Structural origins of adenine-tract bending

Barbič, Andrej; Zimmer, Daniel P.; Crothers, Donald M.

doi:10.1073/pnas.0437877100

Cited by 112 publications

(113 citation statements)

References 39 publications

(34 reference statements)

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“…These observations are in accord with the high conformational variability of alternating ATAT sequences observed in crystal structures (29,30) on one hand, and the structural features of GTAC tetranucleotides (e.g., local major-groove bending) on the other (3). AAAA is relatively rigid and exhibits the maximum bend angle of 10°, which is consistent with previous results (31). Its lowest affinity among the high-affinity class of binding sites may be related to the nonsymmetrical conformation of this target, where the bending direction is one step away from the center, unlike all of the other binding sites.…”

supporting

confidence: 79%

Predicting indirect readout effects in protein–DNA interactions

Zhang

Hegde

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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100

113

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Recognition of DNA by proteins relies on direct interactions with specific DNA-functional groups, along with indirect effects that reflect variable energetics in the response of DNA sequences to twisting and bending distortions induced by proteins. Predicting indirect readout requires knowledge of the variations in DNA curvature and flexibility in the affected region, which we have determined for a series of DNA-binding sites for the E2 regulatory protein by using the cyclization kinetics method. We examined 16 sites containing different noncontacted spacer sequences, which vary by more than three orders of magnitude in binding affinity. For 15 of these sites, the variation in affinity was predicted within a factor of 3, by using experimental curvature and flexibility values and a statistical mechanical theory. The sole exception was traced to differential magnesium ion binding. Because many proteins deform DNA upon binding (1, 2), it is reasonable to expect that protein-DNA association might be facilitated by enhanced ease of DNA deformation and a match between intrinsic DNA shape in solution and the strained DNA conformation in the complex. The lack of a simple correspondence code between amino acids and DNA bases in hydrogen bonding, or direct readout, makes a general prediction of protein-DNA affinity impossible at this time. However, variations in contributions from indirect readout due to sequencedependent shape and mechanical properties may be predictable, yielding a partial structural code for protein-DNA interaction (3). Many attempts to test this idea have been performed during the last two decades with different proteins, such as nucleosome (4-6), cAMP-binding protein (7), 434 repressor (8, 9), TATA box-binding protein (10), and E2 protein (11).Among the impediments to realization of this objective is the difficulty of accurately determining the multiple DNA parameters involved, including magnitude and direction of curvature, helical twist, and bending and torsional flexibilities, for a variety of sequences corresponding to the region of indirect readout. The DNA cyclization method (1, 12, 13), in the high-throughput format we recently described (14), coupled with a statistical mechanical theory (15) for extracting the curvature and flexibility parameters from the data, provides a solution to this problem. Although the extent of variation of DNA flexibility with sequence remains controversial, recent results from the cyclization kinetics method show that a DNA sequence with high histone affinity (TATAAACGCC) has a nearly 2-fold smaller bending force constant and 35% less torsional rigidity than generic DNA (6). Also, an AT repeating sequence has 28% lower bending rigidity (14).Experimental testing of the accuracy of prediction of indirect readout requires that the nucleotides involved not be also engaged in direct interactions. A system that meets this requirement is the noncontacted spacer region in the DNA-binding site for the E2 protein encoded by the human papillomavirus (HPV) type 16 genome (11)....

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supporting

confidence: 79%

Predicting indirect readout effects in protein–DNA interactions

Zhang

Hegde

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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100

113

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“…Interestingly, SarT binds to two regions on the sarS promoter, separated by an extremely AT-rich 23-bp region (20 of 23 bp or 87% AT). Within the AT-rich region is a short stretch of five adenines on the top strand and four adenines on the bottom strand which potentially may play a role in DNA bending (2,44), a process that has been recognized to play a role in growth phase-mediated transcriptional regulation (51). Additionally, the binding sites covered in both the plus and minus strands divulged a 12-bp sequence in region I that was repeated in region II (Fig.…”

Section: Discussionmentioning

confidence: 99%

SarT Influences sarS Expression in Staphylococcus aureus

2003

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Staphylococcus aureus is a gram-positive pathogen that is capable of expressing a variety of virulence proteins in response to environmental signals. Virulence protein expression in S. aureus is controlled by a network of regulatory loci including sarA and agr. The sarA/agr network is associated with the expression of cell wallassociated adhesins during exponential growth and the expression of secreted enzymes and toxins in the transition to post-exponential growth. A number of sarA homologs, including sarT and sarS, have been identified in the S. aureus genome. Previous studies have shown that sarA influences expression of both sarT and sarS in the global regulatory network. SarS has been shown to bind to the spa promoter to induce expression of protein A. SarT, one of the SarA homologs that represses hla expression and is repressible by SarA and agr, was found to induce sarS expression in this report. Northern blot analysis of sarS and spa expression in S. aureus RN6390, and the isogenic sarT, sarT sarA, and sarT agr mutants showed that while sarA regulated spa expression directly, the agr locus used sarT as an intermediary to regulate sarS, thus leading to spa repression in agr-activated cells. Gel shift and footprinting analysis showed that SarT binds to the sarS promoter, indicating that the interaction of the sarT gene product with the upstream region of sarS is likely direct. Induction of sarS and spa by SarT in agr ؉ strains was confirmed by a tetracycline-inducible system to titrate sarT expression.

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“…2) found at the distal and proximal LexA binding sites (Table 3). DNA molecules containing four to six consecutive A or T base pairs are predicted to have an intrinsic structural curvature that can impact their role in transcriptional activation by affecting promoter geometry (Barbic et al, 2003;Perez-Martin & de Lorenzo, 1997). Although increases in promoter strength due to DNA bending are usually associated with sequences upstream of the promoter region (Perez-Martin & de Lorenzo, 1997), it has been shown that bent DNA at or near the transcriptional start site is an important component of T7 RNA polymerase promoter enhancement, suggesting that in order to affect promoter activation, bent DNA should be situated in close proximity to the transcription initiation site (Ujvari & Martin, 2000).…”

Section: Discussionmentioning

confidence: 99%

The role of SOS boxes in enteric bacteriocin regulation

2008

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Bacteriocins are a large and functionally diverse family of toxins found in all major lineages of Bacteria. Colicins, those bacteriocins produced by Escherichia coli, serve as a model system for investigations of bacteriocin structure-function relationships, genetic organization, and their ecological role and evolutionary history. Colicin expression is often dependent on host regulatory pathways (such as the SOS system), is usually confined to times of stress, and results in death of the producing cells. This study investigates the role of the SOS system in mediating this unique form of toxin expression. A comparison of all the sequenced enteric bacteriocin promoters reveals that over 75 % are regulated by dual, overlapping SOS boxes, which serve to bind two LexA repressor proteins. Furthermore, a highly conserved poly-A motif is present in both of the binding sites examined, indicating enhanced affinity of the LexA protein for the binding site. The use of gene expression analysis and deletion mutations further demonstrates that these unique LexA cooperative binding regions result in a fine tuning of bacteriocin production, limiting it to times of stress. These results suggest that the evolution of dual SOS boxes elegantly accomplishes the task of increasing the amount of toxin produced by a cell while decreasing the rate of uninduced production, effectively reducing the cost of colicin production. This hypothesis may explain why such a promoter motif is present at such high frequencies in natural populations of bacteriocin-producing enteric bacteria.

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Structural origins of adenine-tract bending

Cited by 112 publications

References 39 publications

Predicting indirect readout effects in protein–DNA interactions

Predicting indirect readout effects in protein–DNA interactions

SarT Influences sarS Expression in Staphylococcus aureus

The role of SOS boxes in enteric bacteriocin regulation

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