Project description:blanc-08-01_2012_01_rnapaths_03 - rnapaths--3_02/2012 - Identify the transcript overlap and specificity between the PTGS and decapping/exoribonuclease pathways b identifying transcripts that are significantly changed in double mutants versus single mutants, and transcripts that are commonly changed among the single and double mutants compared to WT. - Identify transcripts that are significantly changed in double mutants (L1 vcs sgs2) (xrn4-5/sgs3-11) versus their respective single mutants (L1 vcs and L1 sgs2) (xrn4-5 and sgs3-11) , and identify transcripts that are changed among the single and double mutants compared to WT (Col) reference or to mutant L1 reference. 20 dye-swap - genotype comparaison
Project description:Parkinson disease (PD) is a neurodegenerative disease characterized by the accumulation of alpha-synuclein (SNCA) and other proteins in aggregates termed âLewy Bodiesâ within neurons. PD has both genetic and environmental risk factors, and while processes leading to aberrant protein aggregation are unknown, past work points to abnormal levels of SNCA and other proteins. Although several genome-wide studies have been performed for PD, these have focused on DNA sequence variants by genome-wide association studies (GWAS) and on RNA levels (microarray transcriptomics), while genome-wide proteomics analysis has been lacking. After appropriate filters, proteomics identified 3,558 unique proteins and 283 of these (7.9%) were significantly different between PD and controls (q-value<0.05). RNA-sequencing identified 17,580 protein-coding genes and 1,095 of these (6.2%) were significantly different (FDR p-value<0.05), but only 166 of the FDR significant protein-coding genes (0.94%) were present among the 3,558 proteins characterized. Of these 166, eight genes (4.8%) were significant in both studies, with the same direction of effect. Functional enrichment analysis of the proteomics results strongly supports mitochondrial-related pathways, while comparable analysis of the RNA-sequencing results implicates protein folding pathways and metallothioneins. Ten of the implicated genes or proteins co-localized to GWAS loci. Evidence implicating SNCA was stronger in proteomics than in RNA-sequencing analyses. Notably, differentially expressed protein-coding genes were more likely to not be characterized in the proteomics analysis, which lessens the ability to compare across platforms. Combining multiple genome-wide platforms offers novel insights into the pathological processes responsible for this disease by identifying pathways implicated across methodologies. The study consists of mRNA-Seq (29 PD, 44 neurologically normal controls) and three-stage Mass Spectrometry Tandem Mass Tag Proteomics (12 PD, 12 neurologically normal controls) performed in post-mortem BA9 brain tissue. The proteomics samples are a subset of the RNA-Seq samples.
Project description:Prokaryotes are, due to their moderate complexity, particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant and membrane localized, we could eliminate their initial under-representation compared to the estimated endpoint. A total of 1,250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and around 90% of the expressed protein-coding genes. Genes, whose transcripts were detected, but not their corresponding protein products, were found highly enriched in several genomic islands. Additionally, genes that lacked an ortholog and a functional annotation were not detected at the protein level, and possibly include over-predicted genes in genome annotations. Furthermore, a dramatic membrane proteome re-organization was observed including differential regulation of autotransporters, adhesins and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor. Transcriptome and proteome analysis of B.henselae in two conditions and duplicates: uninduced and induced for host invasion.
Project description:Differently expressed proteins in probiotic Escherichia coli nissle 1917 under mercury stress identified by using a proteomic approach. We applied to separate proteins by using two-dimensional gel electrophoresis and proteins were identified using MALDI-TOF-MS using PMF, by mascot database search using the NCBI database. we identified six proteins after exposure to mercury stress with respect to different functional classes. It is useful to understand the molecular insights into mercury stress in probiotic E. coli. Next we describe a structure generated by homology modelling and functional domain identification; it is interesting to study the impact of stress on protein structures. MS characterization and computational methods together provide the opportunity to examine the impact of stress arising from mercury. The role of these proteins in metal tolerance and structure relation is discussed. To the best of our knowledge, proteomics of E. coli nissle 1917 overview of mercury stress has been reported for the first time.
Project description:To identify substrates of the ubiquitinating E3 enzyme Rsp5 we applied purified Rsp5 to duplicate protein arrays. The Rsp proteins were expressed as fusion proteins to GST. We used as a control Ubr1, a RING domain containing E3 ligase We analyzed Rsp5 from S.cerevisiae on duplicate arrays, with four control chips, two without Rsp5 and two with Ubr1.
Project description:This review is a compilation of proteomic studies on forest tree species published in the last decade (2012-2022), mostly focused on the most investigated species, including Eucalyptus, Pinus, and Quercus. Improvements in equipment, platforms, and methods in addition to the increasing availability of genomic data have favored the biological knowledge of these species at the molecular, organismal, and community levels. Integration of proteomics with physiological, biochemical and other large-scale omics in the direction of the Systems Biology, will provide a comprehensive understanding of different biological processes, from growth and development to responses to biotic and abiotic stresses. As main issue we envisage that proteomics in long-living plants will thrive light on the plant responses and resilience to global climate change, contributing to climate mitigation strategies and molecular breeding programs. Proteomics not only will provide a molecular knowledge of the mechanisms of resilience to either biotic or abiotic stresses, but also will allow the identification on key gene products and its interaction. Proteomics research has also a translational character being applied to the characterization of the variability and biodiversity, as well as to wood and non-wood derived products, traceability, allergen and bioactive peptides identification, among others. Even thought, the full potential of proteomics is far from being fully exploited in forest tree research, with PTMs and interactomics being reserved to plant model systems. The most outstanding achievements in forest tree proteomics in the last decade as well as prospects are discussed.
Project description:The endothelium is the frontline target of multiple metabolic stressors and pharmacological agents. As a consequence, endothelial cells (ECs) display highly dynamic and diverse proteome profiles. We describe here the culture of human aortic ECs from healthy and type 2 diabetic donors, the treatment with a small molecular conformation of trans-resveratrol and hesperetin (tRES+HESP), followed by proteomic analysis of whole-cell lysate. A number of 3666 proteins were presented in all the samples and thus further analyzed. We found that 179 proteins had a significant difference between diabetic ECs vs. healthy ECs, while 81 proteins had a significant change upon the treatment of tRES+HESP in diabetic ECs. Among them, 16 proteins showed a difference between diabetic ECs and healthy ECs and the difference was reversed by the tRES+HESP treatment, with the top 5 drastically altered proteins being ACVRL1, ADAM9, ITGAV, PCCB, and TGFBR2. Follow-up functional assays identified ACVRL1 and TGFBR2 as the most pronounced mediator for tRES+HESP-induced protection of angiogenesis in vitro. Our study has revealed the global changes in proteins and biological pathways in ECs from diabetic donors, which are potentially reversible by the tRES+HESP formula. Furthermore, we have identified the TGFβ signaling axis as a responding mechanism in ECs treated with this formula, shedding light for future studies for deeper molecular characterization
Project description:Ribosomes are essential macromolecular complexes conducting protein biosynthesis in all domains of life. Cells can have heterogeneous ribosomes, i.e. ribosomes with various ribosomal RNA (rRNA) and ribosomal protein (r-protein) composition. However, the functional importance of heterogeneous ribosomes has remained elusive. One of the possible sources for ribosome heterogeneity is provided by paralogous r-proteins. In E. coli, ribosomal protein bL31 has two paralogs: bL31A encoded by rpmE and bL31B encoded by ykgM. This study investigates phenotypic effects of these ribosomal protein paralogs using bacterial strains expressing only bL31A or bL31B. We show that bL31A confers higher fitness to E. coli under lower temperatures. In addition, bL31A and bL31B have different effects on translation reading frame maintenance and apparent translation processivity in vivo as demonstrated by dual luciferase assay. In general, this study demonstrates that ribosomal protein paralog composition (bL31A versus bL31B) can affect cell growth and translation outcome.