Biology subjects

Atomi, H.

Publications and source records attributed to Atomi, H..

6 recordsLinked to original sources

bioRxiv2026

Cryo-electron tomography reveals near-native archaeal chromatin architecture

Most archaea package their genomes using histones, the evolutionary ancestors of eukaryotic chromatin proteins. Yet how archaeal chromatin is organized in cells has remained unknown. Here we provide the first high-resolution view of archaeal chromatin in a near-native state. We combine cryo-electron tomography, subtomogram averaging and single-particle cryo-electron microscopy to study chromatin released from gently lysed cells of the model archaeon Thermococcus kodakarensis. We show that archaeal chromatin is built from closed hypernucleosomes of variable length and determine structures of multiple hypernucleosome species, revealing a variable-beads-on-a-string architecture with flexible local contact geometries. We further show that chromatin organization changes with cellular state: logarithmic-phase cells are enriched in short hypernucleosomes, whereas stationary-phase cells form longer assemblies. Histone HTkB deletion shifts chromatin towards shorter hypernucleosomes in both growth phases and reduces local contact order. These results establish archaeal chromatin as a dynamic and complex system, shaped by growth phase and histone composition.

Molecular Biology↗

bioRxiv2025

Reverse gyrase and 3D genome architecture suppress hyperthermophile genome instability arising from horizontal gene transfer

Reverse gyrase (Rgy), a distinctive topoisomerase conserved in all hyperthermophiles, has the unique ability to introduce positive DNA supercoils. It has long been hypothesized that Rgy overwinds genomic DNA to prevent its detrimental denaturation at high temperature. However, its role in vivo has remained unresolved for more than four decades. In the course of investigating how Rgy affects genome organization in the archaeon Thermococcus kodakarensis, we find that Rgy suppresses heat-induced clustering of AT-rich genes, most of which bear signatures of horizontal gene transfer. This function depends on the topoisomerase active site of Rgy, underscoring a critical role of its action on DNA topology. The clustering of AT-rich genes is accompanied by their aberrant recruitment of the single-stranded DNA-binding protein RPA, indicative of extensive DNA melting. Genetic analysis further provides evidence that RPA sequesters denatured loci and mitigates genome instability in the absence of Rgy. We propose that DNA topology and higher-order genome organization constitute a multilayered mechanism that stabilizes horizontally acquired genes at high temperature.

molecular biology↗

bioRxiv2025

Archaeal histone HTkC hypercompacts DNA

Histones are important organizers of chromatin in eukaryotes and archaea. In eukaryotes, the core histones assemble with DNA to form the octameric nucleosome. In archaea, histones form hypernucleosomes that are not restricted to an octameric histone core but can extend to variable lengths. We previously identified face-to-face (FtF) histones as a widely distributed group of archaeal histones that assemble into toroidal tetramer structures, distinct from nucleosomal histones. Here, we characterize the FtF histone HTkC from Thermococcus kodakarensis, which also encodes the canonical histones HTkA and HTkB. We show that HTkC wraps DNA around its toroidal tetramer and forms highly compact nucleoprotein complexes, achieving a level of compaction approximately twice that of hypernucleosomes. Consistent with a major chromatin-organizing role, htkC is among the most highly expressed genes in T. kodakarensis and its deletion leads to impaired growth. Together, these findings establish FtF histones as important organizers of archaeal chromatin alongside classical histones.

biochemistry↗

bioRxiv2024

Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure

Structural maintenance of chromosomes (SMC) complexes fold genomes by extruding DNA loops. In eukaryotes, loop-extruding SMC complexes form topologically associating domains (TADs) by being stalled by roadblock proteins. It remains unclear whether a similar mechanism of domain formation exists in prokaryotes. Using high-resolution chromosome conformation capture sequencing, we show that an archaeal homolog of the bacterial Smc-ScpAB complex organizes the genome of Thermococcus kodakarensis into TAD-like domains. We also find that TrmBL2, a nucleoid- associated protein that forms a stiff nucleoprotein filament, stalls the T. kodakarensis SMC complex and establishes a boundary at the site-specific recombination site dif. TrmBL2 stalls the SMC complex at tens of additional non-boundary loci with lower efficiency. Intriguingly, the stalling efficiency is correlated with structural properties of underlying DNA sequences. Our study illuminates not only a eukaryotic-like mechanism of domain formation in archaea, but also an unforeseen role of intrinsic DNA structure in large-scale genome organization.

molecular biology↗

bioRxiv2023

Development of a rapid and highly accurate method for 13C tracer-based metabolomics and its application on a hydrogenotrophic methanogen

Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for underivatized proteinogenic amino acids. The method consisting of a ZipChip CE system and a high-resolution Orbitrap Fusion Tribrid mass spectrometer allows us to obtain highly accurate data from 1 L of 100 nmol/L mol amino acids comparable to a mere 1 x 104-5 prokaryotic cells. To validate the capability of the CE-MS method, we analyzed 16 protein-derived amino acids from a methanogenic archaeon Methanothermobacter thermautotrophicus as a model organism, and the mass spectra showed sharp peaks with low mass errors and background noise. Tracer-based metabolome analysis was then performed to identify the central carbon metabolism in M. thermautotrophicus using 13C-labeled substrates. The mass isotopomer distributions of serine, aspartate, and glutamate revealed the co-occurrence of the Wood-Ljungdahl pathway and an incomplete reductive TCA cycle for carbon fixation. In addition, biosynthesis pathways of 15 amino acids were constructed based on the mass isotopomer distributions of the detected protein-derived amino acid, genomic information, and public database. Among them, the presence of the alternative enzymes of alanine dehydrogenase, ornithine cyclodeaminase, and homoserine kinase was suggested in the biosynthesis pathways of alanine, proline, and threonine, respectively. To our knowledge, the novel 13C tracer-based metabolomics using CE-MS is the most efficient method to identify central carbon metabolism and amino acid biosynthesis pathways and is applicable to in any kind of isolated microbe.

microbiology↗

bioRxiv2020

Different Proteins Mediate Step-wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis

Archaeal species encode a variety of distinct lineage-specific chromosomal proteins. We have previously shown that in Thermococcus kodakarensis, histone, Alba, and TrmBL2 play distinct roles in chromosome organization. Although our understanding of individual archaeal chromosomal proteins has been advancing, how archaeal chromosomes are folded into higher-order structures and how they are regulated are largely unknown. Here, we investigated the primary and higher-order structures of archaeal chromosomes from different archaeal lineages. Atomic force microscopy of chromosome spreads out of Thermoplasma acidophilum and Pyrobaculum calidifontis cells revealed 10-nm fibers and 30-40-nm globular structures, suggesting the occurrence of higher-order chromosomal folding. Our results also indicated that chromosome compaction occurs toward the stationary phase. Micrococcal nuclease digestion indicated that fundamental structural units of the chromosome exist in T. acidophilum and T. kodakarensis but not in P. calidifontis or Sulfolobus solfataricus. In vitro reconstitution showed that, in T. acidophilum, the bacterial HU protein homolog HTa formed a 6-nm fiber by wrapping DNA, and that Alba was responsible for the formation of the 10-nm fiber by binding along the DNA without wrapping. Remarkably, Alba could form different higher-order complexes with histone or HTa on DNA in vitro. Mass spectrometry detected HTa in the T. acidophilum chromosome but not in other species. A putative transcriptional regulator of the AsnC/Lrp family (Pcal_1183) was detected on the P. calidifontis chromosome, but not on that of other species studied. Putative membrane-associated proteins were detected in the chromosomes of the three archaeal species studied, including T. acidophilum, P. calidifontis, and T. kodakarensis. Collectively, our data show that Archaea use different combinations of proteins to achieve chromosomal architecture and functional regulation.

microbiology↗