FunSys: Software for functional analysis of prokaryotic transcriptome and proteome

The vast amount of data produced by next-generation sequencing (NGS) has necessitated the development of computational tools to assist in understanding the myriad functions performed by the biological macromolecules involved in heredity. In this work, we developed the FunSys programme, a stand-alone tool with an user friendly interface that enables us to evaluate and correlate differential expression patterns from RNA sequencing and proteomics datasets. The FunSys generates charts and reports based on the results of the analysis of differential expression to aid the interpretation of the results. AVAILABILITY: The database is available for free at https://sourceforge.net/projects/funsysufpa/     

Differential proteome and phosphoproteome signatures in human T‐lymphoblast cells induced by sirolimus

Objectives: The present study was designed to investigate early proteome and phosphoproteome changes during inhibition of lymphocyte proliferation induced by sirolimus (SRL). Materials and methods: Proliferation assays were conducted using human CCRF‐CEM T lymphoblasts under different SRL concentrations. Total protein lysates after SRL treatment were used to identify significantly regulated proteins and phosphorylated proteins by 2‐DE and Q‐TOF Ultima Global mass spectrometer. Results and conclusions: Incubation with 2.5 μmol/l SRL resulted in a ～ 70% inhibition of cell proliferation. Cells incubated with 2.5 μmol/l for 30 min showed a differential phosphorylation pattern with one higher (TCPQ) and six lower phosphorylation signals (TBA1B, VIME, HNRPD, ENPL, SEPT9, PLSL). On investigating the differential protein expression, five proteins were found to be up‐regulated (ECHB, PSB3, MTDC, LDHB and NDKA) and four were down‐regulated (EHD1, AATC, LMNB1 and MDHC). Nine of these differentially regulated proteins/phosphoproteins (TCPQ, TBA1B, VIME, HNRPD, ENPL, ECHB, PSB3, LDHB and LMNB1) showed significant interaction potential, through binding protein YWHAZ using MINT software. Conclusions: We report for the first time the simultaneous early influence of SRL on phosphorylation status and on protein expression in the total proteome of CCRF‐CEM T lymphoblasts and predict that 56% of the proteins interact with each other, highlighting significance of these results.     

ProteoConnections: a bioinformatics platform to facilitate proteome and phosphoproteome analyses

Novel and improved computational tools are required to transform large-scale proteomics data into valuable information of biological relevance. To this end, we developed ProteoConnections, a bioinformatics platform tailored to address the pressing needs of proteomics analyses. The primary focus of this platform is to organize peptide and protein identifications, evaluate the quality of the acquired data set, profile abundance changes, and accelerate data interpretation. Peptide and protein identifications are stored into a relational database to facilitate data mining and to evaluate the quality of data sets using graphical reports. We integrated databases of known PTMs and other bioinformatics tools to facilitate the analysis of phosphoproteomics data sets and to provide insights for subsequent biological validation experiments. Phosphorylation sites are also annotated according to kinase consensus motifs, contextual environment, protein domains, binding motifs, and evolutionary conservation across different species. The practical application of ProteoConnections is further demonstrated for the analysis of the phosphoproteomics data sets from rat intestinal IEC-6 cells where we identified 9615 phosphorylation sites on 2108 phosphoproteins. Combined proteomics and bioinformatics analyses revealed valuable biological insights on the regulation of phosphoprotein functions via the introduction of new binding sites on scaffold proteins or the modulation of protein-protein, protein-DNA, or protein-RNA interactions. Quantitative proteomics data can be integrated into ProteoConnections to determine the changes in protein phosphorylation under different cell stimulation conditions or kinase inhibitors, as demonstrated here for the MEK inhibitor PD184352.     

Large-scale analysis of the human ubiquitin-related proteome

Protein ubiquitylation contributes to the regulation of many cellular processes including protein degradation, receptor internalization, and repair of DNA damage. We now present a comprehensive characterization of ubiquitin-conjugated and ubiquitin-associated proteins in human cells. The proteins were purified by immunoaffinity chromatography under denaturing or native conditions. They were then digested with trypsin, and the resulting peptides were analyzed by 2-D LC and MS/MS. A total of 670 distinct proteins were identified; 345 proteins (51%) were classified as Urp-D (ubiquitin-related proteome under the denaturing condition) and comprised ubiquitin-conjugated molecules, whereas 325 proteins (49%) were classified as Urp-N (ubiquitin-related proteome only under the native condition) and included molecules that associated with ubiquitylated proteins. The proportions of proteins in various functional categories differed substantially between Urp-D and Urp-N. Many ribosomal subunits were detected in the Urp-D group of proteins and several of these subunits were directly shown to be ubiquitylated by mass spectrometric analysis, suggesting that ubiquitylation might play an important role in the regulation and/or quality control of ribosomal proteins. Our results demonstrate the potential of proteomics analysis of protein ubiquitylation to provide important insight into the regulation of protein stability and other ubiquitin-related cellular functions.     

In-depth analysis of the human tear proteome

The tears, a critical body fluid of the surface of the eye, contain an unknown number of molecules including proteins/peptides, lipids, small molecule metabolites, and electrolytes. There have been continued efforts for exploring the human tear proteome to develop biomarkers of disease. In this study, we used the high speed TripleTOF 5600 system as the platform to analyze the human tear proteome from healthy subjects (3 females and 1 male, average age: 36±14). We have identified 1543 proteins in the tears with less than 1% false discovery rate, which represents the largest number of human tear proteins reported to date. The data set was analyzed for gene ontology (GO) and compared with the human plasma proteome, NEIBank lacrimal gland gene dataset and NEIBank cornea gene dataset. This comprehensive tear protein list may serve as a reference list of human tear proteome for biomarker research of ocular diseases or establishment of MRM (Multiple Reaction Monitoring) assays for targeted analysis. Tear fluid is a useful and an accessible source not only for evaluating ocular surface tissues (cornea and conjunctiva), inflammation, lacrimal gland function and a number of disease conditions, such as dry eye as well as response to treatment.     

Insight into the salivary transcriptome and proteome of Dipetalogaster maxima

Dipetalogaster maxima is a blood-sucking Hemiptera that inhabits sylvatic areas in Mexico. It usually takes its blood meal from lizards, but following human population growth, it invaded suburban areas, feeding also on humans and domestic animals. Hematophagous insect salivary glands produce potent pharmacologic compounds that counteract host hemostasis, including anticlotting, antiplatelet, and vasodilatory molecules. To obtain further insight into the salivary biochemical and pharmacologic complexity of this insect, a cDNA library from its salivary glands was randomly sequenced. Salivary proteins were also submitted to one- and two-dimensional gel electrophoresis (1DE and 2DE) followed by mass spectrometry analysis. We present the analysis of a set of 2728 cDNA sequences, 1375 of which coded for proteins of a putative secretory nature. The saliva 2DE proteome displayed approximately 150 spots. The mass spectrometry analysis revealed mainly lipocalins, pallidipins, antigen 5-like proteins, and apyrases. The redundancy of sequence identification of saliva-secreted proteins suggests that proteins are present in multiple isoforms or derive from gene duplications.