Prokaryotic histones

Abstract

Organisms from all domains of life compact and functionally organize their DNA to accommodate the genome within the confines of the cell.

In eukaryotes, the core histones - H2A, H2B, H3, and H4 - serve as major organizers of the genome by forming DNA-wrapping nucleosome structures, while playing additional roles in replication, repair and gene expression.

In prokaryotes, nucleoid-associated proteins (NAPs), a term for referring to any DNA-binding protein that is associated with the nucleoid, shape and organize the genome, playing similar functional roles to histones. In this thesis, I explore the world of prokaryotic histones by first identifying and categorizing histone proteins computationally with the use of AlphaFold2. I identify 24 groups of histones in prokaryotes that either bend, wrap, or bridge DNA. The histones and their categories can be viewed at www.prohistonedb.org. I focussed on two new histones to characterize experimentally: bacterial histone HBb from Bdellovibrio bacteriovorus and archaeal histone HTkC from Thermococcus kodakarensis. Histone HBb is required for the survival of Bdellovibrio bacteriovorus. Instead of wrapping DNA like canonical histones, HBb bends DNA as a dimer. Histone HTkC is important for the growth of Thermococcus kodakarensis. It forms a unique toroidal tetramer structure, characteristic for the face-to-face category that it belongs to. Around this tetramer it can wrap DNA and form highly compact nucleoprotein complexes. Collectively, this work establishes that histones are very diverse and that several new histones, such as HBb and HTkC, function as important organizers of chromatin.