Genome-wide identification of Hfq-regulated small RNAs in the bacterial pathogen Erwinia amylovora. Erwinia amylovora

RNA-seq analysis was performed to examine the sRNA transcripts in wild type E. amylovora 1189 and in the deletion mutant of hfq, at 6 and 12 hours of culture in hrp-inducing minimal medium. Overall design: Total RNA was isolated from wild type Ea1189, and the hfq mutant of Ea1189, at 6 and 12 hours post inoculation in hrp-inducing minimal medium. RNA transcripts that are between 50-350 nucleotides were analyzed by RNA-seq. Intergenic transcripts whose expression was greatly reduced in the hfq mutant than the wild type at both 6 and 12 hours post inoculation in hrp-inducing minimal medium were selected as potential small RNAs.