CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state

A large-scale curated and filterable dataset for cryo-EM foundation model pre-training

Cryo-electron microscopy (cryo-EM) is a transformative imaging technology that enables near-atomic resolution 3D reconstruction of target biomolecule, playing a critical role in structural biology and drug discovery. Cryo-EM faces significant challenges due to its extremely low signal-to-noise ratio (SNR) where the complexity of data processing becomes particularly pronounced. To address this challenge, foundation models have shown great potential in other biological imaging domains. However, their application in cryo-EM has been limited by the lack of large-scale, high-quality datasets. To fill this gap, we introduce CryoCRAB, the first large-scale dataset for cryo-EM foundation models. CryoCRAB includes 746 proteins, comprising 152,385 sets of raw movie frames (116.8 TB in total). To tackle the high-noise nature of cryo-EM data, each movie is split into odd and even frames to generate paired micrographs for denoising tasks. The dataset is stored in HDF5 chunked format, significantly improving random sampling efficiency and training speed. CryoCRAB offers diverse data support for cryo-EM foundation models, enabling advancements in image denoising and general-purpose feature extraction for downstream tasks.

Environmental drivers affecting the dormancy of Paranosema locustae

AIMS

As a gastrotoxic biocontrol agent employed for locust outbreak management, the infectivity of Paranosema locustae demonstrates significant dependence on pre-ingestion environmental exposure conditions, particularly temperature fluctuations, humidity levels, and UV radiation intensity, making the systematic investigation of these abiotic factors crucial for optimal field application.

METHODS AND RESULTS

In this study, we simulated key environmental parameters (temperature, humidity, and UV radiation) that critically influence P. locustae viability during the pre-infection phase of host exposure. Analyzed the locust growth curve post-infection, the pathogen's copy number, dormancy factor Lso2 gene expression, and phosphorylated protein levels. Results show a marked decline in lethality and infectivity of P. locustae after prolonged exposure to water, especially at 20°C for 15 days, the survival curve became similar to that of the negative control group. In contrast, drying at 40°C for 15 days preserved its pathogenicity. The pathogen exhibited strong UV resistance, remaining infectious after 24 h of UV exposure at intensities over 100 µW/cm². After 5-10 days of dry conditions, the significant increase in Lso2 gene expression highlights the entry of P. locustae into true dormancy, which subsequently returns to baseline with extended exposure. Western blot analysis supported that sustained phosphorylation is vital for P. locustae lethality.

CONCLUSIONS

Paranosema locustae demonstrates high-temperature tolerance, with dry heat and UV exposure maintaining infectivity, while wet environments reduce its viability.

Novel archaeal ribosome dimerization factor facilitating unique 30S-30S dimerization

Protein synthesis (translation) consumes a substantial proportion of cellular resources, prompting specialized mechanisms to reduce translation under adverse conditions. Ribosome inactivation often involves ribosome-interacting proteins. In both bacteria and eukaryotes, various ribosome-interacting proteins facilitate ribosome dimerization or hibernation, and/or prevent ribosomal subunits from associating, enabling the organisms to adapt to stress. Despite extensive studies on bacteria and eukaryotes, understanding factor-mediated ribosome dimerization or anti-association in archaea remains elusive. Here, we present cryo-electron microscopy structures of an archaeal 30S dimer complexed with an archaeal ribosome dimerization factor (designated aRDF), from Pyrococcus furiosus, resolved at a resolution of 3.2 Å. The complex features two 30S subunits stabilized by aRDF homodimers in a unique head-to-body architecture, which differs from the disome architecture observed during hibernation in bacteria and eukaryotes. aRDF interacts directly with eS32 ribosomal protein, which is essential for subunit association. The binding mode of aRDF elucidates its anti-association properties, which prevent the assembly of archaeal 70S ribosomes.

Accurate and fast segmentation of filaments and membranes in micrographs and tomograms with TARDIS

It is now possible to generate large volumes of high-quality images of biomolecules at near-atomic resolution and in near-native states using cryogenic electron microscopy/electron tomography (Cryo-EM/ET). However, the precise annotation of structures like filaments and membranes remains a major barrier towards applying these methods in high-throughput. To address this, we present TARDIS (Transformer-based Rapid Dimensionless Instance Segmentation), a machine-learning framework for fast and accurate annotation of micrographs and tomograms. TARDIS combines deep learning for semantic segmentation with a novel geometric model for precise instance segmentation of various macromolecules. We develop pre-trained models within TARDIS for segmenting microtubules and membranes, demonstrating high accuracy across multiple modalities and resolutions, enabling segmentation of over 13,000 tomograms from the CZI Cryo-Electron Tomography data portal. As a modular framework, TARDIS can be extended to new structures and imaging modalities with minimal modification. TARDIS is open-source and freely available at https://github.com/SMLC-NYSBC/TARDIS, and accelerates analysis of high-resolution biomolecular structural imaging data.

Ribosomes hibernate on mitochondria during cellular stress

Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated by mitochondrial fragmentation and sequestration of cytosolic ribosomes on mitochondria. This cellular adaptation promotes survival under harsh environmental conditions; however, the underlying mechanism of this response remains unknown. Here, we demonstrate that upon glucose depletion protein synthesis is halted. Cryo-electron microscopy structure of the ribosomes show that they are devoid of both tRNA and mRNA, and a subset of the particles depicted a conformational change in rRNA H69 that could prevent tRNA binding. Our in situ structural analyses reveal that the hibernating ribosomes tether to fragmented mitochondria and establish eukaryotic-specific, higher-order storage structures by assembling into oligomeric arrays on the mitochondrial surface. Notably, we show that hibernating ribosomes exclusively bind to the outer mitochondrial membrane via the small ribosomal subunit during cellular stress. We identify the ribosomal protein Cpc2/RACK1 as the molecule mediating ribosomal tethering to mitochondria. This study unveils the molecular mechanism connecting mitochondrial stress with the shutdown of protein synthesis and broadens our understanding of cellular responses to nutrient scarcity and cell quiescence.

Staphylococcal exoribonuclease YhaM destabilizes ribosomes by targeting the mRNA of a hibernation factor

The hibernation-promoting factor (Hpf) in Staphylococcus aureus binds to 70S ribosomes and induces the formation of the 100S complex (70S dimer), leading to translational avoidance and occlusion of ribosomes from RNase R-mediated degradation. Here, we show that the 3'-5' exoribonuclease YhaM plays a previously unrecognized role in modulating ribosome stability. Unlike RNase R, which directly degrades the 16S rRNA of ribosomes in S. aureus cells lacking Hpf, YhaM destabilizes ribosomes by indirectly degrading the 3'-hpf mRNA that carries an intrinsic terminator. YhaM adopts an active hexameric assembly and robustly cleaves ssRNA in a manganese-dependent manner. In vivo, YhaM appears to be a low-processive enzyme, trimming the hpf mRNA by only 1 nucleotide. Deletion of yhaM delays cell growth. These findings substantiate the physiological significance of this cryptic enzyme and the protective role of Hpf in ribosome integrity, providing a mechanistic understanding of bacterial ribosome turnover.

Hibernating ribosomes as drug targets?

When ribosome-targeting antibiotics attack actively growing bacteria, they occupy ribosomal active centers, causing the ribosomes to stall or make errors that either halt cellular growth or cause bacterial death. However, emerging research indicates that bacterial ribosomes spend a considerable amount of time in an inactive state known as ribosome hibernation, in which they dissociate from their substrates and bind to specialized proteins called ribosome hibernation factors. Since 60% of microbial biomass exists in a dormant state at any given time, these hibernation factors are likely the most common partners of ribosomes in bacterial cells. Furthermore, some hibernation factors occupy ribosomal drug-binding sites - leading to the question of how ribosome hibernation influences antibiotic efficacy, and vice versa. In this review, we summarize the current state of knowledge on physical and functional interactions between hibernation factors and ribosome-targeting antibiotics and explore the possibility of using antibiotics to target not only active but also hibernating ribosomes. Because ribosome hibernation empowers bacteria to withstand harsh conditions such as starvation, stress, and host immunity, this line of research holds promise for medicine, agriculture, and biotechnology: by learning to regulate ribosome hibernation, we could enhance our capacity to manage the survival of microorganisms in dormancy.

Implications of lytic phage infections inducing persistence

Phage therapy holds much promise as an alternative to antibiotics for fighting infection. However, this approach is no panacea as recent results show that a small fraction of cells survives lytic phage infection due to both dormancy (i.e. formation of persister cells) and resistance (genetic change). In this brief review, we summarize evidence suggesting phages induce the persister state. Therefore, it is predicted that phage cocktails should be combined with antipersister compounds to eradicate bacterial infections.