DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes (2009)
Butala, Matej, Busby, Stephen J. W., Lee, David J.
We describe a protocol, DNA sampling, for the rapid isolation of specific segments of DNA, together with bound proteins, from Escherichia coli K-12. The DNA to be sampled is generated as a discrete...
Shimada, Tomohiro, Ishihama, Akira, Busby, Stephen J. W., Grainger, David C.
The Escherichia coli RutR protein is the master regulator of genes involved in pyrimidine catabolism. Here we have used chromatin immunoprecipitation in combination with DNA microarrays to measure...
Samarasinghe, Shivanthi, El-Robh, Mohamed Samir, Grainger, David C., Zhang, Wenke, Soultanas, Panos, Busby, Stephen J. W.
The Escherichia coli MelR protein is a transcription activator that autoregulates its own promoter by repressing transcription initiation. Optimal repression requires MelR binding to a site that...
Kedzierska, Barbara, Szambowska, Anna, Herman-Antosiewicz, Anna, Lee, David J., Busby, Stephen J.W., Wegrzyn, Grzegorz, ...
The bacteriophage λ pM promoter is required for maintenance of the λ prophage in Escherichia coli, as it facilitates transcription of the cI gene, encoding the λ repressor (CI). CI levels are...
Transcription factor distribution in Escherichia coli: studies with FNR protein (2007)
Grainger, David C., Aiba, Hirofumi, Hurd, Douglas, Browning, Douglas F., Busby, Stephen J. W.
Using chromatin immunoprecipitation (ChIP) and high-density microarrays, we have measured the distribution of the global transcription regulator protein, FNR, across the entire Escherichia coli...
Grainger, David C., Hurd, Douglas, Goldberg, Martin D., Busby, Stephen J. W.
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating...
Grainger, David C., Hurd, Douglas, Goldberg, Martin D., Busby, Stephen J. W.
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating...
Transcription factor distribution in Escherichia coli: studies with FNR protein (2006)
Grainger, David C., Aiba, Hirofumi, Hurd, Douglas, Browning, Douglas F., Busby, Stephen J. W.
Using chromatin immunoprecipitation (ChIP) and high-density microarrays, we have measured the distribution of the global transcription regulator protein, FNR, across the entire Escherichia coli...
Grainger, David C., Hurd, Douglas, Goldberg, Martin D., Busby, Stephen J. W.
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating...
Transcription factor distribution in Escherichia coli: studies with FNR protein (2006)
Grainger, David C., Aiba, Hirofumi, Hurd, Douglas, Browning, Douglas F., Busby, Stephen J. W.
Using chromatin immunoprecipitation (ChIP) and high-density microarrays, we have measured the distribution of the global transcription regulator protein, FNR, across the entire Escherichia coli...
Kedzierska, Barbara, Lee, David J., Wegrzyn, Grzegorz, Busby, Stephen J. W., Thomas, Mark S.
The bacteriophage λ CII protein stimulates the activity of three phage promoters, pE, pI and paQ, upon binding to a site overlapping the –35 element at each promoter. Here we used preparations of...
Identification and analysis of 'extended -10' promoters in Escherichia coli (2003)
Mitchell, Jennie E., Zheng, Dongling, Busby, Stephen J. W., Minchin, Stephen D.
We have compiled and aligned the DNA sequences of 554 promoter regions from Escherichia coli and analysed the alignment for sequence similarities. We have focused on the similarities and differences...
Howard, Victoria J., Belyaeva, Tamara A., Busby, Stephen J. W., Hyde, Eva I.
MelR is an Escherichia coli transcription factor belonging to the AraC family. It activates expression of the melAB operon in response to melibiose. Full-length MelR (MelR303) binds to two pairs of...
Meng, Wenmao, Belyaeva, Tamara, Savery, Nigel J., Busby, Stephen J. W., Ross, Wilma E., Gaal, Tamas, ...
The UP element stimulates transcription from the rrnB P1 promoter through a direct interaction with the C-terminal domain of the RNA polymerase α subunit (αCTD). We investigated the effect on...
Michan, Carmen M., Busby, Stephen J. W., Hyde, Eva I.
A set of nested deletions has been made In the Escherichia coll melR gene, encoding the MelR transcription activator protein. Expression of the resulting meIR derivatives led to the production of...
Murakami, Katsuhiko, Owens, Jeffrey T., Belyaeva, Tamara A., Meares, Claude F., Busby, Stephen J. W., Ishihama, Akira
Interactions between the cAMP receptor protein (CRP) and the carboxy-terminal regulatory domain (CTD) of Escherichia coli RNA polymerase α subunit were analyzed at promoters carrying tandem DNA...
Meng, Wenmao, Belyaeva, Tamara, Savery, Nigel J., Busby, Stephen J. W., Ross, Wilma E., Gaal, Tamas, ...
The UP element stimulates transcription from the rrnB P1 promoter through a direct interaction with the C-terminal domain of the RNA polymerase α subunit (αCTD). We investigated the effect on...
Landini, Paolo, Busby, Stephen J. W.
The methylated form of the Ada protein (meAda) activates transcription from the Escherichia coli ada, aidB, and alkA promoters with different mechanisms. In this study we identify amino acid...
Landini, Paolo, Busby, Stephen J. W.
The Escherichia coli Ada protein activates ς70-dependent transcription at three different promoters (ada, aidB, and alkA) in response to alkylation damage of DNA. During stationary phase, however,...
Regulation of Acetyl Coenzyme A Synthetase in Escherichia coli
Kumari, Suman, Beatty, Christine M., Browning, Douglas F., Busby, Stephen J. W., Simel, Erica J., Hovel-Miner, Galadriel, ...
Cells of Escherichia coli growing on sugars that result in catabolite repression or amino acids that feed into glycolysis undergo a metabolic switch associated with the production and utilization of...
Bown, Jonathan A., Kolb, Annie, Meares, Claude F., Ishihama, Akira, Minchin, Stephen D., Busby, Stephen J. W.
A DNA cleavage reagent, specifically tethered to residue 581 of the Escherichia coli RNA polymerase ς70 subunit, has been used to investigate the location of ς70 region 4 in different complexes at...
Howard, Victoria J., Belyaeva, Tamara A., Busby, Stephen J. W., Hyde, Eva I.
MelR is an Escherichia coli transcription factor belonging to the AraC family. It activates expression of the melAB operon in response to melibiose. Full-length MelR (MelR303) binds to two pairs of...
A simple mechanism for co-dependence on two activators at an Escherichia coli promoter
Wade, Joseph T., Belyaeva, Tamara A., Hyde, Eva I., Busby, Stephen J.W.
The Escherichia coli melAB promoter is co-dependent upon two transcription activators, MelR and the cyclic AMP receptor protein, CRP. In this study we demonstrate positive co-operativity between the...
Savery, Nigel J., Lloyd, Georgina S., Busby, Stephen J. W., Thomas, Mark S., Ebright, Richard H., Gourse, Richard L.
Alanine scanning of the Escherichia coli RNA polymerase α subunit C-terminal domain (αCTD) was used to identify amino acid side chains important for class I cyclic AMP receptor protein...
Transcription Activation by FNR: Evidence for a Functional Activating Region 2
Blake, Timo, Barnard, Anne, Busby, Stephen J. W., Green, Jeffrey
The FNR protein of Escherichia coli controls the transcription of target genes in response to anoxia via the assembly-disassembly of oxygen-labile iron-sulfur clusters. Previous work identified...
Overton, Tim, Reid, Eleanor G. F., Foxall, Robin, Smith, Harry, Busby, Stephen J. W., Cole, Jeffrey A.
The Neisseria gonorrhoeae genome encodes a homologue of the Escherichia coli FNR protein (the fumarate and nitrate reductase regulator). Despite its similarity to E. coli FNR, the gonococcal FNR only...
Identification and analysis of ‘extended –10’ promoters in Escherichia coli
Mitchell, Jennie E., Zheng, Dongling, Busby, Stephen J. W., Minchin, Stephen D.
We have compiled and aligned the DNA sequences of 554 promoter regions from Escherichia coli and analysed the alignment for sequence similarities. We have focused on the similarities and differences...
Beatty, Christine M., Browning, Douglas F., Busby, Stephen J. W., Wolfe, Alan J.
The cyclic AMP receptor protein (CRP) activates transcription of the Escherichia coli acs gene, which encodes an acetate-scavenging enzyme required for fitness during periods of carbon starvation....
Lloyd, Georgina S., Niu, Wei, Tebbutt, John, Ebright, Richard H., Busby, Stephen J.W.
Transcription activation by the Escherichia coli cyclic AMP receptor protein (CRP) at different promoters has been studied using RNA polymerase holoenzyme derivatives containing two full-length α...
Transcription Regulation by Tandem-Bound FNR at Escherichia coli Promoters
Barnard, Anne M. L., Green, Jeffrey, Busby, Stephen J. W.
FNR is an Escherichia coli transcription factor that regulates the transcription of many genes in response to anaerobiosis. We have constructed a series of artificial FNR-dependent promoters, based...
Meng, Wenmao, Savery, Nigel J., Busby, Stephen J.W., Thomas, Mark S.
The C–terminal domain of the Escherichia coli RNA polymerase α subunit (αCTD) plays a key role in transcription initiation at many activator-dependent promoters. This domain is connected to the...
Kedzierska, Barbara, Lee, David J., Węgrzyn, Grzegorz, Busby, Stephen J. W., Thomas, Mark S.
The bacteriophage λ CII protein stimulates the activity of three phage promoters, pE, pI and paQ, upon binding to a site overlapping the –35 element at each promoter. Here we used preparations of...
Grainger, David C., Overton, Timothy W., Reppas, Nikos, Wade, Joseph T., Tamai, Eiji, Hobman, Jon L., ...
Escherichia coli MelR protein is a transcription activator that is essential for melibiose-dependent expression of the melAB genes. We have used chromatin immunoprecipitation to study the binding of...
Kovács, Ákos T., Rákhely, Gábor, Browning, Douglas F., Fülöp, András, Maróti, Gergely, Busby, Stephen J. W., ...
The purple sulfur photosynthetic bacterium Thiocapsa roseopersicina BBS contains a heat-stable membrane-associated hydrogenase encoded by the hyn operon. Expression from the hyn operon regulatory...
El-Robh, Mohamed Samir, Busby, Stephen J W
We report the first detailed quantitative study of divergent promoters dependent on the Escherichia coli cAMP receptor protein (CRP), a factor known to activate transcription initiation at target...
Grainger, David C., Hurd, Douglas, Harrison, Marcus, Holdstock, Jolyon, Busby, Stephen J. W.
Chromatin immunoprecipitation and high-density microarrays have been used to monitor the distribution of the global transcription regulator Escherichia coli cAMP-receptor protein (CRP) and RNA...
Kahramanoglou, Christina, Webster, Christine L., El-Robh, Mohamed Samir, Belyaeva, Tamara A., Busby, Stephen J. W.
Transcription of the Escherichia coli melAB operon is regulated by the MelR protein, an AraC family member whose activity is modulated by the binding of melibiose. In the absence of melibiose, MelR...
Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
Grainger, David C., Hurd, Douglas, Goldberg, Martin D., Busby, Stephen J. W.
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating...
Murakami, Katsuhiko, Owens, Jeffrey T., Belyaeva, Tamara A., Meares, Claude F., Busby, Stephen J. W., Ishihama, Akira
Interactions between the cAMP receptor protein (CRP) and the carboxy-terminal regulatory domain (CTD) of Escherichia coli RNA polymerase α subunit were analyzed at promoters carrying tandem DNA...
Meng, Wenmao, Belyaeva, Tamara, Savery, Nigel J., Busby, Stephen J. W., Ross, Wilma E., Gaal, Tamas, ...
The UP element stimulates transcription from the rrnB P1 promoter through a direct interaction with the C-terminal domain of the RNA polymerase α subunit (αCTD). We investigated the effect on...
Landini, Paolo, Busby, Stephen J. W.
The methylated form of the Ada protein (meAda) activates transcription from the Escherichia coli ada, aidB, and alkA promoters with different mechanisms. In this study we identify amino acid...
Landini, Paolo, Busby, Stephen J. W.
The Escherichia coli Ada protein activates ς70-dependent transcription at three different promoters (ada, aidB, and alkA) in response to alkylation damage of DNA. During stationary phase, however,...
Regulation of Acetyl Coenzyme A Synthetase in Escherichia coli
Kumari, Suman, Beatty, Christine M., Browning, Douglas F., Busby, Stephen J. W., Simel, Erica J., Hovel-Miner, Galadriel, ...
Cells of Escherichia coli growing on sugars that result in catabolite repression or amino acids that feed into glycolysis undergo a metabolic switch associated with the production and utilization of...
Bown, Jonathan A., Kolb, Annie, Meares, Claude F., Ishihama, Akira, Minchin, Stephen D., Busby, Stephen J. W.
A DNA cleavage reagent, specifically tethered to residue 581 of the Escherichia coli RNA polymerase ς70 subunit, has been used to investigate the location of ς70 region 4 in different complexes at...
Howard, Victoria J., Belyaeva, Tamara A., Busby, Stephen J. W., Hyde, Eva I.
MelR is an Escherichia coli transcription factor belonging to the AraC family. It activates expression of the melAB operon in response to melibiose. Full-length MelR (MelR303) binds to two pairs of...
A simple mechanism for co-dependence on two activators at an Escherichia coli promoter
Wade, Joseph T., Belyaeva, Tamara A., Hyde, Eva I., Busby, Stephen J.W.
The Escherichia coli melAB promoter is co-dependent upon two transcription activators, MelR and the cyclic AMP receptor protein, CRP. In this study we demonstrate positive co-operativity between the...
Savery, Nigel J., Lloyd, Georgina S., Busby, Stephen J. W., Thomas, Mark S., Ebright, Richard H., Gourse, Richard L.
Alanine scanning of the Escherichia coli RNA polymerase α subunit C-terminal domain (αCTD) was used to identify amino acid side chains important for class I cyclic AMP receptor protein...
Transcription Activation by FNR: Evidence for a Functional Activating Region 2
Blake, Timo, Barnard, Anne, Busby, Stephen J. W., Green, Jeffrey
The FNR protein of Escherichia coli controls the transcription of target genes in response to anoxia via the assembly-disassembly of oxygen-labile iron-sulfur clusters. Previous work identified...
Overton, Tim, Reid, Eleanor G. F., Foxall, Robin, Smith, Harry, Busby, Stephen J. W., Cole, Jeffrey A.
The Neisseria gonorrhoeae genome encodes a homologue of the Escherichia coli FNR protein (the fumarate and nitrate reductase regulator). Despite its similarity to E. coli FNR, the gonococcal FNR only...
Identification and analysis of ‘extended –10’ promoters in Escherichia coli
Mitchell, Jennie E., Zheng, Dongling, Busby, Stephen J. W., Minchin, Stephen D.
We have compiled and aligned the DNA sequences of 554 promoter regions from Escherichia coli and analysed the alignment for sequence similarities. We have focused on the similarities and differences...
Beatty, Christine M., Browning, Douglas F., Busby, Stephen J. W., Wolfe, Alan J.
The cyclic AMP receptor protein (CRP) activates transcription of the Escherichia coli acs gene, which encodes an acetate-scavenging enzyme required for fitness during periods of carbon starvation....
Lloyd, Georgina S., Niu, Wei, Tebbutt, John, Ebright, Richard H., Busby, Stephen J.W.
Transcription activation by the Escherichia coli cyclic AMP receptor protein (CRP) at different promoters has been studied using RNA polymerase holoenzyme derivatives containing two full-length α...
Transcription Regulation by Tandem-Bound FNR at Escherichia coli Promoters
Barnard, Anne M. L., Green, Jeffrey, Busby, Stephen J. W.
FNR is an Escherichia coli transcription factor that regulates the transcription of many genes in response to anaerobiosis. We have constructed a series of artificial FNR-dependent promoters, based...
Meng, Wenmao, Savery, Nigel J., Busby, Stephen J.W., Thomas, Mark S.
The C–terminal domain of the Escherichia coli RNA polymerase α subunit (αCTD) plays a key role in transcription initiation at many activator-dependent promoters. This domain is connected to the...
Kedzierska, Barbara, Lee, David J., Węgrzyn, Grzegorz, Busby, Stephen J. W., Thomas, Mark S.
The bacteriophage λ CII protein stimulates the activity of three phage promoters, pE, pI and paQ, upon binding to a site overlapping the –35 element at each promoter. Here we used preparations of...
Grainger, David C., Overton, Timothy W., Reppas, Nikos, Wade, Joseph T., Tamai, Eiji, Hobman, Jon L., ...
Escherichia coli MelR protein is a transcription activator that is essential for melibiose-dependent expression of the melAB genes. We have used chromatin immunoprecipitation to study the binding of...
Kovács, Ákos T., Rákhely, Gábor, Browning, Douglas F., Fülöp, András, Maróti, Gergely, Busby, Stephen J. W., ...
The purple sulfur photosynthetic bacterium Thiocapsa roseopersicina BBS contains a heat-stable membrane-associated hydrogenase encoded by the hyn operon. Expression from the hyn operon regulatory...
El-Robh, Mohamed Samir, Busby, Stephen J W
We report the first detailed quantitative study of divergent promoters dependent on the Escherichia coli cAMP receptor protein (CRP), a factor known to activate transcription initiation at target...
Grainger, David C., Hurd, Douglas, Harrison, Marcus, Holdstock, Jolyon, Busby, Stephen J. W.
Chromatin immunoprecipitation and high-density microarrays have been used to monitor the distribution of the global transcription regulator Escherichia coli cAMP-receptor protein (CRP) and RNA...
Kahramanoglou, Christina, Webster, Christine L., El-Robh, Mohamed Samir, Belyaeva, Tamara A., Busby, Stephen J. W.
Transcription of the Escherichia coli melAB operon is regulated by the MelR protein, an AraC family member whose activity is modulated by the binding of melibiose. In the absence of melibiose, MelR...
Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
Grainger, David C., Hurd, Douglas, Goldberg, Martin D., Busby, Stephen J. W.
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating...
Browning, Douglas F., Lee, David J., Wolfe, Alan J., Cole, Jeffrey A., Busby, Stephen J. W.
The Escherichia coli K-12 nrf operon promoter can be activated fully by the FNR protein (regulator of fumarate and nitrate reduction) binding to a site centered at position −41.5. FNR-dependent...
Transcription factor distribution in Escherichia coli: studies with FNR protein
Grainger, David C., Aiba, Hirofumi, Hurd, Douglas, Browning, Douglas F., Busby, Stephen J. W.
Using chromatin immunoprecipitation (ChIP) and high-density microarrays, we have measured the distribution of the global transcription regulator protein, FNR, across the entire Escherichia coli...
Kedzierska, Barbara, Szambowska, Anna, Herman-Antosiewicz, Anna, Lee, David J., Busby, Stephen J.W., Wegrzyn, Grzegorz, ...
The bacteriophage λ pM promoter is required for maintenance of the λ prophage in Escherichia coli, as it facilitates transcription of the cI gene, encoding the λ repressor (CI). CI levels are...
Mitchell, Jennie E., Oshima, Taku, Piper, Sarah E., Webster, Christine L., Westblade, Lars F., Karimova, Gouzel, ...
The Escherichia coli Rsd protein forms complexes with the RNA polymerase σ70 factor, but its biological role is not understood. Transcriptome analysis shows that overexpression of Rsd causes...
Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR
Samarasinghe, Shivanthi, El-Robh, Mohamed Samir, Grainger, David C., Zhang, Wenke, Soultanas, Panos, Busby, Stephen J. W.
The Escherichia coli MelR protein is a transcription activator that autoregulates its own promoter by repressing transcription initiation. Optimal repression requires MelR binding to a site that...
Lee, David J., Busby, Stephen J. W., Westblade, Lars F., Chait, Brian T.
Bacteria contain a single multisubunit RNA polymerase that is responsible for the synthesis of all RNA. Previous studies of the Escherichia coli K-12 laboratory strain identified a group of effector...
Shimada, Tomohiro, Ishihama, Akira, Busby, Stephen J. W., Grainger, David C.
The Escherichia coli RutR protein is the master regulator of genes involved in pyrimidine catabolism. Here we have used chromatin immunoprecipitation in combination with DNA microarrays to measure...
DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes
Butala, Matej, Busby, Stephen J. W., Lee, David J.
We describe a protocol, DNA sampling, for the rapid isolation of specific segments of DNA, together with bound proteins, from Escherichia coli K-12. The DNA to be sampled is generated as a discrete...
Regulation by Nucleoid-Associated Proteins at the Escherichia coli nir Operon Promoter▿
Browning, Douglas F., Cole, Jeffrey A., Busby, Stephen J. W.
The Escherichia coli K-12 nir operon promoter can be fully activated by binding of the regulator of fumarate and nitrate reduction (FNR) to a site centered at position −41.5 upstream of the...
Activation and Repression at the Escherichia coli ynfEFGHI Operon Promoter▿
Xu, Meng, Busby, Stephen J. W., Browning, Douglas F.
Induction of the Escherichia coli K-12 ynfEFGHI operon in response to anaerobiosis is repressed by nitrate ions. In this study, we show that the global transcription factor FNR is a class II...