DNA bending and looping in the transcriptional control of bacteriophage φ29

Camacho, Ana; Salas, Margarita

doi:10.1111/j.1574-6976.2010.00219.x

Cited by 7 publications

(12 citation statements)

References 138 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The data presented here showed that a short central A tract and Arg54 are additional requirements for stable binding of p4 to DNA and agree with the proposed "zipper model" for p4 DNA recognition and binding (6). The distance from GϪ13 to Gϩ13 is ϳ90 Å, while the 75-Å distance from Arg6 of one of the monomers to the Arg6 of the other monomer is too short to explain simultaneous interaction of both monomers with the inverted repeats of site 3.…”

Section: Discussionsupporting

confidence: 69%

“…Cooperative binding of proteins p4 and p6 to the promoter region synchronizes the transition from early to late gene expression by repressing the early promoters A2c and A2b and simultaneously activating promoter A3 (Fig. 5, lane d) (6). p6 did not affect transcription in the absence of p4 (lane b).…”

Section: Resultsmentioning

confidence: 99%

“…In the Bacillus subtilis phage Ø29, three main promoters, the early promoters A2c and A2b and the late promoter A3, are coordinately regulated by two virus-encoded proteins: the transcriptional regulator protein p4 and the nucleoid-associated protein p6 (6,12). Dimers of p4 bind specifically to four targets with the consensus sequence 5=-CTTTTT-15 bp-AAAATG-3= (40).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Functional Specificity of a Protein-DNA Complex Mediated by Two Arginines Bound to the Minor Groove

Mendieta¹,

Pérez‐Lago²,

Salas³

et al. 2012

Journal of Bacteriology

View full text Add to dashboard Cite

A bacteriophage Ø29 transcriptional regulator, protein p4, interacts with its DNA target by employing two mechanisms: by direct readout of the chemical signatures of only one DNA base and by inducing local modification on the topology of short A tracts (indirect readout). p4 binds as a dimer to targets consisting of imperfect inverted repeats. Here we used molecular dynamic simulation to define interactions of a cluster of 12 positively charged amino acids of p4 with DNA and biochemical assays with modified DNA targets and mutated proteins to quantify the contribution of residues in the nucleoprotein complex. Our results show the implication of Arg54, with non-base-specific interaction in the central A tract, in p4 binding affinity. Despite being chemically equivalent and in identical protein monomers, the two Arg54 residues differed in their interactions with DNA. We discuss an indirect-readout mechanism for p4-DNA recognition mediated by dissimilar interaction of arginines penetrating the minor groove and the inherent properties of the A tract. Our findings extend the current understanding of protein-DNA recognition and contribute to the relevance of the sequence-dependent conformational malleability of the DNA, shedding light on the role of arginines in binding affinity. Characterization of mutant p4R54A shows that the residue is required for the activity of the protein as a transcriptional regulator. Specific interactions between proteins and DNA are fundamental for the regulation of key biological processes, such as transcription, replication, and recombination. Understanding the mechanisms used by regulatory proteins to discern their target sequence within the DNA genome requires the consideration of the properties of all interactions with their cognate binding sites. Structural and biological studies of contacts between proteins and DNA have led to the conclusion that sequence-specific DNA recognition involves both direct and indirect readout of the target sequences (10,20,23). In addition to amino acid-base specific interactions (direct readout), the affinity of a protein for its DNA target involves indirect readout of the target, where sequence-dependent variation leads to recognition of aspects of DNA such as topology of major or minor grooves, local geometry of backbone phosphates, flexibility or malleability, intrinsic curvature, or water-mediated hydrogen bonds (18,42,54,57). Indirect readout explains some aspects leading to stability and the affinity of several prokaryotic transcriptional regulators for their target sequences. Among those, the Escherichia coli catabolite activator protein (CAP) is selective for a pyrimidine-purine step involved in sequence effects on the energy of kink formation required for bending the DNA around the protein (14, 24, 34). The trp repressor recognizes its operator sequence indirectly through its effects on the geometry of the phosphate backbone, which in turn permits the formation of a stable interface by water-mediated contacts (3, 36). Bacteriophage 434 repressor...

show abstract

Section: Discussionsupporting

confidence: 69%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Functional Specificity of a Protein-DNA Complex Mediated by Two Arginines Bound to the Minor Groove

Mendieta¹,

Pérez‐Lago²,

Salas³

et al. 2012

Journal of Bacteriology

View full text Add to dashboard Cite

show abstract

“…The DNA polymerase encoded by bacteriophage 29, for example, effectively mediates processive strand-displacement synthesis on duplex DNA without accessory proteins (7). Similarly, the DNA polymerase of bacteriophage T5 alone polymerizes hundreds of nucleotides per binding event (8).…”

mentioning

confidence: 99%

Thioredoxin, the Processivity Factor, Sequesters an Exposed Cysteine in the Thumb Domain of Bacteriophage T7 DNA Polymerase

Tran¹,

Lee²,

Akabayov³

et al. 2012

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: Formation of disulfide bonds between exposed cysteines decreases activity of T7 DNA polymerase. Results: Only Cys-275 and Cys-313 on the thioredoxin binding domain of T7 DNA polymerase are solvent exposed. Conclusion: Cys-313 is critical for the interaction of T7 DNA polymerase with its processivity factor, thioredoxin. Significance: A single cysteine in the thioredoxin binding domain of T7 DNA polymerase is important for activity.

show abstract

“…Regulation of gene expression during the development of Ø29 has proven to be a very powerful system to analyze different molecular mechanisms of transcription regulation based on formation of DNA-protein complexes and on specific DNA sequence recognition [47]. Ø29 suppressor-sensitive mutants in early genes 4 and 6 have impaired transcription when they infect a non-suppressor host [48,49].…”

Section: Molecular Requirements In the Transcriptional Switch From Eamentioning

confidence: 99%

Molecular Interactions and Protein-Induced DNA Hairpin in the Transcriptional Control of Bacteriophage Ø29 DNA

Camacho

Salas

2010

IJMS

Self Cite

View full text Add to dashboard Cite

Studies on the regulation of phage Ø29 gene expression revealed a new mechanism to accomplish simultaneous activation and repression of transcription leading to orderly gene expression. Two phage-encoded early proteins, p4 and p6, bind synergistically to DNA, modifying the topology of the sequences encompassing early promoters A2c and A2b and late promoter A3 in a hairpin that allows the switch from early to late transcription. Protein p6 is a nucleoid-like protein that binds DNA in a non-sequence specific manner. Protein p4 is a sequence-specific DNA binding protein with multifaceted sequence-readout properties. The protein recognizes the chemical signature of only one DNA base on the inverted repeat of its target sequence through a direct-readout mechanism. In addition, p4 specific binding depends on the recognition of three A-tracts by indirect-readout mechanisms. The biological importance of those three A-tracts resides in their individual properties rather than in the global curvature that they may induce.

show abstract

DNA bending and looping in the transcriptional control of bacteriophage φ29

Cited by 7 publications

References 138 publications

Functional Specificity of a Protein-DNA Complex Mediated by Two Arginines Bound to the Minor Groove

Functional Specificity of a Protein-DNA Complex Mediated by Two Arginines Bound to the Minor Groove

Thioredoxin, the Processivity Factor, Sequesters an Exposed Cysteine in the Thumb Domain of Bacteriophage T7 DNA Polymerase

Molecular Interactions and Protein-Induced DNA Hairpin in the Transcriptional Control of Bacteriophage Ø29 DNA

Contact Info

Product

Resources

About