1
|
Ashavaid TF, Todur SP, Kondkar AA, Nair KG, Shalia KK, Dalal JJ, Rajani R, Ponde CK. Platelet polymorphisms: frequency distribution and association with coronary artery disease in an Indian population. Platelets 2010; 22:85-91. [PMID: 21034162 DOI: 10.3109/09537104.2010.522275] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Platelets play a critical role in normal blood hemostasis and thrombus formation in myocardial infarction (MI). Several polymorphisms of genes involved in platelet activation and fibrinolysis have been reported to be associated with MI. The aim of the present study was to determine the frequency distribution and association of polymorphisms in these genes with coronary artery disease (CAD) among Indians. A case-control genetic association study was performed for polymorphisms in platelet glycoprotein receptors (GPIIb/IIIa [HPA1a/1b], GPIb-IX-V [VNTR], and GPIa/IIa [C807T]), fibrinogen β-chain (BclI), α-chain (Aα312), tissue plasminogen activator (tPA) [I/D] and plasminogen activator inhibitor-I (PAI-1) [4G/5G] in 473 healthy controls and 446 patients with stable and unstable angina. Genotyping was either by PCR-based restriction endonuclease digestion or allele-specific primers. The I allele frequency of the tPA I/D polymorphism was significantly higher in our patients (χ(2)=7.33, P<0.01) and no other polymorphisms varied significantly between patients and controls. Also, none of the polymorphisms seemed to affect the severity of the disease, the only exception being the mutant alleles of β chain of fibrinogen gene, which were significantly elevated in single vessel disease. This is the first study to evaluate the role of gene polymorphisms in both the thrombotic and fibrinolytic pathway in the Indian population and suggests that tPA I/D polymorphism confers CAD risk in our population.
Collapse
Affiliation(s)
- Tester F Ashavaid
- Research Laboratories, P D Hinduja National Hospital and Medical Research Centre, V S Marg, Mahim, Mumbai, India.
| | | | | | | | | | | | | | | |
Collapse
|
2
|
Martı́nez AT. Molecular biology and structure-function of lignin-degrading heme peroxidases. Enzyme Microb Technol 2002. [DOI: 10.1016/s0141-0229(01)00521-x] [Citation(s) in RCA: 321] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
3
|
Blodig W, Smith AT, Doyle WA, Piontek K. Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism. J Mol Biol 2001; 305:851-61. [PMID: 11162097 DOI: 10.1006/jmbi.2000.4346] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The heme enzyme lignin peroxidase (LiP) from the white rot fungus Phanerochaete chrysosporium contains a solvent exposed redox active tryptophan residue (Trp171) that carries a unique hydroxy group stereo-specifically attached to its C(beta) atom. A Trp171Phe mutant has no activity at all towards the substrate veratryl alcohol. The mechanism of veratryl alcohol oxidation involving beta-hydroxy-Trp171 is largely unknown. Here, we present the first crystal structures of LiP isozyme H8 at high resolution in its pristine non-hydroxylated form, of the C(beta)-hydroxylated form, and of the Trp171Phe mutant using recombinantly expressed and refolded protein produced from Escherichia coli. As a consequence, all structures are unglycosylated. Structural changes in response to the mutation are marginal and allow us to attribute the complete lack of activity exclusively to the absence of the redox active indole side-chain. The origin of the stereospecificity of the Trp171 hydroxylation can be explained on structural grounds. A reaction mechanism involving Trp171 is proposed and the possible function of the modification is discussed. Another important result regarding the ongoing debate on the co-ordination state of the heme iron in the resting state is that the iron is six co-ordinate in all cases the data being collected at room temperature. The mean distance from the iron to the distal water ligand is 2.18(+/-0.08) A. The radical scavenger orcinol was found to decrease radiation damage to the crystals, during data collection at room temperature.
Collapse
Affiliation(s)
- W Blodig
- Institut für Biochemie, Eidgenössische Technische Hochschule (ETH), Universitätstrasse 16, Zürich, CH-8092, Switzerland
| | | | | | | |
Collapse
|
4
|
Camarero S, Ruiz-Dueñas FJ, Sarkar S, Martínez MJ, Martínez AT. The cloning of a new peroxidase found in lignocellulose cultures of Pleurotus eryngii and sequence comparison with other fungal peroxidases. FEMS Microbiol Lett 2000; 191:37-43. [PMID: 11004397 DOI: 10.1111/j.1574-6968.2000.tb09316.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: 11/29/2022] Open
Abstract
We report cloning and sequencing of gene ps1 encoding a versatile peroxidase combining catalytic properties of lignin peroxidase (LiP) and manganese peroxidase (MnP) isolated from lignocellulose cultures of the white-rot fungus Pleurotus eryngii. The gene contains 15 putative introns, and the deduced amino acid sequence consists of a 339-residue mature protein with a 31-residue signal peptide. Several putative response elements were identified in the promoter region. Amino acid residues involved in oxidation of Mn(2+) and aromatic substrates by direct electron transfer to heme and long-range electron transfer from superficial residues as predicted by analogy with Phanerochaete chrysosporium MnP and LiP, respectively. A dendrogram is presented illustrating sequence relationships between 29 fungal peroxidases.
Collapse
Affiliation(s)
- S Camarero
- Centro de Investigaciones Biológicas, CSIC, Velázquez 144, E-28006, Madrid, Spain
| | | | | | | | | |
Collapse
|
5
|
Abstract
Lignin peroxidase (LiP) from Phanerochaete chrysosporium catalyzes irreversible oxidative damage to ferricytochrome c (Cc3+) in the presence of H2O2 and 3,4-dimethoxybenzyl (veratryl) alcohol (VA). Atomic absorption analysis and UV/vis spectroscopy indicate that the oxidation of Cc3+ is accompanied by a loss of heme iron from the protein and probably oxidation of the porphyrin ring. At H2O2 concentrations of 7.5 microM or higher, this oxidation of Cc3+ by LiP is strictly dependent on the presence of VA. The latter is not oxidized to veratraldehyde at a significant rate in the presence of either ferrocytochrome c (Cc2+) or Cc3+, indicating it is not stimulating the reactions by specifically reducing LiP compound II. LiP is inactivated rapidly in 100 microM H2O2, and the presence of 500 microM VA protects LiP from this inactivation. Neither 20 microM Cc3+ nor 20 microM VA alone can protect LiP from inactivation; however, 20 microM each of VA and Cc3+ together protect LiP fully. This and other results strongly suggest that VA is acting as a protein-bound redox mediator in the oxidation of Cc3+. SDS-PAGE analysis of the Cc3+ oxidation products demonstrates the formation of some covalently linked dimer of Cc3+ in addition to the oxidized Cc3+ monomer. Amino acid analysis of the dimeric and monomeric products indicates the presence of oxidized Met and Tyr residues. This suggests that Tyr residues on the surface of the protein are oxidized to Tyr radicals during LiP oxidation and that some of these radicals subsequently undergo intermolecular radical coupling, resulting in dimerization of some of the Cc3+ molecules. However, most of the Cc3+ molecules appear to be irreversibly oxidized without dimerization. These results demonstrate that Cc3+ can serve as a useful polymeric model of the lignin substrate in studying the enzymatic mechanism of lignin oxidation and the role of VA in the reaction.
Collapse
Affiliation(s)
- D Sheng
- Department of Biochemistry and Molecular Biology, Oregon Graduate Institute of Science and Technology, Portland 97291-1000, USA
| | | |
Collapse
|
6
|
Abstract
This review highlights significant recent advances in the molecular genetics of white-rot fungi and identifies areas where information remains sketchy. The development of critical experimental tools such as genetic mapping techniques is described. A major portion of the text focuses on the structure, genomic organization and transcriptional regulation of the genes encoding peroxidases, laccases and glyoxal oxidase. Finally, recent efforts on heterologous expression of lignin-degrading enzymes are discussed.
Collapse
Affiliation(s)
- D Cullen
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, Madison, WI 53705, USA
| |
Collapse
|
7
|
Molecular evidence of a lignin peroxidase H8 homologue inFusarium oxysporum. Folia Microbiol (Praha) 1996. [DOI: 10.1007/bf02815698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
8
|
Dehrmann FM, Elliott E, Dennison C. Reductive activation markedly increases the stability of cathepsins B and L to extracellular ionic conditions. BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1996; 377:391-4. [PMID: 8839985 DOI: 10.1515/bchm3.1996.377.6.391] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cathepsins B and L are thought to function extracellularly in pathological conditions. pH-Activity profiles of cathepsin B, measured in phosphate and acetate-Mes-Tris buffers of constant ionic strength, indicated that cathepsin B is sensitive to specific buffer ions, as previously reported for cathepsin L. In assessing the activity of these enzymes in vitro the influence of the buffer must therefore be taken into account. In Hank's balanced salt solution, a buffer modeling the extracellular fluid, the half-life of activated human liver cathepsin B at 37 degrees C is 245 +/- 11.3 s, at pH 7.2, and 857 +/- 50.1 s, at pH 6.8 (the peritumor pH), indicating that cathepsin B is markedly stable under these conditions. The stability was increased by the additional presence of proteins. Without immediate activation, however, the stabilities of both cathepsins B and L were markedly decreased, a large proportion of their activity being lost before it could be measured. Enzymes injected into the extracellular space in the unactivated state would therefore survive for only a very short time in their native conformation. It is proposed that the active site thiolate-imidazolium ion pair contributes substantially to the stability of cathepsins B and L to extracellular ionic conditions.
Collapse
Affiliation(s)
- F M Dehrmann
- Department of Biochemistry, University of Natal, Pietermaritzburg, Rep. of South Africa
| | | | | |
Collapse
|
9
|
Johansson T, Nyman PO. A cluster of genes encoding major isozymes of lignin peroxidase and manganese peroxidase from the white-rot fungus Trametes versicolor. Gene 1996; 170:31-8. [PMID: 8621085 DOI: 10.1016/0378-1119(95)00846-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A gene cluster from the white-rot basidiomycete Trametes (Coriolus) versicolor (Tv) PRL 572 containing three structural genes, LPGIII, LPGIV and MPGI, was characterized. The genes are arranged in the same transcriptional direction, within a 10-kb region, and found to encode quantitatively dominant isozymes of lignin peroxidase (LP) and manganese peroxidase (MP). The second gene in sequence, LPGIV, predicts a 346-amino-acid (aa) mature polypeptide (36.9 kDa, pI 4.31) which is identical with the partial aa sequence information available on the LP12 isozyme (43.1 kDa, pI 3.27). The first gene, LPGIII, encodes a 341-aa polypeptide (36.1 kDa, pI 3.93) which has not been identified at the protein level. However, the similarity of LPGIV would suggest that the predicted product is an LP-type enzyme. LPGIII and LPGIV are homologous to the tandemly arranged genes LPGII and LPGI, respectively, recently described by Jönsson and Nyman [Biochim. Biophys. Acta 1218 (1994) 408-412]. The homologous genes, LPGIII/LPGII and LPGIV/LPGI, are 99% and 96% identical in sequence, respectively, and are predicted to encode identical polypeptides, since base substitutions in the predicted exons are all synonymous. The third gene, MPGI, is different in intron-exon organization and predicted to be disrupted by five rather than six introns, as are the LP genes. The deduced polypeptide, 339 aa in size (35.9 kDa, pI 4.07), is identical with the partial aa sequence information available for isozyme MP2 (44.5 kDa, pI 3.09). The MPGI- and LPGIV-encoded polypeptides are 70% identical in sequence which suggests that MP and LP from Tv may be regarded as members of the same family within the plant peroxidase superfamily. Most importantly, this study identifies a gene encoding the MP2 isozyme, and further shows that genes encoding MP and LP can be closely linked on the chromosome and may be coordinately transcribed.
Collapse
Affiliation(s)
- T Johansson
- Department of Biochemistry, Lund University, Sweden.
| | | |
Collapse
|
10
|
Kersten PJ, Witek C, vanden Wymelenberg A, Cullen D. Phanerochaete chrysosporium glyoxal oxidase is encoded by two allelic variants: structure, genomic organization, and heterologous expression of glx1 and glx2. J Bacteriol 1995; 177:6106-10. [PMID: 7592374 PMCID: PMC177449 DOI: 10.1128/jb.177.21.6106-6110.1995] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A cDNA clone (glx-2c) encoding glyoxal oxidase (GLOX) was isolated from a Phanerochaete chrysosporium lambda gt11 library, and its nucleotide sequence was shown to be distinct from that of the previously described clone glx-1c (P. J. Kersten and D. Cullen, Proc. Natl. Acad. Sci. USA 90:7411-7413, 1993). Genomic clones corresponding to both cDNAs were also isolated and sequenced. overall nucleotide sequence identity was 98%, and the predicted proteins differed by a single residue: Lys-308<==>Thr-308. Analyses of parental dikaryotic strain BKM-F-1767 and homokaryotic progeny firmly established allelism for these structural variants. Southern blots of pulsed-field gels localized the GLOX gene (glx) to a dimorphic chromosome separate from the peroxidase and cellobiohydrolase genes of P. chrysosporium. Controlled expression of active GLOX was obtained from Aspergillus nidulans transformants when glx-1c was fused to the promoter and secretion signal of the A. niger glucoamylase gene. The GLOX isozyme corresponding to glx-2c was also efficiently secreted by A. nidulans following site-specific mutagenesis of the expression vector at codon 308 of glx-1c.
Collapse
Affiliation(s)
- P J Kersten
- Forest Products Laboratory, U.S. Department of Agriculture Forest Service, Madison, Wisconsin, USA
| | | | | | | |
Collapse
|
11
|
Lamar RT, Schoenike B, Vanden Wymelenberg A, Stewart P, Dietrich DM, Cullen D. Quantitation of fungal mRNAs in complex substrates by reverse transcription PCR and its application to Phanerochaete chrysosporium-colonized soil. Appl Environ Microbiol 1995; 61:2122-6. [PMID: 7793933 PMCID: PMC167484 DOI: 10.1128/aem.61.6.2122-2126.1995] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Thorough analysis of fungi in complex substrates has been hampered by inadequate experimental tools for assessing physiological activity and estimating biomass. We report a method for the quantitative assessment of specific fungal mRNAs in soil. The method was applied to complex gene families of Phanerochaete chrysosporium, a white-rot fungus widely used in studies of organopollutant degradation. Among the genes implicated in pollutant degradation, two closely related lignin peroxidase transcripts were detected in soil. The pattern of lignin peroxidase gene expression was unexpected; certain transcripts abundant in defined cultures were not detected in soil cultures. Transcripts encoding cellobiohydrolases and beta-tubulin were also detected. The method will aid in defining the roles of specific genes in complex biological processes such as organopollutant degradation, developing strategies for strain improvement, and identifying specific fungi in environmental samples.
Collapse
Affiliation(s)
- R T Lamar
- Forest Products Laboratory, U.S. Department of Agriculture, Madison, Wisconsin 53705, USA
| | | | | | | | | | | |
Collapse
|
12
|
Gaskell J, Stewart P, Kersten PJ, Covert SF, Reiser J, Cullen D. Establishment of genetic linkage by allele-specific polymerase chain reaction: application to the lignin peroxidase gene family of Phanerochaete chrysosporium. BIO/TECHNOLOGY (NATURE PUBLISHING COMPANY) 1994; 12:1372-5. [PMID: 7765568 DOI: 10.1038/nbt1294-1372] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Determining linkage is problematic for genes lacking easily identifiable phenotypes and for organisms without well-defined genetic recombination systems. Phanerochaete chrysosporium with its lignin peroxidase (LiP) gene family typifies these difficulties. We describe an experimental approach whereby the segregation of specific alleles is directly monitored during sexual fruiting. The method establishes linkage relationships among genes for which there are no mutations, and it is applicable to a wide range of genes, gene families and organisms. Using this approach, five P. chrysosporium linkage groups were identified. Ten LiP genes were distributed among three of these groups. One co-segregating group contained eight closely linked LiP genes. Another LiP gene was linked to a cellobiohydrolase gene cluster. These genetic linkages were consistent with physical mapping by pulsed field gel electrophoresis. Based on the identification of allelic relationships, a uniform nomenclature for LiP genes is also described.
Collapse
Affiliation(s)
- J Gaskell
- USDA Forest Service, Forest Products Laboratory, Madison, WI 53705
| | | | | | | | | | | |
Collapse
|
13
|
Orth AB, Rzhetskaya M, Cullen D, Tien M. Characterization of a cDNA encoding a manganese peroxidase from Phanerochaete chrysosporium: genomic organization of lignin and manganese peroxidase-encoding genes. Gene 1994; 148:161-5. [PMID: 7926830 DOI: 10.1016/0378-1119(94)90251-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two heme proteins, manganese peroxidase (MnP) and lignin peroxidase (LiP), play key roles in the fungal depolymerization of lignin. Many cDNA and genomic clones encoding these peroxidases have been published. We report here on the cDNA lambda MP-2 encoding the MnP isozyme H3 from Phanerochaete chrysosporium strain BKM-F-1767. We also demonstrate that the MnP-encoding gene, lambda MP-1, encoding isozyme H4, and lambda MP-2 reside on separate chromosomes from each other and from the LiP-encoding genes. From these results, it is apparent that lambda MP-2 is not linked to lambda MP-1 or other genes believed to be involved in lignin depolymerization, such as the LiP and glyoxal oxidase.
Collapse
Affiliation(s)
- A B Orth
- Department of Molecular and Cell Biology, Pennsylvania State University, University Park 16803
| | | | | | | |
Collapse
|
14
|
Johnston CG, Aust SD. Detection of Phanerochaete chrysosporium in soil by PCR and restriction enzyme analysis. Appl Environ Microbiol 1994; 60:2350-4. [PMID: 8074515 PMCID: PMC201654 DOI: 10.1128/aem.60.7.2350-2354.1994] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A nonradioactive method to detect Phanerochaete chrysosporium grown in a soil matrix was developed. This method involved DNA extraction, PCR amplification, and restriction enzyme analysis. Amplification of ligninase H8 DNA from pure cultures of P. chrysosporium was not as sensitive as amplification of the internal transcribed spacer (ITS) of the highly repetitive nuclear ribosomal DNA. Amplified ITS DNA was digested with restriction enzymes for analysis. The restriction enzyme pattern of PCR-amplified ITS DNA of P. chrysosporium was unique compared with those of unrelated fungi. Two strains of Phanerochaete chrysosporium and two strains of Phanerochaete sordida were indistinguishable by restriction enzyme analysis, while a third strain of P. chrysosporium had an unique pattern. These results were confirmed by sequence information and indicate that species designations of Phanerochaete spp. should be reexamined. The restriction enzyme pattern of DNA extracted and PCR amplified from P. chrysosporium grown in soil was identical to that from P. chrysosporium grown in pure culture. The ITS sequence was detected in 14 ng of the 100 micrograms of total DNA extracted from 1 g of soil.
Collapse
Affiliation(s)
- C G Johnston
- Biotechnology Center, Utah State University, Logan 84322-4705
| | | |
Collapse
|
15
|
Reddy CA, D'Souza TM. Physiology and molecular biology of the lignin peroxidases of Phanerochaete chrysosporium. FEMS Microbiol Rev 1994; 13:137-52. [PMID: 8167033 DOI: 10.1111/j.1574-6976.1994.tb00040.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The white-rot basidiomycete Phanerochaete chrysosporium produces lignin peroxidases (LiPs), a family of extracellular glycosylated heme proteins, as major components of its lignin-degrading system. Up to 15 LiP isozymes, ranging in M(r) values from 38,000 to 43,000, are produced depending on culture conditions and strains employed. Manganese-dependent peroxidases (MnPs) are a second family of extracellular heme proteins produced by P. chrysosporium that are also believed to be important in lignin degradation by this organism. LiP and MnP production is seen during secondary metabolism and is completely suppressed under conditions of excess nitrogen and carbon. Excess Mn(II) in the medium, on the other hand, suppresses LiP production but enhances MnP production. Nitrogen regulation of LiP and MnP production is independent of carbon and Mn(II) regulation. LiP activity is also affected by idiophasic extracellular proteases. Intracellular cAMP levels appear to be important in regulating the production of LiPs and MnPs, although LiP production is affected more than MnP production. Studies on the sequencing and characterization of lip cDNAs and genes of P. chrysosporium have shown that the major LiP isozymes are each encoded by a separate gene. Each lip gene encodes a mature protein that is 343-344 amino acids long, contains 1 putative N-glycosylation site, a number of putative O-glycosylation sites, and is preceded by a 27-28-amino acid leader peptide ending in a Lys-Arg cleavage site. The coding region of each lip gene is interrupted by 8-9 introns (50-63 bp), and the positions of the last two introns appear to be highly conserved. There are substantial differences in the temporal transcription patterns of the major lip genes. The sequence data suggest the presence of three lip gene subfamilies. The genomic DNA of P. chrysosporium strain BKMF-1767 was resolved into 10 chromosomes (genome size of 29 Mb), and that of strain ME-446 into 11 chromosomes (genome size of 32 Mb). The lip genes have been localized to five chromosomes in BKMF-1767 and to four chromosomes in ME-446. DNA transformation studies have reported both integrative and non-integrative transformation in P. chrysosporium.
Collapse
Affiliation(s)
- C A Reddy
- Department of Microbiology, Michigan State University, East Lansing 48824-1101
| | | |
Collapse
|
16
|
Gold MH, Alic M. Molecular biology of the lignin-degrading basidiomycete Phanerochaete chrysosporium. Microbiol Rev 1993; 57:605-22. [PMID: 8246842 PMCID: PMC372928 DOI: 10.1128/mr.57.3.605-622.1993] [Citation(s) in RCA: 164] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The white rot basidiomycete Phanerochaete chrysosporium completely degrades lignin and a variety of aromatic pollutants during the secondary metabolic phase of growth. Two families of secreted heme enzymes, lignin peroxidase (LiP) and manganese peroxidase (MnP), are major components of the extracellular lignin degradative system of this organism. MnP and LiP both are encoded by families of genes, and the lip genes appear to be clustered. The lip genes contain eight or nine short introns; the mnp genes contain six or seven short introns. The sequences surrounding active-site residues are conserved among LiP, MnP, cytochrome c peroxidase, and plant peroxidases. The eight LiP cysteine residues align with 8 of the 10 cysteines in MnP. LiPs are synthesized as preproenzymes with a 21-amino-acid signal sequence followed by a 6- or 7-amino-acid propeptide. MnPs have a 21- or 24-amino-acid signal sequence but apparently lack a propeptide. Both LiP and MnP are regulated at the mRNA level by nitrogen, and the various isozymes may be differentially regulated by carbon and nitrogen. MnP also is regulated at the level of gene transcription by Mn(II), the substrate for the enzyme, and by heat shock. The promoter regions of mnp genes contain multiple heat shock elements as well as sequences that are identical to the consensus metal regulatory elements found in mammalian metallothionein genes. DNA transformation systems have been developed for P. chrysosporium and are being used for studies on gene regulation and for gene replacement experiments.
Collapse
Affiliation(s)
- M H Gold
- Department of Chemistry, Biochemistry, and Molecular Biology, Oregon Graduate Institute of Science and Technology, Portland 97291-1000
| | | |
Collapse
|
17
|
Reiser J, Walther IS, Fraefel C, Fiechter A. Methods to investigate the expression of lignin peroxidase genes by the white rot fungus Phanerochaete chrysosporium. Appl Environ Microbiol 1993; 59:2897-903. [PMID: 8215362 PMCID: PMC182383 DOI: 10.1128/aem.59.9.2897-2903.1993] [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: 01/29/2023] Open
Abstract
Two methods allowing the analysis of expression of specific lignin peroxidase (LPO) genes from white rot fungi are presented. In the first method, degenerate oligonucleotide primers derived from amino acid sequence motifs held in common among all members of the LPO gene family are used to prime the polymerase chain reaction (PCR) amplification of LPO-related nucleotide sequences from cDNA prepared by using RNA from ligninolytic cultures. The PCR products are cloned and analyzed by restriction cleavage and DNA sequencing. This method was applied to the analysis of transcripts from carbon-limited cultures of Phanerochaete chrysosporium BKM-F-1767, revealing two major classes of PCR products. One class showed DNA sequences with a high degree of similarity to the previously described CLG4 cDNA sequence (H. A. De Boer, Y. Zhang, C. Collins, and C. A. Reddy, Gene 60:93-102, 1987), whereas the other harbored DNA sequences with similarities to the L18 cDNA sequence previously described for P. chrysosporium OGC101 (T. G. Ritch, Jr., V. J. Nipper, L. Akileswaran, A. J. Smith, D. G. Pribnow, and M. H. Gold, Gene 107:119-126, 1991). The second method is based on nuclease protection assays involving isoenzyme-specific RNA probes. By using this method, the L18-related gene of P. chrysosporium BKM-F-1767 was found to be expressed under conditions of carbon and of nitrogen limitation, although the transcript levels were found to be higher in carbon-limited cultures. Furthermore, it was found that omission of veratryl alcohol addition to the culture did not affect the levels of the L18-related transcripts in carbon-limited cultures.
Collapse
Affiliation(s)
- J Reiser
- Institute of Biotechnology, Swiss Federal Institute of Technology, Zürich
| | | | | | | |
Collapse
|
18
|
Gaskell J, Cullen D. Recent advances in the organization and regulation of lignin peroxidase genes of Phanerochaete chrysosporium. J Biotechnol 1993. [DOI: 10.1016/0168-1656(93)90031-h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
19
|
Ritch TG, Gold MH. Characterization of a highly expressed lignin peroxidase-encoding gene from the basidiomycete Phanerochaete chrysosporium. Gene X 1992; 118:73-80. [PMID: 1511887 DOI: 10.1016/0378-1119(92)90250-s] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The genomic clone, LG2, encoding LiP2, the major lignin peroxidase (LiP) isozyme from Phanerochaete chrysosporium strain OGC101, was isolated and characterized. The 5'-untranslated region of LG2 contains sequences similar to CRE and XRE promoter elements. Comparison with its transcript indicates that eight introns, each less than 59 bp, interrupt the coding sequence. Comparison with genes encoding other LiP isozymes shows five related patterns of intron location, whose incidence coincides with described LiP structural subfamilies. Codon bias indices calculated for all known P. chrysosporium genes, including trpC and genes encoding LiP, MnP, and exo-cellobiohydrolase I, demonstrate that LG2 has the most biased codon usage. We conclude that subdivisions of the LiP family may be based on intron location in the encoding genes, and that ranking of isozyme production levels can be estimated by the extent of bias in codon usage in the cognate gene.
Collapse
Affiliation(s)
- T G Ritch
- Department of Chemical and Biological Sciences, Oregon Graduate Institute of Science and Technology, Beaverton 97006-1999
| | | |
Collapse
|
20
|
Morosoli R, Durand S, Moreau A. Cloning and expression in Escherichia coli of a xylanase-encoding gene from the yeast Cryptococcus albidus. Gene 1992; 117:145-50. [PMID: 1644307 DOI: 10.1016/0378-1119(92)90504-i] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the yeast, Cryptococcus albidus, a comparison between the sequence of the xylanase (XLN)-encoding chromosomal gene (XLN) and the cDNA sequence reveals the presence of seven introns, ranging in length from 51 to 69 bp. One of their 5' splice site sequences is similar to the consensus sequence for yeast, while the other six resemble the consensus sequence for higher eukaryotes. Their 3' end splice site sequences are representative of the conserved sequence found in eukaryotes. Their putative branching point sequences are different from the well-known conserved sequence, 5'-TACTAAC, observed in yeast, but again resemble the mammalian one. The cDNA encoding XLN is expressed by Escherichia coli, under the control of the lacZ promoter. The gene product remains inside the cell and has a molecular size of 40 kDa, which matches the size of the nonglycosylated protein. When compared to the glycosylated enzyme, the nonglycosylated XLN from E. coli shows twofold less affinity for substrate and its Vmax is 100-fold lower. Moreover, the nonglycosylated XLN only acts on large xylan polymers and very slightly on xylohexaose.
Collapse
Affiliation(s)
- R Morosoli
- Centre de Recherche en Microbiologie Appliquée, Institut Armand-Frappier, Université du Québec, Ville de Laval, Canada
| | | | | |
Collapse
|
21
|
Stewart P, Kersten P, Vanden Wymelenberg A, Gaskell J, Cullen D. Lignin peroxidase gene family of Phanerochaete chrysosporium: complex regulation by carbon and nitrogen limitation and identification of a second dimorphic chromosome. J Bacteriol 1992; 174:5036-42. [PMID: 1629160 PMCID: PMC206318 DOI: 10.1128/jb.174.15.5036-5042.1992] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Lignin peroxidases (LiP) of Phanerochaete chrysosporium are encoded by a family of six closely related genes. Five LiP genes have been localized to the same dimorphic chromosome. In this investigation, relative transcript levels of the LiP genes were determined. Transcripts of the LiPA, LiPB, and O282 genes were at similar levels in both carbon- and nitrogen-limited cultures. In contrast, transcription of the GLG5, V4, and GLG4 genes was dramatically altered by culture conditions. Under carbon-limited conditions, GLG4 transcripts were, by far, the most abundant. Southern blot analyses of clamped homogeneous field gels were used to map the GLG4 gene to a dimorphic chromosome separate from the other LiP genes.
Collapse
Affiliation(s)
- P Stewart
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, Madison, Wisconsin 53705
| | | | | | | | | |
Collapse
|
22
|
Sinclair R, Yamazaki I, Bumpus J, Brock B, Chang CS, Albo A, Powers L. Structure of the active site of lignin peroxidase isozyme H2: native enzyme, compound III, and reduced form. Biochemistry 1992; 31:4892-900. [PMID: 1591249 DOI: 10.1021/bi00135a021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The wood-degrading fungus Phanerochaete chrysosporium secretes a number of extracellular enzymes called lignin peroxidases which are involved in the degradation of both lignin and a number of persistent environmental pollutants. Lignin peroxidase isozyme H2, a glycosylated protein of approximately 40 kDa, contains a single heme. X-ray absorption spectroscopy (XAS) has been used to probe the local environment of the iron in the active site of resting enzyme, reduced enzyme, and compound III. For the native and reduced forms, respectively, the average Fe-pyrrole nitrogen distances are 2.055 and 2.02 A (+/- 0.015 A); the Fe-proximal nitrogen distance is 1.93 and 1.91 A (+/- 0.02 A) while the Fe-distal ligand distance is 2.17 and 2.10 A (+/- 0.03 A). Although the results are not as well-defined, the active-site structure of compound III is largely 2.02 +/- 0.015 A for the average Fe-pyrrole nitrogen distance, 1.90 +/- 0.02 for the Fe-proximal nitrogen, and 1.74 +/- 0.03 A for the Fe-distal ligand distance. The heme iron-pyrrole nitrogen distance is more expanded in ligninase H2 than in other peroxidases. The possible significance of this is discussed in relation to other heme proteins.
Collapse
Affiliation(s)
- R Sinclair
- National Center for the Design of Molecular Function, Utah State University, Logan 84322-4630
| | | | | | | | | | | | | |
Collapse
|
23
|
James CM, Felipe MS, Sims PF, Broda P. Expression of a single lignin peroxidase-encoding gene in Phanerochaete chrysosporium strain ME446. Gene 1992; 114:217-22. [PMID: 1351020 DOI: 10.1016/0378-1119(92)90577-c] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A previously described linked set of lignin peroxidase-encoding genes (Lpo) from Phanerochaete chrysosporium (P.c.) ME446 is not expressed under standard growth conditions for ligninolytic activity. However, a single unlinked Lpo gene, not previously described in P.c. strain ME446, is expressed. The transcription start points of this gene are mapped and the gene is assigned to a genetic linkage group by the use of restriction-site polymorphism segregation analysis. No transcripts from Lpo-related genes, including that normally expressed in ME446, could be detected within RNA extracted from three nonligninolytic mutant strains, but a hyper-ligninolytic strain showed an increased level of Lpo expression. This increase is due to expression of additional Lpo genes, rather than to an increased level of transcription from the normally expressed sequence.
Collapse
Affiliation(s)
- C M James
- Department of Biochemistry and Applied Molecular Biology, University of Manchester Institute of Science and Technology, UK
| | | | | | | |
Collapse
|
24
|
Gaskell J, Vanden Wymelenberg A, Stewart P, Cullen D. Method to identify specific alleles of a Phanerochaete chrysosporium gene encoding lignin peroxidase. Appl Environ Microbiol 1992; 58:1379-81. [PMID: 1599257 PMCID: PMC195604 DOI: 10.1128/aem.58.4.1379-1381.1992] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A method to identify and differentiate allelic variants of the gene encoding lignin peroxidase isozyme H8 is presented. The strategy involves amplifying a variable region of the gene's carboxy terminus by use of the polymerase chain reaction and then probing with allele-specific oligonucleotides.
Collapse
Affiliation(s)
- J Gaskell
- Institute for Microbial and Biochemical Technology, USDA Forest Service, Madison, Wisconsin 53705
| | | | | | | |
Collapse
|
25
|
Ritch TG, Nipper VJ, Akileswaran L, Smith AJ, Pribnow DG, Gold MH. Lignin peroxidase from the basidiomycete Phanerochaete chrysosporium is synthesized as a preproenzyme. Gene 1991; 107:119-26. [PMID: 1743510 DOI: 10.1016/0378-1119(91)90304-t] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The cDNA clone L18 encoding lignin peroxidase LiP2, the most highly expressed LiP isozyme from Phanerochaete chrysosporium strain OGC101, was isolated and sequenced. Comparison of the cDNA sequence with the N-terminal sequence of the mature LiP2 protein isolated from culture medium suggests that the mature protein contains 343 amino acids (aa) and is preceded by a 28-aa leader sequence. In vitro transcription followed by in vitro translation and processing by signal peptidase resulted in cleavage at a site following the Ala21 (counted from the N-terminal Met1 of the initial translation product). The resultant protein contains a 7-aa propeptide, indicating that LiP is synthesized as a preproenzyme.
Collapse
Affiliation(s)
- T G Ritch
- Department of Chemical and Biological Sciences, Oregon Graduate Institute for Science and Technology, Beaverton 97006-1999
| | | | | | | | | | | |
Collapse
|
26
|
Kimura Y, Asada Y, Oka T, Kuwahara M. Molecular analysis of a Bjerkandera adusta lignin peroxidase gene. Appl Microbiol Biotechnol 1991; 35:510-4. [PMID: 1367394 DOI: 10.1007/bf00169758] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A cDNA clone, lambda LPO-1, encoding a major lignin peroxidase from the basidiomycete Bjerkandera adusta was isolated and characterized. The nucleotide sequence of lambda LPO-1 predicts a mature protein consisting of 349 amino acids with a molecular weight of 37,225 preceded by a signal peptide of 23 amino acid residues. We have also cloned and sequenced the gene encoding lignin peroxidase from B. adusta. Comparison of these sequences reveals a lignin peroxidase gene structure consisting of 1,116 bp of protein-encoding DNA that is interrupted by four intervening sequences. The putative eukaryotic regulatory sequence, a TATA box, is present at position -75 relative to the translational initiation codon. Amino acid sequence homology between the coding regions of lambda LPO-1 and of the lignin peroxidase cDNA clone lambda ML-1 from Phanerochaete chrysosporium is 61%.
Collapse
Affiliation(s)
- Y Kimura
- Department of Bioresource Science, Faculty of Agriculture, Kagawa University, Japan
| | | | | | | |
Collapse
|
27
|
Brown JA, Alic M, Gold MH. Manganese peroxidase gene transcription in Phanerochaete chrysosporium: activation by manganese. J Bacteriol 1991; 173:4101-6. [PMID: 2061289 PMCID: PMC208059 DOI: 10.1128/jb.173.13.4101-4106.1991] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The expression of manganese peroxidase in nitrogen-limited cultures of Phanerochaete chrysosporium is dependent on Mn, and initial work suggested that Mn regulates transcription of the mnp gene. In this study, using Northern (RNA) blot analysis of kinetic, dose-response, and inhibitor experiments, we demonstrate unequivocally that Mn regulates mnp gene transcription. The amount of mnp mRNA in cells of 4-day-old nitrogen-limited cultures is a direct function of the concentration of Mn in the culture medium up to a maximum of 180 microM. Addition of Mn to nitrogen-limited Mn-deficient secondary metabolic (4-, 5-, and 6-day-old) cultures results in the appearance of mnp mRNA within 40 min. The appearance of this message is completely inhibited by the RNA synthesis inhibitor dactinomycin but not by the protein synthesis inhibitor cycloheximide. Furthermore, the amount of mnp mRNA produced is a direct function of the concentration of added Mn. In contrast, addition of Mn to low-nitrogen Mn-deficient 2- or 3-day-old cultures does not result in the appearance of mnp mRNA. Manganese peroxidase protein is detected by specific immunoprecipitation of the in vitro translation products of poly(A) RNA isolated from Mn-supplemented (but not from Mn-deficient) cells. All of these results demonstrate that Mn, the substrate for the enzyme, regulates mnp gene transcription via a growth-stage-specific and concentration-dependent mechanism.
Collapse
Affiliation(s)
- J A Brown
- Department of Chemical and Biological Sciences, Oregon Graduate Institute of Science and Technology, Beaverton 97006-1999
| | | | | |
Collapse
|
28
|
Alic M, Mayfield MB, Akileswaran L, Gold MH. Homologous transformation of the lignin-degrading basidiomycete Phanerochaete chrysosporium. Curr Genet 1991. [DOI: 10.1007/bf00312741] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
29
|
Gaskell J, Dieperink E, Cullen D. Genomic organization of lignin peroxidase genes of Phanerochaete chrysosporium. Nucleic Acids Res 1991; 19:599-603. [PMID: 2011531 PMCID: PMC333654 DOI: 10.1093/nar/19.3.599] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Three lignin peroxidase (LiP) genes from the basidiomycete Phanerochaete chrysosporium were cloned on a single 30 kb cosmid insert. One gene, GLG5, is the genomic equivalent of a previously reported cDNA clone, CLG5. The other two LiP genes are transcriptionally convergent and map to a position approximately 15 kb downstream of GLG5. The translational stop codons of these genes are separated by 1.3 kb. Analysis of homokaryons established allelic relationships to previously described LiP clones. Using clamped homogeneous electrical field electrophoresis (CHEF), seven chromosomal bands were resolved from P. chrysosporium genomic DNA. On CHEF gel Southern blots, the LiP gene family was localized to a single, dimorphic chromosome.
Collapse
Affiliation(s)
- J Gaskell
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, Madison, WI 53705
| | | | | |
Collapse
|
30
|
|
31
|
Zhang YZ, Reddy CA, Rasooly A. Cloning of several lignin peroxidase (LIP)-encoding genes: sequence analysis of the LIP6 gene from the white-rot basidiomycete, Phanerochaete chrysosporium. Gene 1991; 97:191-8. [PMID: 1999283 DOI: 10.1016/0378-1119(91)90051-c] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A Phanerochaete chrysosporium BKMF1767 genomic library, constructed in the BamHI site of vector YRp12, was screened with the lignin peroxidase(LIP)-encoding cDNAs, CLG4 and CLG5, that have been shown to encode LIP2 (previously H2) and LIP6 (previously H10), respectively. Six distinct LIP genomic clones, designated pGLG1, pGLG2, pGLG3, pGLG4, pGLG5, and pGLG6, were isolated in this study. Probe CLG4 hybridized only to pGLG1. Probe CLG5 gave intense hybridization to pGLG2 and weaker hybridization to clones pGLG3 through pGLG6, but showed little or no hybridization to pGLG1. These results, in agreement with previous biochemical results, indicate the existence of LIP gene subfamilies. The limits and transcriptional orientation of the LIP gene in each clone were determined. The sequence data showed that pGLG2 contains the LIP6 gene, which encodes a protein identical in amino acid (aa) composition to that encoded by CLG5. It contains a leader sequence of 27 aa and a mature protein of 344 aa (Mr 36,607). Archetypal TATA-box-like and CAAT-box-like sequences in the 5'-noncoding region are located 51 and 97 nt upstream from the cDNA start point, respectively. S1 nuclease analysis of the 5' region of LIP6 revealed two transcription start points 8 nt apart downstream from the TATA box. Comparison of the sequence of LIP6 with its corresponding cDNA CLG5 showed that the gene contains nine small introns which range in size from 50 to 62 bp. These introns contained consensus splice junction sequences similar to those reported in other fungal and yeast introns.
Collapse
Affiliation(s)
- Y Z Zhang
- Department of Microbiology and Public Health, Michigan State University, East Lansing 48824-1101
| | | | | |
Collapse
|
32
|
A novel extrachromosomally maintained transformation vector for the lignin-degrading basidiomycete Phanerochaete chrysosporium. J Bacteriol 1991; 173:776-82. [PMID: 1987163 PMCID: PMC207071 DOI: 10.1128/jb.173.2.776-782.1991] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A stable extrachromosomally maintained transformation vector (pG12-1) for the lignin-degrading filamentous fungus Phanerochaete chrysosporium is described. The vector is 6.3 kb and contains a Kanr marker, pBR322 ori, and a 2.2-kb fragment (ME-1) derived from an endogenous extrachromosomal DNA element of P. chrysosporium. Vector pG12-1 was able to transform P. chrysosporium to G418 resistance and was readily and consistently recoverable from the total DNA of transformants via Escherichia coli transformation. Southern blot analyses indicated that pG12-1 is maintained at a low copy number in the fungal transformants. The vector is demonstrable in the total DNA of individual G418-resistant basidiospore progeny of the transformants only after amplification by polymerase chain reaction. Exonuclease III and dam methylation analyses, respectively, indicated that pG12-I undergoes replication in P. chrysosporium and that it is maintained extrachromosomally in a circular form. The vector is stably maintained in the transformants even after long-term nonselective growth. There is no evidence for integration of the vector into the chromosome at any stage.
Collapse
|
33
|
Cloning, sequence analysis, and expression of ligninolytic phenoloxidase genes of the white-rot basidiomycete Coriolus hirsutus. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)77245-1] [Citation(s) in RCA: 140] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
34
|
Godfrey BJ, Mayfield MB, Brown JA, Gold MH. Characterization of a gene encoding a manganese peroxidase from Phanerochaete chrysosporium. Gene 1990; 93:119-24. [PMID: 2227420 DOI: 10.1016/0378-1119(90)90144-g] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The complete nucleotide (nt) sequence of a gene (mnp-1) encoding manganese peroxidase isozyme 1 (MnP-1) (pI = 4.9) from Phanerochaete chrysosporium has been determined. The sequence of 2539 bp includes 526 bp of 5'-flanking sequence and 368 bp 3' to the poly(A) site. Comparison of cDNA and genomic sequences indicates six introns varying in size from 57-72 bp. Intron splice-junction sequences all adhere to the GT---AG rule. The positions of the introns show little similarity to the intron positions in the closely related lignin peroxidase-encoding genes. The 5' upstream region of the mnp-1 gene contains a TATAA element and three inverted CCAAT elements (ATTGG) at nt positions -81, -181, -195, and -304, respectively, relative to the start codon. In addition, the mnp-1 gene contains three putative heat-shock (HS) elements similar to the consensus C--GAA--TTC--G sequence, and two consensus metal response elements located within 500 bp upstream from the start codon. Furthermore, Northern-blot analysis demonstrates that mnp gene transcription is regulated by HS.
Collapse
Affiliation(s)
- B J Godfrey
- Department of Chemical and Biological Sciences, Oregon Graduate Institute of Science and Technology, Beaverton 97006-1999
| | | | | | | |
Collapse
|
35
|
Kimura Y, Asada Y, Kuwahara M. Screening of basidiomycetes for lignin peroxidase genes using a DNA probe. Appl Microbiol Biotechnol 1990; 32:436-42. [PMID: 1366392 DOI: 10.1007/bf00903779] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Basidiomycetes were screened for lignin peroxidase (LPO) genes using a DNA probe prepared from the LPO restriction fragment of Phanerochaete chrysosporium. Southern blot analysis showed restriction fragments of chromosomal DNA of Bjerkandera adusta and Coriolus consors hybridized with the probe. Bjerkandera adusta produced LPO in a glucose-peptone medium. Ion-exchange chromatography showed that this fungus produced multiple molecular forms of LPO. One of the enzymes, LPO-2, was purified and characterized. The molecular weight of LPO-2 was 41,000 with a pI of 4.2. Spectral analysis demonstrated that LPO-2 is a haem protein. The enzyme cleaved lignin model dimers mainly at the C alpha-C beta position of the side chain. The LPO-2 exhibited close similarity to LPOs of P. chrysosporium with respect to their basic properties.
Collapse
Affiliation(s)
- Y Kimura
- Department of Bioresource Science, Kagawa University, Japan
| | | | | |
Collapse
|
36
|
Brown JA, Glenn JK, Gold MH. Manganese regulates expression of manganese peroxidase by Phanerochaete chrysosporium. J Bacteriol 1990; 172:3125-30. [PMID: 2345139 PMCID: PMC209116 DOI: 10.1128/jb.172.6.3125-3130.1990] [Citation(s) in RCA: 98] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The appearance of manganese peroxidase (MnP) activity in nitrogen-limited cultures of Phanerochaete chrysosporium is dependent on the presence of manganese. Cultures grown in the absence of Mn developed normally and produced normal levels of the secondary metabolite veratryl alcohol but produced no MnP activity. Immunoblot analysis indicated that appearance of MnP protein in the extracellular medium was also dependent on the presence of Mn. Intracellular MnP protein was detectable only in cells grown in the presence of Mn. MnP mRNA was detected by Northern (RNA) blot analysis only in cells grown in the presence of Mn. If Mn was added to 4-day-old nitrogen-limited Mn-deficient cultures, extracellular MnP activity appeared after 6 h and reached a maximum after 18 h. Both actinomycin D and cycloheximide inhibited the induction of MnP activity by Mn. These results indicate that Mn, the substrate of the enzyme, is involved in the transcriptional regulation of the MnP gene.
Collapse
Affiliation(s)
- J A Brown
- Department of Chemical and Biological Sciences, Oregon Graduate Institute of Science and Technology, Beaverton 97006-1999
| | | | | |
Collapse
|
37
|
Forrester IT, Grabski AC, Mishra C, Kelley BD, Strickland WN, Leatham GF, Burgess RR. Characteristics and N-terminal amino acid sequence of a manganese peroxidase purified from Lentinula edodes cultures grown on a commercial wood substrate. Appl Microbiol Biotechnol 1990; 33:359-65. [PMID: 1366641 DOI: 10.1007/bf00164536] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Extracellular culture filtrates from ligninolytic cultures of the lignin-degrading basidiomycete Lentinula (syn. Lentinus) edodes (Berk.) Pegler contained one major peroxidase when grown on a commercial oak-wood substrate. The peroxidase was purified by polyethylenimine clarification, anion-exchange chromatography, and hydrophobic-interaction HPLC. The enzyme (MnP1) was a heme-iron protein with an apparent molecular weight of 44,600 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels and an isoelectric point of pH 3.2. The native enzyme had an absorption maximum at 407 nm, which shifted to 420 nm upon H2O2 addition. The pyridine-hemochrome-absorption spectrum indicated that one heme group was present per enzyme as protoporphyrin IX. N-Terminal amino acid sequencing showed that MnP1 had higher sequence homology with manganese peroxidases than with lignin peroxidases reported from Phanerochaete chrysosporium. L. edodes MnP1 was capable of oxidizing lignin and lignin-model compounds in the presence of manganese and H2O2.
Collapse
Affiliation(s)
- I T Forrester
- Protein Purification Facility, University of Wisconsin Biotechnology Center, Madison 53705
| | | | | | | | | | | | | |
Collapse
|
38
|
Dass SB, Reddy CA. Characterization of extracellular peroxidases produced by acetate-buffered cultures of the lignin-degrading basidiomycete Phanerochaete chrysosporium. FEMS Microbiol Lett 1990; 57:221-4. [PMID: 2210334 DOI: 10.1111/j.1574-6968.1990.tb04233.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Growth of Phanerochaete chrysosporium in a nitrogen-limited medium buffered with sodium acetate, instead of the commonly used 2,2-dimethylsuccinate (DMS), resulted in quantitative and qualitative differences in the production of various extracellular lignin peroxidases (LIPs) and manganese-dependent peroxidases (MNPs) involved in lignin degradation. The results indicate that production of LIPs and MNPs can be selectively enhanced by manipulation of culture conditions. Partial N-terminal analyses of the major LIPs and MNPs have made it possible to assign a specific protein to the specific genes and cDNAs that have been reported recently. The LIPs and MNPs differed widely in their ability to decolorize various dyes that are known to be degraded by the lignin degrading enzyme system of P. chrysosporium.
Collapse
Affiliation(s)
- S B Dass
- Department of Microbiology and Public Health, Michigan State University, East Lansing 48824-1101
| | | |
Collapse
|
39
|
Huoponen K, Ollikka P, Kälin M, Walther I, Mäntsälä P, Reiser J. Characterization of lignin peroxidase-encoding genes from lignin-degrading basidiomycetes. Gene X 1990; 89:145-50. [PMID: 2373364 DOI: 10.1016/0378-1119(90)90218-g] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Two closely linked lignin peroxidase (LPO)-encoding genes (lpo) from Phanerochaete chrysosporium were isolated. Nucleotide sequence studies indicated that the two genes are separated by 1.3 kb of flanking DNA and transcribed in opposite directions. Cloned P. chrysosporium lpo gene probes have been shown to hybridize to multiple sequences present in the DNAs of the white-rot fungi, Bjerkandera adusta, Coriolus versicolor and Fomes lignosus, but no hybridization was detected with DNA from Pleurotus ostreatus. Thus, lpo gene families appear to be common in a number of lignin-degrading basidiomycetes, some of which have not yet been shown to produce LPO proteins.
Collapse
Affiliation(s)
- K Huoponen
- Department of Biochemistry, University of Turku, Finland
| | | | | | | | | | | |
Collapse
|
40
|
Alic M, Clark EK, Kornegay JR, Gold MH. Transformation of Phanerochaete chrysosporium and Neurospora crassa with adenine biosynthetic genes from Schizophyllum commune. Curr Genet 1990. [DOI: 10.1007/bf00314877] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
41
|
Glumoff T, Harvey PJ, Molinari S, Goble M, Frank G, Palmer JM, Smit JD, Leisola MS. Lignin peroxidase from Phanerochaete chrysosporium. Molecular and kinetic characterization of isozymes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 187:515-20. [PMID: 2303054 DOI: 10.1111/j.1432-1033.1990.tb15333.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Five isozymes of lignin peroxidase from Phanerochaete chrysosporium were purified and their physical, molecular and kinetic properties determined. The isozymes differ from each other in terms of their isoelectric point, molecular mass, sugar content, spectral characteristics, substrate specificity and stability. The N-terminal sequence of amino acids was different for each isozyme suggesting they are different gene products. The isozyme with the highest carbohydrate level was most sensitive to changes in environmental factors. The kinetic behaviour of the isozymes varied clearly when tert-butyl hydroperoxide instead of hydrogen peroxide was used as the oxidant. Two out of five isozymes had very similar substrate specificity. The results are discussed in relation to the role which lignin peroxidase isozymes may play in lignin biodegradation.
Collapse
Affiliation(s)
- T Glumoff
- Laboratorium für Biochemie, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Kent Kirk T, Tien M, Kersten PJ, Kalyanaraman B, Hammel KE, Farrell RL. [27] Lignin peroxidase from fungi: Phanerochaete chrysosporium. Methods Enzymol 1990. [DOI: 10.1016/0076-6879(90)88029-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
|
43
|
Boominathan K, Dass SB, Randall TA, Kelley RL, Reddy CA. Lignin peroxidase-negative mutant of the white-rot basidiomycete Phanerochaete chrysosporium. J Bacteriol 1990; 172:260-5. [PMID: 2294087 PMCID: PMC208426 DOI: 10.1128/jb.172.1.260-265.1990] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Phanerochaete chrysosporium produces two classes of extracellular heme proteins, designated lignin peroxidases and manganese peroxidases, that play a key role in lignin degradation. In this study we isolated and characterized a lignin peroxidase-negative mutant (lip mutant) that showed 16% of the ligninolytic activity (14C-labeled synthetic lignin----14CO2) exhibited by the wild type. The lip mutant did not produce detectable levels of lignin peroxidase, whereas the wild type, under identical conditions, produced 96 U of lignin peroxidase per liter. Both the wild type and the mutant produced comparable levels of manganese peroxidase and glucose oxidase, a key H2O2-generating secondary metabolic enzyme in P. chrysosporium. Fast protein liquid chromatographic analysis of the concentrated extracellular fluid of the lip mutant confirmed that it produced only heme proteins with manganese peroxidase activity but no detectable lignin peroxidase activity, whereas both lignin peroxidase and manganese peroxidase activities were produced by the wild type. The lip mutant appears to be a regulatory mutant that is defective in the production of all the lignin peroxidases.
Collapse
Affiliation(s)
- K Boominathan
- Department of Microbiology and Public Health, Michigan State University, East Lansing 48824-1101
| | | | | | | | | |
Collapse
|
44
|
Saloheimo M, Barajas V, Niku-Paavola ML, Knowles JK. A lignin peroxidase-encoding cDNA from the white-rot fungus Phlebia radiata: characterization and expression in Trichoderma reesei. Gene X 1989; 85:343-51. [PMID: 2628172 DOI: 10.1016/0378-1119(89)90427-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The nucleotide sequence of a cDNA coding for a lignin peroxidase (Lgp) of the white-rot fungus, Phlebia radiata, has been determined. By amino acid (aa) sequencing, it has been shown that the protein product of this gene is the LIII Lgp of Pb. radiata. The isolated gene and the putative aa sequence are about 60% homologous to published Lgp sequences from the fungus, Phanerochaete chrysosporium. The aa thought to be involved in the catalysis of LIII are revealed by comparison with the yeast cytochrome c peroxidase. The P. radiata Lgp-encoding gene (lgp3) was expressed in the fungus, Trichoderma reesei, under the cellobiohydrolase-encoding cbh1 gene promoter. Lgp3 mRNA was produced by the T. reesei transformants. No Lgp protein, however, could be detected.
Collapse
Affiliation(s)
- M Saloheimo
- VTT, Biotechnical Laboratory, Espoo, Finland
| | | | | | | |
Collapse
|
45
|
Molecular cloning and sequences of lignin peroxidase genes of Phanerochaete chrysosporium. Mol Cell Biol 1989. [PMID: 2761543 DOI: 10.1128/mcb.9.6.2743] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genomic clones encoding lignin peroxidase isozyme H8 and two closely related genes were isolated from Phanerochaete chrysosporium BKM-1767, and their nucleotide sequences were determined. The positions and approximate lengths of introns were found to be highly conserved in all three clones. Analysis of homokaryotic derivatives indicated that the three clones are not alleles of the same gene(s).
Collapse
|
46
|
Pease EA, Andrawis A, Tien M. Manganese-dependent Peroxidase from Phanerochaete chrysosporium. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)80029-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
47
|
Andrawis A, Pease EA, Kuan IC, Holzbaur E, Tien M. Characterization of two lignin peroxidase clones from Phanerochaete chrysosporium. Biochem Biophys Res Commun 1989; 162:673-80. [PMID: 2474293 DOI: 10.1016/0006-291x(89)92363-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Two cDNA clones encoding lignin peroxidase isozymes from Phanerochaete chrysosporium have been isolated and characterized. One of the clones, lambda ML-4, encodes isozyme H8 as does the previously reported clone lambda ML-1 [Tien, M. and Tu, C.-P.D. Nature 326 (1987) 520-523; 328, 742]. Our data are consistent with lambda ML-1 and lambda ML-4 being allelic variants. The other clone, lambda ML-5, encodes a homologous isozyme. We have also isolated the genomic clone corresponding to lambda ML-4 cDNA. Conserved residues thought to be essential for peroxidase function were identified in the predicted amino acid sequences of both cDNA clones. Northern blot analyses indicate that these isozymes are expressed during secondary metabolism, appearing on day 4 of growth and increasing on days 5 and 6.
Collapse
Affiliation(s)
- A Andrawis
- Department of Molecular and Cell Biology, Pennsylvania State University, University Park 16802
| | | | | | | | | |
Collapse
|
48
|
Gines MJ, Dove MJ, Seligy VL. Aspergillus oryzae has two nearly identical Taka-amylase genes, each containing eight introns. Gene 1989; 79:107-17. [PMID: 2789162 DOI: 10.1016/0378-1119(89)90096-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
cDNA and genomic DNA for two nearly identical genes, AmyI and AmyII, coding for the enzyme Taka-amylase A (TA-A) of the fungus Aspergillus oryzae have been cloned and characterized. These genes are apparently unlinked, differing by only 3 nucleotides (nt) out of the 2720 nt that span the coding regions. The 617-nt 5'-flanking regions differ only at nt -372 (T or A) from the putative ATG start codon and contain four sets of short, inverted repeats (IR) upstream from the putative TATAAA box at nt -100 and the transcription start point at nt -69. The coding regions consist of 499 codons disrupted by eight intervening sequences. The putative proenzymes differ by only two amino acids (aa) and consist of the 478-aa extracellular enzyme plus a 21-aa hydrophobic leader sequence. Except for the replacement site changes in codons 35 (Arg----Gln) and 151 (Phe----Leu), the identity of the two genes continues downstream for 58 nt past the TGA stop codon before diverging. Exon 9 codes for 94 of the 98 aa of the domain B of mature TA-A. Little conservation of TA-A exons was found when these exons were aligned with those of human amylase. The genes are flanked by at least 6 to 10 kb of unrelated chromosomal nucleotide sequence. The Amy genes are co-expressed, since mRNA (cDNA) specific to the 3'-UTR of both genes was recovered from mycelia grown on starch, a known inducer of TA-A biosynthesis. The 3'-UTRs of cDNAs related to AmyI are shorter (128 nt and 145 nt) than those of AmyII (179 nt and 297 nt). The AmyI specific 3'-UTR is characterized by the absence of IR sequences and the presence of a putative 'AATAAA' polyadenylation signal.
Collapse
Affiliation(s)
- M J Gines
- Division of Biological Sciences, National Research Council of Canada, Ottawa
| | | | | |
Collapse
|
49
|
Farrell RL, Murtagh KE, Tien M, Mozuch MD, Kirk T. Physical and enzymatic properties of lignin peroxidase isoenzymes from Phanerochaete chrysosporium. Enzyme Microb Technol 1989. [DOI: 10.1016/0141-0229(89)90014-8] [Citation(s) in RCA: 162] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
50
|
Schalch H, Gaskell J, Smith TL, Cullen D. Molecular cloning and sequences of lignin peroxidase genes of Phanerochaete chrysosporium. Mol Cell Biol 1989; 9:2743-7. [PMID: 2761543 PMCID: PMC362349 DOI: 10.1128/mcb.9.6.2743-2747.1989] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The genomic clones encoding lignin peroxidase isozyme H8 and two closely related genes were isolated from Phanerochaete chrysosporium BKM-1767, and their nucleotide sequences were determined. The positions and approximate lengths of introns were found to be highly conserved in all three clones. Analysis of homokaryotic derivatives indicated that the three clones are not alleles of the same gene(s).
Collapse
Affiliation(s)
- H Schalch
- Department of Bacteriology, University of Wisconsin, Madison 53706
| | | | | | | |
Collapse
|