Author(s): Ichsanto Permadi, Is Helianti, Soemarno Reto Prawiro, Tri Yudani Mardining Raras


DOI: 10.52711/0974-360X.2024.00208   

Address: Ichsanto Permadi1,2, Is Helianti3, Soemarno Reto Prawiro4, Tri Yudani Mardining Raras5*
1Biomedical Science Post Graduate Programs, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia.
2Program Study of Medicine, Faculty of Medicine, Universitas Alkhairaat, Palu, Central Celebes, Indonesia.
3Research Center of Applied Microbiology, National Agency of Research and Innovation, Cibinong Science Center, Jl Raya Bogor km 46, Cibinong, West Java, Indonesia.
4Department Clinical Microbiology, Faculty Medicine, University Brawijaya, Malang, Indonesia.
5Department of Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia.
*Corresponding Author

Published In:   Volume - 17,      Issue - 3,     Year - 2024

There is an increase rate of hypervirulent Klebsiella pneumoniae (hvKP) that urges the need for preventive and effective immunotherapies, such as vaccine. The YidR gene is a new gene for adherence to host that is conserved in many strain of Klebsiella sp, offering its potency as vaccine candidate. This study aims to isolate the YidRhv gene and analyze the YidRhv protein in silico for future work as vaccine candidate against hypervirulent K. pneumoniae Indonesia strain. Klebsiella pneunomiae is tested for hypervirulency using LAMP-PCR method. The YidRhv gene was amplified via PCR method and the fragment produced was cloned and sequenced. The protein structure and epitope prediction for T-cell and B-cell of YidRhv protein was analyzed using bioinformatics approach. DNA sequence of YidRhv gene strain consisted of 1227 base pairs and showed 99,75 % homology to yidR from classical K pneumoniae. However, several single nucleotide polymorphism were found in this gene. The protein structure demonstrated that the YidRhv is possibly outer membrane protein. The protein YidRhv contain predicted epitopes that showed high affinity to B-cell but low affinity to T-cell.

Cite this article:
Ichsanto Permadi, Is Helianti, Soemarno Reto Prawiro, Tri Yudani Mardining Raras. Isolation of yidRhv Gene from Hypervirulent Klebsiella pneumoniae Indonesia Strain and in silico study of Gene product. Research Journal of Pharmacy and Technology. 2024; 17(3):1324-1. doi: 10.52711/0974-360X.2024.00208

Ichsanto Permadi, Is Helianti, Soemarno Reto Prawiro, Tri Yudani Mardining Raras. Isolation of yidRhv Gene from Hypervirulent Klebsiella pneumoniae Indonesia Strain and in silico study of Gene product. Research Journal of Pharmacy and Technology. 2024; 17(3):1324-1. doi: 10.52711/0974-360X.2024.00208   Available on:

1.    Lee CR. Lee JH. Park KS. Jeon JH. Kim YB. Cha CJ. Jeong BC. Lee SH. Antimicrobial Resistance of Hypervirulent Klebsiella pneumoniae: Epidemiology, Hypervirulence-Associated Determinants, and Resistance Mechanisms. Front Cell Infect Microbiol. 2017;
2.    Feldman MF. Mayer Bridwell AE. Scott NE. Vinogradov E. McKee SR. Chavez SM. Twentyman J. Stallings CL. Rosen DA. Harding CM. A promising bioconjugate vaccine against hypervirulent Klebsiella pneumoniae. Proc Natl Acad Sci. 2019; 116(37):
3.    Rodrigues MX. Yang Y. de Souza Meira EB. do Carmo Silva J. Bicalho RC. Development and evaluation of a new recombinant protein vaccine (YidR) against Klebsiella pneumoniae infection. Vaccine. 2020; 38(29): 4640-8.
4.    Assoni L. Girardello R. Converso TR. Darrieux M. Current Stage in the Development of Klebsiella pneumoniae Vaccines. Infect Dis Ther. 2021; 10(4):
5.    Szklarczyk D. Gable AL. Lyon D. Junge A. Wyder S. Huerta-Cepas J. Simonovic M. Doncheva NT. Morris JH. Bork P. Jensen LJ. Mering C von. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019; 47(D1):
6.    Chen N. Li G. Si Y. Zhang W. Ye Y. Wang Y. Wang K. Zong M. Fan L. Evaluation of LAMP assay using phenotypic tests and PCR for detection of bla KPC gene among clinical samples. J Clin Lab Anal. 2022; 36(4).
7.    Makharita RR. El-kholy I. Hetta HF. Abdelaziz M. Hagagy F. Ahmed A. Algammal AM. Antibiogram and Genetic Characterization of Carbapenem-Resistant Gram-Negative Pathogens Incriminated in Healthcare-Associated Infections. Infect Drug Resist. 2020; 13: 3991-4002.
8.    Senthilkumar G. Madhanraj P. Panneerselvam A. Studies on DNA extraction, molecular identification and genetic evolution of Trichoderma harzianum. Asian J Res Chem. 2011; 4(8):1225-30.
9.    Mohamed SH. Khalil MS. Mabrouk MI. Mohamed MSM. Prevalence of antibiotic resistance and biofilm formation in Klebsiella pneumoniae carrying fimbrial genes in Egypt. Res J Pharm Technol. 2020; 13(7): 3051.
10.    Sutar DA. Jain BhavanaU. Kondawar M. A Review Article on Study of Cloning. Asian J Res Pharm Sci. 2019; 9(2): 148.
11.    Mizuguchi H. Nakatsuji M. Fujiwara S. Takagi M. Imanaka T. Characterization and Application to Hot Start PCR of Neutralizing Monoclonal Antibodies against KOD DNA Polymerase. J Biochem (Tokyo). 1999; 126(4): 762-8.
12.    Yadav AR. Mohite SK. Homology modeling and generation of 3d-structure of protein. Res J Pharm Dos FORMS Technol. 2020; 12(4): 313-20.
13.    Altschul SF. Gish W. Miller W. Myers EW. Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215(3): 403-10.
14.    Reddy PP. Rao UMV. Homology modeling and validation of bacterial superoxide dismutase enzyme, an antioxidant. Res J Pharm Technol. 2020; 13(12): 6202-5.
15.    Sowmya H. A Comparative Study of Homology Modeling Algorithms for NPTX2 Structure Prediction. Res J Pharm Technol. 2019; 12(4):1895.
16.    Reynisson B. Alvarez B. Paul S. Peters B. Nielsen M. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 2020; 48(W1):
17.    Rahmahani J. Regilya Fatimah T. Hanny Irawan A. Putri N. Hendrianto E. Abdul Rantam F. Introducing B Cell Epitopes of Newcastle Disease Virus Obtained from Domestic Pigeons (Columba livia domestica) as Sub-Unit Vaccine Candidate to Eradicate Newcastle Disease Virus in Poultry. Res J Pharm Technol. Published online May 30, 2022:
18.    Larsen J. Lund O. Nielsen M. Improved method for predicting linear B-cell epitopes. Immunome Res. 2006; 2(1): 1-7.
19.    Nakajima Y. Ito K. Toshima T. Egawa T. Zheng H. Oyama H. Wu YF. Takahashi E. Kyono K. Yoshimoto T. Dipeptidyl Aminopeptidase IV from Stenotrophomonas maltophilia Exhibits Activity against a Substrate Containing a 4-Hydroxyproline Residue. J Bacteriol. 2008; 190(23):
20.    Bertoni M. Kiefer F. Biasini M. Bordoli L. Schwede T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Sci Rep. 2017; 7(1): 10480.
21.    Oduselu GO. Ajani OO. Ajamma YU. Brors B. Adebiyi E. Homology Modelling and Molecular Docking Studies of Selected Substituted Benzo[ d ]imidazol-1-yl)methyl)benzimidamide Scaffolds on Plasmodium falciparum Adenylosuccinate Lyase Receptor. Bioinforma Biol Insights. 2019;
22.    Chang KY. Yang JR. Analysis and Prediction of Highly Effective Antiviral Peptides Based on Random Forests. Isalan M, ed. PLoS ONE. 2013; 8(8):
23.    Gonzalez-Galarza FF. McCabe A. Santos EJM dos. Jones J. Takeshita L. Ortega-Rivera ND. Cid-Pavon GMD. Ramsbottom K. Ghattaoraya G. Alfirevic A. Middleton D. Jones AR. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools. Nucleic Acids Res. Published online November 13, 2019:
24.    Russo TA. Marr CM. Hypervirulent Klebsiella pneumoniae. Clin Microbiol Rev. 2019; 32(3):
25.    Rana S. Sirwar SB. Vijayaraghavan Prevalence and Antibiogram of Extended Spectrum β-Lactamase Producing Klebsiella pneumoniae and Proteus mirabilis in UTI. Res J Pharm Technol. 2015; 8(11):
26.    Sheela JM. Bhavani RavuriD. Pugazhendhi A. Characterization and Insilico Analysis of Cassia auriculata against Multi drug Resistant Klebsiella pneumoniae Isolated from Inanimate Origin. Asian J Res Pharm Sci. 2021; 11(3): 199-204.
27.    Cortés G. Borrell N. de Astorza B. Gómez C. Sauleda J. Albertí S. Molecular Analysis of the Contribution of the Capsular Polysaccharide and the Lipopolysaccharide O Side Chain to the Virulence of Klebsiella pneumoniae in a Murine Model of Pneumonia. Infect Immun. 2002; 70(5): 2583-90.
28.    Keats BJB. Sherman SL. Population Genetics. In Emery and Rimoin’s Principles and Practice of Medical Genetics. Elsevier; 2013: 1-12.
29.    Junaidin J. Chaerani S. Husniah Fadla N. Studi Homology Modeling Enzim Tirosinase (Homo Sapiens) Dengan Menggunakan Swiss-Model. J Farmagazine. 2019; 6(1): 1.
30.    Zhanhua C. Gan JGK. lei L. Sakharkar MK. Kangueane P. Protein subunit interfaces: heterodimers versus homodimers. Bioinformation. 2005; 1(2): 28-39.
31.    Jensen KK. Andreatta M. Marcatili P. Buus S. Greenbaum JA. Yan Z. Sette A. Peters B. Nielsen M. Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology. 2018; 154(3): 394-406.
32.    Solomon S. Pitossi F. Rao MS. Banking on iPSC- Is it Doable and is it Worthwhile. Stem Cell Rev Rep. 2015; 11(1):1-10.
33.    Vita R. Mahajan S. Overton JA. Dhanda SK. Martini S. Cantrell JR. Wheeler DK. Sette A. Peters B. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 2019; 47(D1):
34.    Crooke SN. Ovsyannikova IG. Kennedy RB. Poland GA. Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome. Sci Rep. 2020; 10(1): 14179.

Recomonded Articles:

Research Journal of Pharmacy and Technology (RJPT) is an international, peer-reviewed, multidisciplinary journal.... Read more >>>

RNI: CHHENG00387/33/1/2008-TC                     
DOI: 10.5958/0974-360X 

56th percentile
Powered by  Scopus

SCImago Journal & Country Rank

Recent Articles


Not Available