Evolutionary and Functional Aspects of Two-Component Signalling Systems
Author(s)
Sheng, Xia
Type
Thesis
Abstract
Two-component systems (TCSs) are critical for bacteria to interact with their extracellular
environment. They define a type of signalling system that is composed of a
transmembrane histidine kinase (HK) and a cytoplasmic response regulator (RR). In
this thesis we have studied the evolutionary and functional aspects of these important
signalling systems. By studying the distribution of the TCS orthologues of E.coli across
more than 900 bacterial organisms, we have found that a pair of TCS proteins does not
always coexist in one organism. The genomic localisation map of TCSs reveals a possible
translocation mechanism for TCS evolution. The alignments of HKs and RRs have
shown that HKs are genetically more divergent, probably due to their signal recognizing
role. An analysis of the steady states of TCS dynamics has shown that the outputs of
the TCSs are bistable if they have positive auto-regulation feedback loops in their transcriptional
regulation. Our analysis has also shown that the phosphorylation process of
a TCS is always monostable and the factors that affect steady states have been studied.
For both orthodox and non-orthodox TCSs, autophosphorylation rates of the HKs are
the most important factor to affect the steady states of the TCSs' outputs. To study the
phosphorelay mechanism of the non-orthodox TCS ArcB/A, we constructed plasmids
carrying different copy numbers of ArcB mutants with different phosphorylation sites
ablated. By fitting our phosphorelay model to the data obtained from mutant ArcB
constructs, we have found that ArcB most likely performs phosphorelay in an allosteric
mechanism. Finally, Approximate Bayesian computation was used in order to evaluate
the potential use of orthodox TCS and non-orthodox TCS architectures in synthetic
biology contexts. Results show that neither of the orthodox TCS model or the nonorthodox
TCS model are superior under all circumstances but that both models have
advantages in some scenarios. In the appendix, we did some study on how the contact
residue disorder would affect protein-ligand binding specificity.
environment. They define a type of signalling system that is composed of a
transmembrane histidine kinase (HK) and a cytoplasmic response regulator (RR). In
this thesis we have studied the evolutionary and functional aspects of these important
signalling systems. By studying the distribution of the TCS orthologues of E.coli across
more than 900 bacterial organisms, we have found that a pair of TCS proteins does not
always coexist in one organism. The genomic localisation map of TCSs reveals a possible
translocation mechanism for TCS evolution. The alignments of HKs and RRs have
shown that HKs are genetically more divergent, probably due to their signal recognizing
role. An analysis of the steady states of TCS dynamics has shown that the outputs of
the TCSs are bistable if they have positive auto-regulation feedback loops in their transcriptional
regulation. Our analysis has also shown that the phosphorylation process of
a TCS is always monostable and the factors that affect steady states have been studied.
For both orthodox and non-orthodox TCSs, autophosphorylation rates of the HKs are
the most important factor to affect the steady states of the TCSs' outputs. To study the
phosphorelay mechanism of the non-orthodox TCS ArcB/A, we constructed plasmids
carrying different copy numbers of ArcB mutants with different phosphorylation sites
ablated. By fitting our phosphorelay model to the data obtained from mutant ArcB
constructs, we have found that ArcB most likely performs phosphorelay in an allosteric
mechanism. Finally, Approximate Bayesian computation was used in order to evaluate
the potential use of orthodox TCS and non-orthodox TCS architectures in synthetic
biology contexts. Results show that neither of the orthodox TCS model or the nonorthodox
TCS model are superior under all circumstances but that both models have
advantages in some scenarios. In the appendix, we did some study on how the contact
residue disorder would affect protein-ligand binding specificity.
Date Issued
2012-10
Date Awarded
2013-05
Copyright Statement
Attribution NoDerivatives 4.0 International Licence (CC BY-ND)
Advisor
Buck, Martin
Stumpf, Michael
Pinney, John
Sponsor
SHKP-KWOK
Publisher Department
Molecular Biosciences
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)