Biology subjects

Burger, G.

Publications and source records attributed to Burger, G..

3 recordsLinked to original sources

bioRxiv2026

A microeukaryotic PPR-DYW protein supports multisite C- and A-deamination RNA editing

RNA editing in mitochondria is vital for many eukaryotes. In plants, mitochondrial C-to-U deamination editing is catalyzed by tens to hundreds of PPR-DYW proteins, each typically dedicated to a specific site. Where retained, PPR-DYW family expanded independently in all eukaryotic groups examined here -- except in marine microeukaryotes diplonemids, which encode a single homolog despite deaminating their mitochondrial RNA at more than 100 sites. Here we characterize this unconventional deaminase, PPRD1, from Diplonema papillatum. Native affinity pulldown of the protein identified 20 predominantly sub-stoichiometric partners, including potential RNA-binding helical-repeat proteins. Among them, the divergent PolX-like protein DAPX1 consistently and reciprocally co-purified with PPRD1 in near-equal proportions. Structural modelling suggests that DAPX1 may stabilize the deaminase catalytic domain and expand its interaction interface. Silencing either PPRD1 or DAPX1 inhibited cell growth and reduced in vivo not only C-to-U, but also A-to-I deamination across five mitochondrial RNA-editing clusters encompassing 110 sites. Together, these results support a model of PPRD1 and DAPX1 forming the core of the Diplonema deamination-editing machinery, with sub-stoichiometric partners acting as specificity factors that guide accurate RNA editing with minimal off-target effects.

molecular biology↗

bioRxiv2025

Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes

Here, we introduce a new annotation pipeline, called Eukan, designed to deliver reliably high-quality results across a broad range of eukaryotes. First, experimental evidence is automatically leveraged to refine predictions, specifically, RNA-Seq coverage to inform gHMM gene prediction, and intron lengths to inform protein sequence alignments. Second, a consensus is created from an empirically optimized weighting of gene models from multiple sources. Third, Eukan runs a post-annotation routine to recover gene models missing from the consensus that otherwise have strong transcript support and appear to be protein-coding. We compare the results of Eukan with those of three popular freely-available pipelines (Maker, Braker, Gemoma) on 17 phylogenetically diverse haploid and diploid nuclear genomes. In addition to the commonly reported annotation accuracy statistics, we define a novel classification system of critical defects commonly observed in automated annotations. Furthermore, we developed a statistical model that demonstrates each of the tested pipelines correctly identified the majority of the validated "Gold Standard" gene models across the test set, but each pipeline uniquely generates a non-negligible portion of either fragmented, artificially fused, or missing gene models. Despite that, we demonstrate that Eukan performs consistently well where other pipelines encounter challenges, such as for compact protist genomes. ContactMatt Sarrasin; matt.sarrasin@umontreal.ca

bioinformatics↗

bioRxiv2018

An updated phylogeny of the Alphaproteobacteria reveals that the Rickettsiales and Holosporales have independent origins

The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. Furthermore, we find that the Rhodospirillales might be paraphyletic and that the Geminicoccaceae could be sister to all ancestrally free-living alphaproteobacteria. Our robust phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.

evolutionary biology↗