Proteomic Analysis of the HCV Encoded Peptide NS5 A Cellular Protein Complex

Aneuploidy, a state of chromosome imbalance, is a hallmark of human tumors, but its role in cancer still remains to be fully elucidated. To understand the consequences of whole chromosome-level aneuploidies on the proteome, we integrated aneuploidy, transcriptomic and proteomic data from hundreds of TCGA/CPTAC tumor samples. We found a surprisingly large number of expression changes happened on other, non-aneuploid chromosomes. Moreover, we identified an association between those changes and co-complex members of proteins from aneuploid chromosomes. This co-abundance association is tightly regulated for aggregation-prone aneuploid proteins and those involved in a smaller number of complexes. On the other hand, we observe that complexes of the cellular core machinery are under functional selection to maintain their stoichiometric balance in aneuploid tumors. Ultimately, we provide evidence that those compensatory and functional maintenance mechanisms are established through post-transcriptional control and that the degree of success of a tumor to deal with aneuploidy-induced stoichiometric imbalance impacts the activation of cellular protein degradation programs and patient survival.

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Quantitative Proteomic Analysis of Duck Embryo Fibroblasts Infected With Novel Duck Reovirus

Frontiers in Veterinary Science ◽

10.3389/fvets.2020.577370 ◽

2020 ◽

Vol 7 ◽

Author(s):

Yudong Yang ◽

Lin Li ◽

Xingpo Liu ◽

Meijie Jiang ◽

Jun Zhao ◽

...

Keyword(s):

Proteomic Analysis ◽

Cellular Protein ◽

Economic Losses ◽

The Novel ◽

Quantitative Proteomic Analysis ◽

Interferon Stimulated Genes ◽

Proteomic Data ◽

Pekin Ducks ◽

Duck Embryo ◽

Embryo Fibroblasts

The novel duck reovirus (NDRV) can cause hemorrhage and necrosis on the spleen of Pekin ducks; this disease has resulted in great economic losses to the duck industry. However, the molecular pathogenesis of NDRV remains poorly understood. In the current study, the quantitative proteomic analysis of NDRV-infected duck embryo fibroblasts was performed to explore the cellular protein changes in response to viral infection through iTRAQ coupled with the liquid chromatography (LC)–tandem mass spectrometry (MS/MS) method. A total of 6,137 proteins were obtained in cell samples at 24 h post-infection. Of these, 179 differentially expressed proteins (DEPs) were identified (cutoff set to 1.5-fold change), including 89 upregulated and 90 downregulated proteins. Bioinformatics analysis showed that DEPs can be divided into the cellular component, molecular function, and biological process; they were mainly involved in signal transduction, infectious diseases, cell growth and death, and the immune system. The subcellular localization of most proteins was in the cytoplasm. Importantly, the expressions of signal transducer and activator of transcription 1 (STAT1) and various interferon-stimulated genes (ISGs) were upregulated after NDRV infection. The mRNA transcripts of some ISGs were consistent with proteomic data, showing an increased trend. Results of our study suggested that NDRV infection can elicit strong expression changes of cellular proteins and activate the expression of ISGs from the point of quantitative proteomic analysis. The study provides a new insight into the understanding of NDRV pathogenesis.

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Proteomic analysis of cellular protein expression profiles in response to grass carp reovirus infection

Fish & Shellfish Immunology ◽

10.1016/j.fsi.2015.03.010 ◽

2015 ◽

Vol 44 (2) ◽

pp. 515-524 ◽

Cited By ~ 13

Author(s):

Dan Xu ◽

Lang Song ◽

Hao Wang ◽

Xiaoyan Xu ◽

Tu Wang ◽

...

Keyword(s):

Protein Expression ◽

Grass Carp ◽

Proteomic Analysis ◽

Expression Profiles ◽

Cellular Protein ◽

Grass Carp Reovirus ◽

Reovirus Infection ◽

Protein Expression Profiles

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Rapid extraction and kinetic analysis of protein complexes from single cells

10.1101/2021.07.07.451367 ◽

2021 ◽

Author(s):

Sena Sarıkaya ◽

Daniel J Dickinson

Keyword(s):

Single Molecule ◽

Protein Complex ◽

Cell Biology ◽

Dynamic Range ◽

Protein Complexes ◽

Single Cells ◽

Cell Lysis ◽

Cellular Protein ◽

In Vitro Assays

Proteins contribute to cell biology by forming dynamic, regulated interactions, and measuring these interactions is a foundational approach in biochemistry. We present a rapid, quantitative in vivo assay for protein-protein interactions, based on optical cell lysis followed by time-resolved single-molecule analysis of protein complex binding to an antibody-coated substrate. We show that our approach has better reproducibility, higher dynamic range, and lower background than previous single-molecule pull-down assays. Furthermore, we demonstrate that by monitoring cellular protein complexes over time after cell lysis, we can measure the dissociation rate constant of a cellular protein complex, providing information about binding affinity and kinetics. Our dynamic single-cell, single-molecule pull-down method thus approaches the biochemical precision that is often sought from in vitro assays, while being applicable to native protein complexes isolated from single cells in vivo.

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TMT-Based Quantitative Proteomic Analysis of Intestinal Organoids Infected by Listeria monocytogenes with Different Virulence

10.1101/2020.06.21.164061 ◽

2020 ◽

Author(s):

Jie Huang ◽

Cong Zhou ◽

Guanghong Zhou ◽

Keping Ye

Keyword(s):

Listeria Monocytogenes ◽

Proteomic Analysis ◽

High Performance ◽

Virulent Strain ◽

Cellular Protein ◽

Quantitative Proteomic Analysis ◽

Intestinal Organoids ◽

Food Borne ◽

Differential Proteins ◽

Fold Change Cutoff

AbstractListeria monocytogenes (Lm) is an opportunistic food-borne pathogen that cause listeriosis. L. monocytogenes belonged to different serovars presents with different virulence in the host and caused different host reactions. To investigate the remodeling of host proteome by differently toxic strains, the cellular protein responses of intestinal organoids were analyzed using TMT labeling and high performance liquid chromatography-mass spectrometry. Quantitative proteomic analysis revealed 6564 differentially expressed proteins, of which 5591 proteins were quantified. The fold-change cutoff was set at 1.3 (Lm vs control), the virulent strain caused 102 up-regulated proteins and 52 down-regulated proteins, while the low virulent strain caused 188 up-regulated proteins and 25 down-regulated proteins. These identified proteins were involved in the regulation of essential processes such as biological metabolism, energy metabolism, and immune system process. Some selected proteins were screened by Real-time PCR and Western blotting. These results revealed that differently toxic L. monocytogenes induced similar biological functions and immune responses while had different regulation on differential proteins in the pathway.

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