The complete genome sequence of Mycobacterium avium subspecies paratuberculosis

Abstract

We describe here the complete genome sequence of a common clone of Mycobacterium avium subspecies paratuberculosis (Map) strain K-10, the causative agent of Johne's disease in cattle and other ruminants. The K-10 genome is a single circular chromosome of 4,829,781 base pairs and encodes 4,350 predicted ORFs, 45 tRNAs, and one rRNA operon. In silico analysis identified >3,000 genes with homologs to the human pathogen, M. tuberculosis (Mtb), and 161 unique genomic regions that encode 39 previously unknown Map genes. Analysis of nucleotide substitution rates with Mtb homologs suggest overall strong selection for a vast majority of these shared mycobacterial genes, with only 68 ORFs with a synonymous to nonsynonymous substitution ratio of >2. Comparative sequence analysis reveals several noteworthy features of the K-10 genome including: a relative paucity of the PE/PPE family of sequences that are implicated as virulence factors and known to be immunostimulatory during Mtb infection; truncation in the EntE domain of a salicyl-AMP ligase (MbtA), the first gene in the mycobactin biosynthesis gene cluster, providing a possible explanation for mycobactin dependence of Map; and Map-specific sequences that are likely to serve as potential targets for sensitive and specific molecular and immunologic diagnostic tests. Taken together, the availability of the complete genome sequence offers a foundation for the study of the genetic basis for virulence and physiology in Map and enables the development of new generations of diagnostic tests for bovine Johne's disease.

Fig. 1.

Circular representation of the Map K-10 genome. From inside: red arrow, rRNA operon; dark purple histogram, GC content; multicolored histogram, MAP ORFs coded according to functional classification (small molecule metabolism, blue; macromolecule metabolism, red; cell processes, purple; other processes, yellow; hypotheticals, green; unknowns, orange). The outer colored histogram indicates the same direction of transcription as the origin of replication. The inner colored histogram indicates the opposite direction of transcription as the origin of replication. Black arrows, 45 tRNAs. Outer circle, scale. The figure was generated with genescene software (DNAstar, Madison, WI).

Fig. 2.

Linear representation of repeat and unique regions within the Map K-10 genome. From the top: Blue histogram, VNTR/DR repeats; red histogram, SSR repeats; green histogram, unique regions; multicolored histogram, insertion sequences (IS900, blue; MAP01, aqua; MAP02, gray; MAP03, pink; MAP04, green; MAP05, purple; MAP06, black, MAP07, orange; MAP08, red; MAP09, light pink; MAP10, light purple; MAP11, beige; MAP12, brown; MAP13, fuschia; MAP14, light aqua; MAP15, light gray; MAP 16, dark green; IS1311, maroon; Mav2, light blue; REP, light green). Purple histogram, GC content. The figure was generated with genescene software (DNAstar, Madison, WI).

Fig. 3.

Homology comparison of the mycobactin gene cluster between Map K-10, Mav 104, and Mtb H37Rv. The gene cluster is shown in gray with amino acid length indicated above each box. Gene names are indicated.