Organelle trans-splicing examples involve group II introns in the chloroplasts and mitochondria of plants and green algae, but discontinuous group I introns have also been reported from plants and early-branching animals (placazoans) [4?]. Nucleus-encoded genes can also undergo trans-splicing, and two broad splicing categories can be defined: the joining of separateprotein-coding exons via fragmented spliceosomal introns, and the splicing of a short UTR exon onto the 59 end of gene Hexaconazole manufacturer transcripts (spliced-leader (SL) trans-splicing) [1]. The former type is found rarely, with examples from Drosophila [7] and the protist Giardia intestinalis [8,9], whereas SL splicing is found broadly in eukaryotes including many metazoans, as well as protists such as dinoflagellates, diplonemids, and kinetoplastids [10?2]. Both nuclear transsplicing types rely on elements of the same spliceosomal machinery involved in classical intron Itacitinib chemical information removal via cis-splicing [12]. In dinoflagellates, SL trans-splicing occurs throughout dinoflagellate diversity, including the basal species Hematodinium sp., Oxyrrhis marina and Perkinsus marinus [13?5]. The dinoflagellate SL transcript is ,50?0 nucleotides long, and contains a 22nucleotide exon at the 59 end as well as downstream intron sequence. A conserved spliceosomal binding site occurs in the exon sequence, and the trans-splicing reaction apparently utilizes canonical GU-AG intron boundaries, with the GU donor dinucleotide encoded on the SL transcript intron. Dinoflagellate SL splicing is thought to be catalysed by components of the nuclear spliceosome [11]. Yet another type of trans-splicing occurs in the tRNA genes of Archaea, and involves reconstitution of introns characterised by a bulge-helix-bulge (B-H-B) motif at the intron-exon junctions; unlike the cases above, removal of B-H-B introns requires an endonuclease and a ligase [16].An Unusual RNA Trans-Splicing TypeRecently a further example of RNA trans-splicing has emerged, occurring in the mitochondrion of the dinoflagellate Karlodinium veneficum (synonym: K. micrum) [17,18]. While dinoflagellate mitochondrial genomes are among the smallest known in terms of gene content, encoding a paltry three proteins, these genomes are otherwise highly complex. The genes occur in multiple copies including numerous and variously fragmented forms, suggesting a genome that is highly recombinatorial [18,19]. For one of the K. veneficum mitochondrial genes, cox3, no intact gene remains on this genome. Despite this, complete transcripts of cox3 have been detected as oligoadenylated cDNAs, implying that the cox3 gene exons are transcribed and trans-spliced together to generate a complete mRNA [17]. Consistent with this, transcriptome data additionally reveal an oligoadenylated but truncated transcript encoding the first 85 (nucleotides 1?31) of this gene, corresponding to the largest cox3 gene fragment found in the genome. The remainder of cox3 occurs as a separate gene fragment (nucleotides 737?58), and a transcript of this fragment was presumed to complete the mRNA [17,18]. Two features of this trans-splicing case are unusual: 1) no genomic sequence around the splice sites could be identified that could participate in a known splicing reaction such as group I/II intron fragments, or bulgehelix-bulge formation; and 2) five, non-encoded adenosine nucleotides bridge the gap in cox3 transcripts between the two gene exons (nts 1?31, 737?58), presumably donated from the oligoadenosin.Organelle trans-splicing examples involve group II introns in the chloroplasts and mitochondria of plants and green algae, but discontinuous group I introns have also been reported from plants and early-branching animals (placazoans) [4?]. Nucleus-encoded genes can also undergo trans-splicing, and two broad splicing categories can be defined: the joining of separateprotein-coding exons via fragmented spliceosomal introns, and the splicing of a short UTR exon onto the 59 end of gene transcripts (spliced-leader (SL) trans-splicing) [1]. The former type is found rarely, with examples from Drosophila [7] and the protist Giardia intestinalis [8,9], whereas SL splicing is found broadly in eukaryotes including many metazoans, as well as protists such as dinoflagellates, diplonemids, and kinetoplastids [10?2]. Both nuclear transsplicing types rely on elements of the same spliceosomal machinery involved in classical intron removal via cis-splicing [12]. In dinoflagellates, SL trans-splicing occurs throughout dinoflagellate diversity, including the basal species Hematodinium sp., Oxyrrhis marina and Perkinsus marinus [13?5]. The dinoflagellate SL transcript is ,50?0 nucleotides long, and contains a 22nucleotide exon at the 59 end as well as downstream intron sequence. A conserved spliceosomal binding site occurs in the exon sequence, and the trans-splicing reaction apparently utilizes canonical GU-AG intron boundaries, with the GU donor dinucleotide encoded on the SL transcript intron. Dinoflagellate SL splicing is thought to be catalysed by components of the nuclear spliceosome [11]. Yet another type of trans-splicing occurs in the tRNA genes of Archaea, and involves reconstitution of introns characterised by a bulge-helix-bulge (B-H-B) motif at the intron-exon junctions; unlike the cases above, removal of B-H-B introns requires an endonuclease and a ligase [16].An Unusual RNA Trans-Splicing TypeRecently a further example of RNA trans-splicing has emerged, occurring in the mitochondrion of the dinoflagellate Karlodinium veneficum (synonym: K. micrum) [17,18]. While dinoflagellate mitochondrial genomes are among the smallest known in terms of gene content, encoding a paltry three proteins, these genomes are otherwise highly complex. The genes occur in multiple copies including numerous and variously fragmented forms, suggesting a genome that is highly recombinatorial [18,19]. For one of the K. veneficum mitochondrial genes, cox3, no intact gene remains on this genome. Despite this, complete transcripts of cox3 have been detected as oligoadenylated cDNAs, implying that the cox3 gene exons are transcribed and trans-spliced together to generate a complete mRNA [17]. Consistent with this, transcriptome data additionally reveal an oligoadenylated but truncated transcript encoding the first 85 (nucleotides 1?31) of this gene, corresponding to the largest cox3 gene fragment found in the genome. The remainder of cox3 occurs as a separate gene fragment (nucleotides 737?58), and a transcript of this fragment was presumed to complete the mRNA [17,18]. Two features of this trans-splicing case are unusual: 1) no genomic sequence around the splice sites could be identified that could participate in a known splicing reaction such as group I/II intron fragments, or bulgehelix-bulge formation; and 2) five, non-encoded adenosine nucleotides bridge the gap in cox3 transcripts between the two gene exons (nts 1?31, 737?58), presumably donated from the oligoadenosin.
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Cathepsins
