Interactions of Archaeal Chromatin Proteins Alba1 and Alba2 with Nucleic Acids

Miha Črnigoj,Gregor Anderluh,Nataša Poklar Ulrih,Mateja Zorko,Roman Jerala,Zdravko Podlesek,Katrin Karbstein

doi:10.1371/journal.pone.0058237

Abstract

BackgroundArchitectural proteins have important roles in compacting and organising chromosomal DNA. There are two potential histone counterpart peptide sequences (Alba1 and Alba2) in the Aeropyrum pernix genome (APE1832.1 and APE1823).Methodology/Principal FindingsThese two peptides were expressed and their interactions with various DNAs were studied using a combination of various experimental techniques: surface plasmon resonance, UV spectrophotometry, circular dichroism–spectropolarimetry, gel-shift assays, and isothermal titration calorimetry.Conclusions/SignificanceOur data indicate that there are significant differences in the properties of the Alba1 and Alba2 proteins. Both of these Alba proteins can thermally stabilise DNA polynucleotides, as seen from UV melting curves. Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT). Surface plasmon resonance sensorgrams for binding of Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 to DNA oligonucleotides show different binding patterns. Circular dichroism indicates that Alba2 has a less-ordered secondary structure than Alba1. The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures. Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.

Highlights

The Alba proteins are part of a protein superfamily that spans all three domains of life
We investigated the conformational changes of the Alba proteins after their binding to the DNA by circular dichroism (CD) spectropolarimetry
Alba1 appeared as a single band in the gel, while Alba2 and the equimolar mixture of both of these Alba proteins showed two bands, where the weaker band is likely to correspond to a monomer, and the stronger band to a dimer (Figure 2, left side)

Summary

Introduction

The Alba (acetylation lowers binding affinity) proteins are part of a protein superfamily that spans all three domains of life. The Alba proteins were first identified as components of chromatin in the thermoacidophilic archaeon Sulfulobus, they were postulated to have additional functions due to their structure and their binding to RNA [1]. The other two branches are eukaryote specific, and these are exemplified by the human and yeast RNase/MRP subunits Rpp20/Pop (Alba and Alba2) and Rpp25/Pop (Alba and Alba4), with the latter including the ciliate protein Mdp2 [2]. Alba domain proteins appear to have had great functional plasticity through the course of evolution. Following their first identification as DNA-binding proteins in Archaea, they were found in association with the nuclear RNase MRP/P in yeast and mammalian cells [2]. There are two potential histone counterpart peptide sequences (Alba and Alba2) in the Aeropyrum pernix genome (APE1832.1 and APE1823)

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