Thesis (PhD (Biochemistry))--University of Stellenbosch, 2009. / ENGLISH ABSTRACT:
The multiplication of cells proceeds through consecutive phases of growth and division
(G1, S, G2 and M phases), in a process known as the cell cycle. The transition between
these phases is regulated by so-called checkpoints, which are important to ensure proper
functioning of the cell cycle. For instance, mutations leading to faulty regulation of the
G1/S transition point are seen as one of the main causes of cancer.
Traditionally, models for biological systems that show rich dynamic behavior, such
as the cell cycle, are studied using dynamical systems analysis. However, using this
analysis method one cannot quantify the extent of control of an individual process in
the system. To understand system properties at the process level, one needs to employ
methods such as metabolic control analysis (MCA). MCA was, however, developed
for steady-state systems, and is thus limited to the analysis of such systems, unless the
necessary extensions would be made to the framework. The central question of this thesis focuses on quantifying the control in mathematical
models of the G1/S transition by the individual cell cycle processes. Since MCA was
never applied to the cell cycle, several new methods needed to be added to the framework.
The most important extension made it possible to follow and quantify, during a
single cell cycle, the control properties of the individual system processes.
Subsequently, these newly developed methods were used to determine the control
by the individual processes of an important checkpoint in mammalian cells, the restriction
point. The positioning of the restriction point in the cell cycle was distributed over
numerous system processes, but the following processes carried most of the control:
reactions involved in the interplay between retinoblastoma protein (Rb) and E2F transcription
factor, reactions responsible for the synthesis of Delayed Response Genes and
Cyclin D/Cdk4 in response to growth signals, the E2F dependent Cyclin E/Cdk2 synthesis
reaction, as well as the reactions involved in p27 formation. In addition it was
shown that these reactions exhibited their control on the restriction point via the Cyclin
E/Cdk2/p27 complex. Any perturbation of the system leading to a change in the
restriction point could be explained via its e ect on the Cyclin E/Cdk2/p27 complex,
showing a causal relation between restriction point positioning and the concentration of
the Cyclin E/Cdk2/p27 complex.
Finally, we applied the new methods, with a modular approach, to compare a number
of cell cycle models for Saccharomyces cerevisiae (budding yeast) and mammalian cells
with respect to the existence of a mass checkpoint. Such a checkpoint ensures that cells
would have a critical mass at the G1/S transition point. Indeed, in budding yeast, a
correction mechanism was observed in the G1 phase, which stabilizes the size of cells
at the G1/S transition point, irrespective of changes in the specific growth rate. This in
contrast to the mammalian cell cycle models in which no such mass checkpoint could
be observed in the G1 phase.
In this thesis it is shown that by casting specific questions on the regulation and
control of cell cycle transition points in the here extended framework of MCA, it is
possible to derive consensus answers for subsets of mathematical models. / AFRIKAANSE OPSOMMING:
Die selsiklus bestaan uit agtereenvolgende groei- en delingsiklusse wat tot selvermeerdering
lei. Die siklus word gekenmerk deur onderskeie fases (G1, S, G2 en M) wat
deur sogenaamde beheerpunte gereguleer word. Hierdie beheerpunte verseker dat selvermeerdering
nie ongekontroleerd kan plaasvind nie en mutasies wat lei tot foutiewe regulering
van die G1/S transisiepunt word as een van die hoofoorsake van kanker beskou.
Die hoofdoel van hierdie studie was om die beheer wat selsiklusprosesse op die G1/S
transisie uitoefen met behulp van wiskundige modelle te kwantifiseer. Omdat biologiese
sisteme soos die selsiklus ryk dinamiese gedrag vertoon, word hulle tradisioneeldeur
middel van dinamiese sisteemanalise bestudeer. Die analisemetode beskik egter nie oor
die vermoë om die hoeveelheid beheer wat afsonderlike sisteemprosesse op 0n sisteemeienskap
uitoefen te kwantifiseer nie. Om sisteemeienskappe op prosesvlak te verstaan
moet metodes soos metaboliese kontrole analise (MKA) ingespan word. MKA was egter
ontwikkel om sisteme in 0n bestendige toestand te analiseer en aangesien MKA nog nooit vantevore vir selsiklus analises gebruik was nie, moes nuwe MKA tegnieke gedurende
die studie ontwikkel word. Die belangrikste van die metodes maak dit moontlik
om beheer (soos uitgeoefen deur die onderskeie sisteemprosesse) oor 0n enkele selsiklus
na te volg en te kwantifiseer. Die nuut-ontwikkelde metodes was vervolgens gebruik
om te bepaal hoe een so 0n beheerpunt in soogdierselle - die restriksiepunt - deur die
onderskeie sisteemprosesse beheer word.
Die studie het aangedui dat die posisie van die restriksiepunt tydens die selsiklus
deur ’n verskeidenheid sisteemprosesse beheer word. Die bevinding was dat vier prosesse
beduidend meer beheer op die posisie van die restriksiepunt uitoefen: Reaksies
wat betrekking het op die wisselwerking tussen retinoblastoma proteïen (Rb) en E2F
transkripsiefaktor; reaksies verantwoordelik vir die sintese van vertraagde responsgene
en Siklien D/Cdk4 in respons tot groeiseine; die E2F afhanklike Siklien E/Cdk2 sintesereaksie;
sowel as die reaksies betrokke in p27 vorming. Daar was ook aangetoon
dat hierdie reaksies hul beheer op die posisie van die restriksiepunt deur die Siklien
E/Cdk2/p27 kompleks uitoefen, siende enige sisteemversteuringe (wat tot veranderinge
in die restriksiepuntposisie aanleiding gee) deur veranderinge in die kompleks verklaar
kon word - 0n observasie wat aandui dat daar 0n kousale verhouding is tussen die posisie
van die restriksiepunt en die Siklien E/Cdk2/p27 kompleks.
Die nuut-ontwikkelde metodes was verder gebruik om 0n verskeidenheid selsiklusmodelle
van Saccharomyces cerevisiae (bakkersgis) en soogdierselle met 0n modulêre
aanpak te vergelyk om te bepaal of daar 0n massa beheerpunt in beide soogdier- en bakkersgisselle
bestaan. Daar word gepostuleer dat hierdie beheerpunt verseker dat selle
0n kritiese massa by die G1/S transisiepunt bereik. Die resultate van die studie dui
daarop dat bakkersgis, anders as soogdierselle, oor so 0n korreksiemeganisme beskik.
Die meganisme stabiliseer die grootte van selle in die G1 fase ondanks veranderinge in
die groeitempo van die selle, sodat massa homeostaties by die G1/S transisiepunt gehandhaaf
word. Die studie het getoon dat moeilike vrae met betrekking tot die selsiklus
beantwoord kan word deur van wiskundige modelle gebruik te maak en die probleme in
die nuut-ontwikkelde metaboliese kontrole analise raamwerk te giet.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/1236 |
| Date | 12 1900 |
| Creators | Conradie, Riaan |
| Contributors | Snoep, J. L., University of Stellenbosch. Faculty of Science. Dept. of Biochemistry. |
| Publisher | Stellenbosch : University of Stellenbosch |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | English |
| Type | Thesis |
| Rights | University of Stellenbosch. |
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