A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif.
BACKGROUND
The Cleavage Stimulation Factor (CstF) is a required protein complex for eukaryotic mRNA 3'-processing. CstF interacts with 3'-processing downstream elements (DSEs) through its 64-kDa subunit, CstF-64; however, the exact nature of this interaction has remained unclear. We used EST-to-genome alignments to identify and extract large sets of putative 3'-processing sites for mRNA from ten metazoan species, including Homo sapiens, Canis familiaris, Rattus norvegicus, Mus musculus, Gallus gallus, Danio rerio, Takifugu rubripes, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans. In order to further delineate the details of the mRNA-protein interaction, we obtained and multiply aligned CstF-64 protein sequences from the same species.


RESULTS
We characterized the sequence content and specific positioning of putative DSEs across the range of organisms studied. Our analysis characterized the downstream element (DSE) as two distinct parts - a proximal UG-rich element and a distal U-rich element. We find that while the U-rich element is largely conserved in all of the organisms studied, the UG-rich element is not. Multiple alignment of the CstF-64 RNA recognition motif revealed that, while it is highly conserved throughout metazoans, we can identify amino acid changes that correlate with observed variation in the sequence content and positioning of the DSEs.


CONCLUSIONS
Our analysis confirms the early reports of separate U- and UG-rich DSEs. The correlated variations in protein sequence and mRNA binding sequences provide novel insights into the interactions between the precursor mRNA and the 3'-processing machinery.
Functional Genomics Program, The University of Maine, Orono, Maine 04469, USA. jesse.salisbury@umit.maine.edu
Jesse
J
Salisbury
Keith W
KW
Hutchison
Joel H
JH
Graber
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D000852:Anopheles; D017173:Caenorhabditis elegans; D002645:Chickens; D039241:Cleavage Stimulation Factor / Q000378:metabolism*; D030561:Databases, Nucleic Acid; D004285:Dogs; D004330:Drosophila; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D010802:Phylogeny; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D026721:RNA 3' End Processing / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D051381:Rats; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D023741:Takifugu; D015027:Zebrafish
D039241:Cleavage Stimulation Factor; D016601:RNA-Binding Proteins