Complete genome of Streptomyces hygroscopicus subsp. limoneus KCTC 1717 (=KCCM 11405), a soil bacterium producing validamycin and diverse secondary metabolites

Lee, Sang-Heon; Choe, Hanna; Bae, Kyung Sook; Park, Doo-Sang; Nasir, Arshan; Kim, Kyung Mo

doi:10.1016/j.jbiotec.2015.12.010

Cited by 8 publications

(6 citation statements)

References 10 publications

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“…The %G+C mean content is 71.77 +/− 0.81, which is an expected characteristic of members of the phylum Actinobacteria ( Supplementary Figure S2 ; Dhakal et al, 2017 ). Most strains have a unique chromosome, although notably, the strain S. hygroscopicus limoneus KCTC 1717 has two chromosomes ( Lee et al, 2016 ); all strains contain between one and four plasmids. Supplementary File S1 comprises all the metadata collected i.e., it contains the information of genome accession numbers, sequencing platform, coverage, and other genomic features such as the number of tRNAs and rRNAs in each genome.…”

Section: Resultsmentioning

confidence: 99%

Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds

2021

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Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.

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Section: Resultsmentioning

confidence: 99%

Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds

2021

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“…Interestingly, we could not localize S. mobaraensis -like orthologues in the genomes of S. lavendulae subsp. lavendulae and S. hygroscopicus that should be closely related to the early characterized chymostatin-producing strains. ,− The most related genes that we found are available in transglutaminase-producing streptoverticillia, S. olivoreticuli and S. rimosus subsp. rimosus (Table S3).…”

Section: Discussionmentioning

confidence: 82%

Decoding the Papain Inhibitor from Streptomyces mobaraensis as Being Hydroxylated Chymostatin Derivatives: Purification, Structure Analysis, and Putative Biosynthetic Pathway

et al. 2020

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Streptomyces mobaraensis produces the papain inhibitor SPI consisting of a 12 kDa protein and small active compounds (SPI ac ). Purification of the papain inhibitory compounds resulted in four diverse chymostatin derivatives that were characterized by NMR and MS analysis. Chymostatins are hydrophobic tetrapeptide aldehydes from streptomycetes, e.g., S. lavendulae and S. hygroscopicus, that reverse chymosin-mediated angiotensin activation and inhibit other serine and cysteine proteases. Chymotrypsin and papain were both inhibited by the SPI ac compounds in the low nanomolar range. SPI ac differs from the characterized chymostatins by the exchange of phenylalanine for tyrosine. The crystal structure of one of these chymostatin variants confirmed its molecular structure and revealed a S-configured hemithioacetal bond with the catalytic Cys25 thiolate as well as close interactions with hydrophobic S1 and S2 subsite amino acids. A model for chymostatin biosynthesis is provided based on the discovery of clustered genes encoding several putative nonribosomal peptide synthetases; among them, there is the unusual CstF enzyme that accommodates two canonical amino acid activation domains as well as three peptide carrier protein domains.

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“…The 16s rDNA sequencing and phylogenetic analysis conducted on the isolates in this study revealed that several of the most suppressive bacteria belonged to the Streptomyces genus, and grouped with species that have been successfully developed as biocontrol products in the past. MH71 and MH243 clustered with Streptomyces hygroscopicus , which produces a range of antibiotics including for some strains rapamycin, nigericin and validamycin ( Lee et al, 2016 ; Yoo et al, 2017 ) and S. lydicus , which has been commercialized for the control of plant fungal pathogens as Actinovate (Novazymes BioAg Ltd) ( Chen et al, 2016 ). MH191 and MH192 clustered with S. griseoviridus , commercialized as a plant antifungal called Mycostop ( Sabaratnam and Traquair, 2002 ), and S. grisaurantiacus , which produces the antibacterial compound diperamycin ( Matsumoto et al, 1998 ).…”

Section: Discussionmentioning

confidence: 99%

Developing Actinobacterial Endophytes as Biocontrol Products for Fusarium pseudograminearum in Wheat

O’Sullivan

Roper

Myers

et al. 2021

Front. Bioeng. Biotechnol.

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Crown rot of wheat, caused by Fusarium pseudograminearum, results in millions of dollars of yield losses globally each year. Management strategies to control crown rot are limited and there are concerns about development of fungicide resistance so novel treatment strategies are desirable. A collection of endophytic Actinobacteria was screened for their ability to suppress the growth of F. pseudograminearum and the development of crown rot symptoms in wheat with the aim of identifying candidates that can be developed into biocontrol products. The ability of the Actinobacteria isolates to suppress the growth of three different F. pseudograminearum strains in vitro was assessed using agar-plate competition assays. Soil-free seedling assays were used to screen for suppression of development of early disease symptoms in the susceptible wheat (Triticum aestivum) cv. Tamaroi. Four of the isolates were tested in a glasshouse pot experiment to assess their ability to decrease disease symptoms and prevent yield losses in wheat cv. Tamaroi grown to maturity in an unsterilized soil. The screening of 53 isolates identified two Streptomyces isolates, MH71 and MH243, with very strong antifungal activity against F. pseudograminearum strains in agar-plate competition and seedling assays. In the glasshouse pot trial, plants treated with seed coatings of either MH71 or MH243 had > 24% lower disease severity than control plants infected with F. pseudograminearum. These two cultures show potential for development as biocontrol products because they are easy to culture, grow on relatively inexpensive media, produce highly durable spores and can be delivered to plants as a seed coat.

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Complete genome of Streptomyces hygroscopicus subsp. limoneus KCTC 1717 (=KCCM 11405), a soil bacterium producing validamycin and diverse secondary metabolites

Cited by 8 publications

References 10 publications

Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds

Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds

Decoding the Papain Inhibitor from Streptomyces mobaraensis as Being Hydroxylated Chymostatin Derivatives: Purification, Structure Analysis, and Putative Biosynthetic Pathway

Developing Actinobacterial Endophytes as Biocontrol Products for Fusarium pseudograminearum in Wheat

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