Biology subjects

Nagy, G.

Publications and source records attributed to Nagy, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Thylakoid plasticity primes photoprotection in diatoms

For many millions of years, diatoms have been major primary producers in marine ecosystems, supporting food webs and contributing to carbon sequestration through the export of photosynthetically fixed carbon to the deep ocean, mitigating atmospheric carbon dioxide levels and global climate. A key factor in their ecological success is their ability to rapidly adapt to fluctuating light, balancing efficient light harvesting under dim conditions with energy dissipation under excess light. However, the mechanisms behind this regulation have not been fully elucidated. This study shows that several processes contribute to dissipating excess excitation energy in diatoms exposed to light stress: (i) the detachment of the oxygen-evolving complex proteins from the PSII core, leading to energy dissipation via charge recombination, (ii) Non-Photochemical Quenching (NPQ) in the antenna, i.e., thermal dissipation of excited states and (iii) excitation energy transfer from PSII to PSI via energy spillover. The latter process is observed in parallel with high light-induced topological changes of the thylakoids that may favor transient interactions between the photosystems. Along with the accumulation of light-stress-protecting carotenoids on longer time-scales, this ensemble of photoprotective mechanisms provides a dynamic and flexible response to the light challenges expected in coastal marine habitats.

biochemistry↗

bioRxiv2026

Combining CHARMM36m with OPC water improves accuracy

Atomistic simulations of intrinsically disordered proteins (IDPs) are notoriously sensitive to force field inaccuracies, either regarding the protein or the water model, yielding inaccurate observables such as compactness, secondary structure propensities, or kinetics. The currently most widely used IDP force fields are Amber99sb-disp (A99disp) and Charmm36m (C36m). A99disp includes a new water model and thus optimized both, the protein and the water interactions. In contrast, C36m used the Tip3p water model and optimized only protein interactions. In many cases, C36m+Tip3p underestimates radii of gyration compared to FRET or SAXS experiments. Such overly compact structural ensembles are believed to arise from an imbalance between protein-protein, protein-water, and water-water interactions, which might be due to Tip3p inaccuracies. Here, we aim at re-balancing these interactions by combining C36m with the Optimal Point Charge (OPC) water model. Recently, this C36m+OPC combination showed improved accuracy for the disordered domain of the measles virus nucleoprotein. Here we present a systematic assessment, comparing C36m+OPC, C36m+Tip3p, C36m+Tip4p, C22*, A03ws, A99sb-ws, and A99disp for five IDPs, as well as a subset of those for five globular proteins, a set of disordered AGQ-repeat peptides, and the fast folding miniprotein CLN025. We compared extensive MD simulations (> 8.5 ms) with SAXS, NMR, circular dichroism, photo-induced electron transfer (PET), T-jump infrared spectroscopy, and X-ray crystallography measurements. We found that combining C36m with OPC improved accuracy over C36m+Tip3p for IDP ensembles without compromising its accuracy for globular proteins. While also the kinetics of the AGQ-peptides were more accurate for C36m+OPC, those of CLN025 folding were less accurate. Overall, C36m+OPC showed similar accuracy as A99sb-ws and A99disp, the latter is currently considered among the most accurate protein force fields.

biophysics↗

bioRxiv2026

Anthropogenic gradients shape Staphylococcus/Mammaliicoccus communities: Bacterial composition and resistance patterns as indicators of landscape hemeroby

Antimicrobial resistance (AMR) is one of the greatest challenges within the One Health continuum. Exploring transmission routes between health domains and determining their driving forces are key priorities for future research. This effort can be effectively supported by landscape epidemiology, a field of science that integrates methods from landscape ecology and epidemiology to unravel the complex interdependencies behind disease transmission. This exploratory study aimed to demonstrate that landscape diversity and the degree of hemeroby (anthropogenic impact) correlate with the composition of bacterial communities and their AMR profiles. To test this hypothesis, submandibular lymph nodes from Cervidae and Suidae were collected to detect Staphylococcus and Mammaliicoccus bacteria and characterise their AMR features using selective culture and the VITEK 2 Compact automated system. As a result, the bacterial community in the more natural landscape was more diverse, characterised by the dominance of Mammaliicoccus sciuri and pan-susceptible isolates of Staphylococcus hyicus, and it displayed a low-level, heterogeneous AMR profile. Within the more hemerobic landscape, the bacterial community was characterised by the dominance of Staphylococcus epidermidis, a human-adapted species, and the AMR profile showed signs of higher antimicrobial pressure from both public health and veterinary origins. Although this study was based on only two study sites and was therefore not suitable for drawing definite conclusions, the findings suggest that human impact manifests itself in both bacterial and AMR profiles. A high prevalence of mammaliicocci and a heterogeneous AMR profile appeared to be indicators of naturalness. Conversely, the dominance of a human-adapted bacterial species and the accumulation of AMR features characteristic of medical environments likely indicate higher degrees of hemeroby.

ecology↗

bioRxiv2026

Climate change and socioeconomic vulnerability: The Carpathian Basin as a potential hotspot in the dissemination of Dirofilaria repens in Europe

BackgroundDirofilaria repens is a zoonotic parasite expanding unnoticed across Europe due to climate change. We hypothesised that in this process, the Carpathian Basin has a facilitating effect. MethodsUsing 426 georeferenced European cases, the probability of infection occurrence was determined in relation to climatic factors, surface water availability, regional social deprivation, and stray dog population density. To analyse the potential impacts of ecological and social factors (deprivation and stray dog population density), the MaxEnt algorithm, and spatial Empirical Bayes smoothing and Bivariate Local Indicators of Spatial Association (BiLISA) index calculation were employed, respectively. ResultsMaxEnt analysis revealed that the mean warmest month temperature (22.8 - 25.1 {degrees}C), winter mean minimum temperature (> -2.1 {degrees}C), and summer precipitation (28.6 - 231 mm) have the strongest impact on the probability of the parasites occurrence in Europe. Social factors have significance in the eastern Balkans and the Carpathian Basin, but not in Western Europe. The Carpathian Basin appears to be a hotspot, similar to Mediterranean coastal areas. Furthermore, the Danube Valley acts as an ecological corridor for subtropical vector-borne parasites. ConclusionsOur findings confirm that summer warmth is the primary ecological driver of the parasites range expansion, which is facilitated by the Carpathian Basin due to climatic and socioeconomic conditions.

ecology↗

bioRxiv2026

Critical amino acid residues in the N-terminal domain of NADPH-dependent assimilatory sulfite reductase flavoprotein mediate octameric assembly

How large, flexible enzymes assemble into defined oligomeric architectures remains a central question in biology. NADPH-dependent assimilatory sulfite reductase (SiR) forms a heterododecamer built on an octameric flavoprotein (SiRFP) core, yet the molecular basis for this assembly has been unresolved because of its disordered N-terminus. Here, we use ion mobility mass spectrometry, small-angle neutron scattering, and mutagenesis to define the mechanism of SiRFP oligomerization. We show that SiRFP forms a discrete, stable octamer in solution. We also report that its N-terminal 52-residue segment is necessary and sufficient to mediate assembly, also mediating oligomerization when fused to a heterologous protein. Structure-guided mutagenesis identifies four residues (Gln22, Tyr39, Phe40, and Gln47) whose substitution disrupts the octamer, producing concentration-dependent lower-order species while retaining catalytic activity. These findings define the determinants of SiRFP assembly with broader implications for engineering homomeric protein complexes. ImportanceThis work seeks to understand the basis for oligomerization of a large oxidoreductase that is important for metabolizing sulfur, an essential chemical for all of biology. A 52-residue long leader peptide is necessary and sufficient for assembly into a particularly stable octamer that is resistant to chemical denaturation under diverse conditions.

biophysics↗

bioRxiv2026

The effect of ULV-based mosquito control on target and non-target organisms in Hungary: an experimental field study

Ultra-low volume (ULV) insecticide spraying with deltamethrin as the active ingredient is widely used in mosquito control programs, yet its effectiveness against target mosquitoes and its ecological side effects remain poorly quantified under field conditions in Central Europe. Here, we experimentally evaluated the short-term impact of ground ULV spraying on both mosquito populations and non-target flying insects in Hungary using a paired before-after-control-impact (BACI) design. Mosquitoes were sampled with BG Sentinel traps, while non-target insects were collected using malaise traps. ULV treatment resulted in a significant reduction in mosquito abundance at treated sites, with an average decline of approximately 45%. Native and invasive mosquito species, including Aedes albopictus and Aedes koreicus, showed similar proportional decreases. However, treatment effectiveness varied substantially among sites and was influenced by initial mosquito abundance and wind conditions. In parallel, malaise trap samples revealed a marked decline in non-target flying insects, with reductions exceeding 40% across multiple taxonomic groups, particularly among small- and medium-sized insects, and also when considering pollinator taxa together. Our results indicate that while ULV spraying can temporarily reduce mosquito abundance, it also imposes considerable short-term impacts on non-target insect communities, highlighting trade-offs between vector control and insect conservation within mosquito management programs.

ecology↗

bioRxiv2025

Hierarchically ordered multi-timescale structural dynamics of the intrinsically disordered p53 transactivation domain

Intrinsically disordered proteins (IDPs) exhibit pronounced structural dynamics, which is crucial for their functional versatility. Yet their dynamics slower than nanoseconds remain largely elusive. We combined high-power relaxation dispersion nuclear magnetic resonance spectroscopy with molecular dynamics simulations to characterize these kinetics and the underlying structural interconversions of a prototypical IDP, the N-terminal transactivation domain of the tumor suppressor p53 (p53-TAD). We find a complex hierarchy of structural dynamics on timescales covering over seven orders of magnitude, ranging from fast nanoseconds backbone re-orientations, via sub-microsecond helix-formation dynamics involving many structural sub-states and transition times, to transient tertiary structure formation slower than 25 microseconds. These rich structural dynamics of p53-TAD, and likely those of other IDPs, parallel the timescale hierarchy of the conformational dynamics of folded proteins. One-Sentence summaryA hierarchical energy landscape governs kinetics and structural dynamics of the disordered p53 transactivation domain.

biophysics↗

bioRxiv2025

Influence of ULK1 activity on the memory of ATG101 auto-activation dynamics

The initiation of autophagy is marked by the prompt convergence of initiation proteins to form super molecular complexes in spatially-defined autophagic hubs. The recruitment and activation of the ULK-kinase complex is a pivotal event in starting the initiation cascade. ULK complex-component ATG101 is required for initiating autophagy in mammalian cells, but its function is unknown. Its HORMA domain interacts with the HORMA domain of ATG13 and transmembrane protein ATG9A to collectively form the essential autophagy initiation complex ATG9A-ATG13-ATG101. ATG101 has structurally malleable elements, reminiscent of topological conversions used in related metamorphic HORMA domain proteins to control the rate of complex formation. To elucidate the function of ATG101, we monitored the interaction kinetics of ATG101 with ATG13 and ATG9A, and observed that the interaction of ATG101 with ATG9A and ATG13 is exceptionally slow. Dramatic acceleration of complex formation is observed upon a change in the fold of ATG101 induced by its transient homo-dimerization, which in turn is initiated by phosphorylation by the ULK1 kinase. In an auto-catalytic mechanism, ATG101 dimers create a positive feedback to propagate activation to further ATG101 molecules in the absence of ULK1 activity. Despite the competitive nature of the interaction interfaces, homo-dimerization of ATG101 surprisingly accelerates its association to ATG13. Memory of ATG101 activation persists for many hours after dephosphorylation and continues to accelerate the assembly of the ATG9A-ATG13-ATG101 complex. Overall, this work proposes an unusual regulatory mechanism where UKL1 initiates an ATG101 auto activation cascade, whose memory creates a responsive positive feedback that dictates the assembly rate of a key complex in autophagy initiation.

biochemistry↗

bioRxiv2024

Identification of TAP2 protein variants resistant to inhibition by the HSV1 ICP47 protein

Herpes Simplex Virus 1 evades the host immune system by expressing a protein, ICP47, that binds to and inhibits the heterodimeric Transporter Associated with Antigen Processing (TAP). We screened a library of 1786 variants in TAP2, one of the components of the TAP heterodimer, and identified 39 variants that were resistant to inhibition by ICP47. Of these 39 variants, five were individually tested, and three (T257I, S274H, and T244R) were confirmed to be significantly resistant to inhibition by ICP47. This resistance to inhibition did not extend to the Epstein Barr Virus BNLF2a protein, another viral factor known to inhibit antigen presentation by targeting TAP. These three residues localize close to the binding site of ICP47, on the 3D structure of TAP, but only Ser274 is spatially close to the antigenic peptide binding site of TAP. These results functionally resolve the TAP2 residues required for peptide binding from those required for ICP47 binding and identify TAP2 residues whose targeting with small molecule inhibitors could effectively prevent Herpes virus downregulation of antigen processing. AUTHOR SUMMARYT cells detect virus infected cells via viral peptides in complex with the major histocompatibility complex type I (MHC-I) on the cell surface. Herpes Simplex Virus 1 expression of the ICP47 protein allows the virus to evade detection and clearance of infected cells by host T cells. ICP47 binds to the TAP1/TAP2 protein complex and prevents the loading of antigenic peptides onto the MHC-I protein complex and thereby blocks the antigen processing. In this study, we screened for and identified variants of TAP2 with single amino acid substitutions that are no longer inhibited by ICP47. TAP2 proteins with the identified amino acid substitutions functioned normally in antigen processing even in the presence of ICP47. Results from this study create the potential strategy for drugs that target the identified portions of the TAP2 protein and block ICP47 inhibition of antigen processing while retaining normal TAP1/TAP2 function and thus suggest a new antiviral therapeutic approach for herpes virus infections.

immunology↗

bioRxiv2024

Multiplexed functional analysis of TAP2 variants in regulating MHC-I cell surface abundance reveals overexpression of PLK1 downregulates antigen presentation.

The abundance of MHC-I on the cell surface depends on its association with antigenic peptides transported to the endoplasmic reticulum by the Transporter Associated with Antigen Processing (TAP), a peptide channel composed of TAP1 and TAP2. We functionally screened over 1400 TAP2 variants for effects on MHC-I cell surface abundance. Amino-acid substitutions of loss of function (LOF) variants clustered in the NTP-binding domain and along the TAP1-TAP2 binding interface, suggesting that these variants interfered with TAP conformational changes associated with peptide transport. Some LOF variants carried potential phosphomimetic substitutions; one such substitution at Ser251 was embedded in a sequence context consistent with the phosphorylation motif of PLK kinases. Inhibition of PLK kinases increased MHC-I surface expression, while overexpression of PLK1 in cells decreased MHC-I in wild type TAP2, but not in TAP2-S251A-expressing cells. Importantly, site-specific phosphorylation of TAP2 in human tumor samples correlated with alterations of gene expression in the cell cycle and antigen presentation pathways, consistent with the notion that phosphorylation downregulates antigenic peptide transport in human tumors. These data strongly support the hypothesis that in cancer cells, TAP2 phosphorylation by PLK1, and perhaps other kinases, can downregulate the antigen presentation process.

cancer biology↗

bioRxiv2024

Transient Non-local Interactions Dominate the Dynamics of Measles Virus NTAIL

The RNA genome of measles virus is encapsidated by the nucleoprotein within a helical nucleocapsid that serves as template for both transcription and replication. The intrinsically disordered domain of the nucleoprotein (NTAIL), partly protruding outward from the nucleocapsid, is essential for binding the polymerase complex responsible for viral transcription and replication. As for many IDPs, binding of NTAIL occurs through a short molecular recognition element (MoRE) that folds upon binding, with the majority of NTAIL remaining disordered. Though NTAIL regions far from the MoRE influence the binding affinity, interactions between them and the MoRE have not been investigated in depth. Using an integrated approach, relying on photo-induced electron transfer (PET) experiments between tryptophan and cysteine pairs placed at different positions in the protein under varying salt and pH conditions, combined with simulations and analytical models, we identified transient interactions between two disordered regions distant in sequence, which dominate NTAIL dynamics, and regulate the conformational preferences of both the MoRE and the entire NTAIL domain. Co-evolutionary analysis corroborates our findings and suggests an important functional role for the same intramolecular interactions. We propose mechanisms by which these non-local interactions may regulate binding to the measles phosphoprotein, polymerase recruitment, and ultimately viral transcription and replication. Our findings may be extended to other IDPs, where non-local intra-protein interactions affect the conformational preferences of intermolecular binding sites.

biophysics↗

bioRxiv2023

A Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models

Circular Dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light, and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.

biophysics↗

bioRxiv2023

Biomolecular condensates form spatially inhomogeneous network fluids

The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.

biophysics↗

bioRxiv2023

DNA Repair Function Scores for 2172 Variants in the BRCA1 Amino-Terminus

Single nucleotide variants are the most frequent type of sequence changes detected in the genome and these are frequently variants of uncertain significance (VUS). VUS are changes in DNA for which disease risk association is unknown. Thus, methods that classify the functional impact of a VUS can be used as evidence for variant interpretation. In the case of the breast and ovarian cancer specific tumor suppressor protein, BRCA1, pathogenic missense variants frequently score as loss of function in an assay for homology-directed repair (HDR) of DNA double-strand breaks. We previously published functional results using a multiplexed assay for 1056 amino acid substitutions residues 2-192 in the amino terminus of BRCA1. In this study, we have re-assessed the data from this multiplexed assay using an improved analysis pipeline. These new analysis methods yield functional scores for more variants in the first 192 amino acids of BRCA1, plus we report new results for BRCA1 amino acid residues 193-302. We now present the functional classification of 2172 BRCA1 variants in BRCA1 residues 2-302 using the multiplexed HDR assay. Comparison of the functional determinations of the missense variants with clinically known benign or pathogenic variants indicated 93% sensitivity and 100% specificity for this assay. The results from BRCA1 variants tested in this assay are a resource for clinical geneticists for evidence to evaluate VUS in BRCA1. AUTHOR SUMMARYMost missense substitutions in BRCA1 are variants of unknown significance (VUS), and individuals with a VUS in BRCA1 cannot know from genetic information alone whether this variant predisposes to breast or ovarian cancer. We apply a multiplexed functional assay for homology directed repair of DNA double strand breaks to assess variant impact on this important BRCA1 protein function. We analyzed 2172 variants in the amino-terminus of BRCA1 and demonstrate that variants that are known as pathogenic have a loss of function in the DNA repair assay. Conversely, variants that are known to be benign are functionally normal in the multiplexed assay. We suggest that these functional determinations of BRCA1 variants can be used to augment the information that clinical cancer geneticists provide to patients who have a VUS in BRCA1.

cancer biology↗

bioRxiv2022

CotH genes are necessary for normal spore formation and virulence in Mucor lusitanicus

Mucormycosis is an invasive fungal infection caused by certain members of the fungal order of Mucorales. The species most frequently identified as the etiological agents of mucormycosis belong to the genera Rhizopus, Lichtheimia and Mucor. The frequency of systemic mucormycosis has been increasing, mainly because of the elevating numbers of susceptible patients. Furthermore, Mucorales display intrinsic resistance to the majority of routinely used antifungal agents (e.g., echinocandins and short-tailed azoles), which limits the number of possible therapeutic options. All the above-mentioned issues urge the improvement of molecular identification methods and the discovery of new antifungal targets and strategies. Spore coat proteins (CotH) constitute a kinase family present in many pathogenic bacteria and fungi and participate in the spore formation in these organisms. Moreover, some of them can act as virulence factors being receptors of the human GRP78 protein during Rhizopus delemar-induced mucormycosis. We identified 17 cotH-like genes in the Mucor lusitanicus genome database. Successful disruption of five cotH genes was performed using the CRISPR-Cas9 system in Mucor. The CotH3 and CotH4 proteins play a role in adaptation to different temperatures as well as in developing the cell wall structure. We also show CotH4 protein is involved in spore wall formation by affecting the total chitin content and thus, the composition of the spore wall. Furthermore, we demonstrate that spore size is dependent on the cotH4 gene. The role of CotH3 and CotH4 proteins in virulence was confirmed in two invertebrate models and DKA mouse model. IMPORTANCECurrent treatment options for mucormycosis are inadequate resulting in high mortality rates especially among immunosuppressed patients. The development of novel therapies for mucormycosis has been hampered by lack of understanding of the pathogenetic mechanisms. The importance of the cell surface CotH proteins in the pathogenesis of Rhizopus-mediated mucormycosis has been recently described. However, the contribution of this family of proteins to the virulence of other mucoralean fungi and their functionality in vital processes remain undefined. Through the use of CRISPR-Case9 gene disruption system, we demonstrate the importance of several of the CotH proteins to the virulence of Mucor lusitanicus by using three infection models. We also report on the importance of one of these proteins, CotH4, to the spore wall formation through affecting the chitin content. Therefore, our studies extend the importance of CotH proteins to Mucor and identifies the mechanism by which one of the CotH proteins contributes to the development of a normal fungal cell wall, thereby indicating that this family of proteins can be targeted for future development of novel therapeutic strategies of mucormycosis.

microbiology↗

bioRxiv2022

Dual RNA-Seq profiling unveils mycoparasitic activities of Trichoderma atroviride against haploid Armillaria ostoyae in antagonistic interaction assays

Armillaria ostoyae, a species among the destructive forest pathogens from the genus Armillaria, causes root rot disease on woody plants worldwide. Efficient control measures to limit the growth and impact of this severe underground pathogen are currently under investigation. In a previous study, a new soilborne fungal isolate, Trichoderma atroviride SZMC 24276, exhibited high antagonistic efficacy, which suggested that it could be utilized as a biocontrol agent. The dual culture assay results indicated that the haploid A. ostoyae derivative SZMC 23085 (C18/9) is highly susceptible to the mycelial invasion of T. atroviride SZMC 24276. In the present study we analyzed the transcriptome of A. ostoyae SZMC 23085 (AO) and that of T. atroviride SZMC 24276 (TA) in in vitro dual culture assays to test the molecular arsenal of Trichoderma antagonism and the defense mechanisms of Armillaria. We conducted time-course analysis, functional annotation, analyzed enriched pathways, and differentially expressed genes (DEGs) including biocontrol-related candidate genes from TA and defense-related candidate genes from AO. The results indicated that TA deployed several biocontrol mechanisms when confronted with AO. In response, AO initiated multiple defense mechanisms to protect against the fungal attack. To our knowledge, the present study offers the first transcriptome analysis of a biocontrol fungus attacking A. ostoyae. Overall, this study provides insights that aid the further exploration of plant pathogen - biocontrol agent interaction mechanisms. IMPORTANCEArmillaria species can survive for decades in the soil on dead woody debris, develop rapidly under favourable conditions, and harmfully infect newly planted forests. Our previous study found Trichoderma atroviride to be highly effective in controlling Armillaria growth; therefore, our current work explored the molecular mechanisms that might play a key role in Trichoderma-Armillaria interactions. Direct confrontation assays combined with time course-based dual transcriptome analysis provided a reliable system for uncovering the interactive molecular dynamics between the fungal plant pathogen and its mycoparasitic partner. Furthermore, using a haploid Armillaria isolate allowed us to survey the deadly prey-invading activities of the mycoparasite and the ultimate defensive strategies of its prey. Our current study provides detailed insights into the essential genes and mechanisms involved in Armillaria defense against Trichoderma and the genes potentially involved in the efficiency of Trichoderma to control Armillaria. In addition, using a sensitive haploid Armillaria strain (C18/9), with its complete genome data already available, also offers the opportunity to test possible variable molecular responses of Armillaria ostoyae towards diverse Trichoderma isolates with varying biocontrol abilities. Initial molecular tests of the dual interactions may soon help to develop a targeted biocontrol intervention with mycoparasites against plant pathogens.

microbiology↗

bioRxiv2021

Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel

The ribosome is a fundamental biomolecular complex responsible for protein production in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiologic consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form an -helix in the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP sequence has a low helical propensity in water and that the propensity is higher in more hydrophobic solvents. We propose that helix formation within the ribosome is driven by the tunnel environment and that a portion of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling the -helix formation, which causes the elongation arrest.

biophysics↗

bioRxiv2021

Oral epithelial cells distinguish between Candida species with high or low pathogenic potential through miRNA regulation

Oral epithelial cells monitor microbiome composition and initiate immune response upon dysbiosis, as in case of Candida imbalances. Comparison of healthy oral epithelial cell responses revealed that the inability of C. parapsilosis to induce a robust antifungal response was due to activation of various inflammation-independent pathways, while C. albicans robustly activated inflammation cascades. Regarding posttranscriptional regulation, several miRNAs were altered by both species. For C. parapsilosis, the applied dose directly correlated with changes in transcriptomic responses. Carbohydrate metabolism, hypoxia- and cardiovascular development-related responses dominate after C. parapsilosis stimulus, whereas C. albicans altered inflammatory responses. Subsequent analyses of HIF1- and HSC-activation pathways predicted target genes through which miRNA-dependent regulation of yeast-specific functions may occur, supporting the observed responses. Thus, C. parapsilosis is recognized as a commensal at low doses by the oral epithelium; however, increased fungal burden activates different pathways, some of which overlap with inflammatory processes induced by C. albicans. Impact statementAltered miRNA regulation discriminates between C. albicans and C. parapsilosis in human oral epithelial cells

microbiology↗