Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis

Cunha

et al. 2021

Nucleic Acids Research

In all cells, DNA topoisomerases dynamically regulate DNA supercoiling allowing essential DNA processes such as transcription and replication to occur. How this complex system emerged in the course of evolution is poorly understood. Intriguingly, a single horizontal gene transfer event led to the successful establishment of bacterial gyrase in Archaea, but its emergent function remains a mystery. To better understand the challenges associated with the establishment of pervasive negative supercoiling activity, we expressed the gyrase of the bacterium Thermotoga maritima in a naïve archaeon Thermococcus kodakarensis which naturally has positively supercoiled DNA. We found that the gyrase was catalytically active in T. kodakarensis leading to strong negative supercoiling of plasmid DNA which was stably maintained over at least eighty generations. An increased sensitivity of gyrase-expressing T. kodakarensis to ciprofloxacin suggested that gyrase also modulated chromosomal topology. Accordingly, global transcriptome analyses revealed large scale gene expression deregulation and identified a subset of genes responding to the negative supercoiling activity of gyrase. Surprisingly, the artificially introduced dominant negative supercoiling activity did not have a measurable effect on T. kodakarensis growth rate. Our data suggest that gyrase can become established in Thermococcales archaea without critically interfering with DNA transaction processes.

Section: Resultssupporting

confidence: 54%

The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to pervasive negative supercoiling activity of DNA gyrase

Cunha

et al. 2021

Nucleic Acids Research

“…These structural data help explain results from in vivo data. MNase digests yield fragments in multiples of 30–60 bp ( 11 , 15–16 ) and gene expression is significantly altered by histone binding ( 11 , 17 ). Like eukaryotic histones, archaeal histones can also hinder elongation ( 18 ) or inhibit the binding of site-specific transcription factors (TFs) through competition ( 19 ) to influence global transcription levels.…”

Section: Introductionmentioning

confidence: 99%

“…This hypothesis has been substantiated in vitro : plasmid DNA strand dissociation is prevented by histone binding at 90°C ( 25 ). Histone point mutants that cannot compact DNA exhibit differential expression of specific genomic regions ( 11 ). Previous work from our group demonstrated an alternative regulatory function for HpyA, the sole histone of the hypersaline-adapted species Halobacterium salinarum ( 26 ).…”

Section: Introductionmentioning

confidence: 99%

An archaeal histone-like protein regulates gene expression in response to salt stress

Sakrikar

Schmid

2021

Nucleic Acids Research

Histones, ubiquitous in eukaryotes as DNA-packing proteins, find their evolutionary origins in archaea. Unlike the characterized histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression and to maintain wild type cell morphology. However, the precise function of halophilic histone-like proteins remain unclear. Here we use quantitative phenotyping, genetics, and functional genomics to investigate HpyA function. These experiments revealed that HpyA is important for growth and rod-shaped morphology in reduced salinity. HpyA preferentially binds DNA at discrete genomic sites under low salt to regulate expression of ion uptake, particularly iron. HpyA also globally but indirectly activates other ion uptake and nucleotide biosynthesis pathways in a salt-dependent manner. Taken together, these results demonstrate an alternative function for an archaeal histone-like protein as a transcriptional regulator, with its function tuned to the physiological stressors of the hypersaline environment.

“…These mutations have led to changes in the expression of several genes [36], but the biological significance of this structure is not yet fully understood. The flexible multimeric structures formed with archaeal histone have been assigned various names including "hypernucleosome" [58], "archaeasome" [61], and "archaeal histone-based chromatin polymers (AHCP)" [62]. In this review, the term "hypernucleosome" was adopted.…”

Section: Histonementioning

confidence: 99%

“…The structure of the hypernucleosome may dynamically change depending on the state of the cell and the environment, thereby regulating gene expression in response to changes in the environment [36,62]. Another important question is the extent to which hypernucleosomes are present on chromosomes in living cells.…”

Section: Histonementioning

confidence: 99%

Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life

Maruyama

Nambu

Mashimo

et al. 2021

IJMS

Comparative structural/molecular biology by single-molecule analyses combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution have been powerful tools for elucidating the mechanisms underlying genome DNA folding. All genomes in the three domains of life undergo stepwise folding from DNA to 30–40 nm fibers. Major protein players are histone (Eukarya and Archaea), Alba (Archaea), and HU (Bacteria) for fundamental structural units of the genome. In Euryarchaeota, a major archaeal phylum, either histone or HTa (the bacterial HU homolog) were found to wrap DNA. This finding divides archaea into two groups: those that use DNA-wrapping as the fundamental step in genome folding and those that do not. Archaeal transcription factor-like protein TrmBL2 has been suggested to be involved in genome folding and repression of horizontally acquired genes, similar to bacterial H-NS protein. Evolutionarily divergent SMC proteins contribute to the establishment of higher-order structures. Recent results are presented, including the use of Hi-C technology to reveal that archaeal SMC proteins are involved in higher-order genome folding, and the use of single-molecule tracking to reveal the detailed functions of bacterial and eukaryotic SMC proteins. Here, we highlight the similarities and differences in the DNA-folding mechanisms in the three domains of life.