Two genes, encoding YK-LiP1 and YK-LiP2, were cloned from the white-rot fungus Phanerochaete sordida YK-624, and a homologous expression system for the gene was constructed. Two full-length cDNAs (ylpA and ylpB) were isolated by degenerate RT-PCR and RACE-PCR. The results of N-terminal amino acid sequence analysis of native YK-LiP1 and YK-LiP2 showed that ylpA and ylpB coded for YK-LiP2 and YK-LiP1 respectively. The promoter of glyceraldehyde-3-phosphate dehydrogenase cloned from P. sordida YK-624 (PsGPD) was used to drive the expression of ylpA. Expression vector pGPD-g-ylpA was transformed into a P. sordida YK-624 uracil auxotrophic mutant, UV-64. The YlpA protein was secreted in active form by the transformants after 4 d of growth in a medium containing an excessive nitrogen source, whereas endogenous YK-LiP1 and YK-LiP2 were not produced. The physical and catalytic properties of the purified YlpA protein were very similar to those of YK-LiP2. These results suggest that homologous expression of recombinant YK-LiP2 was successful.
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"In addition, lignin peroxidase (LiP) and manganese peroxidase (MnP) are considered to be the most effective enzymes for recycling carbon sources fixed as lignin . As genes encoding LiP are quite limited to white rot fungi, including Phanerochaete chrysosporium[4,5], P. sordida, Trametes versicolor, Phlebia radiata[8,9], P. tremellosa, and Bjerkandera sp. , genes encoding MnP have drawn attention as an alternative ligninolytic peroxidase due to their wider distribution among basidiomycetes compared to those encoding LiP. "
[Show abstract][Hide abstract] ABSTRACT: Background
Peroxidases are a group of oxidoreductases which mediate electron transfer from hydrogen peroxide (H2O2) and organic peroxide to various electron acceptors. They possess a broad spectrum of impact on industry and fungal biology. There are numerous industrial applications using peroxidases, such as to catalyse highly reactive pollutants and to breakdown lignin for recycling of carbon sources. Moreover, genes encoding peroxidases play important roles in fungal pathogenicity in both humans and plants. For better understanding of fungal peroxidases at the genome-level, a novel genomics platform is required. To this end, Fungal Peroxidase Database (fPoxDB; http://peroxidase.riceblast.snu.ac.kr/) has been developed to provide such a genomics platform for this important gene family.
In order to identify and classify fungal peroxidases, 24 sequence profiles were built and applied on 331 genomes including 216 from fungi and Oomycetes. In addition, NoxR, which is known to regulate NADPH oxidases (NoxA and NoxB) in fungi, was also added to the pipeline. Collectively, 6,113 genes were predicted to encode 25 gene families, presenting well-separated distribution along the taxonomy. For instance, the genes encoding lignin peroxidase, manganese peroxidase, and versatile peroxidase were concentrated in the rot-causing basidiomycetes, reflecting their ligninolytic capability. As a genomics platform, fPoxDB provides diverse analysis resources, such as gene family predictions based on fungal sequence profiles, pre-computed results of eight bioinformatics programs, similarity search tools, a multiple sequence alignment tool, domain analysis functions, and taxonomic distribution summary, some of which are not available in the previously developed peroxidase resource. In addition, fPoxDB is interconnected with other family web systems, providing extended analysis opportunities.
fPoxDB is a fungi-oriented genomics platform for peroxidases. The sequence-based prediction and diverse analysis toolkits with easy-to-follow web interface offer a useful workbench to study comparative and evolutionary genomics of peroxidases in fungi.
"UV-64 protoplasts were prepared and then transformed with pPsURA5 and pBUNA2pro-mnp4 using standard techniques. The cotransformed clones were selected by PCR, as described previously (Sugiura et al., 2009), with the following modifications: primers bee2proF4 and mnp4R3 were designed to amplify the mnp4 gene fused with the bee2 promoter. "
[Show abstract][Hide abstract] ABSTRACT: We identified a highly expressed protein (BUNA2) by two-dimensional gel electrophoresis from the hyper lignin-degrading fungus Phanerochaete sordida YK-624 under wood-rotting conditions. Partial amino acid sequences of BUNA2 were determined by LC-MS/MS analysis, and BUNA2 gene (bee2) and promoter region were PCR-cloned and sequenced. The bee2 promoter was used to drive the expression of the manganese peroxidase gene (mnp4) in P. sordida YK-624. Eighteen mnp4-expressing clones were obtained, with most showing higher ligninolytic activity and selectivity than wild-type YK-624. Examination of the ligninolytic properties of the most effective lignin-degrading transformant, BM-65, cultured on wood meal revealed that this strain exhibited higher lignin degradation and MnP activities than those of wild type. Transcriptional analysis confirmed the increased expression of recombinant mnp4 in the transformant. These results indicate that use of the bee2 promoter to drive the expression of ligninolytic enzymes may be an effective approach for improving the lignin-degrading properties of white-rot fungi.
"LiPs are secreted as sets of multiple isozymes and isoforms, by P. chrysosporium and a few other corticioid and polyporous white-rot fungi, e.g., Trametes versicolor (Johansson and Nyman 1993), Phlebia radiata (Lundell 1993; Moilanen et al. 1996), Phlebia tremellosa (Vares et al. 1994), Bjerkandera spp. (ten Have et al. 1998), and Phanerochaete sordida (Sugiura et al. 2009). LiP is catalytically the most powerful class II fungal peroxidase with the ability to directly oxidize dimeric lignin model compounds such as the nonphenolic β-O-4 linkagetype arylglycerol-aryl ethers (Scheme 1, reaction 2, substrate A). "
[Show abstract][Hide abstract] ABSTRACT: Heme-containing peroxidases secreted by fungi are a fascinating group of biocatalysts with various ecological and biotechnological implications. For example, they are involved in the biodegradation of lignocelluloses and lignins and participate in the bioconversion of other diverse recalcitrant compounds as well as in the natural turnover of humic substances and organohalogens. The current review focuses on the most recently discovered and novel types of heme-dependent peroxidases, aromatic peroxygenases (APOs), and dye-decolorizing peroxidases (DyPs), which catalyze remarkable reactions such as peroxide-driven oxygen transfer and cleavage of anthraquinone derivatives, respectively, and represent own separate peroxidase superfamilies. Furthermore, several aspects of the "classic" fungal heme-containing peroxidases, i.e., lignin, manganese, and versatile peroxidases (LiP, MnP, and VP), phenol-oxidizing peroxidases as well as chloroperoxidase (CPO), are discussed against the background of recent scientific developments.