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The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Escherichia coli synthetic construct Thermoplasma acidophilum

PROVIDER: GSE127728 | GEO | 2019/03/11

REPOSITORIES: GEO

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The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog.

Project description:Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are widespread but not universal: several lineages have lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we elucidate primary chromatin architecture in an archaeon without histones, Thermoplasma acidophilum, which harbors a HU family protein (HTa) that protects part of the genome from micrococcal nuclease digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa preferentially binds to GC-rich sequences, exhibits invariant positioning throughout the growth cycle, and shows archaeal histone-like oligomerization behavior. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

| S-EPMC6877293 | biostudies-literature

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (RNA-Seq)

Project description:We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. Comparing HTa-based chromatin architecture to that of three histone-encoding archaea, Methanothermus fervidus, Haloferax volcanii, and Thermococcus kodakkarensis, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around the dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization dynamics. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

2019-03-11 | GSE127726 | GEO

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-Seq)

2019-03-11 | GSE127727 | GEO

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-seq and EMSA-seq)

Project description:Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are phylogenetically widespread but not universal: several archaeal lineages have independently lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we use micrococcal nuclease digestion of native and reconstituted chromatin to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. We confirm and extend prior results showing that T. acidophilum harbours a HU family protein, HTa, that protects part of the genome from MNase digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around a conspicuous dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization behaviour. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

2019-10-08 | GSE138576 | GEO

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog

Project description:The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog

| PRJNA525121 | ENA

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (RNA-Seq)

Project description:The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (RNA-Seq)

| PRJNA525128 | ENA

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-Seq)

Project description:The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-Seq)

| PRJNA525129 | ENA

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-seq and EMSA-seq)

Project description:The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-seq and EMSA-seq)

| PRJNA576437 | ENA

Crystal structure of the Thermoplasma acidophilum protein Ta1207.

Project description:The crystal structure of the Ta1207 protein from Thermoplasma acidophilum is reported. Ta1207 was identified in a screen for high-molecular-weight protein complexes in T. acidophilum. In solution, Ta1207 forms homopentamers of 188?kDa. The crystal structure of recombinant Ta1207 solved by Se-MAD at 2.4?Å resolution revealed a complex with fivefold symmetry. In the crystal lattice, calcium ions induce the formation of a nanocage from two pentamers. The Ta1207 protomers comprise two domains with the same novel ?/? topology. A deep pocket with a binding site for a negatively charged group suggests that Ta1207 functions as an intracellular receptor for an unknown ligand. Homologues of Ta1207 occur only in Thermoplasmatales and its function might be related to the extreme lifestyle of these archaea. The thermostable Ta1207 complex might provide a useful fivefold-symmetric scaffold for future nanotechnological applications.

| S-EPMC5458389 | biostudies-literature

Thermoplasma acidophilum 20S

Project description: Not available

| EMPIAR-10218 | biostudies-other