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

REFERENCES

De Clerck, E., Gevers, D., De Ridder, K. & De Vos, P. 2004. Screening of bacterial contamination during gelatin production by means of denaturing gradient gel electrophoresis, focused on Bacillus and related endospore-forming genera. J. App. Microbiol. 96: 1333-1341.

Del Fabbro, C., Scalabrin, S., Morgante, M. & Giorgi, F.M. 2013. An extensive evaluation of read trimming effects on illumina NGS data analysis. PLoS ONE 8(12): e85024.

Desai, A., Marwah, V.S., Yadav, A., Jha, V., Dhaygude, K. & Bangar, U. 2013. Identification of optimum sequencing depth especially for De Novo genome assembly of small genomes using next generation sequencing data. PLoS ONE 8(4): e60204.

Diene, S.M., Merhej, V., Henry, M., Filali, A.E., Roux, V., Robert, C., Azza, S., Gavory, F., Barbe, V., Scola, B.L., Roult, D. & Rolain, J. 2012. The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new 'killer bugs' are created because of a sympatric lifestyle. Mol. Biol. Evol. 30(2): 369-383.

Gaudermann, P., Vogl, I., Zientz, E., Silva, F.J., Moya, A., Gross, R. & Dandekar, T. 2006. Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus. BMC Microbiology 6: 1.

Gudmundsson, M. & Hafsteinsson, H. 1997. Gelatin from cods skin as affected by chemical treatments. J. Food Sci. 62: 37-39.

Hyatt, D., Chen, G-L., LoCascio, P.F., Land, M.L., Larimer, F.W. & Hauser, L.J. 2010. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinfor. 11: 119.

Ismail, N.H., Yusop, S.M., Babji, A.S. & Maskat, M.Y. 2018. Kesan penambahan Kappaphycus alvarezii, gelatin ikan dan gelatin kaki ayam terhadap ciri-ciri kualiti sosej ayam. Sains Malaysiana 47(6): 1157-1165.

Klimpel, K.R., Arora, N. & Leppla, S.H. 1994. Anthrax toxin lethal factor contains a zinc metalloprotease consensus sequence which is required for lethal toxin activity. Molecular Microbiology 13(6): 1093-1100.

Lorenz, T. 2012. Polymerase chain reaction: Basic protocol plus troubleshooting and optimization strategies. J. Vis. Exp. 63: e3998.

Meyer, R. & Candrian, U. 1996. PCR-based DNA analysis for the identification and characterization of food components. Lebensmittel-Wissenschaft undTech. 29(1-2): 1-9.

Mohd Fadly, L. 2016. Pemencilan, pengenalpastian dan aktiviti enzim bagi bakteria gelatinase terhadap pengesanan gelatin bagi tujuan pengesahan halal. Ph.D Tesis, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia (Unpublished).

Mohd Faizal, A.B. 2013. Penentuan saiz dan analisis jujukan genom Glaciozyma antartica. MSc. Tesis, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia (Unpublished).

Mohd Noor, M.I. 2014. Next-generation sequencing data analysis workshop. Bioinformatics Training Laboratory, September 2014. Malaysia Genome Institute. pp. 17-19.

Musto, H., Naya, H., Zavala, A., Romero, H., Alvarez-Valín, F. & Bernardi, G. 2004. Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Lett. 573(1-3): 73-77.

O'Brien, P. & O'Connor, B.F. 2008. Seprase: An overview of an important matrix serine protease. Biochim. Biophys. Acta. 9: 1130-1145.

Reeves, G.A., Talavera, D. & Thornton, J.M. 2009. Genome and proteome annotation: Organization, interpretation and integration. Journal of the Royal Society Interface 6(31): 129-147.

Rul Aisyah, M.R., Sahilah, A.M., Safiyyah, S., Rozida, M.K., Mohd. Khan, A., Mohd. Faizal, A.B. & Mohd. Noor, M.I. 2016. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus. American Institute of Physics 1784: 030044.

Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.A. & Barrell, B. 2000. Artemis: Sequence visualization and annotation. Bioinformatics 16(10): 944-945.

Selina Oh, S.L., Leong, J.M., Abdul Munir, A.M., Nor Muhammad, M. & Farah Diba, A.B. 2011. Cloning and analysis of pyrG gene encoding orotidine 5-monophosphate decarboxylase of Aspergillus oryzae Strain S1. Sains Malaysiana 40(4): 331-337.

Shahimi, S., Abd Mutalib, S., Nazri, W.S.W., Abdullah, A. & Sani, N.A. 2018. Comparison of DNA profiling between fishes and pork meat using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) analysis. Sains Malaysiana 47(7): 1535-1540.

Shin, S.H., Kim, S., Kim, J.Y., Lee, S., Um, Y., Oh, M-K., Kim, Y-R., Lee, J. & Yang, K-S. 2012. Complete genome sequence of Enterobacter aerogenes KCTC 2190. J. Bacteriol. 194: 2373-2374.

Stakebrandt, E., Frederiksen, W. & Garrity, G.M. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbio. 52: 1043-1047.

Su, Y.A., Sulavik, M.C., He, P., Makinen, K.K., Makinen, P.L., Fiedler, S., Wirth, R. & Clewell, D.B. 1991. Nucleotide sequence of the gelatinase gene (gelE) from Enterococcus faecalis subsp. Liquefaciens. Infect. Immun. 59(1): 415-420.

Suhimi, N.M. & Mohammad, A.W. 2012. Pengoptimuman proses pengeringan semburan gelatin dengan menggunakan kaedah sambutan permukaan. Sains Malaysiana 41(8): 983-991.

Xiang, Z. 2006. Advances in homology protein structure modeling. Current Protein & Peptide Science 7(3): 217-227.

 

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

 

 

 

previous