Genomics And Comparative Genomics Of Lysine-Producing Strains

As a workhorse of industrial microorganism,Corynebacterium glutamicum is well known for fermentative production of L-lysine.Lots of hyper-productive strains haves been screened by the means of mutagenesis and successfully applied in the industrial process.However,the mechanism of the hyper-production of lysine in Corynebacterium glutamicum hasn’t been fully understood,which impedes further rational design of strains with higher production performance.With the fast development of sequencing technology,genomics and comparative genomics have been increasingly used to uncover hyper-production mechanism and facilitate direct the rational strain engineering.The genomes of C.glutamicum for lysine production were sequenced by integrating Illumina paired-end sequencing with PacBio single molecule real time sequencing.The genomes were assembled and annotated,and 3 complete genomes and 10 draft genomes were obtained.The full length of genomes ranges from 3.14 Mb to 3.35 Mb which encodes more than 3,000 CDSs.Combining genome annotation information,the first metabolic network of lysine-producing strains was constructed.The metabolic network includes 492 enzymes,956 catalyzed reaction and 1,081 metabolites.Through the comparison of the metabolic network,we discovered the presence of Entner-Doudoroff pathway in C.glutamicum and experimentally validated.We constructed a phylogenetic tree of 17 lysine-producing C.glutamicum strains and accordingly divided them into 4 groups,G1,G2,G3 and G4.Comparative genomics analysis of genomes within each group or across different groups were conducted.Via intergroup comparison,we found that all the lysine-producing strains have a deletion of a large prophage genomic island CGP3(～190 kb)and have more genes on the metabolic reactions and membrane transport than the wild type.Furthermore,many mutations affecting the function of the key enzymes for lysine production are found in the high producing strains,some of which are consistent with the reports in the literation.Through intragroup comparative genomics together with metabolic network and pathway analysis,we identified many potential hyper-production mechanisms such as alleviated feedback inhibition,enhanced of lysine biosynthesis pathway,weaked branch pathway and appropriate carbon flow of "oxaloacetate/TCA cycle".This work builds a solid basis for uncovering lysine hyper-production mechanisms in C.glutamicum and offers great potentials for systems metabolic engineering of lysine-producing industrial strains to improve its production performance in the future.