Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica

Recent fermentation studies have identified actinomycetes of the marine-dwelling genus Salinispora as prolific natural product producers. To further evaluate their biosynthetic potential, we sequenced the 5,183,331-bp S. tropica CNB-440 circular genome and analyzed all identifiable secondary natural product gene clusters. Our analysis shows that S. tropica dedicates a large percentage of its genome ( approximately 9.9%) to natural product assembly, which is greater than previous Streptomyces genome sequences as well as other natural product-producing actinomycetes. The S. tropica genome features polyketide synthase systems of every known formally classified family, nonribosomal peptide synthetases, and several hybrid clusters. Although a few clusters appear to encode molecules previously identified in Streptomyces species, the majority of the 17 biosynthetic loci are novel. Specific chemical information about putative and observed natural product molecules is presented and discussed. In addition, our bioinformatic analysis not only was critical for the structure elucidation of the polyene macrolactam salinilactam A, but its structural analysis aided the genome assembly of the highly repetitive slm loci. This study firmly establishes the genus Salinispora as a rich source of drug-like molecules and importantly reveals the powerful interplay between genomic analysis and traditional natural product isolation studies.

Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora

Here we report associations between secondary metabolite production and phylogenetically distinct but closely related marine actinomycete species belonging to the genus Salinispora. The pattern emerged in a study that included global collection sites, and it indicates that secondary metabolite production can be a species-specific, phenotypic trait associated with broadly distributed bacterial populations. Associations between actinomycete phylotype and chemotype revealed an effective, diversity-based approach to natural product discovery that contradicts the conventional wisdom that secondary metabolite production is strain specific. The structural diversity of the metabolites observed, coupled with gene probing and phylogenetic analyses, implicates lateral gene transfer as a source of the biosynthetic genes responsible for compound production. These results conform to a model of selection-driven pathway fixation occurring subsequent to gene acquisition and provide a rare example in which demonstrable physiological traits have been correlated to the fine-scale phylogenetic architecture of an environmental bacterial community.

Marine actinomycetes as a source of novel secondary metabolites

A set of 600 actinomycetes strains which were isolated from marine sediments from various sites in the Pacific and Atlantic Oceans were screened for the production of bioactive secondary metabolites. Marine streptomycete strains were found to be producers of well known chemically diverse antibiotics isolated from terrestrial streptomycetes, as in the case of marine Micromonospora strains. New marine members of the rare genus Verrucosispora seem to be a promising source for novel bioactive secondary metabolites as shown in the case of the abyssomicin producing strain AB-18-032.

Biotechnology and molecular biology of the alpha-glucosidase inhibitor acarbose

The alpha-glucosidase inhibitor acarbose, O-[4,6-dideoxy-4[1 s-(1,4,6/5)-4,5,6-trihydroxy-3-hydroxymethyl-2-cyclohexen-1-yl]-amino-alpha-D-glucopyranosyl]-(1-->4)- O-alpha-D-glucopyranosyl-(1-->4)-D-glucopyranose, is produced in large-scale fermentation by the use of strains derived from Actinoplanes sp. SE50. It has been used since 1990 in many countries in the therapy of diabetes type II, in order to enable patients to better control blood sugar contents while living with starch-containing diets. Thus, it is one of the latest successful products of bacterial secondary metabolism to be introduced into the pharmaceutical world market. Cultures of Actinoplanes sp. also produce various other acarbose-like components, of which component C is hard to separate during downstream processing, which is one of the most modern work-up processes developed to date. The physiology, genetics and enzymology of acarbose biosynthesis and metabolism in the producer have been studied to some extent, leading to the proposal of a new pathway and metabolic cycle, the "carbophore". These data could give clues for further biotechnological developments, such as the suppression of side-products, enzymological or biocombinatorial production of new metabolites and the engineering of production rates via genetic regulation in future.

New Cytotoxic Salinosporamides from the Marine ActinomyceteSalinisporatropica

An extensive study of the secondary metabolites produced by the obligate marine actinomycete Salinispora tropica (strain CNB-392), the producing microbe of the potent proteasome inhibitor salinosporamide A (1), has led to the isolation of seven related gamma-lactams. The most important of these compounds were salinosporamide B (3), which is the deschloro-analogue of 1, and salinosporamide C (4), which is a decarboxylated pyrrole analogue. New SAR data for all eight compounds, derived from extensive testing against the human colon carcinoma HCT-116 and the 60-cell-line panel at the NCI, indicate that the chloroethyl moiety plays a major role in the enhanced activity of 1.

Isolation and characterization of novel marine-derived actinomycete taxa rich in bioactive metabolites

A unique selective enrichment procedure has resulted in the isolation and identification of two new genera of marine-derived actinobacteria. Approximately 90% of the microorganisms cultured by using the presented method were from the prospective new genera, a result indicative of its high selectivity. In this study, 102 actinomycetes were isolated from subtidal marine sediments collected from the Bismarck Sea and the Solomon Sea off the coast of Papua New Guinea. A combination of physiological parameters, chemotaxonomic characteristics, distinguishing 16S rRNA gene sequences, and phylogenetic analysis based on 16S rRNA genes provided strong evidence for the two new genera (represented by strains of the PNG1 clade and strain UMM518) within the family Micromonosporaceae. Biological activity testing of fermentation products from the new marine-derived actinomycetes revealed that several had activities against multidrug-resistant gram-positive pathogens, malignant cells, and vaccinia virus replication.

Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species

Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.

Organization of the teicoplanin gene cluster in Actinoplanes teichomyceticus

The glycopeptide teicoplanin is used for the treatment of serious infections caused by Gram-positive pathogens. The tcp gene cluster, devoted to teicoplanin biosynthesis in the actinomycete Actinoplanes teichomyceticus, was isolated and characterized. From sequence analysis, the tcp cluster spans approximately 73 kb and includes 39 ORFs participating in teicoplanin biosynthesis, regulation, resistance and export. Of these, 34 ORFs find a match in at least one of the five glycopeptide gene clusters previously characterized. Putative roles could be assigned for most of the tcp genes. The two glycosyltransferases responsible for attaching amino sugars to amino acids 4 and 6 of the teicoplanin aglycon were overexpressed in Escherichia coli and characterized. They both recognize N-acetylglucosamine as the substrate. tGtfA can add a sugar residue in the presence or absence of N-acetylglucosamine at amino acid 4, while tGtfB can only glycosylate the teicoplanin aglycon.

Degradation of keratin and collagen containing wastes by newly isolated thermoactinomycetes or by alkaline hydrolysis

AIMS

The aim of this study was to develop a method for microbial degradation of indigenous keratin wastes and to compare it with a method of alkaline hydrolysis.

METHODS AND RESULTS

Native sheep skin and wool were chosen as a model mixture of collagen and keratin wastes discarded by the leather and fur industries. Suitable conditions were found for hydrolysis of this mixture by four newly isolated thermoactinomycete strains. Another set of experiments was carried out using alkaline hydrolysis of keratin wastes. It was shown that microbial hydrolysates contained predominantly low molecular peptides and amino acids, including essential ones, while the alkaline hydrolysis produced predominantly peptides of higher molecular weight.

CONCLUSION

A simple and a low-cost method was proposed for rapid and effective biodegradation of keratin wastes using Thermoactinomyces strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

The proposed method could find application in agriculture for preparing mixtures containing valuable peptides and amino acids.

Non-Frankia actinomycetes isolated from surface-sterilized roots of Casuarina equisetifolia fix nitrogen

Based on partial 16S sequences, we previously described a novel group of nonsymbiotic, acetylene reduction activity-positive actinomycetes which were isolated from surface-sterilized roots of Casuarina equisetifolia growing in Mexico. An amplified rRNA restriction analysis confirmed that these actinomycetes are distinct from Frankia, a finding substantiated by a 16S rRNA gene phylogenetic analysis of two of the Mexican isolates. Further support for these actinomycetes being separate from Frankia comes from the very low DNA-DNA homology that was found. Nevertheless, the Mexican isolates may be diazotrophs based not only on their ability to grow in N-free medium and reduce acetylene to ethylene but also on the results from (15)N isotope dilution analysis and the finding that a nifH gene was PCR amplified. A comparison of the nifH sequences from the various isolates showed that they are closely related to nifH from Frankia; the similarity was 84 to 98% depending on the host specificity group. An analysis of complete 16S rRNA gene sequences demonstrated that the two strains analyzed in detail are most closely related to actinobacteria in the Thermomonosporaceae and the Micromonosporaceae.

Patterns of antimicrobial activities from soil actinomycetes isolated under different conditions of pH and salinity

AIMS

To evaluate the patterns of the production of antimicrobial compounds by diverse collection of actinomycetes isolated from different geographies under alternative conditions of pH and salinity in the media.

METHODS AND RESULTS

Actinomycetes were grouped based on their method of isolation and their phenotype diversity was determined by total fatty acid analysis. A total of 335 representative isolates, including 235 Streptomyces species and 100 actinomycetes from other taxa, were screened for the production of antimicrobial activities against a panel of bacteria, filamentous fungi and yeasts, including some of clinical relevance. Production of antimicrobial activities was detected in 230 strains. In the case of the genus Streptomyces, 181 antimicrobial activities (77% of the tested isolates) were recorded. The activities observed among the other actinomycetes taxa were lower (49% of the tested isolates).

CONCLUSIONS

The results of this study support the idea that species of actinomycetes isolated in alternative selective conditions of pH and salinity present a significant capacity to produce compounds with antibacterial or antifungal activity. The best group of isolates in terms of production of active secondary metabolites was the one isolated in saline conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results demonstrate that these actinomycetes strains isolated in alternative selective conditions of pH and salinity and collected from diverse geographical locations present a significant capacity to produce compounds with antibacterial or antifungal activity.

Biosynthetic convergence of salinosporamides A and B in the marine actinomycete Salinispora tropica

[structure: see text] Feeding experiments with stable isotopes established that the potent 20S-proteasome inhibitors salinosporamide A and B are biosynthesized in the marine bacterium Salinispora tropica from three biosynthetic building blocks, namely, acetate, beta-hydroxy-2'-cyclohexenylalanine, and either butyrate or a tetrose-derived chlorinated molecule. The unexpected observation that the chlorinated four-carbon residue in salinosporamide A is derived from a different metabolic origin than the non-chlorinated four-carbon unit in salinosporamide B is suggestive of a convergent biosynthesis to these two anticancer natural products.

Sequencing and analysis of the biosynthetic gene cluster of the lipopeptide antibiotic Friulimicin in Actinoplanes friuliensis

Actinoplanes friuliensis produces the lipopeptide antibiotic friulimicin, which is a cyclic peptide with one exocyclic amino acid linked to a branched-chain fatty acid acyl residue. The structural relationship to daptomycin and the excellent antibacterial performance of friulimicin make the antibiotic an attractive drug candidate. The complete friulimicin biosynthetic gene cluster of 24 open reading frames from A. friuliensis was sequenced and analyzed. In addition to genes for regulation, self-resistance, and transport, the cluster contains genes encoding peptide synthetases, proteins involved in the synthesis and linkage of the fatty acid component of the antibiotic, and proteins involved in the synthesis of the nonproteinogenic amino acids pipecolinic acid, methylaspartic acid, and 2,3-diaminobutyric acid. By using heterologous gene expression in Escherichia coli, we provide biochemical evidence for the stereoselective synthesis of L-pipecolinic acid by the deduced protein of the lysine cyclodeaminase gene pip. Furthermore, we show the involvement of the dabA and dabB genes in the biosynthesis of 2,3-diaminobutyric acid by gene inactivation and subsequent feeding experiments.

Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution

The X-ray crystal structures of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) and alpha-amylase 2 (TVAII) have been determined at 1.6 A and 2.3 A resolution, respectively. The structures of TVAI and TVAII have been refined, R-factor of 0.182 (R(free)=0.206) and 0.179 (0.224), respectively, with good chemical geometries. Both TVAI and TVAII have four domains, N, A, B and C, and all very similar in structure. However, there are some differences in the structures between them. Domain N of TVAI interacts strongly with domains A and B, giving a spherical shape structure to the enzyme, while domain N of TVAII is isolated from the other domains, which leads to the formation of a dimer. TVAI has three bound Ca ions, whereas TVAII has only one. TVAI has eight extra loops compared to TVAII, while TVAII has two extra loops compared to TVAI. TVAI can hydrolyze substrates more efficiently than TVAII with a high molecular mass such as starch, while TVAII is much more active against cyclodextrins than TVAI and other alpha-amylases. A structural comparison of the active sites has clearly revealed this difference in substrate specificity.

Polyester-degrading thermophilic actinomycetes isolated from different environment in Taiwan

Thermophilic actinomycetes strains were isolated from various environment in Taiwan and screened for degradation of poly(ethylene succinate) (PES), poly(epsilon-caprolactone) (PCL) and/or poly(beta-hydroxybutyrate) (PHB) by the clear-zone method. Out of 341 strains of thermophilic actinomycetes, 105 isolates were PHB-degraders (30.8%), 198 isolates were PCL-decomposers (58.1%), and 99 isolates could degrade PES (29.0%). Furthermore, 77 isolates could degrade both PHB and PCL (22.6%), 35 isolates could degrade both PHB and PES (10.3%), 81 isolates could degrade both PES and PCL (23.8%) and 31 isolates could degrade the three polyesters used in this study (9.1%). Base on the morphological and chemical characteristics, these 31 isolates belonging to Actinomadura (12.9%), Microbispora (25.8%), Streptomyces (48.4%), Thermoactinomyces (9.7%) and Saccharomonospora genus (3.22%).

Longispora albida gen. nov., sp. nov., a novel genus of the family Micromonosporaceae

A novel actinomycete strain was isolated from a soil sample collected in Japan by using gellan gum as a solidifying agent. Spore-chains from the short sporophores were straight and each had more than 20 spores per chain. Spores possessed no motility. Cell-wall peptidoglycan contained meso-diaminopimelic acid, glycine, alanine and glutamic acid; whole-cell hydrolysates contained arabinose, galactose and xylose. The acyl type of the peptidoglycan was glycolyl. The predominant menaquinones were MK-10(H(4)) and MK-10(H(6)); MK-10(H(8)) was a minor component. Mycolic acids were not detected. The diagostic phospholipid was phosphatidylethanolamine. Cellular fatty acids included heptadecenoic (C(17 : 1)), 14-methylpentadecanoic (i-C(16 : 0)) and octadecenoic (C(18 : 1)) acids. The G+C content of the DNA was 70 mol%. On the basis of morphogical and chemotaxonomic properties and phylogenetic analysis based on 16S rDNA sequence data, it is proposed that this strain should be classified in a novel genus and species, Longispora albida gen. nov., sp. nov., in the family MICROMONOSPORACEAE: The type strain is K97-0003(T) (=NRRL B-24201(T)=JCM 11711(T)).

A scheme for the identification of thermophilic actinomycetes associated with hypersensitivity pneumonitis

A scheme has been developed for the identification of thermophilic actinomycetes associated with hypersensitivity pneumonitis. Eighty strains, 10 Micropolyspora faeni, 6 Saccharomonospora viridis, 52 Thermoactinomyces candidus, 7 T. vulgaris, 4 T. sacchari, and 1 T. dichotomica, either isolated from patients' environment or received as authentic strains, were studied. In addition to the cultural and microscopic morphology in various media, each strain was subjected to an array of biochemical tests. These tests included decomposition of tyrosine, xanthine, hypoxanthine, gelatin, casein, esculin, and arbutin. Using a rapid thin-layer chromatography method, the isomer of diaminopimelic acid and sugar in the whole cell hydrolysate were studied. The thermophilic actinomycetes can be identified in a reasonable period of time using a combination of all these tests.

Luedemannella gen. nov., a new member of the family Micromonosporaceae and description of Luedemannella helvata sp. nov. and Luedemannella flava sp. nov

Three actinomycete strains were isolated from soil samples collected in Bangladesh. The cultures formed spherical sporangia on short sporangiophores directly above the surface of the substrate mycelium. The sporangia developed singly or in clusters and each sporangium contained several nonmotile spherical to oval spores with a smooth surface. The strains 3-9(24)(T), 3-21(27) and 7-40(26)(T) contained meso-diaminopimelic acid in the cell walls, predominant menaquinone MK-9(H(6)) and MK-9(H(4)) and glucose, xylose, galactose, mannose, rhamnose, ribose and arabinose in the whole-cell hydrolysates. Diagnostic phospholipid is phosphatidylethanolamine and branched anteiso-C(17 : 0) (30.0-38.0%), anteiso-C(15 : 0) (12.5-14.0%), iso-C(16 : 0) (10.0-15.0%) and iso-C(15 : 0) (10.0-12.0%) were detected as the major cellular fatty acids. The acyl type of the peptidoglycan was glycolyl and mycolic acids were not detected. The G+C content of the DNA was 71 mol%. The chemotaxonomic data indicate that these strains belong to the family Micromonosporaceae. Phylogenetic analysis based on 16S rRNA gene sequence data suggested that the strains 3-9(24)(T), 3-21(27) and 7-40(26)(T) fall within the family Micromonosporaceae. On the basis of phylogenetic analysis and characteristic patterns of signature nucleotides as well as morphological and chemotaxonomic data, Luedemannella gen. nov. is proposed for our 3 isolates. DNA-DNA hybridization experiment and phenotypic characterization indicated that the new genus was constituted of 2 species, as Luedemannella helvata sp. nov. for the strain 3-9(24)(T) (=JCM 13249(T)=MTCC 8091(T)) and Luedemannella flava for the strain 7-40(26)(T) (=JCM 13250(T)=MTCC 8095(T)) in the family Micromonosporaceae.

The pathway-specific regulatory genes, tei15* and tei16*, are the master switches of teicoplanin production in Actinoplanes teichomyceticus

Pathogenic antibiotic-resistant bacteria are an unprecedented threat to health care worldwide. The range of antibiotics active against these bacteria is narrow; it includes teicoplanin, a "last resort" drug, which is produced by the filamentous actinomycete Actinoplanes teichomyceticus. In this report, we determine the functions of tei15* and tei16*, pathway-specific regulatory genes that code for StrR- and LuxR-type transcriptional factors, respectively. The products of these genes are master switches of teicoplanin biosynthesis, since their inactivation completely abolished antibiotic production. We show that Tei15* positively regulates the transcription of at least 17 genes in the cluster, whereas the targets of Tei16* still remain unknown. Integration of tei15* or tei16* under the control of the aminoglycoside resistance gene aac(3)IV promoter into attBϕC31 site of the A. teichomyceticus chromosome increased teicoplanin productivity to nearly 1 g/L in TM1 industrial medium. The expression of these genes from the moderate copy number episomal vector pKC1139 led to 3-4 g/L teicoplanin, while under the same conditions, wild type produced approximately 100 mg/L. This shows that a significant increase in teicoplanin production can be achieved by a single step of genetic manipulation of the wild-type strain by increasing the expression of the tei regulatory genes. This confirms that natural product yields can be increased using rational engineering once suitable genetic tools have been developed. We propose that this new technology for teicoplanin overproduction might now be transferred to industrial mutants of A. teichomyceticus.

Discovering the recondite secondary metabolome spectrum of Salinispora species: a study of inter-species diversity

Patterns of inter-species secondary metabolite production by bacteria can provide valuable information relating to species ecology and evolution. The complex nature of this chemical diversity has previously been probed via directed analyses of a small number of compounds, identified through targeted assays rather than more comprehensive biochemical profiling approaches such as metabolomics. Insights into ecological and evolutionary relationships within bacterial genera can be derived through comparative analysis of broader secondary metabolite patterns, and this can also eventually assist biodiscovery search strategies for new natural products. Here, we investigated the species-level chemical diversity of the two marine actinobacterial species Salinispora arenicola and Salinispora pacifica, isolated from sponges distributed across the Great Barrier Reef (GBR), via their secondary metabolite profiles using LC-MS-based metabolomics. The chemical profiles of these two species were obtained by UHPLC-QToF-MS based metabolic profiling. The resultant data were interrogated using multivariate data analysis methods to compare their (bio)chemical profiles. We found a high level of inter-species diversity in strains from these two bacterial species. We also found rifamycins and saliniketals were produced exclusively by S. arenicola species, as the main secondary metabolites differentiating the two species. Furthermore, the discovery of 57 candidate compounds greatly increases the small number of secondary metabolites previously known to be produced by these species. In addition, we report the production of rifamycin O and W, a key group of ansamycin compounds, in S. arenicola for the first time. Species of the marine actinobacteria harbour a much wider spectrum of secondary metabolites than suspected, and this knowledge may prove a rich field for biodiscovery as well as a database for understanding relationships between speciation, evolution and chemical ecology.

Mg-2,4-divinyl pheoporphyrin a5: the product of a reaction catalyzed in vitro by developing chloroplasts

The major product of an aerobic reaction mixture containing developing chloroplasts, Mg-protoporphyrin IX, S-adenosylmethionine, and other cofactors was isolated and purified. Structural studies using nuclear magnetic resonance confirmed earlier reports, based on fluorescence and absorption spectra, that this compound is Mg-2,4-divinyl pheoporphyrin a5. The molecular weight determined by secondary-ion mass spectroscopy further confirmed the assigned structure. Absorption and fluorescence spectra indicate that this compound is identical to that reported previously by various workers in less-purified biological extracts. The nuclear magnetic resonance spectrum of the Mg-free base also supports the assigned structure.

Epoxidation of aldrin to exo-dieldrin by soil bacteria

Twenty-two strains of soil bacteria, including representatives of the genera Bacillus, Micromonospora, Mycobacterium, Nocardia, Streptomyces, Thermoactinomyces, and Pseudomonas and 10 unidentified gram-negative, motile, rod-shaped bacteria, were shown to degrade aldrin to its epoxide dieldrin. In every case, the exo-stereoisomer of dieldrin was produced exclusively.

Cochinmicins, novel and potent cyclodepsipeptide endothelin antagonists from a Microbispora sp. II. Structure determination

Cochinmicins I, II, and III are competitive endothelin antagonists produced by Microbispora sp. ATCC 55140. The cochinmicins are cyclic depsipeptides containing six alpha-amino acids and a pyrrolecarboxylic acid. Based upon MS, 1D and 2D NMR, and LC data, the structures and absolute stereochemistries of the cochinmicins have been assigned. All three components have the same basic sequence and contain one equivalent each of D-allo-threonine, D-alanine, L-phenylalanine, D-phenylalanine, 5-chloropyrrole-2-carboxylic acid (or pyrrole-2-carboxylic acid in cochinmicin I), plus two equivalents of 3,5-dihydroxyphenylglycine (DHPG). The phenylalanine residues were differentiated via a methanolysis product which contained only one of the phenylalanine residues. Both DHPG residues have the D configuration in the more active cochinmicins I and III. Cochinmicin II contains both D- and L-DHPG and these residues have been differentiated in the sequence based upon 1H NMR data.

Catenulobactins A and B, Heterocyclic Peptides from Culturing Catenuloplanes sp. with a Mycolic Acid-Containing Bacterium

The production of two new heterocyclic peptide isomers, catenulobactins A (1) and B (2), in cultures of Catenuloplanes sp. RD067331 was significantly increased when it was cocultured with a mycolic acid-containing bacterium. The planar structures and absolute configurations of the catenulobactins were determined based on NMR/MS and chiral-phase GC-MS analyses. Catenulobactin B (2) displayed Fe(III)-chelating activity and moderate cytotoxicity against P388 murine leukemia cells.