Data resources and mining tools for reconstructing gene regulatory networks in Lactococcus lactis

Abstract

food the of the product inhibitor bacteria Lactococci. The global world milk-related products is estimated Abstract DNA is the blueprint and template for tRNA, rRNA, sRNA and mRNA synthesis in all living organisms. Subsequently, the mRNA is translated to proteins a process in which other RNA types, compounds and proteins play important roles. The regulation of transcription and translation is a delicate equilibrium of thousands of factors interacting within an organism. These factors vary from compound- and protein concentrations, to their activity and stability to physical parameters like temperature and pH. Especially the transcription factors and transcription factor binding sites play a central role in the regulation of gene expression. For lactococci lactis several data sets on gene expression and regulation are available in databases or literature. Furthermore, the number of (in-) complete sequenced lactococci genomes is increasing, while the majority of the strains will only be studied in silico. This review focuses on the visualization and mining of the complex transcription and translation systems via interactive graphics and network reconstruction tools and the amalgamation of DNA microarray data with biological data that together lead to the reconstruction of gene regulatory networks (GRN). These networks are a valuable source of information and knowledge that can be used for studying L. lactis physiology and provide clues for improving industrial strains by either non-GMO methods (strain selection, fermentation condition) or by specific engineering.