Proteome Science[JOURNAL]
Sun
200 papers
A quantitative shotgun proteomics analysis of germinated rice embryos and coleoptiles under low-temperature conditions.
Lee J, Lee W, Kwon SW
Proteome Sci · 2015 · PMID 26587012 · Full text
BACKGROUND: At low temperatures, rice grains have a reduced germination rate and grow more slowly, which delays the emergence of rice seedlings from the paddy water surface and significantly increases seedling mortality....
BACKGROUND: At low temperatures, rice grains have a reduced germination rate and grow more slowly, which delays the emergence of rice seedlings from the paddy water surface and significantly increases seedling mortality. In this study, we conducted a shotgun proteomics analysis of geminated embryos and coleoptiles to compare the proteome expression pattern between the low-temperature resistant variety, Tong 88-7, and the low-temperature susceptible variety, Milyang 23. RESULTS: In a shotgun proteomics analysis of low-temperature resistant and susceptible embryos and coleoptiles in both cold and control temperatures, we discovered a total of 2626 non-redundant proteins, with a 0.01 false discovery rate. A comparison of protein expression patterns between resistant and susceptible embryos and coleoptiles under low-temperature and normal conditions revealed that 85 proteins and 196 proteins were expressed by the resistant and susceptible strains, respectively, in response to low temperature. Among them, 12 proteins overlapped. Proteins involved in stress responses, metabolism, and gene expression were expressed in both strains. CONCLUSIONS: Similar molecular functions of the response were detected, suggesting that the resistant and susceptible strain have a similar proteome response to cold temperatures. The resistance of Tong 88-7 to cold-water germination may result from the efficiency of these proteins, rather than activation of additional or different molecular processes. A comparison of protein expression between the resistant and susceptible strains' responses revealed that the more successful low-temperature germination of Tong 88-7 was associated with gibberellin signaling, protein trafficking, and the ABA-mediated stress response.
Long-term consequences of in utero irradiated mice indicate proteomic changes in synaptic plasticity related signalling.
Kempf SJ, von Toerne C, Hauck SM … +3 more , Atkinson MJ, Benotmane MA, Tapio S
Proteome Sci · 2015 · PMID 26578848 · Full text
BACKGROUND: The harmful consequences of in utero irradiation on learning and memory have been recognised but the molecular mechanisms behind the damage are still unknown. RESULTS: Using a mass spectrometry-based approach...
BACKGROUND: The harmful consequences of in utero irradiation on learning and memory have been recognised but the molecular mechanisms behind the damage are still unknown. RESULTS: Using a mass spectrometry-based approach, we investigated the long-term changes in the global cortical and hippocampal proteome 6 months after 0.1, 0.5 and 1.0 Gy in utero X-ray irradiation delivered on embryonic day 11 in male C57Bl/6 J offspring. We noted alterations in several signalling pathways involved in cognition, the transcription factor cAMP response element-binding protein (CREB) playing a central role. Immunoblotting of CREB and phosphorylated CREB (Ser133) showed an altered expression profile at all doses in the hippocampus and at 0.5 and 1.0 Gy in the cortex. The greatest reduction in the phospho-CREB level was seen at 1.0 Gy in the hippocampus. It was accompanied by enhanced expression of postsynaptic density protein 95 (PSD95), suggesting effect on synaptic plasticity in neuronal dendrites. CONCLUSIONS: As the CREB signalling pathway plays a crucial role in neuronal plasticity and long-term memory formation in the brain, the radiation-induced alterations of this pathway seen here are in good agreement with the cognitive dysfunction seen in in utero irradiated populations. These data contribute to a deeper biological understanding of molecular mechanisms behind the long-term damage induced by relatively low doses of ionising radiation during gestation.
Proteomic analysis of Pteropus alecto kidney cells in response to the viral mimic, Poly I:C.
Mok L, Wynne JW, Ford K … +3 more , Shiell B, Bacic A, Michalski WP
Proteome Sci · 2015 · PMID 26535029 · Full text
BACKGROUND: Bats are recognised as an important reservoir for a number of highly pathogenic zoonotic viruses. While many of these viruses cause severe and often fatal disease in humans, bats are able to coexist with thes...
BACKGROUND: Bats are recognised as an important reservoir for a number of highly pathogenic zoonotic viruses. While many of these viruses cause severe and often fatal disease in humans, bats are able to coexist with these viruses without clinical signs of disease. The mechanism conferring this antiviral response is not fully understood. Here, we investigated the differential protein expression of immortalised Pteropus alecto kidney cells (PaKiT03) following transfection with the viral mimic, Poly I:C. Two complementary proteomic approaches, difference gel electrophoresis (DIGE) and isobaric tagging for relative and absolute quantitation (iTRAQ) were used to quantify changes in protein expression following Poly I:C stimulation at 4, 8 and 20 hr post treatment (hpt). RESULTS: The expression of ISG54 gene, a known responder to virus infection and Poly I:C treatment, was significantly induced in transfected cells compared with mock-transfected cells. Through iTRAQ analysis we show that Poly I:C up-regulates key glycolytic enzymes at 4 hpt within PaKiT03 cells. In contrast, at 20 hpt PaKiT03 cells down-regulated ribosomal subunit proteins. The analysis with DIGE of Poly I:C transfected PaKiT03 cells showed over 215 individual spots differentially regulated, however only 25 spots could be unambiguously identified by LC-MS/MS. Immunoblotting confirmed the up-regulation of Eno1 and Tpi1 in PaKiT03 cells following Poly I:C transfection. A comparison with human cells (HEK293T and HeLa) and one additional bat cell line (PaLuT02), demonstrated that glycolytic pathways are also induced in these cell types, but at different intensities. CONCLUSION: The two techniques, DIGE and iTRAQ identified largely overlapping sets of differentially expressed proteins, however DIGE unambiguously identified significantly less proteins than iTRAQ. Poly I:C induced a rapid metabolic shift towards glycolysis within the PaKiT03 cells at 4 hpt, presumably as a consequence of increased energy requirements. On the other hand ribosomal subunit proteins were seen as down-regulated by iTRAQ, these proteins may be the limiting factors in the translational machinery available for virus replication. This study provides new insight into the antiviral response of bat cells, highlighting the importance of energy metabolism.
Profiling post-translational modifications of histones in human monocyte-derived macrophages.
Olszowy P, Donnelly MR, Lee C … +1 more , Ciborowski P
Proteome Sci · 2015 · PMID 26412985 · Full text
BACKGROUND: Histones and their post-translational modifications impact cellular function by acting as key regulators in the maintenance and remodeling of chromatin, thus affecting transcription regulation either positive...
BACKGROUND: Histones and their post-translational modifications impact cellular function by acting as key regulators in the maintenance and remodeling of chromatin, thus affecting transcription regulation either positively (activation) or negatively (repression). In this study we describe a comprehensive, bottom-up proteomics approach to profiling post-translational modifications (acetylation, mono-, di- and tri-methylation, phosphorylation, biotinylation, ubiquitination, citrullination and ADP-ribosylation) in human macrophages, which are primary cells of the innate immune system. As our knowledge expands, it becomes more evident that macrophages are a heterogeneous population with potentially subtle differences in their responses to various stimuli driven by highly complex epigenetic regulatory mechanisms. METHODS: To profile post-translational modifications (PTMs) of histones in macrophages we used two platforms of liquid chromatography and mass spectrometry. One platform was based on Sciex5600 TripleTof and the second one was based on VelosPro Orbitrap Elite ETD mass spectrometers. RESULTS: We provide side-by-side comparison of profiling using two mass spectrometric platforms, ion trap and qTOF, coupled with the application of collisional induced and electron transfer dissociation. We show for the first time methylation of a His residue in macrophages and demonstrate differences in histone PTMs between those currently reported for macrophage cell lines and what we identified in primary cells. We have found a relatively low level of histone PTMs in differentiated but resting human primary monocyte derived macrophages. CONCLUSIONS: This study is the first comprehensive profiling of histone PTMs in primary human MDM. Our study implies that epigenetic regulatory mechanisms operative in transformed cell lines and primary cells are overlapping to a limited extent. Our mass spectrometric approach provides groundwork for the investigation of how histone PTMs contribute to epigenetic regulation in primary human macrophages.
Beads-free protein immunoprecipitation for a mass spectrometry-based interactome and posttranslational modifications analysis.
Mikula M, Rubel T, Karczmarski J … +3 more , Statkiewicz M, Bomsztyk K, Ostrowski J
Proteome Sci · 2015 · PMID 26336360 · Full text
BACKGROUND: Protein immunoprecipitation (IP) coupled with MS provides means to interrogate protein complexes and their posttranslational modifications (PTMs). In a typical protein IP assay antibodies are conjugated to pr...
BACKGROUND: Protein immunoprecipitation (IP) coupled with MS provides means to interrogate protein complexes and their posttranslational modifications (PTMs). In a typical protein IP assay antibodies are conjugated to protein A/G beads requiring large amounts of antibodies, tube transfers and centrifugations. RESULTS: As an alternative, we present Matrix-IP, beads-free microplate-based platform with surface-immobilized antibodies. Assay utilizes standard 96-well polypropylene PCR plates that are laboratory-fabricated with UV-C light and then protein A/G coated prior to IP reaction. We demonstrate application of Matrix-IP platform in MS analysis of heterogeneous nuclear ribonucleoprotein K (hnRNP K) interactome and PTMs. CONCLUSION: Matrix-IP is time-saving, easy to use high throughput method adaptable for low sample amounts and automation.
Proteomic analysis of quail calcified eggshell matrix: a comparison to chicken and turkey eggshell proteomes.
Mann K, Mann M
Proteome Sci · 2015 · PMID 26312056 · Full text
BACKGROUND: Eggshell mineralization in commercially important species such as chicken, turkey or quail is of interest as a general model of calcium carbonate biomineralization. Knowledge of proteins and molecular mechani...
BACKGROUND: Eggshell mineralization in commercially important species such as chicken, turkey or quail is of interest as a general model of calcium carbonate biomineralization. Knowledge of proteins and molecular mechanisms in eggshell assembly may also pave the way to manipulation of thickness of the calcified layer or other features. Comparison of eggshell matrix proteomes of different species may contribute to a better understanding of the mineralization process. The recent publication of the quail genome sequence now enables the proteomic analysis of the quail shell matrix and this comparison with those of chicken and turkey. RESULTS: The quail eggshell proteome comprised 622 identified proteins, 311 of which were shared with chicken and turkey eggshell proteomes. Forty-eight major proteins (iBAQ-derived abundance higher than 0.1 % of total identified proteome) together covered 94 % of total proteome mass. Fifteen of these are also among the most abundant proteins in chicken and turkey eggshell matrix. Only three proteins with a percentage higher than 1.0 % of the total had not previously been identified as eggshell matrix proteins. These were an uncharacterized member of the latexin family, an uncharacterized protease inhibitor containing a Kunitz domain, and gastric intrinsic factor. The most abundant proteins were ovocleidin-116, ovalbumin and ovocalyxin-36 representing approximately 31, 13 and 8 % of the total identified proteome, respectively. The major phosphoproteins were ovocleidin-116 and osteopontin. While osteopontin phosphorylation sites were predominantly conserved between chicken and quail sequences, conservation was less in ovocleidin-116. CONCLUSIONS: Ovocleidin-116 and ovocalyxin-36 are among the most abundant eggshell matrix proteins in all three species of the family Phasianidae analyzed so far, indicating that their presently unknown function is essential for eggshell mineralization. Evidence for other chicken eggshell-specific proteins in quail was inconclusive. Therefore measurement of additional eggshell proteomes, especially from species of different families and preferentially from outside the order Galliformes, will be necessary.
Proteome analysis of shell matrix proteins in the brachiopod Laqueus rubellus.
Isowa Y, Sarashina I, Oshima K … +3 more , Kito K, Hattori M, Endo K
Proteome Sci · 2015 · PMID 26279640 · Full text
BACKGROUND: The calcitic brachipod shells contain proteins that play pivotal roles in shell formation and are important in understanding the evolution of biomineralization. Here, we performed a large-scale exploration of...
BACKGROUND: The calcitic brachipod shells contain proteins that play pivotal roles in shell formation and are important in understanding the evolution of biomineralization. Here, we performed a large-scale exploration of shell matrix proteins in the brachiopod Laqueus rubellus. RESULTS: A total of 40 proteins from the shell were identified. Apart from five proteins, i.e., ICP-1, MSP130, a cysteine protease, a superoxide dismutase, and actin, all other proteins identified had no homologues in public databases. Among these unknown proteins, one shell matrix protein was identified with a domain architecture that includes a NAD(P) binding domain, an ABC-type transport system, a transmembrane region, and an aspartic acid rich region, which has not been detected in other biominerals. We also identified pectin lyase-like, trypsin inhibitor, and saposin B functional domains in the amino acid sequences of the shell matrix proteins. The repertoire of brachiopod shell matrix proteins also contains two basic amino acid-rich proteins and proteins that have a variety of repeat sequences. CONCLUSIONS: Our study suggests an independent origin and unique mechanisms for brachiopod shell formation.
In-depth Proteomic mapping of mouse (Mus musculus) epididymal constructive basis for sperm maturation.
Liu X, Liu FJ, Jin SH … +2 more , Shen XF, Wang YW
Proteome Sci · 2015 · PMID 26225126 · Full text
BACKGROUND: The mouse epididymis performs an essential role in sperm maturation, but global protein expression data in mouse epididymis are still lacking. Here, we reported the first in-depth gel-based profiling of mouse...
BACKGROUND: The mouse epididymis performs an essential role in sperm maturation, but global protein expression data in mouse epididymis are still lacking. Here, we reported the first in-depth gel-based profiling of mouse epididymis proteome and established a 2-DE map. RESULTS: A total of 832 protein spots were detected in the reproducible gels, and 625 spots corresponding to 355 unique protein entries have been successfully identified by MALDI-TOF-MS. The confidence of proteome data was validated by Western blot. Functional annotations showed that these proteins were mainly related to general metabolism, antioxidant and structural molecule activity. Immunohistochemistry disclosed two structural proteins (myosin regulatory light polypeptide 9 and alpha-2 type I collagen) continuously expressed in the myoid cell since postpartum. CONCLUSION: This study provides a first-draft reference map of the mouse epididymis proteome, which will greatly expand the knowledge of the epididymal structural basis and contribute to the better understanding of those proteins in the process of mouse epididymal sperm maturation.
iTRAQ-based proteomic profiling of Vibrio parahaemolyticus under various culture conditions.
Yang W, Ding D, Zhang C … +2 more , Zhou J, Su X
Proteome Sci · 2015 · PMID 26225125 · Full text
BACKGROUND: Vibrio parahaemolyticus is a common pathogen infecting humans and marine animals; this pathogen has become a major concern of marine food products and trade. In this study, V. parahaemolyticus isolated from s...
BACKGROUND: Vibrio parahaemolyticus is a common pathogen infecting humans and marine animals; this pathogen has become a major concern of marine food products and trade. In this study, V. parahaemolyticus isolated from sewage was exposed to different culture conditions and analyzed by isobaric tag for relative and absolute quantitation (iTRAQ) based reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique. Our goal is to gain further insights into the proteomics of V. parahaemolyticus, particularly differentially expressed proteins closely correlated with growth conditions and pathogenicity associated proteins. RESULTS: In this study, a total of 2,717 proteins including numerous membrane proteins were significantly identified, and 616 proteins displayed significant differential expression under different conditions. Of them, 12 proteins mainly participating in metabolism showed the most elastic expression differentiation between different culture conditions. Some membrane proteins such as type I secretion outer membrane protein, TolC, lipoprotein, efflux system proteins iron-regulated protein A and putaive Fe-regulated protein B, ferric siderophore receptor homolog and several V. parahaemolyticus virulence-associated proteins were differentially regulated under different conditions. Some differentially regulated proteins were analyzed and confirmed at gene expression level by quantitative real time polymerase chain reaction (qRT-PCR). CONCLUSIONS: Proteomics analysis results revealed the characteristics of V. parahaemolyticus proteome expression, provided some promising biomarkers related with growth conditions, the results likely advance insights into the mechanism involved in the response of V. parahaemolyticus to different conditions. Some virulence-associated proteins were discovered to be differentially expressed under different conditions.
Discovery of porcine maternal factors related to nuclear reprogramming and early embryo development by proteomic analysis.
Zhao Q, Guo Z, Piao S … +2 more , Wang C, An T
Proteome Sci · 2015 · PMID 26155198 · Full text
BACKGROUND: Differentiated cell nuclei can be reprogrammed to a pluripotent state in several ways, including incubation with oocyte extracts, transfer into enucleated oocytes, and induced pluripotent stem cell technology...
BACKGROUND: Differentiated cell nuclei can be reprogrammed to a pluripotent state in several ways, including incubation with oocyte extracts, transfer into enucleated oocytes, and induced pluripotent stem cell technology. Nuclear transfer-mediated reprogramming has been proven to be the most efficient method. Maternal factors stored in oocytes have critical roles on nuclear reprogramming and early embryo development, but remain elusive. RESULTS: In this study, we showed most of porcine oocytes became nuclear matured at 33 h of IVM and the rate had no significant difference with oocytes at 42 h of IVM (p > 0.05). Moreover, the cleavage and blastocyst rates of SCNT and PA embryos derived from 42O were significantly higher than that of 33O (p < 0.05). But 33O could sustain IVF embryo development with higher cleavage and blastocyst rates comparing to 42O (p < 0.05). To clarify the development potential difference between 33O and 42O, 18 differentially expressed proteins were identified by proteomic analysis, and randomly selected proteins were confirmed by Western blot. Bioinformatic analysis of these proteins revealed that 33O highly synthesized proteins related to fertilization, and 42O was rich in nuclear reprogramming factors. CONCLUSIONS: These results present a unique insight into maternal factors related to nuclear reprogramming and early embryo development.
Proteomic study of different culture medium serum volume fractions on RANKL-dependent RAW264.7 cells differentiating into osteoclasts.
Xiong Q, Zhang L, Xin L … +4 more , Gao Y, Peng Y, Tang P, Ge W
Proteome Sci · 2015 · PMID 25969670 · Full text
BACKGROUND: Cultivation of osteoclasts is a basic tool for investigating osteolytic bone diseases. Fetal bovine serum (FBS) is the standard supplement used for in vitro cell culture medium. Typically, the serum volume fr...
BACKGROUND: Cultivation of osteoclasts is a basic tool for investigating osteolytic bone diseases. Fetal bovine serum (FBS) is the standard supplement used for in vitro cell culture medium. Typically, the serum volume fraction used for osteoclast cultivation is 10%. In this study, we investigated the use of a low serum (1% FBS) model for culturing osteoclasts. RESULTS: To confirm the validity of this model for use in osteoclast research, we compared the capacity for osteoclastogenesis and bone resorption of RANKL-induced RAW 264.7 cells cultured in medium supplemented with 10% FBS and 1% FBS. Osteoclasts were successfully generated in medium supplemented with 1% FBS, and exhibited prolonged longevity and similar bone resorbing ability to those generated in medium supplemented with 10% FBS, although the osteoclasts were smaller in size. Proteomics and bioinformatics analyses were performed to assess the suitability of osteoclasts formed in low serum-containing medium for use in research focusing on osteoclast differentiation and function. Our study demonstrated that a total of 100 proteins were differentially expressed in cells cultured in medium containing 1% FBS, of which 29 proteins were upregulated, and 71 proteins were downregulated. Bioinformatics analysis showed that the electron transport chain and oxidative phosphorylation pathways were downregulated obviously; however, the osteoclast signaling pathway was unaffected. The data have been deposited to the ProteomeXchange with identifier PXD001935. CONCLUSION: Our study provides clear evidence of the validity of the low serum model for use in studying RANKL-dependent osteoclasts differentiation and bone resorption with the advantage of prolonged survival time.
One-dimensional proteomic profiling of Danio rerio embryo vitellogenin to estimate quantum dot toxicity.
Petushkova NA, Kuznetsova GP, Larina OV … +8 more , Kisrieva YS, Samenkova NF, Trifonova OP, Miroshnichenko YV, Zolotarev KV, Karuzina II, Ipatova OM, Lisitsa AV
Proteome Sci · 2015 · PMID 25964724 · Full text
BACKGROUND: Vitellogenin (Vtg) is the major egg yolk protein (YP) in most oviparous species and may be useful as an indicator in ecotoxicological testing at the biochemical level. In this study, we obtained detailed info...
BACKGROUND: Vitellogenin (Vtg) is the major egg yolk protein (YP) in most oviparous species and may be useful as an indicator in ecotoxicological testing at the biochemical level. In this study, we obtained detailed information about the Vtgs of Danio rerio embryos by cutting SDS-PAGE gel lanes into thin slices, and analyzing them slice-by-slice with (MALDI-TOF) mass spectrometry. RESULTS: We conducted three proteomic analyses, comparing embryonic Danio rerio Vtg cleavage products after exposure for 48 h to CdSecore/ZnSshell quantum dots (QDs), after exposure to a mixture of the components used for quantum dot synthesis (MCS-QDs), and in untreated embryos. The Vtg mass spectrometric profiles of the QDs-treated embryos differed from those of the unexposed or MCS-QDs-treated embryos. CONCLUSION: This study demonstrates the possible utility of Vtg profiling in D. rerio embryos as a sensitive diagnostic tool to estimate nanoparticle toxicity.
Comparative proteomics of Bt-transgenic and non-transgenic cotton leaves.
Wang L, Wang X, Jin X … +4 more , Jia R, Huang Q, Tan Y, Guo A
Proteome Sci · 2015 · PMID 25949214 · Full text
BACKGROUND: As the rapid growth of the commercialized acreage in genetically modified (GM) crops, the unintended effects of GM crops' biosafety assessment have been given much attention. To investigate whether transgenic...
BACKGROUND: As the rapid growth of the commercialized acreage in genetically modified (GM) crops, the unintended effects of GM crops' biosafety assessment have been given much attention. To investigate whether transgenic events cause unintended effects, comparative proteomics of cotton leaves between the commercial transgenic Bt + CpTI cotton SGK321 (BT) clone and its non-transgenic parental counterpart SY321 wild type (WT) was performed. RESULTS: Using enzyme linked immunosorbent assay (ELISA), Cry1Ac toxin protein was detected in the BT leaves, while its content was only 0.31 pg/g. By 2-DE, 58 differentially expressed proteins (DEPs) were detected. Among them 35 were identified by MS. These identified DEPs were mainly involved in carbohydrate transport and metabolism, chaperones related to post-translational modification and energy production. Pathway analysis revealed that most of the DEPs were implicated in carbon fixation and photosynthesis, glyoxylate and dicarboxylate metabolism, and oxidative pentose phosphate pathway. Thirteen identified proteins were involved in protein-protein interaction. The protein interactions were mainly involved in photosynthesis and energy metabolite pathway. CONCLUSIONS: Our study demonstrated that exogenous DNA in a host cotton genome can affect the plant growth and photosynthesis. Although some unintended variations of proteins were found between BT and WT cotton, no toxic proteins or allergens were detected. This study verified genetically modified operation did not sharply alter cotton leaf proteome, and the target proteins were hardly checked by traditional proteomic analysis.
A preliminary quantitative proteomic analysis of glioblastoma pseudoprogression.
Zhang P, Guo Z, Zhang Y … +6 more , Gao Z, Ji N, Wang D, Zou L, Sun W, Zhang L
Proteome Sci · 2015 · PMID 25866482 · Full text
BACKGROUNDS: Pseudoprogression disease (PsPD) is commonly observed during glioblastoma (GBM) follow-up after adjuvant therapy. Because it is difficult to differentiate PsPD from true early progression of GBM, we have use...
BACKGROUNDS: Pseudoprogression disease (PsPD) is commonly observed during glioblastoma (GBM) follow-up after adjuvant therapy. Because it is difficult to differentiate PsPD from true early progression of GBM, we have used a quantitative proteomics strategy to identify molecular signatures and develop predictive markers of PsPD. RESULTS: An initial screening of three PsPD and three GBM patients was performed, and from which 530 proteins with significant fold changes were identified. By conducting biological functional analysis of these proteins, we found evidence that the protein synthesis network and the cellular growth and proliferation network were most significantly affected. Moreover, six of the proteins (HNRNPK, ELAVL1, CDH2, FBLN1, CALU and FGB) involved in the two networks were validated (n = 18) in the same six samples and in twelve additional samples using immunohistochemistry methods and the western blot analysis. The receiver operating characteristic (ROC) curve analysis in distinguishing PsPD patients from GBM patients yielded an area under curve (AUC) value of 0.90 (95% confidence interval (CI), 0.662-0.9880) for CDH2 and.0.92 (95% CI, 0.696-0.995) for CDH2 combined with ELAVL1. CONCLUSIONS: The results of the present study both revealed the biological signatures of PsPD from a proteomics perspective and indicated that CDH2 alone or combined with ELAVL1 could be potential biomarkers with high accuracy in the diagnosis of PsPD.
Differential effects of dopamine signalling on long-term memory formation and consolidation in rodent brain.
Reichenbach N, Herrmann U, Kähne T … +7 more , Schicknick H, Pielot R, Naumann M, Dieterich DC, Gundelfinger ED, Smalla KH, Tischmeyer W
Proteome Sci · 2015 · PMID 25852303 · Full text
BACKGROUND: Using auditory discrimination learning in gerbils, we have previously shown that activation of auditory-cortical D1/D5 dopamine receptors facilitates mTOR-mediated, protein synthesis-dependent mechanisms of m...
BACKGROUND: Using auditory discrimination learning in gerbils, we have previously shown that activation of auditory-cortical D1/D5 dopamine receptors facilitates mTOR-mediated, protein synthesis-dependent mechanisms of memory consolidation and anterograde memory formation. To understand molecular mechanisms of this facilitatory effect, we tested the impact of local pharmacological activation of different D1/D5 dopamine receptor signalling modes in the auditory cortex. To this end, protein patterns in soluble and synaptic protein-enriched fractions from cortical, hippocampal and striatal brain regions of ligand- and vehicle-treated gerbils were analysed by 2D gel electrophoresis and mass spectrometry 24 h after intervention. RESULTS: After auditory-cortical injection of SKF38393 - a D1/D5 dopamine receptor-selective agonist reported to activate the downstream effectors adenylyl cyclase and phospholipase C - prominent proteomic alterations compared to vehicle-treated controls appeared in the auditory cortex, striatum, and hippocampus, whereas only minor changes were detectable in the frontal cortex. In contrast, auditory-cortical injection of SKF83959 - a D1/D5 agonist reported to preferentially stimulate phospholipase C - induced pronounced changes in the frontal cortex. At the molecular level, we detected altered regulation of cytoskeletal and scaffolding proteins, changes in proteins with functions in energy metabolism, local protein synthesis, and synaptic signalling. Interestingly, abundance and/or subcellular localisation of the predominantly presynaptic protein α-synuclein displayed dopaminergic regulation. To assess the role of α-synuclein for dopaminergic mechanisms of memory modulation, we tested the impact of post-conditioning systemic pharmacological activation of different D1/D5 dopamine receptor signalling modes on auditory discrimination learning in α-synuclein-mutant mice. In C57BL/6JOlaHsd mice, bearing a spontaneous deletion of the α-synuclein-encoding gene, but not in the related substrains C57BL/6JCrl and C57BL/6JRccHsd, adenylyl cyclase-mediated signalling affected acquisition rates over future learning episodes, whereas phospholipase C-mediated signalling affected final memory performance. CONCLUSIONS: Dopamine signalling modes via D1/D5 receptors in the auditory cortex differentially impact protein profiles related to rearrangement of cytomatrices, energy metabolism, and synaptic neurotransmission in cortical, hippocampal, and basal brain structures. Altered dopamine neurotransmission in α-synuclein-deficient mice revealed that distinct D1/D5 receptor signalling modes may control different aspects of memory consolidation.
Label-free quantitative phosphorylation analysis of human transgelin2 in Jurkat T cells reveals distinct phosphorylation patterns under PKA and PKC activation conditions.
Jang SH, Jun CD, Park ZY
Proteome Sci · 2015 · PMID 25844069 · Full text
BACKGROUND: Transgelin2, one of cytoskeletal actin binding proteins has recently been suggested to be involved in the formation of immune synapses. Although detailed function of transgelin2 is largely unknown, interactio...
BACKGROUND: Transgelin2, one of cytoskeletal actin binding proteins has recently been suggested to be involved in the formation of immune synapses. Although detailed function of transgelin2 is largely unknown, interactions between transgelin2 and actin appear to be important in regulating cellular functions of transgelin2. Because protein phosphorylation can change ability to interact with other proteins, comprehensive phosphorylation analysis of transgelin2 will be helpful in understanding its functional mechanisms. RESULTS: Here, a specific protein label-free quantitative phosphorylation analysis method combining immuno-precipitation, IMAC phosphopeptide enrichment technique and label-free relative quantification analysis was used to monitor the phosphorylation changes of transgelin2 overexpressed in Jurkat T cells under protein kinase C (PKC) and protein kinase A (PKA) activation conditions, two representative intracellular signalling pathways of immune cell activation and homeostasis. A total of six serine/threonine phosphorylation sites were identified including threonine-84, a novel phosphorylation site. Notably, distinct phosphorylation patterns of transgelin2 under the two kinase activation conditions were observed. Most phosphorylation sites showing specific kinase-dependent phosphorylation changes were discretely located in two previously characterized actin-binding regions: actin-binding site (ABS) and calponin repeat domain (CNR). PKC activation increased phosphorylation of threonine-180 and serine-185 in the CNR, and PKA activation increased phosphorylation of serine-163 in the ABS. CONCLUSIONS: Multiple actin-binding regions of transgelin2 participate to accomplish its full actin-binding capability, and the actin-binding affinity of each actin-binding region appears to be modulated by specific kinase-dependent phosphorylation changes. Accordingly, different actin-binding properties or cellular functions of transgelin2 may result from distinct intracellular signalling events under immune response activation or homeostasis conditions.
New interaction partners for Nek4.1 and Nek4.2 isoforms: from the DNA damage response to RNA splicing.
Basei FL, Meirelles GV, Righetto GL … +3 more , Dos Santos Migueleti DL, Smetana JH, Kobarg J
Proteome Sci · 2015 · PMID 25798074 · Full text
BACKGROUND: Neks are serine-threonine kinases that are similar to NIMA, a protein found in Aspergillus nidulans which is essential for cell division. In humans there are eleven Neks which are involved in different biolog...
BACKGROUND: Neks are serine-threonine kinases that are similar to NIMA, a protein found in Aspergillus nidulans which is essential for cell division. In humans there are eleven Neks which are involved in different biological functions besides the cell cycle control. Nek4 is one of the largest members of the Nek family and has been related to the primary cilia formation and in DNA damage response. However, its substrates and interaction partners are still unknown. In an attempt to better understand the role of Nek4, we performed an interactomics study to find new biological processes in which Nek4 is involved. We also described a novel Nek4 isoform which lacks a region of 46 amino acids derived from an insertion of an Alu sequence and showed the interactomics profile of these two Nek4 proteins. RESULTS AND DISCUSSION: Isoform 1 and isoform 2 of Nek4 were expressed in human cells and after an immunoprecipitation followed by mass spectrometry, 474 interacting proteins were identified for isoform 1 and 149 for isoform 2 of Nek4. About 68% of isoform 2 potential interactors (102 proteins) are common between the two Nek4 isoforms. Our results reinforce Nek4 involvement in the DNA damage response, cilia maintenance and microtubule stabilization, and raise the possibility of new functional contexts, including apoptosis signaling, stress response, translation, protein quality control and, most intriguingly, RNA splicing. We show for the first time an unexpected difference between both Nek4 isoforms in RNA splicing control. Among the interacting partners, we found important proteins such as ANT3, Whirlin, PCNA, 14-3-3ε, SRSF1, SRSF2, SRPK1 and hNRNPs proteins. CONCLUSIONS: This study provides new insights into Nek4 functions, identifying new interaction partners and further suggests an interesting difference between isoform 1 and isoform 2 of this kinase. Nek4 isoform 1 may have similar roles compared to other Neks and these roles are not all preserved in isoform 2. Besides, in some processes, both isoforms showed opposite effects, indicating a possible fine controlled regulation.
Towards further defining the proteome of mouse saliva.
Blanchard AA, Ezzati P, Shamshurin D … +4 more , Nistor AC, Leygue E, Wilkins JA, Myal Y
Proteome Sci · 2015 · PMID 25762866 · Full text
BACKGROUND: Knowledge of the mouse salivary proteome is not well documented and as a result, very limited. Currently, several salivary proteins remain unidentified and for some others, their function yet to be determined...
BACKGROUND: Knowledge of the mouse salivary proteome is not well documented and as a result, very limited. Currently, several salivary proteins remain unidentified and for some others, their function yet to be determined. The goal of the present study is to utilize mass spectrometry analysis to widen our knowledge of mouse salivary proteins, and through extensive database searches, provide further insight into the array of proteins that can be found in saliva. A comprehensive mouse salivary proteome will also facilitate the development of mouse models to study specific biomarkers of many human diseases. RESULTS: Individual saliva samples were collected from male and female mice, and later pooled according to sex. Two pools of saliva from female mice (2 samples/pool) and 2 pools of saliva from male mice were used for analysis utilizing high performance liquid chromatograph mass spectrometry (nano-RPLC-MS/MS). The resulting datasets identified 345 proteins: 174 proteins were represented in saliva obtained from both sexes, as well as 82 others that were more female specific and 89 that were more male specific. Of these sex linked proteins, twelve were identified as exclusively sex-limited; 10 unique to males and 2 unique to females. Functional analysis of the 345 proteins identified 128 proteins with catalytic activity characteristics; indicative of proteins involved in digestion, and 35 proteins associated with stress response, host defense, and wound healing functions. Submission of the list of 345 proteins to the BioMart data mining tool in the Ensembl database further allowed us to identify a total of 283 orthologous human genes, of which, 131 proteins were recently reported to be present in the human salivary proteome. CONCLUSIONS: The present study is the most comprehensive list to date of the proteins that constitute the mouse salivary proteome. The data presented can serve as a useful resource for identifying potentially useful biomarkers of human health and disease.
Proteome changes in the small intestinal mucosa of broilers (Gallus gallus) induced by high concentrations of atmospheric ammonia.
Zhang J, Li C, Tang X … +3 more , Lu Q, Sa R, Zhang H
Proteome Sci · 2015 · PMID 25741220 · Full text
BACKGROUND: Ammonia is a well-known toxicant both existing in atmospheric and aquatic system. So far, most studies of ammonia toxicity focused on mammals or aquatic animals. With the development of poultry industry, ammo...
BACKGROUND: Ammonia is a well-known toxicant both existing in atmospheric and aquatic system. So far, most studies of ammonia toxicity focused on mammals or aquatic animals. With the development of poultry industry, ammonia as a main source of contaminant in the air is causing more and more problems on broiler production, especially lower growth rate. The molecular mechanisms that underlie the negative effects of ammonia on the growth and intestine of broilers are yet unclear. We investigated the growth, gut morphology, and mucosal proteome of Arbor Acres broilers (Gallus gallus) exposed to high concentrations of atmospheric ammonia by performing a proteomics approach integrated with traditional methods. RESULTS: Exposure to ammonia interfered with the development of immune organ and gut villi. Meanwhile, it greatly reduced daily weight gain and feed intake, and enhanced feed conversion ratio. A total of 43 intestinal mucosal proteins were found to be differentially abundant. Up-regulated proteins are related to oxidative phosphorylation and apoptosis. Down-regulated proteins are related to cell structure and growth, transcriptional and translational regulation, immune response, oxidative stress and nutrient metabolism. These results indicated that exposure to ammonia triggered oxidative stress, and interfered with nutrient absorption and immune function in the small intestinal mucosa of broilers. CONCLUSIONS: These findings have important implications for understanding the toxic mechanisms of ammonia on intestine of broilers, which provides new information that can be used for intervention using nutritional strategies in the future.
The proteome profiles of the olfactory bulb of juvenile, adult and aged rats - an ontogenetic study.
Wille M, Schümann A, Kreutzer M … +4 more , Glocker MO, Wree A, Mutzbauer G, Schmitt O
Proteome Sci · 2015 · PMID 25709559 · Full text
BACKGROUND: In this study, we searched for proteins that change their expression in the olfactory bulb (oB) of rats during ontogenesis. Up to now, protein expression differences in the developing animal are not fully und...
BACKGROUND: In this study, we searched for proteins that change their expression in the olfactory bulb (oB) of rats during ontogenesis. Up to now, protein expression differences in the developing animal are not fully understood. Our investigation focused on the question whether specific proteins exist which are only expressed during different development stages. This might lead to a better characterization of the microenvironment and to a better determination of factors and candidates that influence the differentiation of neuronal progenitor cells. RESULTS: After analyzing the samples by two-dimensional polyacrylamide gel electrophoresis (2DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), it could be shown that the number of expressed proteins differs depending on the developmental stages. Especially members of the functional classes, like proteins of biosynthesis, regulatory proteins and structural proteins, show the highest differential expression in the stages of development analyzed. CONCLUSION: In this study, quantitative changes in the expression of proteins in the oB at different developmental stages (postnatal days (P) 7, 90 and 637) could be observed. Furthermore, the expression of many proteins was found at specific developmental stages. It was possible to identify these proteins which are involved in processes like support of cell migration and differentiation.
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