Current Proteomics - Volume 12, Issue 1, 2015

In this study, we used a proteomics approach to analyze genetic diversity of a rare plant Anemone shikokiana (Makino) Makino, and further analyzed the influences of habitats and geographic distribution on it. Proteins were separated by two-dimensional electrophoresis (2-DE), visualized by Coomassie Brilliant Blue (CBB) staining, analyzed by ImageMaster software. A total of 1294 protein spots were detected in four gels from four populations across an isoelectric focusing range of 4-7, of which 1143(88.3%) were polymorphic among populations. By comparing analysis we found both of the habitats and geographic distribution influenced the biochemical changes. But the influence of geographic distribution on A. shikokiana was more important than that of habitat. 31 obviously different spots were found among four populations and identified by ESI-LC/MS/MS and homology searched in available database. The understanding of these proteins will increase our knowledge about conservation biology and improve our ability to conserve A. Shikokiana. Therefore proteomics is a powerful approach to analyze genetic diversity and influence the mechanism of habitats on the plants.

The emergence of high throughput data in genomic, proteomic and bioinformatics has increased the necessity to develop large amount of functional analysis tools to facilitate the inference of biologically meaningful data. A promising high throughput strategy, which is the gene-annotation enrichment analysis, can increase the elucidation ability of related biological processes. This paper reviews 35 bioinformatics enrichment tools and 5 gene set databases that are currently available in the field, which include the description of these tools and databases. This information can help tool developers and users to gain a broad view and better understanding on the bioinformatics enrichment tools and databases, enabling a better decision making in choosing tools in particular research interest.

Exposure to UV radiation is a major cause of DNA damage in plants. One of the proteins involved in nucleotide excision repair, as part of a complex that recognizes DNA damage with AtXPC, is RAD23, also involved in Ub/proteasomal degradation pathway. Arabidopsis thaliana has 4 homologues of RAD23, whose 3D structure has been predicted and validated in this study by different bioinformatics tools. Phylogenetic analysis showed that AtRAD23A/B and AtRAD23C/D homologues have significant similarity among themselves. All four homologues have conserved domains identified: UBL, STI1 and 2 UBA domains, with PFAM domain search identifying XPC-binding domains too. Subcellular localization indicated differences among AtRAD23 homologues, with AtRAD23A localized to the nucleus and AtRAD23D to the cytoplasm. The predicted interactome for the homologues indicates a complex role of AtRAD23 in DNA repair mechanisms, beyond simple recognition of DNA damage and supports extensive interactions with various proteasomal subunits, as well as proteins that are to be degraded in order to maintain cellular integrity. Additionally, an interaction with PNG1 enzyme, a link with the ERAD pathway, was predicted. Docking sites prediction and visualization is shown for the AtRAD23D homologue with AtXPC and AtPNG1.

Annulated sea snake, Hydrophis cyanocinctus, venom was investigated using reversed-phase high-performance liquid chromatography coupled to electrospray mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF/TOF). MALDI-TOF/TOF identified three compounds (a short-chain neurotoxin, a long-chain neurotoxin and a basic phospholipase A2); whose molecular weights were estimated to be 7285, 10838, and 14235 Da, respectively. Moreover, evolutionary relationship of each protein (identity more than 70%) was separately investigated via phylogenetic trees. This study was done as complementary investigation on the composition of the venom of H. cyanocinctus, the annulated sea snake from the Persian Gulf.

Labeo rohita (rohu) is one of the most important freshwater carps widely cultured in India, Bangladesh and other adjacent countries in the region. Proteomic analysis from liver tissue samples of riverine L. rohita was carried out with two-dimensional polyacrylamide gel electrophoresis (2-DE). On an average 450 spots were detected in a colloidal Coomassie stained 2-DE gel using PDQuest software. Forty two spots with high abundance and clear separation were selected from the gel and twelve of them were later analyzed with Electronspray Ionization (ESI) - Mass Spectrometry and identified by MASCOT search. The paper describes first attempt for protein profiling of liver tissue samples of L. rohita based on protocol standardized in our lab for optimized yield of total protein as well as 2-D electrophoresis.

Leaves of Vitis amurensis ‘Shuangyou’ (susceptible) and ‘Shuanghong’ (resistant) were inoculated with Plasmopara viticola, the causal agent of downy mildew in grapevine. Key proteins regulated in the response to downy mildew infection were analyzed by differential proteomics and MALDI-TOF/TOF. The leaf proteome changed differentially between the two cultivars following injection by P. viticola. More than 300 protein spots were detected, among which nine differentially expressed proteins were identified. The functions of the identified proteins comprised secondary metabolism, structure, photosynthesis, energy production, and resistance. In the resistant cultivar, photosynthesis proteins and ATP synthase might be down-regulated to restrict fungal growth, and the pathogenesis-related protein 10 may be upregulated to limit the extent of spread of the fungus. Pathogenesis-related protein 10 is proposed to be a key protein in the response of Vitis amurensis to downy mildew infection in the resistant cultivar.

Characterized by susceptibility of rotavirus infectivity to sialidase treatment on host cells, the currently accepted classification scheme divides rotaviruses into two groups: 'sialidase-sensitive' and 'sialidase-insensitive'. However, the significance of sialic acids at early stage of rotavirus cell entry still remains in debate. To better understand the mechanisms mediating rotavirus cell entry and characterize the biological influence of conserved amino acids involved in rotavirus cell recognition, we have undertaken a site-directed mutagenesis study on amino acid residue 100 (Asp to Asn) of the carbohydratebinding domain VP8* of sialidase-sensitive porcine rotavirus OSU. Diffraction data of this VP8* mutant was collected to 2.35 Å and its crystallographic structure was determined by molecular replacement. Though showing a loss in the binding level compared to the wild type OSU VP8*, this Asp100Asn mutant maintains its capability of recognizing sialic acids, which implicates that this single point mutation is unable to alter the recognition phenotype of sialic acids by OSU VP8* directly.