Biology subjects

Deschamps, P.

Publications and source records attributed to Deschamps, P..

8 recordsLinked to original sources

bioRxiv2026

Characterization of starch metabolism pathways in dinoflagellates, chromerids and apicomplexans highlights the presence of a starch accumulating symbiont in their common ancestor

Unlike most other heterotrophic protist lineages which synthesize glycogen, alveolates accumulate -glucan storage polysaccharides in the form of starch. Within Alveolata, ciliates do so by using a simple pathway analogous to that used for glycogen metabolism in eukaryotes. However, Myzozoa have evolved five additional enzymatic steps which are common to Dinoflagellata, Chromerids and Apicomplexa. Moreover, dinoflagellates have acquired seven additional enzymes that distinguish them from the Chromerids-Apicompexa lineages, while chromerids possess only a single enzyme not found in dinoflagellates. Such modifications are not found in other eukaryotic lineages save for those resulting directly from primary or secondary plastid endosymbiosis. The many differences affecting the starch pathway of Myzozoa can be explained by a single secondary or tertiary plastid endosymbiosis of a starch-containing alga followed by distinct compartmentalisation outcomes of starch metabolism in Dinoflagellata relative to chromerids and Apicomplexa.

evolutionary biology↗

bioRxiv2026

Redox distribution of Asgard archaea and co-occurring taxa in microbial mats from an early Proterozoic ecosystem analog

Increasing evidence supports that eukaryotes originated from the symbiosis of an Asgard archaeon, the alphaproteobacterial ancestor of mitochondria, and possibly additional bacterial contributions. Eukaryogenesis likely occurred in redox-transition environments such as microbial mats or shallow sediments [~]2 billion years ago, when atmospheric oxygen was far lower than today, and oceans were euxinic. We investigated Asgardarchaeota-enriched microbial mats from the low-oxygen, sulfidic Catherine volcano lake (Afar region, Ethiopia), mimicking early Proterozoic conditions. 16S rRNA gene metabarcoding, metagenomics, and metagenome-assembled genome (MAG) analyses across redox-stratified layers of in situ and mesocosm-maintained mats revealed that Asgardarchaeota thrived in the sulfate-reduction zone, mainly co-occurring with Desulfurobacterota and Myxococcota, among others. Lokiarchaeia and Thorarchaeia were more abundant in deeper, anoxic layers. Within Heimdallarchaeia, Heimdallarchaeales were enriched in upper layers, correlating with oxygen-tolerant hydrogenase and sulfate-reduction genes, whereas Hodarchaeales were more relatively abundant in anoxic layers, correlating with methanogenesis. Although reactive-oxygen-species defense mechanisms were widespread in Asgardarchaeota MAGs, they lacked genes for aerobic respiration. These results support the hypothesis that Asgard archaea engaged primarily in syntrophic interactions with sulfate-reducers under conditions prevailing on the early Earth at the onset of eukaryogenesis.

microbiology↗

bioRxiv2025

Molecular phylogeny of the SELMA translocation machinery recounts the evolution of complex photosynthetic eukaryotes.

Photosynthetic eukaryotes and their relatives are the result of an intricate evolutionary history involving a series of plastid acquisitions through endosymbiosis, multiple reversions to heterotrophy, and sometimes total plastid losses. Among these events, one of the most debated is the emergence and diversification of the CASH lineages (Cryptophyta, Alveolata, Stramenopiles and Haptophyta). Although they all include species bearing a complex plastid that derived from the endosymbiosis of a red alga, their phylogenetic relationships remain controversial, and the timing and number of plastid acquisitions are still undetermined. The inner metabolism of all plastids is mostly supported by nuclear-encoded proteins, and consequently, mechanisms allowing the relocation of those proteins have evolved or were recycled at each endosymbiotic event. Thus, the study of the composition and origins of those translocation machineries provides important clues for understanding how photosynthetic lineages have emerged and might be related. In CASH species, the SELMA complex, composed of about 20 proteins, is dedicated to the transport of pre-proteins across the periplastidial membrane, the second outermost membrane of secondary red plastids. In this work, we present the comprehensive genomic survey and phylogenetic analysis of the proteins composing the SELMA complex. We confirm the presence, homology and monophyletic origin of SELMA in the four CASH lineages and use these observations to infer a scenario for the serial transmission of secondary red plastids that differs from previous hypotheses and alters how the evolution of photosynthetic eukaryotes is envisioned.

evolutionary biology↗

bioRxiv2024

Starch granule initiation doesnt require a starch synthase 4 isoform in Chlamydomonas reinhardtii.

The initiation of starch granule synthesis remains a relatively poorly understood phenomenon. Recent advances enabled the establishment of a model explaining the synthesis of new starch granules in Arabidopsis thaliana. These characterizations revealed the involvement of both a specific starch synthase isoform (SS4) and of several non-enzymatic proteins in this process. In this work, we investigated whether the initiation of starch synthesis in the green microalga Chlamydomonas reinhardtii involves the same machinery as those uncovered in the plant model. Our extensive phylogenetic analysis revealed that most of the key players that were identified in higher plants are not found in microalgae suggesting that a different pathway is taking place. We showed that restoration of ADP-glucose synthesis in a mutant strain devoid of any endogenous primers allowed normal starch synthesis, revealing the existence of an initiation mechanism in Chlamydomonas. Our biochemical characterizations revealed that starch synthase isoform 3 possesses the intrinsic capacity to initiate polysaccharide synthesis in vitro and could be one of the functions involved in starch initiation. Our work suggests that the initiation of starch synthesis in Chlamydomonas involves a different pathway to that described in Arabidopsis and that further efforts will be required to identify the proteins involved in this process.

biochemistry↗

bioRxiv2024

CXCL8 secreted by immature granulocytes inhibits wildtype hematopoiesis in chronic myelomonocytic leukemia

Chronic myelomonocytic leukemia (CMML) is a severe myeloid malignancy with limited therapeutic options. Single-cell analysis of clonal architecture demonstrated early clonal dominance with few residual wildtype hematopoietic stem cells. Circulating myeloid cells of the leukemic clone and the cytokines they produce generate a deleterious inflammatory climate. Our hypothesis is that therapeutic control of the inflammatory component in CMML could contribute to stepping down disease progression. The present study explores the contribution of immature granulocytes (iGRANs) to CMML progression. iGRANs can be detected and quantified in the peripheral blood of patients by spectral and conventional flow cytometry. Their accumulation is a potent and independent poor prognostic factor. These cells belong to the leukemic clone and behave as myeloid-derived suppressor cells. Bulk and single cell RNA sequencing revealed a pro-inflammatory status of iGRAN that secrete multiple cytokines of which CXCL8 at the highest level. This cytokine inhibits the proliferation of wildtype but not CMML hematopoietic stem and progenitor cells (HSPCs) in which CXCL8 receptors are epigenetically downregulated. CXCL8 receptor inhibitors and CXCL8 blockade restore wildtype HSPC proliferation, suggesting that relieving CXCL8 selective pressure on wildtype HSPCs is a potential strategy to slow CMML progression and restore some healthy hematopoiesis.

cancer biology↗

bioRxiv2024

Culture- and genome-based characterization of a tripartite interaction between patescibacterial epibionts, methylotrophic proteobacteria, and a jumbo phage in freshwater ecosystems

Patescibacteria form a very diverse and widely distributed phylum of small bacteria inferred to have an episymbiotic lifestyle. However, the prevalence of this lifestyle within the phylum and their host specificity remain poorly known due to the scarcity of cultured representatives. Here, we describe a complex system consisting of a patescibacterium, its gammaproteobacterial hosts, and their respective phages based on enrichment cultures and metagenomic data from two shallow, geographically close, freshwater ecosystems. The patescibacterium, Strigamonas methylophilicida sp. nov., defines a new genus within the family Absconditicoccaceae. It grows as epibiont on cells of methanotrophic species of the gammaproteobacterial family Methylophilaceae. Strigamonas cells grow tightly attached to the host, sometimes forming stacks that connect two host cells. Despite a surprisingly large genome (1.9 Mb) compared to many other Patescibacteria, S. methylophilicida lacks many essential biosynthetic pathways, including the complete biosynthesis of phospholipids, amino acids, and nucleic acids, implying a dependence on the host to obtain these molecules. We also identified and assembled the complete genomes of one patescibacterial phage that might represent a new virus family within the class Caudoviricetes, and two Methylophilaceae phages predicted to have head-tailed and filamentous virions, respectively. The patesciphage uses a modified genetic code similar to that of its host and encodes four tRNA genes, including the suppressor tRNA gene for the UGA stop codon, which is reassigned to glycine in many Patescibacteria. Our results confirm a prevalent episymbiotic lifestyle in Absconditicoccaceae and further suggest a clade-specific adaptation of this patescibacterial family for gammaproteobacterial hosts. IMPORTANCEPatescibacteria are ultra-small bacteria with reduced genomes that rely on symbiotic interactions with other prokaryotes, yet their host specificity and associated viral parasites remain poorly characterized due to limited cultured representatives. Here, we describe Strigamonas methylophilicida, a new patescibacterial species of the family Absconditicoccaceae that grows as an epibiont on various methylotrophic Gammaproteobacteria. This expands the host range for this family beyond previously documented photosynthetic partners. Using enrichment cultures and metagenomics, we retrieved complete genomes of novel phages infecting S. methylophilicida and its hosts, including one phage that uses a modified genetic code matching that of the patescibacterium. These findings reveal a previously unrecognized patescibacteria- methylotroph-phage tripartite interaction in freshwater environments, highlight the adaptations of patescibacterial phages, and shed light on the complex ecology and evolution of host-parasite-phage dynamics in understudied bacterial lineages.

microbiology↗

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↗

bioRxiv2021

Viral and parasitic cell ratios per free-living microbe across ecosystems

It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 {micro}m size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by [~]13 fold and in plankton from marine and saline waters by [~]2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.

microbiology↗