scholarly journals Polyketide Synthase Gene Diversity within the Microbiome of the Sponge Arenosclera brasiliensis, Endemic to the Southern Atlantic Ocean

2012 ◽  
Vol 79 (5) ◽  
pp. 1598-1605 ◽  
Author(s):  
Amaro E. Trindade-Silva ◽  
Cintia P. J. Rua ◽  
Bruno G. N. Andrade ◽  
Ana Carolina Paulo Vicente ◽  
Genivaldo G. Z. Silva ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Polyketide Synthase ◽  
Gene Diversity ◽  
Marine Sponges ◽  
Type I ◽  
Content Type ◽  
Phylogenetic Reconstructions ◽  
Polyketide Synthase Gene ◽  
Exclusive Group ◽  
Southern Atlantic Ocean

ABSTRACTMicrobes associated with marine sponges are considered important producers of bioactive, structurally unique polyketides. The synthesis of such secondary metabolites involves type I polyketide synthases (PKSs), which are enzymes that reach a maximum complexity degree in bacteria. The Haplosclerida spongeArenosclera brasiliensishosts a complex microbiota and is the source of arenosclerins, alkaloids with cytotoxic and antibacterial activity. In the present investigation, we performed high-throughput sequencing of the ketosynthase (KS) amplicon to investigate the diversity of PKS genes present in the metagenome ofA. brasiliensis. Almost 4,000 ketosynthase reads were recovered, with about 90% annotated automatically as bacterial. A total of 235 bacterial KS contigs was rigorously assembled from this sequence pool and submitted to phylogenetic analysis. A great diversity of six type I PKS groups has been consistently detected in our phylogenetic reconstructions, including a novel andA. brasiliensis-exclusive group. Our study is the first to reveal the diversity of type I PKS genes inA. brasiliensisas well as the potential of its microbiome to serve as a source of new polyketides.

scholarly journals Cloning, Sequencing, and Functional Analysis of an Iterative Type I Polyketide Synthase Gene Cluster for Biosynthesis of the Antitumor Chlorinated Polyenone Neocarzilin in “Streptomyces carzinostaticus”

2004 ◽  
Vol 48 (9) ◽  
pp. 3468-3476 ◽  
Author(s):  
Miyuki Otsuka ◽  
Koji Ichinose ◽  
Isao Fujii ◽  
Yutaka Ebizuka
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Streptomyces Coelicolor ◽  
Open Reading Frames ◽  
Modular Organization ◽  
Type I ◽  
Orf3 Protein ◽  
Polyketide Synthase Gene ◽  
Polyketide Chain ◽  
Reading Frames

ABSTRACT Neocarzilins (NCZs) are antitumor chlorinated polyenones produced by “Streptomyces carzinostaticus” var. F-41. The gene cluster responsible for the biosynthesis of NCZs was cloned and characterized. DNA sequence analysis of a 33-kb region revealed a cluster of 14 open reading frames (ORFs), three of which (ORF4, ORF5, and ORF6) encode type I polyketide synthase (PKS), which consists of four modules. Unusual features of the modular organization is the lack of an obvious acyltransferase domain on modules 2 and 4 and the presence of longer interdomain regions more than 200 amino acids in length on each module. Involvement of the PKS genes in NCZ biosynthesis was demonstrated by heterologous expression of the cluster in Streptomyces coelicolor CH999, which produced the apparent NCZ biosynthetic intermediates dechloroneocarzillin A and dechloroneocarzilin B. Disruption of ORF5 resulted in a failure of NCZ production, providing further evidence that the cluster is essential for NCZ biosynthesis. Mechanistic consideration of NCZ formation indicates the iterative use of at least one module of the PKS, which subsequently releases its product by decarboxylation to generate an NCZ skeleton, possibly catalyzed by a type II thioesterase encoded by ORF7. This is a novel type I PKS system of bacterial origin for the biosynthesis of a reduced polyketide chain. Additionally, the protein encoded by ORF3, located upstream of the PKS genes, closely resembles the FADH2-dependent halogenases involved in the formation of halometabolites. The ORF3 protein could be responsible for the halogenation of NCZs, presenting a unique example of a halogenase involved in the biosynthesis of an aliphatic halometabolite.

scholarly journals Streptomyces coelicolor DNA homologous with acyltransferase domains of type I polyketide synthase gene complex

2006 ◽  
Vol 157 (1) ◽  
pp. 195-200 ◽  
Author(s):  
Katarzyna Kuczek ◽  
Krzysztof Pawlik ◽  
Magdalena Kotowska ◽  
Marian Mordarski
Keyword(s):  
Polyketide Synthase ◽  
Streptomyces Coelicolor ◽  
Type I ◽  
Gene Complex ◽  
Polyketide Synthase Gene

scholarly journals Identification and Regulation offusA, the Polyketide Synthase Gene Responsible for Fusarin Production in Fusarium fujikuroi

2012 ◽  
Vol 78 (20) ◽  
pp. 7258-7266 ◽  
Author(s):  
Violeta Díaz-Sánchez ◽  
Javier Avalos ◽  
M. Carmen Limón
Keyword(s):  
Nitrogen Availability ◽  
Polyketide Synthase ◽  
High Sensitivity ◽  
Targeted Mutagenesis ◽  
Fusarium Fujikuroi ◽  
Mrna Levels ◽  
Wild Type ◽  
Sequence Comparisons ◽  
Content Type ◽  
Polyketide Synthase Gene

ABSTRACTFusarins are a class of mycotoxins of the polyketide family produced by differentFusariumspecies, including the gibberellin-producing fungusFusarium fujikuroi. Based on sequence comparisons between polyketide synthase (PKS) enzymes for fusarin production in otherFusariumstrains, we have identified theF. fujikuroiorthologue, calledfusA. The participation offusAin fusarin biosynthesis was demonstrated by targeted mutagenesis. Fusarin production is transiently stimulated by nitrogen availability in this fungus, a regulation paralleled by thefusAmRNA levels in the cell. Illumination of the cultures results in a reduction of the fusarin content, an effect partially explained by a high sensitivity of these compounds to light. Mutants of thefusAgene exhibit no external phenotypic alterations, including morphology and conidiation, except for a lack of the characteristic yellow and/or orange pigmentation of fusarins. Moreover, thefusAmutants are less efficient than the wild type at degrading cellophane on agar cultures, a trait associated with pathogenesis functions inFusarium oxysporum. ThefusAmutants, however, are not affected in their capacities to grow on plant tissues.

scholarly journals Biosynthesis of Cell Envelope-Associated Phenolic Glycolipids in Mycobacterium marinum

2015 ◽  
Vol 197 (6) ◽  
pp. 1040-1050 ◽  
Author(s):  
Olivia Vergnolle ◽  
Sivagami Sundaram Chavadi ◽  
Uthamaphani R. Edupuganti ◽  
Poornima Mohandas ◽  
Catherine Chan ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Cell Envelope ◽  
Acyl Chain ◽  
Deep Understanding ◽  
Fatty Acyl ◽  
Chain Extension ◽  
Type I ◽  
Content Type ◽  
Iterative Polyketide Synthase ◽  
Phenolic Glycolipids

Phenolic glycolipids (PGLs) are polyketide synthase-derived glycolipids unique to pathogenic mycobacteria. PGLs are found in several clinically relevant species, including variousMycobacterium tuberculosisstrains,Mycobacterium leprae, and several nontuberculous mycobacterial pathogens, such asM. marinum. Multiple lines of investigation implicate PGLs in virulence, thus underscoring the relevance of a deep understanding of PGL biosynthesis. We report mutational and biochemical studies that interrogate the mechanism by which PGL biosynthetic intermediates (p-hydroxyphenylalkanoates) synthesized by the iterative polyketide synthase Pks15/1 are transferred to the noniterative polyketide synthase PpsA for acyl chain extension inM. marinum. Our findings support a model in which the transfer of the intermediates is dependent on ap-hydroxyphenylalkanoyl-AMP ligase (FadD29) acting as an intermediary between the iterative and the noniterative synthase systems. Our results also establish thep-hydroxyphenylalkanoate extension ability of PpsA, the first-acting enzyme of a multisubunit noniterative polyketide synthase system. Notably, this noniterative system is also loaded with fatty acids by a specific fatty acyl-AMP ligase (FadD26) for biosynthesis of phthiocerol dimycocerosates (PDIMs), which are nonglycosylated lipids structurally related to PGLs. To our knowledge, the partially overlapping PGL and PDIM biosynthetic pathways provide the first example of two distinct, pathway-dedicated acyl-AMP ligases loading the same type I polyketide synthase system with two alternate starter units to produce two structurally different families of metabolites. The studies reported here advance our understanding of the biosynthesis of an important group of mycobacterial glycolipids.

scholarly journals Transcriptomics-Aided Dissection of the Intracellular and Extracellular Roles of Microcystin in Microcystis aeruginosa PCC 7806

2014 ◽  
Vol 81 (2) ◽  
pp. 544-554 ◽  
Author(s):  
A. Katharina Makower ◽  
J. Merijn Schuurmans ◽  
Detlef Groth ◽  
Yvonne Zilliges ◽  
Hans C. P. Matthijs ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Wild Type Strain ◽  
Carbon Limitation ◽  
Light Conditions ◽  
Wild Type ◽  
Low Light ◽  
Content Type ◽  
Expression Of Genes ◽  
Polyketide Synthase Gene

ABSTRACTRecent studies have provided evidence for both intracellular and extracellular roles of the potent hepatotoxin microcystin (MC) in the bloom-forming cyanobacteriumMicrocystis. Here, we surveyed transcriptomes of the wild-type strainM. aeruginosaPCC 7806 and the microcystin-deficient ΔmcyBmutant under low light conditions with and without the addition of external MC of the LR variant (MC-LR). Transcriptomic data acquired by microarray and quantitative PCR revealed substantial differences in the relative expression of genes of the central intermediary metabolism, photosynthesis, and energy metabolism. In particular, the data provide evidence for a lower photosystem I (PSI)-to-photosystem II (PSII) ratio and a more pronounced carbon limitation in the microcystin-deficient mutant. Interestingly, only 6% of the transcriptional differences could be complemented by external microcystin-LR addition. This MC signaling effect was seen exclusively for genes of the secondary metabolism category. The orphan polyketide synthase gene cluster IPF38-51 was specifically downregulated in response to external MC-LR under low light. Our data suggest a hierarchical and light-dependent cross talk of secondary metabolites and support both an intracellular and an extracellular role of MC inMicrocystis.

scholarly journals Breaking the Silence: Protein Stabilization Uncovers Silenced Biosynthetic Gene Clusters in the Fungus Aspergillus nidulans

2012 ◽  
Vol 78 (23) ◽  
pp. 8234-8244 ◽  
Author(s):  
Jennifer Gerke ◽  
Özgür Bayram ◽  
Kirstin Feussner ◽  
Manuel Landesfeind ◽  
Ekaterina Shelest ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Aspergillus Nidulans ◽  
Polyketide Synthase ◽  
Gene Clusters ◽  
Cellular Protein ◽  
Protein Stabilization ◽  
Putative Gene ◽  
Content Type ◽  
Alternative Approach ◽  
Polyketide Synthase Gene

ABSTRACTThe genomes of filamentous fungi comprise numerous putative gene clusters coding for the biosynthesis of chemically and structurally diverse secondary metabolites (SMs), which are rarely expressed under laboratory conditions. Previous approaches to activate these genes were based primarily on artificially targeting the cellular protein synthesis apparatus. Here, we applied an alternative approach of genetically impairing the protein degradation apparatus of the model fungusAspergillus nidulansby deleting the conserved eukaryoticcsnE/CSN5deneddylase subunit of the COP9 signalosome. This defect in protein degradation results in the activation of a previously silenced gene cluster comprising a polyketide synthase gene producing the antibiotic 2,4-dihydroxy-3-methyl-6-(2-oxopropyl)benzaldehyde (DHMBA). ThecsnE/CSN5gene is highly conserved in fungi, and therefore, the deletion is a feasible approach for the identification of new SMs.

scholarly journals Genome Sequence-Guided Finding of Lucensomycin Production by Streptomyces achromogenes Subsp. streptozoticus NBRC14001

2021 ◽  
Vol 10 (1) ◽  
pp. 37
Author(s):  
Sho Nishimura ◽  
Kazune Nakamura ◽  
Miyako Yamamoto ◽  
Daichi Morita ◽  
Teruo Kuroda ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
Gene Cluster ◽  
Genome Sequence ◽  
Polyketide Synthase ◽  
Macrolide Antibiotic ◽  
Biosynthetic Gene Cluster ◽  
Antifungal Compound ◽  
Type I ◽  
Biosynthetic Gene ◽  
Polyketide Synthase Gene

Information on microbial genome sequences is a powerful resource for accessing natural products with significant activities. We herein report the unveiling of lucensomycin production by Streptomyces achromogenes subsp. streptozoticus NBRC14001 based on the genome sequence of the strain. The genome sequence of strain NBRC14001 revealed the presence of a type I polyketide synthase gene cluster with similarities to a biosynthetic gene cluster for natamycin, which is a polyene macrolide antibiotic that exhibits antifungal activity. Therefore, we investigated whether strain NBRC14001 produces antifungal compound(s) and revealed that an extract from the strain inhibited the growth of Candida albicans. A HPLC analysis of a purified compound exhibiting antifungal activity against C. albicans showed that the compound differed from natamycin. Based on HR-ESI-MS spectrometry and a PubChem database search, the compound was predicted to be lucensomycin, which is a tetraene macrolide antibiotic, and this prediction was supported by the results of a MS/MS analysis. Furthermore, the type I polyketide synthase gene cluster in strain NBRC14001 corresponded well to lucesomycin biosynthetic gene cluster (lcm) in S. cyanogenus, which was very recently reported. Therefore, we concluded that the antifungal compound produced by strain NBRC14001 is lucensomycin.

scholarly journals Molecular Basis for Mycophenolic Acid Biosynthesis in Penicillium brevicompactum

2011 ◽  
Vol 77 (9) ◽  
pp. 3035-3043 ◽  
Author(s):  
Torsten Bak Regueira ◽  
Kanchana Rueksomtawin Kildegaard ◽  
Bjarne Gram Hansen ◽  
Uffe H. Mortensen ◽  
Christian Hertweck ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Mycophenolic Acid ◽  
Molecular Basis ◽  
Polyketide Synthase ◽  
Functional Characterization ◽  
Gene Encoding ◽  
Biosynthesis Gene Cluster ◽  
Content Type ◽  
Polyketide Synthase Gene ◽  
Penicillium Brevicompactum

ABSTRACTMycophenolic acid (MPA) is the active ingredient in the increasingly important immunosuppressive pharmaceuticals CellCept (Roche) and Myfortic (Novartis). Despite the long history of MPA, the molecular basis for its biosynthesis has remained enigmatic. Here we report the discovery of a polyketide synthase (PKS), MpaC, which we successfully characterized and identified as responsible for MPA production inPenicillium brevicompactum. mpaCresides in what most likely is a 25-kb gene cluster in the genome ofPenicillium brevicompactum. The gene cluster was successfully localized by targeting putative resistance genes, in this case an additional copy of the gene encoding IMP dehydrogenase (IMPDH). We report the cloning, sequencing, and the functional characterization of the MPA biosynthesis gene cluster by deletion of the polyketide synthase genempaCofP. brevicompactumand bioinformatic analyses. As expected, the gene deletion completely abolished MPA production as well as production of several other metabolites derived from the MPA biosynthesis pathway ofP. brevicompactum. Our work sets the stage for engineering the production of MPA and analogues through metabolic engineering.

scholarly journals Geographic Distribution of Secondary Metabolite Genes in the Marine Actinomycete Salinispora arenicola

2011 ◽  
Vol 77 (17) ◽  
pp. 5916-5925 ◽  
Author(s):  
Anna Edlund ◽  
Sandra Loesgen ◽  
William Fenical ◽  
Paul R. Jensen
Keyword(s):  
Secondary Metabolite ◽  
Geographic Distribution ◽  
Polyketide Synthase ◽  
Transcriptional Analysis ◽  
Type I ◽  
Molecular Fingerprinting ◽  
Biosynthetic Genes ◽  
Content Type ◽  
Marine Actinomycete ◽  
Sea Of Cortez

ABSTRACTThe molecular fingerprinting technique terminal-restriction fragment length polymorphism (T-RFLP) was used in combination with sequence-based approaches to evaluate the geographic distribution of secondary metabolite biosynthetic genes in strains of the marine actinomyceteSalinispora arenicola. This study targeted ketosynthase (KS) domains from type I polyketide synthase (PKS) genes and revealed four distinct clusters, the largest of which was comprised of strains from all six global locations sampled. The remaining strains fell into three smaller clusters comprised of strains derived entirely from the Red Sea, the Sea of Cortez, or around the Island of Guam. These results reveal variation in the secondary metabolite gene collectives maintained by strains that are largely clonal at the 16S rRNA level. The location specificities of the three smaller clusters provide evidence that collections of secondary metabolite genes in subpopulations ofS. arenicolaare endemic to these locations. Cloned KS sequences support the maintenance of distinct sets of biosynthetic genes in the strains associated with each cluster and include four that had not previously been detected inS. arenicola. Two of these new sequences were observed only in strains derived from Guam or the Sea of Cortez. Transcriptional analysis of one of the new KS sequences in conjunction with the production of the polyketide arenicolide A supports a link between this sequence and the associated biosynthetic pathway. From the perspective of natural product discovery, these results suggest that screening populations from distant locations can enhance the discovery of new natural products and provides further support for the use of molecular fingerprinting techniques, such as T-RFLP, to rapidly identify strains that possess distinct sets of biosynthetic genes.

scholarly journals In Silico Analysis of PKS and NRPS Gene Clusters in Arisostatin- and Kosinostatin-Producers and Description of Micromonospora okii sp. nov.

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1447
Author(s):  
Hisayuki Komaki ◽  
Natsuko Ichikawa ◽  
Akira Hosoyama ◽  
Moriyuki Hamada ◽  
Yasuhiro Igarashi
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Sequence Similarity ◽  
In Silico Analysis ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Rrna Gene ◽  
Type I ◽  
Phenotypic Differences ◽  
Polyketide Synthase Gene

Micromonospora sp. TP-A0316 and Micromonospora sp. TP-A0468 are producers of arisostatin and kosinostatin, respectively. Micromonospora sp. TP-A0316 showed a 16S rRNA gene sequence similarity of 100% to Micromonosporaoryzae CP2R9-1T whereas Micromonospora sp. TP-A0468 showed a 99.3% similarity to Micromonospora haikouensis 232617T. A phylogenetic analysis based on gyrB sequences suggested that Micromonospora sp. TP-A0316 is closely related to Micromonospora oryzae whereas Micromonospora TP-A0468 is an independent genomospecies. As Micromonospora sp. TP-A0468 showed some phenotypic differences to its closely related species, it was classified as a novel species, for which the name Micromonospora okii sp. nov. is proposed. The type strain is TP-A0468T (= NBRC 110461T). Micromonospora sp. TP-A0316 and M. okii TP-A0468T were both found to harbor 15 gene clusters for secondary metabolites such as polyketides and nonribosomal peptides in their genomes. Arisostatin-biosynthetic gene cluster (BGC) of Micromonospora sp. TP-A0316 closely resembled tetrocarcin A-BGC of Micromonospora chalcea NRRL 11289. A large type-I polyketide synthase gene cluster was present in each genome of Micromonospora sp. TP-A0316 and M. okii TP-A0468T. It was an ortholog of quinolidomicin-BGC of M. chalcea AK-AN57 and widely distributed in the genus Micromonospora.

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