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Biology subjects

Böck, D.

Publications and source records attributed to Böck, D..

3 recordsLinked to original sources

Predicting prime editing efficiency across diverse edit types and chromatin contexts with machine learning

Prime editing is a powerful genome editing technology, but its efficiency varies depending on the pegRNA design and target locus. Existing computational models for predicting prime editing rates are limited by their focus on specific edit types and by omitting the local chromatin environment. In our study, we developed machine learning models that predict prime editing efficiencies across a wide range of edit types up to 15 bp (PRIDICT2.0) and in different chromatin contexts (ePRIDICT). Both models can be accessed at www.pridict.it.

molecular biology↗

The large GTPase Sey1/atlastin mediates lipid droplet- and FadL-dependent intracellular fatty acid metabolism of Legionella pneumophila

The facultative intracellular bacterium Legionella pneumophila employs the Icm/Dot type IV secretion system (T4SS) to replicate in a unique membrane-bound compartment, the Legionella-containing vacuole (LCV). The endoplasmic reticulum (ER)-resident large fusion GTPase Sey1/atlastin promotes remodeling and expansion of LCVs, and the GTPase is also implicated in the formation of ER-derived lipid droplets (LDs). Here we show that LCVs intimately interact with palmitate-induced LDs in Dictyostelium discoideum amoeba. Comparative proteomics of LDs isolated from the D. discoideum parental strain Ax3 or {otimes}sey1 revealed 144 differentially produced proteins, of which 7 or 22 were exclusively detected in LDs isolated from strain Ax3 or {otimes}sey1, respectively. Using dually fluorescence-labeled amoeba producing the LCV marker P4C-GFP or AmtA-GFP and the LD marker mCherry-perilipin, we discovered that Sey1 and the L. pneumophila Icm/Dot T4SS as well as the effector LegG1 promote LCV-LD interactions. In vitro reconstitution of the LCV-LD interactions using purified LCVs and LDs from D. discoideum Ax3 or {otimes}sey1 revealed that Sey1 and GTP promote this process. The LCV-LD interactions were impaired for {otimes}sey1-derived LDs, suggesting that Sey1 regulates LD composition. Palmitate promoted the growth of (i) L. pneumophila wild-type in D. discoideum Ax3 but not in {otimes}sey1 mutant amoeba and (ii) L. pneumophila wild-type but not {otimes}fadL mutant bacteria lacking a homologue of the E. coli fatty acid transporter FadL. Finally, isotopologue profiling indicated that intracellular L. pneumophila metabolizes 13C-palmitate, and its catabolism was reduced in D. discoideum {otimes}sey1 and L. pneumophila {otimes}fadL. Taken together, our results reveal that Sey1 mediates LD- and FadL-dependent fatty acid metabolism of intracellular L. pneumophila.

microbiology↗

The in situ structures of mono-, di-, and tri-nucleosomes in human heterochromatin

The in situ 3-D organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography (cryo-ET) to determine the in situ structures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level.

cell biology↗