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Saraiva, J.

Publications and source records attributed to Saraiva, J..

2 recordsLinked to original sources

The small GTPase Rab5 inhibits actin polymerization mediated by the Legionella pneumophila effector VipA

Legionella pneumophila is a facultative intracellular Gram-negative bacterium that causes Legionnaires disease, one of the most severe manifestations of atypical pneumonia. L. pneumophila naturally thrives within protozoan hosts in aquatic environments, which serve as reservoirs for bacterial replication and transmission. Inhalation of contaminated aerosols delivers L. pneumophila to the lungs where it is able to infect human alveolar macrophages and multiply intracellularly inside a membrane-bound compartment, the Legionella-containing vacuole (LCV). The main virulence factor of the bacteria is the Icm/Dot type IVb secretion system, responsible for the translocation of over 300 bacterial effector proteins into host cells. These effectors allow the remodelation of the LCV into a replication-competent compartment that seggregates from the phagolysosomal pathway. After being translocated into host cells, L. pneumophila effector VipA associates with early endosomes and F-actin. VipA increases the polymerization of actin filaments in vitro by promoting the nucleation step without the requirement of additional partners, and impairs vesicle trafficking in Saccharomyces cerevisiae. In this work, we sought the interacting partners of VipA in early endosomes and explored the effects of this association. We found that VipA interacts directly to two key components of these organelles, the membrane lipid PI3P and the small GTPase Rab5. Binding to Rab5 requires the N-terminal region of VipA but not the C-terminal/actin-binding region. Furthermore, binding to Rab5 inhibits VipA-mediated actin polymerization by preventing de novo actin filament formation. These findings offer new insights into VipAs mode of action and underscore the intricate interactions between L. pneumophila effectors and their host cell targets, namely the endocytic pathway.

microbiology↗

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery

We hypothesize that sample evenness, sequencing depth and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample evenness, sequencing depth and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results ([~] 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, whilst the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates the scientific community should their findings from MAG recovery, especially when asserting novel species or metabolic traits.

bioinformatics↗