A eukaryotic
messenger RNA (mRNA) undergoes a number of maturation processes such as splicing
and polyadenylation after transcription. Each of these processes is performed
on a large protein complex molecule. Recent studies revealed that mRNAs bind to
several different proteins and form different mRNPs. The components of those
mRNPs are being identified, but the mechanistic detail of the mRNPs remains to
be elucidated. A long polyadenylation of mRNA is a specific process for
eukaryotic cells and it is known to contribute to the stability of mRNA.
Polyadenylation itself is performed by poly(A) polymerase and its mechanism has
been well elucidated, but its initiation process is still unclear. One of the
mRNPs involved in the first step of mRNA polyadenylation process is cleavage
and polyadenylation specificity factor (CPSF), a hetero-tetramer molecule that
binds to the 3'-terminal of mRNA. We analyzed the sequences of each subunit
aiming for the prediction of its entire structure and of its role in
polyadenylation initiation step. By analyzing the amino acid sequences with
molecular phylogenetic method, we found that each subunit of CPSF had
paralogues with completely different function. This finding let us extract
information of paralogue specific mutations that may contain hints for subunit
interaction sites. With three-dimensional structures of each subunit obtained
by comparative modeling, the possible entire structure of CPSF was deduced. We
mapped the experimentally identified characteristics of CPSF onto the
structures and evaluated the accuracy of the structure.