Interdependence of asRNAs and RNase E on gene regulation during phage infection in Prochlorococcus

Control of RNase E activity represents an important aspect of co- and posttranscriptional gene regulation. In E. coli and other proteobacteria, a fundamental coordination of RNase E activity and target selectivity is maintained via the C-terminal structure domain of RNase E and involves protein modification (phosphorylation) or interaction with accessory proteins (degradosome components, DnaK/J, rraA/B, Hfq) [1, 2].

The ecologically important cyanobacterium Prochlorococcus possesses the smallest genome among oxyphototrophs, with a reduced suite of protein regulators and a disproportionately high number of regulatory RNAs. Many of these RNAs are asRNAs. Intriguingly, a reverse correlation of asRNA expression and RNase E activity was observed upon infection by cyanophage P-SSP7 [3]. The indirect regulation of RNase E activity in Prochlorococcus by RNA duplex formation might reflect an alternative mechanism of regulation of enzyme activity that appears to be required for an organism lacking the region modified in other host-phage systems. In an in vitro approach we assigned RNase E cleavage sites for different transcripts located in MED4 genomic island II [3]. There is evidence from RT-PCR and northern hybridization experiments for a full coverage of large parts of genomic island II by an extraordinary long asRNA [3]. Subsequently, in vitro protection assays with mRNA/ asRNA pairs from genomic island II imply asRNA-dependent RNase E activity, linked to mRNA/ asRNA duplex formation [3]. Our results are in agreement with RNase E specificity for single-stranded RNA [3].