Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides

P>Exposure to oxygen and light generates photooxidative stress by the bacteriochlorophyll a mediated formation of singlet oxygen (1O(2)) in Rhodobacter sphaeroides. Our study reports the genome-wide search for small RNAs (sRNAs) involved in the regulatory response to 1O(2). By using 454 pyrosequencing and Northern blot analysis, we identified 20 sRNAs from R. sphaeroides aerobic cultures or following treatment with 1O(2) or superoxide (O-(2)). One sRNA was specifically induced by 1O(2) and its expression depends on the extracytoplasmic function sigma factor RpoE. Two sRNAs induced by 1O(2) and O-(2) were cotranscribed with upstream genes preceded by promoters with target sequences for the alternative sigma factors RpoH(I) and RpoH(II). The most abundant sRNA was processed in the presence of 1O(2) but not by O-(2). From this and a second sRNA a conserved 3'-segment accumulated from a larger precursor. Absence of the RNA chaperone Hfq changed the half-lives, abundance and processing of 1O(2)-affected sRNAs. Orthologues of three sRNA genes are present in different alpha-proteobacteria, but the majority was unique to R. sphaeroides or Rhodobacterales species. Our discovery that abundant sRNAs are affected by 1O(2) exposure extends the knowledge on the role of sRNAs and Hfq in the regulatory response to oxidative stress.