Publications
48 results found
Liu W, Bi J, Ren Y, et al., 2023, Targeting extracellular CIRP with an X-aptamer shows therapeutic potential in acute pancreatitis., iScience, Vol: 26
Severe acute pancreatitis (AP) is associated with a high mortality rate. Cold-inducible RNA binding protein (CIRP) can be released from cells in inflammatory conditions and extracellular CIRP acts as a damage-associated molecular pattern. This study aims to explore the role of CIRP in the pathogenesis of AP and evaluate the therapeutic potential of targeting extracellular CIRP with X-aptamers. Our results showed that serum CIRP concentrations were significantly increased in AP mice. Recombinant CIRP triggered mitochondrial injury and ER stress in pancreatic acinar cells. CIRP-/- mice suffered less severe pancreatic injury and inflammatory responses. Using a bead-based X-aptamer library, we identified an X-aptamer that specifically binds to CIRP (XA-CIRP). Structurally, XA-CIRP blocked the interaction between CIRP and TLR4. Functionally, it reduced CIRP-induced pancreatic acinar cell injury in vitro and L-arginine-induced pancreatic injury and inflammation in vivo. Thus, targeting extracellular CIRP with X-aptamers may be a promising strategy to treat AP.
Yang L, Wang J, Lu S, et al., 2023, Temperature-dependent carrier state mediated by H-NS promotes the long-term coexistence of Y. pestis and a phage in soil., PLoS Pathog, Vol: 19
The study of carrier state phages challenged the canonical lytic-lysogenic binary, and carrier state appears to be ubiquitous and ecologically important. However, the mechanisms of the carrier state are not well elucidated due to the limited phage models. Herein, we reported phage HQ103, similar to Escherichia coli phage P2. In contrast to the temperate P2 phage, the HQ103 phage does not insert its genome into the bacterial chromosome and displays a dual behavior depending on the temperature. At 37°C, HQ103 lyses the host and forms clear plaques due to the truncation of repressor CI and mutation of promoter Pc. In contrast, HQ103 maintains a carrier state lifestyle with Y. pestis at an environmental temperature (21°C). Mechanistically, we found that the host-encoded histone-like nucleoid-structuring protein H-NS, which is highly expressed at 21°C to silence the Cox promoter Pe and inhibits the phage lytic cycle. Subsequently, the HQ103 carrier state Y. pestis could grow and co-exist with the phage in the soil at 21°C for one month. Thus, this study reveals a novel carrier state lifestyle of phage HQ103 due to the H-NS mediated xenogeneic silencing and demonstrates that the carrier state lifestyle could promote long-term phage-host coexist in nature.
Zhang M, Zhang K, Chen Z, et al., 2023, Secretory expression of human thyroid stimulating hormone receptor A subunit in sf9 insect cell system, Journal of Xi'an Jiaotong University (Medical Sciences), Vol: 44, Pages: 409-414, ISSN: 1671-8259
Objective To construct the secretory expression system of insect cells to express the secretory TSHR A subunit protein in the ovarian cells of Spotoma oryzae (sf9). Methods A recombinant plasmid containing the target protein was constructed, and then the positive bacmid was screened out by the blue and white spots experiment. The verified bacmid was transfected into SF9 insect cells to obtain recombinant baculovirus. The virus was amplified, and the titer level was detected by virus plaque assay. Finally, Western blotting was used to identify the expression of the recombinant protein and optimize the expression conditions. Results During the construction of the protein expression system, PCR identification and sequencing results confirmed the correctness of the sequences of the recombinant plasmid and the recombinant bacmid. After the transfection of the bacmid, the signs of virus budding were observed in sf9 cells. The virus was collected and amplified. The titer of P1 generation virus was 2×107pfu/m according to the plaque assay. The recombinant protein was identified by Western blotting and confirmed to be exogenous into the culture medium. The optimal condition for virus infection and protein expression was 72 h after the infection when the multiplicity of infection (MOI) was 1. Conclusion We constructed an insect cell expression system secreting TSHR 22-289 (55 ku), and the protein could be successfully glycolyzed. This system provides a preliminary basis for the construction and production of its industrial platform and also provides a useful tool for studies on TSHR protein and prevention of GO in the future.
Li L, Zhong Q, Zhao Y, et al., 2023, First-in-human application of double-stranded RNA bacteriophage in the treatment of pulmonary Pseudomonas aeruginosa infection, MICROBIAL BIOTECHNOLOGY, ISSN: 1751-7915
Li Y, Zhu F, Li Y, et al., 2022, Bacteriophages allow selective depletion of gut bacteria to produce a targeted-bacterium-depleted mouse model, CELL REPORTS METHODS, Vol: 2, ISSN: 2667-2375
Guo R, Gao J, Hui L, et al., 2022, An Improved Method for Quick Quantification of Unsaturated Transferrin, BIOSENSORS-BASEL, Vol: 12
Wang X, Ji Y, Qiu C, et al., 2022, A phage cocktail combined with the enteric probiotic Lactobacillus reuteri ameliorated mouse colitis caused by S. typhimurium., Food Funct, Vol: 13, Pages: 8509-8523
Salmonella enterica serovar Typhimurium (S. typhimurium) is one of the most important foodborne pathogens that causes colitis in humans. In this study, we compared the effects of a therapeutic treatment using a phage cocktail (Pc) in combination or not with Lactobacillus reuteri (L. reuteri) in an S. typhimurium-induced colitis murine model. An oral administration of 4 × 108 CFU per mouse of S. typhimurium resulted in intestinal barrier disruption and severe inflammatory symptoms. S. typhimurium in the colon of the mice treated with the Pc and L. reuteri (PcLR) combination were completely removed compared to those in the single Pc or single L. reuteri treatment groups. Furthermore, compared with the infected group, the intestinal barrier and colonic pathological damage were significantly improved in the PcLR-treated group. Additionally, the short-chain fatty acid (SCFA) levels in the feces of the mice in the PcLR treatment group were significantly increased compared to those in the feces of the mice in the infected group. In addition, the combination of Pc with acetate and reuterin released by L. reuteri (PcReAc) can also achieve the same effect as PcLR treatment. Thus, these results indicated that the acetate and reuterin released by L. reuteri play an important role in the treatment. The extraordinary therapeutic effects of PcLR and PcReAc depend on the specific bactericidal activity of Pc and the broad-spectrum bactericidal activity and immunomodulation of L. reuteri (or acetate and reuterin) in the host. This study provides a new concept for the treatment of inflammatory diseases caused by intestinal pathogens.
Zhang K, Li S, Wang Y, et al., 2022, Bacteriophage protein PEIP is a potent Bacillus subtilis enolase inhibitor, CELL REPORTS, Vol: 40, ISSN: 2211-1247
Yang H, Yuan H, Zhao X, et al., 2022, Cytoplasmic domain and enzymatic activity of ACE2 are not required for PI4KB dependent endocytosis entry of SARS-CoV-2 into host cells, VIROLOGICA SINICA, Vol: 37, Pages: 380-389, ISSN: 1674-0769
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- Citations: 2
Zhang P, Zhao X, Wang Y, et al., 2022, Bacteriophage protein Gp46 is a cross-species inhibitor of nucleoid-associated HU proteins., Proc Natl Acad Sci U S A, Vol: 119
The architectural protein histone-like protein from Escherichia coli strain U93 (HU) is the most abundant bacterial DNA binding protein and highly conserved among bacteria and Apicomplexan parasites. It not only binds to double-stranded DNA (dsDNA) to maintain DNA stability but also, interacts with RNAs to regulate transcription and translation. Importantly, HU is essential to cell viability for many bacteria; hence, it is an important antibiotic target. Here, we report that Gp46 from bacteriophage SPO1 of Bacillus subtilis is an HU inhibitor whose expression prevents nucleoid segregation and causes filamentous morphology and growth defects in bacteria. We determined the solution structure of Gp46 and revealed a striking negatively charged surface. An NMR-derived structural model for the Gp46-HU complex shows that Gp46 occupies the DNA binding motif of the HU and therefore, occludes DNA binding, revealing a distinct strategy for HU inhibition. We identified the key residues responsible for the interaction that are conserved among HUs of bacteria and Apicomplexans, including clinically significant Mycobacterium tuberculosis, Acinetobacter baumannii, and Plasmodium falciparum, and confirm that Gp46 can also interact with these HUs. Our findings provide detailed insight into a mode of HU inhibition that provides a useful foundation for the development of antibacteria and antimalaria drugs.
Wang M, Wang C, Feng C, et al., 2022, Potent antitumor activity of novel taxoids in anaplastic thyroid cancer., Endocrine, Vol: 75, Pages: 465-477
PURPOSE: Anaplastic thyroid cancer (ATC) is the most aggressive form of thyroid cancers and it is rapidly fatal without any effective therapeutic regimens. There are some clinical trials showing that paclitaxel-based chemotherapy for ATC can achieve a relatively high response rate and low incidence of adverse reaction. The aim of this study was to evaluate potential therapeutic activity of novel taxoids in ATC cells. METHODS: We evaluated antitumor activity of five novel 3'-difluorovinyltaxoids (DFV-taxoids) in anaplastic thyroid cancer cells by a series of in vitro and in vivo experiments. Besides, we also explored the potential mechanism underlying the difference among the taxoids and paclitaxel by molecular docking and tubulin polymerization assays. RESULTS: Our data showed that these novel DFV-taxoids were more effective than paclitaxel in ATC cell lines and xenografts, as reflected by the inhibition of cell proliferation, colony formation and tumorigenic potential in nude mice, and the induction of G2/M phase arrest and cell apoptosis. Using tubulin polymerization assays and molecular docking analysis, we found that these DFV-taxoids promoted more rapid polymerization of β-tubulin than paclitaxel. CONCLUSIONS: Our data demonstrate that these novel taxoids exhibit stronger antitumor activity in ATC cells than paclitaxel, thereby providing a promising therapeutic strategy for the patients with ATC.
Liu B, Li S, Liu Y, et al., 2021, Bacteriophage Twort protein Gp168 is a beta-clamp inhibitor by occupying the DNA sliding channel, NUCLEIC ACIDS RESEARCH, Vol: 49, Pages: 11367-11378, ISSN: 0305-1048
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- Citations: 3
Zhao K, Ke Z, Hu H, et al., 2021, Erratum for Zhao et al., "Structural Basis and Function of the N Terminus of SARS-CoV-2 Nonstructural Protein 1"., Microbiol Spectr, Vol: 9
Zhao K, Ke Z, Hu H, et al., 2021, Structural Basis and Function of the N Terminus of SARS-CoV-2 Nonstructural Protein 1, MICROBIOLOGY SPECTRUM, Vol: 9, ISSN: 2165-0497
Wang Z, Wang H, Mulvenna N, et al., 2021, A bacteriophage DNA mimic protein employs a non-specific strategy to inhibit the bacterial RNA polymerase, Frontiers in Microbiology, Vol: 12, Pages: 1-10, ISSN: 1664-302X
DNA mimicry by proteins is a strategy that employed by some proteins to occupy the binding sites of the DNA-binding proteins and deny further access to these sites by DNA. Such proteins have been found in bacteriophage, eukaryotic virus, prokaryotic, and eukaryotic cells to imitate non-coding functions of DNA. Here, we report another phage protein Gp44 from bacteriophage SPO1 of Bacillus subtilis, employing mimicry as part of unusual strategy to inhibit host RNA polymerase. Consisting of three simple domains, Gp44 contains a DNA binding motif, a flexible DNA mimic domain and a random-coiled domain. Gp44 is able to anchor to host genome and interact bacterial RNA polymerase via the β and β′ subunit, resulting in bacterial growth inhibition. Our findings represent a non-specific strategy that SPO1 phage uses to target different bacterial transcription machinery regardless of the structural variations of RNA polymerases. This feature may have potential applications like generation of genetic engineered phages with Gp44 gene incorporated used in phage therapy to target a range of bacterial hosts.
Zhang K, Li X, Wang Z, et al., 2021, Systemic Expression, Purification, and Initial Structural Characterization of Bacteriophage T4 Proteins Without Known Structure Homologs, FRONTIERS IN MICROBIOLOGY, Vol: 12, ISSN: 1664-302X
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- Citations: 2
Wang Z, Zhao S, Li Y, et al., 2021, RssB-mediated sigma(S) Activation is Regulated by a Two-Tier Mechanism via Phosphorylation and Adaptor Protein - IraD, JOURNAL OF MOLECULAR BIOLOGY, Vol: 433, ISSN: 0022-2836
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- Citations: 1
Li Y, Li G, Wang Z, et al., 2021, Resonance assignments of the cytoplasmic domain of ECF sigma factor W pathway protein YsdB from Bacillus subtilis, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 15, Pages: 103-106, ISSN: 1874-2718
Xu C, Ke Z, Liu C, et al., 2020, Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server, JOURNAL OF CHEMICAL INFORMATION AND MODELING, Vol: 60, Pages: 5735-5745, ISSN: 1549-9596
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- Citations: 14
Zhu F, Guo R, Wang W, et al., 2020, Transplantation of microbiota from drug-free patients with schizophrenia causes schizophrenia-like abnormal behaviors and dysregulated kynurenine metabolism in mice, MOLECULAR PSYCHIATRY, Vol: 25, Pages: 2905-2918, ISSN: 1359-4184
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- Citations: 97
Krishna A, Liu B, Peacock SJ, et al., 2020, The prevalence and implications of single-nucleotide polymorphisms in genes encoding 3 the RNA polymerase of clinical isolates of Staphylococcus aureus, MicrobiologyOpen, Vol: 9, Pages: 1-8, ISSN: 2045-8827
Central to the regulation of bacterial gene expression is the multisubunit enzyme RNA polymerase (RNAP), which is responsible for catalyzing transcription. As all adaptive processes are underpinned by changes in gene expression, the RNAP can be considered the major mediator of any adaptive response in the bacterial cell. In bacterial pathogens, theoretically, single nucleotide polymorphisms (SNPs) in genes that encode subunits of the RNAP and associated factors could mediate adaptation and confer a selective advantage to cope with biotic and abiotic stresses. We investigated this possibility by undertaking a systematic survey of SNPs in genes encoding the RNAP and associated factors in a collection of 1,429 methicillin‐resistant Staphylococcus aureus (MRSA) clinical isolates. We present evidence for the existence of several, hitherto unreported, nonsynonymous SNPs in genes encoding the RNAP and associated factors of MRSA ST22 clinical isolates and propose that the acquisition of amino acid substitutions in the RNAP could represent an adaptive strategy that contributes to the pathogenic success of MRSA.
Yang Y, Ke Z, Wang Z, et al., 2020, H-1, C-13 and (15) N NMR assignments of solubility tag protein Msyb of Escherichia coli, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 14, Pages: 251-254, ISSN: 1874-2718
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- Citations: 2
Wang Z, Liang Y, Liu H, et al., 2020, Resonance assignments of bacteriophage SPO1 Gp49 protein, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 14, Pages: 111-114, ISSN: 1874-2718
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- Citations: 2
Zhang K, Wang Z, Chang G, et al., 2019, Resonance assignments of bacteriophage T4 Y04L protein, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 14, Pages: 51-54, ISSN: 1874-2718
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- Citations: 2
Wang Z, Zhao S, Jiang S, et al., 2019, Resonance assignments of N-terminal receiver domain of sigma factor S regulator RssB from Escherichia coli, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 13, Pages: 333-337, ISSN: 1874-2718
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- Citations: 1
Zhang P, Wang Z, Zhao S, et al., 2019, H-1, C-13 and N-15 NMR assignments of Bacillus subtilis bacteriophage SPO1 protein Gp46, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 13, Pages: 245-247, ISSN: 1874-2718
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- Citations: 3
Zhao S, Zhang K, Jiang S, et al., 2019, Resonance assignments of sigma factor S binding protein Crl from Escherichia coli, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 13, Pages: 223-226, ISSN: 1874-2718
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- Citations: 2
Darvill N, Blake T, Rouse S, et al., 2018, Structural basis of phosphatidic acid sensing by APH in apicomplexan parasites, Structure, Vol: 26, Pages: 1059-1071.e6, ISSN: 0969-2126
Plasmodium falciparum and Toxoplasma gondii are obligate intracellular parasites that belong to the phylum of Apicomplexa and cause major human diseases. Their access to an intracellular lifestyle is reliant on the coordinated release of proteins from the specialized apical organelles called micronemes and rhoptries. A specific phosphatidic acid effector, the acylated pleckstrin homology domain-containing protein (APH) plays a central role in microneme exocytosis and thus is essential for motility, cell entry, and egress. TgAPH is acylated on the surface of the micronemes and recruited to phosphatidic acid (PA)-enriched membranes. Here, we dissect the atomic details of APH PA-sensing hub and its functional interaction with phospholipid membranes. We unravel the key determinant of PA recognition for the first time and show that APH inserts into and clusters multiple phosphate head-groups at the bilayer binding surface.
Liu B, Wang Z, Lan L, et al., 2018, A rapid colorimetric method to visualize protein interactions, Chemistry - A European Journal, Vol: 24, Pages: 6727-6731, ISSN: 0947-6539
As key molecules in most biological pathways, proteins physically contact one or more biomolecules in a highly specific manner. Several driving forces (i.e., electrostatic and hydrophobic) facilitate such interactions and a variety of methods have been developed to monitor these processes both in vivo and in vitro. In this work, a new method is reported for the detection of protein interactions by visualizing a color change of a cyanine compound, a supramolecule complex of 3,3-di-(3-sulfopropyl)-4,5,4',5'-dibenzo-9-methyl-thiacarbocyanine triethylammonium salt (MTC). Nuclear magnetic resonance (NMR) studies suggest that the hydrophobic nature of the protein surfaces drives MTC into different types of aggregates with distinct colors. When proteins interact with other biomolecules, the hydrophobic surface of the complex differs, resulting in a shift in the form of MTC aggregation, which results in a color change. As a result, this in vitro method has the potential to become a rapid tool for the confirmation of protein-biomolecule interactions, without the requirements for sophisticated instrumentation or approaches.
Tabib-Salazar A, Liu B, Declan B, et al., 2018, T7 phage factor required for managing RpoS in Escherichia coli, Proceedings of the National Academy of Sciences, Vol: 115, Pages: E5353-E5362, ISSN: 0027-8424
T7 development in Escherichia coli requires the inhibition of the housekeepingform of the bacterial RNA polymerase (RNAP), Eσ70, by two T7 proteins: Gp2and Gp5.7. While the biological role of Gp2 is well understood, that of Gp5.7remains to be fully deciphered. Here, we present results from functional andstructural analyses to reveal that Gp5.7 primarily serves to inhibit EσS, thepredominant form of the RNAP in the stationary phase of growth, whichaccumulates in exponentially growing E. coli as a consequence of buildup ofguanosine pentaphosphate ((p)ppGpp) during T7 development. We furtherdemonstrate a requirement of Gp5.7 for T7 development in E. coli cells in thestationary phase of growth. Our finding represents a paradigm for how somelytic phages have evolved distinct mechanisms to inhibit the bacterialtranscription machinery to facilitate phage development in bacteria in theexponential and stationary phases of growth.
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