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In Silico Analysis of nsSNPs of Carp TLR22 Gene Affecting its Binding Ability with Poly I:C

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Abstract

Immune response mediated by toll-like receptor 22 (TLR22), only found in teleost/amphibians, is triggered by double-stranded RNA binding to its LRR (leucine-rich repeats) ecto-domain. Accumulated evidences suggested that missense mutations in TLR genes affect its function. However, information on mutation linked pathogen recognition for TLR22 was lacking. The present study was commenced for predicting the effect of non-synonymous single-nucleotide polymorphisms (nsSNPs) on the pathogen recognizable LRR domain of TLR22 of farmed carp, Labeo rohita. The sequence-based algorithms (SIFT, PROVEAN and I-Mutant2.0) indicated that three SNPs (out of 27) such as p.L159F (rs76759876) and p.L529P (rs749355507) of LRR, and p.I836M (rs750758397) of intracellular motifs could potentially disrupt protein function. The 3D structure was generated using MODELLER 9.13 and further validated by SAVEs server. The simulated molecular docking of native TLR22 and mutants with poly I:C ligand indicated that mutations positioned at p.L159F and p.L529P of the LRR region affects the binding affinity significantly. This is the first kind of study of predicting nsSNPs of teleost TLR22 with disturbed ligand binding affinity with its extra-cellular LRR domain and thereby likely hindrance in subsequent signal transduction. This study serves as a guide for in vivo evaluation of impact of mutation on immune response mediated by teleost TLR22 gene.

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Abbreviations

SIFT:

Sorting intolerant from tolerant

SNP:

Single-nucleotide polymorphism

nsSNPs:

Non-synonymous single-nucleotide polymorphisms

AASs:

Amino acid substitutions

PROVEAN:

Protein variation effect analyzer

PDB:

Protein data bank

SAVES:

Structural analysis and verification server

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Acknowledgements

This work was supported by a grant from the National Agricultural Science Fund (NASF), Indian Council of Agricultural Research, Union Ministry of Agriculture, Government of India. Thanks to the Director of this Institute for providing required facilities to carry out this research.

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Authors and Affiliations

  1. Fish Genetics and Biotechnology Division, ICAR, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India

    Vemulawada Chakrapani, Kiran D. Rasal, Shibani D. Mohapatra, Jitendra K. Sundaray, Pallipuram Jayasankar & Hirak K. Barman

  2. ICAR, National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, 275103, India

    Sunil Kumar

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  1. Vemulawada Chakrapani
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  2. Kiran D. Rasal
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  3. Sunil Kumar
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Correspondence to Hirak K. Barman.

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Chakrapani, V., Rasal, K.D., Kumar, S. et al. In Silico Analysis of nsSNPs of Carp TLR22 Gene Affecting its Binding Ability with Poly I:C. Interdiscip Sci Comput Life Sci 10, 641–652 (2018). https://doi.org/10.1007/s12539-017-0247-2

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