Penicillium rubens Wisconsin 54-1255
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PROVIDER: PRJNA246109 | ENA |
REPOSITORIES: ENA
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Project description:Using in silico modelling, such Genome-Scale Metabolic Network (GSMN), represents a promising approach to predicting and understanding the potential for specialised metabolite production in a given organism. To address these questions, we reconstructed a new high-quality GSMN for the Penicillium rubens Wisconsin 54-1255 strain, a commonly used model organism. Our reconstruction, iPrub22, adheres to current convention standards and quality criteria, incorporating updated functional annotations, orthology searches with different GSMN templates, data from previous reconstructions, and manual curation steps targeting basal and specialised metabolites. With a MEMOTE score of 74% and a metabolic coverage of 45%, iPrub22 includes 5,464 metabolites interconnected by 5,919 reactions, of which 5,033 are supported by at least one genomic sequence. Of the metabolites present in iPrub22, 13% are categorised as belonging to specialised metabolism.
2023-06-20 | MODEL2306150001 | BioModels
Project description:Fingerprint-based physical map
| PRJNA29001 | ENA
Project description:WGS and clone-based sequencing
| PRJEA27927 | ENA
Project description:The recent discovery of a velvet complex containing several regulators of secondary metabolism in the model fungus Aspergillus nidulans raises the question whether similar type complexes direct fungal development in genera other than Aspergillus. Penicillium chrysogenum is the industrial producer of the antibiotic penicillin, whose biosynthetic regulation is barely understood. Here we provide a functional analysis of two major homologues of the velvet complex in P. chrysogenum, that we have named PcvelA and PclaeA. Data from array analysis using a ?PcvelA deletion strain indicate a significant role of PcvelA on the expression of biosynthesis and developmental genes, including PclaeA. Northern hybridization and HPLC quantifications of penicillin titres clearly show that both PcvelA and PclaeA play a major role in penicillin biosynthesis. Both regulators are further involved in different and distinct developmental processes. While PcvelA deletion leads to light independent conidial formation, dichotomous branching of hyphae and pellet formation in shaking cultures, a ?PclaeA strain shows a severe impairment in conidiophore formation in both the light and dark. Bimolecular fluorescence complementation assays finally provide evidence for a velvet-like complex in Penicillium chrysogenum, with structurally conserved components that have distinct developmental roles, illustrating the functional plasticity of these regulators within filamentous ascomycetes. Transcriptomes of PcvelA- and PclaeA- deletion mutants were compared with expression data from recipient strain deltaPcku70 and reference strain P2niaD18 as a control
2010-06-17 | E-GEOD-18585 | biostudies-arrayexpress
Project description:Penicillium chrysogenum
| PRJNA257456 | ENA
Project description:The recent discovery of a velvet complex containing several regulators of secondary metabolism in the model fungus Aspergillus nidulans raises the question whether similar type complexes direct fungal development in genera other than Aspergillus. Penicillium chrysogenum is the industrial producer of the antibiotic penicillin, whose biosynthetic regulation is barely understood. Here we provide a functional analysis of two major homologues of the velvet complex in P. chrysogenum, that we have named PcvelA and PclaeA. Data from array analysis using a ΔPcvelA deletion strain indicate a significant role of PcvelA on the expression of biosynthesis and developmental genes, including PclaeA. Northern hybridization and HPLC quantifications of penicillin titres clearly show that both PcvelA and PclaeA play a major role in penicillin biosynthesis. Both regulators are further involved in different and distinct developmental processes. While PcvelA deletion leads to light independent conidial formation, dichotomous branching of hyphae and pellet formation in shaking cultures, a ΔPclaeA strain shows a severe impairment in conidiophore formation in both the light and dark. Bimolecular fluorescence complementation assays finally provide evidence for a velvet-like complex in Penicillium chrysogenum, with structurally conserved components that have distinct developmental roles, illustrating the functional plasticity of these regulators within filamentous ascomycetes.
2010-06-17 | GSE18585 | GEO
Project description:Background: Microbial gene expression is to a large extend determined by environmental growth conditions. Differential gene expression analysis between two conditions has been frequently used to reveal regulatory networks and to assign physiological function to unknown genes. In nature, microorganisms cohabit however these interactions have been rarely studied and reproduced in laboratory set-up. Thus to quantitatively explore the genome-wide responses of microbial interaction, we co-cultivated Penicillium chrysogenum and Bacillus subtilis in chemostat culture. Results: Time course expression analysis of P. chrysogenum to co-cultivation with B. subtilis was carried out to understand the natural responses of P. chrysogenum to prokaryotes. Steady state chemostats of P. chrysogenum in non-B-lactam producing conditions was pulsed with B. subtilis and co-cultivation was followed for 72 hours. The dynamic physiological and transcriptional responses of P. chrysogenum in mixed culture were monitored. B. subtilis outcompeted growth of P. chrysogenum resulting in an increased B. subtilis biomass by more than three fold of its original size and a reduction in P. chrysogenum biomass to half of its original size after 72 h of mixed culture. Genes of the penicillin pathway, synthesis of the side-chain and precursors were overall unresponsive to the presence of B. subtilis. Moreover Penicillium polyketide synthase and nonribosomal peptide synthetase genes either remained silent or down-regulated, whereas genes responsible for protein synthesis, metabolism, energy conservation, respiration and transport were upregulated in the presence of B. subtilis. Among highly responsive genes, two putative B-1,3 endoglucanase (mutanase) genes viz Pc12g07500 and Pc12g13330 were upregulated by more than 15-fold and 8-fold respectively. Measurement of enzyme activity in the supernatant of mixed culture confirmed that the co-cultivation with B. subtilis induced mutanase production in P. chrysogenum. Mutanase activity was not observed in pure cultures of P. chrysogenum and B. subtilis or when P. chrysogenum was co-cultured with B. subtilis supernatant or heat inactivated B. subtilis cells. However, mutanase production was observed in cultures of P. chrysogenum pulsed with filter sterilized supernatants from mixed cultures P. chrysogenum and B. subtilis. Heterologous expression of Pc12g07500 and Pc12g13330 genes in Saccharomyces cerevisiae confirmed that at least Pc12g07500 encoded an B-1,3 endoglucanase. Conclusion: Time course transcriptional profiling of P. chrysogenum revealed several differentially expressed genes during mixed culture, potentially reflecting interactions between the eukaryotic and the prokaryotic systems. M-oM-^AM-!-1,3 endoglucanase produced by P. chrysogenum against B. subtilis signals may have application in improving the efficacy of antibiotics by degrading exopolysacchride biofilms of pathogenic bacteria. The objective of the present study is to investigate the response of P. chrysogenum to co-cultivation with B. subtilis. To trigger an interaction specific behaviour, steady state chemostat of P. chrysogenum Wisconsin 54-1255 was pulsed with B. subtilis. The dynamic, transcriptional and physiological responses of P. chrysogenum in mixed culture were monitored and analyzed. Several differentially expressed genes potentially reflected interactions between the eukaryotic and the prokaryotic systems. To test whether any bacterial signaling molecules are responsible for differential expression of selected fungal genes, P. chrysogenum cultures were inoculated with supernatant of B. subtilis culture, supernatants from mixed culture and with heat-inactivated B. subtilis. The specific transcriptional responses identified using microarray was verified by analysis of fermentation broth and functional characterization by expression of selected genes in S. cerevisiae.
2014-05-12 | E-GEOD-53286 | biostudies-arrayexpress
Project description:Penicillium chrysogenum 4088766 Genome sequencing
| PRJNA210202 | ENA
Project description:Industrial production of penicillin G by Penicillium chrysogenum requires medium supplementation with the side chain precursor phenylacetate. However, P.chrysogenum grown in presence of phenylalanine as sole nitrogen source formed detectable extracellular amounts of phenylacetate and penicillin G. To get more insights in the metabolism implicated, chemostat-cultivation in presence of 13C9-phenylalanine were carried out. Quantification and modeling of the labeled metabolite pools indicated that phenylalanine was i) incorporated in nascent protein, ii) transaminated to phenylpyruvate and further converted by oxidation or by decarboxylation and iii) oxidized into tyrosine and subsequently assimilated in the homogentisate pathway. Comparative transcriptome analysis of phenylalanine and (NH4)2SO4 grown P.chrysogenum cultures enabled to identify two putative 2-oxo acid decarboxylases Pc13g9300 and Pc18g01490. Both cDNAs were cloned and expressed in the decarboxylase-free Saccharomyces cerevisiae CEN.PK711-7C (pdc1delta, 5delta, 6delta, aro10delta, thi3delta) strain that has lost the ability to grow on glucose as sole carbon source or on phenylalanine as sole nitrogen source. Only Pc13g09300 was able to restore growth on glucose and on phenylalanine, demonstrating that this gene encodes a dual substrate pyruvate, phenylpyruvate decarboxylase. This newly identified thiamine-dependent 2-oxo acid decarboxylase provides clues to explain the formation of phenylacetate via an Ehrlich-like pathway in P.chrysogenum. Penicillium chrysogenum DS17690 was grown in aerobic glucose limited chemostat at 25oC, pH 6.5 and a dilution rate of 0.03h-1 with either amonia or phenylalanine
2011-11-05 | E-GEOD-32097 | biostudies-arrayexpress