Draft Genome Sequence of
            <i>Streptomyces</i>
            sp. Strain C8S0, Isolated from a Highly Oligotrophic Sediment

Gallegos-Lopez, S.; Mejía-Ponce, Paulina M.; González-Salazar, Luz Ángela; Rodríguez-Orduña, Lorena; Souza, Valeria

doi:10.1128/mra.01441-19

Cited by 2 publications

(4 citation statements)

References 11 publications

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“…The soils of the Cuatro Cienegas Basin are characterized by a extremely unbalanced N:P (157 : 1) soil stoichiometry, and rich sulfur, magnesium and calcium sulfate concentrations [71]. It has previously been shown that these conditions conserve a great diversity of endemic microbes with novel biosynthetic potential [32, 72]. For instance, our research group has previously described new diversity in desferrioxamine siderophores (propionyl-ferrioxamine, m / z =628.17; aryl-ferrioxamine, m / z =690.26) in species of Microbacterium , Micrococcus and Streptomyces [33].…”

Section: Discussionmentioning

confidence: 99%

“…CC55 and Actinokineospora sp. PR83 were isolated from the Cuatro Cienegas Basin, as previously reported [ 32 ]. Lentzea sp.…”

Section: Methodsmentioning

confidence: 99%

“…This ecosystem shows a nutrient imbalance in nitrogen-to-phosphorus stoichiometry (N:P 157 : 1), with a high calcium accumulation rising from 35 to 90 % across the microbialite matrix [30,31]. Nutrient limitation, for example, the extremely low concentrations of phosphate and iron, generates the environmental conditions to modulate unique metabolic traits in diverse microbial communities [32][33][34]. Evidence of the potential for novel chemical diversity in the Cuatro Cienegas Basin was reported in two strains of Micrococcus sp.…”

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confidence: 99%

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Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments

et al. 2023

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Calculations predict that testing of 5 000–10 000 molecules and >1 billion US dollars (£0.8 billion, £1=$1.2) are required for one single drug to come to the market. A solution to this problem is to establish more efficient protocols that reduce the high rate of re-isolation and continuous rediscovery of natural products during early stages of the drug development process. The study of ‘rare actinobacteria’ has emerged as a possible approach for increasing the discovery rate of drug leads from natural sources. Here, we define a simple genomic metric, defined as biosynthetic novelty index (BiNI), that can be used to rapidly rank strains according to the novelty of the subset of encoding biosynthetic clusters. By comparing a subset of high-quality genomes from strains of different taxonomic and ecological backgrounds, we used the BiNI score to support the notion that rare actinobacteria encode more biosynthetic gene cluster (BGC) novelty. In addition, we present the isolation and genomic characterization, focused on specialized metabolites and phenotypic screening, of two isolates belonging to genera Lentzea and Actinokineospora from a highly oligotrophic environment. Our results show that both strains harbour a unique subset of BGCs compared to other members of the genera Lentzea and Actinokineospora . These BGCs are responsible for potent antimicrobial and cytotoxic bioactivity. The experimental data and analysis presented in this study contribute to the knowledge of genome mining analysis in rare actinobacteria and, most importantly, can serve to direct sampling efforts to accelerate early stages of the drug discovery pipeline.

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Section: Discussionmentioning

confidence: 99%

“…CC55 and Actinokineospora sp. PR83 were isolated from the Cuatro Cienegas Basin, as previously reported [ 32 ]. Lentzea sp.…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments

et al. 2023

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“…23 Environmental strains were isolated from Cuatro Cienegas Basin, and eight strains from Calakmul in Mexico. Genome sequences were obtained using methods previously reported (Gallegos-Lopez et al, 2020). On the other hand, nine genomes of strains isolated from various locations in Chile (4 from Valparaiso, 4 from Comau Fjord, Huinay and 1 from Penas Gulf) were also included.…”

Section: Genome Sequencesmentioning

confidence: 99%

Phylogenetic classification of natural product biosynthetic gene clusters based on regulatory mechanisms

Rodriguez-Sanchez,

Gónzalez-Salazar,

Rodriguez-Orduña

et al. 2023

Front. Microbiol.

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The natural products (NPs) biosynthetic gene clusters (BGCs) represent the adapting biochemical toolkit for microorganisms to thrive different microenvironments. Despite their high diversity, particularly at the genomic level, detecting them in a shake-flask is challenging and remains the primary obstacle limiting our access to valuable chemicals. Studying the molecular mechanisms that regulate BGC expression is crucial to design of artificial conditions that derive on their expression. Here, we propose a phylogenetic analysis of regulatory elements linked to biosynthesis gene clusters, to classify BGCs to regulatory mechanisms based on protein domain information. We utilized Hidden Markov Models from the Pfam database to retrieve regulatory elements, such as histidine kinases and transcription factors, from BGCs in the MIBiG database, focusing on actinobacterial strains from three distinct environments: oligotrophic basins, rainforests, and marine environments. Despite the environmental variations, our isolated microorganisms share similar regulatory mechanisms, suggesting the potential to activate new BGCs using activators known to affect previously characterized BGCs.

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Draft Genome Sequence of Streptomyces sp. Strain C8S0, Isolated from a Highly Oligotrophic Sediment

Cited by 2 publications

References 11 publications

Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments

Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments

Phylogenetic classification of natural product biosynthetic gene clusters based on regulatory mechanisms

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