Enterohaemorrhagic Escherichia coli (EHEC) have recently emerged as significant zoonotic pathogens. O157:H7 is one of the most common EHEC serotypes associated with human disease, which is transmitted faeco-orally from a bovine reservoir. EHEC O157:H7 preferentially colonises the bovine terminal rectum (BTR). Injection of virulence factors by type-III secretion is necessary for colonisation of cattle and results in re-modelling of the host cytoskeleton. Flagella machinery is evolutionarily related to the Type III secretion apparatus and O157 strains lacking H7 flagella show reduced adherence to the BTR. Vaccination with FliC, the main component of H7 flagella, has the potential to protect cattle against E. coli O157:H7 infection. The focus of this work was to investigate the molecular basis for H7 flagella binding to the BTR, in order to understand the basis for FliCH7 being an immuno-protective antigen. H7 flagella were shown to adhere across the surface and penetrate into BTR epithelial cells. Both the FliC shaft and the FliD cap components of flagella filaments showed the capacity to adhere to BTR epithelial cells. Preliminary studies indicate that the current FliCH7 vaccination of cattle results in FliD-specific antibodies where oral challenge with O157:H7 does not. FliD is more conserved than FliCH7, which contains a predicted 88aa structural insertion, but variation occurs along the full length of the FliD protein. There was no evidence for post-translational modification of FliCH7. A number of actin binding proteins were identified as potential FliC and FliD binding partners from BTR epithelial cell lysates. From this, a panel of purified galectin-4, cofilin-1 and βγ-actin was used to compare binding of flagella from different pathogens. H7 flagella bound more to cofilin-1 than βγ-actin, whereas phase-1 and phase-2 flagella from Salmonella Typhimurium bound more to βγ-actin, than to cofilin-1. Size-exclusion chromatography indicated that cofilin-1 alters H7 flagella filament polymerisation dynamics. αβ-ctin polymerisation and depolymerisation experiments indicate that H7, phase-1 and phase-2 flagella interactions with actin affect actin dynamics.

<p>Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen and is the leading cause of preventable blindness worldwide. Chlamydia is particularly intriguing from the perspective of cell biology because it is an obligate intracellular pathogen that manipulates host cellular pathways to ensure its proliferation and survival. This is achieved through a significant remodeling of the host cell’s internal architecture from within a membrane-bound vacuole, termed the inclusion. However, given a previous lack of tools to perform genetic analysis, the mechanisms by which Chlamydia induces host cellular changes remained unclear. Here I present genetic and molecular mechanisms of chlamydial manipulation of the host cytoskeleton and organelles. Using a forward genetics screen, InaC was identified as a necessary factor for the assembly of an F-actin structure surrounding the inclusion. InaC associated with the vacuolar membrane where it recruited Golgi-specific ARF-family GTPases. Actin dynamics and ARF GTPases regulate Golgi morphology and positioning within cells, and InaC acted to redistribute the Golgi to surround the Chlamydia inclusion. These findings suggest that Chlamydia places InaC at the inclusion-cytosolic interface to recruit host ARF GTPases and F-actin to form a platform for rearranging intracellular organelles around the inclusion. The inclusion is also surrounded by the intermediate filament vimentin and the chlamydial protease CPAF cleaves vimentin in vitro. CPAF-dependent remodeling of vimentin occurred selectively in late stages of the infection. In living cells, this cleavage occurred only after a loss of inclusion membrane integrity, suggesting that CPAF cleaves intermediate filaments specifically during chlamydial exit of host cells. In summary, I have implemented recent forward and reverse genetic approaches in Chlamydia to reveal how it employs effector proteins to manipulate the internal organization of cells in novel ways.</p> / Dissertation

Tip growth is the primary form of growth in hyphal organisms and some plant cells. Tip growth in hyphae is highly dependent on F-actin, which acts to regulate and support growth. One of the models suggested for tip growth, the amebae model of tip growth, suggests that F-actin may also be the primary source of protrusive force for tip growth in some conditions, and that proteins with a similar function to animal integrins would be present an involved in tip growth (Heath and Steinberg 1999). In this thesis we examine the role of F-actin in the growth of the oomycete Phytophthora cinnamomi and the effects on growth of the F-actin disrupting compound Latrunculin B. We demonstrate that F-actin plays a critical role in the tip growth of Phytophthora cinnamomi with it's disruption causing rapid cessation in directional growth, followed by significant subapical swelling. Further more we examine Phytophthora cinnamomi for the presence of an B4 integrin like protein that has been previously reported in the oomycete Achlya bisexualis (Chitcholtan & Garrill 2005) and show that the B4 integrin like protein is not present in Phytophthora cinnamomi. These experiments help further our understanding of tip growth in Phytophthora cinnamomi an economically important plant pathogen.

This thesis investigates whether there are alternative mechanisms of tip growth in invasive and non-invasive hyphae of the fungus Neurospora crassa. The cytoskeleton protein actin is thought to play a pivotal role in hyphal tip growth, performing a multitude of tasks, one of which may be the provision of a resistive force to counter turgor pressure. An Actin depleted zone (ADZ) was the dominant feature of invasive hyphal tips, which was largely absent from non-invasive hyphae. The Spitzenkörper was slightly larger in invasive hyphae but this size difference alone was thought insufficient to account for the exclusion of filamentous actin (F-actin) from the tip. The actin nucleating protein formin was found at sites where actin nucleation is occurring, while cofilin, a protein that severs F-actin, was found to localise where F-actin disassembly was likely to be occurring. It is suggested that these proteins are likely to play a role in controlling a dynamic cytoskeleton, rearrangements of which are required for the two modes of growth. Invasive hyphae were found to generate a higher turgor than non-invasive hyphae. These results suggest that the F-actin rearrangements facilitated by cofilin give an ADZ that may play a role in invasive hyphal tip growth; possibly through a reduction of tip resistance; thus enabling the provision of a greater protrusive force by turgor.

In order for cells to migrate, communicate, and facilitate attachment to the surrounding extraceullar matrix, they must form intricate protein complexes called focal adhesions. The number of identified focal adhesion components continues to grow and the field is an area of active study.Lasp-2 is a member of the nebulin family of actin-binding proteins that has been identified as a member of focal adhesion complexes. To gain further insights into the functional role of lasp-2, we identified two additional binding partners of lasp-2, the integral focal adhesion proteins, vinculin and paxillin. Interestingly, the interaction of lasp-2 with its binding partners vinculin and paxillin was significantly reduced in presence of lasp-1, another nebulin family member. The presence of lasp-2 appears to enhance the interaction of vinculin and paxillin with each other, however, as with the interaction of lasp-2 with vinculin or paxillin, this effect is greatly diminished in the presence of excess lasp-1 suggesting the interplay between lasp-2 and lasp-2 could be an adhesion regulatory mechanism. Lasp-2's potential role in metastasis was revealed as overexpression of lasp-2 in SW620 cells, a highly metastatic cancer cell line, increased cell migration, but impeded cell invasion.Lasp-2 transcript and protein is readily detected in neural tissues. Preliminary experiments involving the knockdown of lasp-2- in frog embryos revealed gross morphological abnormalities in the head region as well as the inability to move normally. Neural crest derived melanocytes also failed to migrate normally.Taken together, these data suggest that lasp-2 has an important role in coordinating and regulating the composition and dynamics of focal adhesions.

We study a number of non-equilibrium models of interest to both active matter and biological physicists. Using microscopic agent-based simulation as well as numerical integration of stochastic PDEs, we uncover the non-trivial behaviour exhibited when active transport, or an advection field, is added to out of equilibrium systems. When gravity is included in the celebrated Fisher-Kolmogoro Petrovsky Piscouno (F-KPP) equation, to model sedimentation of active bacteria in a container, we observe a discontinuous phase transition between a `sedimentation' and a `growth' phase, which should in principle be observable in real systems. With the addition of multiplicative noise, the resulting model contains, as its limits, both the bacterial sedimentation previously described and the fluctuating hydrodynamic description of Directed Percolation (DP), an important and well-studied non-equilibrium system whose physics incorporate many universal features which are typical of systems with absorbing states. We map out the phase diagram describing all the systems in between these two limiting cases, finding that adding an advection term, however small, immediately lifts the resulting system out of the DP universality class. Furthermore, we find two distinct low-density phases separated by a dynamical phase transition reminiscent of a spinodal transition. Finally, we attempt to improve the current diffusion-limited model for the growth of filopodia, which are intriguing networks of actin fibres used by moving cells to sense their environment. By the addition of directed transport of actin monomers to the fibre tip complex by myosin molecular motors, we show that, under appropriate conditions, the resulting dynamics may be more efficient that transport by diffusion alone, which would result in filopodial lengths better corresponding to experimental observation.

The trans-differentiation of injury-activated fibroblasts to myofibroblasts is a process that provides contractile strength for wound closure. Persistent myofibroblast differentiation, however, is associated with fibrotic pathologies such as organ fibrosis, vascular remodeling, and atherosclerotic plaque formation. Myofibroblasts acquire a contractile phenotype with biochemical properties characteristic of both smooth muscle cells and stromal fibroblasts. The cyto-contractile protein, smooth muscle α-actin (SMαA) is a biomarker of myofibroblast differentiation. Expression of the SMαA gene, ACTA2, is regulated by cis-acting elements and transcription factors that activate or repress the ACTA2 promoter. Purine-rich element binding proteins A (Purα) and B (Purβ) are sequence-specific, single-stranded DNA (ssDNA)/RNA-binding proteins that act as transcriptional repressors of ACTA2 expression. Both Pur proteins interact with the purine-rich strand of a cryptic muscle-CAT (MCAT) enhancer motif in 5'-flanking region of the ACTA2 promoter. Despite significant sequence homology with Purα, Purβ was identified as the dominant repressor of ACTA2 expression in mouse embryonic fibroblasts and vascular smooth muscle cells by virtue of gain-of function and loss-of-function analyses in cultured cells. Biophysical studies indicated that Purβ reversibly self-associates in solution to form a homodimer. Quantitative DNA-binding assays revealed that Purβ interacts with the purine-rich strand of the ACTA2 MCAT motif via a cooperative, multisite binding mechanism to form a high-affinity 2:1 Purβ-ssDNA complex. In this dissertation, a combination of computational, biochemical, and cell-based approaches were employed to elucidate the molecular basis of Purβ repressor interaction with the ACTA2 gene. Limited proteolysis of recombinant mouse Purβ in the presence and absence of the purine-rich strand of the ACTA2 MCAT element led to the identification of a core ssDNA-binding region that retains the ability to dimerize in solution. Knockdown of endogenous Purβ in mouse embryonic fibroblasts via RNA interference induced SMαA expression and conversion to a myofibroblast-like phenotype. To map the specific structural domains in the core region of Purβ that account for its unique ACTA2 repressor and ssDNA-binding functions, computational homology models of the Purβ monomer and dimer were generated based on the x-ray crystal structure of an intramolecular subdomain of Drosophila melanogaster Purα. Empirical biochemical and cell-based analyses of rationally-designed Purβ truncation proteins revealed that the assembled Purβ homodimer is composed of three separate purine-rich ssDNA-binding subdomains. Evaluation of the effects of anionic detergent and high-salt on the binding of Purβ to ssDNA implicated the involvement of hydrophobic and electrostatic interactions in mediating high-affinity nucleoprotein complex formation. This inference was validated by site-directed mutagenesis experiments, which identified several basic amino acid residues required for the ACTA2 repressor activity of Purβ. Collectively, the findings described herein establish the structural and chemical basis for the cooperative interaction of Purβ with the ACTA2 MCAT enhancer and for Purβ-dependent suppression of myofibroblast differentiation.

Microtubular cytoskeleton is involved in many processes in plant cells, including cell division, growth and development. Other proteins enable its functions by modulation of its dynamics and organization and by mediation of functional and structural interaction with other cell structures. Identification of the mediating proteins and the functions of these interactions under specific conditions were the main aims of the thesis. Membrane proteins interacting with microtubules were identified using biochemical methods. Surprisingly, the identified proteins co-sedimenting with microtubules were not members of the "classical" microtubule associated proteins (MAPs). There were enzymes, chaperones and plant specific proteins among them. For further studies, the identified microtubule-associated heat-shock protein 90 (Hsp90_MT) was chosen. Recombinant Hsp90_MT binds directly to microtubules and tubulin dimers in vitro. The ATP-binding pocket is not responsible for this association. In BY-2, Hsp90_MT co-localizes with phragmoplast and cortical microtubules and is involved in microtubule recovery after their depolymerization during cold treatment. In plants, Hsp90 is involved in cell cycle progression, its inhibition causes cell-cycle arrest in G1 phase. Based on literature search for animal proteins...

Human MYO1C gene encodes three myosin 1c (Myo1c) isoforms which differ only at their N-ends. Interestingly, all three isoforms localize to the nucleus and also to the cytoplasm, where they are anchored to the plasma membrane by the interaction with phosphatidyl inositol-4,5-bisphosphate (PIP2). However, studies reporting functional involvement of these isoforms are inconsistent. While the shortest isoform C (Myo1c-isoC) has been implicated exclusively in the cytoplasmic processes, the longer isoform B (termed the nuclear myosin 1, NM1) has been employed in the nuclear and processes, such as DNA transcription and rRNA maturation. Similarly, the longest isoform A (Myo1c-isoA) exerts its functions in the nucleus solely. To complete the information on the cellular functions of Myo1c isoforms, we searched for the cytoplasmic functions of NM1 and nuclear functions of Myo1c-isoC. In mouse, only two isoforms (NM1 and Myo1c-isoC) are expressed. We prepared the knock-out mouse (KO) which lacks specifically NM1 while retaining Myo1c-isoC unchanged. Surprisingly, this manifested in no phenotype observed. Since we demonstrated that even Myo1c-isoC acts in the transcription in the similar manner as NM1, it suggests that Myo1c- isoC functionally overlap with NM1 in the nuclear functions. Besides its localization...

Neospora caninum é um parasita intracelular obrigatório pertencente ao filo Apicomplexa, conhecido por ser uma das principais causas de aborto parasitário em bovinos e por apresentar transmissão transplacentária. Para locomoverem-se e acessarem o conteúdo intracelular de células hospedeiras, organismos apicomplexas fazem uso de um mecanismo não convencional que se utiliza de uma maquinaria celular cujo papel central é exercido pelo motor actina-miosina, auxiliado por proteínas intermediárias e de acoragem, que realiza a propulsão do parasita na direção do movimento. Para o funcionamento dessa maquinaria, é essencial que actina esteja em sua forma filamentosa (actina-F). Porém, actinas de apicomplexas são conhecidas por serem funcional e estruturalmente não convencionais, formando filamentos pequenos e instáveis in vitro, assim como pelo predomínio de grande maioria de actina monomérica (actin-G) nas células in vivo. Desse modo, para formar e manter actina-F a dinâmica de actina desses organismos requer uma regulação precisa, que, em apicomplexas, é conduzida por um arsenal conhecidamente pequeno de proteínas que se ligam a actina (ABPs). Nosso objetivo neste estudo foi identificar e caracterizar ABPs de N. caninum. Para isso, duas ABPs de N. caninum foram estudadas: fator de despolimerização de actina (NcADF) e proteína associada a ciclase (NcCAP); também, foi gerado e caracterizado soro contra região de actina de N. caninum entre aminoácidos 201 e 310 (anti-NcAct201-310). NcADF (correspondente ao acesso NCLIV_012510 em ToxoDB) foi submetida a caracterização molecular e bioquímica. A sua estrutura terciária foi gerada por modelagem molecular baseada em homologia, apresentando folding conservado, porém com F-loop de menor tamanho, quando comparada a ADF/cofilinas canônicas. A forma recombinante de NcADF foi expressa E. coli BL21 por plasmídeos pET32a(+) e pET28a(+) e solubilizada em tampão desnaturante e nativo, respectivamente. NcADF_pET32 foi purificada e utilizada para geração de soro anti-NcADF, que detectou ambas NcADF recombinantes, assim como proteínas endógenas em western blot 1-D e 2-D com peso molecular e pI próximos aos preditos. O soro anti-NcADF também localizou NcADF difusa no citoplasma, com menos intensidade nos polos de taquizoítas de N. caninum extracelulares. NcADF_pET28 foi purificado na forma nativa e utilizado para caracterização funcional para avaliação de seu papel na dinâmica de actina liofilizada de coelho. Ensaios de cossedimentação, cinética de polimerização e despolimerização, viscosimentria de baixo cisalhamento (queda de bola), estado estacionário e ligação entre actina-G e NcADF, em conjunto, mostraram que NcADF causa despolimerização de actina-F, realiza sequestro de monômeros de actina e quebra de filamentos. NcCAP foi submetida a caracterização molecular e foi identificada como produto de expressão do gene de acesso NCLIV_054140. NcCAP recombinante foi expressa em pET32a(+) e pET28a(+) predominantemente em corpos de inclusão e foi solubilizada em tampão desnaturante. A forma purificada de pET32_NcCAP, identificada por espectrometria de massas, foi utilizada para imunização e o soro resultante detectou NcCAP recombinante e endógena por western blot 1-D e 2-D, apresentando bandas e spots de peso molecular e pI próximos ao esperado. O soro anti-NcCAP também localizou NcCAP em taquizoítas ii extracelulares de N. caninum difusa no citoplasma e/ou com predomínio na região periplasmática da célula. Por fim, o soro anti-NcAct201-310 foi gerado, sendo capaz de detectar proteínas em sua forma nativa e realizar marcação na região periférica e, possivelmente, nuclear de taquizoítas de N. caninum extracelulares. A caracterização de ABPs de N. caninum feita neste trabalho amplia o conhecimento sobre a conservação dessas proteínas ao longo do filo Apicomplexa. Ademais, representa uma contribuição para o entendimento da dinâmica de actina e, por consequência, futuramente, pode colaborar para a elucidação de mecanismos-chave para a sobrevivência e disseminação dos parasitas pelo seu hospedeiro / Neospora caninum is an obligate intracellular parasite that belongs to the phylum Apicomplexa. It is known as one of the main causes of infectious abortion in cows and for its efficient transplacentary transmission. Apicomplexan organisms use a phylum-specific mechanism of invasion and gliding motility, which use an unusual cellular machinery based on an actin myosin motor assisted by intermediary and anchoring proteins that creates the traction force to impulse the parasite forward. Filamentous actin (F-actin) is essential to the appropriate functioning of this machinery, although apicomplexan unconventional actin forms small and unstable filaments in vitro and is found preponderantly as monomer (G-actin) in cells. Thus, the parasites need actin-binding proteins (ABPs) to strictly regulate actin dynamics and to form and maintain F-actin when it is necessary to the cell. Here, we aimed at identifying and characterising ABPs from N. caninum. Two ABPs were characterised: actin-depolymerising factor (NcADF) and cyclase-associated protein (NcCAP) from N. caninum. In addition, a serum against the actin region between amino acids 201 and 310 (anti-NcAct201-310) was raised. NcADF, which corresponds to identification NCLIV_012510 on ToxoDB, was molecular and biochemically characterised. Firstly, the tertiary structure of NcADF was generated by molecular modelling based on homology. Comparing to canonical ADF/cofilins, NcADF presented a conserved folding, albeit its smaller F-loop. The recombinant form of NcADF was expressed in E. coli BL21 using pET32a(+) and pET28a(+) plasmids and solubilized in denaturing and native buffers, respectively. Polyclonal antibodies were raised in mice against purified NcADF_pET32, which was able to detect both forms of recombinant NcADF as well as proteins in 1-D and 2-D western blot with expected molecular weight and isoelectric point (pI). Additionally, NcADF was localised in extracellular N. caninum tachyzoites as a diffuse pattern on cytoplasm with less intensity in both poles. NcADF_pET28 was successfully purified in native form and used for functional characterisation to evaluate the role of recombinant NcADF on lyophilised rabbit actin dynamics. Together, co-sedimentation, polymerisation and depolymerisation kinetic, low shearing viscometry (falling ball), steady state, and G-actin and NcADF binding assays showed that NcADF was able to depolymerise actin-F, sequester actin monomers, and sever filaments. Moreover, NcCAP (identification NCLIV_054140) was also characterised. Recombinant NcCAP was expressed in pET32a(+) and pET28a(+) plasmids predominantly in inclusion bodies and was solubilised in denaturing buffer. NcCAP_pET32 was purified and identified by mass spectrometry. Then, the polyclonal antibodies against this recombinant protein was generated in mice. It was able to detect recombinant and endogenous NcCAP, presenting bands and spots in 1-D and 2-D western blot with molecular weight and pI quite near to the predicted ones. NcCAP was localised as a diffuse pattern on cytoplasm and/or predominantly on periplasmic regions of extracellular taclyzoites of N. caninum. Finally, the serum containing anti-NcAct201-310 polyclonal antibodies was raised in mice. It detected endogenous proteins mainly in native form and localised them on periplasmic and possibly nuclear region in extracellular N. caninum tachyzoites. The characterisation of N. caninum ABPs iv extends our understanding of these proteins conservation and their function throughout the Apicomplexa phylum. Furthrmore, it represents a contribution to the field towards the comprehention of actin dynamics and in the future might provide information for important mechanisms of dissemination and survival of the parasite at its host