Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

Rul Aisyah Mat Repin, Sahilah Abdul Mutalib, Safiyyah Shahimi, Rozida Mohd Khalid, Mohd Khan Ayob, Mohd Faizal Abu Bakar, Mohd Noor Mat Isa

Research output: ResearchConference contribution

Abstract

In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE-71-length-93919-cov-158.931839-21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE-23-length-52851-cov-190.061386-17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE-106-length-32943-cov-169.147919-8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

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
StatePublished - 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

genes
bacteria
amino acids
genome
primers
oligonucleotides
gelatins
enzymes
soils

Keywords

  • Bioinformatics analysis
  • Detection
  • Gelatinase
  • Lysinibacillussphaericus

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Repin, R. A. M., Mutalib, S. A., Shahimi, S., Khalid, R. M., Ayob, M. K., Bakar, M. F. A., & Isa, M. N. M. (2016). Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus. In 2016 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2016 Postgraduate Colloquium (Vol. 1784). [030044] American Institute of Physics Inc.. DOI: 10.1063/1.4966782

Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus. / Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd; Ayob, Mohd Khan; 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. 030044.

Research output: ResearchConference contribution

Repin, RAM, Mutalib, SA, Shahimi, S, Khalid, RM, Ayob, MK, Bakar, MFA & Isa, MNM 2016, Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus. in 2016 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2016 Postgraduate Colloquium. vol. 1784, 030044, 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. DOI: 10.1063/1.4966782
Repin RAM, Mutalib SA, Shahimi S, Khalid RM, Ayob MK, Bakar MFA et al. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus. 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. 030044. Available from, DOI: 10.1063/1.4966782
Repin, Rul Aisyah Mat ; Mutalib, Sahilah Abdul ; Shahimi, Safiyyah ; Khalid, Rozida Mohd ; Ayob, Mohd Khan ; Bakar, Mohd Faizal Abu ; Isa, Mohd Noor Mat. / Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus. 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, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE-71-length-93919-cov-158.931839-21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE-23-length-52851-cov-190.061386-17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE-106-length-32943-cov-169.147919-8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.",
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