Biology subjects

Bompard, C.

Publications and source records attributed to Bompard, C..

4 recordsLinked to original sources

bioRxiv2025

pylifemap: Mapping Data onto the Tree of Life

O_LIThe need to visualize data associated with NCBI Taxonomy Identifiers is growing in various biological fields ranging from comparative genomics to metagenomics and metabarcoding, and even for outreach. C_LIO_LINo tool today allows visualization of such data while still keeping the full vision of the whole taxonomy, possibly causing a biased view of the data at hand. C_LIO_LIHere we introduce pylifemap, a Python package that allows users to map their own data directly on the interactive taxonomic tree proposed by Lifemap. Through a simple syntax, layers (points, lines, icons, heatmaps, etc.) depicting any type of data are superimposed on the Lifemap basemap, producing an interactive map to inspect biological datasets. The produced visualizations can easily be shared with others through notebooks or standalone HTML files, or exported as static images. C_LIO_LIWe illustrate the utility of pylifemap in the exploration of two contrasting datasets: the IUCN Red List of Threatened Species and the output of a large-scale environmental metagenomics experiment. C_LI Data/Code for peer reviewpylifemap is available at PyPI and easily installable with pip or uv. The development version can be found at https://lifemap-tol.github.io/pylifemap/ along with extensive documentation and examples.

evolutionary biology↗

bioRxiv2024

PII1/MRC interaction with Starch Synthase 4 (SS4) from Arabidopsis thaliana inhibits SS4 enzymatic activity

Starch is the major energy storage compound in plants. It accumulates in the form of insoluble, partly crystalline granules whose number and shape are specific to each plant species. These characteristics are defined very early in starch biosynthesis, at the initiation stage. Starch biosynthesis initiation is a complex process that relies on the coordinated action of several proteins that interact together in the so-called complex of initiation. Starch Synthase 4 (SS4) is the only initiation protein with enzymatic activity. It catalyzes the formation of glucan primers, which serve as substrates for the enzymatic machinery that synthesizes starch granules. Previous studies have highlighted the importance of interactions between SS4 and regulatory proteins in this process. Among them, Protein Involved in Initiation 1 (PII1) interacts with SS4 but its function is not yet established. In this study, we explored the structural and functional implications of PII1 on SS4s enzymatic activity. Our findings reveal that PII1 contains a long coiled-coil domain that specifically interacts with SS4, leading to significant inhibition of SS4s glucan elongation activity. Importantly, this inhibition is specific to SS4 and does not affect other known synthases, suggesting a targeted regulatory mechanism. This work describes the structural specificities of PII1 and SS4 and reveals a function for PII1 in the initiation complex. These results allow us to re-examine these complex mechanisms and propose new hypotheses about the important steps in the initiation of starch biosynthesis.

plant biology↗

bioRxiv2023

Structural basis of the interaction between ESV1 and LESV from Arabidopsis thaliana with starch glucans.

Starch is the major energy storage compound in plants. Whether it is transient or stored, it is accumulated in the form of insoluble, semi-crystalline granules. The structure of these granules is related to the structure of the main component: amylopectin. Amylopectin consists of linear polymers of glucose units linked by -1,4 bonds, forming double helices that combine to form the semi-crystalline lamellae of the granules, and -1,6 branching points that form the amorphous lamellae. This particular structure of amylopectin is linked to the action of isoamylases, which cut the excess of branching points and allow the granules to be structured. For a long time, it was thought that the action of these enzymes was responsible for the structuring of starch granules. Recently, two new proteins, LESV and ESV1, have been characterized and are involved in the phase transition of amylopectin (LESV) or in the maintenance of the granule structure (ESV1). These proteins share a tryptophan-rich domain folded into an antiparallel {beta}-sheet that is particularly well suited to bind amylopectin double helices. In this paper we present the structural study of these interactions using integrative structural biology approaches and show that LESV, in contrast to ESV1 can intervenes during amylopectin biosynthesis.

biophysics↗

bioRxiv2023

BE3 is the major branching enzyme isoform required for amylopectin synthesis in Chlamydomonas reinhardtii

Starch-branching enzymes (BEs) are essential for starch synthesis in both plants and algae where they influence the architecture and physical properties of starch granules. Within Embryophytes, BEs are classified as type 1 and type 2 depending on their substrate preference. In this article, we report the characterization of the three BE isoforms encoded in the genome of the starch producing green algae Chlamydomonas reinhardtii: two type 2 BEs (BE2 and BE3) and a single type 1 BE (BE1). Using single mutant strains, we analyzed the consequences of the lack of each isoform on both transitory and storage starches. The transferred glucan substrate and the chain length specificities of each isoform were also determined. We show that only BE2 and BE3 isoforms are involved in starch synthesis and that, although both isoforms possess similar enzymatic properties, BE3 is critical for both transitory and storage starch metabolism. Finally, we propose putative explanations for the strong phenotype differences evidenced between the C. reinhardtii be2 and be3 mutants, including functional redundancy, enzymatic regulation or alterations in the composition of multimeric enzyme complexes.

plant biology↗