Chapter 13 - Shikimate pathway enzymes in human microbiome. Putative gene candidates for gene knockout in diseases caused by infections

Abstract

I annotated the genes encoding enzymes of shikimate pathway in the genome of proteobacteria Escherichia coli (K-12 substrain) isolated in 1922 from the stool of a convalescent diphtheria patient. The current sequence analysis shows that the shikimate pathway genes dispersed on the genome of E. coli K-12. Therefore, the modern healthy human microbiome contains bacteria with shikimate pathway enzymes that can be potentially blocked by metabolic engineering with enhancing flux to and through shikimate pathway. However, microorganisms with no shikimate pathway but possessing aromatic amino acid decarboxylase enzymes may use tryptophan, tyrosine, and phenylalanine from the environment such as products of human protein degradation and food for both decarboxylation and protein biosynthesis. Hypothetically, the blockage of shikimate pathway in the human microbiome can result in the modification of microbial metabolism for the usage of another source for aromatic amino acids. Moreover, microorganisms of the human microbiome can currently use both sources of aromatic amino acids for decarboxylation: the microbial shikimate pathway and ready to use aromatic amino acids derived from human protein degradation and plant shikimate pathway of food.