Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens

Abstract

Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum, a species widely used for the industrial production of amino acids. C. efficiens but not C. glutamicum can grow above 40 degrees C. We sequenced the complete C. efficiens genome to investigate the basis of its thermostability by comparing its genome with that of C. glutamicum. The difference in GC content between the species was reflected in codon usage and nucleotide substitutions. Our comparative genomic study clearly showed that there was tremendous bias in amino acid substitutions in all orthologous ORFs. Analysis of the direction of the amino acid substitutions suggested that three substitutions are important for the stability of the C. efficiens proteins: from lysine to arginine, serine to alanine, and serine to threonine. Our results strongly suggest that the accumulation of these three types of amino acid substitutions correlates with the acquisition of thermostability and is responsible for the greater GC content of C. efficiens.

Figure 1

GC content of three corynebacterial genomes. Window analysis of GC content performed at 20-kb window size and 1-kb step size. Linear representation of GC content along the chromosome. Green, C. efficiens; dark blue, C. glutamicum; light blue, C. diphtheriae.

Figure 2

C. glutamicum GC skew of the three Corynebacteria. Window analysis of GC skew was performed at 20-kb window size and 1-kb step size. C. glutamicum (A), C. efficiens (B), and C. diphtheriae (C).

Figure 3

Proposed hydrophobic interaction in C. glutamicum diaminopimelate dehydrogenase. The residue ¹¹³Ala is substituted to Ser in C. efficiens. This substitution may destroy hydrophobic interaction and destabilize the protein structure. Flat arrows represent β-sheet.