The<i>virF</i>promoter in<i>Shigella</i>: more than just a curved DNA stretch

Prosseda, Gianni; Falconi, Maurizio; Giangrossi, Mara; Gualerzi, Claudio O.; Micheli, Gioacchino; Colonna, Bianca

doi:10.1046/j.1365-2958.2003.03848.x

Cited by 150 publications

(170 citation statements)

References 49 publications

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“…Recently, the role of DNA curvature has been discussed for the promoters of the toxin and rRNA genes in Bacillus anthracis and E. coli, respectively (Hadjifrangiskou & Koehler, 2008;Pul et al, 2008). For example, in the case of virF, encoding an activator of the AraC/XylS familiy, it was found that the intrinsic curvature acts as a thermoswitch, being flanked by two H-NS-binding sites forming a repressor loop (Prosseda et al, 2004). A second example of a curvature-dependent transcription regulation has been reported for the E. coli ompF gene, where IHF has been found to bind upstream of its promoter, increasing the degree of DNA curvature, in a region relevant for negative regulation at high osmolarity (Ramani et al, 1992).…”

Section: Discussionmentioning

confidence: 99%

“…This process is mainly carried out by regulatory proteins that specifically recognize their DNA targets in a sequence-dependent fashion based on the interactions of the regulatory protein with the nucleotides. In addition, it has been demonstrated that primary DNA sequence is not the only recognized feature in the genome for the transcription regulatory process: the DNA topology has been shown to have a relevant role in gene regulation (Ramani et al, 1992;Falconi et al, 1993;Pérez-Martín et al, 1994;Jáuregui et al, 2003;Poore & Mobley, 2003;Prosseda et al, 2004;Olivares-Zavaleta et al, 2006). Recently, the role of DNA curvature has been discussed for the promoters of the toxin and rRNA genes in Bacillus anthracis and E. coli, respectively (Hadjifrangiskou & Koehler, 2008;Pul et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

“…Several groups have reported that DNA static curvature is involved in the thermoregulation and osmoregulation of certain genes (Ramani et al, 1992;Kaji et al, 2003;Prosseda et al, 2004). The expression of the pRO310-mt fusion was therefore analysed in a wild-type and hns background at low and high osmolarity and at 37 u C and 30 u C (Fig.…”

Section: Osmoregulation and Thermoregulation Of Omps1 Is Not Affectedmentioning

confidence: 99%

“…Lanes: M, 100 bp ladder DNA markers; 1, Fa-wt ("304 to "154); 2, Fb-wt ("226 to "76); 3, Fc-wt ("124 to +27); 4, Fb-mt (A151C, G135A); 5, Fb-re (C151G, A135T). The intrinsic bending of each fragment quantified by the k-value (Prosseda et al, 2004) is shown at the bottom of the 4 6C gel. sion of ompS1 is dependent on the concentration of LeuO (De la Cruz et al, 2007).…”

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The DNA static curvature has a role in the regulation of the ompS1 porin gene in Salmonella enterica serovar Typhi

et al. 2009

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The DNA static curvature has been described to play a key role as a regulatory element in the transcription process of several bacterial genes. Here, the role of DNA curvature in the expression of the ompS1 porin gene in Salmonella enterica serovar Typhi is described. The web server MUTACURVE was used to predict mutations that diminished or restored the extent of DNA curvature in the 59 regulatory region of ompS1. Using these predictions, curvature was diminished by sitedirected mutagenesis of only two residues, and curvature was restored by further mutagenesis of the same two residues. Lowering the extent of DNA curvature resulted in an increase in ompS1 expression and in the diminution of the affinity of the silencer proteins H-NS and StpA for the ompS1 59 regulatory region. These mutations were in a region shown not to contain the H-NS nucleation site, consistent with the notion that the effect on expression was due to changes in DNA structural topology. INTRODUCTIONSalmonella enterica serovar Typhi (S. Typhi) is the aetiological agent of typhoid fever in humans (Pang et al., 1998). In our laboratory we have identified the S. Typhi ompS1 gene that encodes the OmpS1 quiescent porin belonging to the OmpC/OmpF superfamily (Fernández-Mora et al., 1995). OmpS1 has been reported to have a role in swarming motility, biofilm formation and virulence in mice (Toguchi et al., 2000;Mireles et al., 2001;Rodríguez-Morales et al., 2006). Expression of ompS1 is dependent on two overlapping promoters, P1 and P2. The P1 promoter is dependent on the OmpR response regulator. The P2 promoter does not require OmpR for activation, being active only in the absence of OmpR (Oropeza et al., 1999; Flores-Valdez et al., 2003;De la Cruz et al., 2007). Another key element in the transcriptional regulation of ompS1 is the global regulatory protein H-NS, a nucleoid protein of 137 amino acids (15 kDa) that negatively regulates its expression (FloresValdez et al., 2003;De la Cruz et al., 2007). In Salmonella, H-NS has been proposed to selectively silence horizontally acquired genes by targeting sequences with a GC content lower than the resident genome, regulating around 12 % of its genes (Lucchini et al., 2006; Navarre et al., 2006). StpA, an H-NS paralogue, was found to repress ompS1 in an hns background; and LeuO, a LysR-type regulator, positively regulates ompS1 expression by antagonizing H-NS and StpA (De la Cruz et al., 2007). LeuO has been implicated in several functions, such as stress resistance, virulence and biofilm formation (VanBogelen et al., 1996;Fang et al., 2000;Majumder et al., 2001;Tenor et al., 2004; Lawley et al., 2006;Moorthy & Watnick, 2005;Rodríguez-Morales et al., 2006). Recently, our group has described several genes regulated by LeuO in S. Typhi (Hernández-Lucas et al., 2008).In bacterial genomes, the recognition of their binding targets by regulatory proteins is commonly considered to be sequence-dependent, although DNA curvature plays a well-characterized role in many transcriptional regulation mechanisms in pr...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Osmoregulation and Thermoregulation Of Omps1 Is Not Affectedmentioning

confidence: 99%

mentioning

confidence: 99%

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The DNA static curvature has a role in the regulation of the ompS1 porin gene in Salmonella enterica serovar Typhi

et al. 2009

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“…The mechanism by which H-NS influences RNA polymerase activity is not fully understood. Its function as a transcription factor is, however, tightly connected with its ability to oligomerize [Rimsky et al, 2001] and condense DNA into stable nucleoprotein complexes [Schroder and Wagner, 2000;Dole et al, 2004;Prosseda et al, 2004], thereby occluding promoter regions or blocking transcription elongation. Recently, atomic force microscopy was used to visualize the effects of H-NS on DNA topology [Dame et al, 2000]: after initial binding at dispersed sites, H-NS assembles into patches of oligomers that interact with each other, thus bridging different DNA regions.…”

Section: Mechansims Of Nucleoid Organizationmentioning

confidence: 99%

The bacterial nucleoid: A highly organized and dynamic structure

Thanbichler

Wang

Shapiro

2005

J of Cellular Biochemistry

122

101

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Recent advances in bacterial cell biology have revealed unanticipated structural and functional complexity, reminiscent of eukaryotic cells. Particular progress has been made in understanding the structure, replication, and segregation of the bacterial chromosome. It emerged that multiple mechanisms cooperate to establish a dynamic assembly of supercoiled domains, which are stacked in consecutive order to adopt a defined higher-level organization. The position of genetic loci on the chromosome is thereby linearly correlated with their position in the cell. SMC complexes and histone-like proteins continuously remodel the nucleoid to reconcile chromatin compaction with DNA replication and gene regulation. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress.

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DNA structural features of eukaryotic TATA‐containing and TATA‐less promoters

Yella

Bansal

2017

FEBS Open Bio

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Eukaryotic genes can be broadly classified as TATA‐containing and TATA‐less based on the presence of TATA box in their promoters. Experiments on both classes of genes have revealed a disparity in the regulation of gene expression and cellular functions between the two classes. In this study, we report characteristic differences in promoter sequences and associated structural properties of the two categories of genes in six different eukaryotes. We have analyzed three structural features, DNA duplex stability, bendability, and curvature along with the distribution of A‐tracts, G‐quadruplex motifs, and CpG islands. The structural feature analyses reveal that while the two classes of gene promoters are distinctly different from each other, the properties are also distinguishable across the six organisms.

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ThevirFpromoter inShigella: more than just a curved DNA stretch

Cited by 150 publications

References 49 publications

The DNA static curvature has a role in the regulation of the ompS1 porin gene in Salmonella enterica serovar Typhi

The DNA static curvature has a role in the regulation of the ompS1 porin gene in Salmonella enterica serovar Typhi

The bacterial nucleoid: A highly organized and dynamic structure

DNA structural features of eukaryotic TATA‐containing and TATA‐less promoters

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