Construction Of E.coli Gene Modification Database And Analysis Of Integrated Networks

As commonly used strain in Prokaryotes, E.coli has been widely used as theobject of gene engineering. With the advent of post genomic and systems biology era,gene engineering starts to combine with systems biology, which promotes furtherdevelopment of E.coli’s gene modification to improve some target products’production, such as amino acids. As a result, the number of relevant literature andpatents has been rapidly increasing, which made all the information numerous andcomplex, which are hard to extract useful information. With the development ofBioinformatics, many biological network databases have been built in several decades,such as KEGG, EcoCyc. Based on the construction concepts of these databases, wehope to construct an E.coli gene modification network database for facilitatingbiologists who study gene engineering of E.coli.This study aimed to build an E.coli gene modification database with data andgraph combined. This database focused on genetically modified genes and targetproducts, including the information of E.coli from literature and patents we collected,as well as corresponding metabolic pathways charts of target products. This databasecontains engineered E.coli strains, gene IDs, the methods of gene modification, results,target products, products’ concentration, productivity and yield, as well as literatureand patents’ source and publish year. Target products in this database focus on aminoacids, especially threonine, lysine, also includes other products, such as ethanol, fattyacid, lactate. The methods of gene modification include deletion, modificationoverexpression of genes and new genes from other bacteria (such as pyc gene fromRhizobium etli). So far, we have collected nearly200published papers and patents,and organized the gene modification information of about60kinds of target products,as well as nearly genetically modified500genes from E.coli and other bacteria.Besides, we also studied on cellular networks of E.coli, namely metabolicnetwork, transcription regulation, signal transduction network and Protein-Proteininteraction data. We came up with a new method about the study of protein-proteininteraction, which can be used to predict protein interactions, guide wet experiments,verify the information on existing biological databases, such as RegulonDB, and alsowe predicted new two-component systems.