The small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Velos
ORGANISM(S): Sinorhizobium Meliloti 2011
SUBMITTER: 
Sandra Maass
LAB HEAD: Dörte Becher
PROVIDER: PXD034931 | Pride | 2023-03-13
REPOSITORIES: Pride
Similar Datasets
Project description:Previous studies demonstrated that carnosine affects signaling molecules of different pathways in a number of experimental models. However, the primary targets of carnosine are still unknown and its effect on complex signal transduction has not been revealed. This is especially the case for pathways that could be responsible for the anti-neoplastic effect of the dipeptide. Therefore, we performed a phosphoprotein antibody array and RNA-seq experiments with U87 glioblastoma cells treated with 50 mM carnosine for 24h, in order to obtain a precise and coherent picture of carnosine’s influence on signal transduction in single tumor cells.
2019-11-30 | E-MTAB-6455 | biostudies-arrayexpress
Project description:Background Metabolic associated fatty liver disease (MAFLD) was recently proposed to replace non-alcoholic fatty liver disease (NAFLD), which is defined as ectopic fat deposition in the liver. Hepatic steatosis is an independent predictor for insulin resistance and cardiovascular risk and hence mortality. The aim of present study was to investigate the urine molecular pattern and potential urine biomarker to distinguish healthy control, mild and severe hepatic steatosis in MAFLD patients using proteomic data. Method Hepatic steatosis was measured by Magnetic resonance imaging (MRI) that measure the proton density fat fraction (MRI-PDFF). Proteomic measurements of urine samples were done by mass spectrometry. Linear regression analyses were used to detect significant associations between the biomarkers and clinical parameters. Western blot and Elisa were performed for validation. Results Multiple pathways have been compromised in MAFLD, including the carbohydrate derivative catabolic process, glycosaminoglycan process, aminoglycan metabolic process, inflammatory response, insulin-like growth factor receptor and GTPase complex. Alpha-1-acid glycoprotein 1 (ORM1) and ceruloplasmin were finally identified to be potential urine biomarkers to detect mild/severe hepatic steatosis.
2022-08-12 | PXD026333 | Pride
Project description:Recent work has shown that small non-coding RNAs, including miRNAs, serve an important role in controlling gene expression during development and disease. However, little detailed information exists concerning the relative expression patterns of small RNAs during development of C. elegans. Here we use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs, including miRNAs, changes dynamically during development and in the different sexes of C. elegans; approximately 16% of known miRNAs changed over 10 fold in expression during C. elegans development and about 12% of miRNAs showed major changes in expression between males and hermaphrodites of C. elegans. These results should lead to a better understanding of the expression and function of small RNAs in C. elegans development. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of small RNA expression in six different developmental stages of hermaphrodites (Embryo, mid-L1, mid-L2, mid-L3, mid-L4, young adult), and young adult males (dpy-28;him-8) and spermatogenesis-defective young adult hermaphrodites (spe-9). The number of sequence reads for miRNA was assessed from the raw sequence data from Solexa sequencing using perfect sequence matching to known miRNAs (miRBase Release 11.0).
2008-12-01 | E-GEOD-13339 | biostudies-arrayexpress
Project description:A commercially available gene array (SABiosciences array PAMM-029ZD-12) was used to assay gene expression in skeletal muscle of SMA mice and control littermates. The Taiwanese severe SMA mouse model was used (Hsieh-Li et al. 2000). The array included 84 genes associated with DNA damage detection, DNA repair, apoptosis, cell cycle, and other functions. SMA group (n=3) vs. control group (n=3) - single technical replicates, triple biological replicates
2014-03-03 | E-GEOD-55481 | biostudies-arrayexpress
Project description:We report a significant number of miRNAs and other non-coding small RNAs show dramatic changes in expression during aging in C. elegans. RNAs were prepared from four diffrent timepoints during adulthood of C. elegans hermaphrodites, Day 0, 5, 8 and 12 post-L4 molt, and used for making cDNA libraries for small RNAs. Each library was sequenced using recent advances in high-throughput sequencing technology, Solexa. This study should lead to a better understanding of the aging process and age-related diseases. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of small RNA expression in four timepoints during adulthood of C. elegans hermaphrodites (spe-9 (hc88), cultured at 23dC), Day 0, 5, 8 and 12 post L4-molt.
2009-12-31 | E-GEOD-18634 | biostudies-arrayexpress
Project description:Continuous exposure to cisplatin can induce drug resistance to limit efficacy, however, the underlying mechanisms correlated to cisplatin resistance are still unclear. Drug-sensitive A549 cells and cisplatin-resistant A549/DDP cells were used to explore the potential metabolic pathways and key targets associated with cisplatin resistance by integrating untargeted metabolomics with transcriptomics. The results of comprehensive analyses showed that 19 metabolites were significantly changed in A549/DDP vs A549 cells, and some pathways had a close relationship with cisplatin resistance, such as the biosynthesis of aminoacyl-tRNA, glycerophospholipid metabolism, and glutathione metabolism. Moreover, transcriptomics analysis showed glutathione metabolism was also obviously affected in A549/DDP, which indicated that glutathione metabolism played an import role in the process of drug resistance. Meanwhile, transcriptomics analysis suggested the four enzymes related to glutathione metabolism - CD13, GPX4, RRM2B, and OPLAH - as potential targets of cisplatin resistance in NSCLC. Further studies identified the over-expressions of these four enzymes in A549/DDP. The elucidation of mechanism and discovery of new potential targets may help us have a better understanding of cisplatin resistance.
2019-08-12 | PXD013265 | Pride
Project description:MICU1 is a Ca2+-binding protein that regulates the mitochondrial Ca2+ uniporter channel (mtCU ) and mitochondrial Ca2+ (mCa2+) uptake. MICU1 knockout mice display perinatal lethality and disorganized mitochondrial architecture. These phenotypes are distinct from other mtCU loss-of-function models and thus are not explained by changes in mCa2+ content. Utilizing multiple proteomic approaches, we found that MICU1 localized to mitochondrial complexes lacking MCU, suggesting that MICU1 has cellular functions independent of mCa2+ uptake. The overall aim of the current project is to identify the global and mtCU independent MICU1 interactome to characterize the MCU independent functions of the MICU1.
2024-01-26 | PXD028462 | Pride
Project description:Here we performed a comprehensive genomic and proteomics analysis of P. stutzeri in aerobic and oxygen-limiting conditions. We combined de novo genome assembly relying on 3rd generation long read sequencing technologies to report the first complete P. stutzeri ATCC14405 genome, which added over 110 kb of sequence and contains 126 full length CDS that were only partially covered in the fragmented short read-based genome assembly available for this strain. With this optimal basis for downstream functional genomics, we next carried out state of the art bottom-up and top-down proteomics analyses to report the most detailed study of proteome remodeling in response to oxygen limitation in P. stutzeri. We identified more than 2900 proteins, i.e. greater than 70% of the theoretical proteome, including 160 annotated small proteins. The proteins included well-established enzymes involved in denitrification and metabolic adaptation to oxygen-limiting conditions, as well as uncharacterized proteins. Notably, we identified 16 novel small proteins that had so far been missed in the genome annotation.
2023-08-04 | PXD037914 | Pride
Project description:Haploinsufficiency of GRN causes frontotemporal dementia (FTD). The GRN locus produces progranulin (PGRN), which is cleaved to lysosomal granulin polypeptides. The function of lysosomal granulins and why their absence causes neurodegeneration are unclear. Here we discover that PGRN-deficient human cells and murine brains, as well as human frontal lobes from GRN-mutation FTD patients have increased levels of gangliosides, glycosphingolipids that contain sialic acid. In these cells and tissues, levels of lysosomal enzymes that catabolize gangliosides were normal, but levels of bis(monoacylglycero)phosphates (BMP), lipids required for ganglioside catabolism, were reduced with PGRN deficiency. Our findings indicate that granulins are required to maintain BMP levels to support ganglioside catabolism, and that PGRN deficiency in lysosomes leads to gangliosidosis. Lysosomal ganglioside accumulation may contribute to neuroinflammation and neurodegeneration susceptibility observed in FTD due to PGRN deficiency and other neurodegenerative diseases.
2022-09-18 | PXD035889 | Pride
Project description:In the advanced stages, malignant melanoma (MM) has a very poor prognosis. Due to tremendous efforts in cancer research, the overall survival of metastatic melanoma has doubled; however, complete eradication of the disease is almost unknown. With the advent of proteomics, deep-mining studies can reach low-abundant expression areas. The complexity of the proteome, however, still surpasses the dynamic range capabilities of current analytical techniques. Consequently, many predicted protein products with potential biological functions have not yet been verified in experimental proteomic data. This category of ‘missing proteins’ (MP) is comprised of all proteins that have been predicted but are currently unverified. As part of the initiative launched in 2016 in the United States, the European Cancer Moonshot Center has performed numerous deep proteomics analyses on samples from MM patients. In this study, nine MPs were clearly identified by mass spectrometry in MM metastases. Some MPs significantly-correlated with proteins that possess identical PFAM structural domains; and other MPs were significantly-associated with cancer-related proteins. This is the first study to our knowledge, where unknown and novel proteins have been annotated within metastasis, from Melanoma Cancer patients.
2020-03-11 | PXD017968 | Pride