Biology subjects

Dai, L.

Publications and source records attributed to Dai, L..

66 records · Page 4Linked to original sources

bioRxiv2020

Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA in association with Cas2

Cas1 and Cas2 are highly conserved proteins across CRISPR-Cas systems and play a significant role in protospacer acquisition. Here we study the protospacer (or ps) DNA binding, recognition, and response to cleavage on the protospacer-adjacent-motif complementary sequence or PAMc by Cas1-Cas2, implementing all-atom molecular dynamics simulations. First, we noticed that two active sites of Cas1&1 bind asymmetrically to two identical PAMc in the simulation. For psDNA containing only one PAMc to be recognized, it is then found that the non-PAMc association site remains destabilized until after the bound PAMc being cleaved. Thus, correlation appears to exist between the two active sites, which can be allosterically mediated by psDNA and Cas2&2 in bridging. To substantiate such findings, we further simulated Cas1-Cas2 in complex with synthesized psDNA sequences psL and psH, which have been measured with low and high efficiency in acquisition, respectively. Notably, such inter-site correlation becomes largely enhanced for Cas1-Cas2 in complex with psH, and remains low with psL. Hence, our studies demonstrate that PAMc recognition and cleavage in one active site of Cas1-Cas2 allosterically regulates non-PAMc association/reaction in the other site, and such allosteric regulation is mediated by non-catalytic Cas 2 and DNA protospacer in acquisition.

biophysics↗

bioRxiv2020

Identification of a peroxidase inhibitor that enhances kanamycin activity

BackgroundThe threat of antimicrobial resistance calls for more efforts in basic science, drug discovery, and clinical development, particularly gram-negative carbapenem-resistant pathogens. Objectives and methodsWhole-cell-based screening was performed to identify novel antibacterial agents against Acinetobacter baumannii ATCC19606. Spontaneously resistant mutant selection, whole-genome sequencing, and surface plasmon resonance were used for target identification and confirmation. Checkerboard titration assay was used for drug combination analysis. ResultsA small molecule named 6D1 with the chemical structure of 6-fluorobenzo[d]isothiazol-3(2H)-one was identified and exhibited activity against A. baumannii ATCC19606 strain (minimal inhibitory concentration, MIC = 1 mg/L). The mutation in the plasmid-derived ohrB gene that encodes a peroxidase was identified in spontaneously resistant mutants. Treatment of the bacteria with 6D1 resulted in increased sensitivity to peroxide such as tert-butyl hydroperoxide. The binding of 6D1 and OhrB was confirmed by surface plasmon resonance. Interestingly, the MIC of kanamycin against spontaneously resistant mutants decreased. Finally, we identified the effect of 6D1 on enhancing the antibacterial activity of kanamycin, including New Delhi metallo-{beta}-lactamase (NDM-1)-producing carbapenem-resistant Klebsiella pneumoniae, but not in strains carrying kanamycin resistance genes. ConclusionsIn this study, we identified a peroxidase inhibitor that suppresses the growth of A. baumannii and enhances the antibacterial activity of kanamycin. We propose that peroxidase may be potentially used as a target for kanamycin adjuvant development.

microbiology↗

bioRxiv2020

SARS-CoV-2 proteins and anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus

An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of Coronavirus Disease-2019 (COVID-19), a respiratory disease, has infected over 34,000,000 people since the end of 2019, killed over 1,000,000, and caused worldwide social and economic disruption. Due to the mechanisms of SARS-CoV-2 infection to host cells and its pathogenesis remain largely unclear, there are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Besides severe respiratory and systematic symptoms, several comorbidities may also increase risk of fatal disease outcome. Therefore, it is required to investigate the impacts of COVID-19 on pre-existing diseases of patients, such as cancer and other infectious diseases. In the current study, we have reported that SARS-CoV-2 encoded proteins and some anti-COVID-19 drugs currently used are able to induce lytic reactivation of Kaposis sarcoma-associated herpesvirus (KSHV), one of major human oncogenic viruses through manipulation of intracellular signaling pathways. Our data indicate that those KSHV+ patients especially in endemic areas exposure to COVID-19 or undergoing the treatment may have increased risks to develop virus-associated cancers, even after they have fully recovered from COVID-19.

microbiology↗

bioRxiv2020

Inchworm stepping of Myc-Max heterodimer protein diffusion along DNA

Oncogenic protein Myc serves as a transcription factor to control cell metabolisms. Myc dimerizes via leucine zipper with its associated partner protein Max to form a heterodimer structure, which then binds target DNA sequences to regulate gene transcription. The regulation depends on by Myc-Max binding to DNA and searching for target sequences via diffusional motions along DNA. Here, we conduct structure-based molecular dynamics (MD) simulations to investigate the diffusion dynamics of the Myc-Max heterodimer along DNA. We found that the heterodimer protein slides on the DNA in a rotation-uncoupled manner in coarse-grained simulations, as its two helical DNA binding basic regions (BRs) alternate between open and closed conformations via inchworm stepping motions. In such motions, the two BRs of the heterodimer step across the DNA strand one by one, with step sizes up about half of a DNA helical pitch length. Atomic MD simulations of the Myc-Max heterodimer in complex with DNA have also been conducted. Hydrogen bond interactions reveal between the two BRs and two complementary DNA strands, respectively. In the non-specific DNA binding, the BR shows an onset of stepping on one association DNA strand and dissociating from the complementary strand. Overall, our simulation studies suggest that the inchworm stepping motions of the Myc-Max heterodimer can be achieved during the protein diffusion along DNA.

biophysics↗

bioRxiv2020

Revealing Atomic-scale Molecular Diffusion of a Plant Transcription Factor WRKY domain protein along DNA

Transcription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here we constructed a TF model system of the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on the DNA employing all-atom molecular dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to the Crick strand of DNA with significantly stronger energetic association than to the Watson strand. The preferential binding becomes highly prominent from non-specific to specific DNA binding, but less distinct from static binding to diffusive movements of WRKY on the DNA. Remarkably, without employing acceleration forces or bias, we captured a complete one-base pair (bp) stepping cycle of WRKY tracking along major groove of DNA with homogenous (AT)n sequence, as individual protein-DNA contacts break and reform at the binding interface. Continuous tracking of WRKY forward or backward, with occasional sliding as well as strand crossing to the minor groove of DNA, have also been captured in the simulation. The processive diffusion of WRKY had been confirmed by accompanied single-molecule fluorescence assays and coarse-grained (CG) structural simulations. The study thus provides unprecedented structural dynamics details on the TF diffusion, suggests how TF possibly approaches to gene target, and supports further high-precision experimental follow-up. The stochastic movements revealed in the TF diffusion also provide general clues on how other nucleic acid walkers step and slide along DNA. Significance StatementHow transcription factors search for target genes impact on how quickly and accurately the genes are transcribed and expressed. To locate target sufficiently fast, 1D diffusion of the protein along DNA appears essential. Experimentally, it remains challenging to determine diffusional steps of protein on DNA. Here, we report all-atom equilibrium simulations of a WRKY protein binding and diffusing on DNA, revealing structural dynamics details which have not been identified previously. We unprecedently demonstrate a complete stepping cycle of the protein for one base pair on DNA within microseconds, along with stochastic stepping or sliding, directional switching, and strand crossing. Additionally, we have found preferential DNA strand association of WRKY. These suggest how protein factors approach toward target DNA sequences.

biophysics↗

bioRxiv2019

Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease

Drug-resistant mutations often have deleterious impacts on replication fitness, posing a fitness cost that can only be overcome by compensatory mutations. However, the role of fitness cost in the evolution of drug resistance has often been overlooked in clinical studies or in vitro selection experiments, as these observations only capture the outcome of drug selection. In this study, we systematically profile the fitness landscape of resistance-associated sites in HIV-1 protease using deep mutational scanning. We construct a mutant library covering combinations of mutations at 11 sites in HIV-1 protease, all of which are associated with resistance to protease inhibitors in clinic. Using deep sequencing, we quantify the fitness of thousands of HIV-1 protease mutants after multiple cycles of replication in human T cells. Although the majority of resistance-associated mutations have deleterious effects on viral replication, we find that epistasis among resistance-associated mutations is predominantly positive. Furthermore, our fitness data are consistent with genetic interactions inferred directly from HIV sequence data of patients. Fitness valleys formed by strong positive epistasis reduce the likelihood of reversal of drug resistance mutations. Overall, our results support the view that strong compensatory effects are involved in the emergence of clinically observed resistance mutations and provide insights to understanding fitness barriers in the evolution and reversion of drug resistance.

evolutionary biology↗

bioRxiv2019

Small molecule activation of metabolic enzyme pyruvate kinase muscle isozyme 2, PKM2, provides photoreceptor neuroprotection

Photoreceptor cell death is the ultimate cause of vision loss in many retinal disorders, and there is an unmet need for neuroprotective modalities to improve photoreceptor survival. Similar to cancer cells, photoreceptors maintain pyruvate kinase muscle isoform 2 (PKM2) expression, which is a critical regulator in aerobic glycolysis. Unlike PKM1, which has constitutively high catalytic activity, PKM2 is under complex regulation. Recently, we demonstrated that genetically reprogramming photoreceptor metabolism via PKM2-to-PKM1 substitution is a promising neuroprotective strategy. Here, we explored the neuroprotective effects of pharmacologically activating PKM2 via ML-265, a small molecule activator of PKM2, during acute outer retinal stress. We found that ML-265 increased PKM2 activity in 661W cells and in vivo in rat eyes without affecting the expression of genes involved in glucose metabolism. ML-265 treatment did, however, alter metabolic intermediates of glucose metabolism and those necessary for biosynthesis in cultured cells. Long-term exposure to ML-265 did not result in decreased photoreceptor function or survival under baseline conditions. Notably, though, ML-265-treatment did reduce entrance into the apoptotic cascade in in vitro and in vivo models of outer retinal stress. These data suggest that reprogramming metabolism via activation of PKM2 is a novel, and promising, therapeutic strategy for photoreceptor neuroprotection.

molecular biology↗

bioRxiv2019

Weak neural signatures of spatial selective auditory attention in hearing-impaired listeners

Spatial attention may be used to select target speech in one location while suppressing irrelevant speech in another. However, if perceptual resolution of spatial cues is weak, spatially focused attention may work poorly, leading to difficulty communicating in noisy settings. In electroencephalography (EEG), the distribution of alpha (8-14 Hz) power over parietal sensors reflects the spatial focus of attention (Banerjee et al., 2011; Foxe and Snyder, 2011). If spatial attention is degraded, however, alpha may not be modulated across parietal sensors. A previously published behavioral and EEG study found that, compared to normal-hearing (NH) listeners, hearing-impaired (HI) listeners often had higher interaural time difference (ITD) thresholds, worse performance when asked to report the content of an acoustic stream from a particular location, and weaker attentional modulation of neural responses evoked by sounds in a mixture (Dai et al., 2018). This study explored whether these same HI listeners also showed weaker alpha lateralization during the previously reported task. In NH listeners, hemispheric parietal alpha power was greater when the ipsilateral location was attended; this lateralization was stronger when competing melodies were separated by a larger spatial difference. In HI listeners, however, alpha was not lateralized across parietal sensors, consistent with a degraded ability to use spatial features to selectively attend.

neuroscience↗

bioRxiv2019

Ibuprofen-mediated potential inhibition of biofilm development and quorum sensing in Pseudomonas aeruginosa

Pseudomonas aeruginosa is one of the leading causes of opportunistic and hospital-acquired infections worldwide. The infection with P. aeruginosa is frequently linked with clinical treatment difficulties given drug resistance and abuse of antibiotics. Ibuprofen, a widely used non-steroidal anti-inflammatory drug, has been previously reported to exert antimicrobial activity, although the specific mechanism of its action requires additional investigation. Given the regulation effects on quorum sensing (QS), we hypothesized that inhibition of P. aeruginosa with ibuprofen is linked with the QS systems. First, we assessed the action of ibuprofen in P. aeruginosa by measuring CFU. The antimicrobial activity of ibuprofen was evaluated by crystal violent staining and acridine orange staining at various drug concentrations (0, 50, 75, and 100 g/mL). Moreover, the effect of ibuprofen on different QS virulence factors, such as pyocyanin, elastase, protease, and rhamnolipids, was assessed revealing a concentration-dependent decrease (P<0.05). The effect of ibuprofen was confirmed by liquid chromatography/mass spectrometry analysis of 3-oxo-C12-HSL and C4-HSL production. In addition, qRT-PCR results identified significant suppression of Las and Rhl gene expression after 18 hours of treatment with ibuprofen (P<0.05), with the most significant suppression observed at the concentration of 75 g/mL. Functional complementation with exogenous 3-oxo-C12-HSL and C4-HSL suggested that C4-HSL can recover the production of virulence factors and biofilm formation in P. aeruginosa. Molecular docking of ibuprofen with QS-associated proteins revealed high binding affinity. In summary, the results suggest that ibuprofen is a candidate drug for the treatment of clinical infections with P. aeruginosa.

microbiology↗

bioRxiv2019

MicroRNA-222 regulates fluid shear stress-induced human nucleus pulposus cells degeneration through affecting c-Fos expression

Intervertebral disc degeneration (IVDD) is a chronic disease that correlates with the deterioration of the nucleus pulposus (NP) cells. However, the molecular mechanism of IVDD remains unclear. In this study, we investigated the function of microRNA-222 in IVDD and the potential molecular mechanism. NP cells treated with fluid shear stress (FSS) were used to simulate a model of IVDD in vitro. MicroRNA-222 was significantly downregulated in NP cells stimulated with FSS compared with that in unstimulated NP cells. Human NP cells were also treated with FSS to induce their degeneration. The mRNA and protein levels of C-FOS, MEK, phosphorylated MEK5 (pMEK5), ERK5, and pERK5 were evaluated with RT-PCR and western blotting, respectively. Enzyme-linked immunosorbent assays were used to investigate type II collagen and Aggrecan expression. NP cell proliferation was determined with the Cell Counting Kit-8. MicroRNA-222 was significantly downregulated in NP cells treated with FSS. The production of c-Fos and MEK5 were markedly reduced or increased in NP cells transfected with the has-microRNA-222 mimic or inhibitor, respectively, whether or not they were stimulated with FSS. The overexpression or inhibition of microRNA-222 markedly accelerated or suppressed the apoptosis of FSS-stimulated NP cells, respectively. In the NP cells, the overexpression or inhibition of microRNA-222 massively inhibited or strengthened Aggrecan and type II collagen expression. Together, our data indicated that c-Fos was a target of microRNA-222, and was negatively regulated by microRNA-222 in NP cells. Our findings also suggested that microRNA-222 is a possible therapeutic target for IVDD because it regulates c-Fos.

cell biology↗

bioRxiv2018

Structural differences between pri-miRNA paralogs promotes alternative Drosha cleavage and expands target repertoires

MicroRNA (miRNA) processing begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the maturation of three pri-miR-9 paralogs, which encode the same mature miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its distorted and flexible stem structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative-miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Analyses of low grade glioma patient samples indicate that the alternative-miR-9 plays a distinct role in preventing tumor progression. To generalize our model, we provide evidence that distortion of pri-miRNA stems correlates with Drosha cleavage at non-canonical sites. Our studies reveal that pri-miRNA paralogs can have distinct functions via differential Drosha processing.

molecular biology↗

bioRxiv2018

Microbial Community Structure and Diversity of Shrimp Paste at Different Fermentation Stages

High-throughput sequencing was used to reveal the highly diverse bacterial populations in shrimp paste at different fermentation stages. We studied three stages of fermentation and obtained 448,916 reads. Using this approach, we revealed the presence of 30 phyla, 55 classes, 86 orders, 206 families and 695 genera of bacteria in the shrimp paste. Shrimp paste in fermentation metaphase had a more diverse microbiota than that in fermentation prophase and fermentation anaphase. Diversity appeared greatest in fermentation anaphase. The four dominant phyla were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The most common genera were Psychrobacter, Halomonas, Bacillus, Alteribacillus, and Lactococcus. Their content varied at different stages of fermentation. All the microbiome presented a variety of changes in the microbial diversity of shrimp paste.\n\nImportanceMost research on the microbial diversity of shrimp paste has focused on the shrimp culture environment, or the chemical composition and sensory attributes of the paste. Little research has been conducted on the microbial diversity and composition of shrimp paste. The relationship between microbes and the flavor and quality of shrimp paste has thus been unknown. We therefore analyzed the microbial composition and variation of shrimp paste at different stages of fermentation. The dominant bacteria in fermentation prophase, metaphase, and anaphase were identified. Our preliminary findings give some insight into which microbes contribute to the flavor of shrimp paste and suggest how to improve its flavor. In addition, our findings are relevant to optimizing the production of shrimp paste and guaranteeing its quality and safety.

microbiology↗