e-Membranome: A Database for Genome-Wide Analysis of Escherichia coli Outer Membrane Proteins

Abstract

Objectives: Lectin-like adhesins of enteric bacterial pathogens such as Escherichia coli are an attractive target for vaccine or drug development. Here, we have developed e-Membranome as a database of genome-wide putative adhesins in Escherichia coli (E. coli). Methods: The outer membrane adhesins were predicted from the annotated genes of Escherichia coli strains using the PSORTb program. Further analysis was performed using Interproscan and the String database. The candidate proteins can be investigated for homology modeling of the three-dimensional (3D) structure (I-TASSER version 5.1), epitope region (ABCpred), and the glycan array. Results: e-Membranome is implemented using the Django (version 2.2.5) framework. The Web Application Server Apache Tomcat 6.0 is integrated in the platform on Ubuntu Linux (version 16.04). MySQL database (version 5.7) is used as a database engine. The information of homology model of the 3D structure, epitope region, and affinity information from the glycan array will be stored in the e-Membranome database. As a case study, we performed a genome-wide screening of outer membrane-embedded proteins from the annotated genes of E. coli using the e-Membranome pipeline. Conclusion: This platform is expected to be a valuable resource for advancing research of outer membrane proteins for the construction of lectin-glycan interaction network of E. coli. In addition, the e-Membranome pipeline can be extended to other similar biological systems that need to address host-pathogen interactions.

Glycan-Adhering Lectins and Experimental Evaluation of a Lectin FimH Inhibitor in Enterohemorrhagic Escherichia coli (EHEC) O157:H7 Strain EDL933

“…Several studies have elucidated the interaction between pathogen lectins and host glycans during the early stages of infection [ 6 , 7 , 26 ]. We established an experimental strategy and method to characterize the systemic LGI of pathogenic intestinal bacteria in the gastrointestinal tract.…”

“…These protein-ligand and sugar chain-lectin ligand docking approaches were used to estimate the binding structure of ligands. Additionally, these strategies were used to identify and optimize binding sites and candidate materials [ 6 , 7 , 26 ].…”

“…Bacterial adhesins, such as lectin, are potential therapeutic targets and can contribute to an understanding of bacterial evolution. In our previous study, we constructed the LGI network of EHEC [ 6 ] and developed an e-Membranome database [ 26 ]. Using an e-Membranome pipeline, we predicted putative adhesins from EHEC genomes and deposited them onto a public database.…”

Systemic Lectin-Glycan Interaction of Pathogenic Enteric Bacteria in the Gastrointestinal Tract

“…PSORTb software is used to predict outer membrane adhesins from annotated genes in E. coli strains. A target outer membrane protein located in the outer membrane is predicted based on intracellular localization analysis using E. coli genetic information, and a candidate outer membrane protein, which is a lipid protein, is predicted as the E. coli outer membrane protein by using a specific formula [55,56]. Figure 3 (bottom) shows a gene-based screening method that is used to search for known adhesins in SugarBindDB.…”