Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Moss Physcomitrella paten endogenous peptides, LC-MS/MS, part 2

ABSTRACT: Short (<100 codons) open reading frames (sORFs) are common features of all genomes. Proof of translation of sORFs is an important step towards finding of functional sORF-encoded peptides (SEPs). We verified translation of our predicted sORFs using mass-spectrometry (MS) analysis which is often considered as the gold standard in detection of proteins or peptides in cell. Taking into account the shortage of proteomic methods in identifying small proteins or peptides, in our study we used “peptidomic” dataset - endogenous peptides, extracted from three types of moss cells – gametophores, protonemata and protoplasts

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Physcomitrella Patens Subsp. Patens (moss)

TISSUE(S): Plant Cell, Protonema, Gametophore

SUBMITTER: Igor Fesenko

LAB HEAD: Vadim M Govorun

PROVIDER: PXD007923 | Pride | 2019-08-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Moss endogenous peptides, LC-MS/MS

Project description:Short (<100 codons) open reading frames (sORFs) are common features of all genomes. Proof of translation of sORFs is an important step towards finding of functional sORF-encoded peptides (SEPs). We verified translation of our predicted sORFs using mass-spectrometry (MS) analysis which is often considered as the gold standard in detection of proteins or peptides in cell. Taking into account the shortage of proteomic methods in identifying small proteins or peptides, in our study we used “peptidomic” dataset - endogenous peptides, extracted from three types of moss cells – gametophores, protonemata and protoplasts

2019-08-08 | PXD007922 | Pride

Moss proteomes, LC-MS/MS - proteome data analysis

2019-08-08 | PXD007973 | Pride

Transcriptomic and proteomic analysis of alternative splicing in Physcomitrella patens moss

Project description:Alternative splicing (AS) has a significant potential to impact on the eukaryotic cell transcriptome and proteome. However, the extent of this influence as well as mechanisms, providing the tissue-specific pattern of AS are poorly studied. Here, we analyzed the AS of two life forms, protonema and gametophores, as well as the protoplasts, of a model organism, the Physcomitrella patens moss, using the data of transcriptome and proteome profiling. Altogether, 12,043 genes subjected to alternative splicing were identified. The alternative splicing patterns of 302 genes involved in stress response, growth, and development are changed considerably in the process of the gametophore development, whereas AS of 276 genes involved in transcription regulation, development, cell interactions, and cell response to biotic and abiotic stresses altered upon protoplastitation. Using mass spectrometry analysis, we studied the extent to which AS contributes to proteome diversity and identified 117 isoform-specific peptides for 36 genes with AS events. Our results indicate that AS event have a little impact on the proteome diversity and mostly result in the addition of extra amino acids rather than editing of existing proteins sequences. Among differentially expressed and spliced genes we found serine/arginine-rich (SR) genes, which are known to regulate AS in cells. We identified new isoforms of these genes and data evidencing their translation were obtained at transcriptome and proteome level. We also found that treatment with abscisic and jasmonic acids led to the isoform-specific response in protonema. Besides, we revealed the potential lncRNAmRNA and lncRNApre-mRNA interactions that can influence both the expression and alternative splicing of genes. It can point at an additional level of gene expression and AS regulation by non-coding transcripts in the Physcomitrella patens moss.

2018-01-15 | PXD005223 | Pride

MOTS-c: A Novel Peptide Encoded by a Short Mitochondrial Open Reading Frame Regulates Metabolic Homeostasis

Project description:Mitochondria are known to be functional organelles, but their role as a signaling unit is increasingly being appreciated. The recent identification of a short open reading frame (sORF) in the mitochondrial DNA (mtDNA) that encodes a signaling peptide, humanin, suggests the possible existence of additional sORFs in the mtDNA that yield bioactive peptides. Here we report the identification of a sORF within the mitochondrial 12S rRNA encoding a 16-amino-acid peptide named MOTS-c (mitochondrial open-reading-frame of the twelve S rRNA -c) that regulates insulin sensitivity and metabolic homeostasis. MOTS-c is detected in various tissues and in circulation in an age-dependent manner. Its primary target organ appears to be the skeletal muscle and its cellular actions inhibit the folate cycle and its tethered de novo purine biosynthesis, causing a significant accumulation of AICAR levels concomitantly with AMPK activation. MOTS-c treatment in mice prevented age-dependent and high-fat diet-induced insulin resistance, as well as diet-induced obesity. These results suggest that mitochondria may be more actively engaged in regulating metabolic homeostasis than previously recognized, through the production of peptides encoded within its genome that act at the cellular and organismal level.

2015-03-07 | GSE65068 | GEO

MHC-I peptidome analysis of human foreskin fibroblasts

Project description:Ribosome profiling (Ribo-seq) recently revealed the expression of thousands of short open reading frames (sORFs) in eukaryotic cells. They encode for a class of instable peptides, which evade experimental validation by whole-proteome mass spectrometry. Here, we show that computational elimination of experimental noise from Ribo-seq data unravels fundamental new aspects of sORF biology. Based on the revised annotation of cellular sORFs, we show that sORF-derived peptides are efficiently incorporated into MHC-I. sORFs thus encode a novel class of stress-responsive antigens in human cells. Our findings have broad implications on the functional, regulatory and immunogenic role of sORFs in fundamental cellular processes like infection and cancer.

2018-04-05 | PXD007203 | Pride

MOTS-c: A Novel Peptide Encoded by a Short Mitochondrial Open Reading Frame Regulates Metabolic Homeostasis

2015-03-07 | E-GEOD-65068 | biostudies-arrayexpress

Genes affected by auxin and decapitation in moss gametophores

Project description:The goal of this study is to identify genes whose expression is affected by decapitation and auxin in moss gametophores Project ngs2017_09_moss1-auxin in CATdb What genes are misregulated in response to decapitation or auxin response?

2022-06-21 | GSE188843 | GEO

Ppatens transcriptome

Project description:We studied peptide generation process in moss Physcomitrella patens. For this purpose, analysis of peptidome and transcriptome of two different life forms (gametophores and protonema) and also of protoplasts were made.

2014-04-22 | E-MTAB-1637 | biostudies-arrayexpress

K562 polyA RNA-Seq

Project description:RNA-Seq reads and TopHat (Trapnell et al. Bioinformatics 2009) alignments of K562 cell-line transcriptome. These were used to validate the expression of short peptides idenitified by Mass-Spectrometry in K562 cells. K562 polyA+ RNA (Batch 1) and total RNA (batch 2) was purchased from Ambion. We used oligo (dT)-selected polyA+ RNA to construct libraries for RNA-Seq.We then profiled the transcriptome of polyadenylated mRNA-Seq using Illumina sequencing platforms. We then used the sequenced reads to reconstruct the transcriptome using the Cufflinks de-novo assembler (Trapnell et al. Nat.Bio.Tech. 2010). Recent computational and ribosome profiling analyses suggest that many short open reading frames (sORFs) in eukaryotic genomes are translated. However, evidence that these sORFs produce stable polypeptides is lacking. Here we develop a strategy to discover and validate novel sORF-encoded polypeptides (SEPs) in human cells. In total, we detect 117 SEPs, 114 of which are novel, varying in length from 15 to 149 amino acids. Of these, 10 SEPs (0.5%) are derived from long intergenic non-coding RNAs (lincRNAs). We also observe the presence of polycistronic genes and the widespread use of non-AUG start codons, which is a phenomenon historically thought to be rare in the mammalian genome. Quantitative measurements reveal that SEPs can be found at concentrations between ~10-2000 copies per cell, which is within the range of typical cellular proteins. We confirm the translation of a number of these SEPs through heterologous expression of their encoding cDNAs. We also discover that several SEPs possess properties characteristic of functional proteins. These results demonstrate that human sORFs produce numerous stable polypeptides, revealing that the human proteome is larger and more diverse than previously appreciated.

2012-11-14 | E-GEOD-34740 | biostudies-arrayexpress

Expression profiling of the moss F. hygrometrica

Project description:We experimentally generated a genome-wide gene expression data. To this end, we first collected samples of three important haploid developmental stages, specifically germinating spores (gametophyte_1), protonemata (gametophyte_2) and young gametophores (gametophyte_3) (four biological replicates each). We also collected three developmental stages of the diploid phase (sporophyte), specifically sporophytes shorter than 5mm (sporophyte_1), elongated needle-like sporophytes (sporophyte_2), and sporophytes with swollen capsules (sporophyte_3)

2013-07-17 | E-MTAB-1664 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data