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Lawrinowitz S, Wurlitzer JM, Weiss D, Arndt HD, Kothe E, Gressler M, Hoffmeister D. Blue Light-Dependent Pre-mRNA Splicing Controls Pigment Biosynthesis in the Mushroom Terana caerulea. Microbiol Spectr 2022; 10:e0106522. [PMID: 36094086 PMCID: PMC9603100 DOI: 10.1128/spectrum.01065-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/18/2022] [Indexed: 12/30/2022] Open
Abstract
Light induces the production of ink-blue pentacyclic natural products, the corticin pigments, in the cobalt crust mushroom Terana caerulea. Here, we describe the genetic locus for corticin biosynthesis and provide evidence for a light-dependent dual transcriptional/cotranscriptional regulatory mechanism. Light selectively induces the expression of the corA gene encoding the gateway enzyme, the first described mushroom polyporic acid synthetase CorA, while other biosynthetic genes for modifying enzymes necessary to complete corticin assembly are induced only at lower levels. The strongest corA induction was observed following exposure to blue and UV light. A second layer of regulation is provided by the light-dependent splicing of the three introns in the pre-mRNA of corA. Our results provide insight into the fundamental organization of how mushrooms regulate natural product biosynthesis. IMPORTANCE The regulation of natural product biosyntheses in mushrooms in response to environmental cues is poorly understood. We addressed this knowledge gap and chose the cobalt crust mushroom Terana caerulea as our model. Our work discovered a dual-level regulatory mechanism that connects light as an abiotic stimulus with a physiological response, i.e., the production of dark-blue pigments. Exposure to blue light elicits strongly increased transcription of the gene encoding the gateway enzyme, the polyporic acid synthetase CorA, that catalyzes the formation of the pigment core structure. Additionally, light is a prerequisite for the full splicing of corA pre-mRNA and, thus, its proper maturation. Dual transcriptional/cotranscriptional light-dependent control of fungal natural product biosynthesis has previously been unknown. As it allows the tight control of a key metabolic step, it may be a much more prevalent mechanism among these organisms.
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Affiliation(s)
- Stefanie Lawrinowitz
- Friedrich-Schiller-Universität Jena, Institute of Pharmacy, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Jacob M. Wurlitzer
- Friedrich-Schiller-Universität Jena, Institute of Pharmacy, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Dieter Weiss
- Friedrich-Schiller-Universität Jena, Institute for Organic Chemistry and Macromolecular Chemistry, Jena, Germany
| | - Hans-Dieter Arndt
- Friedrich-Schiller-Universität Jena, Institute for Organic Chemistry and Macromolecular Chemistry, Jena, Germany
| | - Erika Kothe
- Friedrich-Schiller-Universität Jena, Institute for Microbiology, Jena, Germany
| | - Markus Gressler
- Friedrich-Schiller-Universität Jena, Institute of Pharmacy, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Dirk Hoffmeister
- Friedrich-Schiller-Universität Jena, Institute of Pharmacy, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
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Kumar S, Mutturi S. Alternative splicing regulates the α-glucosidase synthesis in Aspergillus neoniger NCIM 1400. Fungal Biol 2021; 125:658-665. [PMID: 34281659 DOI: 10.1016/j.funbio.2021.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/26/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Aspergillus neoniger NCIM 1400 whose cell-free fraction was earlier established for transglycosylation activity conferred by α-glucosidase gene (agdA), was subjected to sequence analysis. Preliminary results revealed certain dynamics in the intron splicing mechanism, and to ascertain these molecular events, a detailed study was carried. The electrophoresis results from the cDNA portion (B-fragment) of agdA showed multiple bands, indicating the amplification of one or more fragments. The sequence results of cDNA cloned vector revealed the retention type of alternative splicing in the agdA. The splicing mechanism of agdA in NCIM 1400 was compared to different A. niger strains, which harbours agdA orthologues, using PCR. It was observed that effective intron splicing leads to higher α-glucosidase activity from these selected Aspergillus spp. To explore the dynamics of intron retention in A. neoniger NCIM 1400, time-course analysis of intron retention, enzyme activity, and sugar consumption were carried over a period of 168 h of fungal growth. RT-qPCR results revealed that introns retention was not detected during the initial growth phase when the maltose and its hydrolysed product, glucose were consumed. Here we demonstrate that exhaustion of maltose causes increase in retention of introns in the mRNA transcripts of agdA gene, and this could be the possible mode of regulating this gene.
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Affiliation(s)
- Sandeep Kumar
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India; AcSIR-Academy of Scientific & Innovative Research, Ghaziabad, UP, 201002, India
| | - Sarma Mutturi
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India; AcSIR-Academy of Scientific & Innovative Research, Ghaziabad, UP, 201002, India.
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3
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Effects of intron retention on properties of β-glucosidase in Aspergillus niger. Fungal Biol 2019; 123:465-470. [DOI: 10.1016/j.funbio.2019.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 02/03/2019] [Accepted: 04/09/2019] [Indexed: 01/20/2023]
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Li Y, Li Y, Jin W, Sharpton TJ, Mackie RI, Cann I, Cheng Y, Zhu W. Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen. Front Microbiol 2019; 10:435. [PMID: 30894845 PMCID: PMC6414434 DOI: 10.3389/fmicb.2019.00435] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
In this study, the effects of a syntrophic methanogen on the growth of Pecoramyces sp. F1 was investigated by characterizing fermentation profiles, as well as functional genomic, transcriptomic, and proteomic analysis. The estimated genome size, GC content, and protein coding regions of strain F1 are 106.83 Mb, 16.07%, and 23.54%, respectively. Comparison of the fungal monoculture with the methanogen co-culture demonstrated that during the fermentation of glucose, the co-culture initially expressed and then down-regulated a large number of genes encoding both enzymes involved in intermediate metabolism and plant cell wall degradation. However, the number of up-regulated proteins doubled at the late-growth stage in the co-culture. In addition, we provide a mechanistic understanding of the metabolism of this fungus in co-culture with a syntrophic methanogen. Further experiments are needed to explore this interaction during degradation of more complex plant cell wall substrates.
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Affiliation(s)
- Yuanfei Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Wei Jin
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
| | - Thomas J Sharpton
- Department of Microbiology - Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Roderick I Mackie
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
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5
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Kang DU, Lee YS, Lee JW. Enhanced purification of histidine-tagged carboxymethylcellulase produced by Escherichia coli BL21/LBH-10 and comparison of its characteristics with carboxymethylcellulase without histidine-tag. Mol Biol Rep 2019; 46:1973-1983. [PMID: 30712248 DOI: 10.1007/s11033-019-04647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/24/2019] [Indexed: 11/26/2022]
Abstract
To enhance purification yield of the carboxymethylcellulase (CMCase) of P. aquimaris LBH-10, E. coli BL21/LBH-10 was constructed to produce the six histidine-tagged CMCase (CMCase with a His-tag). The purification yield of the CMCase with a His-tag produced by E. coli BL21/LBH-10 was 44.4%. The molecular weight of the CMCase with a His-tag was determined as 56 kDa. Its Km and Vmax were 7.4 g/L and 70.9 g/L min, respectively. The CMCase with a His-tag hydrolyzed avicel, carboxymethylcellulose (CMC), filter paper, pullulan, and xylan but did not hydrolyze cellobiose and p-nitrophenyl-β-D-glucopyranoside. The optimal temperature for reaction was 50 °C and more than 75% of its original activity was maintained at broad temperatures ranging from 20 to 70 °C after 24 h. The optimal pH was 4.0 and more than 60% of its original activity was maintained at pH ranging from 4.0 to 7.0. The activity of the CMCase with a His-tag was enhanced by CoCl2, KCl, PbCl2, RbCl2, and SrCl2 until the concentration of 100 mM, but inhibited by EDTA, HgCl2, MnCl2, and NiCl2. The characteristics of the CMCase with a His-tag produced by E. coli BL21/LBH-10 were little different from the CMCase without a His-tag, which seemed to resulted from the conformational change in the structure due to a His-tag. The purification yield of the CMCase with a His-tag using affinity chromatography from the cell broth after cell breakdown was proven to be more economic than that from the supernatant with its low concentration of cellulase.
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Affiliation(s)
- Duk-Un Kang
- Department of Applied Biology, Graduate School, Dong-A University, Busan, 49315, Korea
| | - Yong-Suk Lee
- Department of Biotechnology, Dong-A University, Busan, 49315, Korea
| | - Jin-Woo Lee
- Department of Applied Biology, Graduate School, Dong-A University, Busan, 49315, Korea.
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6
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Méndez-Líter JA, Gil-Muñoz J, Nieto-Domínguez M, Barriuso J, de Eugenio LI, Martínez MJ. A novel, highly efficient β-glucosidase with a cellulose-binding domain: characterization and properties of native and recombinant proteins. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:256. [PMID: 29142591 PMCID: PMC5674860 DOI: 10.1186/s13068-017-0946-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/26/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Cellulose, the most abundant biopolymer on earth, is an alternative for fossil fuels as a renewable feedstock for the production of second-generation biofuels and other chemicals. The discovery of novel, highly efficient β-glucosidases remains as one of the major bottlenecks for cellulose degradation. In this context, the ascomycete Talaromyces amestolkiae, isolated from cereal samples, has been studied as a promising source for these enzymes. RESULTS BGL-2 is the major β-glucosidase secreted by this fungus in the presence of cellulosic inductors. This enzyme possesses a CBD (Cellulose Binding Domain), an unusual feature among this type of proteins. Besides, when growing on cellulose, the fungus produced two different bgl-2 mRNAs that were cloned and expressed in Pichia pastoris. A complete recombinant protein (BGL-2*) and its truncated form, lacking CBD (BGL-2T*), have been purified, characterized and compared with the native enzyme (BGL-2). The three BGL-2 forms studied are highly stable in a wide pH range, but BGL-2T* showed an improved thermal stability at 50 °C after 72 h. Using p-nitrophenyl-β-d-glucopyranoside as a substrate, the steady-state kinetic characterization of the three proteins showed a similar Km and kcat for BGL-2 and BGL-2*, while the truncated protein displayed a threefold higher value for kcat . All tested BGL-2 enzymes were as well highly efficient using cellobiose and other short oligosaccharides as a substrate. In view of biotechnological applications, the recombinant T. amestolkiae enzymes in saccharification of brewers' spent grain were studied, being comparable to commercial β-glucosidase cocktails. CONCLUSION A new β-glucosidase from T. amestolkiae has been studied. The enzyme, containing a functional CBD, has been expressed in P. pastoris. The comparative analyses of the native protein and its recombinant forms, with and without CBD, suggest that they could be suitable tools for valorization of lignocellulosic biomass.
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Affiliation(s)
- J. A. Méndez-Líter
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - J. Gil-Muñoz
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - M. Nieto-Domínguez
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - J. Barriuso
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - L. I. de Eugenio
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - M. J. Martínez
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Multiple nucleophilic elbows leading to multiple active sites in a single module esterase from Sorangium cellulosum. J Struct Biol 2015; 190:314-27. [DOI: 10.1016/j.jsb.2015.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 03/25/2015] [Accepted: 04/10/2015] [Indexed: 11/17/2022]
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8
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Enhanced production of carboxymethylcellulase of a marine microorganism, Bacillus subtilis subsp. subtilis A-53 in a pilot-scaled bioreactor by a recombinant Escherichia coli JM109/A-53 from rice bran. Mol Biol Rep 2013; 40:3609-21. [DOI: 10.1007/s11033-012-2435-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 12/18/2012] [Indexed: 11/25/2022]
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9
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MacDonald J, Suzuki H, Master ER. Expression and regulation of genes encoding lignocellulose-degrading activity in the genus Phanerochaete. Appl Microbiol Biotechnol 2012; 94:339-51. [PMID: 22391967 DOI: 10.1007/s00253-012-3937-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 10/28/2022]
Abstract
As white-rot basidiomycetes, Phanerochaete species are critical to the cycling of carbon sequestered as woody biomass, and are predicted to encode many enzymes that can be harnessed to promote the conversion of lignocellulose to sugars for fermentation to fuels and chemicals. Advances in genomic, transcriptomic, and proteomic technologies have enabled detailed analyses of different Phanerochaete species and have revealed numerous enzyme families required for lignocellulose utilization, as well as insight into the regulation of corresponding genes. Recent studies of Phanerochaete are also exemplified by molecular analyses following cultivation on different wood preparations, and show substrate-dependent responses that were difficult to predict using model compounds or isolated plant polysaccharides. The aim of this mini-review is to synthesize results from studies that have applied recent advances in molecular tools to evaluate the expression and regulation of proteins that contribute to lignocellulose conversion in Phanerochaete species. The identification of proteins with as yet unknown function are also highlighted and noted as important targets for future investigation of white-rot decay.
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Affiliation(s)
- Jacqueline MacDonald
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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Cellotriose and cellotetraose as inducers of the genes encoding cellobiohydrolases in the basidiomycete Phanerochaete chrysosporium. Appl Environ Microbiol 2010; 76:6164-70. [PMID: 20656867 DOI: 10.1128/aem.00724-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The wood decay basidiomycete Phanerochaete chrysosporium produces a variety of cellobiohydrolases belonging to glycoside hydrolase (GH) families 6 and 7 in the presence of cellulose. However, no inducer of the production of these enzymes has yet been identified. Here, we quantitatively compared the transcript levels of the genes encoding GH family 6 cellobiohydrolase (cel6A) and GH family 7 cellobiohydrolase isozymes (cel7A to cel7F/G) in cultures containing glucose, cellulose, and cellooligosaccharides by real-time quantitative PCR, in order to evaluate the transcription-inducing effect of soluble sugars. Upregulation of transcript levels in the presence of cellulose compared to glucose was observed for cel7B, cel7C, cel7D, cel7F/G, and cel6A at all time points during cultivation. In particular, the transcription of cel7C and cel7D was strongly induced by cellotriose or cellotetraose. The highest level of cel7C transcripts was observed in the presence of cellotetraose, whereas the highest level of cel7D transcripts was found in the presence of cellotriose, amounting to 2.7 x 10(6) and 1.7 x 10(6) copies per 10(5) actin gene transcripts, respectively. These numbers of cel7C and cel7D transcripts were higher than those in the presence of cellulose. In contrast, cellobiose had a weaker transcription-inducing effect than either cellotriose or cellotetraose for cel7C and had little effect in the case of cel7D. These results indicate that cellotriose and cellotetraose, but not cellobiose, are possible natural cellobiohydrolase gene transcription inducers derived from cellulose.
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Pilot-scale production of carboxymethylcellulase from rice hull by Bacillus amyloliquefaciens DL-3. BIOTECHNOL BIOPROC E 2008. [DOI: 10.1007/s12257-007-0149-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Chapter 2 Enzymes of saprotrophic basidiomycetes. BRITISH MYCOLOGICAL SOCIETY SYMPOSIA SERIES 2008. [DOI: 10.1016/s0275-0287(08)80004-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Costanzo S, Ospina-Giraldo MD, Deahl KL, Baker CJ, Jones RW. Alternate intron processing of family 5 endoglucanase transcripts from the genus Phytophthora. Curr Genet 2007; 52:115-23. [PMID: 17661047 DOI: 10.1007/s00294-007-0144-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 07/03/2007] [Accepted: 07/09/2007] [Indexed: 10/23/2022]
Abstract
Twenty-one homologs of family 5 endo-(1-4)-beta-glucanase genes (EGLs) were identified and characterized in the oomycete plant pathogens Phytophthora infestans, P. sojae, and P. ramorum, providing the first comprehensive analysis of this family in Phytophthora. Phylogenetic analysis revealed that these genes constitute a unique eukaryotic group, with closest similarity to bacterial endoglucanases. Many of the identified EGL copies were clustered in a few genomic regions, and contained from zero to three introns. Using reverse transcription PCR to study in vitro and in planta gene expression levels of P. sojae, we detected partially processed RNA transcripts retaining one or more of their introns. In some cases, the positions of intron/exon splicing sites were also found to be variable. The relative proportions of these transcripts remain apparently unchanged under various growing conditions, but differ among orthologous copies of the three Phytophthora species. The alternate processing of introns in this group of EGLs generates both coding and non-coding RNA isoforms. This is the first report on Phytophthora family 5 endoglucanases, and the first record for alternative intron processing of oomycete transcripts.
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Affiliation(s)
- Stefano Costanzo
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
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Baba Y, Shimonaka A, Koga J, Kubota H, Kono T. Alternative splicing produces two endoglucanases with one or two carbohydrate-binding modules in Mucor circinelloides. J Bacteriol 2005; 187:3045-51. [PMID: 15838031 PMCID: PMC1082807 DOI: 10.1128/jb.187.9.3045-3051.2005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously cloned three endoglucanase genes, rce1, rce2, and rce3, that were isolated from Rhizopus oryzae as the first cellulase genes from a member of the subdivision Zygomycota. In this study, two cDNAs homologous to the rce1 gene, designated the mce1 and mce2 cDNAs, were cloned from Mucor circinelloides, a member of the subdivision Zygomycota. The mce1 cDNA encoded an endoglucanase (family 45 glycoside hydrolase) having one carbohydrate-binding module (CBM), designated MCE1, and the mce2 cDNA encoded the same endoglucanase having two tandem repeated CBMs, designated MCE2. The two cDNAs contained the same sequences but with a 147-bp insertion. The corresponding genomic mce gene consisted of four exons. The mce1 cDNA was created from exons 1, 3, and 4, and the mce2 cDNA was created from exons 1, 2, 3, and 4. These results indicate that the mce1 and mce2 cDNAs were created from one genomic mce gene by alternative splicing. MCE1 and MCE2, purified to apparent homogeneity from the culture supernatant of M. circinelloides, had molecular masses of 43 and 47 kDa, respectively. The carboxymethyl cellulase specific activity of MCE2 was almost the same as that of MCE1, whereas the Avicelase specific activity of MCE2 was two times higher than that of MCE1. Furthermore, MCE2, whose two tandem CBMs might be more effective for degradation of crystalline cellulose than one CBM, was secreted only at an early culture stage when crystalline cellulose was abundant.
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Affiliation(s)
- Yuko Baba
- Food and Health R&D Laboratories, Meiji Seika Kaisha, Ltd., 5-3-1, Chiyoda, Sakado-shi, Saitama 350-0289, Japan
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15
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Macarena S, Fernando LL, Mónica V, Rafael V, Bernardo G. Incomplete processing of peroxidase transcripts in the lignin degrading fungus Phanerochaete chrysosporium. FEMS Microbiol Lett 2005; 242:37-44. [PMID: 15621417 DOI: 10.1016/j.femsle.2004.10.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Revised: 10/06/2004] [Accepted: 10/19/2004] [Indexed: 11/17/2022] Open
Abstract
Phanerochaete chrysosporium has been thoroughly studied as a microbial model for lignin degradation. The enzymes lignin peroxidase (LiP) and manganese peroxidase (MnP), both encoded by several genes, play the main role in the cleavage of different lignin substructures. In this work, the expression of specific LiP and MnP transcripts in liquid medium and in a wood-containing soil system was studied by reverse transcription-PCR and subsequent cloning and sequencing of the products obtained. Splice variants of different LiP and MnP transcripts were observed in wood-containing soil incubations and in liquid cultures. The processed transcripts contained different numbers of complete introns. Since the presence of stop codons in several of these introns would prevent the synthesis of active enzyme, we propose that these transcripts arise as a result of incomplete processing rather than alternative splicing. Interestingly, analysis of splice variants from mnp genes led to the identification of a fourth actively transcribed gene coding for MnP in P. chrysosporium.
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MESH Headings
- Codon, Terminator/physiology
- DNA, Complementary/chemistry
- DNA, Fungal/chemistry
- Fungal Proteins/genetics
- Gene Expression Regulation, Fungal
- Introns
- Lignin/metabolism
- Peroxidases/biosynthesis
- Peroxidases/genetics
- Phanerochaete/genetics
- Phanerochaete/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Fungal/genetics
- RNA, Fungal/isolation & purification
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
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Affiliation(s)
- Stuardo Macarena
- Laboratorio de Microbiología, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, and Millennium Institute for Fundamental and Applied Biology, Santiago, Chile
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16
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Larrondo LF, González B, Cullen D, Vicuña R. Characterization of a multicopper oxidase gene cluster in Phanerochaete chrysosporium and evidence of altered splicing of the mco transcripts. MICROBIOLOGY-SGM 2004; 150:2775-2783. [PMID: 15289573 DOI: 10.1099/mic.0.27072-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A cluster of multicopper oxidase genes (mco1, mco2, mco3, mco4) from the lignin-degrading basidiomycete Phanerochaete chrysosporium is described. The four genes share the same transcriptional orientation within a 25 kb region. mco1, mco2 and mco3 are tightly grouped, with intergenic regions of 2.3 and 0.8 kb, respectively, whereas mco4 is located 11 kb upstream of mco1. All are transcriptionally active, as shown by RT-PCR. Comparison of cDNAs and the corresponding genomic sequences identified 14-19 introns within each gene. Based on homology and intron composition, two subfamilies of mco sequences could be identified. The sequences have copper-binding motifs similar to ferroxidase proteins, but different from fungal laccases. Thus, these sequences constitute a novel branch of the multicopper oxidase family. Analysis of several cDNA clones obtained from poly(A) RNA revealed the presence of transcripts of various lengths. Splice variants from mco2, mco3 and mco4 were characterized. They generally exhibited the presence of one to five introns, whereas other transcripts lacked some exons. In all cases, the presence of introns leads to frame shifts that give rise to premature stop codons. In aggregate, these investigations show that P. chrysosporium possesses a novel family of multicopper oxidases which also feature clustering and incomplete processing of some of their transcripts, a phenomenon referred to in this paper as 'altered splicing'.
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Affiliation(s)
- Luis F Larrondo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile and Instituto Milenio de Biología Fundamental y Aplicada, Santiago, Chile
| | - Bernardo González
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile and Instituto Milenio de Biología Fundamental y Aplicada, Santiago, Chile
| | - Dan Cullen
- USDA Forest Products Laboratory, Madison, WI 53705, USA
| | - Rafael Vicuña
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile and Instituto Milenio de Biología Fundamental y Aplicada, Santiago, Chile
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17
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Sims AH, Gent ME, Robson GD, Dunn-Coleman NS, Oliver SG. Combining transcriptome data with genomic and cDNA sequence alignments to make confident functional assignments for Aspergillus nidulans genes. ACTA ACUST UNITED AC 2004; 108:853-7. [PMID: 15449589 DOI: 10.1017/s095375620400067x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Whole genome sequencing of several filamentous ascomycetes is complete or in progress; these species, such as Aspergillus nidulans, are relatives of Saccharomyces cerevisiae. However, their genomes are much larger and their gene structure more complex, with genes often containing multiple introns. Automated annotation programs can quickly identify open reading frames for hypothetical genes, many of which will be conserved across large evolutionary distances, but further information is required to confirm functional assignments. We describe a comparative and functional genomics approach using sequence alignments and gene expression data to predict the function of Aspergillus nidulans genes. By highlighting examples of discrepancies between the automated genome annotation and cDNA or EST sequencing, we demonstrate that the greater complexity of gene structure in filamentous fungi demands independent data on gene expression and the gene sequence be used to make confident functional assignments.
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Affiliation(s)
- Andrew H Sims
- School of Biological Sciences, University of Manchester, The Michael Smith Building, Manchester M13 9PT, UK
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18
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Lodato P, Alcaino J, Barahona S, Retamales P, Cifuentes V. Alternative splicing of transcripts from crtI and crtYB genes of Xanthophyllomyces dendrorhous. Appl Environ Microbiol 2003; 69:4676-82. [PMID: 12902257 PMCID: PMC169127 DOI: 10.1128/aem.69.8.4676-4682.2003] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xanthophyllomyces dendrorhous is one of the relevant sources of the carotenoid astaxanthin. In this paper, we describe for the first time cloning of unexpected cDNAs obtained from the crtI and crtYB genes of X. dendrorhous strain UCD 67-385. The cDNA of the crtI gene conserves 80 bp of the first intron, while the cDNA of the crtYB gene conserves 55 bp of the first intron and lacks 111 bp of the second exon. The crtI and crtYB RNAs could be spliced in alternative splice sites, which produced alternative transcripts which could not be translated to active CRTI and CRTYB proteins since they had numerous stop codons in their sequences. The ratio of mature mRNA to alternative mRNA for the crtI gene decreased as a function of the age of the culture, while the cellular content of carotenoids increased. It is possible that splicing to mature or alternative transcripts could regulate the cellular concentrations of phytoene desaturase and phytoene synthase-lycopene cyclase proteins, depending on the physiological or environmental conditions.
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Affiliation(s)
- P Lodato
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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19
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Wymelenberg AV, Denman S, Dietrich D, Bassett J, Yu X, Atalla R, Predki P, Rudsander U, Teeri TT, Cullen D. Transcript analysis of genes encoding a family 61 endoglucanase and a putative membrane-anchored family 9 glycosyl hydrolase from Phanerochaete chrysosporium. Appl Environ Microbiol 2002; 68:5765-8. [PMID: 12406778 PMCID: PMC129927 DOI: 10.1128/aem.68.11.5765-5768.2002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phanerochaete chrysosporium cellulase genes were cloned and characterized. The cel61A product was structurally similar to fungal endoglucanases of glycoside hydrolase family 61, whereas the cel9A product revealed similarities to Thermobifida fusca Cel9A (E4), an enzyme with both endo- and exocellulase characteristics. The fungal Cel9A is apparently a membrane-bound protein, which is very unusual for microbial cellulases. Transcript levels of both genes were substantially higher in cellulose-grown cultures than in glucose-grown cultures. These results show that P. chrysosporium possesses a wide array of conventional and unconventional cellulase genes.
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Affiliation(s)
- Amber Vanden Wymelenberg
- Department of Bacteriology. Department of Chemical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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20
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Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 2002. [PMID: 12209002 DOI: 10.1128/mmbr.66.3.506] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.
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Affiliation(s)
- Lee R Lynd
- Chemical and Biochemical Engineering, Thayer School of Engineering and Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.
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21
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Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 2002; 66:506-77, table of contents. [PMID: 12209002 PMCID: PMC120791 DOI: 10.1128/mmbr.66.3.506-577.2002] [Citation(s) in RCA: 2319] [Impact Index Per Article: 105.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.
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Affiliation(s)
- Lee R Lynd
- Chemical and Biochemical Engineering, Thayer School of Engineering and Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.
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22
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Stergiopoulos I, Gielkens MMC, Goodall SD, Venema K, De Waard MA. Molecular cloning and characterisation of three new ATP-binding cassette transporter genes from the wheat pathogen Mycosphaerella graminicola. Gene 2002; 289:141-9. [PMID: 12036592 DOI: 10.1016/s0378-1119(02)00505-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Three single copy ATP-binding cassette (ABC) transporter encoding genes, designated MgAtr3, MgAtr4, and MgAtr5, were cloned and sequenced from the plant pathogenic fungus Mycosphaerella graminicola. The encoded ABC proteins all exhibit the [NBD-TMS(6)](2) configuration and can be classified as novel members of the pleiotropic drug resistance (PDR) class of ABC transporters. The three proteins are highly homologous to other fungal and yeast, ABC proteins involved in multidrug resistance or plant pathogenesis. MgAtr4 and MgAtr5 possess a conserved ABC motif at both the N- and C-terminal domain of the protein. In contrast, the Walker A motif in the N-terminal and the ABC signature in the C-terminal domain of MgAtr3, deviate significantly from the consensus sequence found in other members of the PDR class of ABC transporters. Expression of MgAtr3 could not be detected under any of the conditions tested. However, MgAtr4 and MgAtr5 displayed distinct expression profiles when treated with a range of compounds known to be either substrates or inducers of ABC transporters. These included synthetic fungitoxic compounds, such as imazalil and cyproconazole, natural toxic compounds, such as the plant defence compounds eugenol and psoralen, and the antibiotics cycloheximide and neomycin. The expression pattern of the genes was also dependent on the morphological state of the fungus. The findings suggest a role for MgAtr4 and MgAtr5 during plant pathogenesis and in protection against toxic compounds.
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Affiliation(s)
- I Stergiopoulos
- Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University, P.O. Box 8025, 6700 EE Wageningen, The Netherlands
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23
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Muñoz IG, Ubhayasekera W, Henriksson H, Szabó I, Pettersson G, Johansson G, Mowbray SL, Ståhlberg J. Family 7 cellobiohydrolases from Phanerochaete chrysosporium: crystal structure of the catalytic module of Cel7D (CBH58) at 1.32 A resolution and homology models of the isozymes. J Mol Biol 2001; 314:1097-111. [PMID: 11743726 DOI: 10.1006/jmbi.2000.5180] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cellobiohydrolase 58 (Cel7D) is the major cellulase produced by the white-rot fungus Phanerochaete chrysosporium, constituting approximately 10 % of the total secreted protein in liquid culture on cellulose. The enzyme is classified into family 7 of the glycosyl hydrolases, together with cellobiohydrolase I (Cel7A) and endoglucanase I (Cel7B) from Trichoderma reesei. Like those enzymes, it catalyses cellulose hydrolysis with net retention of the anomeric carbon configuration. The structure of the catalytic module (431 residues) of Cel7D was determined at 3.0 A resolution using the structure of Cel7A from T. reesei as a search model in molecular replacement, and ultimately refined at 1.32 A resolution. The core structure is a beta-sandwich composed of two large and mainly antiparallel beta-sheets packed onto each other. A long cellulose-binding groove is formed by loops on one face of the sandwich. The catalytic residues are conserved and the mechanism is expected to be the same as for other family members. The Phanerochaete Cel7D binding site is more open than that of the T. reesei cellobiohydrolase, as a result of deletions and other changes in the loop regions, which may explain observed differences in catalytic properties. The binding site is not, however, as open as the groove of the corresponding endoglucanase. A tyrosine residue at the entrance of the tunnel may be part of an additional subsite not present in the T. reesei cellobiohydrolase. The Cel7D structure was used to model the products of the five other family 7 genes found in P. chrysosporium. The results suggest that at least two of these will have differences in specificity and possibly catalytic mechanism, thus offering some explanation for the presence of Cel7 isozymes in this species, which are differentially expressed in response to various growth conditions.
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Affiliation(s)
- I G Muñoz
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Centre, SE-751 24 Uppsala, Sweden
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Zwiers LH, De Waard MA. Characterization of the ABC transporter genes MgAtr1 and MgAtr2 from the wheat pathogen Mycosphaerella graminicola. Fungal Genet Biol 2000; 30:115-25. [PMID: 11017767 DOI: 10.1006/fgbi.2000.1209] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ATP-binding cassette (ABC) transporters are membrane-bound transporters involved in various physiological processes. In this paper we describe the cloning of the ABC transporter encoding genes MgAtr1 and MgAtr2 from the wheat pathogen Mycosphaerella graminicola (anamorph Septoria tritici). Both deduced proteins MgAtr1 and MgAtr2 are highly homologous to other fungal ABC transporters. RT-PCR revealed that the MgAtr2 mRNA population consists of partially and fully spliced transcripts. Putative substrates of ABC transporters, modulators of ABC transporter activity, and inducers of ABC transporter gene transcription were analyzed for their potential to induce expression of MgAtr1 and MgAtr2 in m. graminicola. The genes are differently upregulated by compounds such as the plant secondary metabolites eugenol and reserpine. Similar results are obtained for several antibiotics and the azole fungicides cyproconazole and imazalil. Moreover, a different expression pattern between yeast-like cells and mycelium of this dimorphic fungus was observed. These results indicate that MgAtr1 and MgAtr2 play a role in protection of m. graminicola against natural toxic compounds and xenobiotics. A putative role in protection against plant defense compounds during pathogenesis is suggested.
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Affiliation(s)
- L H Zwiers
- Laboratory of Phytopathology, Wageningen University, 6700 EE Wageningen, The Netherlands
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Affiliation(s)
- M S Sachs
- Department of Biochemistry and Molecular Biology, Oregon Graduate Institute of Science and Technology, Portland 97291-1000, USA.
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27
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Kullman SW, Matsumura F. Identification of a novel cytochrome P-450 gene from the white rot fungus Phanerochaete chrysosporium. Appl Environ Microbiol 1997; 63:2741-6. [PMID: 9212420 PMCID: PMC168569 DOI: 10.1128/aem.63.7.2741-2746.1997] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A gene fragment belonging to the cytochrome P-450 superfamily has been cloned and identified from stationary cultures of the filamentous fungus Phanerochaete chrysosporium by reverse transcriptase (RT)-PCR. A set of degenerate primers homologous to highly conserved regions of known cytochrome P-450 sequences were used for initial RT-PCRs. Individual PCR products were cloned, sequenced, and identified as those belonging to the cytochrome P-450 superfamily based on amino acid sequence homologies and the presence of the highly conserved heme binding region. The nucleotide sequence of a single cDNA clone indicated the presence of an open reading frame encoding a partial cytochrome P-450 protein of 208 amino acids. Comparisons of the deduced amino acid sequence of the partial protein to other known cytochrome P-450 sequences indicate that it is the first member of a new family of cytochrome P-450s, designated CYP63-1A. Northern blot analysis suggests that CYP63-1A is expressed under both nitrogen-rich and nitrogen-deficient culture conditions and thus not under the same regulatory constraints as the well-studied lignin and manganese peroxidases. Western blot analyses using antibodies raised to the heme binding region of CYP63-1A indicate that the protein has a molecular mass of approximately 44,000 Da.
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Affiliation(s)
- S W Kullman
- Department of Environmental Toxicology, University of California, Davis 95616, USA
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