Biology Reference
In-Depth Information
idine tract, respectively [Abovich and Rosbash, 1997; Berglund
et al.
, 1998].
This mode of
E-complex assembly is reflected by the T-invariants i17, i18 (i64, i65).
(c) The T-invariants i19, i20 (i62, i63) describe a pathway of E-complex assembly, in which
5'ss selection is modulated by the presence of two alternative splicing factors, ASF/SF2
and TIA1, which both have been reported to interact with U1 snRNP proteins, U170K
(
t12.ASFp U170K bdg
) and U1C (
t9.U1C TIA1 bdg1
), respectively [Foerch
et al.
, 2002]. The
splicing factor SC35 compensates for the requisite of the auxiliary factor U2AF and bridges the
5'ss to the branch point via contacts to U1 snRNP and SF1 (
t56.U1 SC35 SF1 bdg
). Subsequent-
ly, U2 snRNP is directly bound to this intermediate complex (
t152.U2 SC35 bdg
). Note that
the ATP dependent helicase UAP56 is prerequisite for conformational changes in transition of
the spliceosome from E to A-complex [Staley and Guthrie, 1998], based on its ATP hydrolyzing
capacity [Shen
et al.
, 2007]. However, although the U2AF component U2AF65 is an essential
cofactor for positioning UAP56 in the branch site region [Fleckner
et al.
, 1997], U2AF65 seems
not to influence UAP56's ATPase activity [Shen
et al.
, 2007], raising the question how UAP56
unfolds its activity in an U2AF independent mode of A-complex assembly.
3. T-invariants i21-i26 (i56-i61) describe 5'ss recognition in the 5' terminal exon. The first donor
splice site within a transcript follows a different mode of recognition. Here, the interaction of U1
snRNP proteins (U1C) to proteins of the cap binding complex (CBC) via LUC7 has been shown
and hence was modeled with a separate reaction (
t10.U1 CBC 5ss bdg
), which triggers another
set of T-invariants. However, except for the interaction with the cap binding complex, these T-
invariants are the same as above (
2 a-c
) and may constitute novel alternative pathways for the initial
spliceosome assembly at newly synthesized transcripts.
4. T-invariants i27-i32 (i50-i55) describe 5'ss recognition via U1C contacts to intron bound splicing
factor TIA1. Alternatively to the proposed joint action of ASF/SF2 and TIA1 in alternative 5'ss
selection and U1 snRNP recruitment, TIA1 was modeled as sole contributing splicing factor to
5'ss selection (
t30.U1C TIA1 bdg2
)[Forch
et al.
, 2002] initiating different ways of downstream
A-complex formation. Thus, two invariants describe A-complex formation independent of U2AF
via exclusive action of SC35 (i27, i54, similar as in
2c
), and four invariants involve U2AF. The
latter set splits further into two groups, one involving FBP11 additionally to SC35 (i29, i52) and
one involving exclusively FBP11 without SC35 in A-complex formation (i31, i50).
5. T-invariants i33-i38 (i44-i49) describe 5'ss recognition without additional splicing factors. These
T-invariants model the 5'ss recognition without the parallel binding of the U1 stabilizing factors
ASF/SF2 or TIA1, which could be described as a mode for strong donor splice site selection.
However, the transition from the E-complex to the A-complex may require conditions as described
for the T-invariants in
2 a-c
.
6. T-invariants i39, i40 (i70, i71) describe binding of U1 snRNP to the 5'ss after initiating contact
to U2 snRNP via Prp5. These T-invariants model a pathway of E-complex formation, where
the ATPase Prp5 bridges U1 and U2 snRNP prior to their binding to the pre-mRNA. Thus, U2
snRNP is already associated with U1 snRNP and Prp5 when it binds to the intron branch site.
This was suggested based on the observation that binding of Prp5 to U1 and U2 snRNP occurs
also in absence of pre-mRNA but depends on the availability of ATP [Xu
et al.
, 2004]. In
accordance, it was shown that Prp5 is required for pre-spliceosome assembly [Xu
et al.
, 2004].
Hence, the T-invariants i39, i40 (i70, i71) contain the reaction
t27.U1 Prp5 U2 bdg
as bridging
step, followed by
t28.U1 5ss U2 U2AF bdg
, describing the contacts with the 5'ss and the branch
point/polypyrimidine tract associated proteins.
The ATP dependent structural rearrangements
