Biology subjects

Haider, S.

Publications and source records attributed to Haider, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Dynamic Differences in Clinically relevant Pen β-Lactamases from Burkholderia spp.

Antimicrobial resistance (AMR) is a global threat, with Burkholderia species contributing significantly to difficult-to-treat infections. Ambler Class A Pen {beta}-lactamases are produced by all Burkholderia spp., and their mutation or overproduction leads to the resistance of {beta}-lactam antibiotics. This study investigates the dynamic differences among four Pen {beta}-lactamases (PenA, PenI, PenL and PenP) using machine learning driven enhanced sampling molecular dynamics simulations, Markov State Models (MSMs), convolutional variational autoencoder-based deep learning (CVAE) and the BindSiteS-CNN model. Although sharing the same catalytic mechanisms, these enzymes exhibit distinct dynamic features due low sequence identity, resulting in different substrate profiles and catalytic turnover. The BindSiteS-CNN model further reveals local active site dynamics, offering insights into the Pen {beta}-lactamase evolutionary adaptation. Our findings reported here identify critical mutations and proposes new hotspots affecting Pen {beta}-lactamase flexibility and function, which can be used to fight emerging resistance in these enzymes.

biophysics↗

bioRxiv2024

Functionally Important Residues from Graph Analysis of Coevolved Dynamic couplings

The relationship between protein dynamics and function is essential for understanding biological processes and developing effective therapeutics. Functional sites within proteins are critical for activities such as substrate binding, catalysis, and structural changes. Existing computational methods for the predictions of functional residues are trained on sequence, structural and experimental data, but they do not explicitly model the influence of evolution on protein dynamics. This overlooked contribution is essential as it is known that evolution can fine tune protein dynamics through compensatory mutations, either to improve the proteins performance or diversify its function while maintaining the same structural scaffold. To model this critical contribution, we introduce DyNoPy, a computational method that combines residue coevolution analysis with molecular dynamics (MD) simulations, revealing hidden correlations between functional sites. DyNoPy constructs a graph model of residue-residue interactions, identifies communities of key residue groups and annotates critical sites based on their roles. By leveraging the concept of coevolved dynamical couplings--residue pairs with critical dynamical interactions that have been preserved during evolution--DyNoPy offers a powerful method for predicting and analysing protein evolution and dynamics. We demonstrate the effectiveness of DyNoPy on SHV-1 and PDC-3, chromosomally encoded {beta}-lactamases linked to antibiotic resistance, highlighting its potential to inform drug design and address pressing healthcare challenges.

evolutionary biology↗

bioRxiv2024

Darwin's Naturalization Conundrum explained by gradients of environmental stress and disturbance

Darwins Naturalization Conundrum (DNC) states that non-native species closely related to the native community are either more likely to succeed because shared adaptations help them overcome environmental filtering, or less likely to succeed because of strong competition with their native relatives. Despite extensive research, no general patterns have so far emerged. One reason may be that the relative importance of competition and environmental filtering depends on environmental conditions. To test this hypothesis, we conducted a global assessment of DNC examining patterns of phylogenetic relatedness of non-native plant species to the native community along gradients of elevation and anthropogenic disturbance in mountains. Phylogenetic distance of non-native to native species decreased with increasing elevation and in disturbed plant communities. Our results help resolve DNC by showing that the environmental context sets expectations for patterns of relatedness between non-native and native species and helps illuminate the ecological and evolutionary processes generating these patterns.

ecology↗

bioRxiv2024

Biomass allocation of trees in response to mono- and heterospecific neighbourhoods

Carbon sequestration by trees is crucial to mitigate the effects of the current climate crisis. The extent to trees sequester and allocate carbon to above- or belowground structures in turn is mediated by neighbouring species. Although many studies have demonstrated positive effects of diverse neighbourhoods on a trees productivity, little is known about biomass allocation responses to mono-vs. heterospecific neighbourhoods. In the present study we quantified above- and belowground biomass production and root-to-shoot ratios (RSR) of trees grown in mono- and heterospecific neighbourhoods. To this end we analysed growth of mono- and heterospecific tree species pairs (TSPs) established in a greenhouse and a field experiment. In the greenhouse experiment response variables were measured after one year of growth after sapling harvest. In the field experiment, conducted in the context of a forest biodiversity experiment in subtropical China, we analysed biomass density and RSR over three years using terrestrial laser scanner and minirhizotrons. RSR of trees in heterospecific TSPs were significantly higher than in monospecific TSPs. In the greenhouse experiment, this was related to a stronger below-than aboveground overyielding in heterospecific TSPs. In the field experiment, trees in heterospecific TSPs showed a stronger increase in aboveground investments over time than in monospecific TSPs, indicating that positive diversity effects became stronger for aboveground structures with progressing tree development. Our findings are consistent with the optimal biomass partitioning theory and highlight the importance of tree-tree interactions on biomass allocation. Higher RSR in mixtures further suggest a higher resistance or resilience of tree saplings against environmental stressors related to climate change (drought, heat waves).

ecology↗

bioRxiv2024

Hypoxia and loss of GCM1 expression prevents differentiation and contact inhibition in human trophoblast stem cells

The placenta develops alongside the embryo and nurtures fetal development to term. During the first stages of embryonic development, due to low blood circulation, the blood and ambient oxygen supply is very low ([~]1-2% O2) and gradually increases upon placental invasion. While a hypoxic environment is associated with stem cell self-renewal and proliferation, persistent hypoxia may have severe effects on differentiating cells and could be the underlying cause of placental disorders. We find that human trophoblast stem cells (hTSC) thrive in low oxygen, whereas differentiation of hTSC to trophoblast to syncytiotrophoblast (STB) and extravillous trophoblast (EVT) is negatively affected by hypoxic conditions. The pro-differentiation factor GCM1 (human Glial Cell Missing-1) is downregulated in low oxygen, and concordantly there is substantial reduction of GCM1-regulated genes in hypoxic conditions. Knockout of GCM1 in hTSC caused impaired EVT and STB formation and function, reduced expression of differentiation-responsive genes, and resulted in maintenance of self-renewal genes. Treatment with a PI3K inhibitor reported to reduce GCM1 protein levels likewise counteracts spontaneous or directed differentiation. Additionally, chromatin immunoprecipitation of GCM1 showed enrichment of GCM1-specific binding near key transcription factors upregulated upon differentiation including the contact inhibition factor CDKN1C. Loss of GCM1 resulted in downregulation of CDKN1C and corresponding loss of contact inhibition, implicating GCM1 in regulation of this critical process.

cell biology↗

bioRxiv2024

Exploiting functional regions in the viral RNA genome as druggable entities

RNA-targeting compounds or small interfering RNAs (siRNAs) offer a potent means for controlling viral infections. An essential prerequisite to their design depends on identifying conserved and functional viral RNA structures in cells. Techniques that probe RNA structures in situ have been developed recently including SHAPE-MaP, which has been helpful in analyzing the secondary structures of RNA. In this study, we report on the application of SHAPE-MaP to the Porcine Epidemic Diarrhoea Virus (PEDV) RNA genome to categorize different functional regions including potential quadruplex forming sequence and target sites of siRNA. Our results show that these structures can be exploited to inhibit viral proliferation and that SHAPE-MaP is an effective method to the identification of secondary structures in RNA genomes.

genomics↗

bioRxiv2024

Diversity-enhanced canopy space occupation and leaf functional diversity jointly promote overyielding in tropical tree communities

Understanding the mechanisms that drive biodiversity-productivity relationships is critical for guiding forest restoration. Although complementarity among trees in the canopy space has been suggested as a key mechanism for greater productivity in mixed-species tree communities, empirical evidence remains limited. Here, we used data from a tropical tree diversity experiment to disentangle the effects of tree species richness and community functional characteristics (community-weighted mean and functional diversity of leaf traits) on canopy space filling, and how these effects are related to overyielding. We found that canopy space filling was largely explained by species identity effects rather than tree diversity effects. Communities with a high abundance of species with conservative leaf traits were those with most densely packed canopies. Overall, a higher canopy space filling translated into an enhanced wood productivity, with communities associated with a high taxonomic and functional diversity being the most productive. Importantly, most communities (83%) produced more wood volume than the average of their constituent species in monoculture (i.e. most communities overyielded). Our results show that overyielding increased with leaf functional diversity and positive net biodiversity effects on canopy space filling, which mainly arose due to a high taxonomic diversity. These findings suggest that both taxonomic diversity-enhanced canopy space filling and canopy leaf diversity are important drivers for overyielding in mixed-species forests. Consequently, restoration initiatives should promote stands with functionally diverse canopies by selecting tree species with large interspecific differences in leaf nutrition, as well as leaf and branch morphology to optimize carbon capture in young forest stands.

ecology↗

bioRxiv2024

A Mechanistic Understanding of the Activity-Stability Trade-off in PETase

Enzymatic degradation of poly(ethylene terephthalate) (PET) has garnered considerable interest in plastic recycling efforts. Despite numerous descriptions of both natural and engineered enzymes, the fundamental mechanism underlying PETase-catalyzed PET depolymerization at the solid-liquid interface remains elusive. This lack of understanding hampers the rational design of highly efficient depolymerases. Here, we employ multiscale simulations and experiments to elucidate the complete catalytic pathway of IsPETase, from enzyme adsorption at the interface to PET fragment capture, conformational refinement, and ester bond cleavage. Both endo- and exo-cleavage modes of the enzyme are identified, indicating its capacity for endo- and exo-lytic activities. We discover that the trade-off between the activity and stability of IsPETases PET-capturing pliers brings compromises to its PET depolymerization performance. Reshaping the loop dynamics of the enzyme can break this trade-off and enhance its stability and activity simultaneously, as demonstrated by the evolved variant HotPETase. Overall, our study offers comprehensive details into how PETase functions at the interface and provides valuable insights for engineering efficient plastic-degrading enzymes.

biochemistry↗

bioRxiv2024

Selective molecular inhibition of the HDAC6 ZnF-UBP binding domain impairs multiple myeloma cell proliferation

Multiple myeloma is a plasma cell malignancy with poor prognosis despite the recent development of new therapeutic options. Histone deacetylase 6 (HDAC6) is overexpressed in multiple myeloma patients and may be involved in the acquisition of resistance to conventional anti-proteasome treatments. Beyond displaying a deacetylase catalytic activity, HDAC6 can recognize ubiquitinated motifs from misfolded proteins through its C-terminal ZnF-UBP binding domain and send the defective proteins to the aggresome for degradation. Here, we explore the role of the ZnF-UBP binding domain of HDAC6 in the function of multiple myeloma cells. A non-functional ZnF-UBP domain containing a 2-residue mutation in the binding site was designed and the absence of ubiquitin binding was confirmed in a cell-free assay. Molecular docking simulations and electrostatic calculations revealed a significant decrease in the electrostatic potential of the mutated peptide, which is crucial for the stability of the complex with ubiquitin. A multiple myeloma cell line containing the non-functional ZnF-UBP domain was then engineered. Although the deacetylase activity of HDAC6 was maintained in these cells, they showed reduced cell growth, impaired aggresome formation and a dysregulated gene expression profile that was more pronounced than cells entirely deficient in HDAC6. These results indicate that a non-functional ZnF-UBP binding domain impacts the function of multiple myeloma cells. Based on these findings, a series of quinazolinylpropanoic acid derivatives was synthesized to explore the inhibitory activity of small molecules to this domain. We propose that ZnF-UBP binding domain inhibitors should be further evaluated as potential therapeutic agents in multiple myeloma.

cancer biology↗

bioRxiv2024

Nutrient addition in grasslands worldwide reveals proportional plant diversity decline across spatial scales but little change in beta diversity

Nutrient enrichment typically causes local plant diversity declines. A common but untested expectation is that nutrient enrichment also reduces variation in nutrient conditions among localities and selects for a smaller pool of species, causing greater diversity declines at larger than local scales and thus biotic homogenization. Here we apply a framework that links changes in species richness across scales to changes in the numbers of spatially restricted and widespread species for a standardized nutrient addition experiment across 72 grasslands on six continents. Overall, we find proportionally similar species loss at local and larger scales, suggesting similar declines of spatially restricted and widespread species, and no biotic homogenization after 4 years and up to 14 years of treatment. These patterns of diversity changes are generally consistent across species groups. Thus, nutrient enrichment poses threats to plant diversity, including for widespread species that are often critical for ecosystem functions.

ecology↗

bioRxiv2024

{Omega}-Loop mutations control the dynamics of the active site by modulating a network of hydrogen bonds in PDC-3 β-lactamase

The expression of antibiotic-inactivating enzymes, such as Pseudomonas-derived cephalosporinase-3 (PDC-3), is a major mechanism of intrinsic resistance in bacteria. Using reinforcement learning-driven molecular dynamics simulations and constant pH MD, we investigate how clinically observed mutations in the {Omega}-loop (at residues V211, G214, E219, and Y221) alter the structure and function of PDC-3. Our findings reveal that these substitutions modulate the dynamic flexibility of the {Omega}-loop and the R2-loop, reshaping the cavity of the active site. In particular, E219K and Y221A disrupt the tridentate hydrogen bond network around K67, thus lowering its pKa and promoting proton transfer to the catalytic residue S64. Markov state models reveal that E219K achieves enhanced catalysis by adopting stable, long-lived active conformations, whereas Y221A facilitates activity by rapidly toggling between bond-formed and bond-broken states. In addition, substitutions influence key hydrogen bonds that control the opening and closure of the active-site pocket, consequently influencing the overall size. The pocket expands in all nine clinically identified variants, creating additional space to accommodate bulkier R1 and R2 cephalosporin side chains. Taken together, these results provide a mechanistic basis for how single residue substitutions in the {Omega}-loop affect catalytic activity. Insights into the structural dynamics of the catalytic site advance our understanding of emerging {beta}-lactamase variants and can inform the rational design of novel inhibitors to combat drug-resistant P. aeruginosa.

biophysics↗

bioRxiv2024

Dysregulated SASS6 expression promotes increased ciliogenesis and cell invasion phenotypes

Centriole and/or cilia defects are characteristic of cancer cells and have been linked to cancer cell invasion. However, the mechanistic basis of these effects is unknown. Spindle assembly abnormal protein 6 homolog (SAS-6) is essential for centriole biogenesis and cilia formation. In cycling cells, SAS-6 undergoes APCCdh1-mediated targeted degradation by the 26S proteasome at the end of mitosis. Little is known about the function of SAS-6 outside of centrosome biogenesis. To examine this, we expressed a non-degradable SAS-6 mutant (SAS-6ND). Expression of SAS-6ND led to an increase in ciliation and cilia-dependent cell invasion, and caused an upregulation of the YAP/TAZ pathway. YAP/TAZ or ciliogenesis inhibition prevented SAS-6-induced invasion. SAS-6ND caused increased actin alignment and stress fiber coherency, and nuclear flattening known to promote YAP nuclear import. Finally, data from The Cancer Genome Atlas showed that SAS-6 overexpression is associated with poor prognosis in various cancers. Our data provide evidence for a defined role of SAS-6 in cancer cell invasion and offers mechanistic insight into the role of YAP/TAZ in this cilia-sensitive process. Synopsis O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/576599v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1cec0daorg.highwire.dtl.DTLVardef@d73051org.highwire.dtl.DTLVardef@1a53e47org.highwire.dtl.DTLVardef@19bb05d_HPS_FORMAT_FIGEXP M_FIG C_FIG SAS-6 overexpressing cells show increased ciliation, actin cytoskeleton reorganization, cell flattening, YAP pathway activation and increased invasion

cell biology↗

bioRxiv2024

Deciphering the co-evolutionary dynamics of L2 β-lactamases via Deep learning

L2 {beta}-lactamases, a serine-based class A {beta}-lactamases expressed by Stenotrophomonas maltophilia plays a pivotal role in antimicrobial resistance. However, limited studies have been conducted on these important enzymes. To understand the co-evolutionary dynamics of L2 {beta}-lactamase, innovative computational methodologies, including adaptive sampling molecular dynamics simulations, and deep learning methods (convolutional variational autoencoders and BindSiteS-CNN) explored conformational changes and correlations within the L2 {beta}-lactamase family together with other representative class A enzymes including SME-1 and KPC-2. This work also investigated the potential role of hydrophobic nodes and binding site residues in facilitating the functional mechanisms. The convergence of analytical approaches utilized in this effort yielded comprehensive insights into the dynamic behaviour of the {beta}-lactamases, specifically from an evolutionary standpoint. In addition, this analysis presents a promising approach for understanding how the class A {beta}-lactamases evolve in response to environmental pressure and establishes a theoretical foundation for forthcoming endeavours in drug development aimed at combating antimicrobial resistance. SynopsisDeep learning is used to reveal the dynamic co-evolutionary patterns of L2 {beta}-lactamases. O_LIAnalysis of hydrophobic nodes and binding site residues provides a detailed understanding of both local and global dynamic evolution, which explain the functional divergences. C_LIO_LIThe employment of two distinct deep learning models, the Convolutional Variational Autoencoder (CVAE) and BindSiteS-CNN, facilitates the investigation of conformational shifts, thereby depicting the dynamic evolution of L2 {beta}-lactamases. C_LIO_LIThe effectiveness of CVAE and BindSiteS-CNN in dynamic classification is corroborated with selected features. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/575584v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1db15forg.highwire.dtl.DTLVardef@168043eorg.highwire.dtl.DTLVardef@1eebb96org.highwire.dtl.DTLVardef@5d8019_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Low land-use intensity buffers grasslands against future climate and inter-annual climate variability in a large field experiment

Climate and land-use change are key drivers of global change. Full-factorial field experiments in which both drivers are manipulated are essential to understand and predict their potentially interactive effects on the structure and functioning of grassland ecosystems. Here, we present eight years of data on grassland dynamics from the Global Change Experimental Facility (GCEF) in Central Germany. On large experimental plots, temperature and seasonal patterns of precipitation are manipulated by superimposing regional climate model projections onto background climate variability. Climate manipulation is factorially crossed with agricultural land-use scenarios, including intensively used meadows and extensively used (i.e. low-intensity) meadows and pastures. Inter-annual variation of background climate during our study years was high, including three of the driest years on record for our region. The effects of this temporal variability far exceeded the effects of the experimentally imposed climate change on plant species diversity and productivity, especially in the intensively used, species-poor grasslands. These changes in productivity and diversity in response to alterations in climate were due to immigrant species replacing the target forage cultivars. This shift from forage cultivars to immigrant species may impose additional economic costs in terms of a decreasing fodder value and the need for more frequent management measures. In contrast, the extensively used, species-rich grasslands showed weaker responses to both experimentally manipulated future climate and inter-annual climate variability, suggesting that these diverse grasslands are more resistant to climate change than intensively used, species-poor grasslands. We therefore conclude that an extensive management of agricultural grasslands, together with other measures to increase species diversity, can stabilize primary productivity under climate change.

ecology↗

bioRxiv2023

Dissecting the Impact of Maternal Androgen Exposure on Offspring Health through Targeting the Androgen Receptor in Developmental Programming

Women with polycystic ovary syndrome (PCOS) exhibit sustained elevation in circulating androgens during pregnancy, an independent risk factor linked to pregnancy complications and adverse neonatal outcomes. Yet, further investigation is required to understand the precise mechanisms and the impact on cell-type specific placental dysfunction. To explore these dynamics, a PCOS-like mice model was induced with continuous androgen exposure throughout pregnancy, mimicking the human-PCOS. This resulted in impaired placental and embryonic development, leading to mid-gestation lethality. Co-treatment with the androgen receptor blocker, flutamide, prevented this lethality. Comprehensive analysis using whole-genome bisulfite and RNA sequencing revealed the diminished proportion of trophoblast precursors by downregulation of Cdx2. The absence of Gcm1, Synb, and Prl3b1 further resulted in decreased numbers of syncytiotrophoblasts and sinusoidal trophoblast giant cells, leading to observed compromised placenta labyrinth formation. Importantly, human trophoblast organoids exposed to androgens exhibited analogous alterations, highlighting impaired trophoblast differentiation as a key feature in PCOS-related pregnancy complications. Remarkably, all effects were mediated through the androgen receptor pathways, as demonstrated by comparable offspring phenotypes to controls when treated with flutamide. These findings provide novel insight into the PCOS-related pregnancy complications, and potential cellular targets for future treatment.

physiology↗

bioRxiv2023

Improving forest ecosystem functions by optimizing tree species spatial arrangement

Reforestation and afforestation programs are promoted as strategies to mitigate rising atmospheric CO2 concentrations and enhance ecosystem services. Planting diverse forests is supposed to foster such benefits, but optimal tree planting techniques, especially regarding species spatial arrangement, are underexplored. Here, using field measurements from the subtropical BEF-China experiment, we simulated leaf litterfall and decomposition, as a function of various spatial arrangements of tree species, from clusters of species to random distributions. We show that increasing tree species spatial heterogeneity in forests composed of nine tree species led to more evenly distributed litterfall, increased litter decomposition and associated nitrogen cycling by 45%. These effects were amplified with increasing plot species richness, while species functional trait identity and diversity modulated these relationships. The spatial arrangement of tree species is a critical component determining biodiversity-ecosystem functioning relationships, and considering such spatial aspects is crucial for operationalizing biodiversity-ecosystem functioning theory in realistic re-/afforestation projects.

ecology↗

bioRxiv2023

Oligomeric states of an Influenza-encoded PB1-F2 viroporin

Influenza Viruses have always been a major health concern due to their highly contagious nature. The PB1-F2 viroporin encoded by the influenza A virus is known to be a pro-apoptotic protein involved in cell death induction of the host immune cells. The structural arrangement and the mode of action of PB1-F2 viroporin have not been fully understood. In this study, we report on the most probable oligomeric structural existences of PB1-F2, investigated by Molecular Dynamics Simulations with improved sampling of conformational states. The simulations provide a channel framework to study the mitochondrial membrane permeation pathway which could initiate the leakage of mitochondrial contents like cytochrome C and induce apoptosis. The structural attributes of the oligomeric states were rigorously evaluated by comparing the experimental reports. Our results reveal a tetrameric form as the preferable state in the lipid environment. This further fulfills the ion transportation criteria by providing a less energetic barrier to ions/water molecules crossing the membrane.

biophysics↗

bioRxiv2023

Pervasive mislocalization of pathogenic coding variants underlying human disorders

Widespread sequencing has yielded thousands of missense variants predicted or confirmed as disease-causing. This creates a new bottleneck: determining the functional impact of each variant - largely a painstaking, customized process undertaken one or a few genes or variants at a time. Here, we established a high-throughput imaging platform to assay the impact of coding variation on protein localization, evaluating 3,547 missense variants of over 1,000 genes and phenotypes. We discovered that mislocalization is a common consequence of coding variation, affecting about one-sixth of all pathogenic missense variants, all cellular compartments, and recessive and dominant disorders alike. Mislocalization is primarily driven by effects on protein stability and membrane insertion rather than disruptions of trafficking signals or specific interactions. Furthermore, mislocalization patterns help explain pleiotropy and disease severity and provide insights on variants of unknown significance. Our publicly available resource will likely accelerate the understanding of coding variation in human diseases.

cell biology↗