Biology subjects

Loseva, E.

Publications and source records attributed to Loseva, E..

3 recordsLinked to original sources

bioRxiv2024

Phages reconstitute NAD+ to counter bacterial immunity

Bacteria defend against phage infection via a variety of antiphage defense systems. Many defense systems were recently shown to deplete cellular nicotinamide adenine dinucleotide (NAD+) in response to infection, by breaking NAD+ to ADP-ribose (ADPR) and nicotinamide. It was demonstrated that NAD+ depletion during infection deprives the phage from this essential molecule and impedes phage replication. Here we show that a substantial fraction of phages possess enzymatic pathways allowing reconstitution of NAD+ from its degradation products in infected cells. We describe NAD+ reconstitution pathway 1 (NARP1), a two-step pathway in which one enzyme phosphorylates ADPR to generate ADPR-pyrophosphate (ADPR-PP), and the second enzyme conjugates ADPR- PP and nicotinamide to generate NAD+. Phages encoding the NARP1 pathway can overcome a diverse set of defense systems, including Thoeris, DSR1, DSR2, SIR2-HerA, and SEFIR, all of which deplete NAD+ as part of their defensive mechanism. Phylogenetic analyses show that NARP1 is primarily encoded on phage genomes, suggesting a phage- specific function in countering bacterial defenses. A second pathway, NARP2, allows phages to overcome bacterial defenses by building NAD+ via metabolites different than ADPR-PP. Our findings report a unique immune evasion strategy where viruses rebuild molecules depleted by defense systems, thus overcoming host immunity.

microbiology↗

bioRxiv2023

IFT cargo and motors associate sequentially with IFT trains to enter cilia

Intraflagellar transport (IFT) orchestrates entry of proteins into primary cilia. At the ciliary base, assembled IFT trains, driven by kinesin-2 motors, can transport cargo proteins into the cilium, across the crowded transition zone (TZ). How trains assemble at the base and how proteins associate with them is far from understood. Here, we use single-molecule imaging in the cilia of C. elegans chemosensory neurons to directly visualize the entry of kinesin-2 motors kinesin-II and OSM-3, as well as anterograde cargo proteins IFT dynein and tubulin. Single-particle tracking shows that IFT components associate with trains sequentially, both in time and space. Super-resolution maps of IFT components in wild-type and mutant worms reveal ciliary ultrastructure and show that kinesin-II is essential for axonemal organization. Finally, imaging cilia lacking kinesin-II and/or TZ function uncovers the interplay of kinesin-II and OSM-3 in driving efficient transport of IFT trains across the TZ.

biophysics↗

bioRxiv2022

A small excitation window allows long-duration imaging of OCR-2-associated vesicles in C. elegans sensory neurons

Single-particle imaging using laser-illuminated widefield epi-fluorescence microscopy is a powerful tool to investigate molecular processes in vivo. Performing high-quality single-molecule imaging in such biological systems, however, remains a challenge due to difficulties in controlling the number of fluorescing molecules, photobleaching, and the autofluorescence background. Here, we show that by exciting only a small, 5-15 {micro}m wide region in chemosensory neurons in live C. elegans, we can significantly improve the duration and quality of single-molecule imaging. Small-window illumination microscopy (SWIM) allows long-duration single-particle imaging since fluorescently labelled proteins are only excited upon entering the small excited area, limiting their photobleaching. Remarkably, we also find that using a small excitation window significantly improves the signal-to-background ratio of individual particles. With the help of theoretical calculations, we explain that the improved signal-to-background ratio is due to reduced background, mostly caused by out-of-focus autofluorescence. We demonstrate the potential of this approach by studying the dendritic transport of a ciliary calcium channel protein, OCR-2, in the chemosensory neurons of C. elegans. We reveal that OCR-2-associated vesicles are continuously transported back and forth along the length of the dendrite and can switch between directed and diffusive states. Furthermore, we perform single-particle tracking of OCR-2-associated vesicles to quantitatively characterize the transport dynamics. SWIM can be readily applied to other in vivo systems where intracellular transport or cytoskeletal dynamics occur in elongated protrusions, such as axons, dendrites, cilia, microvilli and extensions of fibroblasts.

biophysics↗