Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys

@article{Holland2018ExpansionsDA,
  title={Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys},
  author={Stephen J Holland and Lesley M. Berghuis and Justin J King and Lakshminarayan M. Iyer and Katarzyna Sikora and Heather Fifield and Sarah Peter and Emma M. Quinlan and Fumiaki Sugahara and Prashant Shingate and In{\^e}s Trancoso and Norimasa Iwanami and Elena N. Temereva and C M Strohmeier and Shigeru Kuratani and Byrappa Venkatesh and Guillaume Evanno and L. Aravind and Michael Schorpp and Mani Larijani and Thomas Boehm},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={2018},
  volume={115},
  pages={E3211 - E3220}
}
Significance Cytidine deaminases of the AID/APOBEC family mutate the genetic material of pathogens or contribute to the generation and diversification of antibody repertoires in jawed vertebrates. In the extant jawless vertebrate, the lamprey, two members of the AID/APOBEC family are implicated in the somatic diversification of variable lymphocyte receptor (VLR) repertoires. We discovered an unexpected diversity of cytidine deaminase genes within and among lamprey species. The cytidine… 

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References

SHOWING 1-10 OF 84 REFERENCES

Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity

It is proposed that biological conflicts of AADs with viruses and genomic retroelements are drivers of rapid AAD evolution, suggesting a widespread presence of mutagenesis-based immune-defense systems.

The AID/APOBEC family of nucleic acid mutators

SummaryThe AID/APOBECs, a group of cytidine deaminases, represent a somewhat unusual protein family that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to

Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase

Lamprey lymphocytes express two putative deaminases of the AID-APOBEC family that may be involved in VLR diversification, as indicated by in vitro mutagenesis and recombination assays.

Evolution of vertebrate adaptive immunity: Immune cells and tissues, and AID/APOBEC cytidine deaminases

  • M. Hirano
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 2015
These findings suggest that three basic types of lymphocytes, one B‐like and two T‐like, are an essential feature of vertebrate adaptive immunity.

Biochemical Regulatory Features of Activation-Induced Cytidine Deaminase Remain Conserved from Lampreys to Humans

Investigation of the biochemical properties of AID from a sea lamprey, nurse shark, tetraodon, and coelacanth: representative species chosen because their lineages diverged at the earliest critical junctures in evolution of adaptive immunity found that these earliest-diverged AID orthologs are active cytidine deaminases that exhibit unique substrate specificities and thermosensitivities.

AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification

It is shown that expression of AID in Escherichia coli gives a mutator phenotype that yields nucleotide transitions at dC/dG in a context-dependent manner, which indicates that AID functions by deaminating dC residues in DNA.

The mutation spectrum of purified AID is similar to the mutability index in Ramos cells and in ung−/−msh2−/− mice

The activity of AID on single-stranded DNA produces the same mutation pattern as double-Stranded DNA in hypermutating cells, lending support to the DNA deamination model and indicating that AID does not require co-factors for its WRC specificity.

A Novel Regulator of Activation-Induced Cytidine Deaminase/APOBECs in Immunity and Cancer: Schrödinger’s CATalytic Pocket

It is proposed that variable pocket closure rates across AID/APOBEC3s underlie differential activity in immunity and cancer and is compared with the merits of classical approaches of X-ray and NMR, with that of emerging computational–biochemical approaches, for structural elucidation specifically for AID and APOBEC 3.

Organization of lamprey variable lymphocyte receptor C locus and repertoire development

This analysis indicates that VLRC sequences are well conserved in sea lamprey (Petromyzon marinus), L. camtschaticum, and European brook lampreys (Lampetra planeri), and provides insight into the unique molecular strategies used for VL RC gene assembly and repertoire diversification.
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