Potential secondary metabolite biosynthetic gene clusters and antibacterial activity of novel taxa Gandjariella

Abstract

Abstract. Ningsih F, Sari DCAF, Yabe S, Yokota A, Sjamsuridzal W. 2020. Potential secondary metabolite biosynthetic gene clusters and antibacterial activity of novel taxa Gandjariella. Biodiversitas 21: 5674-5684. Microbial resistance to available antibiotics has gained increasing attention in recent years and led to the urgent search for active secondary metabolites from novel microbial taxa. This study aimed to assess putative secondary metabolite biosynthetic gene clusters (BGCs) in the genome of a novel thermophilic Actinobacteria type strain Gandjariella thermophila SL3-2-4T and screen for its antibacterial activity. Four other related novel candidate Actinobacteria strains, isolated from forest soil in the Cisolok geothermal area (West Java, Indonesia), were also screened for antibacterial activity in various media solidified with gellan gum. The genome of the SL3-2-4T strain contained 21 antiSMASH-identified secondary metabolite regions harboring BGCs. These BGCs were for polyketide synthase, non-ribosomal peptide synthase, and ribosomally synthesized and post-translationally modified peptide family clusters. Three BGC regions displayed 50-100% similarity with known secondary metabolites. Thirteen and five regions displayed low (4-35%) and no similarity with known BGCs for secondary metabolites, respectively. Strains SL3-2-4T and SL3-2-7 on MM 2 medium solidified with gellan gum at 45 °C for 14 days demonstrated inhibitory activity against all Gram-positive, but not Gram-negative bacteria. Strain SL3-2-10 on ISP 3 gellan gum medium incubated for seven days only active against K. rhizophila NBRC 12078. Strains SL3-2-6 and SL3-2-9 did not exhibit any antibacterial activity against the tested bacterial strains on the three tested media. The results indicated that novel taxa have the potential for the discovery of active secondary metabolites.

A Novel Carotenoid-Producing Bacterium, Paenibacillus aurantius sp. nov., Isolated from Korean Marine Environment

“…Furthermore, the genome of strain MBLB1776 T had six BGCs for secondary metabolites, including the genes for ectoine, lassopeptide, LAP, and T3PKS, as well as two distinct terpene clusters (Table 4). The ectoine BGC shared 75.0% cluster similarity with Streptomyces chrysomallus ATCC 11523 T (GenBank: AY524544), the lassopeptide BGC shared 80.0% cluster similarity with the paeninodin BGC of Paenibacillus dendritiformis C454 (GenBank: AHKH01000064), and one terpene BGC shared 33.0% cluster similarity with the carotenoid BGC of Halobacillus halophilus DSM 2266 T (GeneBank: FJ040212) [41][42][43]. Overall, genome analysis and secondary metabolite annotation provided a comprehensive characterization of the genetic content of strain MBLB1776 T , offering insights into its potential biological functions and ability to produce secondary metabolites.…”

Detection of Antimicrobial Compounds From Thermophilic Actinomycetes Using One Strain Many Compounds (Osmac) Approach

“…The OSMAC is still considered an effective approach that can induce silent (Lind et al, 2016;Keller, 2019). The genome sequence of strain SL3-2-4 T was also analyzed using the antiSMASH and successfully revealed the presence of low and no-similarity BGCs compared with published known clusters which suggested the high potential of strain SL3-2-4 T to produce novel bioactive compounds (Ningsih et al, 2020).…”

“…et al, 2017).Modificationof the media composition using the OSMAC approach for the discovery of new metabolites from actinomycetes that have potential as antimicrobials has been carried out byNingsih et al, (2020). The study was conducted using rare thermophilic actinomycete, Gandjariella thermophila SL3-2-4 T , and its closely related strains SL3-2-6, SL3-2-7, SL3-2-9, and SL3-2-10.The five strain were obtained from theforest soil under the bamboo trees in Cisolok geothermal area, West Java, Indonesia.…”