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Lip-like genes in Phanerochaete sordida and Ceriporiopsis subvermispora, white rot fungi with no detectable lignin peroxidase activity.

ABSTRACT: Lignin peroxidase-like genes were PCR amplified from Phanerochaete sordida and Ceriporiopsis subvermispora, fungi lacking lignin peroxidase (LiP) activity. Amplification products were highly similar to previously described LiP genes. Using reverse transcription-coupled PCR a LiP-like cDNA clone was amplified from P. sordida RNA. In contrast, no evidence was obtained for transcription of C. subvermispora LiP genes.

SUBMITTER: Rajakumar S

PROVIDER: S-EPMC168048 | biostudies-other | 1996 Jul

REPOSITORIES: biostudies-other

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Lip-like genes in Phanerochaete sordida and Ceriporiopsis subvermispora, white rot fungi with no detectable lignin peroxidase activity.

Rajakumar S S Gaskell J J Cullen D D Lobos S S Karahanian E E Vicuna R R

Applied and environmental microbiology 19960701 7

Lignin peroxidase-like genes were PCR amplified from Phanerochaete sordida and Ceriporiopsis subvermispora, fungi lacking lignin peroxidase (LiP) activity. Amplification products were highly similar to previously described LiP genes. Using reverse transcription-coupled PCR a LiP-like cDNA clone was amplified from P. sordida RNA. In contrast, no evidence was obtained for transcription of C. subvermispora LiP genes. ...[more]

PMID: 8779605

Similar Datasets

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

Project description: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.

| S-EPMC182383 | biostudies-other

Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants.

Project description:A comparison of sequenced Agaricomycotina genomes suggests that efficient degradation of wood lignin was associated with the appearance of secreted peroxidases with a solvent-exposed catalytic tryptophan. This hypothesis is experimentally demonstrated here by resurrecting ancestral fungal peroxidases, after sequence reconstruction from genomes of extant white-rot Polyporales, and evaluating their oxidative attack on the lignin polymer by state-of-the-art analytical techniques. Rapid stopped-flow estimation of the transient-state constants for the 2 successive one-electron transfers from lignin to the peroxide-activated enzyme (k 2app and k 3app ) showed a progressive increase during peroxidase evolution (up to 50-fold higher values for the rate-limiting k 3app ). The above agreed with 2-dimensional NMR analyses during steady-state treatments of hardwood lignin, showing that its degradation (estimated from the normalized aromatic signals of lignin units compared with a control) and syringyl-to-guaiacyl ratio increased with the enzyme evolutionary distance from the first peroxidase ancestor. More interestingly, the stopped-flow estimations of electron transfer rates also showed how the most recent peroxidase ancestors that already incorporated the exposed tryptophan into their molecular structure (as well as the extant lignin peroxidase) were comparatively more efficient at oxidizing hardwood (angiosperm) lignin, while the most ancestral "tryptophanless" enzymes were more efficient at abstracting electrons from softwood (conifer) lignin. A time calibration of the ancestry of Polyporales peroxidases localized the appearance of the first peroxidase with a solvent-exposed catalytic tryptophan to 194 ± 70 Mya, coincident with the diversification of angiosperm plants characterized by the appearance of dimethoxylated syringyl lignin units.

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Intracellular pathways for lignin catabolism in white-rot fungi

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2021-01-15 | GSE151629 | GEO

Intracellular pathways for lignin catabolism in white-rot fungi.

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| S-EPMC7936344 | biostudies-literature

Intracellular pathways for lignin catabolism in white-rot fungi

Project description:White-rot fungi (WRF), considered the most efficient organisms at degrading organic carbon in the biosphere, are found in plant cell wall lignin biopolymer. We employ multi-omics to demonstrate that Trametes versicolor and Gelatoporia subvermispora funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems.

2021-02-10 | PXD019839 | Pride

Genomic organization of lignin peroxidase genes of Phanerochaete chrysosporium.

Project description: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.

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Organization and differential regulation of a cluster of lignin peroxidase genes of Phanerochaete chrysosporium.

Project description:The lignin peroxidases of Phanerochaete chrysosporium are encoded by a minimum of 10 closely related genes. Physical and genetic mapping of a cluster of eight lip genes revealed six genes occurring in pairs and transcriptionally convergent, suggesting that portions of the lip family arose by gene duplication events. The completed sequence of lipG and lipJ, together with previously published sequences, allowed phylogenetic and intron/exon classifications, indicating two main branches within the lip family. Competitive reverse transcription-PCR was used to assess lip transcript levels in both carbon- and nitrogen-limited media. Transcript patterns showed differential regulation of lip genes in response to medium composition. No apparent correlation was observed between genomic organization and transcript levels. Both constitutive and upregulated transcripts, structurally unrelated to peroxidases, were identified within the lip cluster.

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Elucidating lignin catabolism in white rot fungi

Project description:We propose to elucidate new metabolic pathways in fungi - with a special focus on white rot fungi (WRF)- involved in the catabolism of lignin-derived aromatic compounds. Basidiomycete fungi, in particular WRF, are the most efficient organisms for the depolymerization and mineralization of lignin to CO2 and H2O in Nature and thus, WRF play a pivotal role in carbon cycling. Lignin depolymerization by WRF is mediated by the action of extracellular oxidative ligninolytic enzymes, such as laccases and peroxidases, alongside other secreted metabolites. This extracellular process has been studied for decades via analysis of lignin modifications, ligninolytic enzyme activity in fungal broths, enzyme isolation and characterization, and more recently through multi-omics analyses. Despite the massive research effort directed toward understanding how WRF depolymerize lignin, almost no attention has been dedicated to the elucidation of the intracellular metabolism of WRF in catabolizing lignin. In fact, whether or not WRF are able to catabolize lignin remains a matter of discussion and debate. The work (proposal:https://doi.org/10.46936/10.25585/60001176) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

2024-05-16 | MSV000094781 | MassIVE

Temporal expression of the major lignin peroxidase genes of Phanerochaete chrysosporium.

Project description: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.

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Molecular cloning and sequences of lignin peroxidase genes of Phanerochaete chrysosporium.

Project description: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).

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