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Barley newly synthesized ribosomal proteome: E.coli control samples

ABSTRACT: Ribosomal proteome profiling control for project: Plants synthesize new ribosomal proteins and recycle others in cold-acclimated ribosomes and these in turn synthesize a differential proteome in barley root meristems.

INSTRUMENT(S):

ORGANISM(S): Escherichia Coli

SUBMITTER: Federico Martinez-Seidel

LAB HEAD: Berin A. Boughton

PROVIDER: PXD032938 | Pride | 2024-05-23

REPOSITORIES: Pride

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			Action	DRS
	201009_Federico_FMS-1225_1.raw	Raw
	201009_Federico_FMS-1225_2.raw	Raw
	201009_Federico_FMS-1225_3.raw	Raw
	allSpectra.HCD.FTMS.iso_0.apl	Other
	allSpectra.HCD.FTMS.iso_1.apl	Other

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1 - 5 of 63

Publications

Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on the Plant Ribosome.

Gentry-Torfer Dione D Murillo Ester E Barrington Chloe L CL Nie Shuai S Leeming Michael G MG Suwanchaikasem Pipob P Williamson Nicholas A NA Roessner Ute U Boughton Berin A BA Kopka Joachim J Martinez-Seidel Federico F

Bio-protocol 20240505 9

Ribosomes are an archetypal ribonucleoprotein assembly. Due to ribosomal evolution and function, r-proteins share specific physicochemical similarities, making the riboproteome particularly suited for tailored proteome profiling methods. Moreover, the structural proteome of ribonucleoprotein assemblies reflects context-dependent functional features. Thus, characterizing the state of riboproteomes provides insights to uncover the context-dependent functionality of r-protein rearrangements, as the ...[more]

PMID: 38737506

Similar Datasets

Barley newly synthesized ribosomal proteome

Project description:Plants synthesize new ribosomal proteins and recycle others in cold-acclimated ribosomes and these in turn synthesize a differential proteome in barley root meristems.

2024-11-16 | PXD032923 | Pride

E.coli Ribosome protein composition

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.

2020-10-20 | PXD018123 | Pride

Proteomics link translational reprogramming to S-glutathionalytion and induced priming during cold acclimation in barley roots

Project description:Plants due to their sessile nature rely on root systems to mediate many challenging stimuli. A major cornerstone of the responses are root proteomes, shaped to overcome biotic and abiotic cues. Proteome-wide reprogramming events are magnified in root meristems due to their active protein production. Using root meristems as a test system, we here study the major rewiring that plants face during cold acclimation. To achieve that, we performed tandem mass tag (TMT) label-mediated bottom-up proteomics of two consecutive segments of barley root apexes, comparing changes in global protein contents and individual protein abundances. We report an intricate translational reprogramming happening in the distal apex zone. The reprogramming includes all the translational machinery from ribosome biogenesis to protein folding, even suggesting roles for cold-specific ribosomal protein (RP) paralogs. Finally, this event is accompanied by upregulation of glutathione production and S-glutathionylation assemblage machineries. To summarize, we couple previous reports of an alternatively cold-spliced transcriptome to potential cold-specialized ribosomes and subsequent posttranslational modification (PTM), S-glutathione, of proteins. We propose that these PTMs protect the proteome during cold by acting as ROS scavengers, and consequently, provide a mechanistic link to the cold priming capabilities for root-specific biotic stress.

2021-04-14 | PXD021731 | Pride

Transcription profiling of Leymus cinereus and Leymus triticoides negatively orthogeotropic and diageotropic meristems using a barley gene chip

Project description:Compare gene expression profiles of Leymus negatively orthogeotropic and diageotropic meristems in a similar genetic background, identify gene expression polymorphisms specifically associated with the Leymus LG3a rhizome QTL by bulk segregate analysis, and identify other possible genes specifically involved in branch angle differences of otherwise similar negatively orthogeotropic and diageotropic meristems.

2008-04-20 | E-MEXP-1266 | biostudies-arrayexpress

Structure of an Archaeal Ribosome Reveals a Divergent Active Site and Hibernation Factor

Project description:Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase center (PTC), is thought to be nearly universally conserved. Here, we identify clades of archaea that have highly divergent ribosomal RNA sequences in the PTC. To understand how these PTC sequences fold, we determined cryo-EM structures of the 70S and 50S ribosomes to 2.4 Å and 2 Å, respectively, from the hyperthermophilic archaeon Pyrobaculum calidifontis. PTC sequence variation leads to the rearrangement of key base triples and differences between archaeal and bacterial ribosomal proteins enable sequence variation in archaeal PTCs. Finally, we identify a previously undescribed archaeal ribosome hibernation factor, Dri, that differs from known bacterial and eukaryotic hibernation factors and is found in multiple archaeal phyla. Overall, this work identifies factors that regulate ribosome function in archaea and reveals a larger diversity of the most ancient sequences in the ribosome

2025-06-17 | PXD064958 | Pride

Acclimation and stress response of Prochlorococcus to low salinity

Project description:Prochlorococcus is an obligate marine microorganism which are dominant autotroph in tropical and subtropical central oceans. However, what is the low salinity boundary and how Prochlorococcus would response to low salinity exposure is still unknown. In this study, we first tested the growing salinity range of two Prochlorococcus strains, NATL1A and MED4, and then compared the global transcriptome of their low salinity acclimated cells and cells growing in normal seawater salinity. We found that MED4 could be acclimated in the lowest salinity of 25% and NATL1A could be acclimated in the lowest salinity of 28%. Measurement of the effective quantum yield of PSII photochemistry (Fv/Fm) indicated that both strains were stressed when growing in salinity lower than 34%. The transcriptomic response of NATL1A and MED4 were approximately different, with much more genes having changed transcript abundance in NATL1A than in MED4. To cope with low salinity, NATL1A downregulated the transcript of most genes involved in translation, ribosomal structure and biogenesis, while MED4 upregulated those genes. Moreover, low salinity acclimated NATL1A cells suppressed ATP-producing genes and induced the expression of photosynthesis related genes, while low salinity acclimated MED4 upregulated ATP-producing genes and downregulated photosynthesis related genes. These results indicate that the response to low salinity stress of different Prochlorococcus strains could be distinct. The study provided the first glimpse into the growing salinity range of Prochlorococcus cells and their global gene expression changes due to low salinity stress.

2022-02-02 | GSE195946 | GEO

Wheat, Rye, and Barley Genomes Can Associate during Meiosis in Newly Synthesized Trigeneric Hybrids.

Project description:Polyploidization, or whole genome duplication (WGD), has an important role in evolution and speciation. One of the biggest challenges faced by a new polyploid is meiosis, in particular, discriminating between multiple related chromosomes so that only homologs recombine to ensure regular chromosome segregation and fertility. Here, we report the production of two new hybrids formed by the genomes of species from three different genera: a hybrid between Aegilops tauschii (DD), Hordeum chilense (HchHch), and Secale cereale (RR) with the haploid genomic constitution HchDR (n = 7× = 21); and a hybrid between Triticum turgidum spp. durum (AABB), H. chilense, and S. cereale with the constitution ABHchR (n = 7× = 28). We used genomic in situ hybridization and immunolocalization of key meiotic proteins to establish the chromosome composition of the new hybrids and to study their meiotic behavior. Interestingly, there were multiple chromosome associations at metaphase I in both hybrids. A high level of crossover (CO) formation was observed in HchDR, which shows the possibility of meiotic recombination between the different genomes. We succeeded in the duplication of the ABHchR genome, and several amphiploids, AABBHchHchRR, were obtained and characterized. These results indicate that recombination between the genera of three economically important crops is possible.

| S-EPMC7826760 | biostudies-literature

Vibrio vulnificus CMCP6 Proteome Analysis

Project description:Ribosomal proteins and global proteome were quantified by iTRAQ Labeling. Ribosomal proteins in 70S ribosomes purified from ΔrrnI-comp cells compared to those from ΔrrnI cells. Also, WT cells was measured.

2018-11-23 | PXD009215 | Pride

The synthesized peptides were acetlated by seven acetyltransferases from E.coli

Project description:24 polypeptides (21 amino acids long) were synthesized and mixed as a substrate library. Then, these substrates were acetylated by acetyl-CoA or seven E.coli acetyltransferase PatZ.

2022-09-19 | PXD036845 |

DNA microarray analysis of E.coli K12 MG1655 exposed to prolonged stationary phase

Project description:This study explores the effects of prolonged stationary phase, on whole genome expression of Escherichia coli. In summary these results imply that prolonged stationary phase cells have shown less growth rate compared to fresh cells due to the low abundance of transcripts for translation initiation factor infC, and for all the seven rrn operons of 5S, 16S, 23S ribosomal RNA which further delayed in protein synthesis leading to low biomass in prolonged stationary phase cells.

2013-09-12 | GSE50828 | GEO

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