Biochemical and Structural Insights into RNA Binding by Ssh10b, a Member of the Highly Conserved Sac10b Protein Family in Archaea

Abstract

Background: Proteins of the Sac10b family are widespread in Archaea. Results: Ssh10b, a member of the Sac10b family from Sulfolobus shibatae, disrupts base pairing in structured RNA through interactions between adjacently bound protein dimers. Conclusion: Binding by Ssh10b destabilizes RNA secondary structure. Significance: Proteins of the Sac10b family may play a role in RNA transactions requiring destabilization of RNA secondary structure.

Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation

“…3D structure of Ssh10b-RNA complex has been determined by X-ray crystallography (PDB code: 3WBM, illustrated in Figure 1), and structural study results demonstrated that Ssh10b banded the double strands of RNA nonspecifically and several residues played an essential role in stabilizing Shs10b-RNA complex by hydrogen bonds. [14] These results can provide some basic structural information for understanding Shs10b-RNA interaction. However, the molecular details of the dynamic structural and energetic information at the atomic level are still unclear.…”

“…[14] The rational atomic coordinates of the missing loop was modeled and refined by means of Discovery Studio 2.5. [32] The crystal structure of Ssh10b protein consists of 4 identical monomers, each monomer is a mixed a/b structure comprised of 2 a-helices and 4 b-sheets ( Figure 1): b1 from Ser9 to Leu13, a1 from Val19 to Gln32, b2 from Glu36 to Arg42, a2 from Gly43 to Phe60, b3 from Ile65 to Thr78, b4 from Gln84 to Lys96.…”

“…[18,21,24] Except for the research about for DNA, Shs10b could bind exclusively to RNA in S. shibatae cells as physiological binding targets and has higher thermal stability. [12,14] Huang et al [14] proposed that Ssh10b could protect and stabilize RNA through the interaction between protein and RNA. At the same time, the structure of RNA may be transitioned for RNA transactions such as translation and exosome-mediated RNA degradation.…”

“…[14] It can bind DNA with no sequence specific recognition and constrain negative DNA supercoils at elevated temperatures, which are thought to be involved in chromosomal organization or DNA repair/recombination. [18,21,24] Except for the research about for DNA, Shs10b could bind exclusively to RNA in S. shibatae cells as physiological binding targets and has higher thermal stability.…”

“…[9][10][11][12][13] Based on the previous works, some crystal diffractions and mutation experiments have shown that hyperthermophilic proteins were significant for maintaining the structural and functional stability of DNA at high temperature due to their biochemical properties and cellular abundance. [14][15][16][17] However, the structural basis for RNA binding by hyperthermophilic proteins remains to be understood. [12] The hyperthermophilic Ssh10b was generally regarded as a model to explain the folding and the extreme stability of hyperthermophilic proteins, it was also found to bind to nucleic acid including dsDNA, ssDNA, and RNA in a sequence-independent manner.…”