Phase variation in LPS O-antigen biosynthetic gene cluster of the rice pathogen Xanthomonas oryzaepv. oryzae

Bacteria respond to environmental cues in different ways. Phase variation is one such adaptation where heritable and reversible changes in DNA aid bacteria to alter the expression of specific genes. The bacterial plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) causes the serious bacterial blight disease of rice. The mucoid phenotype of Xoo colonies is attributed to the secreted exopolysaccharide (EPS), xanthan gum. Spontaneous non-mucoid variants of Xoo which are deficient in EPS production and virulence were observed to accumulate in long-term stationary phase cultures. This phenomenon was termed stationary phase variation and variant colonies as stationary phase variants (SPV). Several but not all of these SPVs have been earlier described to carry spontaneous insertions of endogenous insertion sequence elements in the gum operon which encodes genes involved in EPS biosynthesis. In this study, we show that a number of SPVs harbour variations in the lipopolysaccharide (LPS) outer antigen (O-antigen) biosynthetic gene cluster. The data revealed that the vast majority of variations are due to either insertion of endogenous insertion sequence (IS) elements or slipped strand mispairing (SSM). Also, it was observed that many of these SPVs exhibited reversion to wild type mucoid phenotype via restoration of the wild type genotype. The results indicate that the phenomenon of phase variation is occurring in the LPS O-antigen biosynthetic gene cluster of Xoo.