634-0377, USA
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31
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Cloning and characterization of a polygalacturonase-encoding gene from Penicillium janthinellum. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0922-338x(97)82065-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Kester HC, Kusters-van Someren MA, Müller Y, Visser J. Primary structure and characterization of an exopolygalacturonase from Aspergillus tubingensis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 240:738-46. [PMID: 8856078 DOI: 10.1111/j.1432-1033.1996.0738h.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
From the culture fluid of the hyphal fungus Aspergillus tubingensis, an exopolygalacturonase with a molecular mass of 78 kDa, an isoelectric point in the pH-range 3.7-4.4 and a pH optimum of 4.2 was purified. The enzyme has been characterized as an exopolygalacturonase [poly(1,4-alpha-D-galacturonide)galacturonohydrolase] that cleaves monomer units from the non-reducing end of the substrate molecule. K(m) and Vmax for polygalacturonic acid hydrolysis were 3.2 mg ml-1 and 3.1 mg ml-1 and 255 U mg-1 and 262 U mg-1 for the wild-type and recombinant enzymes, respectively. The kinetic data of exopolygalacturonase on oligogalacturonates of different degree of polymerization (2-7) were interpreted in terms of a subsite model to obtain more insight into catalysis and substrate binding. On oligogalacturonates of different degrees of polymerization (2-7), the Michaelis constant (K(m)) decreased with increasing chain length (n). The Vmax value increased with chain length up to n = 4, then reached a plateau value. The enzyme was competitively inhibited by galacturonic acid (Ki = 0.3 mM) as well as by reduced digalacturonate (Ki = 0.4 mM). The exopolygalacturonase gene (pgaX) was cloned by reverse genetics and shows only 13% overall amino acid sequence identity with A. niger endopolygalacturonases. The exopolygalacturonase is most related to plant polygalacturonases. Only four small stretches of amino acids are conserved between all known endogalacturonases and exopolygalacturonases. Expression of the pgaX gene is inducible with galacturonic acid and is subject to catabolite repression. A fusion between the promoter of the A. niger glycolytic gene encoding pyruvate kinase and the pgaX-coding region was used to achieve high level production of exopolygalacturonase under conditions where no endopolygalacturonases were produced.
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Affiliation(s)
- H C Kester
- Section Molecular Genetics of Industrial Microorganisms, Wageningen Agricultural University, The Netherlands
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33
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Gao S, Choi GH, Shain L, Nuss DL. Cloning and targeted disruption of enpg-1, encoding the major in vitro extracellular endopolygalacturonase of the chestnut blight fungus, Cryphonectria parasitica. Appl Environ Microbiol 1996; 62:1984-90. [PMID: 8787397 PMCID: PMC167977 DOI: 10.1128/aem.62.6.1984-1990.1996] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The gene enpg-1, encoding the major extracellular endopolygalacturonase (endoPG) purified from culture filtrates of the chestnut blight fungus, Cryphonectria parasitica, was cloned and characterized. The deduced mature enpg-1 protein product, ENPG-1, had a calculated molecular mass of 34.5 kDa and a pI of 7.2, consistent with empirically derived values for the purified enzyme, and had 66% identity with an endoPG from the maize pathogen Cochliobolus carbonum. Targeted disruption of enpg-1 was accomplished by homologous recombination with a cloned copy of the gene that contained the Escherichia coli hygromycin B phosphotransferase gene (hph) inserted into exon 1. enpg-1 disruption resulted in no reduction in canker formation on dormant American chestnut stems. Unexpectedly, the level of polygalacturonase (PG) activity measured in cankered bark tissue infected with enpg-1 disruptants was indistinguishable from that found in canker tissue infected with virulent strain EP155. Isoelectric focusing and activity gel analysis of PG activity extracted from canker bark tissue revealed ENPG-1 to be a minor (less than 5%) activity component in tissue infected with the virulent strain and to be absent in tissue infected with the disruption mutants. The predominant activity in both canker samples consisted of two previously undetected acidic PG forms that appear absent in C. parasitica culture filtrates. We conclude from these results that the major C. parasitica extracellular endoPG produced in culture, ENPG-1, does not play a significant role in fungal virulence. However, the identification of two acidic PG activities expressed predominantly, if not exclusively, in planta provides new opportunities for examining the importance of PGs in C. parasitica pathogenesis.
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Affiliation(s)
- S Gao
- Roche Institute of Molecular Biology, Roche Research Center, Nutley, New Jersey 07110, USA
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34
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Centis S, Dumas B, Fournier J, Marolda M, Esquerré-Tugayé MT. Isolation and sequence analysis of Clpg1, a gene coding for an endopolygalacturonase of the phytopathogenic fungus Colletotrichum lindemuthianum. Gene 1996; 170:125-9. [PMID: 8621072 DOI: 10.1016/0378-1119(95)00867-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Oligodeoxyribonucleotide primers designed from the N-terminal amino acid (aa) sequence of the endopolygalacturonase (EndoPG) of Colletotrichum lindemuthianum (Cl) race beta and from an internal sequence conserved among different fungal EndoPG were used in a polymerase chain reaction (PCR) to amplify genomic related sequences of the fungus. A 542-bp fragment, designated pgA, was obtained and used as a probe to screen a partial genomic library of Cl. Among the positive clones, one was further analyzed. Nucleotide sequencing of this clone revealed on ORF encoding a 363-amino-acid (aa) polypeptide beginning with a signal peptide of 26 aa interrupted by an intron of 70 bp, and showing a high degree of homology to ten fungal EndoPG sequences. Consensus sequences were identified in the 5' non-coding region. This genomic clone was thereafter designated Clpg1. Southern analysis, performed with a Clpg1-specific probe, showed that this gene is present as a single copy in the Cl genome.
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Affiliation(s)
- S Centis
- Université Paul Sabatier, Centre de Biologie et Physiologie Végétale URA 1941 CNRS, Toulouse, France
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35
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Stratilová E, Dzúrová M, Markovic O, Jörnvall H. An essential tyrosine residue of Aspergillus polygalacturonase. FEBS Lett 1996; 382:164-6. [PMID: 8612742 DOI: 10.1016/0014-5793(96)00146-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Based on strict conservation of a tyrosine residue in 24 polygalacturonases, tyrosine modification was assessed in two different forms of the Aspergillus enzyme. The second subform was unknown in structure but submitted to sequence analysis and was found also to have the conserved tyrosine residue. Results of chemical modifications are consistent in showing inactivation of the proteins with all tyrosine-reactive agents tested, acetic anhydride, N-acetyl imidazole, and tetranitromethane. Furthermore, after acetylation, regeneration of enzyme activity was possible with hydroxylamine. Spectrophotometric pH titration showed that one accessible tyrosine residue is ionized at pH 9.3-9.5, whereas the remaining, masked residues are all ionized at pH 10.5. It is concluded that one tyrosine residue is catalytically important, in agreement with the inactivation and reactivation data, that this residue is accessible, and that it is likely to correspond to the strictly conserved residue observed in all forms.
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Affiliation(s)
- E Stratilová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
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36
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Benen J, Parenicova L, Kusters-van Someren M, Kester H, Visser J. Molecular genetic and biochemical aspects of pectin degradation in Aspergillus. PROGRESS IN BIOTECHNOLOGY 1996. [DOI: 10.1016/s0921-0423(96)80265-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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37
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Stratilov� E, Breierov� E, Vadkertiov� R. Effect of cultivation and storage pH on the production of multiple forms of polygalacturonase by Aspergillus niger. Biotechnol Lett 1996. [DOI: 10.1007/bf00137808] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Lang C, Looman AC. Efficient expression and secretion of Aspergillus niger RH5344 polygalacturonase in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 1995; 44:147-56. [PMID: 8579828 DOI: 10.1007/bf00164494] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
An Aspergillus niger endopolygalacturonase (EC 3.2.1.15) cDNA was expressed in the yeast Saccharomyces cerevisiae. Secretion of the protein into the growth medium was efficiently directed by the fungal leader sequence, and processing occurred at the same site as in Aspergillus. The expression level was significantly enhanced by using a "short" version of the yeast ADHI promoter. An additional increase in the yield of heterologous protein was due to a higher plasmid stability and a rise in plasmid copy number. This was achieved by deleting most of the bacterial sequences from the expression vector. The yeast-derived enzyme showed the same enzymatic and biochemical properties as the fungal polygalacturonase, such as substrate specificity, pH and temperature optima and pI value. The yeast-derived enzyme, however, showed a higher degree of glycosylation and exhibited a more pronounced temperature stability than the fungal enzyme.
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Affiliation(s)
- C Lang
- Institut für Gärungsgewerbe und Biotechnologie, Abt. Biotechnologie Hüls, Berlin, Germany
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39
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Whitehead MP, Shieh MT, Cleveland TE, Cary JW, Dean RA. Isolation and characterization of polygalacturonase genes (pecA and pecB) from Aspergillus flavus. Appl Environ Microbiol 1995; 61:3316-22. [PMID: 7574642 PMCID: PMC167612 DOI: 10.1128/aem.61.9.3316-3322.1995] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Two genes, pecA and pecB, encoding endopolyglacturonases were cloned from a highly aggressive strain of Aspergillus flavus. The pecA gene consisted of 1,228 bp encoding a protein of 363 amino acids with a predicted molecular mass of 37.6 kDa, interrupted by two introns of 58 and 81 bp in length. Accumulation of pecA mRNA in both pectin- or glucose-grown mycelia in the highly aggressive strain matched the activity profile of a pectinase previously identified as P2c. Transformants of a weakly aggressive strain containing a functional copy of the pecA gene produced P2c in vitro, confirming that pecA encodes P2c. The coding region of pecB was determined to be 1,217 bp in length interrupted by two introns of 65 and 54 bp in length. The predicted protein of 366 amino acids had an estimated molecular mass of 38 kDa. Transcripts of this gene accumulated in mycelia grown in medium containing pectin alone, never in mycelia grown in glucose-containing medium, for both highly and weakly aggressive strains. Thus, pecB encodes the activity previously identified as P1 or P3. pecA and pecB share a high degree of sequence identity with polygalacturonase genes from Aspergillus parasiticus and Aspergillus oryzae, further establishing the close relationships between members of the A. flavus group. Conservation of intron positions in these genes also indicates that they share a common ancestor with genes encoding endopolyglacturonases of Aspergillus niger.
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Affiliation(s)
- M P Whitehead
- Department of Plant Pathology and Physiology, Clemson University, South Carolina 29634-0377, USA
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Cary JW, Brown R, Cleveland TE, Whitehead M, Dean RA. Cloning and characterization of a novel polygalacturonase-encoding gene from Aspergillus parasiticus. Gene 1995; 153:129-33. [PMID: 7883176 DOI: 10.1016/0378-1119(94)00749-i] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Pectinases produced by Aspergillus flavus and A. parasiticus are believed to play a significant role in the ability of these fungi to spread in cotton bolls and other crops. Utilizing a DNA probe, generated by PCR, of the Aspergillus niger pgaII gene, we have isolated a novel, constitutively expressed polygalacturonase (PG)-encoding gene (pecA) from an A. parasiticus cDNA library. DNA sequence analysis and the deduced amino acid (aa) sequence of pecA demonstrated significant identity at the nucleotide and aa levels with other PG of fungal origin. Northern blot analysis of RNA isolated from A. parasiticus grown on either glucose or pectin as the sole carbon source showed that pecA was expressed during growth in both media.
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Affiliation(s)
- J W Cary
- USDA-ARS, Southern Regional Research Center, New Orleans, LA 70179
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41
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Robert LS, Allard S, Gerster JL, Cass L, Simmonds J. Isolation and characterization of a polygalacturonase gene highly expressed in Brassica napus pollen. PLANT MOLECULAR BIOLOGY 1993; 23:1273-1278. [PMID: 8292791 DOI: 10.1007/bf00042360] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A cDNA clone, Sta 44-4, corresponding to a mRNA highly expressed in Brassica napus cv. Westar stamens, was isolated by differential screening and characterized. Northern blot and in situ analyses demonstrated that Sta 44-4 is synthesized in pollen beginning at the late uninucleate stage and reaches a maximum in trinucleate microspores. Sta 44-4 displayed significant sequence similarity to known pollen polygalacturonase genes. The B. napus pollen polygalacturonase gene was shown to be part of a small gene family and to display some polymorphism among different cultivars.
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Affiliation(s)
- L S Robert
- Plant Research Centre, Centre Experimental Farm, Ottawa, Ontario, Canada
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Kitamoto N, Kimura T, Kito Y, Ohmiya K, Tsukagoshi N. Structural features of a polygalacturonase gene cloned from Aspergillus oryzae KBN616. FEMS Microbiol Lett 1993; 111:37-41. [PMID: 8359678 DOI: 10.1111/j.1574-6968.1993.tb06358.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A genomic gene encoding a polygalacturonase from Aspergillus oryzae, used in soy sauce production, was cloned and sequenced. The structural gene comprises 1227 bp coding for 363 amino acids with a putative prepropeptide of 28 amino acids and the open reading frame is disrupted by two short introns of 57 bp and 81 bp. The deduced amino acid sequence of the mature protein showed 63, 63, 63 and 64% homology with those of Aspergillus niger polygalacturonase I, Aspergillus niger polygalacturonase II, Aspergillus tubingensis polygalacturonase II and Cochliobolus carbonum polygalacturonase, respectively. There is, however, little homology among fungal, plant and bacterial polygalacturonases.
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Affiliation(s)
- N Kitamoto
- Food Research Institute, Aichi Prefectural Government, Nagoya, Japan
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Caprari C, Richter A, Bergmann C, Lo Cicero S, Salvi G, Cervone F, De Lorenzo G. Cloning and characterization of a gene encoding the endopolygalacturonase of Fusarium moniliforme. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/s0953-7562(09)80138-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Shanley N, van den Broek L, Voragen A, Coughlan M. Physicochemical and catalytic properties of three endopolygalacturonases from Penicillium pinophilum. J Biotechnol 1993. [DOI: 10.1016/0168-1656(93)90170-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Stratilová E, Markovic O, Skrovinová D, Rexová-Benková L, Jörnvall H. Pectinase Aspergillus sp. polygalacturonase: multiplicity, divergence, and structural patterns linking fungal, bacterial, and plant polygalacturonases. JOURNAL OF PROTEIN CHEMISTRY 1993; 12:15-22. [PMID: 8427629 DOI: 10.1007/bf01024909] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nine forms of Aspergillus sp. polygalacturonase were purified from a commercial preparation of pectinase Rohament P using chromatographies and chromatofocusing. Individual forms differ in isoelectric point, and at least five differ in structure; whereas molecular masses and enzymatic properties are largely identical. Four forms with free alpha-amino groups have identical start positions but internal amino acid replacements. Therefore, the multiplicity is derived from true heterogeneities and not from N-terminal truncations. Peptide analysis of the major polygalacturonase reveals large variations toward the enzyme from other Aspergillus species (72-75% residue differences, depending on species) but additional similarities with the enzyme from bacterial and plant sources (only 66-71% residue differences toward the Erwinia, tomato, and peach enzymes). Combined with previous data, these facts show polygalacturonase to exhibit extensive multiplicity and much variability, but also unexpected similarities between distantly related forms with conserved functional properties.
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Affiliation(s)
- E Stratilová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Czechoslovakia
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Bussink HJ, Buxton FP, Fraaye BA, de Graaff LH, Visser J. The polygalacturonases of Aspergillus niger are encoded by a family of diverged genes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 208:83-90. [PMID: 1511691 DOI: 10.1111/j.1432-1033.1992.tb17161.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aspergillus niger produces several polygalacturonases that, with other enzymes, are involved in the degradation of pectin. One of the two previously characterized genes coding for the abundant polygalacturonases I and II (PGI and PGII) found in a commercial pectinase preparation was used as a probe to isolate five more genes by screening a genomic DNA library in phage lambda EMBL4 using conditions of moderate stringency. The products of these genes were detected in the culture medium of Aspergillus nidulans transformants on the basis of activity measurements and Western-blot analysis using a polyclonal antibody raised against PGI. These transformants were, with one exception, constructed using phage DNA. A. nidulans transformants secreted high amounts of PGI and PGII in comparison to the previously characterized A. niger transformants and a novel polygalacturonase (PGC) was produced at high levels by A. nidulans transformed with the subcloned pgaC gene. This gene was sequenced and the protein-coding region was found to be interrupted by three introns; the different intron/exon organization of the three sequenced A. niger polygalacturonase genes can be explained by the gain or loss of two single introns. The pgaC gene encodes a putative 383-amino-acid prepro-protein that is cleaved after a pair of basic amino acids and shows approximately 60% amino acid sequence similarity to the other polygalacturonases in the mature protein. The N-terminal amino acid sequences of the A. niger polygalacturonases display characteristic amino acid insertions or deletions that are also observed in polygalacturonases of phytopathogenic fungi. In the upstream regions of the A. niger polygalacturonase genes, a sequence of ten conserved nucleotides comprising a CCAAT sequence was found, which is likely to represent a binding site for a regulatory protein as it shows a high similarity to the yeast CYC1 upstream activation site recognized by the HAP2/3/4 activation complex.
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Affiliation(s)
- H J Bussink
- Department of Genetics, Wageningen Agricultural University, The Netherlands
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Bussink HJD, van den Hombergh JPTW, van den IJssel PRLA, Visser J. Characterization of polygalacturonase-overproducing Aspergillus niger transformants. Appl Microbiol Biotechnol 1992. [DOI: 10.1007/bf00210987] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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