Biology subjects

Guo, P.

Publications and source records attributed to Guo, P..

46 records · Page 3Linked to original sources

bioRxiv2021

Molecular dynamics simulation study of effects of key mutations in SARS-CoV-2 on protein structures

SARS-CoV-2 has been spreading rapidly since 2019 and has produced large-scale mutations in the genomes. The mutation in genes may lead to changes in protein structure, which would have a great impact on the epidemiological characteristics. In this study, we selected the key mutations of SARS-CoV-2 from a real-time monitoring tool, including D614G, A222V, N501Y, T716I, S982A, D1118H of spike (S) protein, and performed molecular dynamics (MD) simulations on single-site mutant D614G, double-site mutant D614G&A222V and penta-site mutant N501Y&D614G&T716I&S982A&D1118H to investigate their effects on protein structure and stability using molecular dynamics (MD) simulations. The results suggested that D614G improved the stability of S protein, while D614G&A222V and N501Y&D614G&T716I&S982A&D1118H showed an increased solvent accessible surface area and they might enhance the ability of protein to react with the outside environment. Our findings could complement the mechanistic link between genotype--phenotype--epidemiological characteristics in the study of SARS-CoV-2. We also found no significant difference between the antigenicity of S protein and the mutants through Ellipro, which may reference for vaccine development and application.

bioinformatics↗

bioRxiv2020

Satellite subgenomic particles are key regulators of adeno-associated virus life cycle

Historically, AAV defective interfering particles (DI) were known as abnormal virions arising from natural replication and encapsidation errors. Through single virion genome analysis, we revealed that a major category of DI particles contains a double stranded DNA genome in a "snapback" configuration (SBG). The 5-SBGs include the P5 promoters and partial rep gene sequences. The 3-SBGs contains the capsid region. The molecular configuration of 5-SBGs allowed double stranded RNA transcription in their dimer configuration, which in turn regulate AAV rep expression and may improve AAV packaging. In contrast, 3-SBGs at its dimer configuration increased levels of cap protein. The generation and accumulation of 5-SBGs and 3-SBGs appears to be coordinated to balance the viral gene expression level. Therefore, the functions of 5-SBGs and 3-SBGs may help maximize the yield of AAV progenies. We postulate that AAV virus population behaved as a colony and utilizes its subgenomic particles to overcome the size limit of viral genome and encodes additional essential functions.

molecular biology↗

bioRxiv2020

Subgenomic satellite particle generation in recombinant AAV vectors results from DNA lesion/breakage and non-homologous end joining

Recombinant AAV (rAAV) vectors have been developed for therapeutic treatment of genetic diseases. Nevertheless, current rAAV vectors administered to patients often contain non-vector related DNA contaminants. Here, we present a thorough molecular analysis of the configuration of non-standard AAV genomes generated during rAAV production. In addition to the sub-vector genomic size particles containing incomplete AAV genomes, our results found that rAAV preparations were contaminated with multiple categories of subgenomic particles with either snapback genomes or vector genomes with deletions in the mid regions. Through CRISPR and restriction enzyme-based in vivo and in vitro modeling, we identified that the main mechanism leading to the formation of non-canonical genome particles occurred through nonhomologous end joining of fragmented vector genomes caused by genome lesions or DNA breaks that were generated by the host cell/environment. The results of this study advance our understanding of AAV vectors and provide new clues on improving vector efficiency and safety profile for use in human gene therapy.

molecular biology↗

bioRxiv2020

An integrative structural model of the full-length gp16 ATPase in bacteriophage phi29 DNA packaging motor

Biological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. Most of these biomotors belong to a group of enzymes known as ATPases, which adopt a multi-subunit ring-shaped structure and hydrolyze adenosine triphosphate (ATP) to generate forces. The gene product 16 (gp16), an ATPase in bacteriophage {square}29, is among the most powerful biomotors known. It can overcome substantial resisting forces from entropic, electrostatic, and DNA bending sources to package double-stranded DNA (dsDNA) into a preformed protein shell (procapsid). Despite numerous studies of the {square}29 packaging mechanism, a structure of the full-length gp16 is still lacking, let alone that of the packaging motor complex that includes two additional molecular components: a connector gp10 protein and a prohead RNA (pRNA). Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment of gp16-CTD with related RNase H-like nuclease domains revealed a nucleic acid binding surface in gp16-CTD, whereas no nuclease activity has been detected for gp16. Subsequent molecular dynamics (MD) simulations showed that this nucleic acid binding surface is likely essential for pRNA binding. Furthermore, our simulations of a full-length gp16 structural model highlighted a dynamic interplay between the N-terminal domain (NTD) and CTD of gp16, which may play a role in driving DNA movement into the procapsid, providing structural support to the previously proposed inchworm model. Lastly, we assembled an atomic structural model of the complete {square}29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage {square}29 and suggested how the individual domains of gp16 work together to power such translocation. ABSTRACT (SHORT)Biological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. The gene product 16 (gp16) in bacteriophage {square}29 is among the most powerful biomotors known, which adopts a multi-subunit ring-shaped structure and hydrolyzes ATP to package double-stranded DNA (dsDNA) into a preformed procapsid. Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment and molecular dynamics (MD) simulations revealed an essential binding surface of gp16-CTD for prohead RNA (pRNA), a unique component of the motor complex. Furthermore, our simulations highlighted a dynamic interplay between the N-terminal domain (NTD) and CTD of gp16, which may play a role in driving DNA movement into the procapsid. Lastly, we assembled an atomic structural model of the complete {square}29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage {square}29 and suggested how the individual domains of gp16 work together to power such translocation.

biophysics↗

bioRxiv2020

Doxycycline has Distinct Apicoplast-Specific Mechanisms of Antimalarial Activity

Doxycycline (DOX) is a key antimalarial drug thought to kill Plasmodium parasites by blocking protein translation in the essential apicoplast organelle. Clinical use is primarily limited to prophylaxis due to delayed second-cycle parasite death at 1-3 M serum concentrations. DOX concentrations >5 M kill parasites with first-cycle activity but have been ascribed to off-target mechanisms outside the apicoplast. We report that 10 M DOX blocks apicoplast biogenesis in the first cycle and is rescued by isopentenyl pyrophosphate, an essential apicoplast product, confirming an apicoplast-specific mechanism. Exogenous iron rescues parasites and apicoplast biogenesis from first-but not second-cycle effects of 10 M DOX, revealing that first-cycle activity involves a metal-dependent mechanism distinct from the delayed-death mechanism. These results critically expand the paradigm for understanding the fundamental antiparasitic mechanisms of DOX and suggest repurposing DOX as a faster-acting antimalarial at higher dosing whose multiple mechanisms would be expected to limit parasite resistance.

microbiology↗

bioRxiv2019

A portable and cost-effective microfluidic system for massively parallel single-cell transcriptome profiling

Single-cell technologies are becoming increasingly widespread and have been revolutionizing our understanding of cell identity, state, diversity and function. However, current platforms can be slow to apply to large-scale studies and resource-limited clinical arenas due to a variety of reasons including cost, infrastructure, sample quality and requirements. Here we report DNBelab C4 (C4), a negative pressure orchestrated, portable and cost-effective device that enables high-throughput single-cell transcriptional profiling. C4 system can efficiently allow discrimination of species-specific cells at high resolution and dissect tissue heterogeneity in different organs, such as murine lung and cerebral cortex. Finally, we show that the C4 system is comparable to existing platforms but has huge benefits in cost and portability and, as such, it will be of great interest for the wider scientific community.

genomics↗

bioRxiv2019

In situ Fucosylation for Modulating Wnt Signaling in Live Cells

Wnt/{beta}-catenin signaling, also known as canonical Wnt signaling, regulates critical, context-dependent transcription in numerous (patho) physiological events. Amongst the well-documented mechanisms of canonical Wnt signaling, modification of N-glycans by L-fucose (Fuc) is the newest and the least understood. Using a combination of Chinese Hamster Ovary (CHO) cell mutants with different fucosylation levels and in situ cell-surface Fuc editing (ISF), we report that (1-3)-fucosylation of N-acetylglucosamine in the LacNAc (Gal{beta}(1-4)-GlcNAc) sequences of complex N-glycans modulates Wnt signaling by regulating the endocytosis of low density lipoprotein receptor-related protein 6 (LRP6). Pulse-chase experiments reveal that increasing N-glycan LacNAc fucosylation elevates endocytosis of lipid-raft-localized LRP6, leading to the suppression of Wnt-{beta}-catenin signaling. Inhibiting endocytosis by inhibiting dynamin 1, a GTPase responsible for endocytosis in eukaryotic cells, partially rescues Wnt signaling. Remarkably, inhibition of Wnt signaling by N-glycan LacNAc fucosylation is fully rescued by the addition of free Fuc to the medium, suggesting that endocytosis of N-glycan fucosylated LRP6 may be mediated by a receptor that recognizes the bound (1-3)-Fuc. This work provides the first evidence that in situ cell-surface fucosylation can be exploited to regulate a specific signaling pathway via endocytosis, revealing a novel regulatory mechanism linking glycosylation of a cell surface receptor with its intracellular signaling.

biochemistry↗

bioRxiv2019

A triple-hybrid cross reveals new a hybrid incompatibility locus between D. melanogaster and D. sechellia

Hybrid incompatibilities are the result of deleterious interactions between diverged genes in the progeny of two species. In Drosophila, crosses between female D. melanogaster and males from the D. simulans clade (D. simulans, D. mauritiana, D. sechellia) fail to produce hybrid F1 males. When attempting to rescue hybrid F1 males by depleting the incompatible allele of a previously identified hybrid incompatibility gene, we observed robust rescue in crosses of D. melanogaster to D. simulans or D. mauritiana, but no rescue in crosses to D. sechellia. To investigate the genetic basis of D. sechellia resistance to hybrid rescue, we designed a triple-hybrid cross to generate recombinant D. sechellia / D. simulans genotypes. We tested the ability of those genotypes to rescue hybrid males with D. melanogaster, and used whole genome sequencing to measure the D. sechellia / D. simulans allele frequency of viable F1 males. We found that recombinant genotypes were rescued when they contained two specific loci from D. simulans - a region containing previously identified Lethal hybrid rescue (Lhr), and an unknown region of chromosome 3L which we name Sechellia aversion to hybrid rescue (Satyr). Our results show that the genetic basis for the recent evolution of this hybrid incompatibility is simple rather than a highly dispersed effect. Further, these data suggest that fixation of differences at Lhr after the split of the D. simulans clade strengthened the hybrid incompatibility between D. sechellia and D. melanogaster.

evolutionary biology↗

bioRxiv2018

Apigenin relaxes rat intrarenal arteries: involvement of Cl- channels and K+ channels

The vasodilator effect of apigenin (API) was demonstrated in a number of vascular beds. We aimed to characterize the vasospasmolytic and electrophysiological effects of apigenin (API) in intrarenal arteries (IRAs). The vascular tone of male rat isolated IRAs was recorded with a myograph. Transmembrane Cl- currents through Ca2+-activated Cl- channels (CaCCs), K+ currents through voltage-gated K+ (Kv) channels and inwardly rectifier K+ (Kir) channels were recorded with patch clamp in the freshly isolated arterial smooth muscle cells (ASMCs). Preincubation with API (10-100 M) concentration-dependently depressed the contractions induced by KCl, 9,11-dideoxy-9,11-methanoepoxy prostaglandin F2 (U46619), phenylephrine and vasopressin without significant preference and the IC50 values were 13.27-26.26 M. Acute application of API elicited instant relaxations in the IRAs precontracted with these vasoconstrictors and the RC50 values were 5.80-24.33 M. API relaxation was attenuated by chloride deprivation, CaCC blockers, Kv blocker and nitric oxide synthase inhibitor, but not by Kir blocker and cyclooxygenase inhibitor. At 10-100 M, API depressed CaCC currents and Kir currents while enhanced Kv currents of IRA ASMCs. The present results demonstrate that API counteracts various vasoconstrictors noncompetitively and nonspecifically and suggest that modulation of CaCCs, Kv and Kir channels of IRA ASMCs is involved in its vasospasmolytic effects.

pharmacology and toxicology↗

bioRxiv2018

PRL-1 is required for neuroprotection against olfactory CO2 stimulation in Drosophila

The Mammalian phosphatase of regenerating liver (PRL) family is primarily recognized for its oncogenic properties. Here we found that in Drosophila, loss of prl-1 resulted in CO2-induced brain disorder presented as irreversible wing hold up with enhancement of Ca2+ responses at the neuron synaptic terminals. Overexpression of Prl-1 in the nervous system could rescue the mutant phenotype. We show that Prl-1 is particularly expressed in CO2-responsive neural circuit and the higher brain centers. Ablation of the CO2 olfactory receptor, Gr21a, suppressed the mutant phenotype, suggesting that CO2 acts as a neuropathological substrate in absence of Prl-1. Further studies found that the wing hold up is an obvious consequence upon knockdown of Uex, a magnesium transporter, which directly interacts with Prl-1. Conditional expression of Uex in the nervous system could rescue the phenotype of prl-1 mutants. We demonstrate that Uex acts genetically downstream of Prl-1. Our findings provide important insights into mechanisms of Prl-1 protection against olfactory CO2 stimulation induced brain disorder at the level of detailed neural circuits and functional molecular connections.

neuroscience↗