Novel small protein identification and quantitative proteomic analysis in Pseudomonas putida KT-­2440

Bacterial cell factories offer an environmental-friendly and sustainable alternative for traditional chemical and fuel-based industry. Better understanding of industrial bacteria in systematic way is meaningful for the application of bacterial cell factories on broader spectrum of industry.This thesis investigated an industrial bacterium, Pseudomonas putida KT-2440, in two aspects. First, the research focused on discovering novel small proteins (s-proteins) in the bacterium. With large-scale approaches for gene identification, groups of novel s-proteins were identified and validated from the genome, transcriptome and proteome of the bacterium. The application of new research approach, ribosome profiling, enabled us to analysis novel open reading frames (ORFs) from different standpoint. Second, by quantitative proteomic approach, the differential expressions of genes were analyzed at proteome level under different environmental conditions. The results yield insights intothe adaptation of P. putida KT-2440 in different environments.Based on bioinformatic, proteomic and transcriptomic approaches, global gene expression was analyzed on both transcriptional and translational levels. Our research for the first time validates novel s-proteins in P. putida KT-2440, and significantly increases the knowledge of P.putida protein expression and environmental adaptation.