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Evolution of a TRIM5-CypA splice isoform in old world monkeys.

Newman RM, Hall L, Kirmaier A, Pozzi LA, Pery E, Farzan M, O'Neil SP, Johnson W - PLoS Pathog. (2008)

Bottom Line: The CypA insertion is linked to a mutation in the 3' splice site upstream of exon 7, which may prevent or reduce expression of the alpha-isoform.HIV-1 infectivity remained significantly lower than SIV infectivity, but was not rescued by treatment with cyclosporine A.Thus, unlike owl monkey TRIMCyp, expression of the macaque TRIM5-CypA isoform does not result in increased restriction of HIV-1.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Molecular Genetics, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America.

ABSTRACT
The TRIM family proteins share a conserved arrangement of three adjacent domains, an N-terminal RING domain, followed by one or two B-boxes and a coiled-coil, which constitutes the tripartite-motif for which the family is named. However, the C-termini of TRIM proteins vary, and include at least nine evolutionarily distinct, unrelated protein domains. Antiviral restriction factor TRIM5alpha has a C-terminal B30.2/SPRY domain, which is the major determinant of viral target specificity. Here, we describe the evolution of a cyclophilin-A encoding exon downstream of the TRIM5 locus of Asian macaques. Alternative splicing gives rise to chimeric transcripts encoding the TRIM motif fused to a C-terminal CypA domain (TRIM5-CypA). We detected TRIM5-CypA chimeric transcripts in primary lymphocytes from two macaque species. These were derived in part from a CypA pseudogene in the TRIM5 locus, which is distinct from the previously described CypA insertion in TRIM5 of owl monkeys. The CypA insertion is linked to a mutation in the 3' splice site upstream of exon 7, which may prevent or reduce expression of the alpha-isoform. All pig-tailed macaques (M. nemestrina) screened were homozygous for the CypA insertion. In contrast, the CypA-containing allele was present in 17% (17/101) of rhesus macaques (M. mulatta). The block to HIV-1 infection in lymphocytes from animals bearing the TRIM5-CypA allele was weaker than that in cells from wild type animals. HIV-1 infectivity remained significantly lower than SIV infectivity, but was not rescued by treatment with cyclosporine A. Thus, unlike owl monkey TRIMCyp, expression of the macaque TRIM5-CypA isoform does not result in increased restriction of HIV-1. Despite its distinct evolutionary origin, Macaca TRIM5-CypA has a similar domain arrangement and shares approximately 80% amino-acid identity with the TRIMCyp protein of owl monkeys. The independent appearance of TRIM5-CypA chimeras in two primate lineages constitutes a remarkable example of convergent evolution. Based on the presence of the CypA insertion in separate macaque lineages, and its absence from sooty mangabeys, we estimate that the Macaca TRIM5-CypA variant appeared 5-10 million years ago in a common ancestor of the Asian macaques. Whether the formation of novel genes through alternative splicing has played a wider role in the evolution of the TRIM family remains to be investigated.

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5′ junction of the inserted CypA pseudogene.The first 56 nucleotides of the insertion are underlined. The first nucleotide of the inserted sequence is indicated with an arrow, and occurs just after nucleotide position 671,500 of rhesus macaque chromosome 14 (accession # NW_001100384, based on M. mulatta reference assembly Mmu1 01212), in or near the 3′UTR of TRIM5. The 3′ss AG dinucleotide and the first methionine codon in the CypA pseudogene are in boldface. Splicing from the end of TRIM5 exon-6 occurs 35 bases upstream of the AUG, but maintains a continuous open reading frame.
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ppat-1000003-g004: 5′ junction of the inserted CypA pseudogene.The first 56 nucleotides of the insertion are underlined. The first nucleotide of the inserted sequence is indicated with an arrow, and occurs just after nucleotide position 671,500 of rhesus macaque chromosome 14 (accession # NW_001100384, based on M. mulatta reference assembly Mmu1 01212), in or near the 3′UTR of TRIM5. The 3′ss AG dinucleotide and the first methionine codon in the CypA pseudogene are in boldface. Splicing from the end of TRIM5 exon-6 occurs 35 bases upstream of the AUG, but maintains a continuous open reading frame.

Mentions: Expression of TRIM5-CypA as the result of splicing from TRIM5 to the downstream CypA must also depend on cis-acting splice signals. The alternative 3′ss AG dinucleotide used for generation of chimeric TRIM5-CypA transcripts was present within the inserted CypA sequence, and the insertion itself occurred immediately downstream of a pyrimidine-rich tract (Figure 4). Thus, insertion resulted in the juxtaposition of two critical elements (a polypyrimidine tract followed by an AG dinucleotide) that are likely to facilitate formation of the TRIM5-CypA transcripts by alternative splicing [33]. Additionally, a single G-to-T substitution in the 3′splice acceptor upstream of TRIM5 exon-7 (AG to AU in the unprocessed RNA), which we always found linked to the CypA insertion, may represent a further adaptation to favor expression of TRIM5-CypA isoforms by preventing or reducing expression of the TRIM5α and TRIM5δ splice-isoforms. However, from the present data, it is not possible to determine whether the G/T substitution in the intron-6 3′ss occurred after insertion of the CypA pseudogene, or whether it was already present at the time of insertion.


Evolution of a TRIM5-CypA splice isoform in old world monkeys.

Newman RM, Hall L, Kirmaier A, Pozzi LA, Pery E, Farzan M, O'Neil SP, Johnson W - PLoS Pathog. (2008)

5′ junction of the inserted CypA pseudogene.The first 56 nucleotides of the insertion are underlined. The first nucleotide of the inserted sequence is indicated with an arrow, and occurs just after nucleotide position 671,500 of rhesus macaque chromosome 14 (accession # NW_001100384, based on M. mulatta reference assembly Mmu1 01212), in or near the 3′UTR of TRIM5. The 3′ss AG dinucleotide and the first methionine codon in the CypA pseudogene are in boldface. Splicing from the end of TRIM5 exon-6 occurs 35 bases upstream of the AUG, but maintains a continuous open reading frame.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2279257&req=5

ppat-1000003-g004: 5′ junction of the inserted CypA pseudogene.The first 56 nucleotides of the insertion are underlined. The first nucleotide of the inserted sequence is indicated with an arrow, and occurs just after nucleotide position 671,500 of rhesus macaque chromosome 14 (accession # NW_001100384, based on M. mulatta reference assembly Mmu1 01212), in or near the 3′UTR of TRIM5. The 3′ss AG dinucleotide and the first methionine codon in the CypA pseudogene are in boldface. Splicing from the end of TRIM5 exon-6 occurs 35 bases upstream of the AUG, but maintains a continuous open reading frame.
Mentions: Expression of TRIM5-CypA as the result of splicing from TRIM5 to the downstream CypA must also depend on cis-acting splice signals. The alternative 3′ss AG dinucleotide used for generation of chimeric TRIM5-CypA transcripts was present within the inserted CypA sequence, and the insertion itself occurred immediately downstream of a pyrimidine-rich tract (Figure 4). Thus, insertion resulted in the juxtaposition of two critical elements (a polypyrimidine tract followed by an AG dinucleotide) that are likely to facilitate formation of the TRIM5-CypA transcripts by alternative splicing [33]. Additionally, a single G-to-T substitution in the 3′splice acceptor upstream of TRIM5 exon-7 (AG to AU in the unprocessed RNA), which we always found linked to the CypA insertion, may represent a further adaptation to favor expression of TRIM5-CypA isoforms by preventing or reducing expression of the TRIM5α and TRIM5δ splice-isoforms. However, from the present data, it is not possible to determine whether the G/T substitution in the intron-6 3′ss occurred after insertion of the CypA pseudogene, or whether it was already present at the time of insertion.

Bottom Line: The CypA insertion is linked to a mutation in the 3' splice site upstream of exon 7, which may prevent or reduce expression of the alpha-isoform.HIV-1 infectivity remained significantly lower than SIV infectivity, but was not rescued by treatment with cyclosporine A.Thus, unlike owl monkey TRIMCyp, expression of the macaque TRIM5-CypA isoform does not result in increased restriction of HIV-1.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Molecular Genetics, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America.

ABSTRACT
The TRIM family proteins share a conserved arrangement of three adjacent domains, an N-terminal RING domain, followed by one or two B-boxes and a coiled-coil, which constitutes the tripartite-motif for which the family is named. However, the C-termini of TRIM proteins vary, and include at least nine evolutionarily distinct, unrelated protein domains. Antiviral restriction factor TRIM5alpha has a C-terminal B30.2/SPRY domain, which is the major determinant of viral target specificity. Here, we describe the evolution of a cyclophilin-A encoding exon downstream of the TRIM5 locus of Asian macaques. Alternative splicing gives rise to chimeric transcripts encoding the TRIM motif fused to a C-terminal CypA domain (TRIM5-CypA). We detected TRIM5-CypA chimeric transcripts in primary lymphocytes from two macaque species. These were derived in part from a CypA pseudogene in the TRIM5 locus, which is distinct from the previously described CypA insertion in TRIM5 of owl monkeys. The CypA insertion is linked to a mutation in the 3' splice site upstream of exon 7, which may prevent or reduce expression of the alpha-isoform. All pig-tailed macaques (M. nemestrina) screened were homozygous for the CypA insertion. In contrast, the CypA-containing allele was present in 17% (17/101) of rhesus macaques (M. mulatta). The block to HIV-1 infection in lymphocytes from animals bearing the TRIM5-CypA allele was weaker than that in cells from wild type animals. HIV-1 infectivity remained significantly lower than SIV infectivity, but was not rescued by treatment with cyclosporine A. Thus, unlike owl monkey TRIMCyp, expression of the macaque TRIM5-CypA isoform does not result in increased restriction of HIV-1. Despite its distinct evolutionary origin, Macaca TRIM5-CypA has a similar domain arrangement and shares approximately 80% amino-acid identity with the TRIMCyp protein of owl monkeys. The independent appearance of TRIM5-CypA chimeras in two primate lineages constitutes a remarkable example of convergent evolution. Based on the presence of the CypA insertion in separate macaque lineages, and its absence from sooty mangabeys, we estimate that the Macaca TRIM5-CypA variant appeared 5-10 million years ago in a common ancestor of the Asian macaques. Whether the formation of novel genes through alternative splicing has played a wider role in the evolution of the TRIM family remains to be investigated.

Show MeSH
Related in: MedlinePlus