Sains Malaysiana 48(4)(2019): 773–780

http://dx.doi.org/10.17576/jsm-2019-4804-09

 

Representative Candidate of Gelatinase Encoded Gene in Enterobacter aerogenes (Strain EA1) for Hydrolyzing Porcine Gelatin

(Calon Wakil Gen yang Mengekod Gelatinase di dalam Enterobacter aerogenes (Strain EA1) bagi Hidrolisis Gelatin Babi)

 

SAFIYYAH SHAHIMI¹, SAHILAH ABD. MUTALIB¹*, ROZIDA MOHD. KHALID¹, MOHD FADLY LAMRI², MAARUF ABDUL GHANI¹, MOHD. FAIZAL ABU BAKAR³ & MOHD. NOOR MAT ISA³

 

¹School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

 

²Politeknik Metro Kuantan, A-5, Jalan Tun Ismail 2, Sri Dagangan 11, 25000 Kuantan, Pahang Darul Makmur, Malaysia

 

³Malaysia Genome Institute, Ministry of Science Technology and Inovasion, Bangi, 43600 Kajang, Selangor Darul Ehsan, Malaysia

 

Received: 2 March 2018/Accepted: 31 January 2019

 

ABSTRACT

Enterobacter aerogenes (Strain EA1) was characterised as gelatinase species-specific bacterium to porcine and fish gelatin. This bacterium offers the possibility of enzymes production to each species gelatin. In this study, a bioinformatic analysis toward genome sequence of E. aerogenes was perfomed to determine genes encoded for gelatinase. E. aerogenes were partially genome sequenced resulting in 5.0 mega basepair total size of sequence. From pre-process pipeline, 78.58% of high quality reads was obtained for E. aerogenes. Genome assembly produced 120 contigs with 55.17% of GC base content. Protein prediction analysis determined 4705 genes from E. aerogenes. Two gelatinase candidate target genes selected from E. aerogenes were NODE_9_length_26866_cov_148.013245_12 containing 1029 bp sequence and NODE_24_length_155103_cov_177.082458_62 containing 717 bp sequence with highest similarity identity percentage against gelatinase enzyme available in Swiss-Prot and NCBI online database. Then, primers were designed for each target genes based on the open reading frame of selected genes. The expected gene candidate showed, 1029 bp and 717 bp amplicons for gen NODE_9_12 and gene NODE_24_62, respectively. Thus, gelatinase candidate encoded genes of E. aerogenes were identified for hydrolyzing porcine gelatin.

 

Keywords: Bioinformatic analysis; Enterobacter aerogenes; gelatinase; hydrolysis; porcine gelatin

 

ABSTRAK

Enterobacter aerogenes (Strain EA1) ialah sejenis bakteria yang menghasilkan gelatinase khusus-spesies terhadap gelatin babi dan ikan. Bakteria ini menawarkan kemungkinan penghasilan enzim yang mencernakan gelatin spesies tertentu. Dalam kajian ini, satu analisis bioinformatik terhadap jujukan genom E. aerogenes telah dilakukan bagi mengenal pasti gen yang mengekod gelatinase. Penjujukan separa genom E. Aerogenes telah menghasilkan saiz keseluruhan sebanyak 5.0 mega pasangan bes. Daripada pemprosesan awal, 78.58% jujukan berkualiti tinggi telah diperoleh bagi E. aerogenes. Penghimpunan genom telah menghasilkan 120 kontig dengan 55.17% kandungan bes. Analisis peramalan protein telah mengenal pasti 4705 gene daripada E. aerogenes. Dua gen sasaran calon gelatinase terpilih ialah NODE_9_length_26866_cov_148.013245_12 mengandungi 1029 bp jujukan dan NODE_24_length_155103_cov_177.082458_62 mengandungi 717 bp jujukan, dengan peratus identiti persamaan tertinggi dengan enzim gelatinase yang terdapat di pangkalan data atas talian Swiss-Prot dan NCBI. Kemudian, pencetus telah direka bentuk bagi setiap gen sasaran berdasarkan rangka bacaan terbuka gen terpilih. Calon gen yang dijangka telah ditunjukkan, 1029 bp dan 717 bp amplikon bagi gen NODE_9_12 dan NODE_24_62. Oleh itu, gen yang mengekod calon gelatinase telah dikenal pasti bagi hidrolisis gelatin babi.

 

Kata kunci: Analisis bioinformatik; Enterobacter aerogenes; gelatin babi; gelatinase; hidrolisis

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*Corresponding author; email: sahilah@ukm.edu.my