Organization of the biosynthetic gene cluster for the macrolide concanamycin A in Streptomyces neyagawaensis ATCC 27449

The macrolide antibiotic concanamycin A has been identified as an exceptionally potent inhibitor of the vacuolar (V-type) ATPase. Such compounds have been mooted as the basis of a potential drug treatment for osteoporosis, since the V-ATPase is involved in the osteoclast-mediated bone resorption that underlies this common condition. To enable combinatorial engineering of altered concanamycins, the biosynthetic gene cluster governing the biosynthesis of concanamycin A has been cloned from Streptomyces neyagawaensis and shown to span a region of over 100 kbp of contiguous DNA. An efficient transformation system has been developed for S. neyagawaensis and used to demonstrate the role of the cloned locus in the formation of concanamycin A. Sequence analysis of the 28 ORFs in the region has revealed key features of the biosynthetic pathway, in particular the biosynthetic origin of portions of the backbone, which arise from the unusual polyketide building blocks ethylmalonyl-CoA and methoxymalonyl-ACP, and the origin of the pendant deoxysugar moiety 4′-O-carbamoyl-2′-deoxyrhamnose, as well as the presence of a modular polyketide synthase (PKS) encoded by six giant ORFs. Examination of the methoxymalonyl-specific acyltransferase (AT) domains has led to recognition of an amino acid sequence motif which can be used to distinguish methylmalonyl-CoA- from methoxymalonyl-ACP-specific AT domains in natural PKSs.

Download Full-text

Organization of the biosynthetic gene cluster for rapamycin in Streptomyces hygroscopicus: Analysis of the enzymatic domains in the modular polyketide synthase

Gene ◽

10.1016/0378-1119(95)00800-4 ◽

1996 ◽

Vol 169 (1) ◽

pp. 9-16 ◽

Cited By ~ 174

Author(s):

Jesús F. Aparicio ◽

István Molnár ◽

Torsten Schwecke ◽

Ariane König ◽

Stephen F. Haydock ◽

...

Keyword(s):

Gene Cluster ◽

Polyketide Synthase ◽

Biosynthetic Gene Cluster ◽

Streptomyces Hygroscopicus ◽

Biosynthetic Gene ◽

Modular Polyketide Synthase

Download Full-text

Organization of the biosynthetic gene cluster in Streptomyces sp. DSM 4137 for the novel neuroprotectant polyketide meridamycin

Microbiology ◽

10.1099/mic.0.29176-0 ◽

2006 ◽

Vol 152 (12) ◽

pp. 3507-3515 ◽

Cited By ~ 21

Author(s):

Yuhui Sun ◽

Hui Hong ◽

Markiyan Samborskyy ◽

Tatiana Mironenko ◽

Peter F. Leadlay ◽

...

Keyword(s):

Neurodegenerative Disorders ◽

Gene Deletion ◽

Polyketide Synthase ◽

Biosynthetic Gene Cluster ◽

Specific Gene ◽

The Novel ◽

Biosynthetic Gene ◽

Modular Polyketide Synthase

Meridamycin is a non-immunosuppressant, FKBP-binding macrocyclic polyketide, which has major potential as a neuroprotectant in a range of neurodegenerative disorders including dementia, Parkinson's disease and ischaemic stroke. A biosynthetic cluster predicted to encode biosynthesis of meridamycin was cloned from the prolific secondary-metabolite-producing strain Streptomyces sp. DSM 4137, not previously known to produce this compound, and specific gene deletion was used to confirm the role of this cluster in the biosynthesis of meridamycin. The meridamycin modular polyketide synthase consists of 14 extension modules distributed between three giant multienzyme proteins. The terminal module is flanked by a highly unusual cytochrome P450-like domain. The characterization of the meridamycin biosynthetic locus in this readily manipulated streptomycete species opens the way to the engineering of new, altered meridamycins of potential therapeutic importance.

Download Full-text

Glycosylation Steps during Spiramycin Biosynthesis in Streptomyces ambofaciens: Involvement of Three Glycosyltransferases and Their Interplay with Two Auxiliary Proteins

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01602-09 ◽

2010 ◽

Vol 54 (7) ◽

pp. 2830-2839 ◽

Cited By ~ 27

Author(s):

Hoang Chuong Nguyen ◽

Fatma Karray ◽

Sylvie Lautru ◽

Josette Gagnat ◽

Ahmed Lebrihi ◽

...

Keyword(s):

Gene Cluster ◽

Polyketide Synthase ◽

Macrolide Antibiotic ◽

Biosynthetic Gene Cluster ◽

Type I ◽

Biosynthetic Gene ◽

Streptomyces Ambofaciens ◽

Mutant Strains ◽

Genes Encoding

ABSTRACT Streptomyces ambofaciens synthesizes spiramycin, a 16-membered macrolide antibiotic used in human medicine. The spiramycin molecule consists of a polyketide lactone ring (platenolide) synthesized by a type I polyketide synthase, to which three deoxyhexoses (mycaminose, forosamine, and mycarose) are attached successively in this order. These sugars are essential to the antibacterial activity of spiramycin. We previously identified four genes in the spiramycin biosynthetic gene cluster predicted to encode glycosyltransferases. We individually deleted each of these four genes and showed that three of them were required for spiramycin biosynthesis. The role of each of the three glycosyltransferases in spiramycin biosynthesis was determined by identifying the biosynthetic intermediates accumulated by the corresponding mutant strains. This led to the identification of the glycosyltransferase responsible for the attachment of each of the three sugars. Moreover, two genes encoding putative glycosyltransferase auxiliary proteins were also identified in the spiramycin biosynthetic gene cluster. When these two genes were deleted, one of them was found to be dispensable for spiramycin biosynthesis. However, analysis of the biosynthetic intermediates accumulated by mutant strains devoid of each of the auxiliary proteins (or of both of them), together with complementation experiments, revealed the interplay of glycosyltransferases with the auxiliary proteins. One of the auxiliary proteins interacted efficiently with the two glycosyltransferases transferring mycaminose and forosamine while the other auxiliary protein interacted only with the mycaminosyltransferase.

Download Full-text

Faculty Opinions recommendation of Expression analysis of the tylosin-biosynthetic gene cluster: pivotal regulatory role of the tylQ product.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1004877.55457 ◽

2002 ◽

Author(s):

Ben Shen

Keyword(s):

Gene Cluster ◽

Expression Analysis ◽

Biosynthetic Gene Cluster ◽

Regulatory Role ◽

Biosynthetic Gene

Download Full-text

Biosynthesis of Chlorinated Lactylates in Sphaerospermopsis sp. LEGE 00249

10.26434/chemrxiv.12885476 ◽

2020 ◽

Author(s):

Kathleen Abt ◽

Raquel Castelo-Branco ◽

Pedro Leao

Keyword(s):

Gene Cluster ◽

Building Blocks ◽

Bioinformatic Analysis ◽

Biosynthetic Gene Cluster ◽

Pathway Engineering ◽

Dodecanoic Acid ◽

Biosynthetic Gene ◽

Precursor Feeding ◽

Alkyl Chains ◽

Important Group

Lactylates are an important group of molecules in the food and cosmetic industries. A series of natural halogenated 1-lactylates – chlorosphaerolactyaltes (1-4) – were recently reported from Sphaerospermopsis sp. LEGE 00249. Here, we identify the cly biosynthetic gene cluster, containing all the necessary functionalities to generate and release the natural lactylates. Using a combination of stable isotope-labeled precursor feeding and bioinformatic analysis, we propose that dodecanoic acid and pyruvate are the key building blocks in the biosynthesis of 1-4. We additionally report minor analogues of these molecules with varying alkyl chains. The discovery of the cly gene cluster paves the way to accessing industrially-relevant lactylates through pathway engineering.

Download Full-text

Biosynthesis of the uridine-derived nucleoside antibiotic A-94964: identification and characterization of the biosynthetic gene cluster provide insight into the biosynthetic pathway

Organic & Biomolecular Chemistry ◽

10.1039/c8ob02765j ◽

2019 ◽

Vol 17 (3) ◽

pp. 461-466 ◽

Cited By ~ 5

Author(s):

Taro Shiraishi ◽

Makoto Nishiyama ◽

Tomohisa Kuzuyama

Keyword(s):

Gene Cluster ◽

In Silico ◽

Biosynthetic Pathway ◽

Gene Deletion ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene ◽

Identification And Characterization ◽

Insight Into

The biosynthetic pathway of the uridine-derived nucleoside antibiotic A-94964 was proposed via in silico analysis coupled with gene deletion experiments.

Download Full-text

Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium

BMC Genomics ◽

10.1186/s12864-020-06896-1 ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 1

Author(s):

Hye-Seon Kim ◽

Jessica M. Lohmar ◽

Mark Busman ◽

Daren W. Brown ◽

Todd A. Naumann ◽

...

Keyword(s):

Polyketide Synthase ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Sphingolipid Metabolism ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Dehydrogenase Gene ◽

Food And Feed ◽

Feed Safety

Abstract Background Sphingolipids are structural components and signaling molecules in eukaryotic membranes, and many organisms produce compounds that inhibit sphingolipid metabolism. Some of the inhibitors are structurally similar to the sphingolipid biosynthetic intermediate sphinganine and are referred to as sphinganine-analog metabolites (SAMs). The mycotoxins fumonisins, which are frequent contaminants in maize, are one family of SAMs. Due to food and feed safety concerns, fumonisin biosynthesis has been investigated extensively, including characterization of the fumonisin biosynthetic gene cluster in the agriculturally important fungi Aspergillus and Fusarium. Production of several other SAMs has also been reported in fungi, but there is almost no information on their biosynthesis. There is also little information on how widely SAM production occurs in fungi or on the extent of structural variation of fungal SAMs. Results Using fumonisin biosynthesis as a model, we predicted that SAM biosynthetic gene clusters in fungi should include a polyketide synthase (PKS), an aminotransferase and a dehydrogenase gene. Surveys of genome sequences identified five putative clusters with this three-gene combination in 92 of 186 Fusarium species examined. Collectively, the putative SAM clusters were distributed widely but discontinuously among the species. We propose that the SAM5 cluster confers production of a previously reported Fusarium SAM, 2-amino-14,16-dimethyloctadecan-3-ol (AOD), based on the occurrence of AOD production only in species with the cluster and on deletion analysis of the SAM5 cluster PKS gene. We also identified SAM clusters in 24 species of other fungal genera, and propose that one of the clusters confers production of sphingofungin, a previously reported Aspergillus SAM. Conclusion Our results provide a genomics approach to identify novel SAM biosynthetic gene clusters in fungi, which should in turn contribute to identification of novel SAMs with applications in medicine and other fields. Information about novel SAMs could also provide insights into the role of SAMs in the ecology of fungi. Such insights have potential to contribute to strategies to reduce fumonisin contamination in crops and to control crop diseases caused by SAM-producing fungi.

Download Full-text

Characterization of the Nodularin Synthetase Gene Cluster and Proposed Theory of the Evolution of Cyanobacterial Hepatotoxins

Applied and Environmental Microbiology ◽

10.1128/aem.70.11.6353-6362.2004 ◽

2004 ◽

Vol 70 (11) ◽

pp. 6353-6362 ◽

Cited By ~ 169

Author(s):

Michelle C. Moffitt ◽

Brett A. Neilan

Keyword(s):

Gene Cluster ◽

Rational Design ◽

Polyketide Synthase ◽

Alternative Hypothesis ◽

Phylogenetic Analyses ◽

Cyanobacterial Bloom ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene ◽

Microcystin Synthetase

ABSTRACT Nodularia spumigena is a bloom-forming cyanobacterium which produces the hepatotoxin nodularin. The complete gene cluster encoding the enzymatic machinery required for the biosynthesis of nodularin in N. spumigena strain NSOR10 was sequenced and characterized. The 48-kb gene cluster consists of nine open reading frames (ORFs), ndaA to ndaI, which are transcribed from a bidirectional regulatory promoter region and encode nonribosomal peptide synthetase modules, polyketide synthase modules, and tailoring enzymes. The ORFs flanking the nda gene cluster in the genome of N. spumigena strain NSOR10 were identified, and one of them was found to encode a protein with homology to previously characterized transposases. Putative transposases are also associated with the structurally related microcystin synthetase (mcy) gene clusters derived from three cyanobacterial strains, indicating a possible mechanism for the distribution of these biosynthetic gene clusters between various cyanobacterial genera. We propose an alternative hypothesis for hepatotoxin evolution in cyanobacteria based on the results of comparative and phylogenetic analyses of the nda and mcy gene clusters. These analyses suggested that nodularin synthetase evolved from a microcystin synthetase progenitor. The identification of the nodularin biosynthetic gene cluster and evolution of hepatotoxicity in cyanobacteria reported in this study may be valuable for future studies on toxic cyanobacterial bloom formation. In addition, an appreciation of the natural evolution of nonribosomal biosynthetic pathways will be vital for future combinatorial engineering and rational design of novel metabolites and pharmaceuticals.

Download Full-text

Cloning and Characterization of the Biosynthetic Gene Cluster for Tomaymycin, an SJG-136 Monomeric Analog

Applied and Environmental Microbiology ◽

10.1128/aem.02325-08 ◽

2009 ◽

Vol 75 (9) ◽

pp. 2958-2963 ◽

Cited By ~ 65

Author(s):

Wei Li ◽

ShenChieh Chou ◽

Ankush Khullar ◽

Barbara Gerratana

Keyword(s):

Cluster Analysis ◽

Gene Cluster ◽

Biosynthetic Pathway ◽

Biosynthetic Gene Cluster ◽

Gene Replacement ◽

Biosynthetic Gene

ABSTRACT Tomaymycin produced by Streptomyces achromogenes is a naturally produced pyrrolobenzodiazepine (PBD). The biosynthetic gene cluster for tomaymycin was identified and sequenced. The gene cluster analysis reveals a novel biosynthetic pathway for the anthranilate moiety of PBDs. Gene replacement and chemical complementation studies were used to confirm the proposed biosynthetic pathway.

Download Full-text