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3 Biotech

, 9:26 | Cite as

Sequence-based structural analysis and evaluation of polymorphism in buffalo Nod-like receptor-1 gene

  • S. K. Mishra
  • P. K. Dubey
  • Asmita Dhiman
  • Shubham Dubey
  • Deepu Verma
  • A. C. Kaushik
  • Ravinder Singh
  • S. K. Niranjan
  • V. Vohra
  • K. L. Mehrara
  • R. S. KatariaEmail author
Original Article
  • 42 Downloads

Abstract

In this study, we have sequence characterized and analyzed the polymorphism in buffalo NOD1 (nucleotide-binding oligomerization domain 1) gene as well as its expression analysis. Full-length sequence analysis of NOD1 revealed this gene in buffalo being conserved with respect to the domain structures, similar to other species. Alternate splice variants having exon3 skipping also identified for the first time in the gene expressed in buffalo-purified peripheral blood mononuclear cells (PBMCs). Phylogenetically ruminant species were found to be clustering together and buffalo displaying maximum similarity with cattle. Sequencing of NOD1 across 12 Indian buffalo breeds identified 23 polymorphic sites within coding region, among which 16 were synonymous and 7 changes found to be non-synonymous. Four SNPs (single nucleotide polymorphisms) of them were genotyped in 393 animals belonging to 12 riverine, swamp and hybrid (riverine × swamp) buffalo populations of diverse phenotypes and utilities, showing variable allelic frequencies. Principal component analysis revealed, riverine and swamp buffaloes being distinctly placed with the distribution of breeds within the group based on the geographical isolation. Further, quantitative real-time PCR detected NOD1 expression in multiple tissues with PBMCs and lungs showing highest expression among the tissues examined. Structural analysis based on the translated amino acid sequence of buffalo NOD1 identified four protein interaction motifs LxxLL important for ligand binding. Molecular interaction analysis of iE-DAP and NOD1-LRR and their complex stability and binding-free energy studies indicated variable binding energies in buffalo and cattle NOD1. Overall, the study reveals unique structural features in buffalo NOD1, important for species-specific ligand interaction.

Keywords

NOD1 Buffalo Polymorphism Alternate splicing Ligand interaction 

Notes

Acknowledgements

The work reported has been carried out under the financial support received from National Agricultural Innovation Project of ICAR, Government of India under the project scheme C2153, which is thankfully acknowledged.

Compliance with ethical standards

Conflict of interest

On behalf of all the authors, the corresponding author states that there is no conflict of interest for publishing this manuscript.

Supplementary material

13205_2018_1534_MOESM1_ESM.docx (29 kb)
Supplementary material 1 (DOCX 29 KB)
13205_2018_1534_MOESM2_ESM.docx (1017 kb)
Supplementary material 2 (DOCX 1017 KB)

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Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  • S. K. Mishra
    • 1
  • P. K. Dubey
    • 1
  • Asmita Dhiman
    • 1
  • Shubham Dubey
    • 1
  • Deepu Verma
    • 2
  • A. C. Kaushik
    • 3
  • Ravinder Singh
    • 1
  • S. K. Niranjan
    • 1
  • V. Vohra
    • 1
  • K. L. Mehrara
    • 4
  • R. S. Kataria
    • 1
    Email author
  1. 1.ICAR-National Bureau of Animal Genetic ResourcesKarnalIndia
  2. 2.ICAR-National Dairy Research InstituteKarnalIndia
  3. 3.School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
  4. 4.ICAR-Central Institute for Research on BuffaloesNabhaIndia

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