Global Identification of Prokaryotic Glycoproteins Based on an Escherichia coli Proteome Microarray

Wang, Zong xiu; Deng, Rui ping; Jiang, He; Guo, Shu Juan; Le, Huang Ying; Zhao, Xiao Dong; Chen, Chien Sheng; Zhang, Ji bin; Tao, Sheng Ce

doi:10.1371/journal.pone.0049080

Cited by 10 publications

(9 citation statements)

References 55 publications

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“…As yet relatively unexplored, these modifications have the potential to impact important processes such as microbe–host interactions and immune escape mechanisms. Mostly driven by the discovery of protein glycans in diverse pathogenic microbes (Morrison and Imperiali 2014), there is now an increasing body of evidence of protein glycosylation, both from the domains of Bacteria and Archaea (here is a selection of most relevant reviews from the past five years: (Børud et al 2011; Giltner, Nguyen and Burrows 2012; Wang et al 2012; Eichler 2013; Iwashkiw et al 2013; Messner, Schäffer and Kosma 2013; Meyer and Albers 2013; Nothaft and Szymanski 2013; Jarrell et al 2014; Tytgat and Lebeer 2014; Kandiba and Eichler 2015; Naegeli and Aebi 2015; Lu, Li and Shao 2015). As more prokaryotic protein glycosylation systems are being identified and characterised, the central question arises as to what governs the biosynthesis and prevalence of particular protein glycans (Table 1).…”

Section: Introductionmentioning

confidence: 99%

Emerging facets of prokaryotic glycosylation

Schäffer¹,

Messner²

2016

FEMS Microbiology Reviews

117

116

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Glycosylation of proteins is one of the most prevalent post-translational modifications occurring in nature, with a wide repertoire of biological implications. Pathways for the main types of this modification, the N-and O-glycosylation, can be found in all three domains of life-the Eukarya, Bacteria and Archaea-thereby following common principles, which are valid also for lipopolysaccharides, lipooligosaccharides and glycopolymers. Thus, studies on any glycoconjugate can unravel novel facets of the still incompletely understood fundamentals of protein N-and O-glycosylation. While it is estimated that more than two-thirds of all eukaryotic proteins would be glycosylated, no such estimate is available for prokaryotic glycoproteins, whose understanding is lagging behind, mainly due to the enormous variability of their glycan structures and variations in the underlying glycosylation processes. Combining glycan structural information with bioinformatic, genetic, biochemical and enzymatic data has opened up an avenue for in-depth analyses of glycosylation processes as a basis for glycoengineering endeavours. Here, the common themes of glycosylation are conceptualised for the major classes of prokaryotic (i.e. bacterial and archaeal) glycoconjugates, with a special focus on glycosylated cell-surface proteins. We describe the current knowledge of biosynthesis and importance of these glycoconjugates in selected pathogenic and beneficial microbes.

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Section: Introductionmentioning

confidence: 99%

Emerging facets of prokaryotic glycosylation

Schäffer¹,

Messner²

2016

FEMS Microbiology Reviews

117

116

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“…The microarrays were spun dry at 250 g for 3 min and were scanned with a GenePix 4200A microarray scanner (Molecular Devices, CA, USA) to visualize and record the results. The proteome microarray data were extracted with GenePix Pro 6.0 (Molecular Devices, CA, USA) and processed as previously described (Wang et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

“…The experiment was designed to conduct two separated proteome microarray assays. The proteome microarray data were extracted with GenePix Pro 6.0 and processed as previously reported (Jeong et al, 2012; Wang et al, 2012). For human proteome microarray data analysis, the signal-to-noise ratio (SNR) was defined as the ratio of median of foreground signal (F-median) deducted of median of Background signal (B-median) to B-median [(F-median-B-median)/B-median] and was calculated for each protein.…”

Section: Methodsmentioning

confidence: 99%

A Two-Way Proteome Microarray Strategy to Identify Novel Mycobacterium tuberculosis-Human Interactors

Cao¹,

Lyu²,

Jia³

et al. 2019

Front. Cell. Infect. Microbiol.

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Tuberculosis (TB) is still a serious threat to human health which is caused by mycobacterium tuberculosis ( Mtb ). The main reason for failure to eliminate TB is lack of clearly understanding the molecular mechanism of Mtb pathogenesis. Determining human Mtb -interacting proteins enables us to characterize the mechanism and identify potential molecular targets for TB diagnosis and treatment. However, experimentally systematic Mtb interactors are not readily available. In this study, we performed an unbiased, comprehensive two-way proteome microarray based approach to systematically screen global human Mtb interactors and determine the binding partners of Mtb effectors. Our results, for the first time, screened 84 potential human Mtb interactors. Bioinformatic analysis further highlighted these protein candidates might engage in a wide range of cellular functions such as activation of DNA endogenous promoters, transcription of DNA/RNA and necrosis, as well as immune-related signaling pathways. Then, using Mtb proteome microarray followed His tagged pull-down assay and Co-IP, we identified one interacting partner (Rv0577) for the protein candidate NRF1 and three binding partners (Rv0577, Rv2117, Rv2423) for SMAD2, respectively. This study gives new insights into the profile of global Mtb interactors potentially involved in Mtb pathogenesis and demonstrates a powerful strategy in the discovery of Mtb effectors.

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“…The proteome microarray data were extracted with GenePix Pro 6.0 and processed as previously described . In brief, the signal‐to‐noise ratio (S/N) of each spot was set as F532 Median/B532 Median.…”

Section: Methodsmentioning

confidence: 99%

Global identification of O‐GlcNAc transferase (OGT) interactors by a human proteome microarray and the construction of an OGT interactome

Deng

Guo

et al. 2014

Proteomics

Self Cite

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O-Linked β-N-acetylglucosamine (O-GlcNAcylation) is an important protein PTM, which is very abundant in mammalian cells. O-GlcNAcylation is catalyzed by O-GlcNAc transferase (OGT), whose substrate specificity is believed to be regulated through interactions with other proteins. There are a handful of known human OGT interactors, which is far from enough for fully elucidating the substrate specificity of OGT. To address this challenge, we used a human proteome microarray containing ~17,000 affinity-purified human proteins to globally identify OGT interactors and identified 25 OGT-binding proteins. Bioinformatics analysis showed that these interacting proteins play a variety of roles in a wide range of cellular functions and are highly enriched in intra-Golgi vesicle-mediated transport and vitamin biosynthetic processes. Combining newly identified OGT interactors with the interactors identified prior to this study, we have constructed the first OGT interactome. Bioinformatics analysis suggests that the OGT interactome plays important roles in protein transportation/localization and transcriptional regulation. The novel OGT interactors that we identified in this study could serve as a starting point for further functional analysis. Because of its high-throughput and parallel analysis capability, we strongly believe that protein microarrays could be easily applied for the global identification of regulators for other key enzymes.

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Global Identification of Prokaryotic Glycoproteins Based on an Escherichia coli Proteome Microarray

Cited by 10 publications

References 55 publications

Emerging facets of prokaryotic glycosylation

Emerging facets of prokaryotic glycosylation

A Two-Way Proteome Microarray Strategy to Identify Novel Mycobacterium tuberculosis-Human Interactors

Global identification of O‐GlcNAc transferase (OGT) interactors by a human proteome microarray and the construction of an OGT interactome

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