Understanding and engineering of microbial cells based on proteomics and its conjunction with other omics studies

The abilities of microorganisms to produce a wide variety of products ranging from human therapeutics to chemicals and to tolerate or detoxify exogenous stresses such as toxic compounds and pollutants are of great importance in fundamental and applied research. Proteomics has become an indispensable tool for large-scale protein analyses and can be used to understand the resulting physiological changes and uncover the mechanisms responsible for the cellular processes under various genetic and environmental conditions. Recent development of a multi-omic approach that combines proteomics with one or more of other omics is allowing us to better understand cellular physiology and metabolism at the systems-wide level, and consequently paving a way toward more efficient metabolic engineering. In this review, we describe the use of proteomics and its combination with other omics to broaden our knowledge on microorganisms in the field of bioscience and biotechnology. With the increasing interest in practical applications, the strategies of employing proteomics for the successful metabolic engineering of microorganisms toward the enhanced production of desired products as well as the approaches taken to identify novel bacterial components are reviewed with corresponding examples.