Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages

Abstract

Although recent studies have provided a wealth of information about archaeal biology, nothing is known about the molecular basis of DNA segregation in these organisms. Here we unveil the machinery and assembly mechanism of the archaeal Sulfolobus pNOB8 partition system. This system employs three proteins; ParA, an atypical ParB adaptor and a centromere-binding component, AspA. AspA utilizes a spreading mechanism to create a DNA superhelix onto which ParB assembles. This supercomplex links to the ParA motor, which contains a bacteria-like Walker motif. The ParB C-domain harbors structural similarity to CenpA, which dictates eukaryotic segregation. Thus, this archaeal system combines bacteria-like and eukarya-like components, suggesting the possible conservation of DNA segregation principles across the three domains of life.

Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation

“…However, how these proteins interact with nsDNA has been unknown. Notably, all Walker-box ParA proteins, including the recently characterized archaeal pNOB8 ParA, show strong structural homology (Leonard et al 2005;Pratto et al 2008;Dunham et al 2009;Schumacher et al 2012Schumacher et al , 2015. The pNOB8 ParA protein is encoded on the pNOB8 plasmid, which is harbored in Sulfolobus NOB8H2 and is part of a partition cassette that also encodes a CBP and adaptor (Schumacher et al 2015).…”

“…Notably, all Walker-box ParA proteins, including the recently characterized archaeal pNOB8 ParA, show strong structural homology (Leonard et al 2005;Pratto et al 2008;Dunham et al 2009;Schumacher et al 2012Schumacher et al , 2015. The pNOB8 ParA protein is encoded on the pNOB8 plasmid, which is harbored in Sulfolobus NOB8H2 and is part of a partition cassette that also encodes a CBP and adaptor (Schumacher et al 2015). Because obtaining structures of protein-nsDNA complexes is challenging, we carried out crystallization trials of multiple ParA proteins, including pNOB8 ParA, with DNA in the presence of ATP or the ATP analog AMPPNP to maximize chances of obtaining a ParA-DNA crystal structure (Materials and Methods).…”

“…The actinlike polymers bind and push apart replicated DNA plasmid cargo in a process termed insertional polymerization, while tubulin-like NTPase filaments undergo treadmilling and pull CBP-bound cargo DNA to cell poles (Egelman 2003;Møller-Jensen et al 2003;Pogliano 2004;Garner et al 2007;Schumacher et al 2007;Gerdes et al 2010;Ni et al 2010;Gayathri et al 2012;Schumacher 2012;Bharat et al 2015;Fink and Löwe 2015). The less well-understood type I Walker-box systems are used by bacterial and archaeal chromosomes and plasmids and hence are arguably the most ubiquitous type of partition system in nature (Gerdes et al 2000;Schumacher et al 2015;Barillà 2016).…”

“…Multiple ParB proteins bind cooperatively to centromere sites on the cargo DNA to form large partition complexes (Rodionov et al 1999;Schumacher and Funnell 2005;Schumacher 2012;Graham et al 2014;Chen et al 2015;Funnell 2016). Data indicate that disordered typically N-terminal regions of ParB proteins displayed on the partition complexes bind their partner ParA proteins to mediate partition dynamics by stimulating ParA-ATP hydrolysis (Barillà et al 2007;Vecchiarelli et al 2013a;Schumacher et al 2015;Volante and Alonso 2015). ParA must be complexed with ATP to bind DNA.…”

Identification, Characterization, and Application of the Replicon Region of the Halophilic Temperate Sphaerolipovirus SNJ1

“…The most widespread and well-understood bacterial DNA segregation system is composed of three components: a DNA centromere, a ParA ATPase, and a centromere-binding protein, ParB (61,62). Similar segregation systems have been reported in Sulfolobus species, which also contain ParAlike ATPase and site-specific DNA-binding proteins that attach to centromere-like sequences (63)(64)(65). Inspection of the ORFs within the stable replicated fragment of SNJ1 (pYC-SHS) did not reveal any ParA-or ParB-like ORFs, nor did we find candidates similar to the identified archaeal centromere-binding proteins.…”