Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double‐stranded DNA complex

Feng, Yingang; Yao, Hongwei; Wang, Jinfeng

doi:10.1002/pro.385

Cited by 23 publications

(21 citation statements)

References 21 publications

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“…49 The Cren7 and Sul7 proteins encoded by these organisms are structural homologues, both inducing rigid bends upon binding to DNA 11 by intercalating into the minor groove. 50−52 Our earlier single-molecule micromanipulation experiments performed at room temperature (∼23 °C) revealed that this bending results in a decrease in the apparent persistence length and thus compaction of DNA molecules. 11 DNA melting experiments revealed that both Cren7 and Sul7 increase the melting temperature, 53,54 which might imply an important role for these proteins in maintaining DNA integrity at high temperatures.…”

Section: Resultsmentioning

confidence: 99%

Effect of Temperature on the Intrinsic Flexibility of DNA and Its Interaction with Architectural Proteins

et al. 2014

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The helical structure of double-stranded DNA is destabilized by increasing temperature. Above a critical temperature (the melting temperature), the two strands in duplex DNA become fully separated. Below this temperature, the structural effects are localized. Using tethered particle motion in a temperature-controlled sample chamber, we systematically investigated the effect of increasing temperature on DNA structure and the interplay between this effect and protein binding. Our measurements revealed that (1) increasing temperature enhances DNA flexibility, effectively leading to more compact folding of the double-stranded DNA chain, and (2) temperature differentially affects different types of DNA-bending chromatin proteins from mesophilic and thermophilic organisms. Thus, our findings aid in understanding genome organization in organisms thriving at moderate as well as extreme temperatures. Moreover, our results underscore the importance of carefully controlling and measuring temperature in single-molecule DNA (micromanipulation) experiments.

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Section: Resultsmentioning

confidence: 99%

Effect of Temperature on the Intrinsic Flexibility of DNA and Its Interaction with Architectural Proteins

et al. 2014

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“…Sac8b itself may be ribosomal protein L14e with an SH3-like structure [14]. The recently discovered protein Cren7 may be a Sac8a family protein because it is an abundant, conserved chromatin protein in Crenarchaea with many properties similar to those of Sac8a, for example unusual CD spectra, a histidine-and tryptophancontaining sequence, and an apparent molecular weight of 8.6 kDa in solution [15][16][17]. The 10 kDa proteins can be divided into Sac10a and Sac10b proteins.…”

Section: Introductionmentioning

confidence: 99%

The Archaeal Sac10b Protein Family: Conserved Proteins with Divergent Functions

Xuan¹,

Feng²

2012

CPPS

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Abstract:Here we review the present state of structural and functional studies of the Sac10b protein family, a class of highly conserved 10 kDa nucleic acid-binding proteins in archaea. Based on biochemical and structural studies, these proteins were originally assigned a role in the structural organization of chromatin; Sac10b proteins of hyperthermophilic archaea, for example, showed tight, unspecific DNA binding. More recently, however, Sac10b proteins of mesophilic archaea were found to interact preferentially with specific DNA sequences thereby affecting the expression of distinct genes. Furthermore, Sac10b proteins of hyperthermophilic, thermophilic and mesophilic archaea were also shown to bind to RNA with distinct affinities and specificities but functional consequences of RNA binding of these proteins, besides perhaps RNA stabilization, have not yet been observed. To better understand the physiological meaning of the various interactions of Sac10b proteins with nucleic acids, future work should concentrate on elucidating the molecular structures of complexes of Sac10b proteins of hyperthermophilic and mesophilic archaea with DNA and RNA. In addition, existing and new X-ray and NMR structures of individual hyperthermophilic Sac10b proteins may represent very good models for introducing thermostability especially in enzymes for industrial use.

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“…In Sulfolobus species, NAPs predominantly organize the genome by bridging or bending DNA. The Sso10b and Sso10a proteins have been shown to bridge or rigidify DNA in EM [52] and AFM studies [26,28], whereas Sac7d/Sso7d [30–32] and Cren7 [33,34] were shown to bend DNA in their complex 3D structures. In our study, Sso7c4 exhibits DNA-binding activity and alters the trajectory of the DNA through bending and bridging.…”

Section: Resultsmentioning

confidence: 99%

“…acidocaldarius ), which are hyperthermophilic crenarchaeal organisms, encode a variety of small, abundant and basic proteins ranging in molecular weight from 7 to 10 kDa that modulate their genome. Five classes of architectural proteins have been characterized and classified as histone-like proteins according to their physical properties: Alba (acetylation lowers binding affinity, also known as the Sso10b [24–26]/Sac10b [27] family), Sso10a [28]/Sac10a [29], Sul7d (Sso7d/Sac7d) [30–32], Cren7 [33,34] and Sso7c4 [35,36]. As observed in atomic force microscopy (AFM) images, Alba proteins form dimers in solution and exhibit two different binding modes by bridging DNA or forming stiff filaments along DNA, depending on the dimer concentration and composition [26].…”

Section: Introductionmentioning

confidence: 99%

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The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA

et al. 2017

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The Sso7c4 from Sulfolobus solfataricus forms a dimer, which is believed to function as a chromosomal protein involved in genomic DNA compaction and gene regulation. Here, we present the crystal structure of wild-type Sso7c4 at a high resolution of 1.63 Å, showing that the two basic C-termini are disordered. Based on the fluorescence polarization (FP) binding assay, two arginine pairs, R11/R22′ and R11′/R22, on the top surface participate in binding DNA. As shown in electron microscopy (EM) images, wild-type Sso7c4 compacts DNA through bridging and bending interactions, whereas the binding of C-terminally truncated proteins rigidifies and opens DNA molecules, and no compaction of the DNA occurs. Moreover, the FP, EM and fluorescence resonance energy transfer (FRET) data indicated that the two basic and flexible C-terminal arms of the Sso7c4 dimer play a crucial role in binding and bending DNA. Sso7c4 has been classified as a repressor-like protein because of its similarity to Escherichia coli Ecrep 6.8 and Ecrep 7.3 as well as Agrobacterium tumefaciens ACCR in amino acid sequence. Based on these data, we proposed a model of the Sso7c4-DNA complex using a curved DNA molecule in the catabolite activator protein-DNA complex. The DNA end-to-end distance measured with FRET upon wild-type Sso7c4 binding is almost equal to the distance measured in the model, which supports the fidelity of the proposed model. The FRET data also confirm the EM observation showing that the binding of wild-type Sso7c4 reduces the DNA length while the C-terminal truncation does not. A functional role for Sso7c4 in the organization of chromosomal DNA and/or the regulation of gene expression through bridging and bending interactions is suggested.

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Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double‐stranded DNA complex

Cited by 23 publications

References 21 publications

Effect of Temperature on the Intrinsic Flexibility of DNA and Its Interaction with Architectural Proteins

Effect of Temperature on the Intrinsic Flexibility of DNA and Its Interaction with Architectural Proteins

The Archaeal Sac10b Protein Family: Conserved Proteins with Divergent Functions

The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA

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