Genome analysis and identification of gelatinase encoded gene in Enterobacter aerogenes

Safiyyah Shahimi, Sahilah Abd. Mutalib, Rozida Mohd. Khalid, Rul Aisyah Mat Repin, Mohd Fadly Lamri, Mohd Faizal Abu Bakar, Mohd Noor Mat Isa

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

In this study, bioinformatic analysis towards genome sequence of E. aerogenes was done to determine gene encoded for gelatinase. Enterobacter aerogenes was isolated from hot spring water and gelatinase species-specific bacterium to porcine and fish gelatin. This bacterium offers the possibility of enzymes production which is specific to both species gelatine, respectively. Enterobacter aerogenes was partially genome sequenced resulting in 5.0 mega basepair (Mbp) total size of sequence. From pre-process pipeline, 87.6 Mbp of total reads, 68.8 Mbp of total high quality reads and 78.58 percent of high quality percentage was determined. Genome assembly produced 120 contigs with 67.5% of contigs over 1 kilo base pair (kbp), 124856 bp of N50 contig length and 55.17 % of GC base content percentage. About 4705 protein gene was identified from protein prediction analysis. Two candidate genes selected have highest similarity identity percentage against gelatinase enzyme available in Swiss-Prot and NCBI online database. They were NODE-9-length-26866-cov-148.013245-12 containing 1029 base pair (bp) sequence with 342 amino acid sequence and NODE-24-length-155103-cov-177.082458-62 which containing 717 bp sequence with 238 amino acid sequence, respectively. Thus, two paired of primers (forward and reverse) were designed, based on the open reading frame (ORF) of selected genes. Genome analysis of E. aerogenes resulting genes encoded gelatinase were identified.

Original languageEnglish
Title of host publication2016 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2016 Postgraduate Colloquium
PublisherAmerican Institute of Physics Inc.
Volume1784
ISBN (Electronic)9780735414464
DOIs
Publication statusPublished - 17 Nov 2016
Event2016 Postgraduate Colloquium of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology, UKM FST 2016 - Selangor, Malaysia
Duration: 13 Apr 201614 Apr 2016

Other

Other2016 Postgraduate Colloquium of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology, UKM FST 2016
CountryMalaysia
CitySelangor
Period13/4/1614/4/16

Fingerprint

genome
genes
bacteria
amino acids
enzymes
springs (water)
proteins
primers
gelatins
fishes
assembly
predictions

Keywords

  • Bioinformatic
  • Enterobacter aerogenes
  • Gelatin
  • Gelatinase

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Shahimi, S., Abd. Mutalib, S., Mohd. Khalid, R., Repin, R. A. M., Lamri, M. F., Bakar, M. F. A., & Isa, M. N. M. (2016). Genome analysis and identification of gelatinase encoded gene in Enterobacter aerogenes. In 2016 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2016 Postgraduate Colloquium (Vol. 1784). [030031] American Institute of Physics Inc.. https://doi.org/10.1063/1.4966769

Genome analysis and identification of gelatinase encoded gene in Enterobacter aerogenes. / Shahimi, Safiyyah; Abd. Mutalib, Sahilah; Mohd. Khalid, Rozida; Repin, Rul Aisyah Mat; Lamri, Mohd Fadly; Bakar, Mohd Faizal Abu; Isa, Mohd Noor Mat.

2016 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2016 Postgraduate Colloquium. Vol. 1784 American Institute of Physics Inc., 2016. 030031.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Shahimi, S, Abd. Mutalib, S, Mohd. Khalid, R, Repin, RAM, Lamri, MF, Bakar, MFA & Isa, MNM 2016, Genome analysis and identification of gelatinase encoded gene in Enterobacter aerogenes. in 2016 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2016 Postgraduate Colloquium. vol. 1784, 030031, American Institute of Physics Inc., 2016 Postgraduate Colloquium of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology, UKM FST 2016, Selangor, Malaysia, 13/4/16. https://doi.org/10.1063/1.4966769
Shahimi S, Abd. Mutalib S, Mohd. Khalid R, Repin RAM, Lamri MF, Bakar MFA et al. Genome analysis and identification of gelatinase encoded gene in Enterobacter aerogenes. In 2016 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2016 Postgraduate Colloquium. Vol. 1784. American Institute of Physics Inc. 2016. 030031 https://doi.org/10.1063/1.4966769
Shahimi, Safiyyah ; Abd. Mutalib, Sahilah ; Mohd. Khalid, Rozida ; Repin, Rul Aisyah Mat ; Lamri, Mohd Fadly ; Bakar, Mohd Faizal Abu ; Isa, Mohd Noor Mat. / Genome analysis and identification of gelatinase encoded gene in Enterobacter aerogenes. 2016 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2016 Postgraduate Colloquium. Vol. 1784 American Institute of Physics Inc., 2016.
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abstract = "In this study, bioinformatic analysis towards genome sequence of E. aerogenes was done to determine gene encoded for gelatinase. Enterobacter aerogenes was isolated from hot spring water and gelatinase species-specific bacterium to porcine and fish gelatin. This bacterium offers the possibility of enzymes production which is specific to both species gelatine, respectively. Enterobacter aerogenes was partially genome sequenced resulting in 5.0 mega basepair (Mbp) total size of sequence. From pre-process pipeline, 87.6 Mbp of total reads, 68.8 Mbp of total high quality reads and 78.58 percent of high quality percentage was determined. Genome assembly produced 120 contigs with 67.5{\%} of contigs over 1 kilo base pair (kbp), 124856 bp of N50 contig length and 55.17 {\%} of GC base content percentage. About 4705 protein gene was identified from protein prediction analysis. Two candidate genes selected have highest similarity identity percentage against gelatinase enzyme available in Swiss-Prot and NCBI online database. They were NODE-9-length-26866-cov-148.013245-12 containing 1029 base pair (bp) sequence with 342 amino acid sequence and NODE-24-length-155103-cov-177.082458-62 which containing 717 bp sequence with 238 amino acid sequence, respectively. Thus, two paired of primers (forward and reverse) were designed, based on the open reading frame (ORF) of selected genes. Genome analysis of E. aerogenes resulting genes encoded gelatinase were identified.",
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