Complete genome sequencing and in silico genome mining reveal the promising metabolic potential in Streptomyces strain CS-7

Alam, Khorshed; Hao, Jinfang; Zhong, Liang; Fan, G. J.; Ouyang, Qi; Islam, Md. Manirul; Islam, Shofiq; Sun, Hongluan; Zhang, Youming; Li, Ruijuan; Li, Aiying

doi:10.3389/fmicb.2022.939919

Cited by 12 publications

(8 citation statements)

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“…An increasing understanding of high-quality genome sequencing and genome mining techniques coupled with the introduction of powerful computational toolkits facilitates the process of connecting these gene clusters with key compounds (Li et al, 2016 ). Comparing the traditional method for the identification of biosynthetic gene clusters by using MS and NMR-based, in silico genome mining has become a crucial strategy for the discovery and characterization of gene clusters (Alam et al, 2022 ). Many web portals contain databases and tools to identify the metabolites by using BLAST, Diamond, and HMMer alignment tools.…”

Section: Strategy To Discover Lichen Natural Productsmentioning

confidence: 99%

Discovery and excavation of lichen bioactive natural products

et al. 2023

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Lichen natural products are a tremendous source of new bioactive chemical entities for drug discovery. The ability to survive in harsh conditions can be directly correlated with the production of some unique lichen metabolites. Despite the potential applications, these unique metabolites have been underutilized by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability, and technical challenges involved in their artificial cultivation. At the same time, DNA sequence data have revealed that the number of encoded biosynthetic gene clusters in a lichen is much higher than in natural products, and the majority of them are silent or poorly expressed. To meet these challenges, the one strain many compounds (OSMAC) strategy, as a comprehensive and powerful tool, has been developed to stimulate the activation of silent or cryptic biosynthetic gene clusters and exploit interesting lichen compounds for industrial applications. Furthermore, the development of molecular network techniques, modern bioinformatics, and genetic tools is opening up a new opportunity for the mining, modification, and production of lichen metabolites, rather than merely using traditional separation and purification techniques to obtain small amounts of chemical compounds. Heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offer a promising means for a sustainable supply of specialized metabolites. In this review, we summarized the known lichen bioactive metabolites and highlighted the application of OSMAC, molecular network, and genome mining-based strategies in lichen-forming fungi for the discovery of new cryptic lichen compounds.

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Section: Strategy To Discover Lichen Natural Productsmentioning

confidence: 99%

Discovery and excavation of lichen bioactive natural products

et al. 2023

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“…Edison et al [31] used in-silico analysis in structural elucidation. Some researchers used comparative genomics in their studies [32][33][34][35][36][37]. Kumar et al [38] used in vitro and insilico analysis using machine learning in their studies.…”

Section: Streptomyces Lividans -Streptomyces Coelicolor Andmentioning

confidence: 99%

Novel Drug Development for Treatment of COVID-19 by In Silico Analysis: Identification of SARS-Cov-2 Inhibiting Streptomyces Compounds

Kumar

Gholap

Pillai

2023

Journal of Cellular Signaling

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In accordance with the present epidemiological paradigm, viral mutations of the virus are on the rise, and their natural effects are being selected for at a higher rate than normal. According to the World Health Organization (WHO), the global COVID-19 pandemic induced by the Delta and Omicron strain of the SARS-CoV-2 virus could propagate and disseminate more rapidly than other viruses thanks to its many mutations, and these also caused some very significant health problems. The established medications would eventually start to lose their efficacy since the variation mutated more quickly than the original stain. As protein spikes are the point of origin or epitome for the mutations to take place, it would be most effective to target the remaining vital enzymes by binding the proteins with the largest pocket sizes. The objective of the current work is to employ in-silico analysis to discover the streptomyces chemicals that suppress the SARS-CoV-2 virus as well as its mutated strains thus promoting a healthy body. Based on the drug likeness property of compounds when subjected to molecular docking, a total of 14 compounds were identified and selected from the PUBCHEM database that showed highest binding energy with the targeted Receptor Binding Domain. The compounds namely - Streptomyces tanashiensis; Thaxtomin A; Bafilomycin A1 from Streptomyces griseus and few others as mentioned further on more research would support and confirm the utilizing of these to create new medications to treat the novel SARS-CoV-2 infectious strains.

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“…This underscores the pivotal role played by the Streptomyces genus in bolstering plant defense mechanisms and their widespread recognition for their biocontrol potential. These bioactive compounds are synthesized by biosynthetic gene clusters (BGCs) comprising genes closely arranged within the bacterial genomes (Zhang et al, 1997;Laiple et al, 2009;Naughton et al, 2017;Alam et al, 2022). Streptomyces not only produce antibiotics but also yield antifungal, antiparasitic, antiviral, anti-tumoral, and immunosuppressive analogs and other essential secondary metabolites (Alam et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

“…13273) (Kamiyama and Kaziro, 1966). Chromomycins, olivomycins, chromocyclomycin, mithramycin, UCH9, and durhamycin A belong to the class of antitumor compounds known as aureolic acids (Alam et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Streptomyces tagetis sp. nov., a chromomycin producing bacteria isolated from the roots of Tagetes patula

Chhetri,

Kim,

Kim

et al. 2024

Front. Microbiol.

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A novel halotolerant actinobacterium, designated as RG38T, capable of producing black extracellular melanin pigment on SP2 agar, was isolated from the roots of Tagetes patula. Comparative analysis of the 16S rRNA gene sequence revealed the highest similarity to Streptomyces collinus NBRC 12759T (99.3%). Phylogenetic analysis showed that strain RG38T clustered within the genus Streptomyces forming a monophyletic cluster with its close relatives. The average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), and amino-acid identity (AAI) values between strain RG38T and related species within the genus Streptomyces were below the standard threshold for prokaryotic species delineation. The DNA G + C content of the strain RG38T was determined to be 73.3%. The genome size measured 7,150,598 bp comprising 17 contigs and encompassed 6,053 protein coding genes. AntiSMASH analysis of the whole genome revealed 35 putative biosynthetic gene clusters (BGCs) responsible for various secondary metabolites. Among these clusters, two gene clusters exhibited 100% similarity to the chromomycin A3, albaflavenone, and anthracimycin, respectively. These compounds were reported to possess significant anticancer and antibacterial activities. LC–MS-based analysis, coupled with further isolation studies, confirmed the production of chromomycins A2 (1), A3 (2), and their derivatives, along with their antibiotic activities. These findings underscore the potential of this novel strain as a novel resource for the discovery of diverse antimicrobial compounds. This study is the first to report an antimicrobial compound producing Streptomyces species isolated from medicinal plant T. patula. Based on a polyphasic study, the strain RG38T isolated from an unexplored habitat with a high potential for new natural products represents a novel species within the genus Streptomyces. Accordingly, we propose the name Streptomyces tagetis sp. nov. for this novel species, with the type strain is RG38T (=KCTC 49624T = TBRC 15113T).

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Complete genome sequencing and in silico genome mining reveal the promising metabolic potential in Streptomyces strain CS-7

Cited by 12 publications

References 100 publications

Discovery and excavation of lichen bioactive natural products

Discovery and excavation of lichen bioactive natural products

Novel Drug Development for Treatment of COVID-19 by In Silico Analysis: Identification of SARS-Cov-2 Inhibiting Streptomyces Compounds

Streptomyces tagetis sp. nov., a chromomycin producing bacteria isolated from the roots of Tagetes patula

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