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Positive evolutionary selection on the RIG-I-like receptor genes in mammals.

Lemos de Matos A, McFadden G, Esteves PJ - PLoS ONE (2013)

Bottom Line: The highest number of positively selected codons was detected in MDA5, but a great percentage of these codons were located outside of the currently defined protein domains for MDA5, which likely reflects the imposition of both functional and structural constraints.Additionally, our results support LGP2 as being the least prone to evolutionary change, since the lowest number of codons under selection was observed for this gene.Furthermore, the RIG-I repressor domain, the region responsible for recognizing and binding to its RNA substrates, exhibited the strongest evidence of selective pressures.

View Article: PubMed Central - PubMed

Affiliation: CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBio Laboratório Associado, Universidade do Porto, Vairão, Portugal ; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal ; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America.

ABSTRACT
The mammalian RIG-I-like receptors, RIG-I, MDA5 and LGP2, are a family of DExD/H box RNA helicases responsible for the cytoplasmic detection of viral RNA. These receptors detect a variety of RNA viruses, or DNA viruses that express unusual RNA species, many of which are responsible for a great number of severe and lethal diseases. Host innate sentinel proteins involved in pathogen recognition must rapidly evolve in a dynamic arms race with pathogens, and thus are subjected to long-term positive selection pressures to avoid potential infections. Using six codon-based Maximum Likelihood methods, we were able to identify specific codons under positive selection in each of these three genes. The highest number of positively selected codons was detected in MDA5, but a great percentage of these codons were located outside of the currently defined protein domains for MDA5, which likely reflects the imposition of both functional and structural constraints. Additionally, our results support LGP2 as being the least prone to evolutionary change, since the lowest number of codons under selection was observed for this gene. On the other hand, the preponderance of positively selected codons for RIG-I were detected in known protein functional domains, suggesting that pressure has been imposed by the vast number of viruses that are recognized by this RNA helicase. Furthermore, the RIG-I repressor domain, the region responsible for recognizing and binding to its RNA substrates, exhibited the strongest evidence of selective pressures. Branch-site analyses were performed and several species branches on the three receptor gene trees showed evidence of episodic positive selection. In conclusion, by looking for evidence of positive evolutionary selection on mammalian RIG-I-like receptor genes, we propose that a multitude of viruses have crafted the receptors biological function in host defense, specifically for the RIG-I gene, contributing to the innate species-specific resistance/susceptibility to diverse viral pathogens.

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Related in: MedlinePlus

Structural representation and identification of positively-selected branches and codons in mammalian MDA5.(A) Based on the human protein structure, the key domains of MDA5 (http://www.uniprot.org/uniprot/Q9BYX4) and the corresponding boundaries are schematically represented. Also, the human domain boundaries while in the mammalian MDA5 deduced protein sequences alignment (Figure S5) are shown in brackets. (B) Cladogram of 26 mammalian MDA5 genes collected from Ensembl and NCBI databases. Branch-site analyses were performed to identify specific branches episodic under positive selection. Branches with statistically significant likelihood ratio tests (LRTs) when performing PAML branch-site model A (Table 3) are colored in green; branches simultaneously identified by PAML branch-site model A and Hyphy branch-site REL method (Table 5) are colored in blue. (C) Positively-selected codons are exhibited in the table and numbered according to the mammalian MDA5 deduced protein sequences alignment (Figure S5). Symbol “?” represents an undetermined amino acid, while “-” symbolizes a deletion. Colors on the codon numbering row correspond to the MDA5 domain with the same color in the protein structural representation (A). The background colors on the identified sites match different amino acid properties: polar positive (yellow), polar negative (orange), polar neutral (green), non-polar neutral (purple), non-polar aliphatic (blue) and non-polar aromatic (pink). The used abbreviations correspond, by order of appearance, to the following species: Hosa – Human; Gogo – Gorilla; Patr – Chimpanzee; Papa – Bonobo; Poab – Orangutan; Nole – Gibbon; Mamu – Rhesus macaque; Sabo – Black-capped squirrel monkey; Caja – Marmoset; Otga – Bushbaby; Bota – Cow; Ovar – Sheep; Susc – Pig; Mupu – Ferret; Aime – Giant panda; Calu – Dog; Eqca – Horse; Mylu – Little brown myotis; Ptal – Black flying fox; Loaf – Elephant; Orcu – European rabbit; Crgr – Chinese hamster; Mumu – Mouse; Rano – Rat; Ictr – Squirrel; Capo – Guinea pig.
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pone-0081864-g005: Structural representation and identification of positively-selected branches and codons in mammalian MDA5.(A) Based on the human protein structure, the key domains of MDA5 (http://www.uniprot.org/uniprot/Q9BYX4) and the corresponding boundaries are schematically represented. Also, the human domain boundaries while in the mammalian MDA5 deduced protein sequences alignment (Figure S5) are shown in brackets. (B) Cladogram of 26 mammalian MDA5 genes collected from Ensembl and NCBI databases. Branch-site analyses were performed to identify specific branches episodic under positive selection. Branches with statistically significant likelihood ratio tests (LRTs) when performing PAML branch-site model A (Table 3) are colored in green; branches simultaneously identified by PAML branch-site model A and Hyphy branch-site REL method (Table 5) are colored in blue. (C) Positively-selected codons are exhibited in the table and numbered according to the mammalian MDA5 deduced protein sequences alignment (Figure S5). Symbol “?” represents an undetermined amino acid, while “-” symbolizes a deletion. Colors on the codon numbering row correspond to the MDA5 domain with the same color in the protein structural representation (A). The background colors on the identified sites match different amino acid properties: polar positive (yellow), polar negative (orange), polar neutral (green), non-polar neutral (purple), non-polar aliphatic (blue) and non-polar aromatic (pink). The used abbreviations correspond, by order of appearance, to the following species: Hosa – Human; Gogo – Gorilla; Patr – Chimpanzee; Papa – Bonobo; Poab – Orangutan; Nole – Gibbon; Mamu – Rhesus macaque; Sabo – Black-capped squirrel monkey; Caja – Marmoset; Otga – Bushbaby; Bota – Cow; Ovar – Sheep; Susc – Pig; Mupu – Ferret; Aime – Giant panda; Calu – Dog; Eqca – Horse; Mylu – Little brown myotis; Ptal – Black flying fox; Loaf – Elephant; Orcu – European rabbit; Crgr – Chinese hamster; Mumu – Mouse; Rano – Rat; Ictr – Squirrel; Capo – Guinea pig.

Mentions: Model M8 implemented in the PAML package [54,55] and Datamonkey web server [52,53] SLAC, FEL, REL, MEME and FUBAR methods [61-63] were used to detect specific codons under selection in the three RLR genes. Based on the methodology adopted by other authors and in previous studies [43,47,48,64], only codons identified by at least three of the six used methods are considered to be under positive selection (Table S3). Since the breadth of species included in each alignment is wide, by applying several methods to detect codons under positive selection and by overlapping the results, we should be decreasing the incidence of false positives. A total of sixteen codons for RIG-I (Figure 4), twenty for MDA5 (Figure 5) and ten for LGP2 (Figure 6) were identified as candidate codons under selective pressure. Regarding their location in each corresponding protein, the greatest number of these codons are located in protein functional domains, more specifically, eleven out of the sixteen RIG-I codons (~ 69%), ten out of the twenty MDA5 codons (50%) and seven out of the ten LGP2 codons (70%). To estimate the percentage of positively selected codons in the three proteins, we used human deduced protein sequences as a reference. Human LGP2 exhibited 1.47% (10/678) of codons under positive selection. Higher values were obtained for human MDA5 and RIG-I, 1.95% (20/1025) and 1.73% (16/925) of codons under selective pressure, respectively.


Positive evolutionary selection on the RIG-I-like receptor genes in mammals.

Lemos de Matos A, McFadden G, Esteves PJ - PLoS ONE (2013)

Structural representation and identification of positively-selected branches and codons in mammalian MDA5.(A) Based on the human protein structure, the key domains of MDA5 (http://www.uniprot.org/uniprot/Q9BYX4) and the corresponding boundaries are schematically represented. Also, the human domain boundaries while in the mammalian MDA5 deduced protein sequences alignment (Figure S5) are shown in brackets. (B) Cladogram of 26 mammalian MDA5 genes collected from Ensembl and NCBI databases. Branch-site analyses were performed to identify specific branches episodic under positive selection. Branches with statistically significant likelihood ratio tests (LRTs) when performing PAML branch-site model A (Table 3) are colored in green; branches simultaneously identified by PAML branch-site model A and Hyphy branch-site REL method (Table 5) are colored in blue. (C) Positively-selected codons are exhibited in the table and numbered according to the mammalian MDA5 deduced protein sequences alignment (Figure S5). Symbol “?” represents an undetermined amino acid, while “-” symbolizes a deletion. Colors on the codon numbering row correspond to the MDA5 domain with the same color in the protein structural representation (A). The background colors on the identified sites match different amino acid properties: polar positive (yellow), polar negative (orange), polar neutral (green), non-polar neutral (purple), non-polar aliphatic (blue) and non-polar aromatic (pink). The used abbreviations correspond, by order of appearance, to the following species: Hosa – Human; Gogo – Gorilla; Patr – Chimpanzee; Papa – Bonobo; Poab – Orangutan; Nole – Gibbon; Mamu – Rhesus macaque; Sabo – Black-capped squirrel monkey; Caja – Marmoset; Otga – Bushbaby; Bota – Cow; Ovar – Sheep; Susc – Pig; Mupu – Ferret; Aime – Giant panda; Calu – Dog; Eqca – Horse; Mylu – Little brown myotis; Ptal – Black flying fox; Loaf – Elephant; Orcu – European rabbit; Crgr – Chinese hamster; Mumu – Mouse; Rano – Rat; Ictr – Squirrel; Capo – Guinea pig.
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Related In: Results  -  Collection

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Show All Figures
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pone-0081864-g005: Structural representation and identification of positively-selected branches and codons in mammalian MDA5.(A) Based on the human protein structure, the key domains of MDA5 (http://www.uniprot.org/uniprot/Q9BYX4) and the corresponding boundaries are schematically represented. Also, the human domain boundaries while in the mammalian MDA5 deduced protein sequences alignment (Figure S5) are shown in brackets. (B) Cladogram of 26 mammalian MDA5 genes collected from Ensembl and NCBI databases. Branch-site analyses were performed to identify specific branches episodic under positive selection. Branches with statistically significant likelihood ratio tests (LRTs) when performing PAML branch-site model A (Table 3) are colored in green; branches simultaneously identified by PAML branch-site model A and Hyphy branch-site REL method (Table 5) are colored in blue. (C) Positively-selected codons are exhibited in the table and numbered according to the mammalian MDA5 deduced protein sequences alignment (Figure S5). Symbol “?” represents an undetermined amino acid, while “-” symbolizes a deletion. Colors on the codon numbering row correspond to the MDA5 domain with the same color in the protein structural representation (A). The background colors on the identified sites match different amino acid properties: polar positive (yellow), polar negative (orange), polar neutral (green), non-polar neutral (purple), non-polar aliphatic (blue) and non-polar aromatic (pink). The used abbreviations correspond, by order of appearance, to the following species: Hosa – Human; Gogo – Gorilla; Patr – Chimpanzee; Papa – Bonobo; Poab – Orangutan; Nole – Gibbon; Mamu – Rhesus macaque; Sabo – Black-capped squirrel monkey; Caja – Marmoset; Otga – Bushbaby; Bota – Cow; Ovar – Sheep; Susc – Pig; Mupu – Ferret; Aime – Giant panda; Calu – Dog; Eqca – Horse; Mylu – Little brown myotis; Ptal – Black flying fox; Loaf – Elephant; Orcu – European rabbit; Crgr – Chinese hamster; Mumu – Mouse; Rano – Rat; Ictr – Squirrel; Capo – Guinea pig.
Mentions: Model M8 implemented in the PAML package [54,55] and Datamonkey web server [52,53] SLAC, FEL, REL, MEME and FUBAR methods [61-63] were used to detect specific codons under selection in the three RLR genes. Based on the methodology adopted by other authors and in previous studies [43,47,48,64], only codons identified by at least three of the six used methods are considered to be under positive selection (Table S3). Since the breadth of species included in each alignment is wide, by applying several methods to detect codons under positive selection and by overlapping the results, we should be decreasing the incidence of false positives. A total of sixteen codons for RIG-I (Figure 4), twenty for MDA5 (Figure 5) and ten for LGP2 (Figure 6) were identified as candidate codons under selective pressure. Regarding their location in each corresponding protein, the greatest number of these codons are located in protein functional domains, more specifically, eleven out of the sixteen RIG-I codons (~ 69%), ten out of the twenty MDA5 codons (50%) and seven out of the ten LGP2 codons (70%). To estimate the percentage of positively selected codons in the three proteins, we used human deduced protein sequences as a reference. Human LGP2 exhibited 1.47% (10/678) of codons under positive selection. Higher values were obtained for human MDA5 and RIG-I, 1.95% (20/1025) and 1.73% (16/925) of codons under selective pressure, respectively.

Bottom Line: The highest number of positively selected codons was detected in MDA5, but a great percentage of these codons were located outside of the currently defined protein domains for MDA5, which likely reflects the imposition of both functional and structural constraints.Additionally, our results support LGP2 as being the least prone to evolutionary change, since the lowest number of codons under selection was observed for this gene.Furthermore, the RIG-I repressor domain, the region responsible for recognizing and binding to its RNA substrates, exhibited the strongest evidence of selective pressures.

View Article: PubMed Central - PubMed

Affiliation: CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos/InBio Laboratório Associado, Universidade do Porto, Vairão, Portugal ; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal ; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America.

ABSTRACT
The mammalian RIG-I-like receptors, RIG-I, MDA5 and LGP2, are a family of DExD/H box RNA helicases responsible for the cytoplasmic detection of viral RNA. These receptors detect a variety of RNA viruses, or DNA viruses that express unusual RNA species, many of which are responsible for a great number of severe and lethal diseases. Host innate sentinel proteins involved in pathogen recognition must rapidly evolve in a dynamic arms race with pathogens, and thus are subjected to long-term positive selection pressures to avoid potential infections. Using six codon-based Maximum Likelihood methods, we were able to identify specific codons under positive selection in each of these three genes. The highest number of positively selected codons was detected in MDA5, but a great percentage of these codons were located outside of the currently defined protein domains for MDA5, which likely reflects the imposition of both functional and structural constraints. Additionally, our results support LGP2 as being the least prone to evolutionary change, since the lowest number of codons under selection was observed for this gene. On the other hand, the preponderance of positively selected codons for RIG-I were detected in known protein functional domains, suggesting that pressure has been imposed by the vast number of viruses that are recognized by this RNA helicase. Furthermore, the RIG-I repressor domain, the region responsible for recognizing and binding to its RNA substrates, exhibited the strongest evidence of selective pressures. Branch-site analyses were performed and several species branches on the three receptor gene trees showed evidence of episodic positive selection. In conclusion, by looking for evidence of positive evolutionary selection on mammalian RIG-I-like receptor genes, we propose that a multitude of viruses have crafted the receptors biological function in host defense, specifically for the RIG-I gene, contributing to the innate species-specific resistance/susceptibility to diverse viral pathogens.

Show MeSH
Related in: MedlinePlus