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1.
Sci Adv ; 9(30): eadi0286, 2023 07 28.
Article in English | MEDLINE | ID: mdl-37506203

ABSTRACT

Polypyrimidine tract binding protein 1 (PTBP1) is thought to be expressed only at embryonic stages in central neurons. Its down-regulation triggers neuronal differentiation in precursor and non-neuronal cells, an approach recently tested for generation of neurons de novo for amelioration of neurodegenerative disorders. Moreover, PTBP1 is replaced by its paralog PTBP2 in mature central neurons. Unexpectedly, we found that both proteins are coexpressed in adult sensory and motor neurons, with PTBP2 restricted mainly to the nucleus, while PTBP1 also shows axonal localization. Levels of axonal PTBP1 increased markedly after peripheral nerve injury, and it associates in axons with mRNAs involved in injury responses and nerve regeneration, including importin ß1 (KPNB1) and RHOA. Perturbation of PTBP1 affects local translation in axons, nociceptor neuron regeneration and both thermal and mechanical sensation. Thus, PTBP1 has functional roles in adult axons. Hence, caution is required before considering targeting of PTBP1 for therapeutic purposes.


Subject(s)
Axons , Nerve Regeneration , Neurons , Peripheral Nerve Injuries , Adult , Humans , Axons/metabolism , Heterogeneous-Nuclear Ribonucleoproteins/genetics , Heterogeneous-Nuclear Ribonucleoproteins/metabolism , Interneurons/metabolism , Nerve Regeneration/genetics , Neurons/metabolism , Peripheral Nerve Injuries/genetics , Peripheral Nerve Injuries/metabolism
2.
Int J Mol Sci ; 24(13)2023 Jun 25.
Article in English | MEDLINE | ID: mdl-37445813

ABSTRACT

The ABC transporter P-glycoprotein (Pgp) has been found to be involved in multidrug resistance in tumor cells. Lipids and cholesterol have a pivotal role in Pgp's conformations; however, it is often difficult to investigate it with conventional structural biology techniques. Here, we applied robust approaches coupled with cross-linking mass spectrometry (XL-MS), where the natural lipid environment remains quasi-intact. Two experimental approaches were carried out using different cross-linkers (i) on living cells, followed by membrane preparation and immunoprecipitation enrichment of Pgp, and (ii) on-bead, subsequent to membrane preparation and immunoprecipitation. Pgp-containing complexes were enriched employing extracellular monoclonal anti-Pgp antibodies on magnetic beads, followed by on-bead enzymatic digestion. The LC-MS/MS results revealed mono-links on Pgp's solvent-accessible residues, while intraprotein cross-links confirmed a complex interplay between extracellular, transmembrane, and intracellular segments of the protein, of which several have been reported to be connected to cholesterol. Harnessing the MS results and those of molecular docking, we suggest an epitope for the 15D3 cholesterol-dependent mouse monoclonal antibody. Additionally, enriched neighbors of Pgp prove the strong connection of Pgp to the cytoskeleton and other cholesterol-regulated proteins. These findings suggest that XL-MS may be utilized for protein structure and network analyses in such convoluted systems as membrane proteins.


Subject(s)
ATP Binding Cassette Transporter, Subfamily B, Member 1 , Tandem Mass Spectrometry , Animals , Mice , ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism , Molecular Docking Simulation , Chromatography, Liquid , ATP Binding Cassette Transporter, Subfamily B/metabolism , Cholesterol/metabolism
3.
Mol Neurobiol ; 60(6): 3158-3174, 2023 Jun.
Article in English | MEDLINE | ID: mdl-36808604

ABSTRACT

Declining cerebral blood flow leads to chronic cerebral hypoperfusion which can induce neurodegenerative disorders, such as vascular dementia. The reduced energy supply of the brain impairs mitochondrial functions that could trigger further damaging cellular processes. We carried out stepwise bilateral common carotid occlusions on rats and investigated long-term mitochondrial, mitochondria-associated membrane (MAM), and cerebrospinal fluid (CSF) proteome changes. Samples were studied by gel-based and mass spectrometry-based proteomic analyses. We found 19, 35, and 12 significantly altered proteins in the mitochondria, MAM, and CSF, respectively. Most of the changed proteins were involved in protein turnover and import in all three sample types. We confirmed decreased levels of proteins involved in protein folding and amino acid catabolism, such as P4hb and Hibadh in the mitochondria by western blot. We detected reduced levels of several components of protein synthesis and degradation in the CSF as well as in the subcellular fractions, implying that hypoperfusion-induced altered protein turnover of brain tissue can be detected in the CSF by proteomic analysis.


Subject(s)
Brain Ischemia , Proteomics , Rats , Animals , Proteostasis , Mitochondria/metabolism , Brain/metabolism , Brain Ischemia/metabolism
4.
Mol Cell Proteomics ; 21(12): 100439, 2022 12.
Article in English | MEDLINE | ID: mdl-36334872

ABSTRACT

While N-glycopeptides are relatively easy to characterize, O-glycosylation analysis is more complex. In this article, we illustrate the multiple layers of O-glycopeptide characterization that make this task so challenging. We believe our carefully curated dataset represents perhaps the largest intact human glycopeptide mixture derived from individuals, not from cell lines. The samples were collected from healthy individuals, patients with superficial or advanced bladder cancer (three of each group), and a single bladder inflammation patient. The data were scrutinized manually and interpreted using three different search engines: Byonic, Protein Prospector, and O-Pair, and the tool MS-Filter. Despite all the recent advances, reliable automatic O-glycopeptide assignment has not been solved yet. Our data reveal such diversity of site-specific O-glycosylation that has not been presented before. In addition to the potential biological implications, this dataset should be a valuable resource for software developers in the same way as some of our previously released data has been used in the development of O-Pair and O-Glycoproteome Analyzer. Based on the manual evaluation of the performance of the existing tools with our data, we lined up a series of recommendations that if implemented could significantly improve the reliability of glycopeptide assignments.


Subject(s)
Search Engine , Software , Humans , Glycosylation , Reproducibility of Results , Glycopeptides/analysis , Proteome/chemistry
5.
Elife ; 102021 03 30.
Article in English | MEDLINE | ID: mdl-33783355

ABSTRACT

Phytochromes are photoreceptors regulating growth and development in plants. Using the model plant Arabidopsis, we identified a novel signalling pathway downstream of the far-red light-sensing phytochrome, phyA, that depends on the highly conserved CCR4-NOT complex. CCR4-NOT is integral to RNA metabolism in yeast and animals, but its function in plants is largely unknown. NOT9B, an Arabidopsis homologue of human CNOT9, is a component of the CCR4-NOT complex, and acts as negative regulator of phyA-specific light signalling when bound to NOT1, the scaffold protein of the complex. Light-activated phyA interacts with and displaces NOT9B from NOT1, suggesting a potential mechanism for light signalling through CCR4-NOT. ARGONAUTE 1 and proteins involved in splicing associate with NOT9B and we show that NOT9B is required for specific phyA-dependent alternative splicing events. Furthermore, association with nuclear localised ARGONAUTE 1 raises the possibility that NOT9B and CCR4-NOT are involved in phyA-modulated gene expression.


Place a seedling on a windowsill, and soon you will notice the fragile stem bending towards the glass to soak in the sun and optimize its growth. Plants can 'sense' light thanks to specialized photoreceptor molecules: for instance, the phytochrome A is responsible for detecting weak and 'far-red' light from the very edge of the visible spectrum. Once the phytochrome has been activated, this message is relayed to the rest of the plant through an intricate process that requires other molecules. The CCR4-NOT protein complex is vital for all plants, animals and fungi, suggesting that it was already present in early life forms. Here, Schwenk et al. examine whether CCR4-NOT could have acquired a new role in plants to help them respond to far-red light. Scanning the genetic information of the plant model Arabidopsis thaliana revealed that the gene encoding the NOT9 subunit of CCR4-NOT had been duplicated in plants during evolution. NOT9B, the protein that the new copy codes for, has a docking site that can attach to both phytochrome A and CCR4-NOT. When NOT9B binds phytochrome A, it is released from the CCR4-NOT complex: this could trigger a cascade of reactions that ultimately changes how A. thaliana responds to far-red light. Plants that had not enough or too much NOT9B were respectively more or less responsive to that type of light, showing that the duplication of the gene coding for this subunit had helped plants respond to certain types of light. The findings by Schwenk et al. illustrate how existing structures can be repurposed during evolution to carry new roles. They also provide a deeper understanding of how plants optimize their growth, a useful piece of information in a world where most people rely on crops as their main source of nutrients.


Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis/physiology , Light , Multigene Family/physiology , Phytochrome A/metabolism , Signal Transduction , Arabidopsis/genetics , Arabidopsis Proteins/metabolism , Gene Expression/physiology
6.
Mol Omics ; 16(2): 147-155, 2020 04 01.
Article in English | MEDLINE | ID: mdl-32065175

ABSTRACT

Intact glycopeptide analysis is becoming more common with developments in mass spectrometry instrumentation and fragmentation approaches. In particular, collision-based fragmentation approaches such as higher energy collisional dissociation (HCD) and radical-driven fragmentation approaches such as electron transfer dissociation (ETD) provide complementary information, but bioinformatic strategies to utilize this combined information are currently lacking. In this work we adapted a software tool, MS-Filter, to search HCD peak list files for predicted Y ions based on matched EThcD results to propose additional glycopeptide assignments. The strategy proved to be extremely powerful for O-glycopeptide data, and also of benefit for N-linked data, where it allowed rescue of low confidence results from database searching.


Subject(s)
Computational Biology/methods , Glycopeptides/urine , Databases, Protein , Humans , Mass Spectrometry , Software
7.
Mol Omics ; 16(2): 156-164, 2020 04 01.
Article in English | MEDLINE | ID: mdl-32022078

ABSTRACT

Glycopeptides represent cross-linked structures between chemically and physically different biomolecules. Mass spectrometric analysis of O-glycopeptides may reveal the identity of the peptide, the composition of the glycan and even the connection between certain sugar units, but usually only the combination of different MS/MS techniques provides sufficient information for reliable assignment. Currently, HCD analysis followed by diagnostic sugar fragment-triggered ETD or EThcD experiments is the most promising data acquisition protocol. However, the information content of the different MS/MS data is handled separately by search engines. We are convinced that these data should be used in concert, as we demonstrate in the present study. First, glycopeptides bearing the most common glycans can be identified from EThcD and/or HCD data. Then, searching for Y0 (the gas-phase deglycosylated peptide) in HCD spectra, the potential glycoforms of these glycopeptides could be lined up. Finally, these spectra and the corresponding EThcD data can be used to verify or discard the tentative assignments and to obtain further structural information about the glycans. We present 18 novel human urinary sialoglycan structures deciphered using this approach. To accomplish this in an automated fashion further software development is necessary.


Subject(s)
Computational Biology/methods , Glycoproteins/chemistry , Glycoproteins/urine , Chromatography, Liquid , Glycosylation , Humans , Search Engine , Tandem Mass Spectrometry
8.
Front Immunol ; 11: 599771, 2020.
Article in English | MEDLINE | ID: mdl-33628204

ABSTRACT

Elements of the immune system particularly that of innate immunity, play important roles beyond their traditional tasks in host defense, including manifold roles in the nervous system. Complement-mediated synaptic pruning is essential in the developing and healthy functioning brain and becomes aberrant in neurodegenerative disorders. C1q, component of the classical complement pathway, plays a central role in tagging synapses for elimination; however, the underlying molecular mechanisms and interaction partners are mostly unknown. Neuronal pentraxins (NPs) are involved in synapse formation and plasticity, moreover, NP1 contributes to cell death and neurodegeneration under adverse conditions. Here, we investigated the potential interaction between C1q and NPs, and its role in microglial phagocytosis of synapses in adult mice. We verified in vitro that NPs interact with C1q, as well as activate the complement system. Flow cytometry, immunostaining and co-immunoprecipitation showed that synapse-bound C1q colocalizes and interacts with NPs. High-resolution confocal microscopy revealed that microglia-surrounded C1q-tagged synapses are NP1 positive. We have also observed the synaptic occurrence of C4 suggesting that activation of the classical pathway cannot be ruled out in synaptic plasticity in healthy adult animals. In summary, our results indicate that NPs play a regulatory role in the synaptic function of C1q. Whether this role can be intensified upon pathological conditions, such as in Alzheimer's disease, is to be disclosed.


Subject(s)
C-Reactive Protein/immunology , Complement C1q/immunology , Microglia/immunology , Nerve Tissue Proteins/immunology , Phagocytosis , Synapses/immunology , Alzheimer Disease/immunology , Animals , Complement C4/immunology , Male , Mice
9.
Int J Mol Sci ; 20(24)2019 Dec 04.
Article in English | MEDLINE | ID: mdl-31817249

ABSTRACT

The fine tuning of hormone (e.g., auxin and gibberellin) levels and hormone signaling is required for maintaining normal embryogenesis. Embryo polarity, for example, is ensured by the directional movement of auxin that is controlled by various types of auxin transporters. Here, we present pieces of evidence for the auxin-gibberellic acid (GA) hormonal crosstalk during embryo development and the regulatory role of the Arabidopsis thaliana Calcium-Dependent Protein Kinase-Related Kinase 5 (AtCRK5) in this regard. It is pointed out that the embryogenesis of the Atcrk5-1 mutant is delayed in comparison to the wild type. This delay is accompanied with a decrease in the levels of GA and auxin, as well as the abundance of the polar auxin transport (PAT) proteins PIN1, PIN4, and PIN7 in the mutant embryos. We have previously showed that AtCRK5 can regulate the PIN2 and PIN3 proteins either directly by phosphorylation or indirectly affecting the GA level during the root gravitropic and hypocotyl hook bending responses. In this manuscript, we provide evidence that the AtCRK5 protein kinase can in vitro phosphorylate the hydrophilic loops of additional PIN proteins that are important for embryogenesis. We propose that AtCRK5 can govern embryo development in Arabidopsis through the fine tuning of auxin-GA level and the accumulation of certain polar auxin transport proteins.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/growth & development , Germination , Protein Serine-Threonine Kinases/metabolism , Receptors, Cell Surface/metabolism , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Enzyme-Linked Immunosorbent Assay , Gene Expression Regulation, Plant , Gibberellins/analysis , Gibberellins/metabolism , Indoleacetic Acids/metabolism , Membrane Transport Proteins/genetics , Membrane Transport Proteins/metabolism , Seeds/anatomy & histology , Seeds/growth & development , Seeds/metabolism
10.
Cell ; 178(6): 1362-1374.e16, 2019 09 05.
Article in English | MEDLINE | ID: mdl-31447178

ABSTRACT

TRPA1 is a chemosensory ion channel that functions as a sentinel for structurally diverse electrophilic irritants. Channel activation occurs through an unusual mechanism involving covalent modification of cysteine residues clustered within an amino-terminal cytoplasmic domain. Here, we describe a peptidergic scorpion toxin (WaTx) that activates TRPA1 by penetrating the plasma membrane to access the same intracellular site modified by reactive electrophiles. WaTx stabilizes TRPA1 in a biophysically distinct active state characterized by prolonged channel openings and low Ca2+ permeability. Consequently, WaTx elicits acute pain and pain hypersensitivity but fails to trigger efferent release of neuropeptides and neurogenic inflammation typically produced by noxious electrophiles. These findings provide a striking example of convergent evolution whereby chemically disparate animal- and plant-derived irritants target the same key allosteric regulatory site to differentially modulate channel activity. WaTx is a unique pharmacological probe for dissecting TRPA1 function and its contribution to acute and persistent pain.


Subject(s)
Scorpion Venoms/pharmacology , TRPA1 Cation Channel/metabolism , Animals , HEK293 Cells , Humans , Mice, Inbred C57BL , Rats, Sprague-Dawley , Scorpions/metabolism
11.
Int J Mol Sci ; 20(14)2019 Jul 12.
Article in English | MEDLINE | ID: mdl-31336871

ABSTRACT

Seedling establishment following germination requires the fine tuning of plant hormone levels including that of auxin. Directional movement of auxin has a central role in the associated processes, among others, in hypocotyl hook development. Regulated auxin transport is ensured by several transporters (PINs, AUX1, ABCB) and their tight cooperation. Here we describe the regulatory role of the Arabidopsis thaliana CRK5 protein kinase during hypocotyl hook formation/opening influencing auxin transport and the auxin-ethylene-GA hormonal crosstalk. It was found that the Atcrk5-1 mutant exhibits an impaired hypocotyl hook establishment phenotype resulting only in limited bending in the dark. The Atcrk5-1 mutant proved to be deficient in the maintenance of local auxin accumulation at the concave side of the hypocotyl hook as demonstrated by decreased fluorescence of the auxin sensor DR5::GFP. Abundance of the polar auxin transport (PAT) proteins PIN3, PIN7, and AUX1 were also decreased in the Atcrk5-1 hypocotyl hook. The AtCRK5 protein kinase was reported to regulate PIN2 protein activity by phosphorylation during the root gravitropic response. Here it is shown that AtCRK5 can also phosphorylate in vitro the hydrophilic loops of PIN3. We propose that AtCRK5 may regulate hypocotyl hook formation in Arabidopsis thaliana through the phosphorylation of polar auxin transport (PAT) proteins, the fine tuning of auxin transport, and consequently the coordination of auxin-ethylene-GA levels.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/physiology , Hypocotyl/physiology , Morphogenesis , Plant Development , Protein Serine-Threonine Kinases/metabolism , Receptors, Cell Surface/metabolism , Arabidopsis/drug effects , Biomarkers , Gene Expression Regulation, Plant , Genes, Reporter , Germination , Morphogenesis/drug effects , Morphogenesis/genetics , Phenotype , Phosphorylation , Plant Development/drug effects , Plant Development/genetics , Signal Transduction , Xanthones/pharmacology
12.
Methods Mol Biol ; 1934: 93-125, 2019.
Article in English | MEDLINE | ID: mdl-31256376

ABSTRACT

Even if a consensus sequence has been identified for a posttranslational modification, the presence of such a sequence motif only indicates the possibility, not the certainty that the modification actually occurs. Proteins can be glycosylated on certain amino acid side chains, and these modifications are designated as C-, N-, and O-glycosylation. C-mannosylation occurs on Trp residues within a relatively loosely defined consensus motif. N-glycosylated species are modified at Asn residues of Asn-Xxx-Ser/Thr/Cys sequons (where Xxx can be any amino acid except proline). N-linked oligosaccharides share a common core structure of GlcNAc2Man3. In addition, an enzyme, peptide N-glycosidase F (PNGase F), removes most of the common N-linked carbohydrates unaltered from proteins while hydrolyzing the originally glycosylated Asn residue to Asp. O-glycosylation occurs at Ser, Thr, and Tyr residues, usually in sequence stretches rich in hydroxy-amino acids. O-glycosylation lacks a common core structure. Mammalian proteins have been reported bearing O-linked N-acetylgalactosamine, fucose, glucose, xylose, mannose, and corresponding elongated structures, as well as N-acetylglucosamine. Chemical methods are used to liberate these oligosaccharides because no enzyme would remove all the different O-linked carbohydrates. Characterization of both N- and O-glycosylation is complicated by the fact that the same positions within a population of protein molecules may feature an array of different carbohydrate structures, or remain unmodified. This site-specific heterogeneity may vary by species and tissue, and may also be affected by physiological changes. For addressing site-specific carbohydrate heterogeneity mass spectrometry has become the method of choice. Reversed-phase HPLC directly coupled with electrospray ionization mass spectrometry (LC/ESI-MS/MS) offers the best solution. Using a mass spectrometer as online detector not only assures the analysis of every component eluting (mass mapping), but also at the same time diagnostic carbohydrate ions can be generated by collisional activation that permits the selective and specific detection of glycopeptides. In addition, ESI-compatible alternative MS/MS techniques, electron-capture and electron-transfer dissociation, aid glycopeptide identification as well as modification site assignments.


Subject(s)
Glycoproteins/chemistry , Proteins/chemistry , Spectrometry, Mass, Electrospray Ionization , Alkylation , Amino Acid Sequence , Chromatography, Liquid , Glycopeptides/chemistry , Glycoproteins/metabolism , Glycosylation , Oligosaccharides/chemistry , Protein Processing, Post-Translational , Proteins/metabolism , Tandem Mass Spectrometry
13.
J Proteome Res ; 18(1): 280-291, 2019 01 04.
Article in English | MEDLINE | ID: mdl-30407017

ABSTRACT

A relatively novel activation technique, electron-transfer/higher-energy collision dissociation (EThcD) was used in the LC-MS/MS analysis of tryptic glycopeptides enriched with wheat germ agglutinin from human urine samples. We focused on the characterization of mucin-type O-glycopeptides. EThcD in a single spectrum provided information on both the peptide modified and the glycan carried. Unexpectedly, glycan oxonium ions indicated the presence of O-acetyl, and even O-diacetyl-sialic acids. B and Y fragment ions revealed that (i) in core 1 structures the Gal residue featured the O-acetyl-sialic acid, when there was only one in the glycan; (ii) several glycopeptides featured core 1 glycans with disialic acids, in certain instances O-acetylated; (iii) the disialic acid was linked to the GalNAc residue whatever the degree of O-acetylation; (iv) core 2 isomers with a single O-acetyl-sialic acid were chromatographically resolved. Glycan fragmentation also helped to decipher additional core 2 oligosaccharides: a LacdiNAc-like structure, glycans carrying sialyl LewisX/A at different stages of O-acetylation, and blood antigens. A sialo core 3 structure was also identified. We believe this is the first study when such structures were characterized from a very complex mixture and were linked not only to a specific protein, but also the sites of modifications have been determined.


Subject(s)
Glycoproteins/urine , Polysaccharides/analysis , Proteomics/methods , Chromatography, Liquid , Glycopeptides/analysis , Humans , N-Acetylneuraminic Acid/chemistry , Polysaccharides/chemistry , Tandem Mass Spectrometry/methods
14.
Electrophoresis ; 39(24): 3142-3147, 2018 12.
Article in English | MEDLINE | ID: mdl-30117533

ABSTRACT

A novel software, Pinnacle was used to reassess the reproducibility of a 2-step lectin-based O-glycopeptide enrichment method. A publicly available dataset consisting of 12 data files representing 3 technical replicates of enriched glycopeptides from human serum was investigated. Previously, an attempt for reproducibility assessment was made utilizing an MS/MS scan (MS2)-based method. However, the stochastic nature of precursor ion selection strongly biased this approach leading to underestimated rate of reproducibility. To bypass this problem, our present method follows the general path to confidently identify O-glycopeptides (database search with MS/MS data) supplemented with full scan/survey scan (MS1)/extracted ion chromatogram (XIC) mining in all files using two software packages, Pinnacle and Skyline. Confident MS/MS identifications were delivered by Protein Prospector. With this input Skyline indicated a 70% reproducibility for our workflow. However, Pinnacle performed better, indicating the presence of 90% of the confidently assigned glycopeptides in all the three replicates. Pinnacle, just like Skyline, performs ion extraction using the high accuracy, high resolution mass measurement data but it also utilizes all the available MS/MS spectra, even from different activation methods, within the same file to make mass spectrometric data evaluation for glycopeptides more reliable.


Subject(s)
Chromatography, Affinity/methods , Glycopeptides/isolation & purification , Software , Glycomics , Glycopeptides/blood , Glycopeptides/chemistry , Glycosylation , Humans , Lectins/chemistry , Lectins/metabolism , Reproducibility of Results , Tandem Mass Spectrometry/methods
15.
J Am Soc Mass Spectrom ; 29(6): 1210-1220, 2018 06.
Article in English | MEDLINE | ID: mdl-29730764

ABSTRACT

A very complex mixture of intact, human N- and O-glycopeptides, enriched from the tryptic digest of urinary proteins of three healthy donors using a two-step lectin affinity enrichment, was analyzed by LC-MS/MS, leading to approximately 45,000 glycopeptide EThcD spectra. Two search engines, Byonic and Protein Prospector, were used for the interpretation of the data, and N- and O-linked glycopeptides were assigned from separate searches. The identification rate was very low in all searches, even when results were combined. Thus, we investigated the reasons why was it so, to help to improve the identification success rate. Focusing on O-linked glycopeptides, we noticed that in EThcD, larger glycan oxonium ions better survive the activation than those in HCD. These fragments, combined with reducing terminal Y ions, provide important information about the glycan(s) present, so we investigated whether filtering the peaklists for glycan oxonium ions indicating the presence of a tetra- or hexasaccharide structure would help to reveal all molecules containing such glycans. Our study showed that intact glycans frequently do not survive even mild supplemental activation, meaning one cannot rely on these oxonium ions exclusively. We found that ETD efficiency is still a limiting factor, and for highly glycosylated peptides, the only information revealed in EThcD was related to the glycan structures. The limited overlap of results delivered by the two search engines draws attention to the fact that automated data interpretation of O-linked glycopeptides is not even close to being solved. Graphical abstract ᅟ.


Subject(s)
Glycopeptides/urine , Tandem Mass Spectrometry/methods , Adult , Carbohydrate Sequence , Chromatography, Liquid/methods , Female , Glycopeptides/analysis , Humans , Male , Middle Aged , Search Engine
16.
eNeuro ; 5(2)2018.
Article in English | MEDLINE | ID: mdl-29756027

ABSTRACT

Transcriptional events leading to outgrowth of neuronal axons have been intensively studied, but the role of translational regulation in this process is not well understood. Here, we use translatome analyses by ribosome pull-down and protein synthesis characterization by metabolic isotopic labeling to study nerve injury and axon outgrowth proteomes in rodent dorsal root ganglia (DRGs) and sensory neurons. We identify over 1600 gene products that are primarily translationally regulated in DRG neurons after nerve injury, many of which contain a 5'UTR cytosine-enriched regulator of translation (CERT) motif, implicating the translation initiation factor Eif4e in the injury response. We further identified approximately 200 proteins that undergo robust de novo synthesis in the initial stages of axon growth. ApoE is one of the highly synthesized proteins in neurons, and its receptor binding inhibition or knockout affects axon outgrowth. These findings provide a resource for future analyses of the role of translational regulation in neuronal injury responses and axon extension.


Subject(s)
Axons/metabolism , Ganglia, Spinal/metabolism , Gene Expression Regulation/genetics , Nerve Regeneration/genetics , Neuronal Outgrowth/genetics , Peripheral Nerve Injuries/genetics , Protein Biosynthesis/genetics , Sensory Receptor Cells/metabolism , Animals , Cell Culture Techniques , Male , Mice , Mice, Inbred C57BL , Proteomics , Rats , Rats, Wistar
17.
FEBS Open Bio ; 8(4): 556-569, 2018 04.
Article in English | MEDLINE | ID: mdl-29632809

ABSTRACT

Oral squamous cell carcinoma (OSCC) is the seventh most common malignancy and the ninth most frequent cause of cancer death in Europe. Within Europe, Hungary has one of the highest rates of OSCC incidence and mortality. Thus, there is an urgent need to improve early detection. Saliva, as a readily available body fluid, became an increasingly important substance for the detection of biomarkers for many diseases. Different research groups have identified salivary biomarkers specific for OSCC for different countries. In this study, saliva samples of Hungarian patients with OSCC were studied to discover disease-specific and perhaps region-specific biomarkers. LC-mass spectrometry (MS)/MS analysis on a linear ion trap-Orbitrap mass spectrometer was used for qualitative and quantitative salivary protein profiling. More than 500 proteins were identified from saliva by shotgun proteomics. The up- and downregulated proteins in the saliva of patients with OSCC highlighted the importance of protein-protein interaction networks involving the immune system and proteolysis in disease development. Two potential biomarkers from our shotgun analysis and a third candidate reported earlier by a Taiwanese group were further examined by ELISA on a larger reference set of samples. Resistin, a biomarker reported in Taiwan but not validated in our study, highlights the necessity of application of standardized analysis methods in different ethnic or geographical populations to identify biomarkers with sufficient specificity and sensitivity.

18.
Development ; 145(6)2018 03 16.
Article in English | MEDLINE | ID: mdl-29487108

ABSTRACT

Regulation of the cytoskeleton is fundamental to the development and function of synaptic terminals, such as neuromuscular junctions. Despite the identification of numerous proteins that regulate synaptic actin and microtubule dynamics, the mechanisms of cytoskeletal control during terminal arbor formation have remained largely elusive. Here, we show that DAAM, a member of the formin family of cytoskeleton organizing factors, is an important presynaptic regulator of neuromuscular junction development in Drosophila We demonstrate that the actin filament assembly activity of DAAM plays a negligible role in terminal formation; rather, DAAM is necessary for synaptic microtubule organization. Genetic interaction studies consistently link DAAM with the Wg/Ank2/Futsch module of microtubule regulation and bouton formation. Finally, we provide evidence that DAAM is tightly associated with the synaptic active zone scaffold, and electrophysiological data point to a role in the modulation of synaptic vesicle release. Based on these results, we propose that DAAM is an important cytoskeletal effector element of the Wg/Ank2 pathway involved in the determination of basic synaptic structures, and, additionally, that DAAM may couple the active zone scaffold to the presynaptic cytoskeleton.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Cytoskeleton/metabolism , Drosophila Proteins/metabolism , Microtubules/metabolism , Presynaptic Terminals/metabolism , Synapses/metabolism , Actin Cytoskeleton/metabolism , Animals , Blotting, Western , Drosophila/metabolism , Immunohistochemistry , Mass Spectrometry , Neuromuscular Junction/metabolism
19.
Mol Cell Proteomics ; 17(1): 2-17, 2018 01.
Article in English | MEDLINE | ID: mdl-29162637

ABSTRACT

Glycosylation is perhaps the most common post-translational modification. Recently there has been growing interest in cataloging the glycan structures, glycoproteins, and specific sites modified and deciphering the biological functions of glycosylation. Although the results are piling up for N-glycosylation, O-glycosylation is seriously trailing behind. In our review we reiterate the difficulties researchers have to overcome in order to characterize O-glycosylation. We describe how an ingenious cell engineering method delivered exciting results, and what could we gain from "wild-type" samples. Although we refer to the biological role(s) of O-glycosylation, we do not provide a complete inventory on this topic.


Subject(s)
Glycopeptides/metabolism , Animals , Glycosylation , Humans
20.
Dev Comp Immunol ; 76: 403-411, 2017 11.
Article in English | MEDLINE | ID: mdl-28713010

ABSTRACT

The identification of molecular markers considerably facilitated the classification and functional analysis of blood cell types. Apis mellifera hemocytes have been classified by morphological criteria and lectin binding properties; however, the use of molecular markers has been minimal. Here we describe a monoclonal antibody to a non-phagocytic subpopulation of A. mellifera hemocytes and to a constituent of the hemolymph clot. We demonstrate that the antibody identifies the A. mellifera hemolectin, a protein carrying human von Willebrand factor homology domains, characteristic of proteins involved in blood coagulation and platelet aggregation in mammals. Hemolectin expressing A. mellifera hemocytes contain the protein as cytoplasmic granules and contribute to the formation of a protein matrix, building up around foreign particles. Consequently, hemolectin as a marker molecule reveals a clear functional heterogeneity of hemocytes, allowing for the analytical separation of hemocyte classes, and could promote the molecular identification of hemocyte lineages in A. mellifera.


Subject(s)
Bees/immunology , Hemocytes/physiology , Hemolymph/metabolism , Lectins/metabolism , Thrombosis/metabolism , Animals , Antibodies, Monoclonal/isolation & purification , Biodiversity , Cell Separation , Lectins/genetics , Lectins/immunology , Mammals , Phagocytosis , Platelet Aggregation/genetics , Sequence Homology, Amino Acid , Transcriptome , von Willebrand Factor/genetics
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