Phylogenomic and Domain Analysis of Iterative Polyketide Synthases in Aspergillus Species

Lin, Shu-Hsi; Yoshimoto, Miwa; Lyu, Ping‐Chiang; Tang, Chuan-Yi; Arita, Masanori

doi:10.4137/ebo.s9796

Cited by 11 publications

(12 citation statements)

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“…Domains were manually assigned by referencing computational predictions using a combination of the Management and Analysis for Polyketide Synthase Type I, ITERDB [ 88 ], and the Conserved Domain Database (CDD) from the NCBI. The PKS types were determined using domain composition and the available literature [ 89 ] and included hybrids of PKS and NRPS, bacterial iPKS (bMSAS or bPRPKS), 6-MSAS, NRPKS, PRPKS, and RPKS. Using the predicted KS domains of P. fici , other reference fungi and outgroups of the homologous FASs from animals and representative type I PKSs from bacteria (Listed in Additional file 2 : Table S9) were aligned by MAFFT6.717b [ 90 ].…”

Section: Methodsmentioning

confidence: 99%

Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products

et al. 2015

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BackgroundIn recent years, the genus Pestalotiopsis is receiving increasing attention, not only because of its economic impact as a plant pathogen but also as a commonly isolated endophyte which is an important source of bioactive natural products. Pestalotiopsis fici Steyaert W106-1/CGMCC3.15140 as an endophyte of tea produces numerous novel secondary metabolites, including chloropupukeananin, a derivative of chlorinated pupukeanane that is first discovered in fungi. Some of them might be important as the drug leads for future pharmaceutics.ResultsHere, we report the genome sequence of the endophytic fungus of tea Pestalotiopsis fici W106-1/CGMCC3.15140. The abundant carbohydrate-active enzymes especially significantly expanding pectinases allow the fungus to utilize the limited intercellular nutrients within the host plants, suggesting adaptation of the fungus to endophytic lifestyle. The P. fici genome encodes a rich set of secondary metabolite synthesis genes, including 27 polyketide synthases (PKSs), 12 non-ribosomal peptide synthases (NRPSs), five dimethylallyl tryptophan synthases, four putative PKS-like enzymes, 15 putative NRPS-like enzymes, 15 terpenoid synthases, seven terpenoid cyclases, seven fatty-acid synthases, and five hybrids of PKS-NRPS. The majority of these core enzymes distributed into 74 secondary metabolite clusters. The putative Diels-Alderase genes have undergone expansion.ConclusionThe significant expansion of pectinase encoding genes provides essential insight in the life strategy of endophytes, and richness of gene clusters for secondary metabolites reveals high potential of natural products of endophytic fungi.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-014-1190-9) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products

et al. 2015

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“…Nutrient limitation is accompanied by fungal developmental changes such as asexual structure formation and sporulation 25 51 . Polyketide synthases are essential for the production of secondary metabolites but have also been shown to be important for melanin production, a pigment pre-dominantly found in the conidia of Aspergillus spp and which protects against environmental stresses such as UV light and radiation 52 53 54 . Indeed, several polyketide synthase-encoding genes of different secondary metabolite clusters were up-regulated in low-glucose conditions in A. nidulans , including one polyketide synthase predicted to be involved in the formation of the conidial green pigment.…”

Section: Discussionmentioning

confidence: 99%

The low affinity glucose transporter HxtB is also involved in glucose signalling and metabolism in Aspergillus nidulans

Reis

Nitsche²,

Lima

et al. 2017

Sci Rep

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One of the drawbacks during second-generation biofuel production from plant lignocellulosic biomass is the accumulation of glucose, the preferred carbon source of microorganisms, which causes the repression of hydrolytic enzyme secretion by industrially relevant filamentous fungi. Glucose sensing, subsequent transport and cellular signalling pathways have been barely elucidated in these organisms. This study therefore characterized the transcriptional response of the filamentous fungus Aspergillus nidulans to the presence of high and low glucose concentrations under continuous chemostat cultivation with the aim to identify novel factors involved in glucose sensing and signalling. Several transcription factor- and transporter-encoding genes were identified as being differentially regulated, including the previously characterized glucose and xylose transporter HxtB. HxtB was confirmed to be a low affinity glucose transporter, localizing to the plasma membrane under low- and high-glucose conditions. Furthermore, HxtB was shown to be involved in conidiation-related processes and may play a role in downstream glucose signalling. A gene predicted to encode the protein kinase PskA was also identified as being important for glucose metabolism. This study identified several proteins with predicted roles in glucose metabolic processes and provides a foundation for further investigation into the response of biotechnologically important filamentous fungi to glucose.

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“…Earlier, phylogenetic studies were performed for type I PKSs of Ascomycota group of fungi, which divided PKSs into 18 clades, indicating that the grouping was based on the presence/absence of reducing and NR domains in PKS. 22 , 57 Distribution of PKS enzymes in Aspergilli is studied by phylogeny, 57 and we have attempted to assign Aspergilli PKS protein to the probable chemical nature of the compound based on sequence homology. In the current study, Aspergillus PKSs fall into eight clades corresponding to the probable chemistry of the end compound they may synthesize based on the rationale of homology.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic and Structural Analysis of Polyketide Synthases inAspergilli

Bhetariya

Prajapati

Bhaduri

et al. 2016

Evolutionary Bioinformatics

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Polyketide synthases (PKSs) of Aspergillus species are multidomain and multifunctional megaenzymes that play an important role in the synthesis of diverse polyketide compounds. Putative PKS protein sequences from Aspergillus species representing medically, agriculturally, and industrially important Aspergillus species were chosen and screened for in silico studies. Six candidate Aspergillus species, Aspergillus fumigatus Af293, Aspergillus flavus NRRL3357, Aspergillus niger CBS 513.88, Aspergillus terreus NIH2624, Aspergillus oryzae RIB40, and Aspergillus clavatus NRRL1, were selected to study the PKS phylogeny. Full-length PKS proteins and only ketosynthase (KS) domain sequence were retrieved for independent phylogenetic analysis from the aforementioned species, and phylogenetic analysis was performed with characterized fungal PKS. This resulted into grouping of Aspergilli PKSs into nonreducing (NR), partially reducing (PR), and highly reducing (HR) PKS enzymes. Eight distinct clades with unique domain arrangements were classified based on homology with functionally characterized PKS enzymes. Conserved motif signatures corresponding to each type of PKS were observed. Three proteins from Protein Data Bank corresponding to NR, PR, and HR type of PKS (XP_002384329.1, XP_753141.2, and XP_001402408.2, respectively) were selected for mapping of conserved motifs on three-dimensional structures of KS domain. Structural variations were found at the active sites on modeled NR, PR, and HR enzymes of Aspergillus. It was observed that the number of iteration cycles was dependent on the size of the cavity in the active site of the PKS enzyme correlating with a type with reducing or NR products, such as pigment, 6MSA, and lovastatin. The current study reports the grouping and classification of PKS proteins of Aspergilli for possible exploration of novel polyketides based on sequence homology; this information can be useful for selection of PKS for polyketide exploration and specific detection of Aspergilli.

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Phylogenomic and Domain Analysis of Iterative Polyketide Synthases in Aspergillus Species

Cited by 11 publications

References 47 publications

Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products

Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products

The low affinity glucose transporter HxtB is also involved in glucose signalling and metabolism in Aspergillus nidulans

Phylogenetic and Structural Analysis of Polyketide Synthases inAspergilli

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