Functional classification of secreted proteins by position specific scoring matrix and auto covariance

Secreted proteins play pivotal biological regulatory roles in eukaryotic cells with different functions, and have the potential for disease biomarkers and protein therapeutics. Furthermore, the comprehension of their functions is not only indispensable for helping genome annotation, but also a supplement to the existing methods. As the rapid increase of protein sequences generated in the post-genomic age, it is urgent to develop a computational method to effectively annotate the function types of numerous newly discovered secreted proteins. In view of this, a support vector machine (SVM)-based predictor is proposed to classify secreted proteins with different functions in this paper, including cytokine, hormone, immune system protein, protease, and protease inhibitor. Here, proteins are represented by position specific scoring matrix (PSSM) and auto covariance (AC), which incorporates the evolution and the sequence-order information of proteins. When distinguishing the five types of secreted proteins, an accuracy of 83.2%, 88.9%, 86.1%, 90.9%, and 90.6% is achieved for cytokine, hormone, immune system protein, protease and protease inhibitor, respectively. Particularly, when performed on an independent test set of 325 proteins, the method also yielded a satisfactory accuracy of 91.2%. It shows that this method can be a complementary tool for identifying different functions of secreted proteins. The code and all datasets used in this article are freely available at http://cic.scu.edu.cn/bioinformatics/fcSecretP.zip.     

Identification and functional analysis of bull (Bos taurus) cauda epididymal fluid proteome

Despite recent advances in bull epididymal fluid proteome research, significant numbers of proteins secreted to epididymal lumen remain unidentified. The objective of this study was to expand the number of identified cauda epididymal fluid proteins in bulls and to contextualize them in a broader view of their mutual interactions and involvement in biological processes and pathways, to fully elucidate the ways in which epididymal fluid proteins are involved in storage and maturation of spermatozoa in epididymis. We collected postmortem cauda epididymal fluid from 6 mature Holstein Friesian bulls. We performed the identification of proteins using 2-dimensional electrophoresis coupled with MALDI mass spectrometry. Analysis of functionality and pathway involvement of identified proteins was performed using Ingenuity Pathway Analysis software. We identified a total of 189 epididymal fluid proteins, out of which 100 were newly identified in bull epididymal fluid. We have combined our data with 2 previously performed bull epididymal fluid proteome identifications, yielding 280 proteins total, and analyzed it. The main canonical pathways involving epididymal proteins were glycolysis, gluconeogenesis, protein ubiquitination pathway, nuclear factor-erythroid 2-related factor 2-mediated oxidative stress response, and farnesoid X receptor/retinoid X receptor activation. The main biological functions potentially performed by epididymal fluid proteins included carbohydrate metabolism, cellular growth and proliferation, cell death and survival, and small molecule biochemistry. Overall, our results have pointed out multiple novel pathways in bull epididymal fluid that might take part in various aspects of maturation and protection processes of epididymal spermatozoa.     

蛋白质组学方法分析不同苯酚浓度下菌株Acinetobacter sp．EDP3的应激机理

Strain EDP3 was isolated from an industrial-activated sludge. It belonged to the gamma group of Pro-teobacteria with an identity of 97.0% to Acinetobacter calcoaceticus according to the 16S rRNA gene sequences. It can tolerate up to 1000mg·L^-1 phenol at room temperature with a much longer lag phase. This indicates that higher phenol concentration has induced some physiological and genotypic changes in the bacterium. The aim of this study is, therefore, to investigate these responses to phenol concentration variations in strain EDP3. Proteome analysis is conducted by means of a two-dimensional polyacrylamide gel electrophoresis （2D PAGE） and matrix-assisted laser desorption ionization time of flight mass spectrometry （MALDI-TOF-MS） was conducted to obtain a deeper insight into the adaptive responses inside the bacterium. Comparative analysis of the proteome profiles of strain EDP3. grown in 400mg·L^-1 and 1000mg·L^-1 phenol allowed us to identify that among all the proteins up-regulated under the higher phenol concentration, oxidative stress proteins were dominant. The synthesis of a heat shock protein, 60000 chaperonin GroEL, was also amplified. In addition, the expression of one membrane protein, adenosine 5＇-triphosphate （ATP）-binding cassette （ABC） type sugar transporter, was found up-regulated. The inhibition of adenosine 5＇-triphosphate （ATP） and RNA/protein synthesis was also observed.     

Identification and proteomic analysis of a novel gossypol-degrading fungal strain

BACKGROUND: Cottonseed meal, an important source of feed raw materials, has limited use in the feed industry because of the presence of the highly toxic gossypol. The aim of the current work was to isolate the gossypol‐degrading fungus from a soil microcosm and investigate the proteins involved in gossypol degradation. RESULTS: A fungal strain, AN‐1, that uses gossypol as its sole carbon source was isolated and identified as Aspergillus niger. A large number of intracellular proteins were detected using sodium dodecyl sulfate–polyacrylamide gel electrophoresis, but no significant difference was observed between the glucose‐containing and gossypol‐containing mycelium extracts. Two‐dimensional gel electrophoresis results showed that the protein spots were concentrated in the 25.0–66.2 kDa range and distributed in different pI gradients. PDQuest software showed that 51 protein spots in the gels were differentially expressed. Of these, 20 differential protein spots, including six special spots expressed in gossypol, were analyzed using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. CONCLUSION: The fungus AN‐1 biodegraded gossypol and the proteomic analysis results indicate that some proteins were involved in the gossypol biodegradation during fungus survival, using gossypol as its sole carbon source. Copyright © 2011 Society of Chemical Industry     

Acute phase serum amyloid A in ovarian cancer as an important component of proteome diagnostic profiling

In the context of serum amyloid A (SAA) identification as ovarian cancer marker derived by SELDI‐MS, its serum levels were measured by immunoassay in different stages of ovarian cancer, in benign gynecological tumors, and in healthy controls. In addition, SELDI‐TOF‐MS spectra were obtained by protocol optimized for the SAA peak intensity. SELDI data on small proteins (5.5–17.5 kDa) and SAA immunoassay data were combined with cancer antigen (CA)125 data in order to study the classification accuracy between cancer and noncancer by support vector machine (SVM), logistic regression, and top scoring pair classifiers. Although an addition of SAA immunoassay data to CA125 data did not significantly improve cancer/noncancer discrimination, SVM applied to combined biomarker data (CA125 and SAA immunoassay variables plus 48 SELDI peak variables) yielded the best classification rate (accuracy 95.2% vs. 86.2% for CA125 alone). Notably, most of discriminatory peaks selected by the classifiers have significant correlation with the major known peaks of SAA (11.7 kDa) and transthyretin (13.9 kDa). Acute phase serum amyloid A (A‐SAA) was proved to be an important member of cancer discriminatory protein profile. Among the eight known ovarian cancer SELDI profile components, A‐SAA is the most relevant to molecular pathogenesis of cancer and it has the highest degree of up‐regulation in disease.