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Immunogenetics2016; 68(5); 353-364; doi: 10.1007/s00251-016-0905-2

Positive selection in the SLC11A1 gene in the family Equidae.

Abstract: Immunity-related genes are a suitable model for studying effects of selection at the genomic level. Some of them are highly conserved due to functional constraints and purifying selection, while others are variable and change quickly to cope with the variation of pathogens. The SLC11A1 gene encodes a transporter protein mediating antimicrobial activity of macrophages. Little is known about the patterns of selection shaping this gene during evolution. Although it is a typical evolutionarily conserved gene, functionally important polymorphisms associated with various diseases were identified in humans and other species. We analyzed the genomic organization, genetic variation, and evolution of the SLC11A1 gene in the family Equidae to identify patterns of selection within this important gene. Nucleotide SLC11A1 sequences were shown to be highly conserved in ten equid species, with more than 97 % sequence identity across the family. Single nucleotide polymorphisms (SNPs) were found in the coding and noncoding regions of the gene. Seven codon sites were identified to be under strong purifying selection. Codons located in three regions, including the glycosylated extracellular loop, were shown to be under diversifying selection. A 3-bp indel resulting in a deletion of the amino acid 321 in the predicted protein was observed in all horses, while it has been maintained in all other equid species. This codon comprised in an N-glycosylation site was found to be under positive selection. Interspecific variation in the presence of predicted N-glycosylation sites was observed.
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Publication Date: 2016-02-04 PubMed ID: 26846480DOI: 10.1007/s00251-016-0905-2Google Scholar: Lookup
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  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The researchers studied the gene SLC11A1 in the family Equidae, which includes horses and related species. Their findings suggest the gene, which is important for immune response, has been under strong evolutionary influence to both preserve and diversify aspects of its makeup.

Background and Purpose of Study

  • The study focuses on the SLC11A1 gene that encodes for a transporter protein that has antimicrobial activities in macrophages, a type of immune cell.
  • This gene has been identified in humans and other species, having numerous polymorphisms tied to various diseases, but relatively little is known about its evolution over time or how natural selection has shaped it.
  • The researchers aimed to analyze the genomic organization, genetic variation, and evolution of this gene in the family Equidae (which includes horses and related species), looking for specific patterns of selection within the gene that may provide insights into its role in immunity.

Research Methods and Findings

  • By analyzing nucleotide sequences of the SLC11A1 gene across ten different species within the family Equidae, the research team found that the gene is highly conserved, having more than 97% identical sequence across all species studied.
  • However, they also identified several single nucleotide polymorphisms (SNPs) in both the coding and noncoding regions of the gene, suggesting some variation.
  • They identified seven codon sites in the gene that are under strong purifying selection – meaning they remain relatively unchanged over time due to the selective pressure to preserve their function.
  • Yet, they also discovered codons (the specific DNA sequence that codes for a protein) in three different regions of the gene that appear to be under diversifying selection, suggesting they have changed over time to adapt to different threats.
  • One such change that occurred uniformly in all horses studied was a deletion of the amino acid 321 in the predicted protein, while this amino acid was maintained in all other species in the family Equidae.
  • This particular codon, part of a site for N-glycosylation (the process where sugars attach to proteins), was under positive selection, suggesting some evolutionary benefit to the change.
  • The research team also noticed interspecific variation in the presence of predicted N-glycosylation sites, meaning these sites differed between species.

Conclusions

  • The findings provide insights into the evolution of the SLC11A1 gene within the Equidae family hinting at its importance in their immune response system and the adaptability required to cope up with varying pathogens.
  • This combination of strong purifying selection and diversifying selection indicates that while the gene’s core function is conserved to a large degree, certain aspects of its structure and function have evolved in response to environmental pressures, possibly including interactions with pathogens. This highlights both the stability and adaptability innate to immune systems.

Cite This Article

APA
Bayerova Z, Janova E, Matiasovic J, Orlando L, Horin P. (2016). Positive selection in the SLC11A1 gene in the family Equidae. Immunogenetics, 68(5), 353-364. https://doi.org/10.1007/s00251-016-0905-2

Publication

Immunogenetics
ISSN: 1432-1211
NlmUniqueID: 0420404
Country: United States
Language: English
Volume: 68
Issue: 5
Pages: 353-364

Researcher Affiliations

Bayerova, Zuzana
  • Department of Animal Genetics, Research Group Immunogenomics, Ceitec VFU, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.
Janova, Eva
  • Department of Animal Genetics, Research Group Immunogenomics, Ceitec VFU, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.
Matiasovic, Jan
  • Department of Immunology, Veterinary Research Institute, Brno, Czech Republic.
Orlando, Ludovic
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Horin, Petr
  • Department of Animal Genetics, Research Group Immunogenomics, Ceitec VFU, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic. horin@dior.ics.muni.cz.

MeSH Terms

  • Animals
  • Cation Transport Proteins / genetics
  • Codon / genetics
  • Equidae / genetics
  • Evolution, Molecular
  • Genomics
  • Phylogeny
  • Polymorphism, Single Nucleotide / genetics
  • Selection, Genetic / genetics

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Citations

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