Characterization of a new lignin peroxidase gene (GLG6) from Phanerochaete chrysosporium

Developments in fungal taxonomy

Fungal infections, especially those caused by opportunistic species, have become substantially more common in recent decades. Numerous species cause human infections, and several new human pathogens are discovered yearly. This situation has created an increasing interest in fungal taxonomy and has led to the development of new methods and approaches to fungal biosystematics which have promoted important practical advances in identification procedures. However, the significance of some data provided by the new approaches is still unclear, and results drawn from such studies may even increase nomenclatural confusion. Analyses of rRNA and rDNA sequences constitute an important complement of the morphological criteria needed to allow clinical fungi to be more easily identified and placed on a single phylogenetic tree. Most of the pathogenic fungi so far described belong to the kingdom Fungi; two belong to the kingdom Chromista. Within the Fungi, they are distributed in three phyla and in 15 orders (Pneumocystidales, Saccharomycetales, Dothideales, Sordariales, Onygenales, Eurotiales, Hypocreales, Ophiostomatales, Microascales, Tremellales, Poriales, Stereales, Agaricales, Schizophyllales, and Ustilaginales).

Characterization of a cDNA encoding a manganese peroxidase from Phanerochaete chrysosporium: genomic organization of lignin and manganese peroxidase-encoding genes

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.

Nucleotide sequence variation of chitin synthase genes among ectomycorrhizal fungi and its potential use in taxonomy

DNA sequences of single-copy genes coding for chitin synthases (UDP-N-acetyl-D-glucosamine:chitin 4-beta-N-acetylglucosaminyltransferase; EC 2.4.1.16) were used to characterize ectomycorrhizal fungi. Degenerate primers deduced from short, completely conserved amino acid stretches flanking a region of about 200 amino acids of zymogenic chitin synthases allowed the amplification of DNA fragments of several members of this gene family. Different DNA band patterns were obtained from basidiomycetes because of variation in the number and length of amplified fragments. Cloning and sequencing of the most prominent DNA fragments revealed that these differences were due to various introns at conserved positions. The presence of introns in basidiomycetous fungi therefore has a potential use in identification of genera by analyzing PCR-generated DNA fragment patterns. Analyses of the nucleotide sequences of cloned fragments revealed variations in nucleotide sequences from 4 to 45%. By comparison of the deduced amino acid sequences, the majority of the DNA fragments were identified as members of genes for chitin synthase class II. The deduced amino acid sequences from species of the same genus differed only in one amino acid residue, whereas identity between the amino acid sequences of ascomycetous and basidiomycetous fungi within the same taxonomic class was found to be approximately 43 to 66%. Phylogenetic analysis of the amino acid sequence of class II chitin synthase-encoding gene fragments by using parsimony confirmed the current taxonomic groupings. In addition, our data revealed a fourth class of putative zymogenic chitin synthesis.

Physiology and molecular biology of the lignin peroxidases of Phanerochaete chrysosporium

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.

Temporal expression of the major lignin peroxidase genes of Phanerochaete chrysosporium

DNA probes specific for the genes encoding major lignin peroxidase (LIP) isozymes H2, H8, and H10 of Phanerochaete chrysosporium were constructed. These probes were used to study the temporal expression of the three lip genes in defined low-nitrogen medium. H2 gene transcripts were produced at high levels on days 4, 5, and 7 and at low levels on day 6, while the H8 gene transcripts peaked on day 4 and were produced in substantially lower amounts thereafter. H10 transcripts, on the other hand, peaked on day 4, dropped precipitously on day 5, and were barely detectable on days 6 and 7. There was no precise correlation between lip transcript and isozyme levels.

Molecular biology of the lignin-degrading basidiomycete Phanerochaete chrysosporium

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.

Methods to investigate the expression of lignin peroxidase genes by the white rot fungus Phanerochaete chrysosporium

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.

An overview of the recent advances on the physiology and molecular biology of lignin peroxidases of Phanerochaete chrysosporium

The lignin-degrading white-rot fungus Phanerochaete chrysosporium produces two families of extracellular peroxidases designated lignin peroxidases (LIPs) and manganese-dependent peroxidases (MNPs) which are components of the lignin degradation system of this organism. The number and types of LIP and MNP isozymes produced vary dramatically in response to changes in culture conditions. Protease-mediated degradation of LIPs was shown to be the major cause for the decay of LIP activity in idiophasic cultures of P. chrysosporium. Use of biochemical mutants has not only yielded information on the relative importance of LIPs and MNPs in lignin degradation but has given us insights into the regulation of production of LIPs and MNPs. The genes encoding the major LIPs have been cloned and sequenced and were shown to have a high degree of homology to each other. Karyotyping studies indicated that heterokaryotic strains contain ten chromosomes and that the LIP genes are distributed on at least two chromosomes.

Is an activator protein-2-like transcription factor involved in regulating gene expression during nitrogen limitation in fungi?

The upstream sequences of all published lignin peroxidase and manganese peroxidase genomic clones from Phanerochaete chrysosporium were analyzed. This analysis revealed the presence of putative activator protein-2 (AP-2) recognition sequences in 11 of 15 lignin peroxidase genes. The lignin peroxidase clone GLG6 and the manganese peroxidase gene (mnp-1) have two copies of putative AP-2 sequence in the upstream region. Interestingly, the lignin peroxidase gene VLG4 of another white rot fungus, Trametes versicolor, and the nit-2 gene of Neurospora crassa also contain putative AP-2-binding sequences. Since all of these genes are regulated by nutrient nitrogen, I hypothesize that an AP-2-like transcription factor may be involved in inducing gene expression during nitrogen limitation in fungi.

Electrophoretic karyotyping of the lignin-degrading basidiomycete Phanerochaete chrysosporium

Electrophoretic karyotyping of the two most widely studied strains of Phanerochaete chrysosporium, BKMF-1767 and ME-446, has been determined using transverse alternating field electrophoresis. The genomic DNA of BKMF-1767 was resolved into 10 chromosomes ranging in size from 1.8-5.0 Mb, amounting to a total genome size of about 29 Mb. The genomic DNA of strain ME-446, on the other hand, was resolved into 11 chromosomes, amounting to a total genome size of about 32 Mb. Lignin peroxidase genes have been localized to five chromosomes in strain BKMF-1767 and to four chromosomes in strain ME-446.

Amino acid sequence of Coprinus macrorhizus peroxidase and cDNA sequence encoding Coprinus cinereus peroxidase. A new family of fungal peroxidases

Sequence analysis and cDNA cloning of Coprinus peroxidase (CIP) were undertaken to expand the understanding of the relationships of structure, function and molecular genetics of the secretory heme peroxidases from fungi and plants. Amino acid sequencing of Coprinus macrorhizus peroxidase, and cDNA sequencing of Coprinus cinereus peroxidase showed that the mature proteins are identical in amino acid sequence, 343 residues in size and preceded by a 20-residue signal peptide. Their likely identity to peroxidase from Arthromyces ramosus is discussed. CIP has an 8-residue, glycine-rich N-terminal extension blocked with a pyroglutamate residue which is absent in other fungal peroxidases. The presence of pyroglutamate, formed by cyclization of glutamine, and the finding of a minor fraction of a variant form lacking the N-terminal residue, indicate that signal peptidase cleavage is followed by further enzymic processing. CIP is 40-45% identical in amino-acid sequence to 11 lignin peroxidases from four fungal species, and 42-43% identical to the two known Mn-peroxidases. Like these white-rot fungal peroxidases, CIP has an additional segment of approximately 40 residues at the C-terminus which is absent in plant peroxidases. Although CIP is much more similar to horseradish peroxidase (HRP C) in substrate specificity, specific activity and pH optimum than to white-rot fungal peroxidases, the sequences of CIP and HRP C showed only 18% identity. Hence, CIP qualifies as the first member of a new family of fungal peroxidases. The nine invariant residues present in all plant, fungal and bacterial heme peroxidases are also found in CIP. The present data support the hypothesis that only one chromosomal CIP gene exists. In contrast, a large number of secretory plant and fungal peroxidases are expressed from several peroxidase gene clusters. Analyses of three batches of CIP protein and of 49 CIP clones revealed the existence of only two highly similar alleles indicating less peroxidase polymorphism in C. cinereus strains than observed in plants and white-rot fungi.

Characterization of a highly expressed lignin peroxidase-encoding gene from the basidiomycete Phanerochaete chrysosporium

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.

cAMP-mediated differential regulation of lignin peroxidase and manganese-dependent peroxidase production in the white-rot basidiomycete Phanerochaete chrysosporium

Lignin peroxidases (LIPs) and manganese-dependent peroxidases (MNPs) are major components of the lignin-degrading enzyme system of Phanerochaete chrysosporium and typically appear during secondary metabolism. The involvement of cAMP in the regulation of production of LIPs and MNPs was investigated in this study. Production of LIPs and MNPs was preceded by a sharp rise in intracellular cAMP concentration. Addition of atropine, theophylline, or histamine to cultures resulted in a drop in intracellular cAMP concentration and a concomitant inhibition of production of LIPs only or of both LIPs and MNPs, depending on the concentration of the inhibitor added. These results were independently confirmed by fast protein liquid chromatographic profiles of the LIPs and MNPs in the extracellular fluid of the inhibitor-treated and untreated control cultures. LIP production was generally more sensitive to the inhibitors than MNP production. Northern blot analyses showed that the inhibitors affect the production of LIPs and MNPs at the level of transcription. Furthermore, LIP and MNP gene expression appears to be differentially regulated depending on the intracellular concentration of cAMP. These results show that cAMP plays a key role in the regulation of production of LIPs and MNPs in P. chrysosporium.

Characterization of a lignin peroxidase gene from the white-rot fungus Trametes versicolor

A genomic library of the white-rot fungus Trametes versicolor has been constructed and a gene coding for a lignin peroxidase has been isolated and sequenced. The gene, which contains 6 introns, encodes a protein of 346 amino acid residues, preceded by a tentative 26-residue signal peptide. The deduced amino-terminal sequence agrees with the amino-terminal end of a lignin peroxidase isozyme previously isolated from carbon-limited cultures of T versicolor.

Cloning and characterization of a lignin peroxidase gene from the white-rot fungus Trametes versicolor

Six putative lignin peroxidase (LIP) genes were isolated from a lambda EMBL3 phage library of the white-rot fungus, Trametes versicolor, using the Phanerochaete chrysosporium LIP cDNA CLG5 as the probe. Sequence analysis of one of the genes, VLG1, showed that its coding region is interrupted by six small introns (49-64 bp) and that it encodes a mature LIP protein (341 aa; Mr: 36,714) that is preceded by a 25 aa signal sequence. This protein has a relatively high degree of aa homology to the N-termini of the LIP proteins purified from T. versicolor and has an aa homology of 55-60% to the LIP proteins of P. chrysosporium, which is comparable to that found between P. chrysosporium and Phlebia radiata LIP proteins.