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RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons.

Kapitonov VV, Jurka J - PLoS Biol. (2005)

Bottom Line: Yet no transposase sequence similar to RAG1 or RAG2 has been found.Our results provide the first direct evidence linking RAG1 and RSSs to a specific superfamily of DNA transposons and indicate that the V(D)J machinery evolved from transposons.We also suggest that the RAG2 protein was not encoded by ancient Transib transposons but emerged in jawed vertebrates as a counterpart of RAG1 necessary for the V(D)J recombination reaction.

View Article: PubMed Central - PubMed

Affiliation: Genetic Information Research Institute, Mountain View, California, USA. vladimir@girinst.org

ABSTRACT
The V(D)J recombination reaction in jawed vertebrates is catalyzed by the RAG1 and RAG2 proteins, which are believed to have emerged approximately 500 million years ago from transposon-encoded proteins. Yet no transposase sequence similar to RAG1 or RAG2 has been found. Here we show that the approximately 600-amino acid "core" region of RAG1 required for its catalytic activity is significantly similar to the transposase encoded by DNA transposons that belong to the Transib superfamily. This superfamily was discovered recently based on computational analysis of the fruit fly and African malaria mosquito genomes. Transib transposons also are present in the genomes of sea urchin, yellow fever mosquito, silkworm, dog hookworm, hydra, and soybean rust. We demonstrate that recombination signal sequences (RSSs) were derived from terminal inverted repeats of an ancient Transib transposon. Furthermore, the critical DDE catalytic triad of RAG1 is shared with the Transib transposase as part of conserved motifs. We also studied several divergent proteins encoded by the sea urchin and lancelet genomes that are 25%-30% identical to the RAG1 N-terminal domain and the RAG1 core. Our results provide the first direct evidence linking RAG1 and RSSs to a specific superfamily of DNA transposons and indicate that the V(D)J machinery evolved from transposons. We propose that only the RAG1 core was derived from the Transib transposase, whereas the N-terminal domain was assembled from separate proteins of unknown function that may still be active in sea urchin, lancelet, hydra, and starlet sea anemone. We also suggest that the RAG2 protein was not encoded by ancient Transib transposons but emerged in jawed vertebrates as a counterpart of RAG1 necessary for the V(D)J recombination reaction.

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Structural Similarities between the Transib TIRs and V(D)J RSS SignalsThe species abbreviations are: AA, yellow fever mosquito; AG, African malaria mosquito; DM, D. melanogaster fruit fly DP, D. pseudoobscura fruit fly; SP, sea urchin. (Transib1 through Transib5 are from the fruit fly D. melanogaster).(A) Frequencies of the most frequent nucleotides at each position of the consensus sequence of the 5′ TIRs of transposons that belong to 20 families of Transib transposons identified in fruit flies and mosquitoes. The RSS23 consensus sequence is shown immediately under the TIRs consensus sequence. The most conserved nucleotides in the RSS23 heptamer and nonamer, which are necessary for efficient V(D)J recombination, are highlighted. The 23 ± 1 bp variable spacer is marked by Ns.(B) Non-gapped alignment of consensus sequences of 5′ TIRs from 21 families of Transib transposons.(C) The 12/23 rule follows from the basic structure of TIRs of the consensus sequences of transposons that belong to the Transib5, Transib2_AG, TransibN1_AG, TransibN2_AG, and TransibN3_AG families. The 5′ TIRs of these transposons are aligned with the corresponding 3′ TIRs. Structures of the 5′ and 3′ TIRs resemble RSS12 and RSS23, respectively.
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pbio-0030181-g004: Structural Similarities between the Transib TIRs and V(D)J RSS SignalsThe species abbreviations are: AA, yellow fever mosquito; AG, African malaria mosquito; DM, D. melanogaster fruit fly DP, D. pseudoobscura fruit fly; SP, sea urchin. (Transib1 through Transib5 are from the fruit fly D. melanogaster).(A) Frequencies of the most frequent nucleotides at each position of the consensus sequence of the 5′ TIRs of transposons that belong to 20 families of Transib transposons identified in fruit flies and mosquitoes. The RSS23 consensus sequence is shown immediately under the TIRs consensus sequence. The most conserved nucleotides in the RSS23 heptamer and nonamer, which are necessary for efficient V(D)J recombination, are highlighted. The 23 ± 1 bp variable spacer is marked by Ns.(B) Non-gapped alignment of consensus sequences of 5′ TIRs from 21 families of Transib transposons.(C) The 12/23 rule follows from the basic structure of TIRs of the consensus sequences of transposons that belong to the Transib5, Transib2_AG, TransibN1_AG, TransibN2_AG, and TransibN3_AG families. The 5′ TIRs of these transposons are aligned with the corresponding 3′ TIRs. Structures of the 5′ and 3′ TIRs resemble RSS12 and RSS23, respectively.

Mentions: All three core residues from the catalytic DDE triad in the RAG1 proteins (residues 603, 711, and 965) that are necessary for V(D)J recombination [21,22] are conserved in the Transib TPases (Figures 3 and Figure S3). This includes the distances between the second D and E residues, which are much longer in Transib transposons (206–214 aa) and RAG1 (253 aa) than in DDE TPases from other studied superfamilies (e.g., approximately 35-aa in Mariner/Tc1 [23], 2-aa in P [23], approximately 35-aa in Harbinger [24], with hAT as an exception (325-aa, [25]). Moreover, each catalytic residue is a part of a motif that is conserved in the Transib TPases and RAG1 (motifs 4, 6, and 10 in Figures 3 and Figure S3). The RAG1 core is composed of the N-terminal region and the central and C-terminal domains ([26,27]. The N-terminal region includes the RSS nonamer-binding regions (residues 387–480), referred to as NBR [28,29]. The two terminal motifs of RAG1 NBR are conserved in the Transib TPases (Figure S3), which indicates that they may be important for their binding to the Transib TIRs during transposition (the RSS-like structure of TIRs is described below; Figure 4). The central domain of the RAG1 core (residues 531–763) includes two aspartic acid residues from the DDE triad and is also thought to be involved in binding to the RSS heptamer and RAG2 [30,31].


RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons.

Kapitonov VV, Jurka J - PLoS Biol. (2005)

Structural Similarities between the Transib TIRs and V(D)J RSS SignalsThe species abbreviations are: AA, yellow fever mosquito; AG, African malaria mosquito; DM, D. melanogaster fruit fly DP, D. pseudoobscura fruit fly; SP, sea urchin. (Transib1 through Transib5 are from the fruit fly D. melanogaster).(A) Frequencies of the most frequent nucleotides at each position of the consensus sequence of the 5′ TIRs of transposons that belong to 20 families of Transib transposons identified in fruit flies and mosquitoes. The RSS23 consensus sequence is shown immediately under the TIRs consensus sequence. The most conserved nucleotides in the RSS23 heptamer and nonamer, which are necessary for efficient V(D)J recombination, are highlighted. The 23 ± 1 bp variable spacer is marked by Ns.(B) Non-gapped alignment of consensus sequences of 5′ TIRs from 21 families of Transib transposons.(C) The 12/23 rule follows from the basic structure of TIRs of the consensus sequences of transposons that belong to the Transib5, Transib2_AG, TransibN1_AG, TransibN2_AG, and TransibN3_AG families. The 5′ TIRs of these transposons are aligned with the corresponding 3′ TIRs. Structures of the 5′ and 3′ TIRs resemble RSS12 and RSS23, respectively.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC1131882&req=5

pbio-0030181-g004: Structural Similarities between the Transib TIRs and V(D)J RSS SignalsThe species abbreviations are: AA, yellow fever mosquito; AG, African malaria mosquito; DM, D. melanogaster fruit fly DP, D. pseudoobscura fruit fly; SP, sea urchin. (Transib1 through Transib5 are from the fruit fly D. melanogaster).(A) Frequencies of the most frequent nucleotides at each position of the consensus sequence of the 5′ TIRs of transposons that belong to 20 families of Transib transposons identified in fruit flies and mosquitoes. The RSS23 consensus sequence is shown immediately under the TIRs consensus sequence. The most conserved nucleotides in the RSS23 heptamer and nonamer, which are necessary for efficient V(D)J recombination, are highlighted. The 23 ± 1 bp variable spacer is marked by Ns.(B) Non-gapped alignment of consensus sequences of 5′ TIRs from 21 families of Transib transposons.(C) The 12/23 rule follows from the basic structure of TIRs of the consensus sequences of transposons that belong to the Transib5, Transib2_AG, TransibN1_AG, TransibN2_AG, and TransibN3_AG families. The 5′ TIRs of these transposons are aligned with the corresponding 3′ TIRs. Structures of the 5′ and 3′ TIRs resemble RSS12 and RSS23, respectively.
Mentions: All three core residues from the catalytic DDE triad in the RAG1 proteins (residues 603, 711, and 965) that are necessary for V(D)J recombination [21,22] are conserved in the Transib TPases (Figures 3 and Figure S3). This includes the distances between the second D and E residues, which are much longer in Transib transposons (206–214 aa) and RAG1 (253 aa) than in DDE TPases from other studied superfamilies (e.g., approximately 35-aa in Mariner/Tc1 [23], 2-aa in P [23], approximately 35-aa in Harbinger [24], with hAT as an exception (325-aa, [25]). Moreover, each catalytic residue is a part of a motif that is conserved in the Transib TPases and RAG1 (motifs 4, 6, and 10 in Figures 3 and Figure S3). The RAG1 core is composed of the N-terminal region and the central and C-terminal domains ([26,27]. The N-terminal region includes the RSS nonamer-binding regions (residues 387–480), referred to as NBR [28,29]. The two terminal motifs of RAG1 NBR are conserved in the Transib TPases (Figure S3), which indicates that they may be important for their binding to the Transib TIRs during transposition (the RSS-like structure of TIRs is described below; Figure 4). The central domain of the RAG1 core (residues 531–763) includes two aspartic acid residues from the DDE triad and is also thought to be involved in binding to the RSS heptamer and RAG2 [30,31].

Bottom Line: Yet no transposase sequence similar to RAG1 or RAG2 has been found.Our results provide the first direct evidence linking RAG1 and RSSs to a specific superfamily of DNA transposons and indicate that the V(D)J machinery evolved from transposons.We also suggest that the RAG2 protein was not encoded by ancient Transib transposons but emerged in jawed vertebrates as a counterpart of RAG1 necessary for the V(D)J recombination reaction.

View Article: PubMed Central - PubMed

Affiliation: Genetic Information Research Institute, Mountain View, California, USA. vladimir@girinst.org

ABSTRACT
The V(D)J recombination reaction in jawed vertebrates is catalyzed by the RAG1 and RAG2 proteins, which are believed to have emerged approximately 500 million years ago from transposon-encoded proteins. Yet no transposase sequence similar to RAG1 or RAG2 has been found. Here we show that the approximately 600-amino acid "core" region of RAG1 required for its catalytic activity is significantly similar to the transposase encoded by DNA transposons that belong to the Transib superfamily. This superfamily was discovered recently based on computational analysis of the fruit fly and African malaria mosquito genomes. Transib transposons also are present in the genomes of sea urchin, yellow fever mosquito, silkworm, dog hookworm, hydra, and soybean rust. We demonstrate that recombination signal sequences (RSSs) were derived from terminal inverted repeats of an ancient Transib transposon. Furthermore, the critical DDE catalytic triad of RAG1 is shared with the Transib transposase as part of conserved motifs. We also studied several divergent proteins encoded by the sea urchin and lancelet genomes that are 25%-30% identical to the RAG1 N-terminal domain and the RAG1 core. Our results provide the first direct evidence linking RAG1 and RSSs to a specific superfamily of DNA transposons and indicate that the V(D)J machinery evolved from transposons. We propose that only the RAG1 core was derived from the Transib transposase, whereas the N-terminal domain was assembled from separate proteins of unknown function that may still be active in sea urchin, lancelet, hydra, and starlet sea anemone. We also suggest that the RAG2 protein was not encoded by ancient Transib transposons but emerged in jawed vertebrates as a counterpart of RAG1 necessary for the V(D)J recombination reaction.

Show MeSH
Related in: MedlinePlus