Mechanism of binding of serum response factor to serum response element

Huet, Alexis; Parlakian, Ara; Arnaud, Marie-Claire; Glandières, Jean-Marie; Valat, P.; Fermandjian, Serge; Paulin, Denise; Alpert, Bernard; Zentz, Christian

doi:10.1111/j.1742-4658.2005.04724.x

Cited by 9 publications

(21 citation statements)

References 49 publications

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“…This correlation time is linked to the time of fluorescein rotation around its link with the oligonucleotide. The correlation time for rotation of the SRE molecule as a whole, estimated to be 10 ns from hydrodynamic measurements [7,52], was hard to detect in our experiments. In any case, the fast depolarization process due to fluorescein motions prevents monitoring of the entire oligonucleotide rotation.…”

Section: Resultsmentioning

confidence: 68%

“…The emission spectrum shifts to 520 nm when fluorescein is conjugated to SRE fos (Fig. 1), the electrostatic potential of DNA generating a new equilibrium between the mono‐ and dianionic populations of the fluorescein [7]. By contrast, the mutations performed in the native SRE fos sequence do not affect the fluorescein emission profile indicating that the fluorescent reporter experiences almost the same environment in SRE fos , SRE Gfos and SRE GGfos .…”

Section: Resultsmentioning

confidence: 99%

“…If the frequency of helix twisting is too high many core‐SRF gather without specific association to DNA (i.e. SRE GGfos ) [7]. We should note that SRE GGfos possesses a hydration state different from the other two oligonucleotides.…”

Section: Discussionmentioning

confidence: 99%

“…The SRE fos sequence, 5′‐d(GGATGTC −5 C −4 A −3 T −2 A −1 T +1 T +2 A +3 G +4 G +5 ACAT)‐3′, embodies the native CArG box of the c‐ fos enhancer (CArG box numbered) [2,27], whereas SRE Gfos carries the single C −5 →G mutation and SRE GGfos the double C −5 C −4 →GG mutation within their CArG box. A previous report has shown that the parent SRE fos bound a core‐SRF homodimer, whereas the single mutant SRE Gfos and the double mutant SRE GGfos bound one and four monomers (on average), respectively [7]. This highlights the role of the base sequence at the border of the A/T track in the specific complex assembly and functional organization.…”

mentioning

confidence: 89%

“…To date, little is known about the relationships between the ability of DNA to bend and its effects on protein binding. Previous studies have shown that association of core-SRF with SRE fos reduces the flexibility of each partner, suggesting a strong role for dynamics in the adjustment of protein-DNA contacts and thereby the specificity of the complex formation [7]. Time-resolved fluorescence anisotropy decays of the modified and native fluoresceinated SREs allow us to assess differences in dynamics among the three oligonucleotides.…”

mentioning

confidence: 99%

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C→G base mutations in the CArG box of c‐fosserum response element alter its bending flexibility

Štěpánek¹,

Vincent²,

Turpin³

et al. 2007

The FEBS Journal

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By binding to the CArG box sequence, the serum response factor (SRF) activates several muscle‐specific genes, as well as genes that respond to mitogens. The core domain of the SRF (core‐SRF) binds as a dimer to the CArG box C−5C−4A−3T−2A−1T+1T+2A+3G+4G+5 of the c‐fos serum response element (SREfos). However, previous studies using 20‐mer DNAs have shown that the binding stoichiometry of core‐SRF is significantly altered by mutations C−5→G (SREGfos) and C−5C−4→GG (SREGGfos) of the CArG box [A Huet, A Parlakian, M‐C Arnaud, J‐M Glandières, P Valat, S Fermandjian, D Paulin, B Alpert & C Zentz (2005) FEBS J272, 3105–3119]. To understand these effects, we carried out a comparative analysis of the three 20‐mer DNAs SREfos, SREGfos and SREGGfos in aqueous solution. Their CD spectra were of the B‐DNA type with small differences generated by variations in the mutual arrangement of the base pairs. Analysis by singular value decomposition of a set of Raman spectra recorded as a function of temperature, revealed a premelting transition associated with a conformational shift in the DNA double helices from a bent to a linear form. Time‐resolved fluorescence anisotropy shows that the fluorescein reporter linked to the oligonucleotide 5′‐ends experiences twisting motions of the double helices related to the interconversion between bent and linear conformers. The three SREs present various bent populations submitted, however, to particular internal dynamics, decisive for the mutual adjustment of binding partners and therefore specific complex formation.

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Section: Resultsmentioning

confidence: 68%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 89%

mentioning

confidence: 99%

See 3 more Smart Citations

C→G base mutations in the CArG box of c‐fosserum response element alter its bending flexibility

Štěpánek¹,

Vincent²,

Turpin³

et al. 2007

The FEBS Journal

Self Cite

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Raman Spectroscopy of Proteins and Nucleoproteins

2013

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A protein Raman spectrum comprises discrete bands representing vibrational modes of the peptide backbone and its side chains. The spectral positions, intensities, and polarizations of the Raman bands are sensitive to protein secondary, tertiary, and quaternary structures and to side-chain orientations and local environments. In favorable cases, the Raman spectrum serves as an empirical signature of protein three-dimensional structure, intramolecular dynamics, and intermolecular interactions. Quantitative analysis of Raman spectral series can be further boosted by advanced statistical approaches of factor analysis that allow fitting of specific theoretical models while reducing the amount of analyzed data. Here, the strengths of Raman spectroscopy are illustrated by considering recent applications from the authors' work that address (1) subunit folding and recognition in assembly of the icosahedral bacteriophages, (2) orientations of subunit main chains and side chains in native filamentous viruses, (3) roles of cysteine hydrogen bonding in the folding, assembly, and function of virus structural proteins, and (4) structural determinants of protein/DNA recognition in gene regulatory complexes. Conventional Raman and polarized Raman techniques are surveyed.

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Characteristics of the CArG-SRF binding context in mammalian genomes

Shen

Tao

2009

Mamm Genome

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Serum response factor (SRF), a member of the MADS family, binds a 10-bp cis element known as the CArG box. However, despite our extensive knowledge of SRF and the CArG box, limited information is available on the CArG-SRF binding context or how CArG flanking sequences are defined. We used statistical tests and computer simulation to find characteristics of the CArG-SRF binding context. Based on the combination of published literature and a search of DBTSS, 150 and 136 functional CArG boxes together with 10 bp flanking on each side were found in mouse and human genomes, respectively. By statistical analysis of the 30 positions we found some new conserved positions of interest (P < 0.005) such as -15, -8, and +8, in addition to the ten highly conserved positions of the CArG box. Intriguingly, studies comparing the flanking positions between consensus CArG boxes and CArG-like boxes showed that there are more conserved positions in the latter. Moreover, CpG content within the CArG-SRF binding context is much higher than that within introns. Collectively, these results suggest that there are some special pre-existing features in the flanking sequences of functional CArG boxes probably contributing to SRF selectively recognizing and binding to the functional CArG from millions of functionless CArG boxes in mammalian genomes. This is a significant step toward understanding the mechanism of transcriptional regulation of SRF-dependent genes.

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Mechanism of binding of serum response factor to serum response element

Cited by 9 publications

References 49 publications

C→G base mutations in the CArG box of c‐fosserum response element alter its bending flexibility

C→G base mutations in the CArG box of c‐fosserum response element alter its bending flexibility

Raman Spectroscopy of Proteins and Nucleoproteins

Characteristics of the CArG-SRF binding context in mammalian genomes

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