Histones and nucleoid-associated proteins in Methanosarcina acetivorans mediate recovery from stress and stasis
- 1Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- 2Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
Abstract
Many archaea encode histones in tandem with nucleoid-associated proteins (NAPs), but the functional overlap between these two classes of non-specific DNA-binding proteins (DBPs) is not well studied. Most in vivo studies of DBPs have been conducted with archaea that only encode histones or NAPs. Here, we characterize the endogenous function of the two families of DBPs in a methanogen, Methanosarcina acetivorans, that encodes a histone and two copies of an archaea-specific NAP called methanogen chromatin Protein 1 (MC1). In M. acetivorans, we found that each DBP is individually dispensable, but at least one copy of mc1 appears to be essential. By and large, the single- and double-DBP knockouts phenocopy the wild-type strain under optimal laboratory growth conditions. Remarkably, mutants lacking the histone, one copy of MC1, or both recover faster than wild-type after being subjected to UV shock or long periods of growth stasis. Overexpression of the DBPs leads to a delay in growth recovery after extended periods in stationary phase, which is abrogated by introducing point mutations in DNA-binding residues. Together, our data suggest that histones and MC1 proteins have partially overlapping roles in M. acetivorans, one of which might be genome maintenance when growth has stalled or stopped.
IMPORTANCE: Though 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 that 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 subjected to stressors or long periods of growth stasis, indicating that DBPs likely function in genome maintenance when growth has stalled or stopped.
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BibTeX
@article{baskevitch2026histones,
title = {{Histones and nucleoid-associated proteins in Methanosarcina acetivorans mediate recovery from stress and stasis}},
author = {Alienor S. Baskevitch and Dipti D. Nayak},
journal = {Microbiology Spectrum},
year = {2026},
month = oct,
doi = {10.1128/spectrum.02785-26},
url = {https://doi.org/10.1128/spectrum.02785-26},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Histones and nucleoid-associated proteins in Methanosarcina acetivorans mediate recovery from stress and stasis
AU - Alienor S. Baskevitch
AU - Dipti D. Nayak
PY - 2026
DA - 2026/10/14
JO - Microbiology Spectrum
DO - 10.1128/spectrum.02785-26
UR - https://doi.org/10.1128/spectrum.02785-26
AB - Many archaea encode histones in tandem with nucleoid-associated proteins (NAPs), but the functional overlap between these two classes of non-specific DNA-binding proteins (DBPs) is not well studied. Most in vivo studies of DBPs have been conducted with archaea that only encode histones or NAPs. Here, we characterize the endogenous function of the two families of DBPs in a methanogen, Methanosarcina acetivorans, that encodes a histone and two copies of an archaea-specific NAP called methanogen chromatin Protein 1 (MC1). In M. acetivorans, we found that each DBP is individually dispensable, but at least one copy of mc1 appears to be essential. By and large, the single- and double-DBP knockouts phenocopy the wild-type strain under optimal laboratory growth conditions. Remarkably, mutants lacking the histone, one copy of MC1, or both recover faster than wild-type after being subjected to UV shock or long periods of growth stasis. Overexpression of the DBPs leads to a delay in growth recovery after extended periods in stationary phase, which is abrogated by introducing point mutations in DNA-binding residues. Together, our data suggest that histones and MC1 proteins have partially overlapping roles in M. acetivorans, one of which might be genome maintenance when growth has stalled or stopped. IMPORTANCE: Though 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 that 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 subjected to stressors or long periods of growth stasis, indicating that DBPs likely function in genome maintenance when growth has stalled or stopped.
SN - 2165-0497
ER -