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RNA editing and alternative splicing of the insect nAChR subunit alpha6 transcript: evolutionary conservation, divergence and regulation.

Jin Y, Tian N, Cao J, Liang J, Yang Z, Lv J - BMC Evol. Biol. (2007)

Bottom Line: The occurrence of alternative splicing was found to be regulated in distinct modes and, in some cases, even correlated with RNA editing.On the basis of comparative analysis of orthologous nAChR alpha6 genes from different insects spanning ~300 million years of evolution, we have documented the existence, evolutionary conservation and divergence, and also regulation of RNA editing and alternative splicing.Phylogenetic analysis of RNA editing and alternative splicing, which can create a multitude of functionally distinct protein isoforms, might have a crucial role in the evolution of complex organisms beyond nucleotide and protein sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, PR of China. jinyf@zju.edu.cn

ABSTRACT

Background: RNA editing and alternative splicing play an important role in expanding protein diversity and this is well illustrated in studies of nicotinic acetylcholine receptors (nAChRs).

Results: Here, we compare the RNA editing and alternative splicing of the nAChR alpha6 subunit genes from different insects spanning ~300 million years of evolution- Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum and Apis mellifera. The conserved and species-specific A-to-I RNA editing occurred across all species except A. gambiae, which displayed extraordinarily short flanking intronic sequences. Interestingly, some A-to-I editing sites were a genomically encoded G in other species. A combination of the experimental data and computational analysis of orthologous alpha6 genes from different species indicated that RNA editing and alternative splicing predated at least the radiation of insect orders spanning ~300 million years of evolution; however, they might have been lost in some species during subsequent evolution. The occurrence of alternative splicing was found to be regulated in distinct modes and, in some cases, even correlated with RNA editing.

Conclusion: On the basis of comparative analysis of orthologous nAChR alpha6 genes from different insects spanning ~300 million years of evolution, we have documented the existence, evolutionary conservation and divergence, and also regulation of RNA editing and alternative splicing. Phylogenetic analysis of RNA editing and alternative splicing, which can create a multitude of functionally distinct protein isoforms, might have a crucial role in the evolution of complex organisms beyond nucleotide and protein sequences.

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Multiple alignments and phylogenetic analysis of duplicated exon nucleotide sequences. (A, B) Multiple alignments of amino acid sequences of duplicated exon 3 (A) and exon 8 (B) sequences and their counterparts from orthologs in other species, respectively. The alternative exons are labeled 'a' and 'b' or 'c'. (C, D) Cladogram of insect duplicated exon DNA sequences and vertebrate orthologous constitutive exons corresponding to the alignments shown in (A, B). For each cluster, the amino acid sequences of each alternative exon from each species were aligned using the Clustal W program and phylogenetic trees generated. The branches contained the vertebrate constitutive exons (CSE), invertebrate alternative exons 8a or exons 3a, alternative exons 8b or exons 3b and alternative exons 8c, respectively. Abbreviations: Hsa, H. sapiens (NM_000746.3); Dre, D. rerio (NP_957513.1); Mmu, M. musculus (NP_031416.2); Gga, G. gallus (NP_989512.1); Tru, T. rubripes (CAG03274.1); Dme, D. melanogaster (CG4128) [16]; Aga, A. gambiae [17]; Bmo, B. mori (CH379590); Tca, T. castaneum (CM000280); Ame, A. mellifera [21].
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Figure 1: Multiple alignments and phylogenetic analysis of duplicated exon nucleotide sequences. (A, B) Multiple alignments of amino acid sequences of duplicated exon 3 (A) and exon 8 (B) sequences and their counterparts from orthologs in other species, respectively. The alternative exons are labeled 'a' and 'b' or 'c'. (C, D) Cladogram of insect duplicated exon DNA sequences and vertebrate orthologous constitutive exons corresponding to the alignments shown in (A, B). For each cluster, the amino acid sequences of each alternative exon from each species were aligned using the Clustal W program and phylogenetic trees generated. The branches contained the vertebrate constitutive exons (CSE), invertebrate alternative exons 8a or exons 3a, alternative exons 8b or exons 3b and alternative exons 8c, respectively. Abbreviations: Hsa, H. sapiens (NM_000746.3); Dre, D. rerio (NP_957513.1); Mmu, M. musculus (NP_031416.2); Gga, G. gallus (NP_989512.1); Tru, T. rubripes (CAG03274.1); Dme, D. melanogaster (CG4128) [16]; Aga, A. gambiae [17]; Bmo, B. mori (CH379590); Tca, T. castaneum (CM000280); Ame, A. mellifera [21].

Mentions: We next analyzed the evolutionary relationship of the alternative exons from D. melanogaster, A. gambiae, B. mori, T. castaneum and A. mellifera nAChR alpha6 genes. For these analyses we used D. melanogaster as the representative Drosophila species. Phylogenetic analyses indicated that A. mellifera did not contain an ortholog to the second alternative exon 3 while B. mori and A. gambiae lacked an ortholog to the first alternative exon 8[17,24] (Figure 1). The orthologs to the second alternative exon 8 were very highly conserved, with all amino acid sequences identical (Figure 1), although they are not highly conserved at the nucleotide level. The hierarchy of amino acid conservation of the alternative exons 8 of nAChR subunit alpha6 genes was exon 8b > exon 8a > exon 8c. Phylogenetic analysis of the protein products of equivalent duplicated exons showed that members of a duplicated pair were more similar to each other than to the exons from other genes (Figure 1). This evidence suggests that exon duplication predated at least the radiation of insect orders spanning ~300 million years of evolution.


RNA editing and alternative splicing of the insect nAChR subunit alpha6 transcript: evolutionary conservation, divergence and regulation.

Jin Y, Tian N, Cao J, Liang J, Yang Z, Lv J - BMC Evol. Biol. (2007)

Multiple alignments and phylogenetic analysis of duplicated exon nucleotide sequences. (A, B) Multiple alignments of amino acid sequences of duplicated exon 3 (A) and exon 8 (B) sequences and their counterparts from orthologs in other species, respectively. The alternative exons are labeled 'a' and 'b' or 'c'. (C, D) Cladogram of insect duplicated exon DNA sequences and vertebrate orthologous constitutive exons corresponding to the alignments shown in (A, B). For each cluster, the amino acid sequences of each alternative exon from each species were aligned using the Clustal W program and phylogenetic trees generated. The branches contained the vertebrate constitutive exons (CSE), invertebrate alternative exons 8a or exons 3a, alternative exons 8b or exons 3b and alternative exons 8c, respectively. Abbreviations: Hsa, H. sapiens (NM_000746.3); Dre, D. rerio (NP_957513.1); Mmu, M. musculus (NP_031416.2); Gga, G. gallus (NP_989512.1); Tru, T. rubripes (CAG03274.1); Dme, D. melanogaster (CG4128) [16]; Aga, A. gambiae [17]; Bmo, B. mori (CH379590); Tca, T. castaneum (CM000280); Ame, A. mellifera [21].
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Figure 1: Multiple alignments and phylogenetic analysis of duplicated exon nucleotide sequences. (A, B) Multiple alignments of amino acid sequences of duplicated exon 3 (A) and exon 8 (B) sequences and their counterparts from orthologs in other species, respectively. The alternative exons are labeled 'a' and 'b' or 'c'. (C, D) Cladogram of insect duplicated exon DNA sequences and vertebrate orthologous constitutive exons corresponding to the alignments shown in (A, B). For each cluster, the amino acid sequences of each alternative exon from each species were aligned using the Clustal W program and phylogenetic trees generated. The branches contained the vertebrate constitutive exons (CSE), invertebrate alternative exons 8a or exons 3a, alternative exons 8b or exons 3b and alternative exons 8c, respectively. Abbreviations: Hsa, H. sapiens (NM_000746.3); Dre, D. rerio (NP_957513.1); Mmu, M. musculus (NP_031416.2); Gga, G. gallus (NP_989512.1); Tru, T. rubripes (CAG03274.1); Dme, D. melanogaster (CG4128) [16]; Aga, A. gambiae [17]; Bmo, B. mori (CH379590); Tca, T. castaneum (CM000280); Ame, A. mellifera [21].
Mentions: We next analyzed the evolutionary relationship of the alternative exons from D. melanogaster, A. gambiae, B. mori, T. castaneum and A. mellifera nAChR alpha6 genes. For these analyses we used D. melanogaster as the representative Drosophila species. Phylogenetic analyses indicated that A. mellifera did not contain an ortholog to the second alternative exon 3 while B. mori and A. gambiae lacked an ortholog to the first alternative exon 8[17,24] (Figure 1). The orthologs to the second alternative exon 8 were very highly conserved, with all amino acid sequences identical (Figure 1), although they are not highly conserved at the nucleotide level. The hierarchy of amino acid conservation of the alternative exons 8 of nAChR subunit alpha6 genes was exon 8b > exon 8a > exon 8c. Phylogenetic analysis of the protein products of equivalent duplicated exons showed that members of a duplicated pair were more similar to each other than to the exons from other genes (Figure 1). This evidence suggests that exon duplication predated at least the radiation of insect orders spanning ~300 million years of evolution.

Bottom Line: The occurrence of alternative splicing was found to be regulated in distinct modes and, in some cases, even correlated with RNA editing.On the basis of comparative analysis of orthologous nAChR alpha6 genes from different insects spanning ~300 million years of evolution, we have documented the existence, evolutionary conservation and divergence, and also regulation of RNA editing and alternative splicing.Phylogenetic analysis of RNA editing and alternative splicing, which can create a multitude of functionally distinct protein isoforms, might have a crucial role in the evolution of complex organisms beyond nucleotide and protein sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, PR of China. jinyf@zju.edu.cn

ABSTRACT

Background: RNA editing and alternative splicing play an important role in expanding protein diversity and this is well illustrated in studies of nicotinic acetylcholine receptors (nAChRs).

Results: Here, we compare the RNA editing and alternative splicing of the nAChR alpha6 subunit genes from different insects spanning ~300 million years of evolution- Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum and Apis mellifera. The conserved and species-specific A-to-I RNA editing occurred across all species except A. gambiae, which displayed extraordinarily short flanking intronic sequences. Interestingly, some A-to-I editing sites were a genomically encoded G in other species. A combination of the experimental data and computational analysis of orthologous alpha6 genes from different species indicated that RNA editing and alternative splicing predated at least the radiation of insect orders spanning ~300 million years of evolution; however, they might have been lost in some species during subsequent evolution. The occurrence of alternative splicing was found to be regulated in distinct modes and, in some cases, even correlated with RNA editing.

Conclusion: On the basis of comparative analysis of orthologous nAChR alpha6 genes from different insects spanning ~300 million years of evolution, we have documented the existence, evolutionary conservation and divergence, and also regulation of RNA editing and alternative splicing. Phylogenetic analysis of RNA editing and alternative splicing, which can create a multitude of functionally distinct protein isoforms, might have a crucial role in the evolution of complex organisms beyond nucleotide and protein sequences.

Show MeSH