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A new family of ribosome hibernation factors in ArchaeaA new family of ribosome hibernation factors in Archaea

ABSTRACT: Ribosome hibernation preserves translation machinery during stress, yet its mechanisms in Archaea remain poorly defined. Here, we identify HibA, a previously unrecognized family of hibernation factors widespread in Archaea. HibA consists of a bacterial-like HPF/RaiA domain fused to a Cystathionine Beta Synthase module. High-resolution cryo-EM structures of HibA:ribosome complexes from Pyrococcus abyssi identify three distinct conformations overlapping A, P and E site tRNA positions. Thus, HibA can inactivate ribosomes in multiple conformational states, providing a structurally robust mechanism for ribosome preservation. Idle ribosomes also frequently accumulate SBDS, suggesting that stressed archaeal cells may engage parallel hibernation routes in which SBDS can complement HibA. Deletion of hibA in Thermococcus barophilus delays recovery from stationary phase and reduces 70S ribosome pools, establishing its role in ribosome preservation. Taxonomic profiling shows that many archaeal lineages encode multiple ribosome-associated protection factors, underscoring the multi-layered nature of archaeal hibernation systems. In addition, a comprehensive phylogenetic analysis highlights the evolutionary relationships between prevalent ribosome hibernation factors across Bacteria and Archaea.

INSTRUMENT(S):

ORGANISM(S): Pyrococcus Abyssi Ge5

SUBMITTER: Magalie Duchateau

LAB HEAD: Emmanuelle Schmitt

PROVIDER: PXD073243 | Pride | 2026-03-24

REPOSITORIES: Pride

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			Action	DRS
	20250317_Q1_MD_ColQ1-146_Emma_70S.raw	Raw
	MQ.zip	Other
	checksum.txt	Txt
	uniprotkb_proteome_UP000009139_2025_03_18_Pyrococcus-abyssi.fasta	Fasta

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Project description:Disruptions of protein homeostasis in the endoplasmic reticulum (ER) elicit activation of the unfolded protein response (UPR), a translation- and transcription-coupled proteostatic stress response pathway. The primary translational control arm of the UPR is initiated by the PERK-dependent phosphorylation of eIF2Î±, leading to a large-scale reprogramming of translation and subsequent activation of an ATF4-mediated transcriptional program. It has remained challenging, however, to accurately evaluate the contribution of each component of the eIF2Î±/ATF4 pathway to the remodelling of transcription and translation. Here, we have used mouse embryonic fibroblasts containing either a knock-in of the non-phosphorylatable eIF2Î± S51A mutant or knock-out for ATF4 by ribosome profiling and mRNA-seq to define the specific contributions of eIF2Î± phosphoryation and ATF4 in controlling the translational and transcriptional components of the UPR. These studies show that the transcriptional and translational targets of each P-eIF2Î±, ATF4, and the other UPR gene expression programs overlapped extensively, leading to a core set of UPR genes whose robust expression in response to ER stress is driven by multiple mechanisms. The identification of other, more factor-specific targets illustrated the potential for functional specialization of the UPR. As the UPR progressed temporally, cells employed distinct combinations of transcriptional and translational mechanisms, initiated by different factors, to adapt to ongoing stress. These effects were accompanied by a buffering effect where changes in mRNA levels were coupled to opposing changes in ribosome loading, a property which makes cooperation between transcription and translation essential to confer robust protein expression. Translational analysis by ribosome profiling and mRNA-seq of PERK pathways mutants during the UPR. Mouse embryonic fibroblasts (MEFs) lacking components of the PERK pathway (eIF2a phosphorylation and ATF4) were subjected to ER stress and analyzed by ribosome profiling.

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A new family of ribosome hibernation factors in ArchaeaA new family of ribosome hibernation factors in Archaea

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