Bioinformatical Analysis On Toxin-antitoxin System In Klebsiella Pneumoniae

Klebsiella pneumoniae is an increasingly important human pathogenic bacteria. It is responsible for nosocomial and community-acquired infections in diverse sites in human body, such as the urinary tract, upper respiratory tract, blood stream and etc. This gramnegative bacterium species became more concerning for its dramatically increased level of antimicrobial resistance, particularly carbapenems.Toxin-antitoxin(TA) system, widespread in bacteria and archaea, is small genetic elements composed of a stable toxin, and a relatively unstable antitoxin which inhibits toxin in multiple ways. TA system has been classified into five types according to the molecular nature of the antitoxin and its mode of interaction with the toxin. It shows that TA system is related to plasmid maintenance, stress resistance, regulation of biofilm formation, programmed cell death. In addition, Hip AB TA system was reported to be involved in the formation of drug tolerant persister cells.The published integrated database TADB for type II TA systems has been cited over 70 times, as it provides a unique compilation of both predicted and experimentally verified type II TA loci. We herein completed the reconstruction and data migration to keep TADB in good working status, and developed a upgraded version for it. 202 new experimentally verified information of TA systems, including type I, III, IV and V TA systems, have been added to achieve the upgradation, which were manually collected by text-mining..An identification tool for type II TA systems, TAfinder, has been developed partly based on data from TADB in this study. Type II TA systems are predicted by TAfinder mainly based on the sequence similarity and domain conservation. Compared with previous works, TAfinder identifies potential TA systems utilizing both standard BLASTP and Hidden Markov Model approach, taking both sequence similarity and conserved domains into account. Apart from the sequence alignment, other TA features are also extracted and applied such as sequence characters, physicochemical features and established a family-specific scoring system. TAfinder provides a functionally flexible interface withmultiple biologist-friendly inputs options. Partial completed sequences such as contigs and scaffolds are also supported. Additional analysis modules including TAfinderCompare and TAfinder-Context are also developed and integrated in TAfinder. TAfinderCompare can show the distribution of certain TA system in subject genomes. Meanwhile, TAfinder-Context is able to find specific genes such as antibiotic resistance genes, virulence factors and other MGE-related genes in TA system context.In this study, we examined the type II TA locus distribution and compared the TA diversity throughout 10 completely sequenced K. pneumoniae genomes by using TAfinder and other integrated tools. 212 putative type II TA loci were identified in 30 replicons of these K. pneumoniae strains. 77 unreported TA systems containing GNAT conserved domain have been found. The amino acid sequence similarity-based grouping shows that these loci distribute differently not only on different K. pneumoniae strains from diverse sources, but also on the type of replicon, say chromosome and plasmid.Besides the TA in K. pneumoniae, 38456 putative TA systems from 2194 bacterial genomes have been identified by TAfinder. Furthermore, TA systems harboured by mobile genetic elements(MGEs) including plasmids, integrative and conjugative elements and genomic islands were all detected. Some species-specific toxin families have been found based on the difference on distribution. The results are hopefully helpful to help gain deeper insight into the bacterial TA system and inspire new ideas for the “wet” research.