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Bacterial protein profiling——Comparison of Three Mass Spectrometry Methodologies

高等学校化学学报 2024年第11期45卷 158-173页

作者： JIANG Yan CHEN Yanlin SONG Gaoyu CHEN Yanyan BAI Jing ZHU Yingdi LI Juan School of Life Sciences Faculty of MedicineTianjin UniversityTianjin 300072China School of Molecular Medicine Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China Hangzhou Institute of Medicine(HIM) Chinese Academy of SciencesHangzhou 310022China School of Information Engineering Zhejiang University of TechnologyHangzhou 310023China

profiling the protein composition of bacteria is essential for understanding their biology,physiology and interaction with *** spectrometry has become a pivotal tool for protein analysis,facilitating the examination of expression levels,molecular masses and structural *** this study,we compared the performance of three widely-used mass spectrometry methods,i.e.,matrix-assisted laser desorption/ionization(MALDI)protein fingerprinting,top-down proteomics and bottom-up proteomics,in the profiling of bacterial protein *** was revealed that bottom-up proteomics provided the highest protein coverage and exhibited the greatest protein profile overlap between bacterial *** contrast,MALDI protein fingerprinting demonstrated superior detection reproducibility and effectiveness in distinguishing between bacterial *** top-down proteomics identified fewer proteins than bottom-up approach,it complemented MALDI fingerprinting in the discovery of bacterial protein markers,both favoring abundant,stable,and hydrophilic bacterial ribosomal *** study represents the most systematic and comprehensive comparison of mass spectrometry-based protein profiling methodologies to *** provides valuable guidelines for the selection of appropriate profiling strategies for specific analytical *** will facilitate studies across various fields,including infection diagnosis,antimicrobial resistance detection and pharmaceutical target discovery.

关键词： Bacteria protein profiling Mass spectrometry

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Proteoform Stability profiling Reveals O-GlcNAcylation as a General protein Stabilization Signal

Proteoform Stability Profiling Reveals O-GlcNAcylation as a ...

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第十一届全国化学生物学学术会议

作者： Jingyang Wang Wei Qin Linghang Peng Xin Zeng Wei Lin Ke Qin Xinqi Fan Weiyao Hong Chu Wang Xing Chen College of Chemistry and Molecular Engineering Peking University Peking-Tsinghua Center for Life Sciences Peking University Synthetic and Functional Biomolecules Center Peking University Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University

Cancer cells endure higher internal proteotoxic stresses through upregulating protein quality control components, regulated by many pathways including post-translational modifications. Glucose-dependent O-GlcNAcylation is elevated on thousands of intracellular proteins in cancer cells, while the direct impact of O-GlcNAc on substrates remained elusive. Here, we developed proteoform stability profiling（PSP） strategies and surprisingly found the degradation of O-GlcNAcylated proteoforms is generally slower. Moreover, proteoform thermal stability profiling reveals O-GlcNAcylated proteoforms also exhibit higher structural stability in general. The extent of protein stabilization is determined by O-GlcNAc localization at intrinsic disorder regions（IDRs） and high stoichiometry, which happen on many oncoproteins including CUGBP1. Most importantly, O-GlcNAc level responds to drugs impairing proteostasis and O-GlcNAc inhibition sensitizes cancer cells to proteotoxic chemotherapies in vivo. These findings demonstrate the physiological and oncogenic roles of O-GlcNAcylation as a protein stabilization signal and highlight the potential of PSP methodology for evaluating the stability of other proteoforms.

关键词： Proteostasis O-GlcNAc protein profiling Stress response Cancer chemotherapy

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The circ_0002538/miR-138-5p/plasmolipin axis regulates Schwann cell migration and myelination in diabetic peripheral neuropathy

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Neural Regeneration Research 2023年第7期18卷 1591-1600页

作者： Yu-Tian Liu Zhao Xu Wei Liu Sen Ren He-Wei Xiong Tao Jiang Jing Chen Yu Kang Qian-Yun Li Zi-Han Wu Hans-GüNther Machens Xiao-Fan Yang Zhen-Bing Chen Department of Hand Surgery Union HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceChina Department of Geriatrics Renmin Hospital of Wuhan UniversityWuhanHubei ProvinceChina Department of Plastic and Hand Surgery Technical University of MunichMunichGermany

Circular RNAs(circRNAs)play a vital role in diabetic peripheral ***,their expression and function in Schwann cells in individuals with diabetic peripheral neuropathy remain poorly ***,we performed protein profiling and circRNA sequencing of sural nerves in patients with diabetic peripheral neuropathy and *** profiling revealed 265 differentially expressed proteins in the diabetic peripheral neuropathy *** Ontology indicated that differentially expressed proteins were mainly enriched in myelination and mitochondrial oxidative phosphorylation.A real-time polymerase chain reaction assay performed to validate the circRNA sequencing results yielded 11 differentially expressed ***_0002538 was markedly downregulated in patients with diabetic peripheral *** in vitro experiments showed that overexpression of circ_0002538 promoted the migration of Schwann cells by upregulating plasmolipin(PLLP)***,overexpression of circ_0002538 in the sciatic nerve in a streptozotocin-induced mouse model of diabetic peripheral neuropathy alleviated demyelination and improved sciatic nerve *** results of a mechanistic experiment showed that circ_0002538 promotes PLLP expression by sponging miR-138-5p,while a lack of circ_0002538 led to a PLLP deficiency that further suppressed Schwann cell *** findings suggest that the circ_0002538/miR-138-5p/PLLP axis can promote the migration of Schwann cells in diabetic peripheral neuropathy patients,improving myelin sheath structure and nerve ***,this axis is a potential target for therapeutic treatment of diabetic peripheral neuropathy.

关键词： circ_0002538 circRNA sequencing competing endogenous RNAs demyelination diabetic peripheral neuropathy miR-138-5 myelination plasmolipin protein profiling Schwann cells

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Current status and prospects of clinical proteomics studies on detection of colorectal cancer:Hopes and fears

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World Journal of Gastroenterology 2006年第41期12卷 6594-6601页

作者： ME de Noo RAEM Tollenaar AM Deelder LH Bouwman Department of Surgery Leiden University Medical CenterLeidenThe Netherlands Biomolecular Mass Spectrometry Unit Department of ParasitologyLeiden University Medical CenterLeidenThe Netherlands

Colorectal adenocarcinoma （CRC） is the third most common type of cancer and the fourth most frequent cause of death due to cancer worldwide. Given the natural history of CRC, early diagnosis appears to be the most appropriate tool to reduce disease-related mortality. A field of recent interest is clinical proteomics, which was reported to lead to high sensitivity and specificities for early detection of several solid tumors. This emerging field uses mass spectrometry-based protein profiles/patterns of easy accessible body fluids to distinguish cancer from non-cancer patients. These discrepancies may be a result of：（i） proteins being abnormally produced or shed and added to the serum proteome, （2） proteins clipped or modified as a consequence of the disease process, or （3） proteins subtracted from the proteome owing to disease-related proteolytic degradation pathways. Therefore, protein pattern diagnostics would provide easy and reliable tools for detection of cancer. This paper focuses on the current status of clinical proteomics research in oncology and in colorectal cancer especially, and will reflect on pitfalls and fears in this relatively new area of clinical medicine, which are reproducibility issues and pre-analytical factors, statistical issues, and identification and nature of discriminating proteins/peptides.

关键词： Proteomics Colorectal cancer protein profiling Diagnosis Biomarkers Statistical issues

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Cancer:A proteomic disease

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Science China(Life Sciences) 2011年第5期54卷 403-408页

作者： LI GuoQing XIAO ZheFeng LIU JianPing LI Cui LI Feng CHEN ZhuChu Key Laboratory of Cancer Proteomics of Chinese Ministry of Health Xiangya Hospital Central South University Changsha 410008 China Department of Biology School of Pharmacy and Life Science University of South China Hengyang 421001 China

The development of cancer is a pathological process involving multiple environmental carcinogenic factors and genetic *** decades,cancer researchers have focused on genomic and transcriptomic *** completion of the Human Genome Project has opened the door to the post-genome era and *** play a critical role in tumorigenesis and influence the differences between normal cells and malignant *** report proposes the concept that cancer is a proteomic *** concept is based on examining protein expression profiles,post-translational modifications,and protein-protein interactions in carcinogenesis using recent advances in comparative,functional and structural *** approach provides a new way of viewing carcinogenesis,presents new clues in biomarker discovery for cancer diagnosis and therapy,and reveals important scientific findings and their significance to clinical applications.

关键词： cancer proteomic disease protein profiling modification-specific proteome protein-protein interaction

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Physiological Evaluation of Wheat (<i>Triticum aestivum</i>L.) Genotypes at Pre-Anthesis Stage under Heat Stress Conditions

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American Journal of Plant Sciences 2021年第12期12卷 1780-1790页

作者： Munazza Nazir Asghari Bano Faizan Ullah Samiullah Khan Naeem Khan Department of Botany University of Azad Jammu & Kashmir Muzaffarabad Azad Kashmir Pakistan Department of Biosciences Quaid Avenue University of Wah Wah Cantt Pakistan Department of Botany University of Science and Technology Bannu Pakistan Department of Agronomy University of Haripur Haripur Pakistan Department of Agronomy University of Florida Gainesville FL USA

Experiments were conducted to analyze effects of high temperature stress on wheat at pre-anthesis growth stage. Twenty four wheat genotypes exposed to a sub optimal temperature (>35°C) which showed altered physiological, biochemical and agronomic characteristics. Accumulation of proline, presence of new protein bands and higher antioxidant enzyme activity in leaves of G.7 and G.17 reflects their better adaptive response under heat stress conditions. G.17 and G.19 showed least reduction in number of spikelets per spike, biological yield and 100 grain weight. It was inferred that the genotypes G.7, G.17 and G.19 exhibited greater heat tolerance and could be recommended for cultivation under heat stress conditions.

关键词： Heat Stress Tolerance Mechanisms protein profiling Osmolytes

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