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Gene regulation models of viral genetic switches
KTH, School of Computer Science and Communication (CSC), Numerical Analysis and Computer Science, NADA.
2007 (English)Licentiate thesis, comprehensive summary (Other scientific)
Abstract [en]

The recent decades of research in molecular biology have resulted in break-throughs concerning our knowledge of the genetic code, protein structures and functions of the different cellular components. With this new information follows an increased interest in constructing computational models of the biological systems. A computational model can range from a description of one specific protein to a complete cell or organism. The aim of a computational model is often to complement the experimental studies and help identify essential mechanisms of a system.

All processes taking place in our cells, from general metabolic processes to cell specific actions, originates from information encoded in our DNA. The first step in transferring the genetic information to a functional protein or RNA, is through the transcription of a gene. The transcription process is controlled by cellular proteins binding to DNA regions called promoters. The term "genetic switch", used in the title of this thesis, refers to a specific change in transcription activity, where one or several promoters get activated or silenced.

In this thesis, I present studies of the regulation mechanisms in two different genetic switches. The first is a switch between two central promoters in the Epstein- Barr virus. This human virus is mostly known for causing the ’kissing disease’, but is also coupled to several cancer types. Infected cells can change between a resting and a proliferating phenotype, depending on which viral promoter is active. In order to understand what causes uncontrolled proliferation in tumors, it is important to understand the regulation of these viral promoters. The other switch is present in the phage λ, a bacterial virus. This virus has one specific promoter region, controlling expression of two proteins that determine if the phage will remain silent (lysogenic) in the host cell, or start producing new viral particles (go lytic). For the Epstein- Barr virus we tested, and confirmed, the hypothesis that the regulation of the two central promoters can be obtained by only one viral and one human protein. Further, we studied the cooperative effects on one of the promoters, showing that steric hindrance at the promoter region results in a more effective switching than with only cooperative binding present. For the bacteriophage λ we studied the genetically altered λ- Lac mutants, presented by Little & Atsumi in 2006. We demonstrate that the experimental results cannot, in terms of its equilibria, be explained by the mechanisms generally believed to be in control of the lysogenic/ lytic switch.

Place, publisher, year, edition, pages
Stockholm: KTH , 2007. , x, 60 p.
Series
Trita-CSC-A, ISSN 1653-5723 ; 2007:20
National Category
Condensed Matter Physics
Identifiers
URN: urn:nbn:se:kth:diva-4528ISBN: 978-91-7178-806-1 (print)OAI: oai:DiVA.org:kth-4528DiVA: diva2:12686
Presentation
2007-11-30, RB35, Hus 16, Albanova, Roslagstullsbacken 35, Stockholm, 13:00 (English)
Opponent
Supervisors
Note
QC 20101119Available from: 2007-11-12 Created: 2007-11-12 Last updated: 2010-11-19Bibliographically approved
List of papers
1. Epstein-Barr virus latency switch in human B-cells: a physico-chemical model
Open this publication in new window or tab >>Epstein-Barr virus latency switch in human B-cells: a physico-chemical model
Show others...
2007 (English)In: BMC SYST BIOL, ISSN 1752-0509, Vol. 1Article in journal (Refereed) Published
Abstract [en]

Background: The Epstein-Barr virus is widespread in all human populations and is strongly associated with human disease, ranging from infectious mononucleosis to cancer. In infected cells the virus can adopt several different latency programs, affecting the cells' behaviour. Experimental results indicate that a specific genetic switch between viral latency programs, reprograms human B-cells between proliferative and resting states. Each of these two latency programs makes use of a different viral promoter, C-P and Q(P), respectively. The hypothesis tested in this study is that this genetic switch is controlled by both human and viral transcription factors; Oct-2 and EBNA-1. We build a physico-chemical model to investigate quantitatively the dynamical properties of the promoter regulation and experimentally examine protein level variations between the two latency programs. Results: Our experimental results display significant differences in EBNA-1 and Oct-2 levels between resting and proliferating programs. With the model we identify two stable latency programs, corresponding to a resting and proliferating cell. The two programs differ in robustness and transcriptional activity. The proliferating state is markedly more stable, with a very high transcriptional activity from its viral promoter. We predict the promoter activities to be mutually exclusive in the two different programs, and our relative promoter activities correlate well with experimental data. Transitions between programs can be induced, by affecting the protein levels of our transcription factors. Simulated time scales are in line with experimental results. Conclusion: We show that fundamental properties of the Epstein-Barr virus involvement in latent infection, with implications for tumor biology, can be modelled and understood mathematically. We conclude that EBNA-1 and Oct-2 regulation of C-P and Q(P) is sufficient to establish mutually exclusive expression patterns. Moreover, the modelled genetic control predict both mono-and bistable behavior and a considerable difference in transition dynamics, based on program stability and promoter activities. Both these phenomena we hope can be further investigated experimentally, to increase the understanding of this important switch. Our results also stress the importance of the little known regulation of human transcription factor Oct-2.

Keyword
MULTIPLE EBNA1-BINDING SITES, BURKITTS-LYMPHOMA CELLS, NUCLEAR ANTIGEN 1, TRANSCRIPTION FACTORS, GENE-TRANSCRIPTION, EBNA-1 GENE, C PROMOTER, BINDING-PROTEIN, DNA-BINDING, I LATENCY
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-12078 (URN)10.1186/1752-0509-1-40 (DOI)000252362900001 ()2-s2.0-37749007113 (Scopus ID)
Note
QC20100720Available from: 2010-03-02 Created: 2010-03-02 Last updated: 2010-07-20Bibliographically approved
2. Cooperative action in eukaryotic gene regulation: Physical properties of a viral example
Open this publication in new window or tab >>Cooperative action in eukaryotic gene regulation: Physical properties of a viral example
2007 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 76, no 6Article in journal (Refereed) Published
Abstract [en]

The Epstein-Barr virus (EBV) infects more than 90% of the human population, and causes glandular fever as well as several more serious diseases. It is a tumor virus, and has been widely studied as a model system for cell transformation in humans. A central feature of the EBV life cycle is its ability to persist in human B cells in different latency states, denoted latency I, II, and III. In latency III the host cell is driven to cell proliferation and hence expansion of the viral population without entering the lytic pathway, while the latency I state is almost completely dormant. We here study the effective cooperativity of the viral C promoter, active in latency III EBV cell lines. We show that the unusually large number of binding sites of two competing transcription factors, one viral and one from the host, serves to make the switch sharper (higher Hill coefficient), either by cooperative binding between molecules of the same species when they bind, or by competition between the two species if there is sufficient steric hindrance.

Keyword
EPSTEIN-BARR-VIRUS, MULTIPLE EBNA1-BINDING SITES, NUCLEAR ANTIGEN-1, TRANSCRIPTIONAL REGULATION, C PROMOTER, DNA, ENHANCER, ORIGIN, REPLICATION, ACTIVATION
National Category
Other Physics Topics Fusion, Plasma and Space Physics
Identifiers
urn:nbn:se:kth:diva-12089 (URN)10.1103/PhysRevE.76.061909 (DOI)000251985600071 ()2-s2.0-37249031032 (Scopus ID)
Note
2007 Licentiatavhandling Acceppted QC20100720Available from: 2010-03-03 Created: 2010-03-03 Last updated: 2017-12-12Bibliographically approved
3. A computational systems biology study of the lambda-lac mutants
Open this publication in new window or tab >>A computational systems biology study of the lambda-lac mutants
2007 (English)Manuscript (preprint) (Other academic)
Abstract [en]

We present a comprehensive computational study of some 900 possible “λ-lac” mutants of thelysogeny maintenance switch in phage λ, of which up to date 19 have been studied experimentally(Atsumi & Little, PNAS 103: 4558-4563, (2006)). We clarify that these mutants realise regulatoryschemes quite different from wild-type λ, and can therefore be expected to behave differently, withinthe conventional mechanistic setting in which this problem has often been framed. We verify thatindeed, within this framework, across this wide selection of mutants the λ-lac mutants for the mostpart either have no stable lytic states, or should only be inducible with difficulty. In particular, thecomputational results contradicts the experimental finding that four λ-lac mutants both show stablelysogeny and are inducible. This work hence suggests either that the four out of 900 mutants are special,or that λ lysogeny and inducibility are holistic effects involving other molecular players or othermechanisms, or both. The approach illustrates the power and versatility of computational systemsbiology to systematically and quickly test a wide variety of examples and alternative hypotheses for future closer experimental studies.

National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-7605 (URN)
Note

QC 20101119

Available from: 2007-11-12 Created: 2007-11-12 Last updated: 2016-02-02Bibliographically approved

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