The E. coli DEAD box ATPase CsdA, is a NAD+ capped RNA binding protein

Abstract

5' nicotinamide adenine dinucleotide (NAD+) caps are one of the most common metabolites derived non-canonical caps reported on bacterial RNAs. Multiple decapping proteins are known to regulate the stability of NAD+ capped transcripts. However, no other proteins have been identified that preferentially interact with these NAD+ caps, and mechanistic details of the cap-dependent recognition remain poorly understood. Using an affinity capture approach, we identified multiple E. coli proteins that selectively recognize NAD+ caps, including the ATP-dependent RNA helicase, CsdA. CsdA preferentially interacts directly with NAD+ capped RNAs and can discriminate between 5' NAD+ capped and 5' triphosphate end transcripts. Binding to NAD+ capped RNA versus 5' triphosphate RNA more greatly enhances the ATPase activity of CsdA and the presence of NAD+ caps on transcripts modulates the ability of CsdA to form RNA condensates. Furthermore, we find that CsdA enhances the decapping activity of the NADH hydrolase NudC, suggesting CsdA plays a role in regulating the degradation of NAD+ capped transcripts. CsdA is the first identified NAD+ cap reader protein and its preference for binding NAD+ capped RNA provides a mechanism by which E. coli cells link RNA stability to the identity of the 5' cap. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/730015v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@115a057org.highwire.dtl.DTLVardef@d1c2c6org.highwire.dtl.DTLVardef@14a6d2dorg.highwire.dtl.DTLVardef@145ccff_HPS_FORMAT_FIGEXP M_FIG C_FIG