Showing papers on "Salinispora arenicola published in 2008"

Biosynthesis and structures of cyclomarins and cyclomarazines, prenylated cyclic peptides of marine actinobacterial origin.

Abstract: Two new diketopiperazine dipeptides, cyclomarazines A and B, were isolated and characterized along with the new cyclic heptapeptide cyclomarin D from the marine bacterium Salinispora arenicola CNS-205. These structurally related cyclic peptides each contain modified amino acid residues, including derivatives of N-(1,1-dimethylallyl)-tryptophan and delta-hydroxyleucine, which are common in the di- and heptapeptide series. Stable isotope incorporation studies in Streptomyces sp. CNB-982, which was first reported to produce the cyclomarin anti-inflammatory agents, illuminated the biosynthetic building blocks associated with the major metabolite cyclomarin A, signifying that this marine microbial peptide is nonribosomally derived largely from nonproteinogenic amino acid residues. DNA sequence analysis of the 5.8 Mb S. arenicola circular genome and PCR-targeted gene inactivation experiments identified the 47 kb cyclomarin/cyclomarazine biosynthetic gene cluster (cym) harboring 23 open reading frames. The cym locus is dominated by the 23 358 bp cymA, which encodes a 7-module nonribosomal peptide synthetase (NRPS) responsible for assembly of the full-length cyclomarin heptapeptides as well as the truncated cyclomarazine dipeptides. The unprecedented biosynthetic feature of the megasynthetase CymA to synthesize differently sized peptides in vivo may be triggered by the level of beta oxidation of the priming tryptophan residue, which is oxidized in the cyclomarin series and unoxidized in the cyclomarazines. Biosynthesis of the N-(1,1-dimethyl-2,3-epoxypropyl)-beta-hydroxytryptophan residue of cyclomarin A was further illuminated through gene inactivation experiments, which suggest that the tryptophan residue is reverse prenylated by CymD prior to release of the cyclic peptide from the CymA megasynthetase, whereas the cytochrome P450 CymV installs the epoxide group on the isoprene of cyclomarin C post-NRPS assembly. Last, the novel amino acid residue 2-amino-3,5-dimethylhex-4-enoic acid in the cyclomarin series was shown by bioinformatics and stable isotope experiments to derive from a new pathway involving condensation of isobutyraldehyde and pyruvate followed by S-adenosylmethionine methylation. Assembly of this unsaturated, branched amino acid is unexpectedly related to the degradation of the environmental pollutant 3-(3-hydroxyphenyl)propionic acid.

S-Adenosyl-L-Methionine Hydrolase (Adenosine-Forming), a Conserved Bacterial and Archeal Protein Related to SAM-Dependent Halogenases

Abstract: S-Adenosyl-L-methionine (SAM) is a ubiquitous molecule that participates in various biochemical reactions, second only to ATP as the most frequently used enzyme substrate.[1] The recently described SAM-dependent halogenases involved in the biosynthesis of secondary metabolites in actinomycetes represent a new family of SAM-binding proteins[2, 3] that catalyze the nucleophilic displacement of L-methionine (L-met) from SAM with halides to form halogenated 5′-deoxyadenosine (5′-XDA).[4, 5] These enzymes belong to a family of over 100 archaeal and bacterial proteins with no assigned function (pfam 01887, DUF62). Here we report that a DUF62 member from the recently sequenced marine bacterium Salinispora arenicola CNS-205 (SaDUF62, Sare_1364, genome accession number NC_ 009953) has no significant halogenase, but instead SAM hydrolase (adenosine-forming) activity in vitro.

Phylogenetic diversity of Gram -positive bacteria and their secondary metabolite genes

Abstract: To assess the bacterial diversity of marine sediments, a culture-dependent approach was employed to assess the diversity of Gram-positive bacteria in marine sediments collected around the islands of Palau. The survey of the total, aerobic Gram-positive bacterial diversity present in tropical marine sediments resulted in the isolation of a diverse assemblage of Gram-positive isolates. Of the 78 operational taxonomic units cultured (OTUs based on ≥ 98% 16S rRNA gene sequence identity), 52 were determined to be members of the order Actinomycetales and 26 were determined to be members of the order Bacillales. Bacterial genome sequencing has provided opportunities to assess the secondary metabolite biosynthetic potential of individual strains. By elucidating entire biosynthetic pathways in the context of all other genes and pathways present, it is also possible to address questions related to the evolution of gene clusters or individual genes within a cluster. The complete genome sequence of Salinispora arenicola strain CNS-205, an actinomycete isolated during the research expedition to Palau, provided an opportunity to investigate the evolution of type I modular polyketide synthase (PKS) gene clusters. While a tremendous amount can be learned from analyzing the entire genetic blueprint of a microorganism, additional natural product discovery approaches are necessary to gain insight into the biosynthetic potential of unsequenced organisms prior to fermentation, extraction and chemical analyses. A PCR based approach has been used successfully to suggest which representative isolates from the 52 Actinomycetales OTUs harbor type I PKS, enediyne PKS and nonribosomal peptide synthetase (NRPS) pathways. Over half of the cultured Actinomycetales OTUs were found to possess genes associated with at least one PKS or NRPS biosynthetic pathway and although some of these actinomycetes represent families well known to produce secondary metabolites, the results suggest that novel secondary metabolites can be isolated from both filamentous and unicellular actinomycete families. In addition to determining if these pathways are present, a phylogenetic approach was used successfully to suggest the number and novelty of type I PKS pathways present. By using the phylogenetic approach, the diversity, novelty and identity of type I PKS metabolites can be predicted.

The First Total Synthesis of Emericellamide A.

Abstract: A highly convergent asymmetric total synthesis of emericellamide A, a 19-membered antibacterial depsipeptide isolated from the co-culture of an Emericella sp. (strain CNL-878) and a Salinispora arenicola (strain CNH-665) is described.