Growth temperature and chromatinization in archaea

Hocher, Antoine; Borrel, Guillaume; Fadhlaoui, Khaled; Brugère, Jean-François; Gribaldo, Simonetta; Warnecke, Tobias

doi:10.1038/s41564-022-01245-2

Cited by 23 publications

(33 citation statements)

References 53 publications

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“…S5). Note that the nucleoid fraction is also enriched for membrane components that have previously been reported to co-sediment with the nucleoid (Portalier and Worcel 1976; Murphy and Zimmerman 1997; Hocher et al . 2022).…”

Section: Resultsmentioning

confidence: 83%

“…Nucleoid enrichment analysis was carried out as in (Hocher et al 2022), comparing soluble and nucleoid enriched fraction using the R package DEP (v1.8.0). Globally, we observe robust enrichment of proteins with predicted membrane localization, providing validation for the approach (Fig.…”

Section: Nucleoid Enrichment Analysismentioning

confidence: 99%

“…2022). In some archaea, histones rank among the most abundant proteins in the cell (Hocher et al . 2022) and their presence is required for viability in the model archaeon Thermococcus kodakarensis (Čuboňová et al .…”

Section: Introductionmentioning

confidence: 99%

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Histone-organized chromatin in bacteria

Hocher

Laursen

Radford

et al. 2023

Preprint

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Histones are the principal constituents of chromatin in eukaryotes and most archaea, while bacteria generally rely on an orthogonal set of proteins to organize their chromosomes. However, several bacterial genomes encode proteins with putative histone fold domains. Whether these proteins are structurally and functionally equivalent to archaeal and eukaryotic histones is unknown. Here, we demonstrate that histones are essential and are major components of chromatin in the bacteriaBdellovibrio bacteriovorusandLeptospira interrogans. Patterns of sequence evolution suggest important roles in several additional bacterial clades. Structural analysis of theB. bacteriovorushistone (Bd0055) dimer shows that histone fold topology is conserved between bacteria, archaea, and eukaryotes. Yet, unexpectedly, Bd0055 binds DNA end-on and forms a sheath of tightly packed histone dimers to encase straight DNA. This binding mode is in stark contrast to that employed by archaeal, eukaryotic, and viral histones, which invariably bend and wrap DNA around their outer surface. Our results demonstrate that histones are integral chromatin components across the tree of life and highlight organizational innovation in the domain Bacteria.

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Section: Resultsmentioning

confidence: 83%

Section: Nucleoid Enrichment Analysismentioning

confidence: 99%

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Histone-organized chromatin in bacteria

Hocher

Laursen

Radford

et al. 2023

Preprint

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“…Furthermore, the chromosome of S. acidocaldarius and other Crenarchaeota is compacted by a large array of small bacterial-like NAPs (47). NAPs seem to play an important role in preventing DNA denaturation at heat-shock temperatures as observed and proposed for other hyperthermophilic archaea (57), however, they might also play a role in temperature-responsive global gene regulation. Previously, it was shown that cold shock leads to altered short-range and long-range interactions and an associated decreased ClsN occupancy and transcriptional activity in the chromosome of S. islandicus (58).…”

Section: Discussionmentioning

confidence: 88%

“…Previously, it was shown that cold shock leads to altered short-range and long-range interactions and an associated decreased ClsN occupancy and transcriptional activity in the chromosome of S. islandicus (58). Here, it is shown that heat shock induces altered levels of various chromatin proteins, not only ClsN, but also classical NAPs and Lrs14-family proteins, with the latter type also being involved in transcription regulation (41, 42, 46, 57). In conclusion, we hypothesize that in contrast to histone-harboring Euryarchaeota that have heat-shock transcription factors such as Phr, Sulfolobales and other histone-lacking thermophilic archaea employ an evolutionary ancient mechanism relying on temperature-responsive changes in DNA organization and compaction, induced by the action of NAPs and in combination with a considerable portion of post-transcriptional and -translational regulation.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional and translational dynamics underlying heat shock response in the thermophilic CrenarchaeonSulfolobus acidocaldarius

Baes

Grünberger

Ruys

et al. 2022

Preprint

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High-temperature stress is critical for all organisms and induces a profound cellular response. For Crenarchaeota, little information is available on how heat shock affects cellular processes and on how this response is regulated. In this work, we set out to study heat shock response in the thermoacidophilic model crenarchaeonSulfolobus acidocaldarius, which thrives in volcanic hot springs and has an optimal growth temperature of 75°C. Pulse-labeling experiments demonstrated that a temperature shift to 86°C induces a drastic reduction of the transcriptional and translational activity, but that RNA and protein neosynthesis still occurs. By combining RNA sequencing and TMT-labeled mass spectrometry, an integrated mapping of the transcriptome and proteome was performed. This revealed that heat shock causes an immediate change in the gene expression profile, with RNA levels of half of the genes being affected, followed by the more subtle reprogramming of the protein landscape. A limited correlation was observed in differential expression on the RNA and protein level, suggesting that there is a prevalence of post-transcriptional and post-translational regulation upon heat shock. Furthermore, based on the finding that promoter regions of heat shock regulon genes lack a conserved DNA-binding motif, we propose that heat-shock responsive transcription regulation is likely not to be accomplished by a classical transcription factor. Instead, in contrast to histone-harboring Euryarchaeota that have heat-shock transcription factors, it is hypothesized that Sulfolobales and other histone-lacking thermophilic archaea employ an evolutionary ancient mechanism relying on temperature-responsive changes in DNA organization and compaction, induced by the action of nucleoid-associated proteins.

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