Pre-mRNA trans-splicing: from kinetoplastids to mammals, an easy language for life diversity

Abstract

Since the discovery that genes are split into intron and exons, the studies of the mechanisms involved in splicing pointed to presence of consensus signals in an attempt to generalize the process for all living cells. However, as discussed in the present review, splicing is a theme full of variations. The trans-splicing of pre-mRNAs, the joining of exons from distinct transcripts, is one of these variations with broad distribution in the phylogenetic tree. The biological meaning of this phenomenon is discussed encompassing reactions resembling a possible noise to mechanisms of gene expression regulation. All of them however, can contribute to the generation of life diversity.Key words: RNA processing -alternative trans-splicing -spliced leader RNA -trypanosomatids -nematodes -mammalian Most of the protein-coding eukaryotic genes display an interrupted structure alternating exons and introns. After transcription, introns must be removed from the primary transcript (pre-mRNA) to generate a translatable mature mRNA. It is interesting to note that the mature mRNA is constituted of 5' and 3' untranslatable regions (UTR) flanking the open reading frame (ORF) and that UTR are also exons. The precise excision of the introns and the joining of neighboring exons is a complex process generally named splicing, and when this processing occurs within a single pre-mRNA molecule it can also be called cis-splicing (Moore et al. 1993, Burge et al. 1999.Cis-splicing occurs in a two-step mechanism, each step consisting of a transesterification reaction (Moore et al. 1993) (Fig. 1A). The spliceosome, a ribonucleoprotein machinery composed of five small ribonucleoproteins (U1, U2, U4, U5, U6 snRNPs, named in relation to the kind of associated RNA molecule) and approximately 300 distinct proteins, is responsible for the splicing catalysis (Burge et al. 1999).Much effort was expended on the comprehension of the structure and dynamics of this complex machine during the splicing process, but the rules that discriminate introns and exons within the message are still poorly understood. Nevertheless, four conserved pre-mRNA sequence elements, which interact with the spliceosome, have been characterized as determinants in the splicing process (Moore et al. 1993, Burge et al. 1999 (Fig. 1C). In mammals, the 5' splice site consensus is AG/GURAGU (R for purine, /for splice site, bold for the dinucleotide 5' intron boundary) while the 3' splice site consensus is YAG/G (Y for pyrimidine, /for splice site, bold for the dinucleotides 3' intron boundary). There is also a conservation of nucleotide sequence around the branch point, CURAY (Y for pyrimidine, R for purine and A for branch Recently, other cis-regulatory elements were implicated in splice site recognition, e.g. the exonic splicing enhancers (ESEs) (Fig. 1C). ESEs are localized within exons and interact with a family of proteins rich in serine and arginine (SR proteins) that recruits the spliceosome to the proximal splice site .Although the presence of those consensuses was observed, it i...

Ancient linkage of a POU class 6 and an anterior hox‐like gene in cnidaria: implications for the evolution of homeobox genes

“…Although the occurrence of chimeric transcripts has been reported for a variety of metazoan taxa (Mayer and Floeter-Winter, 2005), we cannot entirely rule out the possibility that the fusion of the two genes is the result of a chromosomal aberration. However, a possible chromosomal aberration must have affected the whole Eleutheria strain because the genomic DNA and mRNA were obtained from several hundred individual medusae.…”

RNA polymerase I promoter and splice acceptor site recognition affect gene expression in non-pathogenic Leishmania species

“…1C-3), positioned upstream the CAT gene. In addition, the tb sequence presents more than one AG that can assure the occurrence of trans-splicing, a fact already observed for other trypanosomatid genes (Mayer & Floeter-Winter 2005). Transient transfection of the same Leishmania species with pAB3.0tbCAT showed positive expression results (Fig.…”

“…A particular biological feature of Kinetoplastidae species is the polycistronic transcription of protein-coding genes followed by trans-splicing, and regulation of gene expression almost exclusively at the post-transcriptional level (Clayton 2002, Campbell et al 2003, Mayer & Floeter-Winter 2005. Unlike most eukaryotes, almost all trypanosomatid protein-coding genes are transcribed constitutively as polycistronic pre-mRNAs from a few non-conventional RNA polymerase (RNA pol) II promoter regions (Palenchar & Bellofatto 2006).…”

Spliced Leader (SL) RNA: análises de genes e regiões intergênicas com aportes na filogenia, taxonomia e genotipagem de <i>Trypanosoma</i> spp. de todas as classes de vertebrados.

“…Desta maneira, as principais funções do mecanismo de trans-splicing são a individualização dos mRNAs de transcritos policistrônicos longos e a adição de uma estrutura "cap4" na extremidade 5' dos mRNAs nascentes, a qual é essencial no metabolismo e processamento dos mRNAs para sua estabilidade, transporte intracelular e tradução (Liang et al, 2003;Mayer, Floeter-Winter, 2005;Haile, Papadopoulou, 2007;Lasda, Blumenthal, 2011).…”

“…Além de usar os mesmos componentes do spliceossomo, ambos os processos envolvem os mesmos sinais presentes na sequência de RNA, que indicam os sítios de clivagem (Lasda, Blumenthal, 2011). Por estes motivos e considerando a ampla distribuição do mecanismo de trans-splicing entre os eucariotos (Figura 10), discute-se se este processo surgiu diversas vezes de forma independente durante a evolução do grupo, ou se um mecanismo ancestral comum dos eucariotas foi perdido em várias linhagens (Hastings, 2005;Mayer, Floeter-Winter, 2005;Douris et al, 2010).…”