Nov 30, 2016

Structural and evolutionary analyses reveal determinants of DNA binding specificities of nucleoid-associated proteins HU and IHF

Molecular Phylogenetics and Evolution
Debayan DeySuryanarayanarao Ramakumar

Abstract

Nucleoid-associated proteins (NAPs) are chromosome-organizing factors, which affect the transcriptional landscape of a bacterial cell. HU is an NAP, which binds to DNA with a broad specificity while homologous IHF (Integration Host Factor), binds DNA with moderately higher specificity. Specificity and differential binding affinity of HU/IHF proteins towards their target binding sites play a crucial role in their regulatory dynamics. Decades of biochemical and genomic studies have been carried out for HU and IHF like proteins. Yet, questions related to their DNA binding specificity, and differential ability to bend DNA thus affecting the binding site length remained unanswered. In addition, the problem has not been investigated from an evolutionary perspective. Our phylogenetic analysis revealed three major clades belonging to HU, IHFα and IHFβ like proteins with reference to E. coli. We carried out a comparative analysis of three-dimensional structures of HU/IHF proteins to gain insight into the structural basis of clade division. The present study revealed three major features which contribute to differential DNA binding specificity of HU/IHF proteins, (I) conformational restriction of DNA binding residues due to salt-bridge f...Continue Reading

Mentioned in this Paper

Study
Conserved Sequence
Bacterial cell
Protein Binding
Bacterial Proteins
Alkalescens-Dispar Group
Genome
Transcription, Genetic
Body Image
N-(4-aminophenethyl)spiroperidol

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