July 7, 2019  |  

The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island.

The complete genome sequence of the original isolate of the model actinomycete Streptomyces lividans 66, also referred to as 1326, was deciphered after a combination of next-generation sequencing platforms and a hybrid assembly pipeline. Comparative analysis of the genomes of S. lividans 66 and closely related strains, including S. coelicolor M145 and S. lividans TK24, was used to identify strain-specific genes. The genetic diversity identified included a large genomic island with a mosaic structure, present in S. lividans 66 but not in the strain TK24. Sequence analyses showed that this genomic island has an anomalous (G + C) content, suggesting recent acquisition and that it is rich in metal-related genes. Sequences previously linked to a mobile conjugative element, termed plasmid SLP3 and defined here as a 94 kb region, could also be identified within this locus. Transcriptional analysis of the response of S. lividans 66 to copper was used to corroborate a role of this large genomic island, including two SLP3-borne “cryptic” peptide biosynthetic gene clusters, in metal homeostasis. Notably, one of these predicted biosynthetic systems includes an unprecedented nonribosomal peptide synthetase–tRNA-dependent transferase biosynthetic hybrid organization. This observation implies the recruitment of members of the leucyl/phenylalanyl-tRNA-protein transferase family to catalyze peptide bond formation within the biosynthesis of natural products. Thus, the genome sequence of S. lividans 66 not only explains long-standing genetic and phenotypic differences but also opens the door for further in-depth comparative genomic analyses of model Streptomyces strains, as well as for the discovery of novel natural products following genome-mining approaches.


July 7, 2019  |  

Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis.

Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.


July 7, 2019  |  

Genome sequence of Streptomyces sp. H-KF8, a marine actinobacterium isolated from a northern Chilean Patagonian fjord.

Streptomyces sp. H-KF8 is a fjord-derived marine actinobacterium capable of producing antimicrobial activity. Streptomyces sp. H-KF8 was isolated from sediments of the Comau fjord, located in the northern Chilean Patagonia. Here, we report the 7.7-Mb genome assembly, which represents the first genome of a Chilean marine actinobacterium. Copyright © 2017 Undabarrena et al.


July 7, 2019  |  

Plant growth-promoting effect and genomic analysis of the beneficial endophyte Streptomyces sp. KLBMP 5084 isolated from halophyte Limonium sinense

Background and aims: Soil salinity is a worldwide environmental problem that can hinder plant development and therefore negatively impact crop production. Inoculation of halophytic plants with plant growth-promoting (PGP) actinobacteria has been suggested as one strategy to improve salt tolerance. Here we performed a glasshouse experiment to test the effect of a PGP halotolerant endophytic actinomycete strain, KLBMP 5084 on the performance of the halophyte Limonium sinense under conditions of salt stress. Methods: Strain KLBMP 5084 was identified and screened for multiple PGP traits. The complete genome of strain KLBMP 5084 was sequenced and analyzed. L. sinense control seedlings (no inoculation) and seedlings inoculated with KLBMP 5084 were given different NaCl (0, 100 and 250 mM) salt-stress treatments. Growth parameters and physiological responses of L. sinense were determined after harvest. Results: Compared with the control, plants inoculated with strain KLBMP 5084 had greater in fresh weight, root length, leaf length and total chlorophyll and proline contents under both normal and high salinity conditions. Compared with control, inoculated plants had significantly lower leaf malondialdehyde (MDA) content and significantly more antioxidant enzymes. Moreover, inoculated plants had significantly lower accumulation of Na+ in both leaves and roots under high salt-stress conditions. Genomic analysis of strain KLBMP 5084 revealed many PGP related genes, including some genes putatively involved in salt tolerance and harsh environment adaptation. Conclusion: Strain KLBMP 5084 seems to confer salt tolerance to host plant L. sinense through more than one mechanism, suggesting KLBMP 5084 could be a strong PGP agent to improve plant yields and tolerance to salinity stress.


July 7, 2019  |  

Complete genome sequencing of Streptomyces sp. strain MOE7, which produces an extracellular polysaccharide with antioxidant and antitumor activities.

Streptomyces sp. strain MOE7 is a Gram-positive filamentous bacterium isolated from agricultural soil in Columbia, Missouri, USA. Strain MOE7 produces an extracellular polysaccharide with antioxidant and antitumor activities. Through PacBio RSII sequencing, the MOE7 genome was found to be a linear chromosome of 8,399,509 bp with 6,782 protein-coding sequences. Copyright © 2017 Elnahas et al.


July 7, 2019  |  

Genome sequences for Streptomyces spp. isolated from disease-suppressive soils and long-term ecological research sites.

We report here the high-quality genome sequences of three Streptomyces spp. isolated as part of a long-term study of microbial soil ecology. Streptomyces sp. strain GS93-23 was isolated from naturally disease-suppressive soil (DSS) in Grand Rapids, MN, and Streptomyces sp. strains S3-4 and 3211-3 were isolated from experimental plots in the Cedar Creek Ecosystem Science Reserve (CCESR). Copyright © 2017 Heinsch et al.


July 7, 2019  |  

Identification and characterization of a biosynthetic gene cluster for tryptophan dimers in deep sea-derived Streptomyces sp. SCSIO 03032.

Tryptophan dimers (TDs) are an important class of natural products with diverse bioactivities and share conserved biosynthetic pathways. We report the identification of a partial gene cluster (spm) responsible for the biosynthesis of a class of unusual TDs with non-planar skeletons including spiroindimicins (SPMs), indimicins (IDMs), and lynamicins (LNMs) from the deep-sea derived Streptomyces sp. SCSIO 03032. Bioinformatics analysis, targeted gene disruptions, and heterologous expression studies confirmed the involvement of the spm gene cluster in the biosynthesis of SPM/IDM/LNMs, and revealed the indispensable roles for the halogenase/reductase pair SpmHF, the amino acid oxidase SpmO, and the chromopyrrolic acid (CPA) synthase SpmD, as well as the positive regulator SpmR and the putative transporter SpmA. However, the spm gene cluster was unable to confer a heterologous host the ability to produce SPM/IDM/LNMs. In addition, the P450 enzyme SpmP and the monooxygenase SpmX2 were found to be non-relevant to the biosynthesis of SPM/IDM/LNMs. Sequence alignment and structure modeling suggested the lack of key conserved amino acid residues in the substrate-binding pocket of SpmP. Furthermore, feeding experiments in the non-producing ?spmO mutant revealed several biosynthetic precursors en route to SPMs, indicating that key enzymes responsible for the biosynthesis of SPMs should be encoded by genes outside of the identified spm gene cluster. Finally, the biosynthetic pathways of SPM/IDM/LNMs are proposed to lay a basis for further insights into their intriguing biosynthetic machinery.


July 7, 2019  |  

Identification of a gene cluster for telomestatin biosynthesis and heterologous expression using a specific promoter in a clean host.

Telomestatin, a strong telomerase inhibitor with G-quadruplex stabilizing activity, is a potential therapeutic agent for treating cancers. Difficulties in isolating telomestatin from microbial cultures and in chemical synthesis are bottlenecks impeding the wider use. Therefore, improvement in telomestatin production and structural diversification are required for further utilization and application. Here, we discovered the gene cluster responsible for telomestatin biosynthesis, and achieved production of telomestatin by heterologous expression of this cluster in the engineered Streptomyces avermitilis SUKA strain. Utilization of an optimal promoter was essential for successful production. Gene disruption studies revealed that the tlsB, tlsC, and tlsO-T genes play key roles in telomestatin biosynthesis. Moreover, exchanging TlsC core peptide sequences resulted in the production of novel telomestatin derivatives. This study sheds light on the expansion of chemical diversity of natural peptide products for drug development.


July 7, 2019  |  

Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants.

We report a new Streptomyces species named S. formicae that was isolated from the African fungus-growing plant-ant Tetraponera penzigi and show that it produces novel pentacyclic polyketides that are active against MRSA and VRE. The chemical scaffold of these compounds, which we have called the formicamycins, is similar to the fasamycins identified from the heterologous expression of clones isolated from environmental DNA, but has significant differences that allow the scaffold to be decorated with up to four halogen atoms. We report the structures and bioactivities of 16 new molecules and show, using CRISPR/Cas9 genome editing, that biosynthesis of these compounds is encoded by a single type 2 polyketide synthase biosynthetic gene cluster in the S. formicae genome. Our work has identified the first antibiotic from the Tetraponera system and highlights the benefits of exploring unusual ecological niches for new actinomycete strains and novel natural products.


July 7, 2019  |  

Identification of three homologous latex-clearing protein (lcp) genes from the genome of Streptomyces sp. strain CFMR 7.

Rubber materials have greatly contributed to human civilization. However, being a polymeric material does not decompose easily, it has caused huge environmental problems. On the other hand, only few bacteria are known to degrade rubber, with studies pertaining them being intensively focusing on the mechanism involved in microbial rubber degradation. The Streptomyces sp. strain CFMR 7, which was previously confirmed to possess rubber-degrading ability, was subjected to whole genome sequencing using the single molecule sequencing technology of the PacBio® RS II system. The genome was further analyzed and compared with previously reported rubber-degrading bacteria in order to identify the potential genes involved in rubber degradation. This led to the interesting discovery of three homologues of latex-clearing protein (Lcp) on the chromosome of this strain, which are probably responsible for rubber degrading activities. Genes encoding oxidoreductase a-subunit (oxiA) and oxidoreductase ß-subunit (oxiB) were also found downstream of two lcp genes which are located adjacent to each other. In silico analysis reveals genes that have been identified to be involved in the microbial degradation of rubber in the Streptomyces sp. strain CFMR 7. This is the first whole genome sequence of a clear-zone-forming natural rubber- degrading Streptomyces sp., which harbours three Lcp homologous genes with the presence of oxiA and oxiB genes compared to the previously reported Gordonia polyisoprenivorans strain VH2 (with two Lcp homologous genes) and Nocardia nova SH22a (with only one Lcp gene). Copyright © 2017. Published by Elsevier B.V.


July 7, 2019  |  

Draft genome sequence of Streptomyces scabrisporus NF3, an endophyte isolated from Amphipterygium adstringens.

We report the draft genome sequence of Streptomyces scabrisporus NF3, an endophyte isolated from Amphipterygium adstringens in Chiapas, Mexico. This strain produces a new modified linaridin peptide. The genome harbors at least 50 gene clusters for synthases of polyketide and nonribosomal peptides, suggesting a prospective production of various secondary metabolites. Copyright © 2017 Vazquez-Hernandez et al.


July 7, 2019  |  

Complete genome sequence of a natural compounds producer, Streptomyces violaceus S21.

The complete genome sequence of Streptomyces violaceus strain S21, a valuable natural compounds producer isolated from the forest soil, is firstly presented here. The genome comprised 7.91M bp, with a G + C content of 72.65%. A range of genes involved in pathways of secondary product biosynthesis were predicted. The genome sequence is available at DDBJ/EMBL/Genbank under the accession number CP020570. This genome is annotated with 6856 predicted genes identifying the natural product biosynthetic gene clusters in S. violaceus.


July 7, 2019  |  

Comparative genomic and regulatory analyses of natamycin production of Streptomyces lydicus A02.

Streptomyces lydicus A02 is used by industry because it has a higher natamycin-producing capacity than the reference strain S. natalensis ATCC 27448. We sequenced the complete genome of A02 using next-generation sequencing platforms, and to achieve better sequence coverage and genome assembly, we utilized single-molecule real-time (SMRT) sequencing. The assembled genome comprises a 9,307,519-bp linear chromosome with a GC content of 70.67%, and contained 8,888 predicted genes. Comparative genomics and natamycin biosynthetic gene cluster (BGC) analysis showed that BGC are highly conserved among evolutionarily diverse strains, and they also shared closer genome evolution compared with other Streptomyces species. Forty gene clusters were predicted to involve in the secondary metabolism of A02, and it was richly displayed in two-component signal transduction systems (TCS) in the genome, indicating a complex regulatory systems and high diversity of metabolites. Disruption of the phoP gene of the phoR-phoP TCS and nsdA gene confirmed phosphate sensitivity and global negative regulation of natamycin production. The genome sequence and analyses presented in this study provide an important molecular basis for research on natamycin production in Streptomyces, which could facilitate rational genome modification to improve the industrial use of A02.


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