Text S4 Small RNAs.docVIP

Text S4: Small RNAs Brian C. Tjaden1 and Heidi Goodrich-Blair2 1Department of Computer Science, Wellesley College, Wellesley, Massachusetts, United States of America 2Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America E-mail: hgblair@bact.wisc.edu Small RNAs have recently been recognized as important regulatory factors controlling gene expression in bacteria. Many are part of regulatory hierarchies that control adaptations to environmental changes [1], and it is likely that they will be increasingly found to control symbiotic gene expression in response to the host environment. In E. coli, small RNAs regulate translation of the sigma transcription factor RpoS (reviewed in [2]). This sigma factor is essential for X. nematophila colonization of its nematode host [3,4]. sRNAs can modulate RNA polymerase, protein degradation, and translation regulation [5]. Prediction algorithms were used to examine the small RNA coding capacity of Xenorhabdus spp. Using conserved RNA structure and primary sequence similarity search parameters, of the 59 E. coli small RNAs reported in the Rfam database [6], 23 were found either in X. nematophila or X. bovienii (Table 1, below). These 23 include those involved in gene expression machinery (e.g. 6S RNA, a regulator of transcription [7]; RNaseP necessary for tRNA processing; tmRNA, which releases stalled ribosomes; 4.5S RNA, a component of the secretion apparatus). Of those small RNAs known to regulate RpoS in E. coli, DsrA, RprA, and OxyS [8], only an RprA homolog was apparent in Xenorhabdus spp., with E-values 0.00046 and 0.0011 in X. nematophila and X. bovienii respectively and truncated lengths relative to E. coli. Therefore, regulatory control of RpoS expression in Xenorhabdus is distinct from that occurring in E. coli. Small RNA genes were predicted throughout the genomes of X. nematophila and X. bovienii using a Markov model approach combining primary sequence data (e.g