10 research outputs found
IST Austria Thesis
Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past
Evolution of new regulatory functions on biophysically realistic fitness landscapes
Regulatory networks consist of interacting molecules with a high degree of
mutual chemical specificity. How can these molecules evolve when their function
depends on maintenance of interactions with cognate partners and simultaneous
avoidance of deleterious "crosstalk" with non-cognate molecules? Although
physical models of molecular interactions provide a framework in which
co-evolution of network components can be analyzed, most theoretical studies
have focused on the evolution of individual alleles, neglecting the network. In
contrast, we study the elementary step in the evolution of gene regulatory
networks: duplication of a transcription factor followed by selection for TFs
to specialize their inputs as well as the regulation of their downstream genes.
We show how to coarse grain the complete, biophysically realistic
genotype-phenotype map for this process into macroscopic functional outcomes
and quantify the probability of attaining each. We determine which evolutionary
and biophysical parameters bias evolutionary trajectories towards fast
emergence of new functions and show that this can be greatly facilitated by the
availability of "promiscuity-promoting" mutations that affect TF specificity
Intrinsic limits to gene regulation by global crosstalk
Gene regulation relies on the specificity of transcription factor (TF) - DNA
interactions. In equilibrium, limited specificity may lead to crosstalk: a
regulatory state in which a gene is either incorrectly activated due to
noncognate TF-DNA interactions or remains erroneously inactive. We present a
tractable biophysical model of global crosstalk, where many genes are
simultaneously regulated by many TFs. We show that in the simplest regulatory
scenario, a lower bound on crosstalk severity can be analytically derived
solely from the number of (co)regulated genes and a suitable parameter that
describes binding site similarity. Estimates show that crosstalk could present
a significant challenge for organisms with low-specificity TFs, such as
metazoans, unless they use appropriate regulation schemes. Strong cooperativity
substantially decreases crosstalk, while joint regulation by activators and
repressors, surprisingly, does not; moreover, certain microscopic details about
promoter architecture emerge as globally important determinants of crosstalk
strength. Our results suggest that crosstalk imposes a new type of global
constraint on the functioning and evolution of regulatory networks, which is
qualitatively distinct from the known constraints acting at the level of
individual gene regulatory elements
Receptor crosstalk improves concentration sensing of multiple ligands
Cells need to reliably sense external ligand concentrations to achieve
various biological functions such as chemotaxis or signaling. The molecular
recognition of ligands by surface receptors is degenerate in many systems
leading to crosstalk between different receptors. Crosstalk is often thought of
as a deviation from optimal specific recognition, as the binding of non-cognate
ligands can interfere with the detection of the receptor's cognate ligand,
possibly leading to a false triggering of a downstream signaling pathway. Here
we quantify the optimal precision of sensing the concentrations of multiple
ligands by a collection of promiscuous receptors. We demonstrate that crosstalk
can improve precision in concentration sensing and discrimination tasks. To
achieve superior precision, the additional information about ligand
concentrations contained in short binding events of the non-cognate ligand
should be exploited. We present a proofreading scheme to realize an approximate
estimation of multiple ligand concentrations that reaches a precision close to
the derived optimal bounds. Our results help rationalize the observed ubiquity
of receptor crosstalk in molecular sensing
Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants
In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes
Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants
In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes
MATLAB simulation routine to modify the quantitative genetic reaction norm approach of Lande (2009) to include maternal effects and stochastic flipping environment. - See more at: http://figshare.com/preview/_preview/894436#sthash.2emuq1Ue.dpuf
<p>The code modifies the reaction norm approach of Lande (2009) to include maternal effects (Hoyle & Ezard 2012) and then explores different models of environmental change that are correlated across generations.</p>
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<p>This is the script for the sinusoidal environment.</p>
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<p>The model is explained fully in Ezard et al. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. <em>Func. Ecol</em>. doi: 10.1111/1365-2435.12207. The core was published as Hoyle, R.B. & Ezard, T.H.G. (2012). The benefits of maternal effects in novel and in stable environments. J<em>. Roy. Soc. Interface</em><strong>9</strong>, 2403-2413. doi:10.1098/rsif.2012.0183. See links below. </p>
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MATLAB simulation routines that modify the reaction norm approach of Lande (2009) to include maternal effects.
<p>MATLAB simulation routines as used in:</p>
<p>Hoyle, R.B. & Ezard, T.H.G. (2012). The benefits of maternal effects in novel and in stable environments. <em>J. Roy. Soc. Interface</em> <strong>9</strong>, 2403-2413. doi:10.1098/rsif.2012.0183.</p>
<p>Ezard <em>et al</em>. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. <em>Func. Ecol</em>. doi: 10.1111/1365-2435.12207. </p>
<p>Prizak<em> et al</em>. (2014). Fitness consequences of maternal and grandmaternal effects. <em>Ecol. Evol</em>. doi: 10.1002/ece3.1150.</p