Abstract
Throughout the kingdoms of life cells face a similar problem, namely the size of their genome is very large compared to the volume of the cell. Although each organism employs its own set of proteins to compact their genome, up to a factor of 10.000, the method of compaction seems highly conserved. Besides, DNA organization is known to be a key regulatory mechanism involved in many important processes such as gene regulation and DNA replication. The protein Alba, one of the most abundant proteins in Archaea, has been suggested to play an important role in DNA organization. Previous studies have shown that Alba binds as a dimer to non-specific DNA sequences and is able to condense DNA. However, little is known about its mechanism and structural role in DNA-organization. Here we show, using several single-molecule imaging and manipulation techniques such as AFM, double and quadruple optical tweezers, the condensing and possible regulation mechanism of Alba. From the surprising structural changes to the protein-bound DNA the binding constant, footprint and cooperativity factor are obtained by using a McGhee von Hippel analysis. We furthermore prove that the Archaea protein Alba II, which is thought to have a regulatory function, controls the binding efficiency of Alba I by changing the cooperativity of the Alba & Alba II protein mix.
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