Evolution of CCL11: genetic characterization in lagomorphs and evidence of positive and purifying selection in mammals

Neves, Fabiana; Abrantes, Joana; Esteves, Pedro J.

doi:10.1177/1753425916647471

Cited by 7 publications

(7 citation statements)

References 57 publications

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“…Our outcomes reveal that several sites in other proteins, which are under substantial positive selection have been developing more swiftly than the mature protein [43][44][45]. As a result, the dynamic selection forces its change which concerns to improve the protein secretion efficacy, which is true in case of PD-L2 protein ( Figure 3C), which is unlike than the matured protein [46,47].…”

Section: Agingmentioning

confidence: 89%

Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates

Ahmad¹,

Zhou²,

Ahmad

et al. 2020

Aging

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Programmed cell death-1 (PD-1) and its ligands, particularly PD-L1 and PD-L2, are the most important proteins responsible for signaling T-cell inhibition and arbitrating immune homeostasis and tolerance mechanisms. However, the adaptive evolution of these genes is poorly understood. In this study, we aligned protein-coding genes from vertebrate species to evaluate positive selection constraints and evolution in the PD1, PD-L1 and PD-L2 genes conserved across up to 166 vertebrate species, with an average of 55 species per gene. We determined that although the positive selection was obvious, an average of 5.3% of codons underwent positive selection in the three genes across vertebrate lineages, and increased positive selection pressure was detected in both the Ig-like domains and transmembrane domains of the proteins. Moreover, the PD1, PD-L1 and PD-L2 genes were highly expressed in almost all tissues of the selected species indicating a distinct expression pattern in different tissues among most species. Our study reveals that adaptive selection plays a key role in the evolution of PD1 and its ligands in the majority of vertebrate species, which is in agreement with the contribution of these residues to the mechanisms of pathogen identification and coevolution in the complexity and novelties of vertebrate immune systems.

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Section: Agingmentioning

confidence: 89%

Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates

Ahmad¹,

Zhou²,

Ahmad

et al. 2020

Aging

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“…Virtual transcripts of Lepus and Ochotona TRIM5 PRYSPRY domains were created by splicing together the exons reads (~ 600 bp) and have been deposited in the GenBank database under the following accession numbers: #MN605824 ( Ochotona hoffmanni ), #MN605825 ( Ochotona hyperborean) , #MN605826 ( Ochotona mantchurica ), #MN605827 ( Ochotona pallasi ), #MN605828 ( Ochotona rutila ), #MN605829 ( Ochotona turuchanensis ), #MN605830 ( Ochotona alpina ), #MN605831 ( Ochotona pusilla ), #MN605832 ( Ochotona dauurica ), #MN605833 ( Lepus capensis ), #MN605834 ( Lepus castroviejoi ), #MN605835 ( Lepus corsicanus ), #MN605836 ( Lepus timidus ), #MN605837 ( Lepus townsendii ), #MN605838 ( Lepus americanus ), #MN605839 ( Lepus californicus ). Lepus and Ochotona samples have been used in previous publications [49–52]…”

Section: Methodsmentioning

confidence: 99%

Not so unique to Primates: The independent adaptive evolution of TRIM5 in Lagomorpha lineage

et al. 2019

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The plethora of restriction factors with the ability to inhibit the replication of retroviruses have been widely studied and genetic hallmarks of evolutionary selective pressures in Primates have been well documented. One example is the tripartite motif-containing protein 5 alpha (TRIM5α), a cytoplasmic factor that restricts retroviral infection in a species-specific fashion. In Lagomorphs, similarly to what has been observed in Primates, the specificity of TRIM5 restriction has been assigned to the PRYSPRY domain. In this study, we present the first insight of an intra-genus variability within the Lagomorpha TRIM5 PRYSPRY domain. Remarkably, and considering just the 32 residue-long v1 region of this domain, the deduced amino acid sequences of Daurian pika (Ochotona dauurica) and steppe pika (O. pusilla) evidenced a high divergence when compared to the remaining Ochotona species, presenting values of 44% and 66% of amino acid differences, respectively. The same evolutionary pattern was also observed when comparing the v1 region of two Sylvilagus species members (47% divergence). However, and unexpectedly, the PRYSPRY domain of Lepus species exhibited a great conservation. Our results show a high level of variation in the PRYSPRY domain of Lagomorpha species that belong to the same genus. This suggests that, throughout evolution, the Lagomorpha TRIM5 should have been influenced by constant selective pressures, likely as a result of multiple different retroviral infections.

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“…The remaining samples were available in the CIBIO tissue samples collection. Approval from an ethics committee was unnecessary since no animals were killed for the purpose of this study and these samples have been described and used in previous publications [15, 19, 22, 39–41]. Total RNA was extracted from liver tissue of one specimen of American pika by using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.…”

Section: Methodsmentioning

confidence: 99%

“…The study of CCL8 , a prime ligand of CCR5, revealed that this gene was pseudogenized only in those species that underwent the CCR5 alteration, while it remained intact in hares and Eastern cottontail ( S. floridanus ) [16, 17]. In contrast, CCL3, CCL4, CCL5 and CCL11 genes were found to be functional in all studied leporids [18, 19]. While in rabbit, mouse and rat CCL3 and CCL4 are encoded by a single functional gene, they are duplicated in other rodents such as squirrel and guinea pig, being either functional or inactivated [20, 21].…”

Section: Introductionmentioning

confidence: 99%

Evolution of CCL16 in Glires (Rodentia and Lagomorpha) shows an unusual random pseudogenization pattern

et al. 2019

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Background The C-C motif chemokine ligand 16 (CCL16) is a potent pro-inflammatory chemokine and a chemoattractant for monocytes and lymphocytes. In normal plasma, it is present at high concentrations and elicits its effects on cells by interacting with cell surface chemokine receptors. In the European rabbit and in rodents such as mouse, rat and guinea pig, CCL16 was identified as a pseudogene, while in the thirteen-lined ground squirrel it appears to be potentially functional. To gain insight into the evolution of this gene in the superorder Glires (rodents and lagomorphs), we amplified the CCL16 gene from eleven Leporidae and seven Ochotonidae species. Results We compared our sequences with CCL16 sequences of twelve rodent species retrieved from public databases. The data show that for all leporid species studied CCL16 is a pseudogene. This is primarily due to mutations at the canonical Cys Cys motif, creating either premature stop codons, or disrupting amino acid replacements. In the Mexican cottontail, CCL16 is pseudogenized due to a frameshift deletion. Additionally, in the exon 1 (signal peptide), there are frameshift deletions present in all leporids studied. In contrast, in Ochotona species, CCL16 is potentially functional, except for an allele in Hoffmann’s pika. In rodents, CCL16 is functional in a number of species, but patterns of pseudogenization similar to those observed in lagomorphs also exist. Conclusions Our results suggest that while functional in the Glires ancestor, CCL16 underwent pseudogenization in some species. This process occurred stochastically or in specific lineages at different moments in the evolution of Glires. These observations suggest that the CCL16 had different evolutionary constrains in the Glires group that could be associated with the CCL16 biological function. Electronic supplementary material The online version of this article (10.1186/s12862-019-1390-7) contains supplementary material, which is available to authorized users.

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Evolution of CCL11: genetic characterization in lagomorphs and evidence of positive and purifying selection in mammals

Cited by 7 publications

References 57 publications

Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates

Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates

Not so unique to Primates: The independent adaptive evolution of TRIM5 in Lagomorpha lineage

Evolution of CCL16 in Glires (Rodentia and Lagomorpha) shows an unusual random pseudogenization pattern

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