Biology subjects

Zottig, X.

Publications and source records attributed to Zottig, X..

4 recordsLinked to original sources

bioRxiv2025

Structural basis for non-AUG translation regulation by 5MPs

The cellular proteome is regulated by translation initiation on AUG or non-canonical (non-AUG) start codons1-3. Non-AUG initiation remodels proteome during stress and is implicated in cancer and other diseases4-6. The eIF5-mimic proteins (5MPs) restrict non-AUG start codon usage and thereby reprogram proteoform expression from mRNAs with alternative start sites, such as the oncogenic c-Myc7-10. The mechanism by which 5MPs induce such translational reprogramming remains unknown. Here, using in extracto cryo-electron microscopy (cryo-EM) and biochemical assays, we report that translational repression by 5MP strongly depends on the sequence context near the AUG or non-AUG codons. Cryo-EM structures of 5MP-bound 48S pre-initiation complexes (PICs) from native cell extracts reveal that 5MP binds at the A site of the small ribosomal subunit, stabilizing an expanded open-head conformation of the PIC scanning along mRNA. The N-terminal region of 5MP blocks the A site, whereas the C-terminal domain docks at eIF2{beta} and the initiator tRNAMet outside the P site (i.e., Pout). These findings indicate that 5MP protein directly biases the initiating 48S complexes toward the open conformation, promoting mRNA scanning and inhibiting initiation at suboptimal start codons.

biophysics↗

bioRxiv2025

In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles

Cryogenic electron microscopy (cryo-EM) made impressive progress in resolving cellular macromolecules and their detailed interactions. Single-particle cryo-EM traditionally relies on purified macromolecules and lacks the complexity of cellular environments, whereas in situ cryo-EM or cryo-ET require extensive sample preparation and data acquisition, presenting challenges in achieving high resolution. We describe cryo-EM of cellular lysates--in extracto cryo-EM--allowing the flexibility and high-resolution of cryo-EM in the context of cellular components. High-resolution 2D template matching (2DTM) yields [~]2.2 [A] maps of the mammalian translational apparatus. Elongating ribosome abundances in primate cell lines (MCF-7 and BSC-1) and rabbit reticulocyte lysates range from [~]70% to [~]10%, reflecting translational stress responses. Non-translating (hibernating) ribosomes carrying no mRNA, feature numerous proteins shielding ribosomal functional centers. Elongation factor 2 (eEF2) is the most abundant hibernation factor bound to >95% of ribosomes and, unexpectedly, to 60S subunits. eEF2*GDP is stabilized by interactions with the sarcin-ricin loop and protein uL14. Hibernating ribosomes also feature LARP1 involved in initiation and mTOR signaling; eIF5A implicated in elongation and termination; and other factors, exposing the variety of hibernation scenarios. Our work underscores the efficiency and potential of in extracto cryo-EM to discover native cellular complexes and mechanisms at near-atomic resolution.

molecular biology↗

bioRxiv2025

Unbend: Correction of local beam-induced sample motion in cryo-EM images using a 3D spline model

The exposure of frozen biological samples to the high-energy electron beam in a cryo-electron microscope commonly leads to beam-induced sample motion and distortions. Previously, we described Unblur, which is part of our cisTEM software to correct for beam-induced motion based on the alignment of full frames in a movie collected during the beam exposure (Grant et al., 2015). However, Unblur cannot accommodate motion due to more localized sample bending and distortions. Here, we present Unbend, extending Unblur by incorporating local motion correction using a three-dimensional cubic spline model. The 3D spline model is constructed using cubic B-splines along the exposure time axis, and bicubic B-splines within movie frames. Unbend is integrated into our cisTEM software with a new local motion visualization panel within the cisTEM graphical user interface. We processed movie frames from various in-situ sample types, including whole cells, lamellae, and cell lysates, to analyze motion behavior across different specimen types. To quantify the improvement in high-resolution signal, we utilized the 2D template matching method, which operates independently of the motion correction process, to search large ribosomal subunits from the motion-corrected micrographs. Overall, the signal-to-noise ratio of detected particles improved by 3-8% across different samples compared with full-frame aligned micrographs, while the number of detected target particles increased by up to [~]300%. The total and Von Mises equivalent strain shows a deformation scale of less than 1% in most of the samples, confirming that our model induces minimal additional distortion. Furthermore, we processed micrograph montages to study motion patterns across an entire sample, revealing considerable variance in distortion scale within the same sample, suggesting a complex underlying mechanism.

biophysics↗

bioRxiv2024

CTFFIND5 provides improved insight into quality, tilt and thickness of TEM samples

Images taken by transmission electron microscopes are usually affected by lens aberrations and image defocus, among other factors. These distortions can be modeled in reciprocal space using the contrast transfer function (CTF). Accurate estimation and correction of the CTF is essential for restoring the high-resolution signal in cryogenic electron microscopy (cryoEM). Previously, we described the implementation of algorithms for this task in the cisTEM software package (Grant et al., 2018). Here we show that taking sample characteristics, such as thickness and tilt, into account can improve CTF estimation. This is particularly important when imaging cellular samples, where measurement of sample thickness and geometry derived from accurate modeling of the Thon ring pattern helps judging the quality of the sample. This improved CTF estimation has been implemented in CTFFIND5, a new version of the cisTEM program CTFFIND. We evaluated the accuracy of these estimates using images of tilted aquaporin crystals and eukaryotic cells thinned by focused ion beam milling. We estimate that with micrographs of sufficient quality CTFFIND5 can measure sample tilt with an accuracy of 3{degrees} and sample thickness with an accuracy of 5 nm.

biophysics↗