Genomes and Genome-Level Engineering of Amino Acid-Producing Bacteria

Abstract

The complete nucleotide sequence of the genomes of several strains of Escherichia coli and Corynebacterium glutamicum reveal the genetic blueprint of these industrial organisms including their structural genetic organization and their metabolic networks and conversion capabilities, refine the understanding of their phylogenetic positions, and open the possibility to assess the expected size of their pan-genomes in order to harness their diversity. The genome of C. glutamicum R codes for approximately 3000 genes, a minimum of 5.3% of which are related to amino acid transport and metabolism and 4.6% to carbohydrate transport and metabolism. The genome of E. coli K-12 encodes approximately 4450 genes, 7.5% of which are involved in amino acid transport and metabolism and 6.1% in carbohydrate transport and metabolism. Global techniques were enabled by these complete genomic sequences, including analyses by global transcription profiling, proteomics and metabolomics to gather biological data, and megabase molecular biology tools to engineer at will these organisms at various scales, from the level of single base pairs to that of chromosomes. Systems biology represents the next technological paradigm necessary on the one hand to efficiently integrate and process the large volume of global biological information thus attained, in order to understand bacterial physiology and organization at a higher level; and on the other hand to enable in silico models useful for generating optimization strategies of increasing complexity and relevance, in the hope to lead faster towards improved metabolic engineering solutions with the aim of attaining expanded industrial process scope and superior economics.