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Insight into buffalo (Bubalus bubalis) RIG1 and MDA5 receptors: a comparative study on dsRNA recognition and in-vitro antiviral response.

Singh M, Brahma B, Maharana J, Patra MC, Kumar S, Mishra P, Saini M, De BC, Mahanty S, Datta TK, De S - PLoS ONE (2014)

Bottom Line: Moreover, binding free energy calculation revealed that MDA5 had a greater affinity towards dsRNA compared to RIG1.Poly I:C stimulation induced elevated expressions of IFN-β and IFN-stimulated genes (ISGs) through interferon regulatory factors (IRFs) mediated pathway in buffalo foetal fibroblast cells.The present study provides crucial insights into the structure and function of RIG1 and MDA5 receptors in buffalo.

View Article: PubMed Central - PubMed

Affiliation: Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India.

ABSTRACT
RIG1 and MDA5 have emerged as important intracellular innate pattern recognition receptors that recognize viral RNA and mediate cellular signals controlling Type I interferon (IFN-I) response. Buffalo RIG1 and MDA5 genes were investigated to understand the mechanism of receptor induced antiviral response. Sequence analysis revealed that RIG1 and MDA5 maintain a domain arrangement that is common in mammals. Critical binding site residues of the receptors are evolutionary conserved among mammals. Molecular dynamics simulations suggested that RIG1 and MDA5 follow a similar, if not identical, dsRNA binding pattern that has been previously reported in human. Moreover, binding free energy calculation revealed that MDA5 had a greater affinity towards dsRNA compared to RIG1. Constitutive expressions of RLR genes were ubiquitous in different tissues without being specific to immune organs. Poly I:C stimulation induced elevated expressions of IFN-β and IFN-stimulated genes (ISGs) through interferon regulatory factors (IRFs) mediated pathway in buffalo foetal fibroblast cells. The present study provides crucial insights into the structure and function of RIG1 and MDA5 receptors in buffalo.

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Amino acid sequence analysis of RIG1 and MDA5 receptors.(A) Sequence comparison of functional domains and binding residues of RIG1 and MDA5. Multiple sequence alignment was performed by MAFFT web server and binding site residues (highlighted) were identified by DELTA-BLAST and CDD database of NCBI. (B) The evolutionary history was inferred by using the Maximum Likelihood method of MEGA5 based on the JTT matrix-based model. The trees with the highest log likelihood are shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. Sequences used for analysis are provided in Table S2 in File S1.
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pone-0089788-g001: Amino acid sequence analysis of RIG1 and MDA5 receptors.(A) Sequence comparison of functional domains and binding residues of RIG1 and MDA5. Multiple sequence alignment was performed by MAFFT web server and binding site residues (highlighted) were identified by DELTA-BLAST and CDD database of NCBI. (B) The evolutionary history was inferred by using the Maximum Likelihood method of MEGA5 based on the JTT matrix-based model. The trees with the highest log likelihood are shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. Sequences used for analysis are provided in Table S2 in File S1.

Mentions: The amino acid sequences of buffalo RIG1 and MDA5 were translated from respective nucleotide sequences identified in this study (GenBank Accession ID: KF517376 and KF517377; Text S3 in File S1). The putative conserved domains and critical binding site residues within RIG1 and MDA5 were identified using DELTA BLAST and Conserved Domain Database (CDD) of NCBI. Comparison of amino acid conservation among different domains of buffalo RIG1 and MDA5 sequences revealed that CARD, helicase, and CTDs of these genes share 31.1, 34.9 and 21.5% homology, respectively (Figure 1). Putative conserved domains along with conservation of critical binding site residues among buffalo RIG1, MDA5 and different model organism has been shown in Figure 1A. From Figure 1A it is clear that critical binding site residues of both RIG1 and MDA5 are conserved across mammals. Moreover, the residues responsible for ATP, Mg++, and RNA binding are almost identical. Phylogenetic trees constructed by maximum likelihood method (MEGA5.2 software) [29] revealed a similar pattern of evolution for RIG1 and MDA5 in different model organisms except perrisodactyla (horse), where, RIG1 was clustered with cetartiodactyla and MDA5 with primates (Figure 1B).


Insight into buffalo (Bubalus bubalis) RIG1 and MDA5 receptors: a comparative study on dsRNA recognition and in-vitro antiviral response.

Singh M, Brahma B, Maharana J, Patra MC, Kumar S, Mishra P, Saini M, De BC, Mahanty S, Datta TK, De S - PLoS ONE (2014)

Amino acid sequence analysis of RIG1 and MDA5 receptors.(A) Sequence comparison of functional domains and binding residues of RIG1 and MDA5. Multiple sequence alignment was performed by MAFFT web server and binding site residues (highlighted) were identified by DELTA-BLAST and CDD database of NCBI. (B) The evolutionary history was inferred by using the Maximum Likelihood method of MEGA5 based on the JTT matrix-based model. The trees with the highest log likelihood are shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. Sequences used for analysis are provided in Table S2 in File S1.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3935933&req=5

pone-0089788-g001: Amino acid sequence analysis of RIG1 and MDA5 receptors.(A) Sequence comparison of functional domains and binding residues of RIG1 and MDA5. Multiple sequence alignment was performed by MAFFT web server and binding site residues (highlighted) were identified by DELTA-BLAST and CDD database of NCBI. (B) The evolutionary history was inferred by using the Maximum Likelihood method of MEGA5 based on the JTT matrix-based model. The trees with the highest log likelihood are shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. Sequences used for analysis are provided in Table S2 in File S1.
Mentions: The amino acid sequences of buffalo RIG1 and MDA5 were translated from respective nucleotide sequences identified in this study (GenBank Accession ID: KF517376 and KF517377; Text S3 in File S1). The putative conserved domains and critical binding site residues within RIG1 and MDA5 were identified using DELTA BLAST and Conserved Domain Database (CDD) of NCBI. Comparison of amino acid conservation among different domains of buffalo RIG1 and MDA5 sequences revealed that CARD, helicase, and CTDs of these genes share 31.1, 34.9 and 21.5% homology, respectively (Figure 1). Putative conserved domains along with conservation of critical binding site residues among buffalo RIG1, MDA5 and different model organism has been shown in Figure 1A. From Figure 1A it is clear that critical binding site residues of both RIG1 and MDA5 are conserved across mammals. Moreover, the residues responsible for ATP, Mg++, and RNA binding are almost identical. Phylogenetic trees constructed by maximum likelihood method (MEGA5.2 software) [29] revealed a similar pattern of evolution for RIG1 and MDA5 in different model organisms except perrisodactyla (horse), where, RIG1 was clustered with cetartiodactyla and MDA5 with primates (Figure 1B).

Bottom Line: Moreover, binding free energy calculation revealed that MDA5 had a greater affinity towards dsRNA compared to RIG1.Poly I:C stimulation induced elevated expressions of IFN-β and IFN-stimulated genes (ISGs) through interferon regulatory factors (IRFs) mediated pathway in buffalo foetal fibroblast cells.The present study provides crucial insights into the structure and function of RIG1 and MDA5 receptors in buffalo.

View Article: PubMed Central - PubMed

Affiliation: Animal Genomics Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India.

ABSTRACT
RIG1 and MDA5 have emerged as important intracellular innate pattern recognition receptors that recognize viral RNA and mediate cellular signals controlling Type I interferon (IFN-I) response. Buffalo RIG1 and MDA5 genes were investigated to understand the mechanism of receptor induced antiviral response. Sequence analysis revealed that RIG1 and MDA5 maintain a domain arrangement that is common in mammals. Critical binding site residues of the receptors are evolutionary conserved among mammals. Molecular dynamics simulations suggested that RIG1 and MDA5 follow a similar, if not identical, dsRNA binding pattern that has been previously reported in human. Moreover, binding free energy calculation revealed that MDA5 had a greater affinity towards dsRNA compared to RIG1. Constitutive expressions of RLR genes were ubiquitous in different tissues without being specific to immune organs. Poly I:C stimulation induced elevated expressions of IFN-β and IFN-stimulated genes (ISGs) through interferon regulatory factors (IRFs) mediated pathway in buffalo foetal fibroblast cells. The present study provides crucial insights into the structure and function of RIG1 and MDA5 receptors in buffalo.

Show MeSH