Biology subjects

Lukacs, A.

Publications and source records attributed to Lukacs, A..

9 recordsLinked to original sources

bioRxiv2026

Hybrid Drosophila cell lines show selective genome instabilities

Background: Post-zygotic reproductive isolation is thought to be caused by genomic conflict. However, the exact nature of these detrimental incompatibilities is largely unknown. To identify genomic regions that became incompatible during the formation of species and are therefore prone to get lost in hybrids, we established hybrid cell lines derived from an authentic interspecies cross between Drosophila melanogaster and Drosophila simulans. Results: All four independently derived lines selectively lost the D. melanogaster allele of the hybrid incompatibility gene Hmr, confirming its incompatibility with cellular viability. Moreover, each line underwent distinct but directionally biased erosion of additional D. melanogaster chromosomal regions, preferentially affecting the X chromosome, chromosome 4, and chromosome 3R. Loss of the D. melanogaster X was dosage compensated by upregulation of genes on the hemizygous D. simulans X, while D. melanogaster rDNA was paradoxically amplified across all lines. Nucleolar dominance was driven by relative rDNA copy number rather than species identity, overturning the prevailing view of fixed species-based dominance. Finally, the measurements of the species-specific proteome revealed species specific differences in the RNA to protein coefficient K_p as novel and yet undescribed sources of molecular conflict in hybrids. Conclusions: These findings reveal a hierarchical, constraint-driven mechanism of hybrid genome resolution.

evolutionary biology↗

bioRxiv2024

Crystal structure of a bacterial photoactivated adenylate cyclase determined at room temperature by serial femtosecond crystallography

OaPAC is a recently discovered blue-light using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report the crystal structures of the enzyme in the absence of its natural substrate determined from room temperature serial crystallography data collected at both an X-ray free electron laser and a synchrotron and we compare them with the cryo macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6 mutation in the blue-light using flavin adenosine dinucleotide domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side-chain of the critical Q48 residue. These studies pave the way for ps - ms time-resolved serial crystallography experiments at X-ray free electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well-studied ps - ms spectroscopic intermediates. SynopsisStructures of the dark-adapted state of a photoactivated adenylate cyclase are determined from serial crystallography (SX) data collected at room temperature at an X-ray free electron laser (XFEL) and a synchrotron and are compared with cryo macromolecular crystallography (MX) synchrotron structures obtained by us and others. These structures of the wild-type enzyme in combination with the cryo MX synchrotron structure of a light-sensor domain mutant provide insight into the hydrogen bond network rearrangement upon blue-light illumination and pave the way for the determination of structural intermediates of the enzyme by time-resolved SX.

biophysics↗

bioRxiv2022

A possible way to relate the effects of SARS-CoV-2 induced changes in transferrin to severe COVID-19 associated diseases

The potentially life-threatening Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is responsible for the coronavirus pandemic in 2019 (COVID-19). The transferrin as an essential component of iron-metabolism was suggested to be a link between iron transport associated diseases and COVID-19 infection. The effect of SARS-CoV-2 on human whole blood was studied by differential scanning calorimetry. The analysis and deconvolution of the thermal transition curves showed that the Tm of transferrin related second peak decreased by 5.16 {degrees}C (6.4%) in the presence of SARS-CoV-2 virus. The ratio of the under-curve area of the two main peaks was greatly affected while the total enthalpy of the heat denaturation was nearly unchanged in the presence of the virus. Based on the results it is possible to conclude that SARS-CoV-2 through binding to transferrin can influence its Fe3+ uptake by inducing thermodynamic changes. Transferrin may stay in iron-free apo-conformational state, which probably depends on the SARS-CoV-2 concentration. SARS-CoV-2 might induce disturbance in the erythropoiesis due to the free iron overload generated iron toxicity. As a late consequence iron toxicity related hepatocellular carcinoma can even develop. Our work can support the basic role of transferrin in COVID-19 related severe diseases.

biophysics↗

bioRxiv2022

Uncertainties of cell number estimation in cyanobacterial colonies and the potential use of sphere packing

Cyanobacteria are notorious bloom formers causing various water quality concerns, such as toxin production, extreme diurnal variation of oxygen, or pH, etc., therefore, their monitoring is essential to protect the ecological status of aquatic systems. Cyanobacterial cell counts and biovolumes are currently being used in water management and water quality alert systems. In this study, we investigated the accuracy of colonial biovolume and cell count estimation approaches used in the everyday practice. Using real like 3-dimensional images of cyanobacterial colonies, we demonstrated that their shape cannot be approximated by ellipsoids. We also showed that despite the significant relationship between overall colony volume and cell biovolumes because of the considerable scatter of cell count data the regressions give biased estimates for cyanobacterial cell counts. We proposed a novel approach to estimate cell counts in colonies that was based on the random close sphere packing method. This method provided good results only in those cases when overall colony volumes could be accurately measured. The visual investigation of colonies done by skilled experts has given precise but lower estimates for cell counts. Estimation results of several experts were surprisingly good which suggest that this capability can be improved, and estimation bias can be reduced to the level acceptable for water quality estimations. HighlightsCyanobacterial colony - cell biovolume relationships provide biased estimates for cellbiovolumes. Sphere packing approach provides good cellcount estimates if colony volumes are accurately measured. Considering cyanobacterial colonies as ellipsoids gives inaccurate volume estimates. Skilled experts slightly underestimate the cellcounts but dispersion of their estimates is low.

ecology↗

bioRxiv2021

The Integrity of the Speciation Core Complex is necessary for centromeric binding and reproductive isolation in Drosophila

Postzygotic isolation by genomic conflict is a major cause for the formation of species. Despite its importance, the molecular mechanisms that result in the lethality of interspecies hybrids are still largely unclear. The genus Drosophila, which contains over 1600 different species, is one of the best characterized model systems to study these questions. We showed in the past that the expression levels of the two hybrid incompatibility factors Hmr and Lhr diverged in the two closely related Drosophila species, D. melanogaster and D. simulans, resulting in an increased level of both proteins in interspecies hybrids. This overexpression leads to mitotic defects, a misregulation in the expression of transposable elements and a decreased fertility. In this work, we describe a distinct six subunit Speciation Core Complex (SCC) containing HMR and LHR and analyse the effect of Hmr mutations on complex function and integrity. Our experiments suggest that HMR acts as a bridging factor between centromeric chromatin and pericentromeric heterochromatin, which is required for both its physiological function and its ability to cause hybrid male lethality.

biochemistry↗

bioRxiv2020

Does rhythmic priming improve grammatical processing in Hungarian-speaking children with and without Developmental Language Disorder?

Research has described several features shared between musical rhythm and speech or language, and experimental studies consistently show associations between performance on tasks in the two domains as well as impaired rhythm processing in children with language disorders. Motivated by these results, in the current study our first aim was to explore whether the activation of the shared system underlying rhythm and language processing with a regular musical rhythm can improve subsequent grammatical processing in preschool-aged Hungarianspeaking children with and without Developmental Language Disorder (DLD). Second, we investigated whether rhythmic priming is specific to grammar processing by assessing priming in two additional domains: a linguistic but non-grammatical task (picture naming) and a non-linguistic task (nonverbal Stroop task). Third, to confirm that the rhythmic priming effect originates from the facilitating effect of the regular rhythm and not the negative effect of the control condition, we added a third condition, silence, for all the three tasks. Both groups of children showed better performance on the grammaticality judgment task in the regular compared to both the irregular and the silent conditions but no such effect appeared in the non-grammatical and non-linguistic tasks. These results suggest that 1) rhythmic priming can improve grammatical processing in Hungarian, a language with complex morphosyntax, both in children with and without DLD, 2) the effect is specific to grammar and 3) is a result of the facilitating effect of the regular rhythm.Research Highlights6-year-old Hungarian-speaking children with and without Developmental Language Disorder perform better on a grammatical task subsequent to exposure to a regular rhythm vs. an irregular rhythm/silenceThe effect of regular rhythm is specific: it improves performance on a grammatical task but not on a word retrieval or a non-linguistic taskDifference between performance following regular vs. irregular rhythm originates from the facilitating effect of the regular rhythm (not the negative effect of the irregular rhythm)The results highlight the importance of rhythm in speech processing, and point towards a possible intervention tool in language disordersCompeting Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗

bioRxiv2020

Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix

Light-activated protein domains provide a convenient, modular, and genetically encodable sensor for optogenetics and optobiology. Although these domains have now been deployed in numerous systems, the precise mechanism of photoactivation and the accompanying structural dynamics that modulate output domain activity remain to be fully elucidated. In the C-terminal light, oxygen, voltage (LOV) domain of plant phototropins (LOV2), blue light activation leads to formation of an adduct between a conserved Cys residue and the embedded FMN chromophore, rotation of a conserved Gln (Q513), and unfolding of a helix (J-helix) which is coupled to the output partner. In the present work, we focus on the allosteric pathways leading to J helix unfolding in Avena sativa LOV2 (AsLOV2) using an interdisciplinary approach involving molecular dynamics simulations extending to 7 s, time-resolved infrared spectroscopy, solution NMR spectroscopy, and in-cell optogenetic experiments. In the dark state, the side chain of N414 is hydrogen bonded to the backbone N-H of Q513. The simulations predict a lever-like motion of Q513 after Cys adduct formation resulting in loss of the interaction between the side chain of N414 and the backbone C=O of Q513, and formation of a transient hydrogen bond between the Q513 and N414 side chains. The central role of N414 in signal transduction was evaluated by site-directed mutagenesis supporting a direct link between J helix unfolding dynamics and the cellular function of the Zdk2-AsLOV2 optogenetic construct. Through this multifaceted approach, we show that Q513 and N414 are critical mediators of protein structural dynamics, linking the ultrafast (sub-ps) excitation of the FMN chromophore to the microsecond conformational changes that result in photoreceptor activation and biological function.

biophysics↗

bioRxiv2018

Intricate structure of the interphase chromocenter revealed by the analysis of a factor involved in species formation

In higher eukaryotes centromeres often coalesce into a large intranuclear domain called the chromocenter. Chromocenters are important for the organization of pericentric heterochromatin and a disturbance of their formation results in an upregulation of repetitive elements and causes defects in chromosome segregation. Mutations in the gene encoding for the centromere associated Drosophila speciation factor HMR show very similar phenotypes suggesting a role of HMR in chromocenter architecture and function. We performed confocal and super resolution microscopy as well as proximity based biotinylation experiments of HMR and its associated protein HP1a to generate a molecular map of HMR and HP1a bound chromatin. Our work reveals an intricate internal structure of the centromeric chromatin region, which suggests a role of HMR in separating heterochromatin from centromeric chromatin.

biochemistry↗

bioRxiv2018

Altered chromatin localization of hybrid lethality proteins in Drosophila

Understanding hybrid incompatibilities is a fundamental pursuit in evolutionary genetics. In crosses between Drosophila melanogaster females and Drosophila simulans males, the interaction of at least three genes is necessary for hybrid male lethality: Hmr mel, Lhr sim, and gfzf sim. All three hybrid incompatibility genes are chromatin associated factors. While HMR and LHR physically bind each other and function together in a single complex, the connection between either of these proteins and gfzf remains mysterious. Here, we investigate the allele specific chromatin binding patterns of gfzf. First, our cytological analyses show that there is little difference in protein localization of GFZF between the two species except at telomeric sequences. In particular, GFZF binds the telomeric retrotransposon repeat arrays, and the differential binding of GFZF at telomeres reflects the rapid changes in sequence composition at telomeres between D. melanogaster and D. simulans. Second, we investigate the patterns of GFZF and HMR co-localization and find that the two proteins do not normally co-localize in D. melanogaster. However, in inter-species hybrids, HMR shows extensive mis-localization to GFZF sites, and this altered localization requires the presence of gfzf sim. Third, we find by ChIP-Seq that over-expression of HMR and LHR within species is sufficient to cause HMR to mis-localize to GFZF binding sites, indicating that HMR has a natural low affinity for GFZF sites. Together, these studies provide the first insights into the different properties of gfzf between D. melanogaster and D. simulans as well as a molecular interaction between gfzf and Hmr in the form of altered protein localization.

molecular biology↗