Analisis bioinformatik gen pensintesis poly gamma glutamic acid pada genom Bacillus subtilis IFP1.1 = Bioinformatic analysis of poly gamma glutamic acid synthesis in genom Bacillus subtilis IFP1.1

Karema, Anastasia Veronica (2020) Analisis bioinformatik gen pensintesis poly gamma glutamic acid pada genom Bacillus subtilis IFP1.1 = Bioinformatic analysis of poly gamma glutamic acid synthesis in genom Bacillus subtilis IFP1.1. Bachelor thesis, Universitas Pelita Harapan.

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Abstract

B. subtilis IFP1.1 merupakan salah satu strain B. subtilis yang diisolasi dari saluran pencernaan babi. Babi tersebut diperlihara secara tradisional dan tidak diberi antibiotik. Menurut penelitian yang telah dilakukan sebelumnya, B. subtilis IFP1.1 memiliki kemampuan sebagai agen fibrinolitik seperti B. subtilis subsp. natto. Salah satu keunikan B. subtilis subsp. natto yaitu memiliki struktur lengket pada hasil fermentasi kacang kedelai. Struktur lengket ini terbentuk akibat adanya produksi γPGA. Analisis whole genome sequencing penting dilakukan untuk mengassembly dan menganotasi whole genome B. subtilis IFP1.1, serta menganalisis genom B. subtilis dan menganalisis gen – gen yang terkait produksi γ-PGA pada B. subtilis IFP1.1. Assembly genom dilakukan dengan menggunakan program SPAdes, Mauve, dan Artemis. Sedangkan untuk anotasi genom dilakukan dengan menggunakan program RAST. Selain itu, juga dilakukan analisis genom dengan menggunakan BRIG, serta analisis pohon filogenetik dengan menggunakan NCBI BLAST dan ClustalW. Alignment sequence juga dilakukan untuk melihat mutasi pada gen yang terkait produksi γ-PGA. Ukuran genom B. subtilis IFP1.1 adalah 4.094.105 bp, dengan GC content 43,2 %, number of subsystem 477, number of coding sequence 4628, dan number of RNAs adalah 63. Secara genomik B. subtilis IFP1.1 lebih mirip dengan B. subtilis 168. Berdasarkan analisis pada gen - gen yang terkait produksi γ-PGA yaitu swrA dan degQ serta berdasarkan analisis pohon filogenetik, B. subtilis IFP1.1 berada pada kelompok yang sama dengan B. subtilis subsp. natto BEST195 dan B. subtilis subsp. natto CGMCC2108. Sehingga diduga B. subtilis IFP1.1 dapat memproduksi struktur lengket seperti B. subtilis subsp. natto. / B. subtilis IFP1.1 is a strain of B. subtilis isolated from the digestive tract of pigs. The pigs are traditionally raised and not given antibiotics. According to previous studies, B. subtilis IFP1.1 has the ability as a fibrinolytic agent like B. subtilis subsp. natto. One of the uniqueness of B. subtilissubsp. natto is that it has a sticky structure on the fermented soybeans. This sticky structure is formed due to the production of γ-PGA. Analysis of whole genome sequencing is important for assembling and annotating the whole genome of B. subtilis IFP1.1, as well as analyzing the genome of B. subtilis and analyzing genes associated with γ-PGA production in B. subtilis IFP1.1. Genome assembly was carried out using the SPAdes, Mauve, and Artemis programs. Meanwhile, genome annotation was carried out using the RAST program. In addition, genome analysis was also carried out using BRIG, as well as phylogenetic tree analysis using NCBI BLAST and ClustalW. Sequence alignment was also carried out to look for mutations in genes associated with γ-PGA production. The genome size of B. subtilis IFP1.1 is 4,094,105 bp, with a GC content of 43.2 %, number of subsystem 477, number of coding sequence 4628, and number of RNAs is 63. Genomically, B. subtilisIFP1.1 is more similar to B. subtilis 168. Based on the analysis of genes associated with γ-PGA production, namely swrA and degQ and based on phylogenetic tree analysis, B. subtilis IFP1.1 is in the same group as B. subtilis subsp. natto BEST195 and B. subtilis subsp. natto CGMCC2108. So it is suspected that B. subtilis IFP1.1 can produce a sticky structure like B. subtilis subsp. natto.

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