Missing proteins Dotaz Zobrazit nápovědu
Integral membrane proteins are under-represented in standard proteomic analyses, mostly because of their low expression and absence of trypsin-cleavage sites in their hydrophobic transmembrane segments. Novel and effective strategies for membrane proteomic analysis aim at soluble N-glycosylated segments of integral membrane proteins (CSC, SPEG, N-glyco-FASP) or selectively target the hydrophobic transmembrane alpha-helical segments employing chemical peptide cleavage by CNBr (hpTC). We combined a solid phase enrichment of glycopeptides (SPEG) with a transmembrane segment-oriented hpTC method and a standard "detergent and trypsin" approach into a three-pronged "Pitchfork" strategy to maximize the membrane proteome coverage in human lymphoma cells. This strategy enabled the identification of >1200 integral membrane proteins from all cellular compartments, including 105 CD antigens, 24 G protein-coupled receptors, and 141 solute carrier transporters. The advantage of the combination lies in the complementarity of the methods. SPEG and hpTC target different sets of membrane proteins. HpTC provided identifications of proteins and peptides with significantly higher hydrophobicity compared to SPEG and detergent-trypsin approaches. Among all identified proteins, we observed 32 so-called "missing proteins". The Pitchfork strategy presented here is universally applicable and enables deep and fast description of membrane proteomes in only 3 LC-MS/MS runs per replicate. SIGNIFICANCE: Integral membrane proteins (IMPs) are encoded by roughly a quarter of human coding genes. Their functions and their specific localization makes IMPs highly attractive drug targets. In fact, roughly half of the currently approved drugs in medicine target IMPs. Our knowledge of membrane proteomes is, however, limited. We present a new strategy for the membrane proteome analysis that combines three complementary methods targeting different features of IMPs. Using the combined strategy, we identified over 1200 IMPs in human lymphoma tissue from all sub-cellular compartments in only 3 LC-MS/MS runs per replicate. The three-pronged "Pitchfork" strategy is universally applicable, and offers a fast way toward a reasonably concise description of membrane proteomes in multiple samples.
- MeSH
- chromatografie kapalinová MeSH
- heterografty MeSH
- lidé MeSH
- lymfom z plášťových buněk metabolismus MeSH
- membránové proteiny metabolismus MeSH
- myši MeSH
- nádorové proteiny metabolismus MeSH
- proteom metabolismus MeSH
- tandemová hmotnostní spektrometrie MeSH
- transplantace nádorů MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Nejlepší definice epigenetiky říká, že se zabývá studiem vlastností, jež jsou předávány prostřednictvím meiózy nebo mitózy a přitom nejsou závislé na primární struktuře DNA Britský genetik Adrian Bird k tomu dodává: „Epigenetika je užitečný termín, pokud nevíte, o co jde. Pokud to víte, nazvete to úplně jinak“ (Anonymus 2010).
The best working definition for the epigenetics is that it is the study of traits heritable through meiosis or mitosis that are not dependent on the primary DNA sequence. Even so, British geneticist Adrian Bird has commented: “Epigenetics is useful word if you don't know what's going on – if you do, you use something else” (Anonymus 2010).
- Klíčová slova
- gen aguti,
- MeSH
- dědičnost genetika MeSH
- endokrinní disruptory MeSH
- epigenomika * MeSH
- histony fyziologie MeSH
- hlad MeSH
- lidé MeSH
- metylace DNA fyziologie MeSH
- nekódující RNA MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- populární práce MeSH
Genomic rearrangements involving the peripheral myelin protein gene (PMP22) in human chromosome 17p12 are associated with neuropathy: duplications cause Charcot-Marie-Tooth disease type 1A (CMT1A), whereas deletions lead to hereditary neuropathy with liability to pressure palsies (HNPP). Our previous studies showed that >99% of these rearrangements are recurrent and mediated by nonallelic homologous recombination (NAHR). Rare copy number variations (CNVs) generated by nonrecurrent rearrangements also exist in 17p12, but their underlying mechanisms are not well understood. We investigated 21 subjects with rare CNVs associated with CMT1A or HNPP by oligonucleotide-based comparative genomic hybridization microarrays and breakpoint sequence analyses, and we identified 17 unique CNVs, including two genomic deletions, ten genomic duplications, two complex rearrangements, and three small exonic deletions. Each of these CNVs includes either the entire PMP22 gene, or exon(s) only, or ultraconserved potential regulatory sequences upstream of PMP22, further supporting the contention that PMP22 is the critical gene mediating the neuropathy phenotypes associated with 17p12 rearrangements. Breakpoint sequence analysis reveals that, different from the predominant NAHR mechanism in recurrent rearrangement, various molecular mechanisms, including nonhomologous end joining, Alu-Alu-mediated recombination, and replication-based mechanisms (e.g., FoSTeS and/or MMBIR), can generate nonrecurrent 17p12 rearrangements associated with neuropathy. We document a multitude of ways in which gene function can be altered by CNVs. Given the characteristics, including small size, structural complexity, and location outside of coding regions, of selected rare CNVs, their identification remains a challenge for genome analysis. Rare CNVs may potentially represent an important portion of "missing heritability" for human diseases. Copyright 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
BACKGROUND: Fibrinogen-related proteins with lectin activity are believed to be part of the tick innate immune system. Several fibrinogen-related proteins have been described and characterised mainly on the basis of their cDNA sequences while direct biochemical evidence is missing. One of them, the haemolymph lectin Dorin M from the tick Ornithodoros moubata was isolated and characterised in more depth. RESULTS: Several fibrinogen-related proteins were detected in the haemolymph of ixodid ticks Dermacentor marginatus, Rhipicephalus appendiculatus, R. pulchellus, and R. sanguineus. These proteins were recognised by sera directed against the tick lectin Dorin M and the haemagglutination activity of the ticks R. appendiculatus and D. marginatus. Cross-reactivity of the identified proteins with antibodies against the fibrinogen domain of the human ficolin was also shown. The carbohydrate-binding ability of tick haemolymph was confirmed by haemagglutination activity assays, and this activity was shown to be inhibited by neuraminic acid and sialylated glycoproteins as well as by N-acetylated hexosamines. The fibrinogen-related proteins were shown to be glycosylated and they were localised in salivary glands, midguts, and haemocytes of D. marginatus. Hemelipoglycoprotein was also recognised by sera directed against the fibrinogen-related proteins in all three Rhipicephalus species as well as in D. marginatus. However, this protein does not contain the fibrinogen domain and thus, the binding possibly results from the structure similarity between hemelipoglycoprotein and the fibrinogen domain. CONCLUSIONS: The presence of fibrinogen-related proteins was shown in the haemolymph of four tick species in high abundance. Reactivity of antibodies directed against ficolin or fibrinogen-related proteins with proteins which do not contain the fibrinogen domain points out the importance of sequence analysis of the identified proteins in further studies. Previously observed expression of fibrinogen-related proteins in haemocytes together with the results of this study suggest involvement of fibrinogen-related proteins in tick immunity processes. Thus, they have potential as targets for anti-tick vaccines and as antimicrobial proteins in pharmacology. Research on fibrinogen-related proteins could reveal further details of tick innate immunity processes.
- MeSH
- anatomické struktury zvířat chemie MeSH
- Dermacentor chemie MeSH
- fibrinogen imunologie MeSH
- glykoproteiny imunologie metabolismus MeSH
- hemaglutininy imunologie metabolismus MeSH
- hmyzí proteiny imunologie metabolismus MeSH
- lektiny imunologie metabolismus MeSH
- lidé MeSH
- metabolismus sacharidů MeSH
- Ornithodoros chemie MeSH
- protilátky imunologie MeSH
- Rhipicephalus chemie MeSH
- vazba proteinů MeSH
- zkřížené reakce MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Integral membrane proteins are generally under-represented in routine proteomic analyses, mostly because of their relatively low abundance, hydrophobicity and lack of trypsin-cleavage sites. To increase the coverage of membrane proteomes, various strategies have been developed, targeting mostly the extra-membrane segments of membrane proteins. We focused our attention to the rather overlooked hydrophobic transmembrane segments. Such peptides can be isolated after carbonate stripping and protease "shaving" of membranes isolated by simple centrifugation procedure. The treated membranes with embedded hydrophobic peptides can then be solubilized in organic solvents, re-digested with CNBr, delipidated and subjected to LC-MS/MS analysis. We modified the original "hppK" method, and applied it for the analysis of human lymphoma cells. We identified 1224 proteins of which two-thirds were IMPs with 1-16 transmembrane segments. This method allowed us to identify 13 "missing proteins" - proteins with no previous evidence on protein level. BIOLOGICAL SIGNIFICANCE: Integral membrane proteins execute numerous essential functions and represent substantial part of eukaryotic proteomes. Our knowledge of their function and expression is, however, limited. Novel approaches extending our knowledge of membrane proteome are therefore highly desired. As we demonstrate here, a non-conventional method which targets rather overlooked hydrophobic transmembrane segments of integral membrane proteins has wide potential to provide the missing information on the membrane proteome. We show that it can deliver identification and potentially also quantification of hundreds of integral membrane proteins including the so called "missing proteins".
- MeSH
- chromatografie kapalinová metody MeSH
- hydrofobní a hydrofilní interakce MeSH
- lidé MeSH
- lymfom z plášťových buněk chemie MeSH
- membránové proteiny analýza MeSH
- nádorové proteiny analýza MeSH
- peptidy analýza MeSH
- proteom chemie MeSH
- proteomika metody MeSH
- tandemová hmotnostní spektrometrie metody MeSH
- trypsin chemie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Dinaciclib is a multi-specific cyclin-dependent kinase (CDK) inhibitor with significant preclinical and clinical activity. It inhibits CDK1, CDK2, CDK5, CDK9 and CDK12 in the nanomolar range and exhibits potent antiproliferative effects on various cancers in vitro and in vivo. Aldo-keto reductases (AKR) and carbonyl reductases (CBR) are enzymes involved at the biosynthesis, intermediary metabolism and detoxification processes, but can also play a significant role in cancer resistance. Here, we report that dinaciclib is a strong inhibitor of aldo-keto reductase 1C3 (AKR1C3), an enzyme that is known to be an important regulator of cell proliferation and differentiation. AKR1C3 is overexpressed in a range of cancer types and is also involved in tumour cell resistance to anthracyclines. In our study, dinaciclib displayed tight-binding inhibition of human recombinant AKR1C3 (Kiapp = 0.07 µM) and was also active at the cellular level (IC50 = 0.23 µM). Dinaciclib acts as a noncompetitive inhibitor with respect to daunorubicin and as an uncompetitive inhibitor with respect to the NADPH. In subsequent experiments, pretreatment with dinaciclib (0.1 µM) significantly sensitized AKR1C3-overexpressing anthracycline-resistant cancer cells to daunorubicin. In conclusion, our results indicate that dinaciclib may potentially increase the therapeutic efficacy and safety of anthracyclines by preventing anthracycline resistance and minimizing their adverse effects.
- MeSH
- antracykliny aplikace a dávkování MeSH
- bicyklické sloučeniny heterocyklické aplikace a dávkování farmakologie MeSH
- buňky Hep G2 MeSH
- chemorezistence účinky léků MeSH
- daunomycin metabolismus farmakokinetika MeSH
- HCT116 buňky MeSH
- inhibitory enzymů farmakologie MeSH
- lidé MeSH
- protein AKR1C3 antagonisté a inhibitory genetika metabolismus MeSH
- protokoly protinádorové kombinované chemoterapie farmakologie MeSH
- pyridinové sloučeniny aplikace a dávkování farmakologie MeSH
- regulace genové exprese enzymů účinky léků MeSH
- rekombinantní proteiny genetika metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
The journey undertaken by the pollen tube in angiosperms to reach the deeply embedded female gametophyte for fertilization involves persistent guidance by the female gametophyte and accurate perception of the signals by the pollen tube. Several ovule-secreted peptides have been identified. Nevertheless, there are no exact findings on how these signals are perceived by the pollen tube. As a novel approach, we have improvised a modified SIV (semi-in vivo) technique, SIV-PS (SIV pollen tube secretome), to perform gel-free LC-MS/MS for high-throughput analysis of pollen-tube-secreted proteins. Our approach has led to the identification of over 1400 protein groups. Among them are pollen-tube-secreted ligands and receptor proteins representing potential male components in perceiving ovule-emitted cues for guidance. The present article reviews the missing link in pollen tube perception and showcases the improvised SIV-PS as a tool for high-throughput and targeted study of the pollen tube secretome.
The study aim was to compare molecular-level effects (blood-dialyzer interactions) of heparin and citrate anticoagulation using proteome-wide analysis of biofilm adsorbed to dialysis membrane. Ten patients receiving maintenance hemodialysis were examined in a crossover design under three different anticoagulation regimens, namely citrate, heparin, and anticoagulation-free (control). Following a regular hemodialysis session (4 hours, polysulfone membrane), dialyzers were flushed and the surface biofilm eluted by acetic acid. Protein composition of the eluates was determined by 2-dimensional gel electrophoresis and resulting patterns compared between regimens. Proteins responsible for the difference were identified by mass spectrometry. Citrate anticoagulation was associated with significantly less protein adsorption to the membrane than heparin (2.2 [1.1-2.9] mg vs. 6.5 [2.9-11.6] mg, P = 0.009). Among the proteins identified as major discriminators between citrate and the other regimens, fibrin α-chain fragments of molecular weight below 40 kDa prevailed. In these fragments, an analysis of the amino acid sequence has been performed by comparison with the UniProt database. It showed missing α-chain cross-links. On the contrary, heparin prevented adsorption and cleavage of several heparin-binding proteins; especially complement factor H-related protein 3, insulin-like growth factor binding proteins (2, 4, and 5), and chemerin. Compared to heparin, citrate is associated with less protein adsorption and imperfectly crosslinked fibrin clot formation. Membrane adsorptive properties are significantly modified by the anticoagulation regimen.
- MeSH
- adsorpce MeSH
- antikoagulancia farmakologie MeSH
- dialýza ledvin přístrojové vybavení metody MeSH
- hemokoagulace účinky léků MeSH
- heparin farmakologie MeSH
- krevní proteiny analýza MeSH
- kyselina citronová farmakologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- membrány umělé MeSH
- polymery chemie MeSH
- proteomika MeSH
- senioři MeSH
- sulfony chemie MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Undesirable effects of the pathogen Botrytis cinerea include reduced quality and quantity of wine grapes. Winemaking is also complicated by the formation of a protein haze in white wines and oxidative browning of red wines. We analyzed proteins in experimental Moravian white wines characterized by their instability and haze formation in bottles during storage despite prior bentonite treatment. To study the relationship of wine proteins and haze, we carried out proteomics on hazy and clear white wines produced with partly or largely botrytized grapes and standard reference wines. Wine proteins were identified after their extraction, electrophoresis, and tryptic digestion by reversed-phase liquid chromatography of peptides, coupled with tandem mass spectrometry. Plant defense proteins, yeast glycoproteins, and various enzymes from Botrytis, particularly hydrolases, were found. As the content of the known haze-active thaumatin-like proteins and chitinases was visually low on stained gels (missing bands) compared to previous studies with unfined wines, other proteins are discussed in terms of the haze formation. As the main novelty, this work reveals the role of high proline-containing proteins in the propensity of white wines to turbidity following prior Botrytis damage of grapes.
Estrogens are steroid hormones that affect a wide range of physiological functions. The effect of estrogens on male reproductive tissues and sperm cells through specific receptors is essential for sperm development, maturation, and function. Although estrogen receptors (ERs) have been studied in several mammalian species, including humans, they have not yet been described in bull spermatozoa and reproductive tissues. In this study, we analyzed the presence of all types of ERs (ESR1, ESR2, and GPER1) in bull testicular and epididymal tissues and epididymal and ejaculated spermatozoa, and we characterize them here for the first time. We observed different localizations of each type of ER in the sperm head by immunofluorescent microscopy. Additionally, using a selected polyclonal antibody, we found that each type of ER in bull sperm extracts had two isoforms with different molecular masses. The detailed detection of ERs is a prerequisite not only for understanding the effect of estrogen on all reproductive events but also for further studying the negative effect of environmental estrogens (endocrine disruptors) on processes that lead to fertilization.
- MeSH
- epididymis metabolismus MeSH
- receptory pro estrogeny metabolismus MeSH
- receptory spřažené s G-proteiny metabolismus MeSH
- rozmnožování * MeSH
- skot metabolismus MeSH
- spermie metabolismus MeSH
- testis metabolismus MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- skot metabolismus MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
