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translational proteomics

Sravanth K Hindupur, Marco Colombi, Stephen R Fuhs, Matthias S Matter, Yakir Guri, Kevin Adam, Marion Cornu, Salvatore Piscuoglio, Charlotte K Y Ng, Charles Betz, Dritan Liko, Luca Quagliata, Suzette Moes, Paul Jenoe, Luigi M Terracciano, Markus H Heim, Tony Hunter, Michael N Hall
Histidine phosphorylation, the so-called hidden phosphoproteome, is a poorly characterized post-translational modification of proteins. Here we describe a role of histidine phosphorylation in tumorigenesis. Proteomic analysis of 12 tumours from an mTOR-driven hepatocellular carcinoma mouse model revealed that NME1 and NME2, the only known mammalian histidine kinases, were upregulated. Conversely, expression of the putative histidine phosphatase LHPP was downregulated specifically in the tumours. We demonstrate that LHPP is indeed a protein histidine phosphatase...
March 21, 2018: Nature
Dillon F Da Fonte, Chris J Martyniuk, Lei Xing, Vance L Trudeau
Radial glial cells (RGCs) are the main macroglia in the teleost brain and have established roles in neurogenesis and neurosteroidogenesis. They are the only brain cell type expressing aromatase B ( cyp19a1b ), the enzyme that synthesizes estrogens from androgen precursors. There are few studies on the regulation of RGC functions, but our previous investigations demonstrated that dopamine stimulates cyp19a1b expression in goldfish RGCs, while secretoneurin A (SNa) inhibits the expression of this enzyme. Here, we determine the range of proteins and cellular processes responsive to SNa treatments in these steroidogenic cells...
2018: Frontiers in Endocrinology
Jorge Ruiz-Orera, Pol Verdaguer-Grau, José Luis Villanueva-Cañas, Xavier Messeguer, M Mar Albà
Accumulating evidence indicates that some protein-coding genes have originated de novo from previously non-coding genomic sequences. However, the processes underlying de novo gene birth are still enigmatic. In particular, the appearance of a new functional protein seems highly improbable unless there is already a pool of neutrally evolving peptides that are translated at significant levels and that can at some point acquire new functions. Here, we use deep ribosome-profiling sequencing data, together with proteomics and single nucleotide polymorphism information, to search for these peptides...
March 19, 2018: Nature Ecology & Evolution
Davoud Mozhdehi, Kelli M Luginbuhl, Joseph R Simon, Michael Dzuricky, Rüdiger Berger, H Samet Varol, Fred C Huang, Kristen L Buehne, Nicholas R Mayne, Isaac Weitzhandler, Mischa Bonn, Sapun H Parekh, Ashutosh Chilkoti
Post-translational modification of proteins is a strategy widely used in biological systems. It expands the diversity of the proteome and allows for tailoring of both the function and localization of proteins within cells as well as the material properties of structural proteins and matrices. Despite their ubiquity in biology, with a few exceptions, the potential of post-translational modifications in biomaterials synthesis has remained largely untapped. As a proof of concept to demonstrate the feasibility of creating a genetically encoded biohybrid material through post-translational modification, we report here the generation of a family of three stimulus-responsive hybrid materials-fatty-acid-modified elastin-like polypeptides-using a one-pot recombinant expression and post-translational lipidation methodology...
March 19, 2018: Nature Chemistry
Kiyomichi Imamura, Hikari Yoshitane, Kazuki Hattori, Mitsuo Yamaguchi, Kento Yoshida, Takenori Okubo, Isao Naguro, Hidenori Ichijo, Yoshitaka Fukada
Daily rhythms of behaviors and physiologies are generated by the circadian clock, which is composed of clock genes and the encoded proteins forming transcriptional/translational feedback loops (TTFLs). The circadian clock is a self-sustained oscillator and flexibly responds to various time cues to synchronize with environmental 24-h cycles. However, the key molecule that transmits cellular stress to the circadian clockwork is unknown. Here we identified apoptosis signal-regulating kinase (ASK), a member of the MAPKKK family, as an essential mediator determining the circadian period and phase of cultured cells in response to osmotic changes of the medium...
March 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
Michał Rurek, Magdalena Czołpińska, Tomasz Andrzej Pawłowski, Włodzimierz Krzesiński, Tomasz Spiżewski
Complex proteomic and physiological approaches for studying cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower ( Brassica oleracea var. botrytis ) curds after cold and heat and after stress recovery were assayed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) in relation to mRNA abundance and respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold, major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed...
March 16, 2018: International Journal of Molecular Sciences
Weiyang Chen, Longfa Fang, Xiahe Huang, Haitao Ge, Jinlong Wang, Xiaorong Wang, Yuanya Zhang, Na Sui, Wu Xu, Yingchun Wang
Differential expression of cold-responsive proteins is necessary for cyanobacteria to acclimate to cold stress frequently occurring in their natural habitats. Accumulating evidence indicates that cold-induced expression of certain proteins is dependent on light illumination, but a systematic identification of light-dependent and/or light-independent cold-responsive proteins in cyanobacteria is still lacking. Herein, we comprehensively identified cold-responsive proteins in a model cyanobacterium Synechocystis sp...
March 12, 2018: Journal of Proteomics
Tong Liu, Dong-Wei Tian, Li-Juan Zou, Fang-Yu Liu, Qi-Yan Can, Jin-Kui Yang, Jian-Ping Xu, Xiao-Wei Huang, Jia-Qin Xi, Ming-Liang Zhu, Ming-He Mo, Ke-Qin Zhang
Ammonia is one of the fungistatic factors in soil that can suppress conidial germination, but the molecular mechanism underlying the suppression is unknown. In this study, the proteomes of fungistatic conidia, fresh conidia and germinated conidia of Arthrobotrys oligospora ATCC24927 were determined and quantified. The protein expression profile of fungistatic conidia was significantly different from those in the other two conditions. 281 proteins were down expressed in fungistatic conidia and characterized by GO annotation...
March 12, 2018: International Journal of Biochemistry & Cell Biology
Charlotte E Teunissen, Markus Otto, Sebastiaan Engelborghs, Sanna-Kaisa Herukka, Sylvain Lehmann, Piotr Lewczuk, Alberto Lleó, Armand Perret-Liaudet, Hayrettin Tumani, Martin R Turner, Marcel M Verbeek, Jens Wiltfang, Henrik Zetterberg, Lucilla Parnetti, Kaj Blennow
Body fluid biomarkers have great potential for different clinical purposes, including diagnosis, prognosis, patient stratification and treatment effect monitoring. This is exemplified by current use of several excellent biomarkers, such as the Alzheimer's disease cerebrospinal fluid (CSF) biomarkers, anti-neuromyelitis optica antibodies and blood neurofilament light. We still, however, have a strong need for additional biomarkers and several gaps in their development and implementation should be filled. Examples of such gaps are i) limited knowledge of the causes of neurological diseases, and thus hypotheses about the best biomarkers to detect subclinical stages of these diseases; ii) the limited success translating discoveries obtained by e...
March 15, 2018: Alzheimer's Research & Therapy
Alexander Hogrebe, Louise von Stechow, Dorte B Bekker-Jensen, Brian T Weinert, Christian D Kelstrup, Jesper V Olsen
Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible quantification remains challenging, especially for post-translational modifications such as phosphorylation. Here, we compare the most popular quantification techniques for global phosphoproteomics: label-free quantification (LFQ), stable isotope labeling by amino acids in cell culture (SILAC) and MS2 - and MS3 -measured tandem mass tags (TMT). In a mixed species comparison with fixed phosphopeptide ratios, we find LFQ and SILAC to be the most accurate techniques...
March 13, 2018: Nature Communications
Zhonghua Li, Wei Zeng, Shiyi Ye, Jian Lv, Axiu Nie, Bingzhou Zhang, Yumei Sun, Heyou Han, Qigai He
The nucleocapsid (N) protein is a major structural component of porcine epidemic diarrhea virus (PEDV), which is predicted to be a multifunctional protein in viral replication. Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a cellular protein participating in the splicing of pre-mRNA in the nucleus and translation regulation in the cytoplasm. According to our previous proteomic study about PEDV infection in vivo, hnRNP A1 was thought to be a cellular factor influencing PEDV replication. In this report, PEDV N protein was discovered to colocalize with cellular hnRNP A1 in perinuclear region of PEDV infected cells...
March 13, 2018: Viruses
Ying Zhu, Qing Lei, Dan Li, Yang Zhang, Xiaogang Jiang, Zhanhong Hu, Guoqiang Xu
Protein post-translational modification by ubiquitin-fold modifier 1, UFM1, regulates many biological processes such as response to endoplasmic reticulum stress and regulation of tumor progression. Recent study has indicated that the UFM1-binding and PCI domain-containing protein 1 (UFBP1) is required for the conjugation of UFM1 to a substrate. However, other biological functions of UFBP1 have not been explored. Here, we use immunoprecipitation and label-free quantitative proteomics to identify UFBP1-interacting proteins in a mammalian cell line...
March 13, 2018: Journal of Proteome Research
Jinho Lee, Gary K Geiss, Gokhan Demirkan, Christopher P Vellano, Brian Filanoski, Yiling Lu, Zhenlin Ju, Shuangxing Yu, Huifang Guo, Lisa Y Bogatzki, Warren E Carter, Rhonda K Meredith, Savitri Krishnamurthy, Zhiyong Ding, Joseph M Beechem, Gordon Mills
Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy.  Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application.  Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples...
March 12, 2018: Molecular & Cellular Proteomics: MCP
Jeng-Ting Chen, Chien-Chun Liu, Jau-Song Yu, Hung-Hsuan Li, Ming-Chih Lai
Hypoxia is associated with poor prognosis in most solid tumors due to its multiple effects on therapy resistance, angiogenesis, apoptotic resistance, and tumor invasion/metastasis. Here we used a comprehensive omics profiling to investigate hypoxia-regulated gene expression in HCT116 colon cancer cells. Quantitative analyses of proteome and secretome were performed in HCT116 cells cultured under hypoxic or normoxic conditions. A total of 5700 proteins were quantified in proteome analysis and 722 proteins were quantified in secretome analysis...
March 7, 2018: Journal of Proteomics
Marc Planas, Martí Bernardo-Faura, Judith Katharina Paulus, Farnusch Kaschani, Markus Kaiser, Marc Valls, Renier van der Hoorn, Nuria Sanchez Coll
Activity-based protein profiling (ABPP) is a powerful proteomic technique to display protein activities in a proteome. It is based on the use of small molecular probes that react with the active site of proteins in an activity-dependent manner. We used ABPP to dissect the protein activity changes that occur in the intercellular spaces of tolerant (Hawaii 7996) and susceptible (Marmande) tomato plants in response to R. solanacearum, the causing agent of bacterial wilt, one of the most destructive bacterial diseases in plants...
March 9, 2018: Molecular & Cellular Proteomics: MCP
K Johanna R Hoyer, Sebastian Dittrich, Malte P Bartram, Markus M Rinschen
Renal diseases are driven by alterations in the entity of proteins within the kidney, at the level of single cells, nephron subunits (such as glomerulus and tubule), tissues and body fluids. Histologically, kidney diseases are extremely heterogeneous. Mass-spectrometry based proteomics provides a unique opportunity to interrogate heterogeneity and dynamics of various proteome layers within the kidney to better understand physiology and pathophysiology, and to translate signaling networks into therapies. Yet, the success of this endeavor will largely depend on improving proteomic data acquisition methods toward increased reproducibility...
March 6, 2018: Journal of Proteomics
Guang Xu, Jacek Stupak, Li Yang, Luokai Hu, Bo Guo, Jianjun Li
Mass spectrometry (MS) has played a vital role across a broad range of fields and applications in proteomics. The development of high-resolution MS for the past decades has significantly advanced biology, such as protein structure, function, post translational modification and global protein dynamics. In MS, two ionization techniques are often used-electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). ESI mass spectra are generally crowded by signals of multiple charge values for each molecular mass and an isotopic cluster for each nominal mass-to-charge (m/z) value...
March 8, 2018: Rapid Communications in Mass Spectrometry: RCM
Sander Bekeschus, Jan-Wilm Lackmann, Denis Gümbel, Matthias Napp, Anke Schmidt, Kristian Wende
Non-healing wounds continue to be a clinical challenge for patients and medical staff. These wounds have a heterogeneous etiology, including diabetes and surgical trauma wounds. It is therefore important to decipher molecular signatures that reflect the macroscopic process of wound healing. To this end, we collected wound sponge dressings routinely used in vacuum assisted therapy after surgical trauma to generate wound-derived protein profiles via global mass spectrometry. We confidently identified 311 proteins in exudates...
March 7, 2018: International Journal of Molecular Sciences
Taewook Kang, Pia Jensen, Vita Solovyeva, Jonathan R Brewer, Martin R Larsen
Characterization of molecular mechanisms underlying pancreatic β-cell function in relation to glucose-stimulated insulin secretion is incomplete, especially with respect to global response in the nuclear environment. Here, we focus on the characterization of proteins in the nuclear environment of β-cells after brief, high glucose-stimulation. We compared purified nuclei derived from β-cells stimulated with 17mM glucose for 0, 2, and 5 minutes using quantitative proteomics, a time frame that most likely does not result in translation of new protein in the cell...
March 8, 2018: Journal of Proteome Research
Erik H A Rikkerink
Organisms face stress from multiple sources simultaneously and require mechanisms to respond to these scenarios if they are to survive in the long term. This overview focuses on a series of key points that illustrate how disorder and post-translational changes can combine to play a critical role in orchestrating the response of organisms to the stress of a changing environment. Increasingly, protein complexes are thought of as dynamic multi-component molecular machines able to adapt through compositional, conformational and/or post-translational modifications to control their largely metabolic outputs...
March 8, 2018: International Journal of Molecular Sciences
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