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: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:we profiled small RNAs binding to phosphorylated Serine (p-Ser), Threonine (p-Thr) and Tyrosine (p-Tyr) residues of proteins in human lung bronchial epithelial (HBE) and lung squamous cell carcinoma (SCC) cells. A total of 1986 unique p-Proteins interacted piRNAs and piRNA-Likes were called.
2020-01-31 | GSE94337 | GEO
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:Insulin signaling is mediated via a network of protein phosphorylation. Dysregulation of this network is central to obesity, type 2 diabetes and metabolic syndrome. Here we have investigated the role of phosphatase binding protein Alpha4 (α4) that is essential for the Ser/Thr protein phosphatase PP2A in insulin action/resistance in adipocytes. Unexpectedly, adipocyte-specific inactivation of α4 impairs insulin-induced Akt-mediated Ser/Thr phosphorylation despite a decrease in the PP2A levels. Interestingly, loss of α4 also reduces insulin-induced insulin receptor Tyr phosphorylation. This occurs through decreased association of α4 with Y-box protein 1 (YBX1), resulting in the enhancement of the Tyr phosphatase PTP1B expression. Moreover, adipocyte-specific knockout of α4 results in impaired adipogenesis and altered mitochondrial oxidation leading to increased inflammation, systemic insulin resistance, hepatosteatosis, islet hyperplasia, and impaired thermogenesis. Thus, the α4 /YBX1-mediated pathway of insulin receptor signaling is essential for maintaining insulin sensitivity, normal adipose tissue homeostasis and systemic metabolism.
2022-09-21 | GSE210407 | GEO
Project description:Sinorhizobium meliloti, a facultative microsymbiont of alfalfa, should fine-tune its cellular processes to live saprophytically in soils characterized with limited nutrients and diverse stresses. In this study, TiO2 enrichment and LC-MS/MS were used to uncover the site-specific Ser/Thr/Tyr phosphoproteome of S. meliloti in minimum medium at stationary phase. There are a total of 96 unique phosphorylated sites, with a Ser/Thr/Tyr distribution of 65:32:5, in 78 proteins. Phosphoproteins identified in S. meliloti showed a wide distribution pattern regarding to functional categories, such as replication, transcription, translation, posttranslational modification, transport and metabolism of amino acids, carbohydrate, inorganic ion, succinoglycan etc. Ser/Thr/Tyr phosphosites identified within the conserved motif in proteins of key cellular function indicate a crucial role of phosphorylation in modulating cellular physiology. Moreover, phosphorylation events potentially involved in rhizobial adaptation to diverse stresses were also discussed, such as those identified in SMa0114 and PhaP2 (polyhydroxybutyrate synthesis), ActR (pH stress and microaerobic adaption), SupA (potassium stress), chaperonin GroEL2 (viability and potentially symbiosis), and ExoP (succinoglycan synthesis and secretion). These Ser/Thr/Tyr phosphosites identified herein would be helpful for our further investigation and understanding of the role of phosphorylation in rhizobial physiology.
2015-10-05 | PXD002064 | Pride
Project description:We report the mRNA expression profile of Streptococcus pneumoniae Type 2 D39 strain-derived mutant lacking the phpP gene encoding eukaryote-type ser/thr phosphatase and the stkP gene encoding Ser/Thr protein kinase.
2019-04-13 | GSE113337 | 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: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:This work focus on in the role of Ser/Thr/Tyr protein phosphorylation in Streptococcus thermophilus, the only streptococcal species used in food fermentation. During technological processes, S. thermophilus has to adapt to various nutrition and physical-chemical stresses that require rapid adjustments. In this study, we investigated a way for S. thermophilus to regulate specific pathways namely post-translational protein modifications and more specifically protein serine/threonine/tyrosine phosphorylation. We would like to assess the specific role of the only predicted Hanks-type kinase, named PknB. We performed in parallel a global shotgun proteomics and a specific phosphoproteomics analyses on both the wild type strain and its Hanks-type kinase deletion mutant. All the analysis were performed on an Orbitrap Fusion Lumos Tribrid. We showed that the S. thermophilus Ser/Thr/Tyr phosphoproteome is of the same order of magnitude than the other streptococci ones as peptides belonging to 106 proteins (410 phosphopeptides corresponding to 161 peptide sequences with different phosphosite positions) from various metabolic pathways were found phosphorylated in one bacterial growth condition. The phosphorylation occurred for 43 % on serine, 33 % on threonine and 23 % on tyrosine. We demonstrated that the Hanks-type kinase, named PknB in S. thermophilus, targets the divisome and is only one of the players in the Ser/Thr/Tyr phosphorylation process. Consistent with these results, the pknB deletion mutant exhibits a clear phenotype with longer whimsical chains and affected division process.
2019-07-08 | PXD011391 | Pride
Project description:Cyanobacteria have shaped the earth’s biosphere as the first oxygenic photoautotrophs and still play an important role in many ecosystems. The ability to adapt to changing environmental conditions is an essential characteristic in order to ensure survival. To this end, numerous studies have shown that bacteria use protein post-translational modifications such as Ser/Thr/Tyr phosphorylation in cell signalling, adaptation and regulation. Nevertheless, our knowledge of cyanobacterial phosphoproteomes and their dynamic response to environmental stimuli is relatively limited. In this study, we applied gel-free methods and high accuracy mass spectrometry towards the unbiased detection of Ser/Thr/Tyr phosphorylation events in the model cyanobacterium Synechocystis sp. PCC 6803. We could identify over 300 phosphorylation events in cultures grown on nitrate as exclusive nitrogen source. Chemical dimethylation labelling was applied to investigate proteome and phosphoproteome dynamics during nitrogen starvation. Our dataset describes the most comprehensive (phospho)proteome of Synechocystis to date, identifying 2,382 proteins and 183 phosphorylation events and quantifying 2,111 proteins and 148 phosphorylation events during nitrogen starvation. Global protein phosphorylation levels were increased in response to nitrogen depletion after 24 hours. Among the proteins with increased phosphorylation, the PII signalling protein showed the highest fold-change, serving as positive control. Other proteins with increased phosphorylation levels comprised functions in photosynthesis and in carbon and nitrogen metabolism. This study reveals dynamics of Synechocystis phosphoproteome in response to environmental stimuli and suggests an important role of protein Ser/Thr/Tyr phosphorylation in fundamental mechanisms of homeostatic control in cyanobacteria.
2016-05-09 | PXD001831 | Pride