Publications
197 results found
Huvet M, Toni T, Sheng X, et al., 2010, The evolution of the Phage shock protein (Psp) response system: interplay between protein function, genomic organization and system function., Mol Biol Evol
Joly N, Burrows PC, Engl C, et al., 2009, A Lower-Order Oligomer Form of Phage Shock Protein A (PspA) Stably Associates with the Hexameric AAA<SUP>+</SUP> Transcription Activator Protein PspF for Negative Regulation, JOURNAL OF MOLECULAR BIOLOGY, Vol: 394, Pages: 764-775, ISSN: 0022-2836
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- Citations: 44
Zhang N, Joly N, Burrows PC, et al., 2009, The role of the conserved phenylalanine in the σ<SUP>54</SUP>-interacting GAFTGA motif of bacterial enhancer binding proteins, NUCLEIC ACIDS RESEARCH, Vol: 37, Pages: 5981-5992, ISSN: 0305-1048
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- Citations: 28
Jovanovic G, Engl C, Buck M, 2009, Physical, functional and conditional interactions between ArcAB and phage shock proteins upon secretin-induced stress in <i>Escherichia coli</i>, MOLECULAR MICROBIOLOGY, Vol: 74, Pages: 16-28, ISSN: 0950-382X
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- Citations: 27
Burrows PC, Schumacher J, Amartey S, et al., 2009, Functional roles of the pre-sensor I insertion sequence in an AAA plus bacterial enhancer binding protein, Molecular Microbiology, Vol: 73, Pages: 519-533, ISSN: 0950-382X
Molecular machines belonging to the AAA+ superfamily of ATPases use NTP hydrolysis to remodel their versatile substrates. The presence of an insertion sequence defines the major phylogenetic pre‐sensor I insertion (pre‐SIi) AAA+ superclade. In the bacterial σ54‐dependent enhancer binding protein phage shock protein F (PspF) the pre‐SIi loop adopts different conformations depending on the nucleotide‐bound state. Single amino acid substitutions within the dynamic pre‐SIi loop of PspF drastically change the ATP hydrolysis parameters, indicating a structural link to the distant hydrolysis site. We used a site‐specific protein–DNA proximity assay to measure the contribution of the pre‐SIi loop in σ54‐dependent transcription and demonstrate that the pre‐SIi loop is a major structural feature mediating nucleotide state‐dependent differential engagement with Eσ54. We suggest that much, if not all, of the action of the pre‐SIi loop is mediated through the L1 loop and relies on a conserved molecular switch, identified in a crystal structure of one pre‐SIi variant and in accordance with the high covariance between some pre‐SIi residues and distinct residues outside the pre‐SIi sequence.
, 2009, Nucleic Acids Research: VOLUME 37 ISSUE 15 2009, Nucleic Acids Research, Vol: 37, Pages: i-i, ISSN: 0305-1048
Burrows PC, Joly N, Nixon BT, et al., 2009, Comparative analysis of activator-Eσ<SUP>54</SUP> complexes formed with nucleotide-metal fluoride analogues, NUCLEIC ACIDS RESEARCH, Vol: 37, Pages: 5138-5150, ISSN: 0305-1048
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- Citations: 5
Huvet M, Toni T, Tan H, et al., 2009, Model-based evolutionary analysis: the natural history of phage-shock stress response, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 37, Pages: 762-767, ISSN: 0300-5127
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- Citations: 8
Xiao Y, Wigneshweraraj SR, Weinzierl R, et al., 2009, Construction and functional analyses of a comprehensive Σ<SUP>54</SUP> site-directed mutant library using alanine-cysteine mutagenesis, NUCLEIC ACIDS RESEARCH, Vol: 37, Pages: 4482-4497, ISSN: 0305-1048
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- Citations: 7
Huo Y-X, Zhang Y-T, Xiao Y, et al., 2009, IHF-binding sites inhibit DNA loop formation and transcription initiation, NUCLEIC ACIDS RESEARCH, Vol: 37, Pages: 3878-3886, ISSN: 0305-1048
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- Citations: 22
Engl C, Jovanovic G, Lloyd LJ, et al., 2009, In vivo localizations of membrane stress controllers PspA and PspG in Escherichia coli, Molecular Microbiology, Vol: 73, Pages: 382-396, ISSN: 1365-2958
The phage shock protein (Psp) response in Gram-negative bacteria counteracts membrane stress. Transcription of the PspF regulon (pspABCDE and pspG) in Escherichia coli is induced upon stresses that dissipate the proton motive force (pmf). Using GFP fusions we have visualized the subcellular localizations of PspA (a negative regulator and effector of Psp) and PspG (an effector of Psp). It has previously been proposed that PspA evenly coates the inner membrane of the cell. We now demonstrate that instead of uniformly covering the entire cell, PspA (and PspG) is highly organized into what appear to be distinct functional classes (complexes at the cell pole and the lateral cell wall). Real-time observations revealed lateral PspA and PspG complexes are highly mobile, but absent in cells lacking MreB. Without the MreB cytoskeleton, induction of the Psp response is still observed, yet these cells fail to maintain pmf under stress conditions. The two spatial subspecies therefore appear to be dynamically and functionally distinct with the polar clusters being associated with sensory function and the mobile complexes with maintenance of pmf.
Burrows PC, Joly N, Cannon WV, et al., 2009, Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting, JOURNAL OF MOLECULAR BIOLOGY, Vol: 387, Pages: 306-319, ISSN: 0022-2836
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- Citations: 12
Wang B, Kitney R, Buck M, et al., 2009, The Design and Construction of a Set of Modular Synthetic BioLogic Devices for Programming Cells, World Congress on Medical Physics and Biomedical Engineering, Publisher: Springer Berlin Heidelberg, Pages: 289-292
Modularity is an essential property for rationally engineered standard parts and devices. This principle is now being extended to biological based parts and devices for programming cells. However, the design principles and building blocks which are currently in Synthetic Biology are somewhat limited. In addition, it is important to explore the underlying mechanisms of existing, natural biological systems in order to utilise them in designing novel genetic circuit modules. In this paper, we will describe a set of modular synthetic biological parts and devices that are based in rational design. Particularly, a modular tight-controlled and hypersensitive genetic circuit with digital logic AND function is rationally designed and engineered. They use a sigma factor 54( σ 54 ) dependent hetero-regulation module in the hrp (hypersensitive response and pathogenicity) gene regulatory system for Type III secretion in Pseudomonas syringae . Their inputs and outputs are both promoters and thus do not rely on specific inducible promoters and could drive various cellular responses. It shows that the hrp system has significant potential for building a range of biological parts and devices with good performance and flexibility.
Bose D, Pape T, Burrows PC, et al., 2008, Organization of an Activator-Bound RNA Polymerase Holoenzyme, MOLECULAR CELL, Vol: 32, Pages: 337-346, ISSN: 1097-2765
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- Citations: 59
Schumacher J, Joly N, Claeys-Bouuaert IL, et al., 2008, Mechanism of homotropic control to coordinate hydrolysis in a hexameric AAA plus ring ATPase, JOURNAL OF MOLECULAR BIOLOGY, Vol: 381, Pages: 1-12, ISSN: 0022-2836
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- Citations: 9
Burrows PC, Wigneshweraraj S, Bose D, et al., 2008, Visualizing the organization and reorganization of transcription complexes for gene expression, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 36, Pages: 776-779, ISSN: 0300-5127
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- Citations: 4
Joly N, Burrows PC, Buck M, 2008, An intramolecular route for coupling ATPase activity in AAA<SUP>+</SUP> proteins for transcription activation, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 283, Pages: 13725-13735
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- Citations: 27
Wigneshweraraj S, Bose D, Burrows PC, et al., 2008, <i>Modus operandi</i> of the bacterial RNA polymerase containing the σ<SUP>54</SUP> promoter-specificity factor, MOLECULAR MICROBIOLOGY, Vol: 68, Pages: 538-546, ISSN: 0950-382X
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- Citations: 101
Joly N, Rappas M, Buck M, et al., 2008, Trapping of a transcription complex using a new nucleotide analogue: AMP aluminium fluoride, JOURNAL OF MOLECULAR BIOLOGY, Vol: 375, Pages: 1206-1211, ISSN: 0022-2836
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- Citations: 14
Bose D, Joly N, Pape T, et al., 2008, Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 36, Pages: 83-88, ISSN: 0300-5127
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- Citations: 20
Burrows PC, Wigneshweraraj SR, Buck M, 2008, Protein-DNA interactions that govern AAA<SUP>+</SUP> activator-dependent bacterial transcription initiation, JOURNAL OF MOLECULAR BIOLOGY, Vol: 375, Pages: 43-58, ISSN: 0022-2836
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- Citations: 19
Wigneshweraraj S, Burrows P, Bose D, et al., 2008, THE MECHANISTIC BASIS OF <i>nif</i> GENE ACTIVATION, Joint Conference of the 15th International Congress on Nitrogen Fixation/12 International Conference of the African-Association-for-Biological-Nitrogen-Fixation, Publisher: SPRINGER, Pages: 339-+, ISSN: 0924-1949
Joly N, Rappas M, Wigneshweraraj SR, et al., 2007, Coupling nucleotide hydrolysis to transcription activation performance in a bacterial enhancer binding protein, MOLECULAR MICROBIOLOGY, Vol: 66, Pages: 583-595, ISSN: 0950-382X
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- Citations: 31
Schumacher J, Joly N, Rappas M, et al., 2007, Sensor I threonine of the AAA plus ATPase transcriptional activator PspF is involved in coupling nucleoticle triphosphate hydrolysis to the restructuring of σ<SUP>54</SUP>-RNA polymerase, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 282, Pages: 9825-9833
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- Citations: 16
Dago AE, Wigneshweraraj SR, Buck M, et al., 2007, A role for the conserved GAFTGA motif of AAA plus transcription activators in sensing promoter DNA conformation, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 282, Pages: 1087-1097
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- Citations: 18
Mao X-J, Huo Y-X, Buck M, et al., 2007, Interplay between CRP-cAMP and PII-Ntr systems forms novel regulatory network between carbon metabolism and nitrogen assimilation in <i>Escherichia coli</i>, NUCLEIC ACIDS RESEARCH, Vol: 35, Pages: 1432-1440, ISSN: 0305-1048
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- Citations: 46
Heilemann M, Lymperopoulos K, Wigneshweraraj SR, et al., 2007, Studying σ<SUP>54</SUP>-dependent transcription at the single-molecule level using alternating-laser excitation (ALEX) spectroscopy, Biophotonics 2007 Conference, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
Buck M, Bose D, Burrows P, et al., 2006, A second paradigm for gene activation in bacteria, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 34, Pages: 1067-1071, ISSN: 0300-5127
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- Citations: 27
Joly N, Schumacher J, Buck M, 2006, Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA plus transcriptional activator, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 281, Pages: 34997-35007, ISSN: 0021-9258
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- Citations: 46
Leach RN, Gell C, Wigneshweraraj S, et al., 2006, Mapping ATP-dependent activation at σ<SUP>54</SUP> promoter, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 281, Pages: 33717-33726
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- Citations: 16
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