Fungal cytochrome P450 database

Park, Jongsun; Lee, Seungmin; Choi, Jaeyoung; Ahn, Kyohun; Park, Bong Soo; Park, Jaejin; Kang, Seogchan; Lee, Yong Hwan

doi:10.1186/1471-2164-9-402

Cited by 146 publications

(137 citation statements)

References 46 publications

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“…The particular transporters and cytochrome P450s involved in lignin degrada- tion remain unknown, but our results identify candidates for future investigation: genes encoding 27 putative transporters (see Table S3 in the supplemental material) and 18 cytochrome P450s (see Table S4) (46,47) were upregulated, in some cases with high RPKM values, at the onset of extracellular oxidation. An additional potential contributor to lignin fragment metabolism is the upregulated gene encoding protein Phach ID 2922705 (Table 2).…”

Section: Resultsmentioning

confidence: 99%

Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood

Korripally

Hunt

Houtman

et al. 2015

Appl Environ Microbiol

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Since uncertainty remains about how white rot fungi oxidize and degrade lignin in wood, it would be useful to monitor changes in fungal gene expression during the onset of ligninolysis on a natural substrate. We grew Phanerochaete chrysosporium on solid spruce wood and included oxidant-sensing beads bearing the fluorometric dye BODIPY 581/591 in the cultures. Confocal fluorescence microscopy of the beads showed that extracellular oxidation commenced 2 to 3 days after inoculation, coincident with cessation of fungal growth. Whole transcriptome shotgun sequencing (RNA-seq) analyses based on the v.2.2 P. chrysosporium genome identified 356 genes whose transcripts accumulated to relatively high levels at 96 h and were at least four times the levels found at 40 h. Transcripts encoding some lignin peroxidases, manganese peroxidases, and auxiliary enzymes thought to support their activity showed marked apparent upregulation. The data were also consistent with the production of ligninolytic extracellular reactive oxygen species by the action of manganese peroxidase-catalyzed lipid peroxidation, cellobiose dehydrogenase-catalyzed Fe 3؉ reduction, and oxidase-catalyzed H 2 O 2 production, but the data do not support a role for iron-chelating glycopeptides. In addition, transcripts encoding a variety of proteins with possible roles in lignin fragment uptake and processing, including 27 likely transporters and 18 cytochrome P450s, became more abundant after the onset of extracellular oxidation. Genes encoding cellulases showed little apparent upregulation and thus may be expressed constitutively. Transcripts corresponding to 165 genes of unknown function accumulated more than 4-fold after oxidation commenced, and some of them may merit investigation as possible contributors to ligninolysis. T he biodegradation of lignocellulose requires the disruption of its lignin, which shields the metabolically assimilable polysaccharides in this recalcitrant natural composite. Although a variety of microorganisms can attack lignocellulose, white rot basidiomycetes are uniquely efficient at this process, cleaving the recalcitrant intermonomer linkages of lignin via extracellular oxidative mechanisms and mineralizing many of the resulting fragments to carbon dioxide (1). Considerable progress has been made in understanding this process in the extensively researched white rot fungus Phanerochaete chrysosporium, which expresses important components of its ligninolytic system in response to nutrient limitation as part of its secondary metabolism. Biochemical and genetic evidence points to an important role in P. chrysosporium for secreted lignin peroxidases (LiPs), manganese peroxidases (MnPs), and H 2 O 2 -producing oxidases, which are thought to work together to cleave lignin into low-molecular-weight fragments (2). However, many aspects of ligninolysis by P. chrysosporium remain poorly understood.First, uncertainty remains about the process of lignin depolymerization. White rot fungi remove lignin not only from the surface of the wood cel...

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Section: Resultsmentioning

confidence: 99%

Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood

Korripally

Hunt

Houtman

et al. 2015

Appl Environ Microbiol

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“…We have included two new SLRP classes containing members that are not “true” proteoglycans, as they are not substituted GAG chains, with the exception of chondroadherin [8]. However, in common with class I–III, class IV and V SLRPs possess functional similarity, extracellular localization and overall high homology [1, 3]. …”

Section: Introductionmentioning

confidence: 99%

Key roles for the small leucine-rich proteoglycans in renal and pulmonary pathophysiology

Nastase

Iozzo

Schaefer

2014

Biochimica et Biophysica Acta (BBA) - General Subjects

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Background Small leucine-rich proteoglycans (SLRPs) are molecules that have signaling roles in a multitude of biological processes. In this respect, SLRPs play key roles in the evolution of a variety of diseases throughout the human body. Scope of Review We will critically review current developments in the roles of SLRPs in several types of disease of the kidney and lungs. Particular emphasis will be given to the roles of decorin and biglycan, the best characterized members of the SLRP gene family. Major Conclusions In both renal and pulmonary disorders, SLRPs are essential elements that regulate several pathophysiological processes including fibrosis, inflammation and tumor progression. Decorin has remarkable antifibrotic and antitumorigenic properties and is considered a valuable potential treatment of these diseases. Biglycan can modulate inflammatory processes in lung and renal inflammation and is a potential target in the treatment of inflammatory conditions. General significance SLRPs can serve as either treatment targets or as potential treatment in renal or lung disease.

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“…Accordingly, the large-scale divergence of P450s is currently being explored. [3][4][5][6] The fungal kingdom consists of a wide variety of eukaryotic microorganisms including yeasts, molds, and basidiomycetes, and it has been estimated that there may be 1.5 million fungal species. 7) Fungi inhabit a broad range of environments, and some play fundamental roles in nutrient cycling by decomposing organic matter.…”

Section: Introductionmentioning

confidence: 99%

Molecular and Functional Diversity of Fungal Cytochrome P450s

Ichinose

2012

Biological & Pharmaceutical Bulletin

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A series of genome projects have uncovered an astonishing molecular diversity of cytochrome P450s in the fungal kingdom. Fungal P450s discovered from such projects are often categorized into novel families and subfamilies. It thus appears that the divergence of fungal P450s is greater than of animal, plant, or bacterial P450s. The tremendous variation implies that fungi have vigorously diversified P450 functions to meet novel metabolic needs. To better understand the metabolic diversity of fungi, one must undertake the challenging task of exploiting the catalytic functions of numerous P450s. A compilation of P450 functions will also enable us to utilize their catalytic potentials in biotechnology. Experimental screening remains essential however, to elucidate the catalytic potentials of individual P450s. This review outlines the molecular and genomic aspects of fungal P450s, and introduces new functions revealed by functionomic studies using a recently developed, rapid, functional screening system.

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Fungal cytochrome P450 database

Cited by 146 publications

References 46 publications

Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood

Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood

Key roles for the small leucine-rich proteoglycans in renal and pulmonary pathophysiology

Molecular and Functional Diversity of Fungal Cytochrome P450s

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