Zhuofei Xu

Followers

Following

Co-authors

Public Views

Let's do something for a better and better world!

less

Interests

Uploads

Papers by Zhuofei Xu

RESEARCH ARTICLE Open Access Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033

Background: Strains of extraintestinal pathogenic Escherichia coli (ExPEC) can invade and coloniz... more Background: Strains of extraintestinal pathogenic Escherichia coli (ExPEC) can invade and colonize extraintestinal sites and cause a wide range of infections. Genomic analysis of ExPEC has mainly focused on isolates of human and avian origins, with porcine ExPEC isolates yet to be sequenced. To better understand the genomic attributes underlying the pathogenicity of porcine ExPEC, we isolated two E. coli strains PCN033 and PCN061 from pigs, assessed their in vivo virulence, and completed and compared their genomes. Results: Animal experiments demonstrated that strain PCN033, but not PCN061, was pathogenic in a pig model. The chromosome of PCN033 was 384 kb larger than that of PCN061. Among the PCN033-specific sequences, genes encoding adhesins, unique lipopolysaccharide, unique capsular polysaccharide, iron acquisition and transport systems, and metabolism were identified. Additionally, a large plasmid PCN033p3 harboring many typical ExPEC virulence factors was identified in PCN033....

Download

RESEARCH ARTICLE Open Access

Background: Actinobacillus pleuropneumoniae is an economically important animal pathogen that cau... more Background: Actinobacillus pleuropneumoniae is an economically important animal pathogen that causes contagious pleuropneumonia in pigs. Currently, the molecular evolutionary trajectories for this pathogenic bacterium remain to require a better elucidation under the help of comparative genomics data. For this reason, we employed a comparative phylogenomic approach to obtain a comprehensive understanding of roles of natural selective pressure and homologous recombination during adaptation of this pathogen to its swine host. Results: In this study, 12 A. pleuropneumoniae genomes were used to carry out a phylogenomic analyses. We identified 1,587 orthologous core genes as an initial data set for the estimation of genetic recombination and positive selection. Based on the analyses of four recombination tests, 23 % of the core genome of A. pleuropneumoniae showed strong signals for intragenic homologous recombination. Furthermore, the selection analyses indicated that 57 genes were under...

Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig

Frontiers in Microbiology

Tibetan pig is an important domestic mammal, providing products of high nutritional value for mil... more Tibetan pig is an important domestic mammal, providing products of high nutritional value for millions of people living in the Qinghai-Tibet Plateau. The genomes of mammalian gut microbiota encode a large number of carbohydrate-active enzymes, which are essential for the digestion of complex polysaccharides through fermentation. However, the current understanding of microbial degradation of dietary carbohydrates in the Tibetan pig gut is limited. In this study, we produced approximately 145 gigabases of metagenomic sequence data for the fecal samples from 11 Tibetan pigs. De novo assembly and binning recovered 322 metagenome-assembled genomes taxonomically assigned to 11 bacterial phyla and two archaeal phyla. Of these genomes, 191 represented the uncultivated microbes derived from novel prokaryotic taxa. Twenty-three genomes were identified as metagenomic biomarkers that were significantly abundant in the gut ecosystem of Tibetan pigs compared to the other low-altitude relatives. F...

Download

Functional characterization of murB-potABCD operon for polyamine uptake and peptidoglycan synthesis in Streptococcus suis

Microbiological research, 2018

Spermidine (Spd), spermine (Spm), and putrescine (Put), which are the most widely distributed cel... more Spermidine (Spd), spermine (Spm), and putrescine (Put), which are the most widely distributed cellular polyamines, are essential for normal growth and multiplication of both eukaryotic and prokaryotic cells. In this study, we identified the only putative polyamine transport system PotABCD in Streptococcus suis, a worldwide zoonotic Gram-positive pathogen causing lethal infections in humans and pigs. It was discovered that S. suis could uptake polyamines preferably Spd and Spm. By constructing a potA deleted mutant, we confirmed that PotABCD was responsible for polyamine uptake, and PotD bound to the protein of polyamines. The four PotABCD genes were co-transcribed with murB, a gene involved in peptidoglycan (PG) synthesis. Furthermore the roles of polyamine transport system in maintaining the PG structure were detected to understand the biological significance of this co-transcription. In contrast to the wild type, the mutant ΔpotA exhibited elongated chain length and abnormal cell ...

Erratum to: Genome-Wide Detection of Selection and Other Evolutionary Forces

Methods in molecular biology (Clifton, N.J.), 2015

The GTP binding sites interacted with RNA-dependent RNA polymerase of classical swine fever virus in de novo initiation

In silico biology, 2008

The NS5B protein of classical swine fever virus (CSFV) is an important enzyme bearing a unique RN... more The NS5B protein of classical swine fever virus (CSFV) is an important enzyme bearing a unique RNA-dependent RNA polymerase (RdRp) activity. The RdRp plays a crucial role in the viral replication cycle and in forming a replicase complex. However, the initiating synthesis mechanism of the CSFV RNA polymerase is unclearly described at present. Our aim is to reveal the RdRp-GTP docking sites and the effective modules of GTP initially bound to the polymerase in starting initiation of replication according to a well predicted CSFV RdRp model. Based on some known crystal structures of RNA polymerase, computational methods were used to establish the model of a CSFV RdRp. An analogous mechanism of CSFV RNA polymerase in de novo initiation was subsequently represented through docking a GTP into the structure model. The unique GTP binding pocket of the polymerase was pointed out: five residues E227, S408, R427, K435, and R439 involved in steady hydrogen bonds and two residues C407 and L232 in...

Download

Actinobacillus pleuropneumoniae two-component system QseB/QseC regulates the transcription of PilM, an important determinant of bacterial adherence and virulence

Veterinary microbiology, Jan 9, 2015

QseB/QseC is one of the five predicted two-component systems (TCSs) in Actinobacillus pleuropneum... more QseB/QseC is one of the five predicted two-component systems (TCSs) in Actinobacillus pleuropneumoniae. To understand the roles of this TCS in A. pleuropneumoniae, a markerless gene-deletion mutant ΔqseBC was constructed. Differentially expressed (DE) genes in ΔqseBC were filtered by microarray analysis. A total of 44 DE genes were found to be regulated by QseB/QseC system. The transcriptional profile of A. pleuropneumoniae ΔqseBC was compared with that of ΔluxS and catecholamine (CA) stimulations, 13 genes regulated by QseB/QseC were found also regulated by LuxS, and 3 Qse-regulons were co-regulated by CA stimulations, respectively. Binding of QseB to the promoters of three regulons (pilM, glpK and hugZ), which were co-regulated by QseB/QseC and LuxS, was evaluated by electrophoretic mobility-shift assay. Results indicated that pilM was directly regulated by phosphorylated-QseB. Then the pilM deletion mutant ΔpilM was constructed and characterized. Data presented here revealed that...

Synergistic inhibition of pseudorabies virus replication by porcine alpha/beta interferon and gamma interferon in vitro

European cytokine network, 2007

Interferon (IFN) is crucial for initiating the innate immune response and for the generation of t... more Interferon (IFN) is crucial for initiating the innate immune response and for the generation of the adaptive response. IFN, in most species, comprises IFN-alpha (IFN-alpha), IFN-beta (IFN-beta) and IFN-gamma (IFN-gamma). In this study, we compared the capacity of porcine IFN-alpha, -beta and -gamma, or a combination of them, to protect IBRS-2 cells (porcine kidney cells) from infection with pseudorabies virus (PRV). The results demonstrated that porcine IFN-beta (PoIFN-beta) was the most efficient of the three IFNs in conferring resistance PRV infection; 100 U/mL PoIFN-beta inhibited PRV plaque formation 5.3-fold. Compared with PoIFN-beta, porcine IFN-gamma (PoIFN-gamma) was less capable of inhibiting PRV plaque formation (3.3-fold inhibition). Porcine IFN-alpha (PoIFN-alpha) had the least capability of the three PoIFNs, and inhibited PRV plaque formation only 1.26-fold. The inhibitory capacity increased to only 2.3-fold with a treatment of 12,800 U/mL PoIFN-alpha. A combination of ...

Secreting expression of porcine interferon-alpha in Pichia pastoris and its antiviral activity

To highly express secreted porcine interferon-alpha(PoIFNα),the signal peptide was excised from t... more To highly express secreted porcine interferon-alpha(PoIFNα),the signal peptide was excised from the interferon-alpha gene and the mature gene(mPoIFNα,501bp) was cloned into the yeast-Escherichia shuttle vector pPIC9K to construct secreting recombinant expressing plasmid of pPIC9K-mPoIFNα.The pPIC9K-mPoIFNα was linearized by SalⅠ and co-transformed with ssDNA into Pichia pastoris cells GS115(defective with histidine) with LiCl.The transformants were selected with MD culture plate and identified by PCR.And then,the multicopy recombinant Pichia pastoris strain was selected by G418 resistance.The selected strain could specifically secret 20 000 mPoIFNα proteins which was demonstrated by SDS-PAGE and Western-blot.The mPoIFNα proteins were about 40.1% of total secreted proteins with the concentration of about 40 mg/L.The results of physicochemical property of the secreted protein indicated that the recombinant protein was insensitive to acid(pH2),partly sensitive to heat(56℃),and the antiviral activity could be neutralized by anti-PoIFNα serum and not by anti-PoIFNγ serum.The antiviral activity of mPoIFNα was tested by CPE50 method.The results showed that the rPoIFNα was of high antiviral activity,which was 8.0×106 U/mg against VSV in MDBK cells.

Secreting expression of porcine interferon-# beta# in Pichia pastoris and its antiviral activity

Draft genome sequence of Burkholderia sordidicola S170, a potential plant growth promoter isolated from coniferous forest soil in the Czech Republic

Burkholderia species are key players in the accumulation of carbon from cellulose decomposition i... more Burkholderia species are key players in the accumulation of carbon from cellulose decomposition in coniferous forest ecosystems. We report here the draft genome of Burkholderia sordidicola strain S170, containing features associated with known genes involved in plant growth promotion, the biological control of plant diseases, and green remediation technologies.

Download

Plasmid-mediated multidrug resistance and virulence in an avian pathogenic Escherichia coli strain isolated in China

Journal of Global Antimicrobial Resistance, 2014

Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colisepticaemia and has ... more Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colisepticaemia and has been previously reported as a potential zoonotic risk [1]. APEC strains often display a multidrug resistance pattern including resistance to aminoglycosides, blactams, chloramphenicol, fluoroquinolones, tetracyclines and trimethoprim/sulfamethoxazole [2]. In this study, an APEC strain (ACN001) isolated from the liver of a diseased chicken in China in 2010 was characterised. ACN001 was shown to belong to phylogenetic group B2 and was confirmed to be highly virulent in chicken and mouse models using previously described methods [3–5]. Antimicrobial susceptibility testing performed according to Clinical and Laboratory Standards Institute (CLSI) standards [6] revealed that the strain was multidrug-resistant, with high minimum inhibitory concentrations to amikacin (>16 mg/mL), ampicillin (256 mg/mL), chloramphenicol (256 mg/mL), ciprofloxacin (64 mg/mL), florfenicol (256 mg/mL), gentamicin (256 mg/ mL), norfloxacin (64 mg/mL), streptomycin (256 mg/mL) and tetracycline (256 mg/mL). To investigate further whether these resistance and virulence phenotypes were plasmid-mediated, the draft whole genome of ACN001 was sequenced using a Roche 454 GS-FLX Sequencer (Roche, Basel, Switzerland), and all contigs were analysed using Cytoscape software v.2.8.2 (http://www.cytoscape.org/). The predicted plasmid-related contigs were all BLASTed with the National Center for Biotechnology Information (NCBI) database (http://blast.ncbi.nlm.nih.gov/Blast.cgi) to confirm their accuracy. The gaps between these contigs were filled by sequencing PCR products and were assembled using Newbler v.2.3 (454 Life Sciences, Branford, CT). A total of six plasmids were obtained (pACN001-A, 60 043 bp; pACN001-B, 168 543 bp; pACN001-C, 5784 bp; pACN001-D, 6747 bp; pACN001-E, 6822 bp; pACN001F, 92 447 bp). The sequences were analysed using Glimmer 3.0

Changes in gene expression of Actinobacillus pleuropneumoniae in response to anaerobic stress reveal induction of central metabolism and biofilm formation

Journal of Microbiology, 2014

Actinobacillus pleuropneumoniae is an important porcine respiratory pathogen causing great econom... more Actinobacillus pleuropneumoniae is an important porcine respiratory pathogen causing great economic losses in the pig industry worldwide. Oxygen deprivation is a stress that A. pleuropneumoniae will encounter during both early infection and the later, persistent stage. To understand modulation of A. pleuropneumoniae gene expression in response to the stress caused by anaerobic conditions, gene expression profiles under anaerobic and aerobic conditions were compared in this study. The microarray results showed that 631 genes (27.7% of the total ORFs) were differentially expressed in anaerobic conditions. Many genes encoding proteins involved in glycolysis, carbon source uptake systems, pyruvate metabolism, fermentation and the electron respiration transport chain were up-regulated. These changes led to an increased amount of pyruvate, lactate, ethanol and acetate in the bacterial cells as confirmed by metabolite detection. Genes encoding proteins involved in cell surface structures, especially biofilm formation, peptidoglycan biosynthesis and lipopolysaccharide biosynthesis were up-regulated as well. Biofilm formation was significantly enhanced under anaerobic conditions. These results indicate that induction of central metabolism is important for basic survival of A. pleuropneumoniae after a shift to an anaerobic environment. Enhanced biofilm formation may contribute to the persistence of this pathogen in the damaged anaerobic host tissue and also in the early colonization stage. These discoveries give new insights into adaptation mechanisms of A. pleuropneumoniae in response to environmental stress.

Genomic Characterization of Haemophilus parasuis SH0165, a Highly Virulent Strain of Serovar 5 Prevalent in China

PLoS ONE, 2011

Haemophilus parasuis can be either a commensal bacterium of the porcine respiratory tract or an o... more Haemophilus parasuis can be either a commensal bacterium of the porcine respiratory tract or an opportunistic pathogen causing Gla ¨sser's disease, a severe systemic disease that has led to significant economical losses in the pig industry worldwide. We determined the complete genomic sequence of H. parasuis SH0165, a highly virulent strain of serovar 5, which was isolated from a hog pen in North China. The single circular chromosome was 2,269,156 base pairs in length and contained 2,031 protein-coding genes. Together with the full spectrum of genes detected by the analysis of metabolic pathways, we confirmed that H. parasuis generates ATP via both fermentation and respiration, and possesses an intact TCA cycle for anabolism. In addition to possessing the complete pathway essential for the biosynthesis of heme, this pathogen was also found to be well-equipped with different iron acquisition systems, such as the TonB system and ABC-type transport complexes, to overcome iron limitation during infection and persistence. We identified a number of genes encoding potential virulence factors, such as type IV fimbriae and surface polysaccharides. Analysis of the genome confirmed that H. parasuis is naturally competent, as genes related to DNA uptake are present. A nine-mer DNA uptake signal sequence (ACAAGCGGT), identical to that found in Actinobacillus pleuropneumoniae and Mannheimia haemolytica, followed by similar downstream motifs, was identified in the SH0165 genome. Genomic and phylogenetic comparisons with other Pasteurellaceae species further indicated that H. parasuis was closely related to another swine pathogenic bacteria A. pleuropneumoniae. The comprehensive genetic analysis presented here provides a foundation for future research on the metabolism, natural competence and virulence of H. parasuis.

Download

Genome comparison of a novel classical swine fever virus isolated in China in 2004 with other CSFV strains

Virus Genes, 2006

The genome of a novel classical swine fever virus (CSFV), SWH/CA/2004, isolated from a hog pen in... more The genome of a novel classical swine fever virus (CSFV), SWH/CA/2004, isolated from a hog pen in Henan Province, central China, is 12,296 nucleotides (nt) in length. It is composed of a 373-nt 5&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; terminal non-translated region (NTR), a 11,697-nt open reading frame (ORF) encoding a polyprotein of 3,898 amino acids (aa), and a 226-nt 3&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-NTR. Genome comparison of the SWH/CA/2004 isolate (GenBank Accession: DQ127910) with other known CSFV isolates was performed and analyzed. Corresponding segments from SWH/CA/2004 and other reported strains shared 80.4-99.8% identity at the nucleotide level and 89.5-99.8% identity at the amino acid level. From an evolutionary point of view, isolate SWH/CA/2004 is closely related to the highly virulent isolate cF114/CA/2001, with a pairwise distance of 0.013; and distantly related to the moderately virulent isolate GXWZ02/CA/2003, with pairwise distance 0.170. The phylogenetic trees of the full-length genome and the following region E(rns), E1, E2, and NS5B-based neighbor-joining (NJ) method were constructed and approximately divided into different genetic groups according to avirulence, moderate virulence and high virulence, while other region-based NJ trees demonstrated sequence conservation between these groups. The four genomic regions may constitute important criteria for genetic typing of diverse CSFV isolates. Based on these analyses, isolate SWH/CA/2004 was deduced to belong to the highly virulent isolate group. However, SWH/CA/2004 also contains a 14-U deletion in the 3&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;-NTR that is characteristic of avirulent isolates. These analyses constitute a comprehensive study of the phylogenetics of CSF based on distinct regions of the genome and may provide the basis for future molecular epidemiology research to identify virulent strain outbreaks and trigger implementation of appropriate control measures.

Diagnosis and molecular characterization of rabies virus from a buffalo in China: a case report

Virology Journal, 2011

Background Rabies virus (RABV) can infect many different species of warm-blooded animals. Glycopr... more Background Rabies virus (RABV) can infect many different species of warm-blooded animals. Glycoprotein G plays a key role in viral pathogenicity and neurotropism, and includes antigenic domains that are responsible for membrane fusion and host cell receptor recognition. Case presentation A case of buffalo rabies in China was diagnosed by direct fluorescent antibody test, G gene reverse-transcriptase polymerase chain reaction, and RABV mouse inoculation test. Molecular characterization of the RABV was performed using DNA sequencing, phylogenetic analysis and amino acid sequence comparison based on the G gene from different species of animals. Conclusion The results confirmed that the buffalo with suspected rabies was infected by RABV, which was genetically closely related to HNC (FJ602451) that was isolated from cattle in China in 2007. Comparison of the G gene among different species of animal showed that there were almost no amino acid changes among RABVs isolated from the same spe...

Download

Contribution of glutamine synthetase to the virulence of Streptococcus suis serotype 2

Veterinary Microbiology, 2009

Streptococcus suis serotype 2 (S. suis 2) is an important pathogen, responsible for diverse disea... more Streptococcus suis serotype 2 (S. suis 2) is an important pathogen, responsible for diverse diseases in swine and human. In this study, we investigated the role of the glutamine synthetase (GlnA) in the pathogenesis of S. suis 2 in mice. To assess the contribution of glutamine synthetase (GlnA) to the virulence of S. suis 2, an knockout mutant (DeltaglnA) unable to produce GlnA was constructed, and the virulence level of wild-type (WT) SC19 and the DeltaglnA mutant strain were compared in an in vitro adherence assay and murine infection models. The data showed that DeltaglnA mutant exhibited a significant decrease in adherence to the epithelial cells HEp-2. The DeltaglnA mutant strain was attenuated and could reduce mortality and morbidity in murine infection models. Furthermore, organ cultures showed that GlnA plays a role in the colonization of the specific organs involved in S. suis infection. Functional complementation of the glnA gene into the knockout mutant DeltaglnA or incubated with extracellular glutamine restored its ability to adhere to the epithelial cells HEp-2. These findings suggested that glnA is required for the full virulence in S. suis 2. Therefore, the DeltaglnA mutant was considered as an attenuated mutant.

Novel Insight into the Genetic Context of the cadAB Genes from a 4-chloro-2-methylphenoxyacetic Acid-Degrading Sphingomonas

PLoS ONE, 2013

The 2-methyl-4-chlorophenoxyacetic (MCPA) acid-degrader Sphingomonas sp. ERG5 has recently been i... more The 2-methyl-4-chlorophenoxyacetic (MCPA) acid-degrader Sphingomonas sp. ERG5 has recently been isolated from MCPAdegrading bacterial communities. Using Illumina-sequencing, the 5.7 Mb genome of this isolate was sequenced in this study, revealing the 138 kbp plasmid pCADAB1 harboring the 32.5 kbp composite transposon Tn6228 which contains genes encoding proteins for the removal of 2,4-dichlorophenoxyacetic acid (2,4-D) and MCPA, as well as the regulation of this pathway. Transposon Tn6228 was confirmed by PCR to be situated on the plasmid and also exist in a circular intermediate state-typical of IS3 elements. The canonical tfdAa-gene of group III 2,4-D degraders, encoding the first step in degradation of 2,4-D and related compounds, was not present in the chromosomal contigs. However, the alternative cadAB genes, also providing the initial degradation step, were found in Tn6228, along with the 2,4-D-degradation-associated genes tfdBCDEFKR and cadR. Putative reductase and ferredoxin genes cadCD of Rieske non-heme iron oxygenases were also present in close proximity to cadAB, suggesting that these might have an unknown role in the initial degradation reaction. Parts of the composite transposon contain sequence displaying high similarity to previously analyzed 2,4-D degradation genes, suggesting rapid dissemination and high conservation of the chlorinated-phenoxyacetic acid (PAA)-degradation genotype among the sphingomonads.

Download

Complete Genome Sequence of Pasteurella multocida HN06, a Toxigenic Strain of Serogroup D

Journal of Bacteriology, 2012

Pasteurella multocida is an important etiological agent that can cause many economically importan... more

Download

Enhanced biofilm formation and reduced virulence of Actinobacillus pleuropneumoniae luxS mutant

Microbial Pathogenesis, 2008

Actinobacillus pleuropneumoniae is the pathogen of porcine contagious pleuropneumonia causing gre... more Actinobacillus pleuropneumoniae is the pathogen of porcine contagious pleuropneumonia causing great economic losses globally. LuxS is known to be involved in the interspecies quorum sensing by mediating the production of AI-2 signal molecule and play important roles in regulating various behaviors of bacteria. In this study, A. pleuropneumoniae was tested to be able to produce AI-2 like molecule. A luxS

Download

Zhuofei Xu

Uploads

Papers by Zhuofei Xu

Log In