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Molecular & Cellular Proteomics: MCP

Kerstin Thriene, Björn Andreas Grüning, Olivier Bornert, Anika Erxleben, Juna Leppert, Ioannis Athanasiou, Ekkehard Weber, Dimitra Kiritsi, Alexander Nyström, Thomas Reinheckel, Rolf Backofen, Cristina Has, Leena Bruckner-Tuderman, Joern Dengjel
The extracellular matrix protein collagen VII is part of the microenvironment of stratified epithelia and critical in organismal homeostasis. Mutations in the encoding gene COL7A1 lead to the skin disorder dystrophic epidermolysis bullosa (DEB), are linked to skin fragility and progressive inflammation-driven fibrosis that facilitates aggressive skin cancer. So far, these changes have been linked to mesenchymal alterations, the epithelial consequences of collagen VII loss remaining under-addressed. As epithelial dysfunction is a principal initiator of fibrosis, we performed a comprehensive transcriptome and proteome profiling of primary human keratinocytes to generate global and detailed images of dysregulated epidermal molecular pathways linked to loss of collagen VII...
January 11, 2018: Molecular & Cellular Proteomics: MCP
Krystyna Cwiklinski, Heather Jewhurst, Paul McVeigh, Tara Barbour, Aaron G Maule, Jose Tort, Sandra M O'Neill, Mark W Robinson, Sheila Donnelly, John P Dalton
The parasite Fasciola hepatica infects a broad range of mammals with impunity.  Following ingestion of parasites (metacercariae) by the host, newly excysted juveniles (NEJ) emerge from their cysts, rapidly penetrate the duodenal wall and migrate to the liver.  Successful infection takes just a few hours and involves negotiating hurdles presented by host macromolecules, tissues and micro-environments, as well as the immune system.  Here, transcriptome and proteome analysis of ex vivo F. hepatica metacercariae and NEJ reveal the rapidity and multitude of metabolic and developmental alterations that take place in order for the parasite to establish infection...
January 10, 2018: Molecular & Cellular Proteomics: MCP
Kyle Swovick, Kevin A Welle, Jennifer Hryhorenko, Andrei Seluanov, Vera Gorbunova, Sina Ghaemmaghami
The constitutive process of protein turnover plays a key role in maintaining cellular homeostasis. Recent technological advances in mass spectrometry have enabled the measurement of protein turnover kinetics across the proteome. However, it is not known if turnover kinetics of individual proteins are highly conserved or if they have evolved to meet the physiological demands of individual species. Here, we conducted systematic analyses of proteome turnover kinetics in primary dermal fibroblasts isolated from eight different rodent species...
January 10, 2018: Molecular & Cellular Proteomics: MCP
Veronique Jonckheere, Daria Fijałkowska, Petra Van Damme
Excision of the N-terminal initiator methionine (iMet) residue from nascent peptide chains is an essential and omnipresent protein modification carried out by methionine aminopeptidases (MetAPs) that accounts for a major source of N-terminal proteoform diversity. While MetAP2 is known to be implicated in processes such as angiogenesis and proliferation in mammals, the physiological role of MetAP1 is much less clear. In this report we studied the omics-wide effects of human MetAP1 deletion and general MetAP inhibition...
January 9, 2018: Molecular & Cellular Proteomics: MCP
Valentin Voillet, Magali San Cristobal, Marie-Christine Pere, Yvon Billon, Laurianne Canario, Laurence Liaubet, Louis Lefaucheur
BACKGROUND: In pigs, the perinatal period is the most critical time for survival. Piglet maturation, which occurs at the end of gestation, leads to a state of full development after birth. Maturity is thus an important determinant of early survival. Skeletal muscle plays a key role in adaptation to extra-uterine life, e.g. motor function and thermoregulation. Progeny from two breeds with extreme neonatal mortality rates were analyzed at 90 and 110 days of gestation (dg). The Large White breed is a highly selected breed for lean growth with a high rate of mortality at birth, whereas the Chinese Meishan breed is fatter and more robust and has a low mortality rate...
January 8, 2018: Molecular & Cellular Proteomics: MCP
Silin Ren, Mingkun Yang, Yuewei Yue, Feng Ge, Yu Li, Xiaodong Guo, Jia Zhang, Feng Zhang, Xinyi Nie, Shihua Wang
Aspergillus flavus (A. flavus) is a ubiquitous saprophytic and pathogenic fungus that produces the aflatoxin carcinogen, and A. flavus can have tremendous economic and health impacts worldwide. Increasing evidence demonstrates that lysine succinylation plays an important regulatory role in metabolic processes in both bacterial and human cells. However, little is known about the extent and function of lysine succinylation in A. flavus Here, we performed a global succinylome analysis of A. flavus using high accuracy nano-LC-MS/MS in combination with the enrichment of succinylated peptides from digested cell lysates and subsequent peptide identification...
January 3, 2018: Molecular & Cellular Proteomics: MCP
Hanyang Dong, Zhenchang Guo, Wei Feng, Tao Zhang, Guijin Zhai, Agata Palusiak, Antoni Rozalski, Shanshan Tian, Xue Bai, Lijin Shen, Pu Chen, Quan Wang, Enguo Fan, Zhongyi Cheng, Kai Zhang
Lysine 2-hydroxyisobutyrylation (Khib) is a novel post-translational modification (PTM), which was thought to play a role in active gene transcription and cellular proliferation. Here we report a comprehensive identification of Khib in Proteus mirabilis (P. mirabilis). By combining affinity enrichment with two-dimensional liquid chromatography and high-resolution mass spectrometry, 4735 2-hydroxyisobutyrylation sites were identified on 1051 proteins in P. mirabilis. These proteins bearing modifications were further characterized in abundance, distribution and functions...
January 3, 2018: Molecular & Cellular Proteomics: MCP
Te-Yao Hsu, Jyun-Mu Lin, Mai-Huong Thi Nguyen, Feng-Hsiang Chung, Ching-Chang Tsai, Hsin-Hsin Cheng, Yun-Ju Lai, Hsuan-Ning Hung, Chien-Sheng Chen
Pre-eclampsia is one of the main causes of perinatal mortality and morbidity. Many biomarkers for diagnosing pre-eclampsia have been found but most have low accuracy. Therefore, a potential marker that can detect pre-eclampsia with high accuracy is required. Infection has been reported as a cause of pre-eclampsia. In recent years, protein microarray chips have been recognized as a strong and robust tool for profiling antibodies for infection diagnoses. The purpose of the present study was to profile antibodies in the human plasma of healthy and pre-eclamptic pregnancies to identify suitable biomarkers...
December 28, 2017: Molecular & Cellular Proteomics: MCP
Wolin Hou, Xiyan Meng, Aihua Zhao, Weijing Zhao, Jiemin Pan, Junling Tang, Yajuan Huang, Huaping Li, Wei Jia, Fang Liu, Weiping Jia
Although metabolomics are desirable to understand the pathophysiology of gestational diabetes mellitus (GDM), comprehensive metabolomic studies of GDM are rare. We aimed to offer a holistic view of metabolites alteration in GDM patients and investigate the possible multimarker models for GDM diagnosis. Biochemical parameters and perinatal data of 131 GDM cases and 138 controls were collected. Fasting serum samples at 75 g oral glucose tolerance test were used for metabolites by ultra performance liquid chromatography-quadrupole-time of flight-mass spectrometry, ultra performance liquid chromatography-triple triple-quadrupole-mass spectrometry and gas chromatography- time-of- flight mass spectrometry platforms...
December 27, 2017: Molecular & Cellular Proteomics: MCP
Tiphaine Cecchini, Eun-Jeong Yoon, Yannick Charretier, Chloé Bardet, Corinne Beaulieu, Xavier Lacoux, Jean-Denis Docquier, Jerome Lemoine, Patrice Courvalin, Catherine Grillot-Courvalin, Jean-Philippe Charrier
Resistance to β-lactams in Acinetobacter baumannii involves various mechanisms. To decipher them, whole genome sequencing (WGS) and real-time quantitative polymerase chain reaction (RT-qPCR) were complemented by mass spectrometry (MS) in selected reaction monitoring mode (SRM) in 39 clinical isolates. The targeted label-free proteomic approach enabled, in one hour and using a single method, the quantitative detection of 16 proteins associated with antibiotic resistance: eight acquired β-lactamases (i.e. GES, NDM-1, OXA-23, OXA-24, OXA-58, PER, TEM-1 and VEB), two resident β-lactamases (i...
December 19, 2017: Molecular & Cellular Proteomics: MCP
Joel Basken, Scott A Stuart, Andrew J Kavran, Thomas Lee, Christopher C Ebmeier, William Old, Natalie G Ahn
The BRAF-MKK1/2-ERK1/2 pathway is constitutively activated in response to oncogenic mutations of BRAF in many cancer types, including melanoma. Although small molecules that inhibit oncogenic BRAF and MKK1/2 have been successful in clinical settings, resistance invariably develops. High affinity inhibitors of ERK1/2 have been shown in preclinical studies to bypass the resistance of melanoma and colon cancer cells to BRAF and MKK1/2 inhibitors, and are thus promising additions to current treatment protocols...
December 18, 2017: Molecular & Cellular Proteomics: MCP
Ho-Chang Kuo, Ying-Hsien Huang, Feng-Hsiang Chung, Po-Chung Chen, Tzu-Cheng Sung, Yi-Wen Chen, Kai-Sheng Hsieh, Chien-Sheng Chen, Guan-Da Syu
Kawasaki disease (KD) is a form of systemic vasculitis that generally occurs in children under 5 years old. Currently, KD is still diagnosed according to its clinical symptoms, including prolonged fever, skin rash, conjunctivitis, neck lymphadenopathy, palm erythema, and oral mucosa changes. Since KD is a type of inflammation without specific marker for diagnosis, we plan to profile the plasma antibodies by using E. coli proteome microarray and analyze the differences between KD and healthy subjects. Plasmas were collected from KD patient before intravenous immunoglobulin treatment (KD1), at least 3 weeks after treatment (KD3), non-fever control (NC), and fever control (FC) children...
December 15, 2017: Molecular & Cellular Proteomics: MCP
Safinur Atay, Daniel W Wilkey, Mohammed M Milhem, Michael Merchant, Andrew K Godwin
Developing tumors continuously release nano-sized vesicles that represent circulating "fingerprints" of the tumor's identity.  In gastrointestinal stromal tumor (GIST), we have previously reported that these tumors release "oncosomes" carrying the constitutively activated tyrosine kinase (TK) receptor KIT.  Despite the clinical utility of TK inhibitors, such as imatinib mesylate (IM), recurrence and metastasis are clinical problems that urge the need to identify new tumor-derived molecules.  To this aim, we performed the first high quality proteomic study of GIST-derived exosomes (GDEs) and identified 1,060 proteins composing the core GDE proteome (cGDEp)...
December 14, 2017: Molecular & Cellular Proteomics: MCP
Chloe Chong, Fabio Marino, Hui-Song Pak, Julien Racle, Roy T Daniel, Markus Müller, David Gfeller, George Coukos, Michal Bassani-Sternberg
Comprehensive knowledge of the human leukocyte antigen (HLA) class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer and other diseases. However methodologies for their purification for mass-spectrometry analysis have been a major limitation. We designed a novel high-throughput, reproducible and sensitive method for sequential immuno-affinity purification of HLA-I and -II peptides from up to 96 samples in a plate format, suitable for both cell lines and tissues...
December 14, 2017: Molecular & Cellular Proteomics: MCP
Wei Zeng, Kristina L Ford, Tony Bacic, Joshua L Heazlewood
N-glycosylation is one of the most common protein post-translational modifications in eukaryotes and has a relatively conserved core structure between fungi, animals and plants. In plants, the biosynthesis of N-glycans has been extensively studied with all the major biosynthetic enzymes characterized. However, few studies have applied advanced mass spectrometry to profile intact plant N-glycopeptides. In this study, we use hydrophilic enrichment, high-resolution tandem mass spectrometry with complementary and triggered fragmentation to profile Arabidopsis N-glycopeptides from microsomal membranes of aerial tissues...
December 13, 2017: Molecular & Cellular Proteomics: MCP
Jitka Štáfková, Petr Rada, Dionigia Meloni, Vojtěch Žárský, Tamara Smutná, Nadine Zimmann, Karel Harant, Petr Pompach, Ivan Hrdý, Jan Tachezy
The secretion of virulence factors by parasitic protists into the host environment plays a fundamental role in multifactorial host-parasite interactions. Several effector proteins are known to be secreted by Trichomonas vaginalis, a human parasite of the urogenital tract. However, a comprehensive profiling of the T. vaginalis secretome remains elusive, as do the mechanisms of protein secretion. In this study, we used high-resolution label-free quantitative MS to analyze the T. vaginalis secretome, considering that secretion is a time- and temperature-dependent process, to define the cutoff for secreted proteins...
December 12, 2017: Molecular & Cellular Proteomics: MCP
Kathrin Stavenhagen, H Mehmet Kayili, Stephanie Holst, Carolien Koeleman, Ruchira Engel, Diana Wouters, Sacha Zeerleder, Bekir Salih, Manfred Wuhrer
Human C1-inhibitor (C1-Inh) is a serine protease inhibitor and the major regulator of the contact activation pathway as well as the classical and lectin complement pathways. It is known to be a highly glycosylated plasma glycoprotein. However, both the structural features and biological role of C1-Inh glycosylation are largely unknown. Here, we performed for the first time an in-depth site-specific N- and O-glycosylation analysis of C1-Inh combining various mass spectrometric approaches, including C18-porous graphitized carbon (PGC)-LC-ESI-QTOF-MS/MS applying stepping-energy collision-induced dissociation (CID) and electron-transfer dissociation (ETD)...
December 12, 2017: Molecular & Cellular Proteomics: MCP
Xiaojing Wang, Simona G Codreanu, Bo Wen, Kai Li, Matthew Chambers, Daniel C Liebler, Bing Zhang
Alternative splicing dramatically increases transcriptome complexity but its contribution to proteome diversity remains controversial. Exon-exon junction spanning peptides provide direct evidence for the translation of specific splice isoforms and are critical for delineating protein isoform complexity. Here we found that junction-spanning peptides are underrepresented in publicly available mass spectrometry-based shotgun proteomics data sets. Further analysis showed that evolutionarily conserved preferential nucleotide usage at exon boundaries increases the occurrence of lysine- and arginine-coding triplets at the end of exons...
December 8, 2017: Molecular & Cellular Proteomics: MCP
Fan Liu, Philip Lössl, Beverley M Rabbitts, Robert S Balaban, Albert J R Heck
Mitochondria exert an immense amount of cytophysiological functions, but the structural basis of most of these processes is still poorly understood. Here we use cross-linking mass spectrometry to probe the organization of proteins in native mouse heart mitochondria. Our approach provides the largest survey of mitochondrial protein interactions reported so far. In total, we identify 3,322 unique residue-to-residue contacts involving half of the mitochondrial proteome detected by bottom-up proteomics. The obtained mitochondrial protein interactome gives insights in the architecture of defined protein assemblies, the sub-mitochondrial localization, and the mitochondrial localization of five proteins not yet included in the MitoCarta database...
December 8, 2017: Molecular & Cellular Proteomics: MCP
Xiaomin Zhao, Xiaoyuan Bai, Lijuan Guan, Juejun Li, Xiangjun Song, Xuelian Ma, Jianxiong Guo, Zhichao Zhang, Qian Du, Yong Huang, Dewen Tong
Transmissible gastroenteritis virus (TGEV), a member of the coronaviridae family, could cause fatal diarrhea of piglets and result in numerous economic losses. Previous studies demonstrated that TGEV infection could lead to mitochondrial damage and up-regulate miR-4331 level. So miR-4331 may play an important regulatory role in the control of mitochondrial function. To explore the potential role of miR-4331 in mitochondrial damage, we adopted a strategy consisting of quantitative proteomic analysis of porcine kidney (PK-15) cells in response to miR-4331 and TGEV infection...
December 7, 2017: Molecular & Cellular Proteomics: MCP
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