Isolation and In-Silico Analysis of the Polyketide Synthase (PKS) Gene Fragment from Actinobacteria Kocuria palustris 19C38A1

DOI

10.2991/978-94-6463-730-4_23How to use a DOI?

Keywords

polyketide synthase (PKS); gene; fragment; Kocuria palustris 19C38A1; in silico analysis

Abstract

Marine sponges also known with able to produce antibiotic compounds which are widely used medically, but unfortunatelly they are difficult to cultivate en masse, so symbiont microbes that can be obtained from sponge tissue such as actinobacteria are utilized. One of marine sponge actinobacteria symbiont that has been successfully cultured is Kocuria palustris 19C38A1 which reported able to inhibit the growth of pathogenic fungi, characterized by the polyketide synthase (PKS) gene. This research was carried out to isolate and carry out in silico expression analysis to the PKS gene fragment from the marine actinobacteria Kocuria palustris 19C38A1, began with culturing and rejuvenating the culture of Kocuria palustris 19C38A1 isolates using ISP-2 media. Continued by observing microscopically, DNA extraction, gene amplification by PCR using specially designed specific primers, visualization by electrophoresis, and sequencing of the PKS 2 gene. The sequencing results were analyzed using BIOEDIT software and continued by characterizing the expression/conformation in silico via the NCBI website. The similarities were analyzed to look for matches with the deposited PKS genes in the UNIPROT database. Furthermore, the ligand binding domain is predicted using the conformation that has been deposited in the PUBCHEM database using SWISSMODEL. Through ORFFINDER, 3 potential regions coding for a protein were found, namely ORF1 (498 nt), ORF2 (447 nt), and ORF3 (84 nt). It was discovered that only the ORF 1 region was confirmed have 53.74% similarity to the Multidrugs Efflux gene RND Transporter Permease Subunit of Shewanella oneidensis bacteria (ID: WP_011073987.1).

Copyright

© 2025 The Author(s)

Open Access

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TY  - CONF
AU  - Wawan Abdullah Setiawan
AU  - Bambang Irawan
AU  - Kusuma Handayani
AU  - Fitria Salsabila Adna
AU  - Adinda Nurulita Putri
AU  - Andi Setiawan
PY  - 2025
DA  - 2025/05/27
TI  - Isolation and In-Silico Analysis of the Polyketide Synthase (PKS) Gene Fragment from Actinobacteria Kocuria palustris 19C38A1
BT  - Proceedings of the 5th International Conference on Applied Sciences, Mathematics, and Informatics (ICASMI 2024)
PB  - Atlantis Press
SP  - 263
EP  - 279
SN  - 2352-541X
UR  - https://doi.org/10.2991/978-94-6463-730-4_23
DO  - 10.2991/978-94-6463-730-4_23
ID  - Setiawan2025
ER  -