CMMC Feb 01 2024 Carboxylic Acids Conjugated with Amino Acids - 1
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Not Applicable
SUBMITTER: 
Pieter C Dorrestein
PROVIDER: MSV000094220 | MassIVE | Fri Mar 01 19:20:00 GMT 2024
REPOSITORIES: MassIVE
Similar Datasets
Project description:Amidation reaction was used. Acyl chlorides and amines were used to create these compounds. The following reactants are: Palmitoyl, Tetradecanoyl, Decanoyl, Octanoyl, Hexanoyl, Butyryl, Acetyl chlorides with Arg, Phe, Tyr, Trp, Ser, Met, Gly, Homoserine, Leu, GABA, 5-aminobutanoic acid, His, Lys, Thr.
2024-03-01 | MSV000094220 | GNPS
Project description:Amino acids (AA) are essential molecules for life because they are precursors for the synthesis of proteins and other organic compounds. Their metabolism in plants involves more than one cellular compartment, among which the chloroplast plays a key role. From the 20 essential AA, ten (Arg, Lys, Thr, Leu, Ile, Val, Trp, Phe, Tyr and His) are only synthesized in the plastids and seven (Asp, Cys, Gln, Glu, Gly, Ser and Met) can be synthesized in both chloroplast and other parts of the cell. Despite knowing the roles of AA in plant physiology, little has been assessed in plants with albino phenotypes, lacking chloroplasts. To assess the effect of chloroplast biogenesis disturbances on AA metabolism in albino and variegated somaclonal variations of Agave angustifolia Haw., a comparative proteomic based TMT- synchronous precursor selection (SPS)-MS3 strategy was used to determine the status of AA biosynthetic pathways. Besides the 20 essential AA was quantified to underpin proteomics finding. A total of 2,442 different proteins were identified in the proteome of the somaclonal variants, from which 82 correspond to enzymes participating in AA biosynthesis. From these 82, 32 proteins were differentially accumulated. On the other hand, the concentration of 16 and 12 of the AA synthesized by the chloroplast were over-accumulated in the variegated and albino somaclonal variant, respectively. In plantlets devoid of functional chloroplasts, there is a surprising increase of AA and key enzymes of the AA biosyntethic pathways, compared to green plantlets. This could suggest que la activation of AA biosynthesis is key to sustaining albino and variegated plantlets survival that lack chloroplasts.
2024-01-29 | PXD039512 | Pride
Project description:N-terminal acetylation is one of the most common protein modifications in eukaryotes, with emerging roles in regulating protein quality and stoichiometry and targeting and complex formation. The NatC complex is one of the three major N-terminal acetyltransferases (NATs). Here, we partially defined the in vivo human NatC Nt-acetylome by combining siNAA30 mediated knockdown with positional proteomics. We identified 51 human NatC substrates and expanded our current knowledge on the substrate repertoire of NatC which now includes proteins harboring Met-Leu, Met-Ile, Met-Phe, Met-Trp, Met-Tyr, Met-Trp, Met-Met, Met-His and Met-Lys N-termini. Next to cytosolic proteins, several organellar proteins were identified as NatC substrates. Interestingly, upon Naa30 depletion, the levels of several organellar proteins were reduced, in particular those of mitochondrial proteins. Further, knockdown of Naa30 induced the loss of membrane potential, clearing and fragmentation of mitochondria. Naa30 depletion also led to disassembly of the Golgi apparatus. However, Naa30 depletion did not affect ER morphology, endosome or peroxisome distribution or microtubule and actin cytoskeletal architecture, suggesting that the observed mitochondrial fragmentation and clearance and Golgi scattering are not due to general disruption of organelles or microtubules. In conclusion, NatC Nt-acetylates a large variety of cytosolic and organellar proteins and is essential for cis-Golgi integrity and mitochondrial function.
2016-10-05 | PXD000930 | Pride
Project description:Liquid biopsy is noninvasive and convenient to detect cancer-derived materials in blood or other body fluids. The aim of this study was to identify tRNA-derived small RNAs (tsRNAs) in plasma that could distinguish patients with breast cancer (BC) from healthy controls. Basing on high-throughput sequencing, 15 significantly upregulated tsRNAs were selected and assessed in cell supernatants and cell lines. 6 tsRNAs were identified and verified in a large cohort of 120 patients with BC and 112 healthy controls. tRF-Arg-CCT-017, tRF-Gly-CCC-001 and tiRNA-Phe-GAA-003 could serve as novel diagnostic biomarkers. Meanwhile, tRF-Arg-CCT-017 and tiRNA-Phe-GAA-003 could also act as prognostic biomarkers. Target genes of these tsRNAs were related to the development of cancer. These results suggest that specific tsRNAs in plasma might serve as diagnostic and prognostic biomarkers of BC.
2020-10-08 | GSE158945 | GEO
Project description:Scope: As a result of population ageing, the number of Alzheimer’s disease (AD) patients has rapidly increased. There are many hypothesises on the pathogenesis of AD, but its detailed molecular mechanism is still unknown, and so no effective preventive or therapeutic measures have been established. Some reports showed a decrease in levels of norepinephrine (NE) has been suspected to be involved in the decline of cognitive function in AD patients and NE concentrations were decreased in postmortem AD patient brains. Tyr-Trp was identified as being the most effective dipeptide in enhancing norepinephrine (NE) synthesis and metabolism. And Tyr-Trp treatment ameliorated the short-term memory dysfunction in AD model mice caused by amyloid beta (Aβ) 25-35. So, the purpose of this study was to investigate the preventive or/and protective effects of Tyr-Trp administration in AD model mice. Methods and results: ddY mice were fed normal diet. After 7 days of feeding, mice were divided into 3 groups (n=10 per group) as follows: the sham group, which received saline administration and distilled water injection; the Aβ group, which received saline administration and Aβ peptides 25–35 injection; and the Aβ+YW group, which received Tyr-Trp administration and Aβ peptides 25–35 injection. Tyr-Trp was orally administered Tyr-Trp (100 mg kg-1 day-1, twice a day), starting 7 days before Aβ peptides injection. The other groups received oral administration of saline (5 mL kg-1). After Aβ peptides injection or sham operation, each groups received every oral administration. DAN microarray showed that Tyrosine hydroxylase, dopa decarboxylase and dopamine receptor D2 mRNA expressions which were downregulated in Aβ group comparing with sham group were upregulated in Aβ+YW group comparing with Aβ group. In addition, quinoid dihydropteridine reductase mRNA expression which wasn’t changed in Aβ group comparing with sham group was upregulated in Aβ+YW group comparing with Aβ group. Conclusions: These results suggest that Tyr-Trp administration might ameliorate the short-term memory dysfunction in AD model mice because of enhancing norepinephrine (NE) synthesis and metabolism through metabolism of both Tyr and Trp.
2020-04-30 | GSE146400 | GEO
Project description:Mothers contribute cytoplasmic components to their progeny in a process called maternal provisioning. Provisioning is influenced by the parental environment, but the molecular pathways that transmit environmental cues between generations are not well understood. Here we show that in C. elegans, social cues modulate maternal provisioning to regulate gene silencing in offspring. Intergenerational signal transmission depends on a pheromone-sensing neuron and neuronal FMRFamide (Phe-Met-Arg-Phe)-like peptides. Parental FMRFamide-like peptide signaling dampens oxidative stress resistance and promotes the deposition of mRNAs for translational components in progeny, which in turn reduces gene silencing. This study identifies a new pathway for intergenerational communication that links neuronal responses to maternal provisioning. We suggest that loss of social cues in the parental environment represents an adverse environment that stimulates stress responses across generations.
2021-05-19 | GSE174646 | GEO
Project description:To identify molecular effects of the dual PI3K/mTOR inhibitor omipalisib (GSK2126458), we applied gene expression profiling in human leukemic cell lines OCI-AML3 using Whole Transcriptome Shotgun Sequencing (RNA-seq). After OCI-AML3 cell were treated with 50 nM omipalisib for 24 h, differentially expressed genes (DEGs) of 1245 genes upregulated and 811 were downregulated were found compared with vehicle group. Down-regulated genes enriched in cell cycle, DNA metabolic process, PI3K/AKT/mTOR signaling, MYC pathway, E2F pathway, Gly, Ser and Thr metabolism, Cys and Met metabolism, carbon metabolism, oxidative phosphorylation, mitochondrial biogenesis and respiratory electron transporter chain.
2023-09-15 | GSE224155 | GEO
Project description:To determine differences in kidney and renal F4/80+ macrophage gene expression between mice homozygous for the Arg-encoding versus the Trp-encoding rs3184504 polymorphism after 4 weeks of angiotensin II infusion.
2022-10-13 | GSE205031 | GEO
Project description:Co-translational N-terminal (Nt-) acetylation of nascent polypeptides is catalyzed by N-terminal acetyltransferases (NATs). The very N-terminal amino acid sequence is the major factor determining whether or not a given protein is Nt-acetylated. In humans, six different NATs, denoted NatA-NatF, are identified. In the current study we used N-terminal COFRADIC analysis to define the in vivo substrate specificity of Naa50 (Nat5)/NatE as this has long remained elusive. Three yeast strains were generated; a control strain endogenously expressing yNaa50, a deletion strain depleted of yNaa50 and a strain deleted of yNaa50 but ectopically expressing human Naa50. When comparing the Nt-acetylation status of different N-termini in the control strain with the deletion strain, a reduction in Nt-acetylation for several yeast proteins was observed. To our surprise, these substrates were not of the predicted NatE-type substrates, but rather canonical NatA substrates. Further, ectopic expression of hNaa50 mainly resulted in the Nt-acetylation of a selected class of otherwise Nt-free yeast N-termini besides increasing the degree of Nt-acetylation of several other yeast proteins, and as such (partially) complementing those N-termini displaying reduced Nt-acetylation upon yNAA50-deletion. The preferred substrates of hNaa50 were predominantly Met-starting N-termini including Met-Lys-, Met-Val-, Met-Ala-, Met-Tyr-, Met-Phe-, Met-Leu-, Met-Ser- and Met-Thr, and highly overlapped with the previously identified human Naa60/NatF substrate specificity profile. Identification of several hNaa50 substrates with a small amino acid in the second position also revealed a potential interplay between the NATs and methionine aminopeptidases (MetAPs). The initiator Methionine (iMet) is normally cleaved off by MetAPs when the second amino acid is small, but our in vitro data suggest that in contrast to a free iMet, an Nt-acetylated iMet is not hydrolyzed by MetAPs. Thus, Naa50-mediated Nt-acetylation may potentially act as a mechanism to retain the iMet of proteins with a small amino acid at the second position that normally would be hydrolyzed.
2015-05-29 | PXD001437 | Pride
Project description:Tyrosine (Tyr, Y) and phenylalanine (Phe, F) synthesis is shared by the pea aphid and its symbiont Buchnera aphidicola.These aromatic amino acids are essential for the pea aphid growth and development. To characterize the molecular mechanisms, at gene transcriptional level, underlying this symbiotic integrated network pea aphids (Acyrthosyphon pisum, clone LL01) were reared on (i) standard artificial diet (AP3) and (ii) on the same AP3 medium depleted of Tyr (Y) and Phe (F). From each of the two groups, aphids were collected at specific time points and dissected: 12 h (D0), 1 day (D1), 2 days (D2), 3 days (D3), 4 days (D4), 5 days (D5) and 7 days (D7). Total RNA, to be used in gene expression analysis by arrays, was extracted, under the two rearing conditions, from two tissues: gut [from 20 aphids per sample at all 7 time points] and bacteriocytes [from 25 aphids per sample at 4 time points: 3 days (D3), 4 days (D4), 5 days (D5) and 7 days (D7)]. At each time point we included three biological replicates.
2017-07-18 | E-MTAB-4456 | biostudies-arrayexpress