Xingye Xu

Peking Union Medical College Hospital, Peping, Beijing, China

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Publications (33)

  • Xingye Xu · Tao Liu · Xianwen Ren · [...] · Qi Jin
    [Show abstract] [Hide abstract] ABSTRACT: Infections caused by dermatophytes, Trichophyton rubrum (T. rubrum) in particular, are among the most common diseases in humans. In this study, we present a proteogenomic analysis of T. rubrum based on whole-genome proteomics and RNA-Seq studies. We confirmed 4,291 expressed proteins in T. rubrum and validated their annotated gene structures based on 35,874 supporting peptides. In addition, we identified 323 novel peptides (not present in the current annotated protein database of T. rubrum) that can be used to enhance current T. rubrum annotations. A total of 104 predicted genes supported by novel peptides were identified, and 127 gene models suggested by the novel peptides that conflicted with existing annotations were manually assigned based on transcriptomic evidence. RNA-Seq confirmed the validity of 95% of the total peptides. Our study provides evidence that confirms and improves the genome annotation of T. rubrum and represents the first survey of T. rubrum genome annotations based on experimental evidence. Additionally, our integrated proteomics and multi-sourced transcriptomics approach provides stronger evidence for annotation refinement than proteomic data alone, which helps to address the dilemma of "one-hit wonders" (uncertainties supported by only one peptide).
    Article · Apr 2015 · Journal of Proteome Research
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    Tao Liu · Xingye Xu · Wenchuan Leng · [...] · Qi Jin
    [Show abstract] [Hide abstract] ABSTRACT: Trichophyton rubrum, an anthropophilic and cosmopolitan fungus, is the most common agent of superficial mycoses. In this study, T. rubrum infection was modeled by adding human skin sections to a limited medium containing glucose, and cDNA microarrays were used to monitor T. rubrum gene expression patterns on a global level. We observed that exposure to human skin resulted in up-regulation of the expression levels of T. rubrum genes related to many cellular and biological processes, including transcription and translation; metabolism and secondary transport; stress response; and signaling pathways. These results provide a reference set of T. rubrum genes whose expression patterns change upon infection and reveal previously unknown genes that probably correspond to proteins that should be considered as virulence factor candidates and potential new drug targets for T. rubrum infection.
    Full-text Article · Feb 2014 · Journal of Medical Microbiology
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    [Show abstract] [Hide abstract] ABSTRACT: Accumulating evidence demonstrates that non-coding RNAs (ncRNAs) are indispensable components of many organisms and play important roles in cellular events, regulation, and development. Here, we analysed the small non-coding RNA (ncRNA) transcriptome of Trichophyton rubrum by constructing and sequencing a cDNA library from conidia and mycelia. We identified 352 ncRNAs and their corresponding genomic loci. These ncRNA candidates included 198 entirely novel ncRNAs and 154 known ncRNAs classified as snRNAs, snoRNAs and other known ncRNAs. Further bioinformatic analysis detected 96 snoRNAs, including 56 snoRNAs that had been annotated in other organisms and 40 novel snoRNAs. All snoRNAs belonged to two major classes--C/D box snoRNAs and H/ACA snoRNAs--and their potential target sites in rRNAs and snRNAs were predicted. To analyse the evolutionary conservation of the ncRNAs in T. rubrum, we aligned all 352 ncRNAs to the genomes of six dermatophytes and to the NCBI non-redundant nucleotide database (NT). The results showed that most of the identified snRNAs were conserved in dermatophytes. Of the 352 ncRNAs, 102 also had genomic loci in other dermatophytes, and 27 were dermatophyte-specific. Our systematic analysis may provide important clues to the function and evolution of ncRNAs in T. rubrum. These results also provide important information to complement the current annotation of the T. rubrum genome, which primarily comprises protein-coding genes.
    Full-text Article · Dec 2013 · BMC Genomics
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    [Show abstract] [Hide abstract] ABSTRACT: Tuberculosis (TB) is an infectious bacterial disease that causes morbidity and mortality, especially in developing countries. Although the efficacy against TB has displayed a high degree of variability (0-80%) in different trials, Mycobacterium bovis bacillus Calmette-Guerin (BCG) has been recognized as an important weapon for preventing TB worldwide for over 80 years. Because secreted proteins often play vital roles in the interaction between bacteria and host cells, the secretome of mycobacteria is considered to be an attractive reservoir of potential candidate antigens for the development of novel vaccines and diagnostic reagents. In this study, we performed a proteomic analysis of BCG culture filtrate proteins using SDS-PAGE and high-resolution Fourier transform mass spectrometry. In total, 239 proteins (1555 unique peptides) were identified, including 185 secreted proteins or lipoproteins. Furthermore, 17 novel protein products not annotated in the BCG database were detected and validated by RT-PCR at the transcriptional level. Additionally, the translational start sites of 52 proteins were confirmed, and 22 proteins were validated by extension of the translational start sites based on N-terminus-derived peptides. Compared with previous studies on the mycobacterial secretome, there are 103 secreted proteins that have not been reported that are unique to our study. The physicochemical characteristics of the secreted proteins were determined. Major components from the culture supernatant, including low-molecular-weight antigens, lipoproteins, PE and PPE family proteins and Mce family proteins, were discussed; some components represent potential predominant antigens in the humoral and cellular immune responses.
    Full-text Article · Apr 2013 · Molecular & Cellular Proteomics
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    XingYe Xu · Tao Liu · WenChuan Leng · [...] · Qi Jin
    [Show abstract] [Hide abstract] ABSTRACT: Trichophyton rubrum (T. rubrum) is a common superficial fungus. Molecular and genetic studies of T. rubrum are still limited. In this paper, we report the global analysis of gene expression profiles at different growth phases using cDNA microarray technology. A total of 2044 differentially expressed genes were obtained and clustered into three expression patterns. Our data confirmed previous results that many mRNAs were pre-stored in the conidia of T. rubrum. Transcriptional profiling and function analysis showed that some glycolytic enzymes share similar expression patterns and may be coregulated during the transition of growth phases. Some genes involved in small GTPase signaling pathways, and in cAMP-dependent and MAPK regulation pathways were induced in response to the growth dynamics of T. rubrum. Although the detailed biological roles of these T. rubrum genes are still unknown, our results suggest that these genes may be involved in regulation mechanisms in the life cycle of the fungus.
    Full-text Article · Jun 2011 · Science China. Life sciences
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    [Show abstract] [Hide abstract] ABSTRACT: Bacillus cereus strain Q1 was isolated from a deep-subsurface oil reservoir in the Daqing oil field in northeastern China. This strain is able to produce biosurfactants and to survive in extreme environments. Here we report the finished and annotated genome sequence of this organism.
    Full-text Article · Feb 2009 · Journal of bacteriology
  • [Show abstract] [Hide abstract] ABSTRACT: In China, comparatively little research has been directed at serogroup B meningococci, which are mainly isolated from healthy individuals. We attempted to study the genotypic characterization of Neisseria meningitidis serogroup B strains. We analyzed 150 N. meningitidis strains isolated in China during 1975-2005 by multilocus sequence typing (MLST) and porA typing. A total of 88 different sequence types (STs) were identified by MLST, 73 of which were newly identified. Seven complexes previously identified in other countries and three unique clonal lineages first identified in China were detected, seven of which had previously been described as 'hyperinvasive meningococcal lineages'. Several lineages were found in specified period. A total of 63 different porA types were found, 11 of which were novel. The most common porA types were P1.5-1,2-2 (17 isolates), P1.5-1,10-4 (12 isolates), P1.5-2,2-2 (eight isolates) and P1.7-2,4 (seven isolates). In this context, serogroup B meningococci provide a diverse, continually reassorted gene pool from which new genotypes arise. The most important mechanism is probably horizontal genetic exchange among N. meningitidis serogroup B strains, possibly resulting in the emergence of new meningococcal clones. These results may help our understanding of the genotypic distribution of serogroup B meningococci and provide clues for further study of this organism.
    Article · Apr 2008 · The Journal of infection
  • [Show abstract] [Hide abstract] ABSTRACT: An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 complex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak.
    Article · Feb 2008 · Science in China Series C Life Sciences
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    Junping Peng · Li Yang · Fan Yang · [...] · Qi Jin
    [Show abstract] [Hide abstract] ABSTRACT: Ten outbreaks of a new serogroup C meningococcal disease emerged during 2003-2005 in China. The multilocus sequence typing results indicated that unique sequence type 4821 clone meningococci were responsible for these outbreaks. Herein, we determined the entire genomic DNA sequence of serogroup C isolate 053442, which belongs to ST-4821. Comparison of 053442 gene contents with other meningococcal genomes shows that they have similar characteristics, including thousands of repetitive elements and simple sequence repeats, numerous phase-variable genes, and similar virulence-related factors. However, many strain-specific regions were found in each genome. We also present the results of a genomic comparison of 28 ST-4821 complex isolates that were isolated from different serogroups using comparative genomic hybridization analysis. Genome comparison between the newly emerged hyperinvasive isolates belonging to different serogroups will further our understanding of their respective pathogenetic mechanisms.
    Full-text Article · Feb 2008 · Genomics
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    [Show abstract] [Hide abstract] ABSTRACT: An increase in the number of serogroup C meningococcal disease cases occurred in China from September 2003 to January 2006 as a result of several successive outbreaks. In addition, the proportion of serogroup C Neisseria meningitidis isolates from sporadic cases and carriers has also increased. In this study, 113 serogroup C meningococcal isolates were characterized by multilocus sequence typing (MLST) and PorA typing. These isolates comprised those from outbreak cases and their close contacts, the national carriage survey conducted during the same period and some historical isolates from 1966-2002. Twenty MLST sequence types (STs) and 21 PorA variable region (VR) types were identified in the collection. The ST-4821 complex, a newly identified lineage, was the most prevalent lineage (95/113). These data also showed a high level of diversification of serogroup C isolates, as indicated by the number of variants of the ST-4821 clone and the VR types present. There were ten PorA VR types among the ST-4821 isolates, and certain VR types (P1.7-2,14, P1.12-1,16-8) were associated with isolates from outbreak cases. The results of this study allow us to draw a profile of the molecular characteristics of serogroup C strains in China. These data are helpful for monitoring the spread of virulent strains and will provide valuable information for the prevention of bacterial meningitis in China.
    Full-text Article · Oct 2007 · Journal of Medical Microbiology
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    [Show abstract] [Hide abstract] ABSTRACT: Conidia are considered to be the primary cause of infections by Trichophyton rubrum. We have developed a cDNA microarray containing 10250 ESTs to monitor the transcriptional strategy of conidial germination. A total of 1561 genes that had their expression levels specially altered in the process were obtained and hierarchically clustered with respect to their expression profiles. By functional analysis, we provided a global view of an important biological system related to conidial germination, including characterization of the pattern of gene expression at sequential developmental phases, and changes of gene expression profiles corresponding to morphological transitions. We matched the EST sequences to GO terms in the Saccharomyces Genome Database (SGD). A number of homologues of Saccharomyces cerevisiae genes related to signalling pathways and some important cellular processes were found to be involved in T. rubrum germination. These genes and signalling pathways may play roles in distinct steps, such as activating conidial germination, maintenance of isotropic growth, establishment of cell polarity and morphological transitions. Our results may provide insights into molecular mechanisms of conidial germination at the cell level, and may enhance our understanding of regulation of gene expression related to the morphological construction of T. rubrum.
    Full-text Article · Apr 2007 · BMC Genomics
  • Jie Yang · Xiaobing Zhang · Xingye Xu · [...] · Qi Jin
    [Show abstract] [Hide abstract] ABSTRACT: To serologically and genetically characterize other serogroups (except A, B, and C) of Neisseria meningitidis isolates in China, we collected 56 strains of other serogroups, identified by serogroup typing and multilocus sequence typing (MLST). All of them are non-invasive isolates. The serogroups of the 56 Chinese isolates were W135 (11 isolates), Y (4), X (15), 29E (15), D (1), H (4), I (3), K (2), and non-groupable (1). By MLST, 34 different sequence types (STs) were identified, 28 of which were not found in the MLST database as of July 2006 and seemed to be unique to China. Statistical analysis of the MLST results revealed that, although the Chinese isolates seemed to be genetically divergent, they could be classified into 5 major clonal groups and other minor groups. Among these isolates, none of the well-documented ST complexes found worldwide was present.
    Article · Feb 2007 · Infectious Diseases
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    Jian Yang · Huan Nie · Lihong Chen · [...] · Qi Jin
    [Show abstract] [Hide abstract] ABSTRACT: The theory that Shigella is derived from multiple independent origins of Escherichia coli (Pupo et al. 2000) has been challenged by recent findings that the virulence plasmids (VPs) and the chromosomes share a similar evolutionary history (Escobar-Paramo et al. 2003), which suggests that an ancestral VP entered an E. coli strain only once, which gave rise to Shigella spp. In an attempt to resolve these conflicting theories, we constructed three phylogenetic trees in this study: a robust chromosomal tree using 23 housekeeping genes from 46 strains of Shigella and enteroinvasive E. coli (EIEC), a chromosomal tree using 4 housekeeping genes from 19 EcoR strains and 46 Shigella/EIEC strains, and a VP tree using 5 genes outside of the VP cell-entry region from 38 Shigella/EIEC strains. Both chromosomal trees group Shigella into three main clusters and five outliers, and strongly suggest that Shigella has multiple origins within E. coli. Most strikingly, the VP tree shows that the VPs from two main Shigella clusters, C1 and C2, are more closely related, which contradicts the chromosomal trees that place C2 and C3 next to each other but C1 at a distance. Additionally, we have identified a complete tra operon of the F-plasmid in the genome sequence of an EIEC strain and found that two other EIEC strains are also likely to possess a complete tra operon. All lines of evidence support an alternative multiorigin theory that transferable diverse ancestral VPs entered diverse origins of E. coli multiple times during a prolonged period of time, resulting in Shigella species with diverse genomes but similar pathogenic properties.
    Full-text Article · Feb 2007 · Journal of Molecular Evolution
  • Jian Yang · Huan Nie · Lihong Chen · [...] · Qi Jin
    Dataset · Jan 2007
  • [Show abstract] [Hide abstract] ABSTRACT: Sexual and asexual development.
    Dataset · Oct 2006
  • [Show abstract] [Hide abstract] ABSTRACT: ESTs Comparison.
    Dataset · Oct 2006
  • [Show abstract] [Hide abstract] ABSTRACT: secondary metabolism.
    Dataset · Oct 2006
  • [Show abstract] [Hide abstract] ABSTRACT: signal transduction.
    Dataset · Oct 2006
  • [Show abstract] [Hide abstract] ABSTRACT: secreted proteins.
    Dataset · Oct 2006
  • [Show abstract] [Hide abstract] ABSTRACT: metabolism overview.
    Dataset · Oct 2006

Publication Stats

697 Citations

Institutions

  • 2015
    • Peking Union Medical College Hospital
      Peping, Beijing, China