Biology subjects

Gaullier, G.

Publications and source records attributed to Gaullier, G..

6 recordsLinked to original sources

bioRxiv2026

Molecular mechanism of redox regulation of the alpha-carboxysomal carbonic anhydrase CsoSCA

Carboxysomes are protein-based organelles that form the core of the bacterial CO2-concentrating mechanism (CCM) by elevating CO2 levels around Rubisco. They encapsulate Rubisco and carbonic anhydrase (CA) within a protein shell that, after closure, excludes cytosolic reductants. Because cytosolic CA activity would short-circuit the CCM, CA activity must be confined to the carboxysome, yet how -carboxysomes achieve this has remained unknown. Here we show that CsoSCA, the -carboxysomal CA, is redox-regulated: inactive under reducing conditions, active under oxidizing. This regulation is mediated by a conserved vicinal cysteine pair distal from the active site. CryoEM structures of Halothiobacillus neapolitanus CsoSCA under active and inactive conditions, and of an inactive cysteine variant, reveal that redox conditions modulate global conformational dynamics that reorganize the active site for catalysis. These findings advance the understanding of -carboxysome regulation and couple CsoSCA activation to lumenal oxidation during carboxysome maturation.

biochemistry↗

bioRxiv2025

Atomic resolution structure of spinach rubisco reveals protons and dynamics

Photosynthetic organisms sustain life on Earth by storing solar energy in biomass. Central to this process is rubisco, the enzyme that catalyses the fixation of CO2 to ribulose-1,5-bisphosphate, providing the primary gateway for inorganic carbon into the biosphere. Rubiscos catalytic efficiency is a major determinant of crop productivity and global carbon flux, making it a longstanding target for protein engineering.1-4 Yet, attempts to enhance its performance through rational design have met limited success due to an incomplete understanding of rubiscos catalytic mechanism. Here, we report an atomic resolution (1.25 [A]) cryo-EM structure of spinach rubisco in complex with the transition-state analogue 2-carboxyarabinitol-1,5-bisphosphate. Supported by large-scale quantum/classical (QM/MM) calculations, our structural analysis reveals protonation equilibria within the active site and unexpected structural flexibility across large protein regions despite the exceptionally tight ligand binding. Our findings provide new insight into the complex interplay of protonation equilibria and conformational sampling, suggesting a novel basis for rubiscos rational redesign utilizing strategies that rely on a combination of dynamic and electrostatic control.

biochemistry↗

bioRxiv2025

ALC1 Finds a New Foothold on the Nucleosome's Super-Groove

Nucleosomes act as recognition platforms for chromatin-binding factors that coordinate genome maintenance. A distinct structural feature of the nucleosome is the alignment of the DNA major and minor grooves across both gyres, forming continuous major and minor super-grooves. Despite this prominent feature, only one example of a naturally occurring protein binding to a super-groove is documented at the structural level to date. The chromatin remodeler Amplified in Liver Cancer 1 (ALC1) is a key component of the DNA damage response and a promising therapeutic target in cancer. Through extensive classification of our cryo-electron microscopy data, we identified a previously unresolved ALC1-nucleosome complex characterized by a loosely bound conformation of ALC1. This conformation represents an intermediate between the auto-inhibited and active states, and provides new structural insights into the conformational transitions that regulate ALC1 activity. In this intermediate state, the linker of ALC1 engages the nucleosomes minor DNA super-groove across both gyres in a recognition mode observed for the first time in a naturally occurring protein. SynopsisRe-analysis of a publicly available cryo-EM dataset identifies an intermediate state of the oncogenic chromatin remodeler ALC1, revealing the conformational change leading to its activation upon binding to a PARylated nucleosome. The remodeler recognizes the nucleosomes super-groove.

biophysics↗

bioRxiv2025

Structural basis of ATP release and ion selectivity in Pannexin1 channels

This study investigated the structural basis of adenosine triphosphate (ATP) release and ion selectivity by Pannexin1 (Panx1). The microinjection of active SRC tyrosine kinase increased Panx1-mediated currents in Panx1-expressing oocytes. Furthermore, a mutation mimicking phosphorylation at Y308 turned Panx1 into a constitutively open ATP-releasing channel with broad ion permeability. Cryogenic electron microscopy showed that for most maps, the channel alternated between wide and narrow conformations. However, in the map of the phosphomimetic Y308E mutation, Panx1 remains in a wide ATP-releasing conformation. The pore-lining residues, W74 and R75, are flexible and create, in concert with the sequestered N-terminal helix, a path for ATP. The data point to phosphorylation as a reversible switch that activates ATP permeability by stabilizing Panx1 in the ATP-releasing conformation, which is crucial for developing modulators for diseases such as cancer and chronic pain.

biophysics↗

bioRxiv2021

Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome

The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a candidate drug target for cancer therapy as its loss confers synthetic lethality in homologous recombination-deficient cells. However, structure-based drug design and molecular analysis of ALC1 have been hindered by the requirement for PARylation and the highly heterogeneous nature of this post-translational modification. Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro using PARP2 and HPF1. This complex was amenable to cryo-EM structure determination without cross-linking, which enabled visualization of several intermediate states of ALC1 from the recognition of the PARylated nucleosome to the tight binding and activation of the remodeler. Functional biochemical assays with PARylated nucleosomes highlight the importance of nucleosomal epitopes for productive remodeling and reveal that ALC1 preferentially slides nucleosomes away from DNA breaks.

biophysics↗

bioRxiv2019

Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1

Poly(ADP-ribose) Polymerase 2 (PARP2) is one of three DNA-dependent PARPs involved in the detection of DNA damage. Upon binding to DNA double-strand breaks, PARP2 uses nicotinamide adenine dinucleotide to synthesize poly(ADP-ribose) (PAR) onto itself and other proteins, including histones. PAR chains in turn promote the DNA damage response by recruiting downstream repair factors. These early steps of DNA damage signaling are relevant for understanding how genome integrity is maintained and how their failure leads to genome instability or cancer. There is no structural information on DNA double-strand break detection in the context of chromatin. Here we present a cryo-EM structure of two nucleosomes bridged by human PARP2 and confirm that PARP2 bridges DNA ends in the context of nucleosomes bearing short linker DNA. We demonstrate that the conformation of PARP2 bound to damaged chromatin provides a binding platform for the regulatory protein Histone PARylation Factor 1 (HPF1), and that the resulting HPF1*PARP2*nucleosome complex is enzymatically active. Our results contribute to a structural view of the early steps of the DNA damage response in chromatin.

biochemistry↗