LmTDRM Database: A Comprehensive Database on Thiol Metabolic Gene/Gene Products in Listeria monocytogenes EGDe

Abstract

SummaryThere are a number of databases on the Listeria species and about their genome. However, these databases do not specifically address a set of network that is important in defence mechanism of the bacteria. Listeria monocytogenes EGDe is a well-established intracellular model organism to study host pathogenicity because of its versatility in the host environment. Here, we have focused on thiol disulphide redox metabolic network proteins, specifically in L. monocytogenes EGDe. The thiol redox metabolism is involved in oxidative stress mechanism and is found in all living cells. It functions to maintain the thiol disulphide balance required for protein folding by providing reducing power. Nevertheless, they are involved in the reversible oxidation of thiol groups in biomolecules by creating disulphide bonds; therefore, the term thiol disulphide redox metabolism (TDRM). TDRM network genes play an important role in oxidative stress mechanism and during host-pathogen interaction. Therefore, it is essential to have detailed information on these proteins with regard to other bacteria and its genome analysis to understand the presence of tRNA, transposons, and insertion elements for horizontal gene transfer. LmTDRM database is a new comprehensive web-based database on thiol proteins and their functions. It includes: Description, Search, TDRM analysis, and genome viewer. The quality of these data has been evaluated before they were aggregated to produce a final representation. The web interface allows for various queries to understand the protein function and their annotation with respect to their relationship with other bacteria. LmTDRM is a major step towards the development of databases on thiol disulphide redox proteins; it would definitely help researchers to understand the mechanism of these proteins and their interaction. Database URL: www.lmtdrm.com IntroductionBacteria during their interaction with the host or during other conditions generate reactive oxygen species (ROS) and reactive nitrogen species (RNS). These serve as secondary messengers and/or can also damage proteins, nucleic acids, and lipids [1,2]. To avoid cellular damage by these processes, most bacteria have developed a series of antioxidants that can convert ROS and RNS to unreactive derivatives. They are (i) a number of enzymes such as catalase, glutathione peroxidase, glutathione-S-transferase, thiol-specific peroxidase, methionine sulphoxide reductase, thioredoxin peroxidase, glutathione reductase, and glutaredoxins; (ii) various metal binding proteins such as ceruloplasmin, ferritin, transferrin, various metabolites, and cofactors (NADs, lipoic acid, uric acid, bilirubin, etc); (iii) a number of dietary components (vitamin A, C, E, quercetin, etc.) and (iv) metal ions (Mg 2+ , Mn 2+ , Zn 2+ ) with enzymes or metalloenzymes like superoxide dismutase. Among them, thiol proteins are the major ones [3,4].