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PubMed2005

Clostridium perfringens: insight into virulence evolution and population structure.

Clostridium perfringens is an important pathogen in veterinary and medical fields. Diseases caused by this organism are in many cases life threatening or fatal. At the same time, it is part of the ecological community of the intestinal tract of man and animals. Virulence in this species is not fully understood and it does seem that there is erratic distribution of the toxin/enzyme genes within C. perfringens population. We used the recently developed multiple-locus variable-number tandem repeat analysis (MLVA) scheme to investigate the evolution of virulence and population structure of this species. Analysis of the phylogenetic signal indicates that acquisition of the major toxin genes as well as other plasmid-borne toxin genes is a recent evolutionary event and their maintenance is essentially a function of the selective advantage they confer in certain niches under different conditions. In addition, it indicates the ability of virulent strains to cause disease in different host species. More interestingly, there is evidence that certain normal flora strains are virulent when they gain access to a different host species. Analysis of the population structure indicates that recombination events are the major tool that shapes the population and this panmixia is interrupted by frequent clonal expansion that mostly corresponds to disease processes. The signature of positive selection was detected in alpha toxin gene, suggesting the possibility of adaptive alleles on the other chromosomally encoded determinants. Finally, C. perfringens proved to have a dynamic population and availability of more genome sequences and use of comparative proteomics and animal modeling would provide more insight into the virulence of this organism.

Animals↗
PubMed2004

Characterization of human TMEM16G gene in silico.

TMEM16A, TMEM16B, TMEM16C, TMEM16D, TMEM16E, TMEM16F and TP53I5 are TMEM16 family eight-transmembrane proteins with N- and C-terminal tails facing the cytoplasm. TMEM16A gene at human chromosome 11q13.3 is amplified in head and neck tumors, and TMEM16E gene at human chromosome 11p14.3 is mutated in gnathodiaphyseal dysplasia (GDD). Ngep cDNA (NM_207031.1) is derived from mouse Tmem16g gene. Here, we characterized human TMEM16G gene by using bioinformatics. TMEM16G gene, consisting of 25 exons, was located at human chromosome 2q37.3. Intra-species comparative genomics revealed that the PASK-PPP1R7-TMEM16G-HDLBP-NEDD5 locus was the unique region without paralogous region. TMEM16G mRNA was preferentially expressed in normal prostate and prostate cancer. Complete coding sequence of TMEM16G cDNA was determined by assembling 25 exons of TMEM16G gene. Human TMEM16G gene was found to encode 932-amino-acid TMEM16G protein with TM16H1, TM16H2 and TM16H3 domains. Comparative proteomics revealed that T844N amino-acid substitution occurred in human TMEM16G during evolution. TMHMM2 program predicted that mouse Tmem16g and artificial human TMEM16G (844T) were eight-transmembrane proteins, but that wild-type human TMEM16G (844N) was a seven-transmembrane protein. These facts indicate that amino-acid substitution at codon 844 of human TMEM16G resulted in the mis-folding of the eighth transmembrane helix. Human TMEM16G with altered membrane topology might show functional divergence compared with other members of the TMEM16 family.

Amino Acid Sequence↗
PubMed2005

[Identification of biomarkers in serum of early rheumatoid arthritis by proteomic methods].

OBJECTIVE: To discover the biomarkers of early rheumatoid arthritis (RA) patients and healthy person were analyzed by proteomic methods to discover serum biomarkers. METHODS: Samples of peripheral blood were collected form 10 newly diagnosed active RA patients, 5 males and 5 females, aged 54.3 +/- 12.78, with a disease course of 4.08 +/- 1.9 months, and 10 age and sex matched healthy persons. The samples were divided into 10 groups containing 1 sample of patient serum and 1 sample of healthy serum to undergo. High-molecular-weight protein (HMWP) was enriched by depletion of albumin with HiTrap Blue column and depletion of immunoglobulin G with HiTrap rProtein A column. Low-molecular-weight protein (LMWP) was enriched by C18 absorbent binding and elution. After comparative proteomic analysis, the different protein spots were identified using matrix-assisted laser desorption ionization-time of flight-ionization-mass spectrometry. (MALDI-TOF-MS). RESULTS: Marrow-related protein (MRP) 14, a protein of the S100 family was 100% positive in the RA patient sera and 100% negative in the sera of the healthy controls. MRP8, another protein of the S100 family, was 100% positive in the RA patient sera and 50% positive in the sera of the healthy controls. Ubiquitin was 90% positive in the RA patient sera and 10% positive in the sera of the healthy controls. The levels of apolipoprotein A-I (ApoA-I), serum amyloid A1 and A2 (SAA1/SAA2), and transthyretin of the RA patients were all significantly higher than those of the healthy controls. CONCLUSION: MRP14/MRP8, SAA1/SAA2 and ubiquitin may play important roles in development of RA and their determination may benefit early diagnosis, evaluation of disease activity and investigation of new therapy targets.

Adult↗
PubMed2024

Analysis of Antibiotic Response in Clinical Wound Pseudomonas aeruginosa Isolates: Unveiling Proteome Dynamics of Tobramycin-Tolerant Phenotype.

Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic human pathogen, causing serious chronic infections. P. aeruginosa can adapt efficiently to antibiotic stressors via different genotypic or phenotypic strategies such as resistance and tolerance. The adaptation regulatory system is not always very well understood. In this study, we use shotgun proteomics to investigate the system-level response to tobramycin in two clinical wound P. aeruginosa isolates and PAO1. We profiled each strain for its antibiotic drug-tolerant phenotype using supra-minimum inhibitory concentrations (supra-MICs) of tobramycin and applied proteomics to investigate the protein expression profiles. The MIC revealed that all isolates were susceptible to tobramycin but at supra-MICs at stationary growth, a degree of tolerance was observed for the isolates. We identified around 40% of the total proteins encoded by the P. aeruginosa genome and highlighted shared and unique protein signatures for all isolates. Comparative proteome profiling in the absence of antibiotic treatment showed divergent fingerprints, despite similarities in the growth behavior of the isolates. In the presence of tobramycin, the isolates shared a common response in the downregulation of proteins involved in the two-component system, whereas stress response proteins were present at higher levels. Our findings provide insight into the use of proteomic tools to dissect the system-level response in clinical isolates in the absence and presence of antibiotic stress.

Pseudomonas aeruginosa↗
PubMed2006

Mitochondrial uncoupling proteins: new insights from functional and proteomic studies.

Mitochondria are the major sites of ATP synthesis through oxidative phosphorylation, a process that is weakened by proton leak. Uncoupling proteins are mitochondrial membrane proteins specialized in inducible proton conductance. They dissipate the proton electrochemical gradient established by the respiratory chain at the expense of reducing substrates. Several physiological roles have been suggested for uncoupling proteins, including roles in the control of the cellular energy balance and in preventive action against oxidative stress. This review focuses on new leads emerging from comparative proteomics about the involvement of uncoupling protein in the mitochondrial physiology. A brief overview on uncoupling proteins and on proteomics applied to mitochondria is also presented herein.

Animals↗
PubMed2006

Porcine pregnancy-associated glycoprotein family (pPAGs) - as in vitro-produced chorionic ligands for luteal and uterine gonadotropin receptors.

This paper compares proteomic interaction-types and binding-effectiveness of secretory chorionic ligands (including pPAGs) with other proteins, i.e. gonadotropin membrane receptors (Rc) isolated from luteal-phase corpora lutea, uterine myometrium and endometrium of cyclic (cCLRc, cMYORc and cENDRc) or pregnant (pCLRc, pMYORc and pENDRc) pigs. Binding-effectiveness of miscellaneous in vitro-produced chorionic ligands (+pPAGs) was compared by radioreceptor assay (RRA) with endometrial (END) proteins of cyclic, pseudopregnant and pregnant gilts - as negative control ligands and porcine LH and hCG - as positive control ligands. The binding-comparison suggests that the pPAGs may play an important role as potential antiluteolytic or luteoprotective chorionic-origin signals during pregnancy, according to the binding-effectiveness of secretory chorionic ligands (+pPAGs) that was relatively comparable to LH/hCG - as classical ligands competing for luteal and uterine gonadotropin receptors of cyclic and pregnant pigs.

Animals↗
PubMed2007

Proteomic analysis of vascular smooth muscle cells treated with ouabain.

Apoptosis of vascular smooth muscle cells (VSMC) plays an important role in remodeling the vessel walls, one of the major determinants of long-term blood pressure elevation and an independent risk factor for cardiovascular morbidity and mortality. Apoptosis in VSMC can be inhibited by inversion of the intracellular [Na+]/[K+] ratio after the sustained blockage of the Na+,K+-ATPase by ouabain. Using two-dimensional gel electrophoresis followed by tandem mass spectroscopy, we compared proteomes of control VSMC and of those with ouabain-inhibited Na+,K+-ATPase and found that ouabain treatment led to overexpression of numerous soluble and membrane-bound proteins. Among proteins, which showed the highest level of ouabain-induced expression, we identified mortalin (also known as GRP75 or PBP-74), a member of the heat shock protein 70 superfamily and a marker for cellular mortal and immortal phenotypes. Further experiments showed that mortalin RNA and protein levels are induced in ouabain-treated VSMC, and that transient transfection of cells with mortalin cDNA inhibited serum deprivation-induced apoptosis via inactivation of the tumor suppressor gene, p53.

Animals↗
PubMed2004

Decreased pyruvate kinase M2 activity linked to cisplatin resistance in human gastric carcinoma cell lines.

Resistance to anticancer drugs is a major obstacle preventing effective treatment of disseminated cancers. Understanding the molecular basis to chemoresistance is likely to provide better treatment. Cell lines resistant to cisplatin or 5-fluorouracil (5-FU) were established from human gastric carcinoma cell lines SNU-638 and SNU-620. Comparative proteomics involving 2-dimensional gel electrophoresis (2-DE) and matrix-associated laser desorption ionization-mass spectroscopy (MALDI-MS) was performed on protein extracts from these parental and drug-resistant derivative lines to screen drug resistance-related proteins. Pyruvate kinase M2 (PK-M2) was identified as a protein showing lower expression in cisplatin-resistant cells compared to parental cells. Consistent with this finding, PK-M2 activity was also lower in cisplatin-resistant cells. Suppression of PK-M2 expression by antisense oligonucleotide resulted in acquired cisplatin resistance in SNU-638 cells. Furthermore, PK-M2 activity in 11 individual human gastric carcinoma cell lines positively correlated with cisplatin sensitivity. Taken together, PK-M2 protein and activity levels were lower in cisplatin-resistant human gastric carcinoma cell lines compared to their parental cell lines. Furthermore, suppression of PK-M2 expression using antisense oligonucleotides increased cisplatin resistance. These data clearly link PK-M2 and cisplatin resistance mechanisms.

Antimetabolites, Antineoplastic↗
PubMed2006

Proteomic analysis of urine in kidney transplant patients with BK virus nephropathy.

The differentiation of BK virus-associated renal allograft nephropathy (BKVAN) from acute allograft rejection (AR) in renal transplant recipients is an important clinical problem because the treatment can be diametrically opposite for the two conditions. The aim of this discovery-phase biomarker development study was to examine feasibility of developing a noninvasive method to differentiate BKVAN from AR. Surface-enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry analysis was used to compare proteomic profiles of urine samples of 21 patients with BKVAN, 28 patients with AR (Banff Ia to IIb), and 29 patients with stable graft function. SELDI analysis showed proteomic profiles that were significantly different in the BKVAN group versus the AR and stable transplant groups. Peaks that corresponded to m/z values of 5.872, 11.311, 11.929, 12.727, and 13.349 kD were significantly higher in patients with BKVAN. Bioinformatics analyses allowed distinction of profiles of patients with BKVAN from patients with AR and stable patients. SELDI profiles also showed a high degree of reproducibility. Proteomic analysis of urine may offer a noninvasive way to differentiate BKVAN from AR in clinical practice. The identification of individual proteomic peaks can improve further the clinical utility of this screening method.

Adult↗
PubMed2005

Comparative genomics on SOX2 orthologs.

SOX2 and POU5F1 (OCT3 or OCT4) transcription factors are implicated in FGF4 expression in embryonic stem (ES) cells. SOX2, POU5F1, and FGF4 are key molecules for the integrome network in oncology and stem cell biology. SOX2 gene at human chromosome 3q26.33, SOX1 gene at 13q34, and SOX3 gene at Xq27.1 constitute a subfamily among the SOX gene family. Here, rat Sox2 and Xenopus sox2 genes were identified and characterized by using bioinformatics for comparative genomics and comparative proteomics analyses. Rat Sox2 gene, encoding a 319-aa protein, was located around the nucleotide position 73213-75621 of rat genome sequence AC123231.4. Xenopus tropicalis sox2 complete coding sequence, encoding a 311-aa protein, was derived from CR760314.1 cDNA. Rat Sox2 showed 98.4%, 97.8%, 92.2%, 88.1% and 86.8% total amino-acid identity with mouse Sox2, human SOX2, chicken sox2, Xenopus sox2 and zebrafish sox2, respectively. SOX123C domain was identified as the novel domain corresponding to the C-terminal region conserved among SOX1, SOX2 and SOX3 orthologs. Vertebrate SOX1, SOX2 and SOX3 orthologs were found consisting of HMG box and SOX123C domain. SOX9, TCF/LEF, POU2F1 and COMP1 binding sites were conserved among human SOX2 promoter, rat Sox2 promoter, and mouse Sox2 promoter. SOX2 mRNA was expressed in ES cells, fetal brain, anaplastic oligodendroglioma, rhabdomyosarcoma, and small cell lung carcinoma. Due to the pivotal role of SOX2 in the early embryogenesis, SOX2 promoter and SOX2 protein were well conserved during vertebrate evolution. This is the first report on comparative integromics analyses on the SOX2 orthologs.

Amino Acid Sequence↗
PubMed2003

Global protein identification and quantification technology using two-dimensional liquid chromatography nanospray mass spectrometry.

A simple and reliable method is described here for the identification and relative quantification of proteins in complex mixtures using two-dimensional liquid chromatography/tandem mass spectrometry. The method is based on the classical proteomic analysis where proteins are digested with trypsin and the resulting peptides are separated by multidimensional liquid chromatography. The separated peptides are analyzed by tandem mass spectrometry and identified via a database search algorithm such as SEQUEST. The peak areas (integrated ion counts over the peptide elution time) of all identified peptides are calculated, and the relative concentration of each protein is determined by comparing the peak areas of all peptides from that protein in one sample versus those from the other. Using this strategy, we compared the relative level of protein expression of A431 cells (an epidermal cell line) grown in the presence or absence of epidermal growth factor (EGF). Our results are consistent with the published observations of the transient effects of EGF. In addition, the difference in the concentrations of several phosphopeptides determined in our studies suggests the possibility of several new targets involved in the EGF cell-signaling pathway. This global protein identification and quantification technology should prove to be a valuable means for comparing proteomes in biological samples subjected to differential treatments.

Amino Acid Sequence↗
PubMed2005

Comparative genomics on FGF7, FGF10, FGF22 orthologs, and identification of fgf25.

FGF family members are key molecules for the integrome network in the fields of oncology and regenerative medicine. Based on the comparative genomics on the CCND1-ORAOV1-FGF19-FGF4 locus, we demonstrated that rodent Fgf15 is the ortholog of human FGF19 in 2003. FGF7 (KGF), FGF10, and FGF22 constitute a subfamily among FGF family members. Here, comparative genomics analyses and comparative proteomics analyses on FGF7, FGF10, and FGF22 orthologs were performed. Chicken fgf22, zebrafish fgf22 and fgf25 genes, consisting of three exons, were identified within AC150066.1, BX927243.9 and CR854981.2 genome sequences, respectively. Zebrafish fgf22 (207 aa) showed 46.9%, 48.6% and 53.5% total amino-acid identity with human FGF7, FGF10 and FGF22, respectively. Zebrafish fgf25 (186 aa) showed 39.2%, 52.9% and 45.9% total amino-acid identity with human FGF7, FGF10 and FGF22, respectively. Phylogenetic analyses revealed that zebrafish fgf25 belongs to the FGF10 ortholog group. Zebrafish fgf25 was a novel FGF family member generated by the duplication of fgf10. FGF10-MRPS30-HCN1 locus at human chromosome 5p12 and FGF22-POLRMT-HCN2 locus at 19p13.3 were paralogous regions within the human genome. FGF7 mRNA was expressed in fetal heart, placenta, lung, kidney, and blood vessels. FGF10 mRNA was expressed in fetal lung, placenta, and uterus. FGF22 mRNA was expressed in hippocampus and ovarian fibrotheoma. FGF7 promoter with bHLH biding site and CCAAT box and FGF10 promoter with double bHLH biding sites were conserved well, while FGF22 promoter was significantly divergent. This is the first report on fgf25 gene and also on the comparative integromics analyses of FGF7, FGF10 and FGF22 orthologs.

5' Flanking Region↗
PubMed2006

Protein expression profiling identifies maspin and stathmin as potential biomarkers of adenoid cystic carcinoma of the salivary glands.

Adenoid cystic carcinoma (ACC) is one of the most common malignant tumors of the salivary glands. It tends to grow slowly but is associated with a poor prognosis compared to other malignant salivary gland tumors. To identify specific markers of ACC, we examined protein expression profiling in ACC xenograft and normal salivary glands (NSG) using fluorescent 2-dimensional differential in-gel electrophoresis (2-D-DIGE), an emerging technique for comparative proteomics, that improves the reproducibility and reliability of differential protein expression analysis between the samples. To identify the proteins, matrix-assisted laser desorption/ionization time-of-flight peptide mass fingerprinting was carried out. Using these strategies, we detected 4 upregulated proteins and 5 downregulated proteins in ACC xenograft. Maspin and stathmin were selected for further analyses. Western blotting and immunohistochemical staining showed a higher expression of these proteins in ACC xenograft and clinical ACC tissue compared to NSG. Furthermore, Expression of these proteins was correlated with the histologic grading of ACC (n = 10). Therefore, our data indicate that maspin and stathmin may be not only useful biomarkers of ACC but also markers of biologic behavior in this tumor.

Animals↗
PubMed2006

Identification of proinflammatory flagellin proteins in supernatants of Vibrio cholerae O1 by proteomics analysis.

The genome of Vibrio cholerae contains five flagellin genes that encode proteins (FlaA-E) of 39-41 kDa with 61-82% identity among them. Although the existing live oral attenuated vaccine strains against cholera are protective in humans, there is an intrinsic residual cytotoxic and inflammatory component associated with these candidate vaccine strains. Bacterial flagellins are known to be potent inducers of proinflammatory molecules via activation of Toll-like receptor 5. Here we found that purified flagella from wild type V. cholerae 395 induced significant release of interleukin (IL)-8 from cultured HT-29 human colonic epithelial cells. Furthermore we found that filtered supernatants of KKV90, a DeltaflaA isogenic strain unable to produce flagella, were still able to activate production of IL-8 albeit to significantly lower levels than the wild type, suggesting that other activators of proinflammatory molecules were still present in these supernatants. A comparative proteomics analysis of secreted proteins of V. cholerae 395 and KKV90 identified additional proteins with potential to induce IL-8 release in HT-29 cells. Secreted proteins in the range of 30-45 kDa identified by two-dimensional electrophoresis and mass spectrometry revealed the presence of two additional flagellins, FlaC and FlaD, that appeared to be secreted 3- and 6-fold more, respectively, in the mutant compared with the wild type. Double isogenic mutants flaAC and flaAD were unable to trigger IL-8 release from HT-29 cells. In sum, we have shown that purified flagella and secreted flagellin proteins (FlaC and FlaD) are inducers of IL-8 release from epithelial cells via Toll-like receptor 5. This observation may explain, in part, the observed reactogenicity of cholera vaccine strains in humans.

Culture Media, Conditioned↗
PubMed2004

Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry.

We have developed an integrated suite of algorithms, statistical methods, and computer applications to support large-scale LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures. The programs automatically detect and quantify large numbers of peptide peaks in feature-rich ion mass chromatograms, compensate for spurious fluctuations in peptide signal intensities and retention times, and reliably match related peaks across many different datasets. Application of this toolkit markedly facilitates pattern recognition and biomarker discovery in global comparative proteomic studies, simplifying mechanistic investigation of physiological responses and the detection of proteomic signatures of disease.

Algorithms↗
PubMed2006

Proteomic analysis of tumor establishment and growth in the B16-F10 mouse melanoma model.

The B16-F10 mouse model of melanoma is a widely used model to study many aspects of cancer biology and therapeutics in a solid tumor. Melanomas aggressively progress within a dynamic microenvironment containing in addition to tumor cells, stroma cells and components such as fibroblasts, immune cells, vascular cells, extracellular matrix (ECM) and extracellular molecules. The goal of this study was to elucidate the processes of tumor progression by identifying differentially expressed proteins in the tumor mass during specific stages of tumor growth. A comparative proteome analysis was performed on B16-F10 derived tumors in C57BL/6 mice at days 3, 5, 7, and 10. Statistical approaches were used to determine quantitative differential protein expression at each tumor time stage. Hierarchical clustering of 44 protein spots (p < 0.01) revealed a progressive change in the tumor mass when all 4 time stages were classified together, but there was a clear switch in expression of these proteins between the day 5 and the day 7 tumors. A trend analysis showed 53 protein spots (p < 0.001) following 6 predominant kinetic paths of expression as the tumor progressed. The protein spots were then identified using MALDI-TOF mass spectrometry. Proteins involved in glycolysis, inflammation, wounding, superoxide metabolism, and chemotaxis increased during tumorigenesis. From day 3 to day 7 VEGF and active cathepsin D were induced 7-fold and 4-fold, respectively. Proteins involved in electron transport, protein folding, blood coagulation, and transport decreased during tumorigenesis. This work illustrates changes in the biology of the B16-F10 tumor mass during tumor progression.

Animals↗
PubMed2006

Proteome analysis of gametophores identified a metallothionein involved in various abiotic stress responses in Physcomitrella patens.

Physcomitrella patens is a model plant for studying gene function using a knockout strategy. To establish a proteome database for P. patens, we resolved over 1,500 soluble proteins from gametophore and protonema tissues by two-dimensional electrophoresis (2-DE) and obtained peptide mass fingerprints (PMFs) by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). Using expressed sequence tags (ESTs), we were able to predict the identities of 90 protein spots. Most of these were related to energy or primary metabolism. Comparative proteome analysis was used to identify proteins specific for each of the tissue types. One of these was a metallothionein type-2 (PpMT2) protein that was highly upregulated in gametophore tissue. PpMT2 was induced in both the gametophore and protonema following culture on solid media and in response to various abiotic stresses such as copper, cadmium, cold, indole-3-acetic acid, and ethylene. We suggest that PpMT2 is not only involved in metal binding and detoxification, but also in many biological aspects as a metal messenger or a protein with additional functions.

Amino Acid Sequence↗
PubMed2004

Proteomic characterization of host response to Yersinia pestis and near neighbors.

Host-pathogen interactions result in protein expression changes within both the host and the pathogen. Here, results from proteomic characterization of host response following exposure to Yersinia pestis, the causative agent of plague, and to two near neighbors, Yersinia pseudotuberculosis and Yersinia enterocolitica, are reported. Human monocyte-like cells were chosen as a model for macrophage immune response to pathogen exposure. Two-dimensional electrophoresis followed by mass spectrometry was used to identify host proteins with differential expression following exposure to these three closely related Yersinia species. This comparative proteomic characterization of host response clearly shows that host protein expression patterns are distinct for the different pathogen exposures, and contributes to further understanding of Y. pestis virulence and host defense mechanisms. This work also lays the foundation for future studies aimed at defining biomarkers for presymptomatic detection of plague.

Bacterial Proteins↗