Biology subjects

Marek, M.

Publications and source records attributed to Marek, M..

26 records · Page 2Linked to original sources

bioRxiv2024

The majority of somatic mutations in fruit trees are layer-specific

BackgroundAll plant tissues and organs develop from meristems. Plant meristems are structured organs consisting of distinct layers of stem cells. Somatic mutations occurring in one of these layers can propagate into large sectors of the plant. However, the frequency and characteristics of meristematic mutations that form the basis of somaclonal phenotypic variation remain unclear. ResultsHere, we analysed the frequency and distribution of somatic mutations in an individual Apricot tree. For this, we sequenced the genomes of fruit samples corresponding to distinct meristematic cell layers selected across the entire tree. Most somatic mutations (>90%) were specific to individual layers. Genotyping the somatic mutations in leaves sampled next to the fruits confirmed their meristematic origin. Interestingly, layer 1 (epidermis) had a higher mutation load than layer 2 (mesocarp), implying differential mutational dynamics between the layers. The somatic mutations followed the branching pattern of the tree. These factors led to the unexpected observation that the layer 1 samples from different branches were more similar to each other than to layer 2 samples of the same branch. Further, using single-cell RNA sequencing, we demonstrated that the layer-specific mutant alleles could only be found in the transcripts of the respective, layer-specific cell clusters and could form the basis for somaclonal phenotypic variation. ConclusionsHere, we analyzed the prevalence and distribution of somatic mutations with meristematic origin. Our insights into the yet unexplored layer-specificity of such somatic mutations outlined how they can be identified and how they impact the breeding of clonally propagated crops.

genomics↗

bioRxiv2023

Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning

Centromeres strongly affect (epi)genomic architecture and meiotic recombination dynamics influencing the overall distribution and frequency of crossovers. Here, we studied how recombination is regulated and distributed in the holocentric plant Rhynchospora breviuscula, a species lacking localised centromeres. Combining immunocytochemistry, chromatin analysis and high-throughput single-pollen sequencing, we discovered that crossover frequency is higher at ends related to centred chromosomal regions. Contrasting the diffused distribution of (epi)genetic features and hundreds of repeat-based centromeric units. Remarkably, we found that crossovers were abolished at core centromeric units but not at their vicinity indicating the absence of a centromere effect across repeat-based holocentromeres. We further show that telomere-led pairing and synapsis of homologous chromosomes appear to be the primary force determining the observed U-shaped recombination landscape. While centromere and (epi)genetic properties only affect crossover positioning locally. Our results suggest that the conserved U-shaped crossover distribution of eukaryotes is independent of chromosome compartmentalisation and centromere organisation.

genomics↗

bioRxiv2022

Illuminating the mechanism and allosteric behavior of NanoLuc luciferase

NanoLuc, a superior {beta}-barrel fold luciferase, was engineered 10 years ago but the nature of its catalysis remains puzzling. Here experimental and computational techniques were combined, revealing that imidazopyrazinone luciferins bind to an intra-barrel catalytic site but also to an allosteric site shaped on the enzyme surface. Structurally, binding to the allosteric site prevents simultaneous binding to the catalytic site, and vice versa, through concerted conformational changes. We demonstrate that restructuration of the allosteric site can boost the luminescent reaction in the remote active site. Mechanistically, an intra-barrel arginine coordinates the imidazopyrazinone component of luciferin, which reacts with O2 via a radical charge-transfer mechanism, and then it also protonates the resulting excited amide product to form a light-emitting neutral species. Concomitantly, an aspartate, supported by two tyrosines, fine-tunes the blue color emitter to secure a high emission intensity. This information is critical to engineering the next-generation of ultrasensitive bioluminescent reporters.

biochemistry↗

bioRxiv2022

Domino-like Effect of C112R Mutation on APOE4 Aggregation and Its Suppression by Alzheimer's Disease Drug Candidate

BackgroundApolipoprotein E (ApoE) {varepsilon}4 genotype is the most prevalent risk factor for late-onset Alzheimers Disease (AD). Although ApoE4 differs from its non-pathological ApoE3 isoform only by the C112R mutation, the molecular mechanism of its proteinopathy is unknown. MethodsHere, we reveal the molecular mechanism of ApoE4 aggregation using a combination of experimental and computational techniques, including X-ray crystallography, site-directed mutagenesis, hydrogen-deuterium mass spectrometry (HDX-MS), static light scattering and molecular dynamics simulations. Treatment of ApoE {varepsilon}3/{varepsilon}3 and {varepsilon}4/{varepsilon}4 cerebral organoids with tramiprosate was used to compare the effect of tramiprosate on ApoE4 aggregation at the cellular level. ResultsWe found that C112R substitution in ApoE4 induces long-distance (>15 [A]) conformational changes leading to the formation of a V-shaped dimeric unit that is geometrically different and more aggregation-prone than the ApoE3 structure. AD drug candidate tramiprosate and its metabolite 3-sulfopropanoic acid induce ApoE3-like conformational behavior in ApoE4 and reduce its aggregation propensity. Analysis of ApoE {varepsilon}4/{varepsilon}4 cerebral organoids treated with tramiprosate revealed its effect on cholesteryl esters, the storage products of excess cholesterol. ConclusionsOur results connect the ApoE4 structure with its aggregation propensity, providing a new druggable target for neurodegeneration and ageing.

neuroscience↗

bioRxiv2022

A catalytic mechanism for Renilla-type bioluminescence

The widely used coelenterazine-powered Renilla luciferase was discovered over 40 years ago but the oxidative mechanism by which it generates blue photons remains unclear. Here we decipher Renilla-type bioluminescence through crystallographic, spectroscopic, and computational experiments. Structures of ancestral and extant luciferases complexed with the substrate-like analogue azacoelenterazine or a reaction product were obtained, providing unprecedented snapshots of coelenterazine-to-coelenteramide oxidation. Bound coelenterazine adopts a Y-shaped conformation, enabling the deprotonated imidazopyrazinone component to attack O2 via a radical charge-transfer mechanism. A high emission intensity is secured by an aspartate from a conserved proton-relay system, which protonates the excited coelenteramide product. Another aspartate on the rim of the catalytic pocket fine-tunes the electronic state of coelenteramide and promotes the formation of the blue light-emitting phenolate anion. The results obtained also reveal structural features distinguishing flash-type from glow-type bioluminescence, providing insights that will guide the engineering of next-generation luciferase-luciferin pairs for ultrasensitive optical bioassays.

biochemistry↗

bioRxiv2021

Increased Occurrence of Treponema spp. and Double-species Infections in Patients with Alzheimer's Disease

ObjectiveAlthough the link between microbial infections and Alzheimers disease (AD) has been demonstrated in multiple studies, the involvement of pathogens in the development of AD remains unclear. Therefore, this theory beckons further systematic investigation. In this study, we have examined the association between the 10 most widely discussed viral and bacterial pathogens found in serum and cerebrospinal fluid (CSF) from patients with AD. MethodsWe have used an in-house developed multiplex PCR kit for simultaneous detection of five bacterial and five viral pathogens in serum and CSF from 50 AD patients and 53 healthy controls. Data analysis was performed with multiple statistical methods: Fishers exact test, chisquare goodness of fit test, and one-sample proportion test. ResultsWe observed an increased frequency of AD patients tested positive for Treponema spp. (AD: 62.2%; CTRL: 30.3%; p-value = 0.007). Furthermore, we confirmed a significantly higher prevalence of cases with two and more simultaneous infections in AD patients compared to controls (AD: 24%; CTRL 7.5%; p-value = 0.029). The studied pathogens were widespread equally in serum and CSF. Borrelia burgdorferi, human herpesvirus 7, and human cytomegalovirus were not detected in any of the studied samples. DiscussionAn increased prevalence of Treponema spp. and double-species infections in AD patients compared to the healthy controls provides further evidence of the association between microbial infections and AD. Paralleled analysis of multiple sample specimens provides complementary information and is advisable for future studies.

microbiology↗

bioRxiv2019

A toolbox of Stable Integration Vectors (SIV) in the fission yeast Schizosaccharomyces pombe

Schizosaccharomyces pombe is a widely used model organism that resembles higher eukaryotes in many aspects of cell physiology. Its popularity as an experimental system partially stems from the ease of genetic manipulations, where the innate homology-targeted repair is exploited to precisely edit the genome. While vectors to incorporate exogenous sequences into the chromosomes are available, most are poorly characterized. Here we show that commonly used fission yeast vectors, which upon integration produce repetitive genomic regions, yield unstable genomic loci. We overcome this problem by designing a new series of Stable Integration Vectors (SIV) that target four different prototrophy genes. SIV produce non-repetitive, stable genomic loci and integrate predominantly as single copy. Additionally, we develop a set of complementary auxotrophic alleles that preclude false-positive integration events. We expand the vector series to include antibiotic resistance markers, promoters, fluorescent tags and terminators, and build a highly modular toolbox to introduce heterologous sequences. Finally, as proof of concept, we generate a large set of ready-to-use, fluorescent probes to mark organelles and cellular processes with a wide range of applications in fission yeast research.

cell biology↗

bioRxiv2019

Sterol flow between the plasma membrane and the endosome is regulated by the LAM family protein Ltc1

Sterols are crucial components of biological membranes that help maintain membrane integrity and regulate various processes such as endocytosis, protein oligomerization and signaling. Although synthetized in the ER, sterols are at highest concentrations at the plasma membrane (PM) in all eukaryotic organisms. Here, by applying a genetically encoded sterol biosensor (D4H), we visualize a sterol flow between PM and endosomes in the fission yeast Schizosaccharomyces pombe. While D4H is detected at the PM during steady-state growth, inhibition of Arp2/3-dependent F-actin assembly unexpectedly promotes the reversible re-localization of the probe to internal sterol rich compartments (STRIC), as shown by correlative light-electron microscopy. Time-lapse imaging identifies STRIC as a late secretory, endosomal compartment labelled by the synaptobrevin Syb1. Retrograde sterol internalization to STRIC is independent of endocytosis or an intact Golgi. Instead, it depends on Ltc1, a LAM/StARkin-family protein that localizes to ER-PM contact sites. In ltc1{Delta}, sterols over-accumulate at the PM, which forms extended ER-interacting invaginations, indicating that sterol transfer by Ltc1 contributes to PM size homeostasis. Anterograde sterol movement from STRIC is independent of canonical vesicular trafficking components but requires Arp2/3 activity, suggesting a novel physiological role for this complex. Thus, transfer routes orthogonal to vesicular trafficking govern the retrograde and anterograde flow of sterols in the cell.

cell biology↗