Biology subjects

wu, y.

Publications and source records attributed to wu, y..

9 recordsLinked to original sources

bioRxiv2025

HPV16 E2 protein possesses intrinsic helicase activity and sterically hinders E1 function through direct interaction

HPV16 E2 protein is a key regulatory protein essential for viral replication, yet no enzymatic activity had been attributed to it until now. In this study, we report for the first time that E2 possesses intrinsic ATP-dependent DNA unwinding activity. Mutational analysis identified residues K299, Y303, and K306 as critical for this helicase function. We further demonstrate that podophyllotoxin directly binds to E2 and inhibits its unwinding activity with an IC50 of 0.1074 {micro}M, mediated primarily by residues Q320 and H342. Comparative analysis revealed that the ATPase and helicase activities of E2 are considerably weaker than those of E1. Notably, we discovered that E2 potently inhibits the helicase activity of E1. This suppression is facilitated by the N-terminal domain of E2 (amino acids 1-245) through direct interaction with E1, with residue E39 playing a critical role. Our findings not only unveil a previously unrecognized enzymatic function of E2 but also suggest its role as a potential antiviral target. Moreover, the observed inhibitory effect of E2 on E1 highlights a novel regulatory mechanism for HPV DNA replication. Synopsis O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/676238v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@12fd0aforg.highwire.dtl.DTLVardef@2dc50forg.highwire.dtl.DTLVardef@e46f5eorg.highwire.dtl.DTLVardef@14b87da_HPS_FORMAT_FIGEXP M_FIG C_FIG E2 protein has traditionally been recognized primarily for its DNA-binding and transcriptional regulatory functions. This study provides the first evidence that E2 protein possesses intrinsic enzymatic activity, identifies a small-molecule inhibitor targeting this activity, and reveals a novel mechanism of E1-E2 interaction. O_LIHPV16 E2 Protein Exhibits ATPase and Helicase Activities C_LIO_LIIdentification of Key Amino Acid Residues for HPV16 E2 Protein Enzymatic Activity C_LIO_LIPPT Effectively Inhibits E2 Protein Helicase Activity In Vitro C_LIO_LIE2 Protein Exhibits Weaker Enzymatic Activity Than E1 and Inhibits E1 Helicase Activity C_LIO_LIE2 Inhibits E1 Helicase Activity Through Protein-Protein Interaction C_LI

molecular biology↗

bioRxiv2025

Spatiotemporal dynamics of Hemerocallis citrina habitat suitability in China under climate change scenarios

ObjectiveHemerocailis citrina, a perennial herb belonging to the Hemerocailis genus in the Apophaceae family, has been utilized as both food and medicine for thousands of years. Additionally, it is considered a traditional dominant cash crop in China. Therefore, analyzing the spatio-temporal distribution characteristics of climate sustability of H. citrina in current and future climatic conditions is crucial for its stable industry development in China. MethodENMTools was used to screen the data of 287 distribution points of H. citrina. 37 environmental variables affecting the distribution of H. citrina were selected, the MaxEnt model and Geographic Information System (ArcGIS) were used to simulate the potential distribution patterns of H. citrina in 5 periods (current, future 2040 s, 2060 s, 2080 s, and 2100 s), and the dominant climate factors affecting the distribution of H. citrina were analyzed through contribution rate, displacement importance value, and jackknife test. Results(1) The average AUC value of 10 cross-validated fits under the ROC curve for the training dataset was 0.933, and the average AUC value of 10 cross-validated fits for the test dataset was 0.901, this indicates that the simulation stability and reliability are highest when incorporating all three types of environmental variables. (2) The main environmental factors identified affecting their distribution include the lowest temperature of the coldest month, average temperature of the coldest quarter, slope, elevation, and carbonate or lime content, as determined by the contribution rate of cutting method, displacement contribution rate, and single factor response curve. (3) The model prediction showed that H. citrina was widely distributed in 34 provincial regions of China under the current climate conditions, with a suitable area of 646.81 km2. (4) Under the future emission scenarios, the suitable habitat for H. citrina is projected to shrink and not shift to higher latitudes, indicating a negative impact of climate warming on its distribution, which will reduce the suitable habitat and narrow the ecological niche. Temperature and precipitation have been identified as important factors affecting the distribution of H. citrina. Although H. citrinas suitable habitat is expected to decrease to varying degrees in the future, the distribution area is relatively stable and there will still be a broad natural habitat in the future. ConclusionThe species distribution model was used to predict the future temporal and spatial distribution of climate-suitable areas for H. citrina in China. Based on the models simulation results, it is recommended that north and southeast China become the main planting areas for H. citrina in the future, with Sichuan and other regions as key development areas. Additionally, other regions should prioritize developing suitable cash crops based on local conditions.

bioinformatics↗

bioRxiv2023

Molecular mechanism of acid stress response of A. acidoterrestris DSM 3922T under sublethal pH environment

Acid-responsive proteome expression profiles of Alicyclobacillus acidoterrestris (A. acidoterrestris) were analysed using label-free quantitative mass spectrometry to investigate its acid resistance mechanism at sublethal pH. Totally, 325 differential expression proteins were identified during acid stress at pH2.5 condition for 15 min, of which the expressions of 83 proteins were up-regulated and the other 242 proteins expressions were down-regulated. Differentially expressed proteins were mainly involved in organic nitrogen compounds metabolism, small molecule metabolism, organic acid metabolism and signal transduction. Overall, they were mapped into 97 metabolic pathways. Combination of KEGG pathway analysis and protein functional analysis suggested that the pH homeostasis system, changes in metabolic pathways, cell membrane permeability and DNA repair are the main acid resistance mechanisms of A. acidoterrestris at sublethal pH conditions. It is speculated that A. acidoterrestris may sense and transmit pH signals from the external environment through the nhaB protein which holds histidine-dependent acid resistance system, initiating a series of acid tolerance reactions. Our study demonstrated global physiological response of A. acidoterrestris to sublethal pH, which provided a better understanding of acid adaption mechanism of A. acidoterrestris.

microbiology↗

bioRxiv2022

ame-miR-34 modulates the larval body weight and immune response of Apis mellifera workers to Ascosphara apis invasion

MiRNAs are critical regulators of numerous physiological and pathological processes. Ascosphaera apis exclusively infects bee larvae and causes chalkbrood disease. However, the function and mechanism of miRNAs in the bee larval response to A. apis infection is poorly understood. Here, ame-miR-34, a previously predicted miRNA involved in the response of Apis mellifera ligustica larvae to A. apis invasion, was subjected to molecular validation, and overexpression and knockdown were then conducted to explore the regulatory functions of ame-miR-34 in larval body weight and immune response. Stem-loop RT-PCR and Sanger sequencing confirmed the authenticity of ame-miR-34 in the larval gut of A. m. ligustica. RT-qPCR results demonstrated that compared with that in the uninfected larval guts, the expression level of ame-miR-34 was significantly downregulated (P < 0.001) in the guts of A. apis-infected 4-, 5-, and 6-day-old larvae, indicative of the remarkable suppression of host ame-miR-34 due to A. apis infection. In comparison with the corresponding negative control (NC) groups, the expression level of ame-miR-34 in the larval guts in the mimic-miR-34 group was significantly upregulated (P < 0.001), while that in the inhibi- tor-miR-34 group was significantly downregulated (P < 0.01). Similarly, effective overexpression and knockdown of ame-miR-34 were achieved. In addition, the body weights of 5- and 6-day-old larvae were significantly increased compared with those in the mimic-NC group; the weights of 5-day-old larvae in the inhibitor-miR-34 group were significantly decreased in comparison with those in the inhibitor-NC group, while the weights of 4- and 6-day-old larvae in the inhibi- tor-miR-34 group were significantly increased, indicating the involvement of ame-miR-34 in modulating larval body weight. Furthermore, the expression levels of both hsp and abct in the guts of A. apis-infected 4-, 5- and 6-day-old larvae were significantly upregulated after ame-miR-34 overexpression. In contrast, after ame-miR-34 knockdown, the expression levels of the aforementioned two key genes in the A. apis-infected 4-, 5- and 6-day-old larval guts were significantly downregu- lated. Together, the results demonstrated that effective overexpression and knockdown of ame-miR-34 in both noninfected and A. apis-infected A. m. ligustica larval guts could be achieved by the feeding method, and ame-miR-34 exerted a regulatory function in the host immune response to A. apis invasion through positive regulation of the expression of hsp and abct. Our findings not only provide a valuable reference for the functional investigation of bee larval miRNAs but also reveal the regulatory role of ame-miR-34 in A. mellifera larval weight and immune response. Additionally, the results of this study may provide a promising molecular target for the treatment of chalkbrood disease.

molecular biology↗

bioRxiv2021

Nrf2 mediated ER-phagy protects against oxidative damage in intervertebral disc degeneration

Intervertebral disc degeneration (IDD) increases the risk of low back pain (LBP). Oxidative stress may induce cellular damage and contribute to various diseases including IDD. Endoplasmic reticulum autophagy (ER-phagy) is a specific type of autophagy, its role in oxidative stress induced damage as well as in IDD is unknown. This study explores the role of ER-phagy in oxidative damage in intervertebral disc nucleus pulposus cells (NPCs), as well as the Nrf2/FAM134B axis in ER-phagy regulation and IDD therapy. We found ER-phagy was decreased in NPCs during oxidative stress; while FAM134B may promote ER-phagy and alleviate oxidative stress induced ER-stress and apoptosis. In addition, the nuclear transcription factor Nrf2 may promote the expression of FAM134B as well as ER-phagy, and suppress ER-stress and apoptosis in NPCs. Furthermore, overexpression of FAM134B and Nrf2 could effectively attenuate the progression of IDD in rats in vivo. These results suggest Nrf2/FAM134B mediated ER-phagy may combat oxidative damage in cells; meanwhile, ER-phagy as well as Nrf2 could be potential therapeutic targets for IDD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/469451v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@188b390org.highwire.dtl.DTLVardef@1c4e4f6org.highwire.dtl.DTLVardef@193fe77org.highwire.dtl.DTLVardef@12770e2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2020

Sterilizing immunity against SARS-CoV-2 in hamsters conferred by a novel recombinant subunit vaccine

A safe and effective SARS-CoV-2 vaccine is essential to avert the on-going COVID-19 pandemic. Here, we developed a subunit vaccine, which is comprised of CHO-expressed spike ectodomain protein (StriFK) and nitrogen bisphosphonates-modified zinc-aluminum hybrid adjuvant (FH002C). This vaccine candidate rapidly elicited the robust humoral response, Th1/Th2 balanced helper CD4 T cell and CD8 T cell immune response in animal models. In mice, hamsters, and non-human primates, 2-shot and 3-shot immunization of StriFK-FH002C generated 28- to 38-fold and 47- to 269-fold higher neutralizing antibody titers than the human COVID-19 convalescent plasmas, respectively. More importantly, the StriFK-FH002C immunization conferred sterilizing immunity to prevent SARS-CoV-2 infection and transmission, which also protected animals from virus-induced weight loss, COVID-19-like symptoms, and pneumonia in hamsters. Vaccine-induced neutralizing and cell-based receptor-blocking antibody titers correlated well with protective efficacy in hamsters, suggesting vaccine-elicited protection is immune-associated. The StriFK-FH002C provided a promising SARS-CoV-2 vaccine candidate for further clinical evaluation.

microbiology↗

bioRxiv2020

Rigorous anterograde trans-monosynaptic tracing of genetic defined neurons with retargeted HSV1 H129

Neuroanatomical tracing technology is fundamental for unraveling the complex network of brain connectome. Tracing tools that could spread between neurons are urgently needed, especially the rigorous trans-monosynaptic anterograde tracer is still lacking. HSV1 strain H129 was proved to be an anterograde tracer and has been used to trace neuronal networks in several reports. However, H129 has a serious defect that it was demonstrated to infect neurons via axon terminals. Thus, when using H129 to dissect output neural circuit, its terminal take up capacity should be carefully considered. Here, we report a recombinant H129 that carrying the anti-Her2 scFv in glycoprotein D to target genetically defined neurons. With the usage of helper virus complementarily expressing Her2 and gD, we can realize the elucidation of direct projection regions of either a given brain nucleus or a specific neuron type. The retargeted H129 system complements the current neural circuit tracer arsenal, which provides a rigorous and practical anterograde trans-monosynaptic tool.

neuroscience↗

bioRxiv2020

Popularizing recombinant baculovirus-derived OneBac system for scaling-up production of all recombinant adeno-associated virus vector serotypes

Recombinant adeno-associated virus (rAAV) has been widely used as an efficient transgenic vector in biomedical research, as well as gene therapy. Serotype-associated transduction efficiency, tissue- or cell-type tropism and immunological profile are major considerations in the various applications of rAAVs. There are increasing needs for different serotypes of rAAV, either naturally isolated or artificially engineered. However, affordable and scalable production of a desired serotype of rAAV remains very difficult, especially for researchers lacking relevant experience. On the basis of our previously established single recombinant baculovirus expression vector (BEV)-derived OneBac system, we have optimized the process and expanded the rAAV production range to the full range of serotypes rAAV1-13. Firstly, the AAV Cap gene was optimized to translate by ribosome leaky scanning and the gene of interest (GOI) was cloned into the pFD/Cap-(ITR-GOI)-Rep2 shutte plasmid. Following the classical Bac-to-Bac method, sufficient BEV stock containing all rAAV packaging elements can be quickly obtained. Finally, we can repeatedly scale up production of rAAVs in one week by using a single BEV to infect suspension-cultured Sf9 cells. The rAAV1-13 show relatively high yields ranging from 5x104 to 4x105 VG/cell. More than 1x1015 VG purified rAAVs can be easily obtained from 5 L suspension-cultured Sf9 cells. As expected, rAAV serotypes 1-13 show different potencies for in vitro transduction and cell-type tropisms. In summary, the single BEV-derived OneBac system should prove popular for laboratory scaling-up production of any serotype of rAAV.

microbiology↗

bioRxiv2020

Introduction of a precocious metamorphosis BmNPV infection in the latter half of the fifth instar silkworm larvae

The silkworm, Bombyx mori, is a complete metamorphosis insect, the model to study insect physiology and biochemistry. Bombyx mori nucleopolyhedrovirus (BmNPV) is a principal pathogen of the silkworm and its host range is restricted to silkworm larvae, requiring interaction with larvae to accomplish virus replication. Prothoracic glands (PGs) are a model for synthetic ecdysone with regulating insect growth and development. This study performed a transcriptome analysis of silkworm PGs after BmNPV infection. Transcriptome data were annotated with KEGG, GO, and shown to be of high quality by RT-qPCR. The spatial expression profiles of BmJing and BmAryl indicate that they may be specifically expressed in silkworm PGs. The RT-qPCR results of the DEGs in the PGs of BmNPV-infected larvae at 24, 48, and 72 h and at the developmental stages of days-6 and 7, comparing to day-3, reveal that the DEGs may be related to the BmNPV infection via promoting early maturation in the latter half of the silkworm fifth instar. This study is the first report on the identification of possible genes in PGs correlating with the precocious molting and metamorphosis of silkworm larvae under BmNPV infection in the latter half of the fifth instar. Our findings will help to address the interactions between BmNPV infection and host developmental response. This work provides a new perspective on BmNPV infection and host developmental response, as well as suggesting candidate genes for further research.

molecular biology↗