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Antonie Van Leeuwenhoek Dec 2020A putative novel clade within the genus Streptomyces was discovered following antifungal screening against Pseudogymnoascus destructans, the causative agent of...
A putative novel clade within the genus Streptomyces was discovered following antifungal screening against Pseudogymnoascus destructans, the causative agent of white-nose syndrome, and described using multi-locus sequencing analysis. Swabs from both the cave myotis bat (Myotis velifer) and the Brazilian free-tailed bat (Tadarida brasiliensis) in southern New Mexico bore isolates AC536, AC541 and AC563, which were characterised using phylogenetic, morphological, and phenotypic analyses. Multi-locus sequence analysis positions AC541 with neighbors Streptomyces rubidus (NRRL B-24619), Streptomyces guanduensis (NRRL B-24617), and Streptomyces yeochonensis (NRRL B-24245). A complete genome of the type strain was assembled to determine its taxonomy and secondary metabolite potential. ANI comparisons between all closely related types strains are shown to be well below the 95-96% species delineation. DNA-DNA relatedness between AC541 and its nearest neighbors ranged between 23.7 and 24.1% confirming novelty. Approximately 1.49 Mb or 17.76% of the whole genome is devoted to natural product biosynthesis. The DNA G + C content of the genomic DNA of the type strain is 73.13 mol %. Micromorphology depicts ovoid spores with smooth surfaces in flexuous chains. Strains presented an ivory to yellow hue on most ISP media except inorganic salts-starch agar (ISP4) and can grow on D-glucose, mannitol, and D-fructose, but exhibited little to no growth on L-arabinose, sucrose, D-xylose, inositol, L-rhamnose, D-raffinose, and cellulose. This clade possesses the capability to grow from 10 to 45 °C and 12.5% (w/v) NaCl. There was strain growth variation in pH, but all isolates thrive at alkaline levels. Based on our polyphasic study of AC541, the strain warrants the assignment to a novel species, for which the name Streptomyces buecherae sp. nov. is proposed. The type strain is AC541 (= JCM 34263, = ATCC TSD201).
Topics: Animals; Ascomycota; Bacterial Typing Techniques; Base Composition; Chiroptera; DNA, Bacterial; New Mexico; Phylogeny; Sequence Analysis, DNA; Streptomyces
PubMed: 33200278
DOI: 10.1007/s10482-020-01493-4 -
Biosynthesis Gene Cluster and Oxazole Ring Formation Enzyme for Inthomycins in sp. Strain SYP-A7193.Applied and Environmental Microbiology Oct 2020Inthomycins belong to a growing family of oxazole-containing polyketides and exhibit a broad spectrum of anti-oomycete and herbicidal activities. In this study, we...
Inthomycins belong to a growing family of oxazole-containing polyketides and exhibit a broad spectrum of anti-oomycete and herbicidal activities. In this study, we purified inthomycins A and B from the metabolites of sp. strain SYP-A7193 and determined their chemical structures. Genome sequencing, comparative genomic analysis, and gene disruption of sp. SYP-A7193 showed that the inthomycin biosynthetic gene cluster () belonged to the hybrid polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) system. Functional domain comparison and disruption/complementation experiments of resulted in the complete loss of inthomycins A and B and the subsequent restoration of their production, confirming that encodes a discrete acyltransferase (AT), and hence, was considered to belong to the -AT type I PKS system. Moreover, the disruption/complementation experiments of also resulted in the loss and restoration of inthomycin A and B formation. Further gene cloning, expression, purification, and activity verification of revealed that Itm15 is a cyclodehydratase that catalyzes a straight-chain dehydration reaction to form an oxazole ring for the biosynthesis of inthomycins A and B. Thus, we discovered a novel enzyme that catalyzes oxazole ring formation and elucidated the complete biosynthetic pathway of inthomycins. species produce numerous secondary metabolites with diverse structures and pharmacological activities that are beneficial for human health and have several applications in agriculture. In this study, hybrid nonribosomal peptide synthetase/polyketide synthase metabolites inthomycins A and B were isolated from after fermenting sp. SYP-A7193. Genome sequencing, gene disruption, gene complementation, heterologous expression, and activity assay revealed that the biosynthesis gene assembly line of inthomycins A and B was a 95.3-kb -AT type I PKS system in the strain SYP-A7193. More importantly, Itm15, a cyclodehydratase, was identified to be an oxazole ring formation enzyme required for the biosynthesis of inthomycins A and B; it is significant to discover this catalyzation reaction in the PKS/NRPS system in the field of microbiology. Our findings could provide further insights into the diversity of -AT type I PKS systems and the mechanism of oxazole cyclization involved in the biosynthesis of natural products.
Topics: Fatty Acids, Unsaturated; Genes, Bacterial; Multigene Family; Oxazoles; Streptomyces
PubMed: 32801183
DOI: 10.1128/AEM.01388-20 -
Journal of Natural Products Feb 2024Marine-derived have long been recognized as a source of novel, pharmaceutically relevant natural products. Among these bacteria, the MAR4 clade within the genus has... (Review)
Review
Marine-derived have long been recognized as a source of novel, pharmaceutically relevant natural products. Among these bacteria, the MAR4 clade within the genus has been identified as metabolically rich, yielding over 93 different compounds to date. MAR4 strains are particularly noteworthy for the production of halogenated hybrid isoprenoid natural products, a relatively rare class of bacterial metabolites that possess a wide range of biological activities. MAR4 genomes are enriched in vanadium haloperoxidase and prenyltransferase genes, thus accounting for the production of these compounds. Functional characterization of the enzymes encoded in MAR4 genomes has advanced our understanding of halogenated, hybrid isoprenoid biosynthesis. Despite the exceptional biosynthetic capabilities of MAR4 bacteria, the large body of research they have stimulated has yet to be compiled. Here we review 35 years of natural product research on MAR4 strains and update the molecular diversity of this unique group of bacteria.
Topics: Streptomyces; Biological Products; Terpenes; Multigene Family
PubMed: 38353658
DOI: 10.1021/acs.jnatprod.3c01007 -
Polish Journal of Microbiology Jun 2021is a genus with known biocontrol activity, producing a broad range of biologically active substances. Our goal was to isolate local species, evaluate their capacity to...
is a genus with known biocontrol activity, producing a broad range of biologically active substances. Our goal was to isolate local species, evaluate their capacity to biocontrol the selected phytopathogens, and promote the plant growth via siderophore and indole acetic acid (IAA) production and phosphate solubilization. Eleven isolates were obtained from local soil samples in Saudi Arabia via the standard serial dilution method and identified morphologically by scanning electron microscope (SEM) and 16S rRNA amplicon sequencing. The biocontrol of phytopathogens was screened against known soil-borne fungi and bacteria. Plant growth promotion capacity was evaluated based on siderophore and IAA production and phosphate solubilization capacity. From eleven isolates obtained, one showed 99.77% homology with the type strain AS 4.1867, and was designated strain HM10. It showed aerial hyphae in SEM, growth inhibition of ten known phytopathogens in experiments, and the production of plant growth promoting compounds such as siderophores, IAA, and phosphate solubilization capacity. strain HM10 exhibited high antagonism against the fungi tested (i.e., with an inhibition zone exceeding 18 mm), whereas the lowest antagonistic effect was against (an inhibition zone equal to 8 mm). Furthermore, the most efficient siderophore production was recorded to strain HM8, followed by strain HM10 with 64 and 22.56 h/c (halo zone area/colony area), respectively. Concerning IAA production, strain HM10 was the most effective producer with a value of 273.02 μg/ml. An autochthonous strain HM10 should be an important biological agent to control phytopathogens and promote plant growth.
Topics: Bacteria; Bacterial Physiological Phenomena; Fungi; Microbial Interactions; Plants; Saudi Arabia; Streptomyces
PubMed: 34349814
DOI: 10.33073/pjm-2021-023 -
Proceedings of the National Academy of... Nov 2003In this article we briefly review theories about the ecological roles of microbial secondary metabolites and discuss the prevalence of multiple secondary metabolite... (Review)
Review
In this article we briefly review theories about the ecological roles of microbial secondary metabolites and discuss the prevalence of multiple secondary metabolite production by strains of Streptomyces, highlighting results from analysis of the recently sequenced Streptomyces coelicolor and Streptomyces avermitilis genomes. We address this question: Why is multiple secondary metabolite production in Streptomyces species so commonplace? We argue that synergy or contingency in the action of individual metabolites against biological competitors may, in some cases, be a powerful driving force for the evolution of multiple secondary metabolite production. This argument is illustrated with examples of the coproduction of synergistically acting antibiotics and contingently acting siderophores: two well-known classes of secondary metabolite. We focus, in particular, on the coproduction of beta-lactam antibiotics and beta-lactamase inhibitors, the coproduction of type A and type B streptogramins, and the coregulated production and independent uptake of structurally distinct siderophores by species of Streptomyces. Possible mechanisms for the evolution of multiple synergistic and contingent metabolite production in Streptomyces species are discussed. It is concluded that the production by Streptomyces species of two or more secondary metabolites that act synergistically or contingently against biological competitors may be far more common than has previously been recognized, and that synergy and contingency may be common driving forces for the evolution of multiple secondary metabolite production by these sessile saprophytes.
Topics: Anti-Bacterial Agents; Ecosystem; Evolution, Molecular; Multigene Family; Siderophores; Streptomyces
PubMed: 12970466
DOI: 10.1073/pnas.1934677100 -
Chembiochem : a European Journal of... Mar 2023The gene cluster in Streptomyces calvus associated with the biosynthesis of the fluoro- and sulfamyl-metabolite nucleocidin was interrogated by systematic gene...
The gene cluster in Streptomyces calvus associated with the biosynthesis of the fluoro- and sulfamyl-metabolite nucleocidin was interrogated by systematic gene knockouts. Out of the 26 gene deletions, most did not affect fluorometabolite production, nine abolished sulfamylation but not fluorination, and three precluded fluorination, but had no effect on sulfamylation. In addition to nucI, nucG, nucJ, nucK, nucL, nucN, nucO, nucQ and nucP, we identified two genes (nucW nucA), belonging to a phosphoadenosine phosphosulfate (PAPS) gene cluster, as required for sulfamyl assembly. Three genes (orf(-3), orf2 and orf3) were found to be essential for fluorination, although the activities of their protein products are unknown. These genes as well as nucK, nucN, nucO and nucPNP, whose knockouts produced results differing from those described in a recent report, were also deleted in Streptomyces virens - with confirmatory outcomes. This genetic profile should inform biochemistry aimed at uncovering the enzymology behind nucleocidin biosynthesis.
Topics: Streptomyces; Multigene Family
PubMed: 36548247
DOI: 10.1002/cbic.202200684 -
Environmental Monitoring and Assessment Dec 2014Both Streptomyces species and mold species have previously been isolated from moisture-damaged building materials; however, an association between these two groups of...
Both Streptomyces species and mold species have previously been isolated from moisture-damaged building materials; however, an association between these two groups of microorganisms in indoor environments is not clear. In this study, we used a culture-independent method, PCR-denaturing gradient gel electrophoresis (PCR-DGGE), to investigate the composition of the Streptomyces community in house dust. Twenty-three dust samples each from two sets of homes categorized as high-mold and low-mold based on mold-specific quantitative PCR analysis were used in the study. Taxonomic identification of prominent bands was performed by cloning and sequencing. Associations between DGGE amplicon band intensities and home mold status were assessed using univariate analyses as well as multivariate recursive partitioning (decision trees) to test the predictive value of combinations of bands intensities. In the final classification tree, a combination of two bands was significantly associated with mold status of the home (p = 0.001). The sequence corresponding to one of the bands in the final decision tree matched a group of Streptomyces species that included Streptomyces coelicolor and Streptomyces sampsonii, both of which have been isolated from moisture-damaged buildings previously. The closest match for the majority of sequences corresponding to a second band consisted of a group of Streptomyces species that included Streptomyces hygroscopicus, an important producer of antibiotics and immunosuppressors. Taken together, the study showed that DGGE can be a useful tool for identifying bacterial species that may be more prevalent in mold-damaged buildings.
Topics: Air Microbiology; Air Pollution, Indoor; Denaturing Gradient Gel Electrophoresis; Dust; Environmental Monitoring; Fungi; Polymerase Chain Reaction; Streptomyces
PubMed: 25331035
DOI: 10.1007/s10661-014-4071-4 -
World Journal of Microbiology &... Sep 2021Filamentous microorganisms are potent sources of bioactive secondary metabolites, the molecules formed in response to complex environmental signals. The chemical... (Review)
Review
Filamentous microorganisms are potent sources of bioactive secondary metabolites, the molecules formed in response to complex environmental signals. The chemical diversity encoded in microbial genomes is only partially revealed by following the standard microbiological approaches. Mimicking the natural stimuli through laboratory co-cultivation is one of the most effective methods of awakening the formation of high-value metabolic products. Whereas the biosynthetic outcomes of co-cultures are reviewed extensively, the bioprocess aspects of such efforts are often overlooked. The aim of the present review is to discuss the submerged co-cultivation strategies used for triggering and enhancing secondary metabolites production in Streptomyces, a heavily investigated bacterial genus exhibiting an impressive repertoire of secondary metabolites, including a vast array of antibiotics. The previously published studies on influencing the biosynthetic capabilities of Streptomyces through co-cultivation are comparatively analyzed in the bioprocess perspective, mainly with the focus on the approaches of co-culture initiation, the experimental setup, the design of experimental controls and the ways of influencing the outcomes of co-cultivation processes. These topics are discussed in the general context of secondary metabolites production in submerged microbial co-cultures by referring to the Streptomyces-related studies as illustrative examples.
Topics: Biological Products; Coculture Techniques; Secondary Metabolism; Streptomyces
PubMed: 34490503
DOI: 10.1007/s11274-021-03141-z -
Antonie Van Leeuwenhoek Sep 2017A polyphasic study was undertaken to establish the taxonomic status of Streptomyces strains isolated from hyper-arid Atacama Desert soils. Analysis of the 16S rRNA gene...
A polyphasic study was undertaken to establish the taxonomic status of Streptomyces strains isolated from hyper-arid Atacama Desert soils. Analysis of the 16S rRNA gene sequences of the isolates showed that they formed a well-defined lineage that was loosely associated with the type strains of several Streptomyces species. Multi-locus sequence analysis based on five housekeeping gene alleles showed that the strains form a homogeneous taxon that is closely related to the type strains of Streptomyces ghanaensis and Streptomyces viridosporus. Representative isolates were shown to have chemotaxonomic and morphological properties consistent with their classification in the genus Streptomyces. The isolates have many phenotypic features in common, some of which distinguish them from S. ghanaensis NRRL B-12104, their near phylogenetic neighbour. On the basis of these genotypic and phenotypic data it is proposed that the isolates be recognised as a new species within the genus Streptomyces, named Streptomyces asenjonii sp. nov. The type strain of the species is KNN35.1b (NCIMB 15082 = NRRL B-65050). Some of the isolates, including the type strain, showed antibacterial activity in standard plug assays. In addition, MLSA, average nucleotide identity and phenotypic data show that the type strains of S. ghanaensis and S. viridosporus belong to the same species. Consequently, it is proposed that the former be recognised as a heterotypic synonym of the latter and an emended description is given for S. viridosporus.
Topics: Amino Acids; Anti-Bacterial Agents; Chile; Desert Climate; Diaminopimelic Acid; Fatty Acids; Genome, Bacterial; Multilocus Sequence Typing; Phenotype; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Soil Microbiology; Species Specificity; Streptomyces; Sugars
PubMed: 28589342
DOI: 10.1007/s10482-017-0886-7 -
BMC Microbiology Oct 2011Streptomyces species are a major source of antibiotics. They usually grow slowly at their optimal temperature and fermentation of industrial strains in a large scale...
Development of a gene cloning system in a fast-growing and moderately thermophilic Streptomyces species and heterologous expression of Streptomyces antibiotic biosynthetic gene clusters.
BACKGROUND
Streptomyces species are a major source of antibiotics. They usually grow slowly at their optimal temperature and fermentation of industrial strains in a large scale often takes a long time, consuming more energy and materials than some other bacterial industrial strains (e.g., E. coli and Bacillus). Most thermophilic Streptomyces species grow fast, but no gene cloning systems have been developed in such strains.
RESULTS
We report here the isolation of 41 fast-growing (about twice the rate of S. coelicolor), moderately thermophilic (growing at both 30°C and 50°C) Streptomyces strains, detection of one linear and three circular plasmids in them, and sequencing of a 6996-bp plasmid, pTSC1, from one of them. pTSC1-derived pCWH1 could replicate in both thermophilic and mesophilic Streptomyces strains. On the other hand, several Streptomyces replicons function in thermophilic Streptomyces species. By examining ten well-sporulating strains, we found two promising cloning hosts, 2C and 4F. A gene cloning system was established by using the two strains. The actinorhodin and anthramycin biosynthetic gene clusters from mesophilic S. coelicolor A3(2) and thermophilic S. refuineus were heterologously expressed in one of the hosts.
CONCLUSIONS
We have developed a gene cloning and expression system in a fast-growing and moderately thermophilic Streptomyces species. Although just a few plasmids and one antibiotic biosynthetic gene cluster from mesophilic Streptomyces were successfully expressed in thermophilic Streptomyces species, we expect that by utilizing thermophilic Streptomyces-specific promoters, more genes and especially antibiotic genes clusters of mesophilic Streptomyces should be heterologously expressed.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Cloning, Molecular; Gene Expression; Hot Temperature; Multigene Family; Streptomyces
PubMed: 22032628
DOI: 10.1186/1471-2180-11-243