Biology Reference
In-Depth Information
towards A-complex assembly are modeled by
t55.unwind1 U2 stl2
- a step that releases the U2
factor SF3a60 [Staley and Guthrie, 1998]. The UAP56-catalyzed conformational changes in the
U1/U2 pre-mRNA complex are modeled by
t29.U1U2 BPS bdg
and complete the transition from
the E-complex to the A-complex.
Shortly after or in parallel to the recognition of 5'ss by U1 snRNP, U2 snRNP joins the assembly
pathway and defines the branch point region. Maturation of the 17S U2 snRNP was proposed to proceed
via two different actions of the putative DExD/H box helicase SF3b125. This enzyme either acts in early
stage of the 17S U2 maturation pathway by catalyzing a conformational change, when SF3b is integrated
into the 12S U2 snRNP to form the intermediate 15S U2 snRNP subcomplex (
t13.17S U2 matur2
).
Alternatively, SF3b125 may act subsequent to the binding of SF3b, in this way supporting the con-
formational rearrangement to integrate the SF3a subcomplex into the U2 snRNP (
22.17S U2 matur1
).
Experimental evidence suggests that this putative enzyme is largely dissociating during 17S U2 assembly
[Will
et al.
, 2002]. Hence, at least one of the alternative reactions was modeled to set SF3b125 free from
the U2 snRNP maturation subpathway. Due to the two different U2 snRNP maturation scenarios, the
number of T-invariants is doubled for all subsystems, which require the presence of a mature U2 snRNP.
This demonstrates the emergence of combinatorial complexity in the modeled system.
A similar behavior can be observed during late spliceosome assembly, where a branching of the pathway
was modeled according to the proposed function of the Prp16 DExD/H box helicase. Although the model
does not reflect the kinetic behavior of Prp16 in detail, the outcome of two different possible kinetics can
be described. The proper kinetics of Prp16 requires a specific substrate of pre-mRNA and snRNP confor-
mations and may channel spliceosome assembly into a productive pathway of C-complex assembly, such
that the second step of splicing and exon ligation can proceed (
via t101.Prp16 remod
step). In contrast,
mutations in the involved RNA species or unfavorable conformations due to missing proteins, can result
in slowed Prp16 kinetics, which was proposed to activate a discard pathway [Burgess and Guthrie, 1993;
Konarska and Query, 2005; Pandit
et al.
, 2006] reflected by transition
t100.premature ATP hydrol
. This
must not necessarily be a degradation pathway as some of the involved factors (Spp382, Prp43) are also
active in recycling spliceosomal components [Staley and Guthrie, 1998; Villa and Guthrie, 2005] mod-
eled by transition
t96.Spp382 hPrp43 act
. In consequence, two possible and different major outcomes
of spliceosome assembly are captured by the model and cause a doubling of observed T-invariants:
i
) the
productive (T-invariants i13-i43) or
ii
) the unproductive (T-invariants i44-i71) branch of late spliceosome
assembly, which fall into line with all subpathways passing through E- and A-complex assembly.
Conservation relations corresponding to P-invariants
Compared to the number of T-invariants the network structure generates only four place invariants. A
trivial P-invariant exists for the serine protein kinase 1 (SRPK1), which was modeled as a loop connected
to the transition that describes the phosphorylation of the splicing factor ASF/SF2. In contrast to other
putative enzymes, which act within the spliceosomal subcomplexes, SRPK1 is active at an early stage,
activating individual splicing factors. Thus, it is assumed not to participate in further spliceosome
assembly and has been modeled as available in a non-limited amount. Two other P-invariants are related
to the factors Prp31 and Prp38, which are present in the B-complex. Prp31 binds the U4 snRNA and the
U4/U6 snRNA duplex in presence of another factor, Snu13. Hence, Prp31 enters spliceosomal assembly
at least in the stage of U4/U6 subcomplex formation [Nottrott
et al.
, 2002; Schaffert
et al.
, 2004].
Furthermore it was shown that Prp31 is destabilized at the time of catalytic activation of the spliceosome.
Thus, it was modeled to leave the spliceosomal main complex through the reaction
t68.B complex act
.
