Biology subjects

Colin, L.

Publications and source records attributed to Colin, L..

11 recordsLinked to original sources

bioRxiv2026

Genomic and oceanographic evidence of reef connectivity across the western and central Indian Ocean

Connectivity among coral populations, via larval dispersal, is one of the key mechanisms supporting reef recovery after climate-driven bleaching events. This study examines reef connectivity of remote atolls of the understudied central and western Indian Ocean seascape, focusing on a key reef-building species, Acropora aff. tenuis. Using genomic data from ultra-conserved elements alongside particle-tracking simulations, we investigate patterns of population structure and gene flow, and the influence of ocean currents. Results show asymmetrical connectivity: strong gene flow occurs within the Chagos Archipelago and between Chagos and the Inner Seychelles, highlighting their importance as regional larval sources. In contrast, the Outer Seychelles mainly functions as a larval sink, and IIes Glorieuses appears to be the least connected. Whilst population structure suggests a partially permeable dispersal barrier between the Inner and Outer Seychelles. Differences between genetic patterns and simulated ocean-driven dispersal suggest that ocean currents are not the only important driver of connectivity patterns. Additional factors, such as stepping-stone dispersal among atolls, fine-scale oceanographic processes, and species biology likely play important roles. Overall, we find widespread genomic connectivity across this seascape, which has positive implications for reef resilience, though future resilience will depend on frequency and severity of future bleaching events.

ecology↗

bioRxiv2026

The genome of the coral model sea anemone Exaiptasia diaphana (Aiptasia) strain F003

We present a genome assembly of Aiptasia strain F003, a broadly used laboratory strain of the sea anemone and coral model organism Exaiptasia diaphana (Cnidaria; Anthozoa; Hexacorallia; Actiniaria; Aiptasiidae; Exaiptasia). The genome assembly spans 237.34 Mb across 12,480 contigs with a contig N50 of 76.47 kb (12,423 scaffolds with a scaffold N50 of 77.93 kb), including a single-contig mitochondrial genome with a length of 19.79 kb. The assembly is highly complete with a BUSCO completeness of 96.50% based on the metazoa dataset, including 94.80% single-copy, 1.70% duplicated, 1.70% fragmented, and 1.80% missing BUSCO genes. Genome annotation identified 29,589 protein-coding genes (including 2 pseudogenes) and a repeat content of 32.89%. The genome of the female Aiptasia strain F003 enhances the utility of a key cnidarian model organism by enabling comparisons among Aiptasia strains in studies of symbiosis, microbiomes, and thermal stress. It thereby strengthens the value of Aiptasia as a model for investigating the mechanisms underlying coral holobiont function, response, and resilience to environmental change.

genomics↗

bioRxiv2026

Phosphorylation of TTL3 by BIK1 Functions as a Molecular Switch to Control Cellulose Biosynthesis under Salt Stress

Cellulose, a central structural component of plant cell walls, is produced by cellulose synthase complexes (CSCs) at the plasma membrane. Salinity stress is particularly damaging to cellulose biosynthesis, and therefore, plants have developed adaptive mechanisms to cope with these conditions. TETRATRICOPEPTIDE THIOREDOXIN-LIKE (TTL) proteins are essential for growth under salt stress and show a salt-dependent association with CSCs through an as-yet unknown mechanism. Here, we identify a phosphorylation-dependent regulatory mechanism linking salt stress signaling to cellulose biosynthesis through the coordinated action of TTL3 and the receptor-like cytoplasmic kinase BOTRYTIS-INDUCED KINASE 1 (BIK1). Phosphorylation of Serine 93 in the N-terminal intrinsically disordered region of TTL3 controls its localization, retaining it in the cytosol, while dephosphorylation promotes association with CSCs at the plasma membrane. Biochemical and genetic analysis identified BIK1 as the kinase responsible for TTL3-S93 phosphorylation, with bik1 mutants phenocopying the phosphoablative TTL3S93A in vivo. Transcriptomic analyses reveal a strong overlap of differentially expressed genes between bik1 and a cellulose-deficient mutant, supporting a broader role for BIK1 in cell wall regulation. Notably, TTL proteins do not appear to be involved in the assayed canonical immune responses, suggesting pathway specificity downstream of BIK1. Together, these findings define a signaling module that connects salt stress perception to CSCs regulation and establish BIK1-dependent TTL3 phosphorylation as a molecular switch for maintaining cell wall integrity under abiotic stress.

Plant Biology↗

bioRxiv2026

Pathogen priming reveals host immune training and microbiome conditioning in corals

UNSTRUCTURED ABSTRACTIn several species, vaccine-like approaches, where hosts are primed through controlled pathogen exposure, have proven effective in enhancing responses to subsequent infections. This principle remains unexplored in corals. Here, we demonstrate that chronic exposure to non-lethal concentrations of live or inactivated Vibrio coralliilyticus primes the coral holobiont to counter subsequent infections under heat stress. Non-primed corals experienced greater heat stress pathogen-driven bleaching and a significant decline in their photosynthetic efficiency compared to primed samples. These results were linked to microbiome conditioning and host gene expression modulation, including a layered, fine-tuned immune and cellular response to microbial invasion. This proof-of-concept challenges strictly innate immune responses in corals and positions immune priming and microbiome conditioning as integrated mechanisms of coral holobiont resilience. Together, these findings can contribute to redefine coral immunity concepts and lay the groundwork for developing new microbiome-based strategies to enhance coral health for reef conservation under climate change. LAY SUMMARYCoral reefs are increasingly threatened by rising seawater temperatures and disease. Unlike vertebrates, corals do not possess a classical adaptive immune system, so they have been thought to rely only on innate defenses. However, our study shows that corals may be more capable than previously believed. We demonstrate that exposing corals to non-lethal doses of a widespread bacterial pathogen can train them to better withstand subsequent infections under heat stress. Corals that were not pre-exposed suffered more pathogen caused bleaching and showed a stronger decline in physiological performance, while those that were primed were more resilient. This improved resistance appears to come from two coordinated processes. First, the corals associated bacterial community shifted in a way that seems to help protect the host. Second, the coral itself adjusted its gene expression, mounting a more effective and controlled response to infection. These findings suggest that corals may be able to remember past exposures and respond more effectively to future infections, even without a traditional adaptive immune system, providing a foundation for developing new strategies to support coral resilience.

microbiology↗

bioRxiv2024

IQD2 recruits KLCR1 to the membrane-microtubule nexus to promote cytoskeletal mechano-responsiveness in leaf epidermis pavement cells

Plant cells experience a variety of mechanical stresses from both internal and external sources, including turgor pressure, mechanical strains arising from heterogeneous growth between neighboring cells, and environmental factors like touch from soil, rain, or wind [1,2]. These stresses serve as signals at the cell-, tissue- and organismal level to coordinate plant growth during development and stress responses [3]. In plants, the physical cell wall-plasma membrane-microtubule continuum is proposed to be integral in transducing mechanical signals from the exterior to intracellular components [4-6]. Cortical microtubules (CMTs) rapidly reorient in response to mechanical stress to align with the maximal tensile stress direction [7,8]. Several studies proposed that CMTs themselves may act as stress sensors; the precise mechanisms involved in the regulation of CMTs and the modes of sensing, however, are still not clearly understood. Here, we show that IQD2 and KLCR1 are enriched at CMTs in proximity to the plasma membrane. IQD2, which is a bona fide microtubule-associated protein, promotes microtubule localization of KLCR1. By combining cross-linking mass spectrometry (XL-MS) and computational modeling with structure-function studies, we present first experimental insights into the composition and structure of IQD2-KLCR1 complexes. Further, we demonstrate that the IQD2-KLCR1 module is a positive regulator of microtubule mechano-responses in pavement cells. Collectively, our work identifies the IQD2-KLCR1 module as novel regulator of mechanostress-mediated CMT reorientation and provides a framework for future mechanistic studies aimed at a functional dissection of mechanotransduction at the plasma membrane-CMT interface during growth and plant morphogenesis. HighlightsO_LIIQD2 and KLCR1 localize to the plasma membrane-microtubule nexus C_LIO_LIIQD2 is required for efficient microtubule targeting of KLCR1 in planta C_LIO_LIIQD2 physically interacts with KLCR1 and microtubules C_LIO_LIThe IQD2-KLCR1 module promotes mechano-stress induced microtubule reorganization C_LI

plant biology↗

bioRxiv2023

RNA Pol II antagonises mitotic chromatin folding and chromosome segregation by condensin

Condensin shapes mitotic chromosomes by folding chromatin into loops but whether it does so by DNA-loop extrusion remains speculative. While loop-extruding cohesin is stalled by transcription, no conclusive evidence has been provided regarding the impact of transcription on condensin despite its conserved enrichment at highly expressed genes. Using degrons of Rpb1 or the torpedo nuclease Dhp1XRN2, we depleted or displaced RNAP2 on chromatin in fission yeast metaphase cells. We show that RNAP2 does not load condensin on DNA but instead retains condensin and hinders its ability to fold mitotic chromatin and to support chromosome segregation, consistent with the stalling of a loop-extruder. Transcription termination by Dhp1 limits such a hindrance. Our results shed a new light on the integrated functioning of condensin and we argue that a tight control of transcription underlies mitotic chromosome assembly by loop-extruding condensin.

genomics↗

bioRxiv2022

Condensin positioning at telomeres by Taz1 promotes telomere disjunction in anaphase

The localization of condensin along chromosomes is crucial for their accurate segregation in anaphase. Condensin is enriched at telomeres but how and for what purpose had remained elusive. Here we show that fission yeast condensin accumulates at telomere repeats through the balancing acts of Taz1, a core component of the shelterin complex that ensures telomeric functions, and Mit1, a nucleosome-remodeler associated with shelterin. We further show that condensin takes part in sister-telomere separation in anaphase, and that this event can be uncoupled from the prior separation of chromosome arms, implying a telomere-specific separation mechanism. Consistent with a cis-acting process, increasing or decreasing condensin occupancy specifically at telomeres modifies accordingly the efficiency of their separation in anaphase. Genetic evidence suggests that condensin promotes sister-telomere separation by counteracting cohesin. Thus, our results reveal a shelterin-based mechanism that enriches condensin at telomeres to drive in cis their separation during mitosis.

cell biology↗

bioRxiv2020

What's left in the tank? Identification of non-ascribed aquarium's coral collections with DNA barcodes as part of an integrated diagnostic approach

The unprecedented threats to coral reef ecosystems from global climate change (GCC) require an urgent response from the aquarium community, which is becoming an increasingly vital coral conservation resource. Unfortunately, many hermatypic corals in aquaria are not identified to species level, which hinders assessment of their conservation significance. Traditional methods of species identification using morphology can be challenging, especially to non-taxonomists. DNA barcoding is an option for species identification of Scleractinian corals, especially when used in concert with morphology-based assessment. This study uses DNA barcodes to try to identify aquarium specimens of the diverse reef-forming genus Acropora from 127 samples. We identified to our best current knowledge, to species name 44% of the analysed samples and provided provisional identification for 80% of them (101/127, in the form of a list of species names with associate confidence values). We highlighted a sampling bias in public nucleotide sequences repertories (e.g.: GenBank) towards more charismatic and more studied species, even inside a well-studied genus like Acropora. In addition, we showed a potential "single observer" effect with over a quarter of the reference sequences used for these identifications coming from the same study. We propose the use of barcoding and query matching as an additional tool for taxonomic experts and general aquarists, as an additional tool to increase their chances of making high confidence species-level identifications. We produce a standardised and easily repeatable methodology to increase the capacity of aquariums and other facilities to assess non-ascribed species, emphasising the value of integrating this approach with morphological identification optimising usage of authoritative identification guides and expert opinion.

genetics↗

bioRxiv2020

iDePP: a genetically encoded system for the inducible depletion of PI(4,5)P2 in Arabidopsis thaliana.

Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is a low abundant lipid present at the plasma membrane of eukaryotic cells. Extensive studies in animal cells revealed the pleiotropic functions of PI(4,5)P2. In plant cells, PI(4,5)P2 is involved in various cellular processes including the regulation of cell polarity and tip growth, clathrin-mediated endocytosis, polar auxin transport, actin dynamics or membrane-contact sites. To date, most studies investigating the role of PI(4,5)P2 in plants have relied on mutants lacking enzymes responsible for PI(4,5)P2 synthesis and degradation. However, such genetic perturbations only allow steady-state analysis of plants undergoing their life cycle in PI(4,5)P2 deficient conditions and the corresponding mutants are likely to induce a range of non-causal (untargeted) effects driven by compensatory mechanisms. In addition, there are no small molecule inhibitors that are available in plants to specifically block the production of this lipid. Thus, there is currently no system to fine tune PI(4,5)P2 content in plant cells. Here we report a genetically encoded and inducible synthetic system, iDePP (Inducible Depletion of PI(4,5)P2 in Plants), that efficiently removes PI(4,5)P2 from the plasma membrane in different organs of Arabidopsis thaliana, including root meristem, root hair and shoot apical meristem. We show that iDePP allows the inducible depletion of PI(4,5)P2 in less than three hours. Using this strategy, we reveal that PI(4,5)P2 is critical for cortical microtubule organization. Together, we propose that iDePP is a simple and efficient genetic tool to test the importance of PI(4,5)P2 in given cellular or developmental responses but also to evaluate the importance of this lipid in protein localization. Research OrganismA. thaliana

plant biology↗

bioRxiv2020

The chromatin remodeler LSH controls genome-wide cytosine hydroxymethylation

TET proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), leading to a dynamic epigenetic state of DNA that can influence transcription. While TET proteins have been associated with either epigenetic repression or activation complexes, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene transcription still remains limited. Here, we show that TET proteins interact with lymphoid-specific helicase (LSH), a chromatin remodeling factor belonging to the SNF2 super family. Lsh knock-out leads to a significant reduction of 5-hydroxymethylation global level in mouse embryonic fibroblasts (MEFs) and in embryonic stem cells (ESC). Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with not much effect on gene expression. We further show that 5hmC modifications upon Lsh loss is not a direct consequence of 5mC decrease, as differentially hydroxymethylated regions (DhMR) did not overlap with DMR (differentially methylated regions), underlying that these modifications occurred at different genomic loci. Altogether, our results suggest that LSH is a key regulator of 5hmC in both MEFs and ESC and that TET proteins rely on specific factors to establish genome-wide 5hmC patterns.

molecular biology↗

bioRxiv2019

Record highest mesophotic fish diversity found in Raja Ampat

Mesophotic coral ecosystems (MCEs; reefs 30-150 m depth) are poorly studied, with existing research heavily geographically biased away from the most species-rich reef regions. Yet, MCEs are of high interest because of their unique species and potential to act as refuges from the impacts of fishing. Using baited remote underwater video systems, we surveyed reef fish communities from 2 to 85 m depths throughout the Raja Ampat archipelago in West Papua, Indonesia - an area considered the heart of the Coral Triangle where coral reef biodiversity is greatest. We sought to provide the first assessment of fish communities across this depth gradient in the region and identify whether human population density and market access differently affected fish abundance based on depth. Here we show that--similar to shallow reefs--Raja Ampat MCEs are exceptionally diverse, with 152 fish species recorded at depths greater than 40 m. We found that fish community structures were highly depth driven, with declines in fish abundance at increased depth. In contrast to previous studies elsewhere in the world, we found that the proportion of planktivores declined across the shallow reef to MCE depth gradient. While greater human population density correlated with lower Epinephelidae and Lutjanidae abundance (two key fisheries families), we did not find evidence that MCEs provide a depth refuge from fishing. Surprisingly, we also found that fish abundance declined at greater distances from the major regional market - likely caused by historical fisheries pressure in more remote areas. These results both expand upon and contrast some previously established MCE-depth patterns and human impact patterns on fish communities, suggesting that regional context and historical pressures matters. Our findings highlight the need for future MCE studies within the Coral Triangle region.

ecology↗