Histones and nucleoid-associated proteins in Methanosarcina acetivorans mediate recovery from stress and stasis

Abstract

Many archaea encode both histones and Nucleoid-Associated Proteins (NAPs), which we refer to collectively as archaeal DNA Binding Proteins (DBPs). Whether these DBPs jointly work to compact the genome or have distinct functions remains unknown. Here, we have developed the methanogen, Methanosarcina acetivorans, as a platform to study the function of archaeal DBPs in vivo. M. acetivorans encodes one archaeal histone, hmaA, and two copies of the archaea-specific NAP, mc1 (mc1a & mc1b). We found that each DBP is individually dispensable, but at least one copy of mc1 appears to be required for growth. The growth of the single and double DBP deletion mutants was, by and large, like the parent strain under optimal growth conditions. However, after exposure to stresses or extended periods of incubation in stationary phase, the DBP deletion strains often recovered growth much faster than the parent strain. Conversely, over-expression of DBPs led to a delay in growth recovery that could be abrogated by introducing point mutations in DNA-binding residues. Together, our data suggest that histone and archaea-specific NAPs have partially overlapping roles in M. acetivorans and likely protect the genome after exposure to stress or during prolonged periods of growth stasis. Our findings emphasize that there is no unified function for histones across the tree of life and instead imply that archaeal histones join the ranks of other archaeal NAPs in having strain-specific functions. ImportanceThough it is known that many archaea encode histones in tandem with archaea-specific Nucleoid-Associated Proteins (NAPs), the interplay between these two classes of DNA-Binding Proteins (DBPs) in vivo is not known. Most studies on archaeal DBPs have focused either on archaea known to form histone-based chromatin, or on strains which lack histones and compact their genomes exclusively with archaea-specific NAPs. Our study, therefore, fills an important gap in the literature by characterizing DBPs in a model methanogen, Methanosarcina acetivorans, which encodes both histones and archaea-specific NAPs. While no DBP is essential, at least one copy of MC1 appears to be needed, likely for genome compaction. In addition, mutants lacking DBPs had a growth advantage after being subject to stresses or long periods of growth stasis, indicating that DBPs likely function in genome maintenance when growth has stalled or stopped.