Gel-based proteomics in disease research: Is it still valuable?

Kim, Yong In; Cho, Je‐Yoel

doi:10.1016/j.bbapap.2018.08.001

Cited by 35 publications

(26 citation statements)

References 97 publications

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“…Not surprisingly, we found 18 diglycine modification sites on a total of 12 histone isoforms and variants, including those of nine H2As (M5VKW3, M5VRK7, M5W1M5, M5W1N0, M5W1R5, M5WDC2, M5X0T3, M5X7W0 and M5Y070), one H2B (M5WQC2), one H3 (M5WKJ0) and one H4 (M5VRN0). These findings echoed several earlier profiling analyses that similarly indicated extensive ubiquitination of histone proteins 18,45,46 . More importantly, as shown in (Supplementary Table S5), the majority of these ubiquitinated lysine residues were revealed to be located at the C-terminal histone tails, known to play a critical role in nucleosome assembly and thus gene expression [47][48][49] .…”

Section: Discussionsupporting

confidence: 84%

Proteome-wide identification and functional analysis of ubiquitinated proteins in peach leaves

Song

Shi

Zou

et al. 2020

Sci Rep

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Ubiquitination is a critical post-translational modification machinery that governs a wide range of cellular functions by regulating protein homeostasis. Identification of ubiquitinated proteins and lysine residues can help researchers better understand the physiological roles of ubiquitin modification in different biological systems. In this study, we report the first comprehensive analysis of the peach ubiquitome by liquid chromatography-tandem mass spectrometry-based diglycine remnant affinity proteomics. Our systematic profiling revealed a total of 544 ubiquitination sites on a total of 352 protein substrates. Protein annotation and functional analysis suggested that ubiquitination is involved in modulating a variety of essential cellular and physiological processes in peach, including but not limited to carbon metabolism, histone assembly, translation and vesicular trafficking. Our results could facilitate future studies on how ubiquitination regulates the agricultural traits of different peach cultivars and other crop species.Peach is a highly popular and well-recognized fruit first cultivated in China during ancient times. It is considered an excellent source of vitamin C, niacin, potassium and dietary fiber. As a result, the recent global trend of healthy eating has greatly stimulated the demand for peach and the related food products. As of 2014, the combined area of peach orchards in China is estimated at around 7,260 square kilometers, with a total production of 12.4 million tons 1 . The long history of peach cultivation has resulted in hundreds of distinct cultivars. Peach growers have spent decades in a continuous quest to enhance the quality of different peach cultivars through crossbreeding. Recently, biotechnology-facilitated engineering has shown enormous promise in rapidly generating new peach varieties with desirable agricultural traits. Still, further accomplishments would depend on improved understanding of the diverse molecular pathways in peach and their connections to its physiology.Ubiquitination is one of the most critical post-translational modification mechanisms with a wide range of cellular functions that center on the control of protein load 2,3 . Ubiquitin is a small but abundantly present protein consisting of 76 amino acids with a C-terminal diglycine tail. The ubiquitination pathway is essentially an enzymatic cascade involving the cooperative action of three enzymes, including the E1, E2 and E3 ligases 2,4 . During this process, the C-terminal carboxyl group of ubiquitin is first adenylated by E1 in the presence of ATP and then forms a thioester linkage with the catalytic cysteine residue of the ligase 5 . The E1 then binds a second ubiquitin with its adenylation domain and recruits its cognate E2.This triggers a transthioesterification reaction where the E1-conjugated ubiquitin unit is transferred to the catalytic cysteine of the E2 6 . Finally, an E3 is involved in the transfer of ubiquitin from E2 to the ε-amino group of one or more lysine residues in the protein substrate 7...

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Section: Discussionsupporting

confidence: 84%

Proteome-wide identification and functional analysis of ubiquitinated proteins in peach leaves

Song

Shi

Zou

et al. 2020

Sci Rep

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“…Peptides go through the process of enrichment and cleanup. Then, dried peptides are resuspended and injected into LC-ms/ms [21]. Second, for In-sol digestion, lysed exosomes are kept in an aqueous state.…”

Section: Exosome Isolation and Protein Digestion For Proteomicsmentioning

confidence: 99%

“…Overall, each method has its advantages and disadvantages. Here, we summarized methodological properties in Table 1 [21,22]. Cho (2015) et al, suggested that the biggest issues in exosome research arise from the exosome isolation method.…”

Section: Exosome Isolation and Protein Digestion For Proteomicsmentioning

confidence: 99%

Exploring the key communicator role of exosomes in cancer microenvironment through proteomics

Kim

Cho

2019

Proteome Sci

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There have been many attempts to fully understand the mechanism of cancer behavior. Yet, how cancers develop and metastasize still remain elusive. Emerging concepts of cancer biology in recent years have focused on the communication of cancer with its microenvironment, since cancer cannot grow and live alone. Cancer needs to communicate with other cells for survival, and thus they secrete various messengers, including exosomes that contain many proteins, miRNAs, mRNAs, etc., for construction of the tumor microenvironment. Moreover, these intercellular communications between cancer and its microenvironment, including stromal cells or distant cells, can promote tumor growth, metastasis, and escape from immune surveillance. In this review, we summarized the role of proteins in the exosome as communicators between cancer and its microenvironment. Consequently, we present cancer specific exosome proteins and their unique roles in the interaction between cancer and its microenvironment. Clinically, these exosomes might provide useful biomarkers for cancer diagnosis and therapeutic tools for cancer treatment.

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“…2DE is unrivaled by other proteomic approach because it consents the simultaneous detection and quantification of thousands of proteins isoforms, not predictable through other techniques including genome analysis [41,42].…”

Section: Author Detailsmentioning

confidence: 99%

2D Gel Electrophoresis to Address Biological Issues

Scumaci¹,

Cuda²

2019

Proteomics Technologies and Applications

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Two-dimensional (2D) gel electrophoresis is a high-resolution technique for the study of proteome. This chapter describes how it can be applied to characterize specific differences in the proteome profile of breast cancer cells following gene target interference. The proteome is the complete set of proteins encoded by a genome, and proteomic analysis consists in profiling the whole proteins expressed in a given cell, tissue, organ, or organism. Proteomic expression has the main purpose of qualitatively and quantitatively comparing proteins expressed under physiological and/or pathological conditions. Although it is not the unique approach used in modern proteomics, two-dimensional electrophoresis (2DE) is unrivaled allowing simultaneous separation of thousands of proteins and the detection of posttranslational modification, not predictable through genome analysis. 2DE combines two physical principles to separate complex protein mixtures: the isoelectric point and the molecular weight. The result is a gel map in which each protein isoform present in the sample can be visualized as a spot, analyzed, quantified, and identified by mass spectrometry analysis. Here we outline features and advantages of the 2DE-based proteomic approach and we describe how 2DE meets biochemistry and molecular biology to address specific issues.

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Gel-based proteomics in disease research: Is it still valuable?

Cited by 35 publications

References 97 publications

Proteome-wide identification and functional analysis of ubiquitinated proteins in peach leaves

Proteome-wide identification and functional analysis of ubiquitinated proteins in peach leaves

Exploring the key communicator role of exosomes in cancer microenvironment through proteomics

2D Gel Electrophoresis to Address Biological Issues

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