Biology subjects

LEVASSEUR, A.

Publications and source records attributed to LEVASSEUR, A..

3 recordsLinked to original sources

bioRxiv2023

Identification and characterization of an HtrA sheddase produced by Coxiella burnetii

Having previously shown that soluble E-cadherin (sE-cad) is found in sera of Q fever patients, and that infection of BeWo cells by C. burnetii leads to modulation of the E-cad/{beta}-cat pathway, our purpose was to identify which sheddase(s) might catalyze the cleavage of E-cad. Here, we searched for a direct mechanism of cleavage initiated by the bacterium itself, assuming the possible synthesis of a sheddase encoded in the genome of C. burnetii or an indirect mechanism based on the activation of a human sheddase. Using a straightforward bioinformatics approach to scan the complete genomes of four laboratory strains of C. burnetii, we demonstrate that C. burnetii encodes a 451 amino acid sheddase (CbHtrA) belonging to the HtrA family and differently expressed according to the bacterial virulence. An artificial CbHtrA gene (CoxbHtrA) was expressed and the CoxbHtrA recombinant protein was found to have sheddase activity. We also found evidence that the C. burnetii infection triggers an over-induction of the human HuHtrA gene expression. Finally, we demonstrate that cleavage of E-cad by CoxbHtrA on THP-1-cells leads to an M2 polarization of the target cells and the induction of their secretion of IL-10, which disarms the target cells and improves C. burnetii replication. Taken together these results demonstrate that the genome of C. burnetii encodes a functional HtrA sheddase and establish a link between the HtrA sheddase-induced cleavage of E-cad, the M2 polarization of the target cells and their secretion of IL-10, and the intracellular replication of C. burnetii.

microbiology↗

bioRxiv2022

Detection of horizontal sequence transfer in microorganisms in the genomic era

Sequence transfer and genome remodeling are very frequent events in microorganisms, especially prokaryotes. This is due to the mosaic structure of the genomes, which calls into question the correct classification of genomes in terms of a single gene or a group of genes. We started here, as a first step, the inventory of bioinformatics tools applied to the detection of horizontal sequence transfers in microorganisms in the genomic era by applying bibliometric survey. Our bibliographic analysis allowed us to identify 17 main tools for the detection of chimeras. The first Bellerophon developed in 2004, followed by CCode and Pintail in 2005; Mallard in 2006; Mothur in 2009; Blackbox Chimera in 2010; Perseus, ChimeraSlayer, UCHIME 1 and UCHIME2, and ChimeraScan in 2011; Decipher in 2012; EBARDenovo and FunFrame in 2013; CATCh in 2015; Uchime 2 in 2016 and ChimeraMiner in April 2019. We then described each of these tools, highlighting their operating principles as well as the advantages and limitations of each (specificities, sensitivity, rapidity and frequent updates). The number of articles citing these tools has increased over the years especially for Mothur, Uchime, VSEARCH and ChimeraSlayer, thus demonstrating the interest of researchers in these tools and the need to decipher chimeras in genomic era.

bioinformatics↗

bioRxiv2020

Tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: Is it still a virus?

Since the discovery of Acanthamoeba polyphaga Mimivirus, the first giant virus of amoeba, the historical hallmarks defining a virus have been challenged. Giant virion sizes can reach up to 2.3 {micro}m, making them visible by optical microscopy. They have large genomes of up to 2.5 Mb that encode proteins involved in the translation apparatus. Herein, we investigated possible energy production in Pandoravirus massiliensis, the largest of our giant virus collection. MitoTracker and TMRM mitochondrial membrane markers allowed for the detection of a membrane potential in virions that could be abolished by the use of the depolarizing agent CCCP. An attempt to identify enzymes involved in energy metabolism revealed that 8 predicted proteins of P. massiliensis exhibited low sequence identities with defined proteins involved in the universal tricarboxylic acid cycle (acetyl Co-A synthase; citrate synthase; aconitase; isocitrate dehydrogenase; -ketoglutarate decarboxylase; succinate dehydrogenase; fumarase). All 8 viral predicted ORFs were transcribed together during viral replication, mainly at the end of the replication cycle. Two of these proteins were detected in mature viral particles by proteomics. The product of the ORF132, a predicted protein of P. massiliensis, cloned and expressed in Escherichia coli, provided a functional isocitrate dehydrogenase, a key enzyme of the tricarboxylic acid cycle, which converts isocitrate to -ketoglutarate. We observed that membrane potential was enhanced by low concentrations of Acetyl-CoA, a regulator of the tricarboxylic acid cycle. Our findings show for the first time that energy production can occur in viruses, namely, pandoraviruses, and the involved enzymes are related to tricarboxylic acid cycle enzymes. The presence of a proton gradient in P. massiliensis coupled with the observation of genes of the tricarboxylic acid cycle make this virus a form a life for which it is legitimate to question what is a virus?.

microbiology↗