Biology subjects

Nagy, V.

Publications and source records attributed to Nagy, V..

4 recordsLinked to original sources

bioRxiv2022

D27-LIKE1 carotenoid isomerase has a preference towards trans/cis and cis/cis conversions in Arabidopsis

Carotenoids are colourful isoprenoids that contribute to a variety of physiological processes in plants. They also function as biosynthesis precursors of abscisic acid (ABA) and strigolactones (SLs). SL biosynthesis starts with the enzymatic conversion of all-trans-{beta}-carotene to 9-cis-{beta}-carotene by the DWARF27 (D27) isomerase. In Arabidopsis, D27 has two closely related paralogs, D27-LIKE1 and D27-LIKE2 which were predicted to be {beta}-carotene-isomerases. Here we characterised D27-LIKE1 and identified some key aspects of its function. Arabidopsis d27-like1-1 mutant does not display any SL or karrikin-deficient traits, however, it exhibits a substantially higher 9-cis-violaxanthin content. In vitro feeding assays with recombinant D27-LIKE1 revealed that the protein exhibits affinity to all {beta}-carotene isoforms but with an exclusive preference towards trans/cis conversions and the interconversion between 9-cis, 13-cis and 15-cis-{beta}-carotene forms. Feeding experiments with zeaxanthin and violaxanthin isomers revealed that D27-LIKE1 accepts these xanthophylls as substrates. The remarkably higher 9-cis-violaxanthin content of the mutant is accompanied by a slightly higher ABA level. Finally, we presented evidence that D27-LIKE1 mRNA is phloem mobile and D27-LIKE1 is an ancient isomerase with long evolutionary history. In summary, we demonstrated that D27-LIKE1 is a carotenoid isomerase with multi-substrate specificity and has a characteristic preference towards the catalysation of cis/cis interconversion of carotenoids. Therefore, D27-LIKE1 is a potential regulator of carotenoid cis pools and eventually, SL and ABA biosynthesis pathways.

plant biology↗

bioRxiv2021

A novel PSII photosynthetic control is activated in anoxic cultures of green algae

Photosynthetic green algae face an ever-changing environment of fluctuating light as well as unstable oxygen levels, which via the production of free radicals constantly challenges the integrity of the photosynthetic complexes. To face such challenges, a complex photosynthetic control network monitors and tightly control the membrane redox potential. Here, we show that not only that the photosynthetic control set the rate limiting step of photosynthetic linear electron flow, but also, upon its ultimate dissipation, it triggers intrinsic alternations in the activity of the photosynthetic complexes. These changes have a grave and prolonged effect on the activity of photosystem II, leading to a massive 3-fold decrease in its electron output. We came into this conclusion via studying a variety of green algae species and applying advance mass-spectrometry and diverse spectroscopic techniques. Our results shed new light on the mechanism of photosynthetic regulation, and provide new target for improving photosynthesis.

plant biology↗

bioRxiv2021

FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder

The brain extracellular matrix (ECM) is enriched in chondroitin sulphate proteoglycans (CSPGs) with variable sulphate modifications that intimately participate in brain maturation and function. Very little is known about how the changing biophysical properties of the CSPGs are signalled to neurons. Here, we report Fibrinogen C Domain Containing 1 (FIBCD1), a known chitin-binding receptor of the innate immune system, to be highly expressed in the hippocampus and to specifically bind CSPGs containing 4-O sulphate modification (CS-4S). Cultured Fibcd1 knockout (KO) neurons lack phenotypic and transcriptomic responses to CSPG stimulation. Further, Fibcd1 KO mice exhibit accumulation of CS-4S, likely resulting in deficits of hippocampal-dependent learning tasks and abrogated synaptic remodelling, a phenotype rescued by enzymatic digestion of CSPGs. Likewise, neuronal specific knockdown of a Fibcd1 orthologue in flies results in neuronal morphological changes at the neuromuscular junctions and behavioural defects. Finally, we report two undiagnosed patients with a complex neurodevelopmental disorder with deleterious variants in FIBCD1, strongly implicating FIBCD1 in the development of the disease. Taken together, our results demonstrate that FIBCD1 is a novel, evolutionarily conserved component of ECM sulphation recognition that is crucial for neuronal development and function.

neuroscience↗

bioRxiv2021

BioProfiling.jl: Profiling biological perturbations with high-content imaging in single cells and heterogeneous populations

MotivationHigh-content imaging screens provide a cost-effective and scalable way to assess cell states across diverse experimental conditions. The analysis of the acquired microscopy images involves assembling and curating morphological measurements of individual cells into morphological profiles suitable for testing biological hypotheses. Despite being a critical step, there is currently no standard approach to morphological profiling and no solution is available for the high-performance Julia programming language. ResultsHere, we introduce BioProfiling.jl, an efficient end-to-end solution for compiling and filtering informative morphological profiles in Julia. The package contains all the necessary data structures to curate morphological measurements and helper functions to transform, normalize and visualize profiles. Robust statistical distances and permutation tests enable quantification of the significance of the observed changes despite the high fraction of outliers inherent to high-content screens. This package also simplifies visual artifact diagnostics, thus streamlining a bottleneck of morphological analyses. We showcase the features of the package by analyzing a chemical imaging screen, in which the morphological profiles prove to be informative about the compounds mechanisms of action and can be conveniently integrated with the network localization of molecular targets. AvailabilityThe Julia package is available on GitHub: https://github.com/menchelab/BioProfiling.jl We also provide Jupyter notebooks reproducing our analyses: https://github.com/menchelab/BioProfilingNotebooks Contactjoerg.menche@univie.ac.at

bioinformatics↗