Community-Based Network Study of Protein-Carbohydrate Interactions in Plant Lectins Using Glycan Array Data

Malik, Adeel; Lee, Juyong; Lee, Jooyoung

doi:10.1371/journal.pone.0095480

Cited by 20 publications

(14 citation statements)

References 76 publications

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“…Network-based studies offer a framework to get a broad overview of data that includes several interacting groups. This potential of a community-based network analysis allows researchers to investigate and compare a diverse set of proteins and their interactions within the context of modules or communities identified in the network [ 54 ]. Therefore, we attempted to identify the modular structure of the interaction network and identified that the network could be divided into 12 modules or communities (clusters) ( Figure 5 ).…”

Section: Resultsmentioning

confidence: 99%

Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets

Malik

Kim

2021

Biology

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Chinese mitten crab (CMC) or Eriocheir sinensis is a strong osmoregulator that can keep rigorous cellular homeostasis. CMC can flourish in freshwater, as well as seawater, habitats and represents the most important species for freshwater aquaculture. Salt stress can have direct effects on several stages (e.g., reproduction, molting, growth, etc.) of the CMC life cycle. To get a better overview of the genes involved in the gills of CMC under different salinity conditions, we conducted an RNA-Seq meta-analysis on the transcriptomes of four publicly available datasets. The meta-analysis identified 405 differentially expressed transcripts (DETs), of which 40% were classified into various transporter classes, including accessory factors and primary active transporters as the major transport classes. A network analysis of the DETs revealed that adaptation to salinity is a highly regulated mechanism in which different functional modules play essential roles. To the best of our knowledge, this study is the first to conduct a transcriptome meta-analysis of gills from crab RNA-Seq datasets under salinity. Additionally, this study is also the first to focus on the differential expression of diverse transporters and channels (transportome) in CMC. Our meta-analysis opens new avenues for a better understanding of the osmoregulation mechanism and the selection of potential transporters associated with salinity change.

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Section: Resultsmentioning

confidence: 99%

Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets

Malik

Kim

2021

Biology

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“…Expression of the Arabidopsis homolog PP2-A1 is enhanced by ethylene treatment and Pseudomonas infection [40]. In a computational study [106] Arabidopsis PP2-A1 was shown to exhibit specificity for a diverse range of glycans including chitin oligomers and the Man 3 GlcNAc 2 core of high mannose N -glycans [106,107]. Consistent with a role in plant defense, PP2-A1 represses feeding of the aphid Myzus persicae and aphid borne yellow virus transmission [40].…”

Section: Non-prr Function Of Lectins In the Immune Responsementioning

confidence: 99%

Protein-Carbohydrate Interactions as Part of Plant Defense and Animal Immunity

Schutter

Damme

2015

Molecules

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Abstract:The immune system consists of a complex network of cells and molecules that interact with each other to initiate the host defense system. Many of these interactions involve specific carbohydrate structures and proteins that specifically recognize and bind them, in particular lectins. It is well established that lectin-carbohydrate interactions play a major role in the immune system, in that they mediate and regulate several interactions that are part of the immune response. Despite obvious differences between the immune system in animals and plants, there are also striking similarities. In both cases, lectins can play a role as pattern recognition receptors, recognizing the pathogens and initiating the stress response. Although plants do not possess an adaptive immune system, they are able to imprint a stress memory, a mechanism in which lectins can be involved. This review will focus on the role of lectins in the immune system of animals and plants.

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“…To understand how glycosylation is functionally involved in these physiological and pathological processes, knowledge of the three-dimensional structures of glycans, their dynamic properties, and their interactions with proteins is essential (Malik and Ahmad 2007;Nagae and Yamaguchi 2012;Malik et al 2014;Jo et al 2016;Qi et al 2016;Dong et al 2018). Experimental methods such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy have been widely used to provide the atomic details of biomolecular structural information (Wormald et al 2002).…”

Section: Introductionmentioning

confidence: 99%

CHARMM-GUIGlycan Modelerfor modeling and simulation of carbohydrates and glycoconjugates

et al. 2019

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Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. Computational modeling and molecular simulation have become an essential tool complementary to experimental methods. Here, we present a computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems. In our previous study, we developed Glycan Reader, a web-based tool for detecting carbohydrate molecules from a PDB structure and generation of simulation system and input files. As integrated into Glycan Reader in CHARMM-GUI, Glycan Modeler (Glycan Reader & Modeler) enables to generate the structures of glycans and glycoconjugates for given glycan sequences and glycosylation sites using PDB glycan template structures from Glycan Fragment Database (http://glycanstructure.org/ fragment-db). Our benchmark tests demonstrate the universal applicability of Glycan Reader & Modeler to various glycan sequences and target proteins. We also investigated the structural properties of modeled glycan structures by running 2-μs molecular dynamics simulations of HIV envelope protein. The simulations show that the modeled glycan structures built by Glycan Reader & Modeler have the similar structural features compared to the ones solved by X-ray crystallography. We also describe the representative examples of glycoconjugate modeling with video demos to illustrate the practical applications of Glycan Reader & Modeler. Glycan Reader & Modeler is freely available at http://charmm-gui.org/input/glycan.

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Community-Based Network Study of Protein-Carbohydrate Interactions in Plant Lectins Using Glycan Array Data

Cited by 20 publications

References 76 publications

Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets

Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets

Protein-Carbohydrate Interactions as Part of Plant Defense and Animal Immunity

CHARMM-GUIGlycan Modelerfor modeling and simulation of carbohydrates and glycoconjugates

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