A Shared, Non-canonical DNA Conformation Detected at DNA/Protein Contact Sites and Bent DNA in the Absence of Supercoiling or Cognate Protein Binding

Economides, Aris N.; Everdeen, Dan; Panayotatos, Nikos

doi:10.1074/jbc.271.40.24836

Cited by 3 publications

(3 citation statements)

References 43 publications

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“…This resembles the organization of the DeoR-regulated dra-nupC-pdp operon in Bacillus subtilis, operators of which consist of one perfect IR and a sequence matching only to one arm of this IR (77). Third, many repressors bend DNA at the center of their operators (17,37,52,53,62,78), and DNA molecules containing a bend at the end migrate faster in the gels than those with the same bend in the middle (74). Consistent with this, AccR-O2 complexes, with accO2 at the end of the fragment, migrated faster than the complexes formed with fragment O1, which contains accO1 in the middle (Fig.…”

Section: Discussionsupporting

confidence: 73%

Opine-BasedAgrobacteriumCompetitiveness: Dual Expression Control of the Agrocinopine Catabolism (acc) Operon by Agrocinopines and Phosphate Levels

Kim

Myung

et al. 2008

J Bacteriol

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Agrobacterium tumefaciens strain C58 can transform plant cells to produce and secrete the sugar-phosphate conjugate opines agrocinopines A and B. The bacterium then moves in response to the opines and utilizes them as exclusive sources of carbon, energy, and phosphate via the functions encoded by the acc operon. These privileged opine-involved activities contribute to the formation of agrobacterial niches in the environment. We found that the expression of the acc operon is induced by agrocinopines and also by limitation of phosphate. The main promoter is present in front of the first gene, accR, which codes for a repressor. This operon structure enables efficient repression when opine levels are low. The promoter contains two putative operators, one overlapping the ؊10 sequence and the other in the further upstream from it; two partly overlapped putative pho boxes between the two operators; and two consecutive transcription start sites. DNA fragments containing either of the operators bound purified repressor AccR in the absence of agrocinopines but not in the presence of the opines, demonstrating the on-off switch of the promoter. Induction of the acc operon can occur under low-phosphate conditions in the absence of agrocinopines and further increases when the opines also are present. Such opine-phosphate dual regulatory system of the operon may ensure maximum utilization of agrocinopines when available and thereby increase the chances of agrobacterial survival in the highly competitive environment with limited general food sources.During agrobacterial infection of susceptible plants, a copy of the T region in a tumor-inducing plasmid (Ti plasmid), called the T-DNA, is transferred from the bacterium to the plant where it becomes integrated into the chromosome (10)(11)(12)25). Expression of the genes on the integrated T-DNA results in the tumorous phenotype and also the production of unusual low-molecular-weight carbon compounds that belong to a large group of plant tumor-specific metabolites collectively called opines (15,20,58,66).Crown gall tumors induced by the classic nopaline-type Agrobacterium tumefaciens strain C58 synthesize and secrete two families of tumor metabolites: agrocinopines A and B and nopaline (20,43). The genes responsible for the biosynthesis of agrocinopines and of nopaline are carried on the T region of pTiC58, harbored by the strain C58 (7,14,29). Strain C58 can catabolize nopaline and agrocinopines by using functions encoded by two different sets of genes located on the nontransferred region of the Ti plasmid (6, 27, 34, 76). These loci, called acc (agrocinopine catabolism) and noc (nopaline catabolism), code for the transport and catabolism of, as well as chemotaxis to, their cognate opines (34,35,51,76).The process by which A. tumefaciens transforms plant cells to produce opines has been termed genetic colonization of the plant (60). The genetic colonization theory leads to the opine concept, proposed by Tempé et al. (68), which states that the opines are the chemical mediators of t...

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Section: Discussionsupporting

confidence: 73%

Opine-BasedAgrobacteriumCompetitiveness: Dual Expression Control of the Agrocinopine Catabolism (acc) Operon by Agrocinopines and Phosphate Levels

Kim

Myung

et al. 2008

J Bacteriol

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“…Both AT‐rich sequences and phased A‐tracts show supercoiling‐dependent flexibility so as to be localized preferentially in the terminal loops of superhelical domains (Tsen and Levene, 1997). They exhibit characteristic properties, strand opening or transition to a pre‐melting state, under low ionic conditions or upon binding to proteins (Chan et al ., 1993; Bowater et al ., 1994; Economides et al ., 1996; Miao and Wang, 1996). Such similarities have raised controversy as to whether bent DNA is or is not responsible for the functions suggested so far.…”

Section: Introductionmentioning

confidence: 99%

Promoter upstream bent DNA activates the transcription of the Clostridium perfringens phospholipase C gene in a low temperature-dependent manner

et al. 1999

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The phospholipase C gene (plc) of Clostridium perfringens possesses three phased A-tracts forming bent DNA upstream of the promoter. An in vitro transcription assay involving C.perfringens RNA polymerase (RNAP) showed that the phased A-tracts have a stimulatory effect on the plc promoter, and that the effect is proportional to the number of A-tracts, and more prominent at lower temperature. A gel retardation assay and hydroxyl radical footprinting revealed that the phased A-tracts facilitate the formation of the RNAP-plc promoter complex through extension of the contact region. The upstream (UP) element of the Escherichia coli rrnB P1 promoter stimulated the downstream promoter activity temperature independently, differing from the phased A-tracts. When the UP element was placed upstream of the plc promoter, low temperature-dependent stimulation was observed, although this effect was less prominent than that of the phased A-tracts. These results suggest that both the phased A-tracts and UP element cause low temperature-dependent activation of the plc promoter through a similar mechanism, and that the more efficient low temperature-dependent activation by the phased A-tracts may be due to an increase in the bending angle at a lower temperature.

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“…Investigation of the telomeric binding protein(s) could provide insight into the nature of recombination in H. polymorpha. Involvement of intrinsically bent DNA elements in the enhanced recombination has also been reported for other organisms (11,29). Though the exact biological function of the bent structure in the DNA is still unclear, it has been speculated that it modifies the chromatin structure of DNA and thus facilitates the binding of related protein factors for DNA replication, transcription, and recombination (17).…”

Section: Discussionmentioning

confidence: 82%

A Family of Telomere-Associated Autonomously Replicating Sequences and Their Functions in Targeted Recombination in Hansenula polymorpha DL-1

et al. 1999

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A family of multiple autonomously replicating sequences (ARSs) which are located at several chromosomal ends of Hansenula polymorpha DL-1 has been identified and characterized. Genomic Southern blotting with an ARS, HARS36, originating from the end of a chromosome, as a probe showed several homologues in the genome ofH. polymorpha. Nucleotide sequences of the three fragments obtained by a selective cloning for chromosomal ends were nearly identical to that of HARS36. All three fragments harbored an ARS motif and ended with 18 to 23 identical repetitions of 5′-GGGTGGCG-3′ which resemble the telomeric repeat sequence in other eukaryotes. Transformation of H. polymorpha with nonlinearized plasmids containing the newly obtained telomeric ARSs almost exclusively resulted in the targeted integration of a single copy or multiple tandem copies of the plasmid into the chromosomes. The sensitivity to exonuclease Bal31 digestion of the common DNA fragment in all integrants confirmed the telomeric origin of HARS36 homologues, suggesting that several chromosomal ends, if not all of them, consisted of the same ARS motif and highly conserved sequences observed in HARS36. Even though the frequencies of targeted recombination were varied among the ends of the chromosomes, the overall frequency was over 96%. The results suggested that the integration of the plasmids containing telemeric ARSs occurred largely through homologous recombination at the telomeric repeats, which serve as high-frequency recombination targets.

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A Shared, Non-canonical DNA Conformation Detected at DNA/Protein Contact Sites and Bent DNA in the Absence of Supercoiling or Cognate Protein Binding

Cited by 3 publications

References 43 publications

Opine-BasedAgrobacteriumCompetitiveness: Dual Expression Control of the Agrocinopine Catabolism (acc) Operon by Agrocinopines and Phosphate Levels

Opine-BasedAgrobacteriumCompetitiveness: Dual Expression Control of the Agrocinopine Catabolism (acc) Operon by Agrocinopines and Phosphate Levels

Promoter upstream bent DNA activates the transcription of the Clostridium perfringens phospholipase C gene in a low temperature-dependent manner

A Family of Telomere-Associated Autonomously Replicating Sequences and Their Functions in Targeted Recombination in Hansenula polymorpha DL-1

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