Biology subjects

Royer, L.

Publications and source records attributed to Royer, L..

10 recordsLinked to original sources

bioRxiv2026

Molecular interplay between Integrative Mobile Elements exploiting Xer drives the evolution of cholera pandemics

XerC and XerD are ubiquitous bacterial recombinases dedicated to chromosome dimer resolution. They add a crossover at a specific chromosomal site, dif, when activated by the FtsK cell division protein. Several integrative mobile elements exploiting Xer (IMEXs) have been reported. IMEXs hijack XerCD to integrate at dif in an FtsK-independent manner. The most notable IMEX is the CTX{Phi} bacteriophage of Vibrio cholerae, which encodes the Cholera toxin. V. cholerae isolates often contain several sequentially integrated IMEX, forming arrays. In the current cholera pandemic lineage, CTX{Phi} integrated in the dif site of the primary V. cholerae chromosome, difI, after the integration of another IMEX, TLC{Phi} (Toxin-Linked Cryptic). The strict order of TLC{Phi} and CTX{Phi} integration has been explained via a dif site-correction hypothesis, where the difI site of the environmental ancestor of the current pandemic isolates was non-functional and was corrected by the integration of TLC{Phi}. Here, we traced the inheritance of difI variants and IMEXs in environmental and pandemic isolates. We show that IMEX arrays undergo rearrangements not congruent with the core genome phylogeny and that TLC{Phi} integration preceded CTX{Phi} integration in pandemic lineages. We demonstrate that the difI sites of environmental and pandemic isolates are equally functional for dimer resolution and CTX{Phi} integration, and show that TLC{Phi} and another IMEX, VGJ{Phi}, encode a Xer activation factor that facilitates CTX{Phi} integration, suggesting an alternate explanation for the integration order of IMEX in environmental and pandemic isolates. Significance statementCholera is an increasing threat due to climate change. Vibrio cholerae pandemic potential is intricately linked to its infection by a lysogenic phage, the CTX{Phi}, which encodes the Cholera Toxin. CTX{Phi} uses the Xer recombination of its host for genomic integration. We established that CTX{Phi} is integrated downstream of the TLC{Phi} phage satellite in pandemic lineages and that it is frequently integrated downstream of the VGJ{Phi} phage in environmental strains. Our results show that TLC{Phi} and VGJ{Phi} encode for distinct Xer activator proteins (Xafs) that facilitate CTX{Phi} integration, providing a mechanistic explanation for the observed integration order. This novel molecular interplay is crucial to understanding the development of pandemic V. cholerae, with a view to preventing future expansions.

microbiology↗

bioRxiv2026

xTracer: Integrating chromatogram and mobiligram correlations for untargeted peptide identification in SLIM-based PAMAF data

Parallel Accumulation with Mobility-Aligned Fragmentation (PAMAF) achieves near-complete ion utilization and high spectral specificity by fragmenting all mobility-separated precursors without quadrupole isolation. Leveraging the ultrahigh mobility resolution of SLIM, this quadrupole-free strategy maximizes ion utilization efficiency and offers a promising approach in mass spectrometry-based proteomics, particularly for low-abundance peptides or low-input samples. However, the unique data structure of PAMAF where precursor-fragment relationships are encoded along the mobility dimension renders it incompatible with existing peptide identification tools. Here, we present xTracer, the first untargeted peptide identification algorithm developed specifically for PAMAF data. xTracer integrates correlations across both chromatographic and mobility dimensions to associate precursor and fragment ions, reconstruct pseudo-spectra, and enable database searching using well-established DDA search engines. Applied to datasets with varying sample loads and acquisition throughputs, xTracer consistently achieved robust and reproducible peptide identifications, outperforming single-domain correlation strategies. Overall, xTracer provides a versatile and high-efficiency computational framework for reconstructing pseudo-spectra from quadrupole-free, mobility-aligned fragmentation data, enhancing the analytical power of high-resolution ion mobility (HRIM)-based proteomics.

systems biology↗

bioRxiv2026

A Parallel Accumulation-Mobility Aligned Fragmentation Strategy Utilizing High-Resolution Ion Mobility for High Performance Proteomics Analysis

Here we present a novel data independent acquisition (DIA) mass spectrometry (MS) operating mode termed parallel accumulation-mobility aligned fragmentation (PAMAF) that offers enhanced speed and sensitivity of ion fragmentation analysis for nontargeted discovery workflows such as bottom-up proteomics. This mode of operation leverages high-resolution ion mobility (HRIM) separation capabilities of the structures for lossless ion manipulation (SLIM) technology to achieve HRIM-based precursor isolation in place of traditional quadrupole filtering approaches. This PAMAF mode of operation increases the number of features that can be identified per MS1/MS2 acquisition cycle by employing mobility-based time alignment to associate fragment ions with their corresponding precursor ions. By using a high-speed, lossless separation technique for precursor isolation instead of the comparatively slow and wasteful quadrupole filtering method, we can avoid ion losses up to 99% while simultaneously increasing the rate at which precursor ions are sequentially fragmented and detected. Additionally, by storing ions in a trapping region while the previous packet of ions is being analyzed, the PAMAF mode achieves [~]100% ion utilization efficiency. Benchmarking results of LC-PAMAF-MS analysis of a whole cell protein digest showed approximately 6x more protein group identifications compared to a standard data-dependent acquisition (DDA) analysis without HRIM on the same QTOF instrument, and to over 100x improvement for low-load workflows. Quantitative evaluations demonstrated that PAMAF mode could quantify low abundance peptides, including those undetectable by DDA. Additionally, since precursor isolation in PAMAF mode is size-based rather than m/z-based, many coeluting isobars and isomers can be resolved prior to fragmentation to eliminate chimeric spectra that compromise identification accuracy. In this work we also explored the benefits of combining HRIM and quadrupole isolation to achieve improved specificity. This approach, known as DIA-PAMAF mode, further reduces the frequency of chimeric fragmentation spectra, and enabled the detection of over 8,000 protein groups from a HeLa digest analysis. PAMAF mode brings a powerful new technique to the field of proteomics that has the potential to improve the sensitivity and selectivity of mass spectrometry-based proteomics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/704896v1_ufig1.gif" ALT="Figure 1"> View larger version (114K): org.highwire.dtl.DTLVardef@7984c3org.highwire.dtl.DTLVardef@1fb2fe3org.highwire.dtl.DTLVardef@50d35org.highwire.dtl.DTLVardef@1a62926_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Novel high-resolution ion mobility mass spectrometry for site-specific quantification of the sirtuin-5 regulated kidney succinylome

Protein post-translational modifications (PTMs) dynamically regulate essential biological and cellular processes. Lysine succinylation changes the amino acid charge, potentially affecting protein structures and functions, and dysregulation of protein succinylation may lead to metabolic disorders. Proteome-wide succinylation quantification using proteomic tools remains challenging, especially due to the low abundance of succinylated peptides and the frequent presence of isomeric PTM forms. Ion mobility spectrometry workflows that can differentiate peptidoforms with different PTM distributions represent a powerful strategy to alleviate these challenges. Recently, a new Parallel Accumulation with Mobility Aligned Fragmentation (PAMAF) operating mode for high-resolution ion mobility-mass spectrometry (HRIM-MS) analysis based on the structures for lossless ion manipulation (SLIM) technology was introduced. Here, we first assessed the performance of PAMAF mode for protein succinylation analysis using synthetic succinylated peptides, demonstrating residue-level differentiation of co-eluting isomers and isobars and precise PTM site localization. We leveraged this novel approach to investigate succinylome remodeling in kidney tissues from wild-type and Sirtuin-5 (Sirt5) knock-out mice, a NAD+-dependent lysine de-succinylase. PAMAF acquisitions yielded [~]1,000 confidently identified and accurately quantified succinylated peptides and sites from mouse kidney. Sirt5 regulated succinylation of mitochondrial proteins involved in metabolic processes, including fatty acid oxidation, the tricarboxylic acid cycle, and propionate metabolism.

cell biology↗

bioRxiv2025

Plasmodium falciparum PP1 phosphatase is a key regulator of malaria parasite transmission

For the successful transmission of malaria parasites from humans to mosquitoes, Plasmodium falciparum gametocytes must remain in the bloodstream long enough to be taken up by a mosquito. Once ingested, they are then activated into gametes to continue the parasite life cycle in the mosquito midgut. Both persistence of gametocytes in the blood and their activation into gametes are tightly regulated by phospho-signaling. While the serine-threonine phosphatase PfPP1 is an essential enzyme for parasite asexual proliferation, its role during transmission of sexual stages remains elusive. Here, we employed a conditional depletion strategy to conduct a functional analysis of PfPP1 during gametocyte development, gamete activation and transmission to mosquitoes. We show that PfPP1 regulates the deformability and the permeability of mature gametocyte-infected erythrocytes through the dephosphorylation of PKA substrates, thus highlighting a key role for PfPP1 in modulating the host cell mechanical properties, which are crucial for gametocyte persistence in the bloodstream. We also provide evidence that PfPP1 controls crucial steps of gamete activation via stimulation of the cGMP/ PKG pathway. Collectively, these results underscore the pivotal role of PfPP1 in the transmission of P. falciparum to the mosquito during both sexual development and gamete activation. AUTHOR SUMMARYThe protein phosphatase PP1 is a major contributor to total cellular phosphatase activity in eukaryotes and plays a critical role during various cellular processes. Here, we have unraveled novel mechanisms regulated by the phosphatase PfPP1 in the human malaria parasite Plasmodium falciparum. While PfPP1 is known to be essential for the parasite asexual proliferation, in the present study we demonstrate that PfPP1 is also required during the sexual parasite stages, called gametocytes, that ensure parasite transmission from humans to mosquitoes. PfPP1 is involved in regulating the mechanical properties of the gametocyte-infected host cell, a process necessary for the persistence of gametocytes in blood circulation. Moreover, PfPP1 also contributes to the activation of gametocytes into gametes, the stages able to pursue the parasite life cycle in mosquitoes. In addition to providing insights into novel mechanisms involved in parasite transmission, this study also highlights the possibility of interfering with PfPP1 signaling pathway for blocking malarial parasite transmission.

microbiology↗

bioRxiv2023

Length-weight relationships of the French pikes Esox spp (Teleostei, Esocidae)

Length-weight relationships for Pike Esox aquitanicus and Esox lucius from France are provided. A total of 9,070 specimens were collected, measured and weighted from 1981 to 2022 throughout France by Departmental Angling Federations and the French Biodiversity Agency during their survey by electrofishing. For all species, the values of b are 2.960 for E. aquitanicus and 2.987 for Esox lucius. We hypothetize this difference by the poor environment where live the Aquitanian pike with no abundant available food and small prey fish species which do not contribute to good conditions for the growth. The study provides the first reference of length-weight relationships for E. aquitanicus.

ecology↗

bioRxiv2017

Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy

Fluorescence microscopy is a key driver of discoveries in the life-sciences, with observable phenomena being limited by the optics of the microscope, the chemistry of the fluorophores, and the maximum photon exposure tolerated by the sample. These limits necessitate trade-offs between imaging speed, spatial resolution, light exposure, and imaging depth. In this work we show how image restoration based on deep learning extends the range of biological phenomena observable by microscopy. On seven concrete examples we demonstrate how microscopy images can be restored even if 60-fold fewer photons are used during acquisition, how near isotropic resolution can be achieved with up to 10-fold under-sampling along the axial direction, and how tubular and granular structures smaller than the diffraction limit can be resolved at 20-times higher frame-rates compared to state-of-the-art methods. All developed image restoration methods are freely available as open source software in Python, FO_SCPLOWIJIC_SCPLOW, and KO_SCPLOWNIMEC_SCPLOW.

bioinformatics↗

bioRxiv2017

Rem2 regulates distinct homeostatic mechanisms in visual circuit plasticity

Activity-regulated genes sculpt neural circuits in response to sensory experience. These calcium-sensitive genes generally fall into two categories: transcription factors and proteins that function at synapses. Yet little is known about activity-regulated, cytosolic proteins that transduce signals between the neuronal membrane and the nucleus. Using the visual system as a model, we investigated the role of the activity-regulated, non-canonical Ras-like GTPase Rem2 in vivo. We demonstrate that Rem2-/- mice fail to exhibit normal ocular dominance plasticity during the critical period. At the circuit level, cortical layer 2/3 neurons in Rem2-/- mice show deficits in both postsynaptic scaling up of excitatory synapses and misregulation of intrinsic excitability. Further, we reveal that Rem2 plays a novel, cell-autonomous role in regulating neuronal intrinsic excitability. Thus, Rem2 is a critical regulator of neural circuit function and distinct homeostatic plasticity mechanisms in vivo.\n\nHIGHLIGHTSO_LIRem2 is required in excitatory cortical neurons for normal ocular dominance plasticity\nC_LIO_LIRem2 regulates postsynaptic homoeostatic synaptic scaling up\nC_LIO_LIRem2 alters the intrinsic excitability of neurons in a cell-autonomous manner\nC_LI

neuroscience↗

bioRxiv2017

The Ras-like GTPase Rem2 is a potent endogenous inhibitor of calcium/calmodulin-dependent kinase II activity

CaMKII is a well-characterized, abundant protein kinase that regulates a diverse set of functions in a tissue specific manner. For example, in heart muscle, CaMKII regulates Ca2+ homeostasis while in neurons CaMKII regulates activity-dependent dendritic remodeling and Long Term Potentiation (LTP), a biological correlate of learning and memory. Previously, we identified the noncanonical GTPase Rem2 as a critical regulator of dendrite branching and synapse formation in the vertebrate nervous system. Here, we report that Rem2 directly interacts with CaMKII and potently inhibits the activity of the intact holoenzyme, a previously undescribed function for the Rem2 protein. To date, only one other endogenous inhibitor of CaMKII has been described: CaMKIIN, which blocks CaMKII activity through binding to the catalytic domain. Our data suggest that Rem2 inhibits CaMKII through a novel mechanism, as inhibition requires the presence of the association domain of CaMKII. Our biochemical finding that Rem2 is a direct, endogenous inhibitor of CaMKII activity, coupled with known functions of Rem2 in neurons, provides a framework which will enable future experiments probing the physiological role of CaMKII inhibition in a cellular context.

biochemistry↗

bioRxiv2017

With Our Powers Combined: Integrating Behavioral And Genetic Data To Estimate Mating Success And Sexual Selection

The analysis of sexual selection classically relies on the regression of individual phenotypes against the marginal sums of a males x females matrix of pairwise reproductive success, assessed by genetic parentage analysis. When the matrix is binarized, the marginal sums give the individual mating success. Because such analysis treats male and female mating/reproductive success independently, it ignores that the success of a male x female sexual interaction can be attributable to the phenotype of both individuals. Also, because it is based on genetic data only, it is oblivious to costly yet unproductive matings, which may be documented by behavioral observations. To solve these problems, we propose a statistical model which combines matrices of offspring numbers and behavioral observations. It models reproduction on each mating occasion of a mating season as three stochastic and interdependent pairwise processes, each potentially affected by the phenotype of both individuals and by random individual effect: encounter (Bernoulli), concomitant gamete emission (Bernoulli), and offspring production (Poisson). Applied to data from a mating experiment on brown trout, the model yielded different results from the classical regression analysis, with only a limited effect of male body size on the probability of gamete release and a negative effect of female body size on the probability of encounter and gamete release. Because the general structure of the model can be adapted to other partitioning of the reproductive process, it can be used for a variety of biological systems where behavioral and genetic data are available.

evolutionary biology↗