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AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity.

MacDuff DA, Demorest ZL, Harris RS - Nucleic Acids Res. (2009)

Bottom Line: We found that AID can inhibit the retrotransposition of L1 through a DNA deamination-independent mechanism.This mechanism may manifest in the cytoplasmic compartment co- or posttranslationally.Together with evidence for AID expression in the ovary, our data combined to suggest that AID has innate immune functions in addition to its integral roles in creating antibody diversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.

ABSTRACT
Retrotransposons make up over 40% of the mammalian genome. Some copies are still capable of mobilizing and new insertions promote genetic variation. Several members of the APOBEC3 family of DNA cytosine deaminases function to limit the replication of a variety of retroelements, such as the long-terminal repeat (LTR)-containing MusD and Ty1 elements, and that of the non-LTR retrotransposons, L1 and Alu. However, the APOBEC3 genes are limited to mammalian lineages, whereas retrotransposons are far more widespread. This raises the question of what cellular factors control retroelement transposition in species that lack APOBEC3 genes. A strong phylogenetic case can be made that an ancestral activation-induced deaminase (AID)-like gene duplicated and diverged to root the APOBEC3 lineage in mammals. Therefore, we tested the hypothesis that present-day AID proteins possess anti-retroelement activity. We found that AID can inhibit the retrotransposition of L1 through a DNA deamination-independent mechanism. This mechanism may manifest in the cytoplasmic compartment co- or posttranslationally. Together with evidence for AID expression in the ovary, our data combined to suggest that AID has innate immune functions in addition to its integral roles in creating antibody diversity.

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(A) AID amino acid sequence alignments. Identical and similar residues are indicated by asterisks and colons, respectively. Positions of amino acid substitutions are indicated with filled circles, and the C-terminal deletion is indicated with a horizontal line. (B) Phylogenetic tree of the AID genes used. Branch lengths represent the evolutionary distance in nucleotide changes per codon (see scale bar). The bootstrap (confidence) value for each branch is indicated. (C) Mutation of E. coli genomic DNA by various vertebrate AID proteins. Each ‘x’ represents the mutation frequency of an independent culture, calculated as the number of RifR colonies per viable cell. Six independent cultures were assayed for each AID variant, and the median mutation frequencies are indicated by the horizontal bars. Vector represents the background level of mutation in ung-deficient E. coli.
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Figure 1: (A) AID amino acid sequence alignments. Identical and similar residues are indicated by asterisks and colons, respectively. Positions of amino acid substitutions are indicated with filled circles, and the C-terminal deletion is indicated with a horizontal line. (B) Phylogenetic tree of the AID genes used. Branch lengths represent the evolutionary distance in nucleotide changes per codon (see scale bar). The bootstrap (confidence) value for each branch is indicated. (C) Mutation of E. coli genomic DNA by various vertebrate AID proteins. Each ‘x’ represents the mutation frequency of an independent culture, calculated as the number of RifR colonies per viable cell. Six independent cultures were assayed for each AID variant, and the median mutation frequencies are indicated by the horizontal bars. Vector represents the background level of mutation in ung-deficient E. coli.

Mentions: We hypothesized that present day AID (either mammalian or non-mammalian) has the ability to inhibit the replication of retroelements, similar to that of the related APOBEC3 (A3) proteins. Towards testing this hypothesis, we acquired and (sub)cloned AID cDNAs from eight representative vertebrate species (Figures 1A and B) and confirmed their ability to mutate DNA using an E. coli-based DNA mutation assay (Figure 1C and Supplementary Figure S2). Expression of all of the AID proteins in E. coli increased the frequency of occurrence of Rifampicin-resistant (RifR) E. coli colonies, ranging from 2.2-fold (pufferfish AID) to 12.4-fold (zebrafish AID) over the empty vector. Almost all of these proteins have been shown to elicit activity in E. coli previously and, as discussed in these studies, the variation in the mutation frequencies observed here may be due to differences in protein expression, optimal temperatures for enzymatic activity, intrinsic enzymatic activity and/or other factors (43,56–58). Regardless of the multiple explanations, the most important points from these initial studies were that all of these AID cDNAs were capable of encoding a catalytically active protein and that they were therefore suitable for subsequent experimentation.Figure 1.


AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity.

MacDuff DA, Demorest ZL, Harris RS - Nucleic Acids Res. (2009)

(A) AID amino acid sequence alignments. Identical and similar residues are indicated by asterisks and colons, respectively. Positions of amino acid substitutions are indicated with filled circles, and the C-terminal deletion is indicated with a horizontal line. (B) Phylogenetic tree of the AID genes used. Branch lengths represent the evolutionary distance in nucleotide changes per codon (see scale bar). The bootstrap (confidence) value for each branch is indicated. (C) Mutation of E. coli genomic DNA by various vertebrate AID proteins. Each ‘x’ represents the mutation frequency of an independent culture, calculated as the number of RifR colonies per viable cell. Six independent cultures were assayed for each AID variant, and the median mutation frequencies are indicated by the horizontal bars. Vector represents the background level of mutation in ung-deficient E. coli.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2665220&req=5

Figure 1: (A) AID amino acid sequence alignments. Identical and similar residues are indicated by asterisks and colons, respectively. Positions of amino acid substitutions are indicated with filled circles, and the C-terminal deletion is indicated with a horizontal line. (B) Phylogenetic tree of the AID genes used. Branch lengths represent the evolutionary distance in nucleotide changes per codon (see scale bar). The bootstrap (confidence) value for each branch is indicated. (C) Mutation of E. coli genomic DNA by various vertebrate AID proteins. Each ‘x’ represents the mutation frequency of an independent culture, calculated as the number of RifR colonies per viable cell. Six independent cultures were assayed for each AID variant, and the median mutation frequencies are indicated by the horizontal bars. Vector represents the background level of mutation in ung-deficient E. coli.
Mentions: We hypothesized that present day AID (either mammalian or non-mammalian) has the ability to inhibit the replication of retroelements, similar to that of the related APOBEC3 (A3) proteins. Towards testing this hypothesis, we acquired and (sub)cloned AID cDNAs from eight representative vertebrate species (Figures 1A and B) and confirmed their ability to mutate DNA using an E. coli-based DNA mutation assay (Figure 1C and Supplementary Figure S2). Expression of all of the AID proteins in E. coli increased the frequency of occurrence of Rifampicin-resistant (RifR) E. coli colonies, ranging from 2.2-fold (pufferfish AID) to 12.4-fold (zebrafish AID) over the empty vector. Almost all of these proteins have been shown to elicit activity in E. coli previously and, as discussed in these studies, the variation in the mutation frequencies observed here may be due to differences in protein expression, optimal temperatures for enzymatic activity, intrinsic enzymatic activity and/or other factors (43,56–58). Regardless of the multiple explanations, the most important points from these initial studies were that all of these AID cDNAs were capable of encoding a catalytically active protein and that they were therefore suitable for subsequent experimentation.Figure 1.

Bottom Line: We found that AID can inhibit the retrotransposition of L1 through a DNA deamination-independent mechanism.This mechanism may manifest in the cytoplasmic compartment co- or posttranslationally.Together with evidence for AID expression in the ovary, our data combined to suggest that AID has innate immune functions in addition to its integral roles in creating antibody diversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.

ABSTRACT
Retrotransposons make up over 40% of the mammalian genome. Some copies are still capable of mobilizing and new insertions promote genetic variation. Several members of the APOBEC3 family of DNA cytosine deaminases function to limit the replication of a variety of retroelements, such as the long-terminal repeat (LTR)-containing MusD and Ty1 elements, and that of the non-LTR retrotransposons, L1 and Alu. However, the APOBEC3 genes are limited to mammalian lineages, whereas retrotransposons are far more widespread. This raises the question of what cellular factors control retroelement transposition in species that lack APOBEC3 genes. A strong phylogenetic case can be made that an ancestral activation-induced deaminase (AID)-like gene duplicated and diverged to root the APOBEC3 lineage in mammals. Therefore, we tested the hypothesis that present-day AID proteins possess anti-retroelement activity. We found that AID can inhibit the retrotransposition of L1 through a DNA deamination-independent mechanism. This mechanism may manifest in the cytoplasmic compartment co- or posttranslationally. Together with evidence for AID expression in the ovary, our data combined to suggest that AID has innate immune functions in addition to its integral roles in creating antibody diversity.

Show MeSH
Related in: MedlinePlus