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Articles 1 - 30 of 41
Full-Text Articles in Social and Behavioral Sciences
Single-Molecule Specific Mislocalization Of Red Fluorescent Proteins In Live Escherichia Coli, Harshad Ghodke, Victor E. A Caldas, Christiaan M. Punter, Antoine M. Van Oijen, Andrew Robinson
Single-Molecule Specific Mislocalization Of Red Fluorescent Proteins In Live Escherichia Coli, Harshad Ghodke, Victor E. A Caldas, Christiaan M. Punter, Antoine M. Van Oijen, Andrew Robinson
Faculty of Science, Medicine and Health - Papers: part A
Tagging of individual proteins with genetically encoded fluorescent proteins (FPs) has been used extensively to study localization and interactions in live cells. Recent developments in single-molecule localization microscopy have enabled the dynamic visualization of individual tagged proteins inside living cells. However, tagging proteins with FPs is not without problems: formation of insoluble aggregates and inhibition of native functions of the protein are well-known issues. Previously reported artifacts manifest themselves at all expression levels of the FP-tagged proteins, making the design of control experiments relatively straightforward. Here, we describe a previously uncharacterized mislocalization artifact of Entacmaea quadricolor red fluorescent protein variants …
Solution Structure Of Domains Iva And V Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii And Interaction With The Alpha Subunit, Xun-Cheng Su, Slobodan Jergic, Max A Keniry, Nicholas E. Dixon, Gottfried Otting
Solution Structure Of Domains Iva And V Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii And Interaction With The Alpha Subunit, Xun-Cheng Su, Slobodan Jergic, Max A Keniry, Nicholas E. Dixon, Gottfried Otting
Professor Nick E Dixon
The solution structure of the C-terminal Domain V of the τ subunit of E. coli DNA polymerase III was determined by nuclear magnetic resonance (NMR) spectroscopy. The fold is unique to τ subunits. Amino acid sequence conservation is pronounced for hydrophobic residues that form the structural core of the protein, indicating that the fold is representative for τ subunits from a wide range of different bacteria. The interaction between the polymerase subunits τ and α was studied by NMR experiments where α was incubated with full-length C-terminal domain (τC16), and domains shortened at the C-terminus by 11 and 18 residues, …
Escherichia Coli Single-Stranded Dna-Binding Protein: Nanoesi-Ms Studies Of Salt-Modulated Subunit Exchange And Dna Binding Transactions, Claire E. Mason, Slobodan Jergic, Allen Lo, Yao Wang, Nicholas E. Dixon, Jennifer L. Beck
Escherichia Coli Single-Stranded Dna-Binding Protein: Nanoesi-Ms Studies Of Salt-Modulated Subunit Exchange And Dna Binding Transactions, Claire E. Mason, Slobodan Jergic, Allen Lo, Yao Wang, Nicholas E. Dixon, Jennifer L. Beck
Professor Nick E Dixon
Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in …
The Unstructured C-Terminus Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii Holoenzyme Is The Site Of Interaction With The Alpha Subunit, Slobodan Jergic, Kiyoshi Ozawa, Neal K. Williams, Xun-Cheng Su, Daniel D. Scott, Samir M. Hamdan, Jeffrey A. Crowther, Gottfried Otting, Nicholas E. Dixon
The Unstructured C-Terminus Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii Holoenzyme Is The Site Of Interaction With The Alpha Subunit, Slobodan Jergic, Kiyoshi Ozawa, Neal K. Williams, Xun-Cheng Su, Daniel D. Scott, Samir M. Hamdan, Jeffrey A. Crowther, Gottfried Otting, Nicholas E. Dixon
Professor Nick E Dixon
The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τC16. We show that the extreme C-terminal region of τC16 constitutes the site of interaction with α. The τC16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τC16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (KD) of the α−τC16 complex to be ∼260 pM. Competition with immobilized τC16 by τC16 derivatives for binding to α gave values of KD of 7 μM for the …
Structure Of The Theta Subunit Of Escherichia Coli Dna Polymerase Iii In Complex With The Epsilon Subunit, Max A Keniry, Ah-Young Park, Elisabeth A. Owen, Samir M. Hamdan, Guido Pintacuda, Gottfried Otting, Nicholas E. Dixon
Structure Of The Theta Subunit Of Escherichia Coli Dna Polymerase Iii In Complex With The Epsilon Subunit, Max A Keniry, Ah-Young Park, Elisabeth A. Owen, Samir M. Hamdan, Guido Pintacuda, Gottfried Otting, Nicholas E. Dixon
Professor Nick E Dixon
The catalytic core of Escherichia coli DNA polymerase III contains three tightly associated subunits, the α, ε, and θ subunits. The θ subunit is the smallest and least understood subunit. The three-dimensional structure of θ in a complex with the unlabeled N-terminal domain of the ε subunit, ε186, was determined by multidimensional nuclear magnetic resonance spectroscopy. The structure was refined using pseudocontact shifts that resulted from inserting a lanthanide ion (Dy3+, Er3+, or Ho3+) at the active site of ε186. The structure determination revealed a three-helix bundle fold that is similar to the solution structures of θ in a methanol-water …
The Proofreading Exonuclease Subunit E Of Escherichia Coli Dna Polymerase Iii Is Tethered To The Polymerase Subunit A Via A Flexible Linker, Kiyoshi Ozawa, Slobodan Jergic, Ah-Young Park, Nicholas E. Dixon, Gottfried Otting
The Proofreading Exonuclease Subunit E Of Escherichia Coli Dna Polymerase Iii Is Tethered To The Polymerase Subunit A Via A Flexible Linker, Kiyoshi Ozawa, Slobodan Jergic, Ah-Young Park, Nicholas E. Dixon, Gottfried Otting
Professor Nick E Dixon
Escherichia coli DNA polymerase III holoenzyme is composed of 10 different subunits linked by noncovalent interactions. The polymerase activity resides in the α-subunit. The ε-subunit, which contains the proofreading exonuclease site within its N-terminal 185 residues, binds to α via a segment of 57 additional C-terminal residues, and also to θ, whose function is less well defined. The present study shows that θ greatly enhances the solubility of ε during cell-free synthesis. In addition, synthesis of ε in the presence of θ and α resulted in a soluble ternary complex that could readily be purified and analyzed by NMR spectroscopy. …
Replication Termination In Escherichia Coli: Structure And Anti-Helicase Activity Of The Tus-Ter Complex, Cameron Neylon, Andrew V. Kralicek, Thomas M. Hill, Nicholas E. Dixon
Replication Termination In Escherichia Coli: Structure And Anti-Helicase Activity Of The Tus-Ter Complex, Cameron Neylon, Andrew V. Kralicek, Thomas M. Hill, Nicholas E. Dixon
Professor Nick E Dixon
The arrest of DNA replication in Escherichia coli is triggered by the encounter of a replisome with a Tus protein-Ter DNA complex. A replication fork can pass through a Tus-Ter complex when traveling in one direction but not the other, and the chromosomal Ter sites are oriented so replication forks can enter, but not exit, the terminus region. The Tus-Ter complex acts by blocking the action of the replicative DnaB helicase, but details of the mechanism are uncertain. One proposed mechanism involves a specific interaction between Tus-Ter and the helicase that prevents further DNA unwinding, while another is that the …
Proofreading Exonuclease On A Tether: The Complex Between The E. Coli Dna Polymerase Iii Subunits Α, Ε, Θ And Β Reveals A Highly Flexible Arrangement Of The Proofreading Domain, Kiyoshi Ozawa, Nicholas P. Horan, Andrew Robinson, Hiromasa Yagi, Flynn R. Hill, Slobodan Jergic, Zhi-Qiang Xu, Karin V. Loscha, Nan Li, Moeava Tehei, Aaron J. Oakley, Gottfried Otting, Thomas Huber, Nicholas E. Dixon
Proofreading Exonuclease On A Tether: The Complex Between The E. Coli Dna Polymerase Iii Subunits Α, Ε, Θ And Β Reveals A Highly Flexible Arrangement Of The Proofreading Domain, Kiyoshi Ozawa, Nicholas P. Horan, Andrew Robinson, Hiromasa Yagi, Flynn R. Hill, Slobodan Jergic, Zhi-Qiang Xu, Karin V. Loscha, Nan Li, Moeava Tehei, Aaron J. Oakley, Gottfried Otting, Thomas Huber, Nicholas E. Dixon
Professor Nick E Dixon
A complex of the three (αεθ) core subunits and the β2 sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of ε (proofreading exonuclease) subunits shows that ε is attached to α at a site far from the polymerase active site. Both α and ε contain clamp-binding motifs (CBMs) that interact simultaneously with β2 in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable αεθ:β2 complexes. …
Flexibility Revealed By The 1.85 Å Crystal Structure Of The Β Sliding-Clamp Subunit Of Escherichia Coli Dna Polymerase Iii, Aaron J. Oakley, Pavel Prosselkov, Gene Wijffels, Jennifer L. Beck, Matthew Cj Wilce, Nicholas E. Dixon
Flexibility Revealed By The 1.85 Å Crystal Structure Of The Β Sliding-Clamp Subunit Of Escherichia Coli Dna Polymerase Iii, Aaron J. Oakley, Pavel Prosselkov, Gene Wijffels, Jennifer L. Beck, Matthew Cj Wilce, Nicholas E. Dixon
Professor Nick E Dixon
The subunit of the Escherichia coli replicative DNA polymerase III holoenzyme is the sliding clamp that interacts with the (polymerase) subunit to maintain the high processivity of the enzyme. The protein is a ring-shaped dimer of 40.6 kDa subunits whose structure has previously been determined at a resolution of 2.5 Å [Kong et al. (1992), Cell, 69, 425-437]. Here, the construction of a new plasmid that directs overproduction of to very high levels and a simple procedure for large-scale purification of the protein are described. Crystals grown under slightly modified conditions diffracted to beyond 1.9 Å at 100 K at …
Structural And Thermodynamic Dissection Of Linear Motif Recognition By The E. Coli Sliding Clamp, Zhou Yin, Michael J. Kelso, Jennifer L. Beck, Aaron J. Oakley
Structural And Thermodynamic Dissection Of Linear Motif Recognition By The E. Coli Sliding Clamp, Zhou Yin, Michael J. Kelso, Jennifer L. Beck, Aaron J. Oakley
Faculty of Science, Medicine and Health - Papers: part A
Protein-protein interactions based on linear motif (LM) recognition play roles in many cell regulatory processes. The E. coli sliding clamp is a protein mediator of replisome formation, which uses a common surface pocket composed of two subsites (I and II) to interact with LMs in multiple binding partners. A structural and thermodynamic dissection of sliding clamp-LM recognition has been performed, providing support for a sequential binding model. According to the model, a hydrophobic C-terminal LM dipeptide submotif acts as an anchor to establish initial contacts within subsite I, and this is followed by formation of a stabilizing hydrogen-bonding network between …
Escherichia Coli Single-Stranded Dna-Binding Protein: Nanoesi-Ms Studies Of Salt-Modulated Subunit Exchange And Dna Binding Transactions, Claire E. Mason, Slobodan Jergic, Allen Lo, Yao Wang, Nicholas E. Dixon, Jennifer L. Beck
Escherichia Coli Single-Stranded Dna-Binding Protein: Nanoesi-Ms Studies Of Salt-Modulated Subunit Exchange And Dna Binding Transactions, Claire E. Mason, Slobodan Jergic, Allen Lo, Yao Wang, Nicholas E. Dixon, Jennifer L. Beck
Faculty of Science, Medicine and Health - Papers: part A
Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in …
Proofreading Exonuclease On A Tether: The Complex Between The E. Coli Dna Polymerase Iii Subunits Α, Ε, Θ And Β Reveals A Highly Flexible Arrangement Of The Proofreading Domain, Kiyoshi Ozawa, Nicholas P. Horan, Andrew Robinson, Hiromasa Yagi, Flynn R. Hill, Slobodan Jergic, Zhi-Qiang Xu, Karin V. Loscha, Nan Li, Moeava Tehei, Aaron J. Oakley, Gottfried Otting, Thomas Huber, Nicholas E. Dixon
Proofreading Exonuclease On A Tether: The Complex Between The E. Coli Dna Polymerase Iii Subunits Α, Ε, Θ And Β Reveals A Highly Flexible Arrangement Of The Proofreading Domain, Kiyoshi Ozawa, Nicholas P. Horan, Andrew Robinson, Hiromasa Yagi, Flynn R. Hill, Slobodan Jergic, Zhi-Qiang Xu, Karin V. Loscha, Nan Li, Moeava Tehei, Aaron J. Oakley, Gottfried Otting, Thomas Huber, Nicholas E. Dixon
Faculty of Science, Medicine and Health - Papers: part A
A complex of the three (αεθ) core subunits and the β2 sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of ε (proofreading exonuclease) subunits shows that ε is attached to α at a site far from the polymerase active site. Both α and ε contain clamp-binding motifs (CBMs) that interact simultaneously with β2 in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable αεθ:β2 complexes. …
Improving Promoter Prediction For The Nnpp2.2 Algorithm: A Case Study Using Escherichia Coli Dna Sequences, Ren Zhang, Alexandra Burden, Yan-Xia Lin
Improving Promoter Prediction For The Nnpp2.2 Algorithm: A Case Study Using Escherichia Coli Dna Sequences, Ren Zhang, Alexandra Burden, Yan-Xia Lin
Associate Professor Yan-Xia Lin
No abstract provided.
Improving Promoter Prediction For The Nnpp2.2 Algorithm: A Case Study Using Escherichia Coli Dna Sequences, Ren Zhang, Alexandra Burden, Yan-Xia Lin
Improving Promoter Prediction For The Nnpp2.2 Algorithm: A Case Study Using Escherichia Coli Dna Sequences, Ren Zhang, Alexandra Burden, Yan-Xia Lin
Alexandra Burden, Lecturer, School of Mathematics and Applied Statistics, Faculty of Informatics
No abstract provided.
Influence Of 18ghz Microwave Radiation On The Enzymatic Activity Of Escherichia Coli Lactate Dehydrogenase And Cytochrome C Oxidase, Yuri Shamis, Alex Traub, Rodney J. Croft, Russell Crawford, Elena Ivanova
Influence Of 18ghz Microwave Radiation On The Enzymatic Activity Of Escherichia Coli Lactate Dehydrogenase And Cytochrome C Oxidase, Yuri Shamis, Alex Traub, Rodney J. Croft, Russell Crawford, Elena Ivanova
Faculty of Health and Behavioural Sciences - Papers (Archive)
The catalytic activity of two common bacterial enzymes, lactate dehydrogenase (LDH) and cytochrome c oxidase (COX) from Escherichia coli, was examined following bacterial exposure to microwave (MW) radiation under well-defined experimental conditions. The experiments were conducted in a specialised microwave processing apparatus, with an exposure frequency of 18 GHz, and a temperature profile that was restricted to below 40oC to avoid thermal degradation of the bacteria. The absorbed power was calculated to be 1500 kW/m3 and the electric field was determined to be 300 V/m. Both values were theoretically confirmed using Computer Simulation Technology (CST) Microwave Studio 3D Electromagnetic Stimulation …
Molecular Characterization Of A 21.4 Kilobase Antibiotic Resistance Plasmid From An Hemolytic Escherichia Coli O108:H-Human Clinical Isolate, Fay E. Dawes, Dieter M. Bulach, Alexander Kuzevski, Karl A. Bettelheim, Carola Venturini, Steven P. Djordjevic, Mark J. Walker
Molecular Characterization Of A 21.4 Kilobase Antibiotic Resistance Plasmid From An Hemolytic Escherichia Coli O108:H-Human Clinical Isolate, Fay E. Dawes, Dieter M. Bulach, Alexander Kuzevski, Karl A. Bettelheim, Carola Venturini, Steven P. Djordjevic, Mark J. Walker
Faculty of Science - Papers (Archive)
This study characterizes the 21.4 kilobase plasmid pECTm80 isolated from Escherichia coli strain 80, an α hemolytic human clinical diarrhoeal isolate (serotype O108:H-). DNA sequence analysis of pECTm80 revealed it belonged to incompatibility group X1, and contained plasmid partition and toxin-antitoxin systems, an R6K-like triple origin (ori) replication system, genes required for replication regulation, insertion sequences IS1R, ISEc37 and a truncated transposase gene (Tn3-like ΔtnpA) of the Tn3 family, and carried a class 2 integron. The class 2 integron of pECTm80 contains an intact cassette array dfrA1-sat2, encoding resistance to trimethoprim and streptothricin, …
Molecular Characterization Of Escherichia Coli Strains That Cause Symptomatic And Asymptomatic Urinary Tract Infections, Sam Abraham, Toni A. Chapman, Ren Zhang, James Chin, Amanda N. Mabbett, Makrina Totsika, Mark A. Schembri
Molecular Characterization Of Escherichia Coli Strains That Cause Symptomatic And Asymptomatic Urinary Tract Infections, Sam Abraham, Toni A. Chapman, Ren Zhang, James Chin, Amanda N. Mabbett, Makrina Totsika, Mark A. Schembri
Faculty of Science - Papers (Archive)
The differences between Escherichia coli strains associated with symptomatic and asymptomatic urinary tract infections (UTIs) remain to be properly determined. Here we examined the prevalence of plasmid types and bacteriocins, as well as genetic relatedness, in a defined collection of E. coli strains that cause UTIs. Comparative analysis identified a subgroup of strains with a high number of virulence genes (VGs) and microcins M/H47. We also identified associations between microcin genes, VGs, and specific plasmid types.
Molecular Characterization Of Commensal Escherichia Coli Adapted To Different Compartments Of The Porcine Gastrointestinal Tract, Sam Abraham, David M. Gordon, James Chin, Huub J. M Brouwers, Peter Njuguna, Mitchell D. Groves, Ren Zhang, Toni A. Chapman
Molecular Characterization Of Commensal Escherichia Coli Adapted To Different Compartments Of The Porcine Gastrointestinal Tract, Sam Abraham, David M. Gordon, James Chin, Huub J. M Brouwers, Peter Njuguna, Mitchell D. Groves, Ren Zhang, Toni A. Chapman
Faculty of Science - Papers (Archive)
The role of Escherichia coli as a pathogen has been the focus of considerable study, while much less is known about it as a commensal and how it adapts to and colonizes different environmental niches within the mammalian gut. In this study, we characterize Escherichia coli organisms (n=146) isolated from different regions of the intestinal tracts of eight pigs (dueodenum, ileum, colon, and feces). The isolates were typed using the method of random amplified polymorphic DNA (RAPD) and screened for the presence of bacteriocin genes and plasmid replicon types. Molecular analysis of variance using the RAPD data showed that E. …
Specific Electromagnetic Effects Of Microwave Radiation On Escherichia Coli, Yury Shamis, Alex Taube, Natasa Mitik-Dineva, Rodney Croft, Russell J. Crawford, Elena P. Ivanova
Specific Electromagnetic Effects Of Microwave Radiation On Escherichia Coli, Yury Shamis, Alex Taube, Natasa Mitik-Dineva, Rodney Croft, Russell J. Crawford, Elena P. Ivanova
Faculty of Health and Behavioural Sciences - Papers (Archive)
The present study investigated the effects of microwave (MW) radiation on Escherichia coli applied under a sub-lethal temperature. The experiments were conducted at a frequency of 18 GHz and performed at a temperature below 40oC to avoid the thermal degradation of bacterial cells during exposure. The absorbed power was calculated to be 1500 kW/m3 and the electric field was determined to be 300 V/m. Both values were theoretically confirmed using CST Microwave Studio 3D Electromagnetic Simulation Software. As a negative control, E. coli cells were also thermally heated up to temperatures up to 40oC using Peltier Plate heating. Scanning Electron …
Distribution Of Class 1 Integrons With Is26-Mediated Deletions In Their 3'-Conserved Segments In Escherichia Coli Of Human And Animal Origin., Fay E. Dawes, Alexander Kuzevski, Karl A Bettelheim, Michael A Hornitzky, Steven P Djordjevic, Mark J. Walker
Distribution Of Class 1 Integrons With Is26-Mediated Deletions In Their 3'-Conserved Segments In Escherichia Coli Of Human And Animal Origin., Fay E. Dawes, Alexander Kuzevski, Karl A Bettelheim, Michael A Hornitzky, Steven P Djordjevic, Mark J. Walker
Faculty of Science - Papers (Archive)
Class 1 integrons play a role in the emergence of multi-resistant bacteria by facilitating the recruitment of gene cassettes encoding antibiotic resistance genes. 512 E. coli strains sourced from humans (n = 202), animals (n = 304) and the environment (n = 6) were screened for the presence of the intI1 gene. In 31/79 integron positive E. coli strains, the gene cassette regions could not be PCR amplified using standard primers. DNA sequence analysis of 6 serologically diverse strains revealed atypical integrons harboured the dfrA5 cassette gene and only 24 bp of the integron 3'-conserved segment (CS) remained, due to …
Interactive Visualization Of Clusters In Microarray Data: An Efficient Tool For Improved Metabolic Analysis Of E. Coli, Theresa Scharl, Gerald Striedner, Florentina Potschacher, Friedrich Leisch, Karl Bayer
Interactive Visualization Of Clusters In Microarray Data: An Efficient Tool For Improved Metabolic Analysis Of E. Coli, Theresa Scharl, Gerald Striedner, Florentina Potschacher, Friedrich Leisch, Karl Bayer
Faculty of Commerce - Papers (Archive)
Background Interpretation of comprehensive DNA microarray data sets is a challenging task for biologists and process engineers where scientific assistance of statistics and bioinformatics is essential. Interdisciplinary cooperation and concerted development of software-tools for simplified and accelerated data analysis and interpretation is the key to overcome the bottleneck in data-analysis workflows. This approach is exemplified by gcExplorer an interactive visualization toolbox based on cluster analysis. Clustering is an important tool in gene expression data analysis to find groups of co-expressed genes which can finally suggest functional pathways and interactions between genes. The visualization of gene clusters gives practitioners an understanding …
Using Neighborhood Graphs For The Investigation Of E. Coli Gene Clusters, Theresa Scharl, Friedrich Leisch
Using Neighborhood Graphs For The Investigation Of E. Coli Gene Clusters, Theresa Scharl, Friedrich Leisch
Faculty of Commerce - Papers (Archive)
Clustering is commonly used in the analysis of geneexpression data to nd groups of co{expressed genes.The denition of gene clusters is not very clear asgenetic interactions are extremely complex. For thisreason the relationship between clusters is very importantas co{expressed genes can end up in dierentclusters. The neighborhood graph is a useful tool tovisualize the cluster structure. In this paper the Rpackage gcExplorer is presented which is an interactivetoolbox for the exploration of gene clusters. Additionalinformation about the gene clusters like theannotation of genes to functional groups (e.g., GOcategories) can easily be investigated. The new visualizationtoolbox is demonstrated on microarray datafrom …
The Proofreading Exonuclease Subunit E Of Escherichia Coli Dna Polymerase Iii Is Tethered To The Polymerase Subunit A Via A Flexible Linker, Kiyoshi Ozawa, Slobodan Jergic, Ah-Young Park, Nicholas E. Dixon, Gottfried Otting
The Proofreading Exonuclease Subunit E Of Escherichia Coli Dna Polymerase Iii Is Tethered To The Polymerase Subunit A Via A Flexible Linker, Kiyoshi Ozawa, Slobodan Jergic, Ah-Young Park, Nicholas E. Dixon, Gottfried Otting
Faculty of Science - Papers (Archive)
Escherichia coli DNA polymerase III holoenzyme is composed of 10 different subunits linked by noncovalent interactions. The polymerase activity resides in the α-subunit. The ε-subunit, which contains the proofreading exonuclease site within its N-terminal 185 residues, binds to α via a segment of 57 additional C-terminal residues, and also to θ, whose function is less well defined. The present study shows that θ greatly enhances the solubility of ε during cell-free synthesis. In addition, synthesis of ε in the presence of θ and α resulted in a soluble ternary complex that could readily be purified and analyzed by …
The Unstructured C-Terminus Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii Holoenzyme Is The Site Of Interaction With The Alpha Subunit, Slobodan Jergic, Kiyoshi Ozawa, Neal K. Williams, Xun-Cheng Su, Daniel D. Scott, Samir M. Hamdan, Jeffrey A. Crowther, Gottfried Otting, Nicholas E. Dixon
The Unstructured C-Terminus Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii Holoenzyme Is The Site Of Interaction With The Alpha Subunit, Slobodan Jergic, Kiyoshi Ozawa, Neal K. Williams, Xun-Cheng Su, Daniel D. Scott, Samir M. Hamdan, Jeffrey A. Crowther, Gottfried Otting, Nicholas E. Dixon
Faculty of Science - Papers (Archive)
The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τC16. We show that the extreme C-terminal region of τC16 constitutes the site of interaction with α. The τC16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τC16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (KD) of the α−τC16 complex to be ∼260 pM. Competition with immobilized τC16 by …
Comparative Analysis Of Virulence Genes, Genetic Diversity, And Phylogeny Of Commensal And Enterotoxigenic Escherichia Coli Isolates From Weaned Pigs, Xi-Yang Wu, Toni A. Chapman, Darren J. Trott, Karl A Bettelheim, Thuy N. Do, Steve Driesen, Mark J. Walker, James Chin
Comparative Analysis Of Virulence Genes, Genetic Diversity, And Phylogeny Of Commensal And Enterotoxigenic Escherichia Coli Isolates From Weaned Pigs, Xi-Yang Wu, Toni A. Chapman, Darren J. Trott, Karl A Bettelheim, Thuy N. Do, Steve Driesen, Mark J. Walker, James Chin
Faculty of Science - Papers (Archive)
If the acquisition of virulence genes (VGs) for pathogenicity were not solely acquired through horizontal gene transfers of pathogenicity islands, transposons, and phages, then clonal clusters of enterotoxigenic Escherichia coli (ETEC) would contain few or even none of the VGs found in strains responsible for extraintestinal infections. To evaluate this possibility, 47 postweaning diarrhea (PWD) ETEC strains from different geographical origins and 158 commensal E. coli isolates from the gastrointestinal tracts of eight group-housed healthy pigs were screened for 36 extraintestinal and 18 enteric VGs using multiplex PCR assays. Of 36 extraintestinal VGs, only 8 were detected (fimH, …
Solution Structure Of Domains Iva And V Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii And Interaction With The Alpha Subunit, Xun-Cheng Su, Slobodan Jergic, Max A Keniry, Nicholas E. Dixon, Gottfried Otting
Solution Structure Of Domains Iva And V Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii And Interaction With The Alpha Subunit, Xun-Cheng Su, Slobodan Jergic, Max A Keniry, Nicholas E. Dixon, Gottfried Otting
Faculty of Science - Papers (Archive)
The solution structure of the C-terminal Domain V of the τ subunit of E. coli DNA polymerase III was determined by nuclear magnetic resonance (NMR) spectroscopy. The fold is unique to τ subunits. Amino acid sequence conservation is pronounced for hydrophobic residues that form the structural core of the protein, indicating that the fold is representative for τ subunits from a wide range of different bacteria. The interaction between the polymerase subunits τ and α was studied by NMR experiments where α was incubated with full-length C-terminal domain (τC16), and domains shortened at the C-terminus by 11 …
Comparison Of Virulence Gene Profiles Between Escherichia Coli Strains Isolated From Healthy And Diarrheic Swine, Mark R. Wilson, Xi Yang Wu, Idris Barchia, Karl A Bettelheim, Steven Driesen, Darren J. Trott, Toni A. Chapman, James J C Chin
Comparison Of Virulence Gene Profiles Between Escherichia Coli Strains Isolated From Healthy And Diarrheic Swine, Mark R. Wilson, Xi Yang Wu, Idris Barchia, Karl A Bettelheim, Steven Driesen, Darren J. Trott, Toni A. Chapman, James J C Chin
Faculty of Science - Papers (Archive)
A combination of uni- and multiplex PCR assays targeting 58 virulence genes (VGs) associated with Escherichia coli strains causing intestinal and extraintestinal disease in humans and other mammals was used to analyze the VG repertoire of 23 commensal E. coli isolates from healthy pigs and 52 clinical isolates associated with porcine neonatal diarrhea (ND) and postweaning diarrhea (PWD). The relationship between the presence and absence of VGs was interrogated using three statistical methods. According to the generalized linear model, 17 of 58 VGs were found to be significant (P < 0.05) in distinguishing between commensal and clinical isolates. Nine of the 17 genes represented by iha, hlyA, aidA, east1, aah, fimH, iroN(E. coli), traT, and saa have not been previously identified as important VGs in clinical porcine isolates in Australia. The remaining eight VGs code for fimbriae (F4, F5, F18, and F41) and toxins (STa, STb, LT, and Stx2), normally associated with porcine enterotoxigenic E. coli. Agglomerative hierarchical algorithm analysis grouped E. coli strains into subclusters based primarily on their serogroup. Multivariate analyses of clonal relationships based on the 17 VGs were collapsed into two-dimensional space by principal coordinate analysis. PWD clones were distributed in two quadrants, separated from ND and commensal clones, which tended to cluster within one quadrant. Clonal subclusters within quadrants were highly correlated with serogroups. These methods of analysis provide different perspectives in our attempts to understand how commensal and clinical porcine enterotoxigenic E. coli strains have evolved and are engaged in the dynamic process of losing or acquiring VGs within the pig population.
Structure Of The Theta Subunit Of Escherichia Coli Dna Polymerase Iii In Complex With The Epsilon Subunit, Max A Keniry, Ah-Young Park, Elisabeth A. Owen, Samir M. Hamdan, Guido Pintacuda, Gottfried Otting, Nicholas E. Dixon
Structure Of The Theta Subunit Of Escherichia Coli Dna Polymerase Iii In Complex With The Epsilon Subunit, Max A Keniry, Ah-Young Park, Elisabeth A. Owen, Samir M. Hamdan, Guido Pintacuda, Gottfried Otting, Nicholas E. Dixon
Faculty of Science, Medicine and Health - Papers: part A
The catalytic core of Escherichia coli DNA polymerase III contains three tightly associated subunits, the α, ε, and θ subunits. The θ subunit is the smallest and least understood subunit. The three-dimensional structure of θ in a complex with the unlabeled N-terminal domain of the ε subunit, ε186, was determined by multidimensional nuclear magnetic resonance spectroscopy. The structure was refined using pseudocontact shifts that resulted from inserting a lanthanide ion (Dy3+, Er3+, or Ho3+) at the active site of ε186. The structure determination revealed a three-helix bundle fold that is similar to the solution …
Comparison Of Virulence Gene Profiles Between Escherichia Coli Strains Isolated From Healthy And Diarrheic Swine, Mark Wilson, Karl A Bettelheim, X Y Wu, S Driesen, James Chin, Toni Chapman, I Barchia, D Trott
Comparison Of Virulence Gene Profiles Between Escherichia Coli Strains Isolated From Healthy And Diarrheic Swine, Mark Wilson, Karl A Bettelheim, X Y Wu, S Driesen, James Chin, Toni Chapman, I Barchia, D Trott
Mark R Wilson
No abstract provided.
Bovine Feces From Animals With Gastrointestinal Infections Are A Source Of Serologically Diverse Atypical Enteropathogenic Escherichia Coli And Shiga Toxin-Producing E. Coli Strains That Commonly Possess Intimin, Michael A Hornitzky, Kim Mercieca, Karl A Bettelheim, Steven P. Djordjevic
Bovine Feces From Animals With Gastrointestinal Infections Are A Source Of Serologically Diverse Atypical Enteropathogenic Escherichia Coli And Shiga Toxin-Producing E. Coli Strains That Commonly Possess Intimin, Michael A Hornitzky, Kim Mercieca, Karl A Bettelheim, Steven P. Djordjevic
Faculty of Science, Medicine and Health - Papers: part A
Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) cells were isolated from 191 fecal samples from cattle with gastrointestinal infections (diagnostic samples) collected in New South Wales, Australia. By using a multiplex PCR, E. coli cells possessing combinations of stx1, stx2, eae, and ehxA were detected by a combination of direct culture and enrichment in E. coli (EC) (modified) broth followed by plating on vancomycin-cefixime-cefsulodin blood (BVCC) agar for the presence of enterohemolytic colonies and on sorbitol MacConkey agar for the presence of non-sorbitol-fermenting colonies. The high prevalence of the intimin gene eae …