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New Report: Genome Mining Untaps the Antibiotics Biosynthetic Gene Cluster of Pseudoalteromonas xiamenensis STKMTI.2 from a Mangrove Soil Sediment

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Abstract

The marine bacterium Pseudoalteromonas xiamenensis STKMTI.2 was isolated from a mangrove soil sediment on Setokok Island, Batam, Indonesia. The genome of this bacterium consisted of 4,563,326 bp (GC content: 43.2%) with 1 chromosome, 2 circular plasmids, 2 linear plasmids, 4,824 protein-coding sequences, 25 rRNAs, 104 tRNAs, 4 ncRNAs, and 1 clustered, regularly interspaced, short palindromic repeated (CRISPR). This strain possessed cluster genes which are responsible for the production of brominated marine pyrroles/phenols (bmp), namely, bmp8 and bmp9. Other gene clusters responsible for the synthesis of secondary metabolites were identified using antiSMASH and BAGEL4, which yielded five results, namely, non-ribosomal peptides, polyketide-like butyrolactone, Lant class I, and RiPP-like, detected in chromosome 1, while prodigiosin was detected in the unnamed plasmid 5. This suggests that these whole genome data will be of remarkable importance for the improved understanding of the biosynthesis of industrially important bioactive and antibacterial compounds produced by P. xiamenensis STKMTI.2.

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Data Availability

The following is information regarding the deposition of whole-genome sequences:

The complete genome sequence has been deposited at GenBank under the following accession number Chromosome 1 (CP072133.1); Plasmid Unnamed1 (CP072131.1); Plasmid Unnamed2 (CP072132.1); Plasmid Unnamed4 (CP072134.1); and Plasmid Unnamed5 (CP072135.1), BioProject PRJNA716124, and Biosample SAMN18395665. The raw sequencing reads have been deposited in the SRA under accession number SRR14179988.

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Funding

Part of the work in this research was financially supported by the Global Alliance for TB Drug Development (TB ALLIANCE), PMDSU program of the KEMENRISTEKDIKTI Republic of Indonesia, and KRUPT program of the KEMENRISTEKDIKTI Republic of Indonesia (contract number: 3847/UN1/DITLIT/DIT-LIT/PT/2020).

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Authors and Affiliations

  1. Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia

    Desy Putri Handayani, Alim Isnansetyo & Indah Istiqomah

  2. Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia

    Jumina Jumina

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  1. Desy Putri Handayani
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  2. Alim Isnansetyo
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Contributions

Desy Putri Handayani: designed the experiment method, conducted the experiments, prepared the figures and/or tables, analyzed the data, and wrote the paper. Alim Isnansetyo: prepared and submitted a proposal for the research grant, designed the experiment method, analyzed the data, reviewed the paper, and approved for the final draft. Indah Istiqomah: analyzed the data, reviewed the paper, and gave approval for the final draft. Jumina: reviewed the paper and approved the final draft.

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Correspondence to Alim Isnansetyo.

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Handayani, D.P., Isnansetyo, A., Istiqomah, I. et al. New Report: Genome Mining Untaps the Antibiotics Biosynthetic Gene Cluster of Pseudoalteromonas xiamenensis STKMTI.2 from a Mangrove Soil Sediment. Mar Biotechnol 24, 190–202 (2022). https://doi.org/10.1007/s10126-022-10096-1

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