Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I

Structure of Escherichia coli Hfq bound to polyriboadenylate RNA

“…Regardless, the significant gain in affinity of Hfq for longer A-R-N tracts can be attributed to an increase in the local concentration of these triplets, thus allowing the tract to zipper cooperatively into place, and the positive electrostatic nature of the distal face (56), which through electrostatic steering (41,42) can attract longer nucleotides more effectively. Although the distal face can accommodate 6 (A-R-N) triplets, once 5 A-R-E sites are filled, the presence of additional triplets does not affect binding affinity (compare A 16 and A 27 , the values of which parallel those reported previously) (refs. 35 and 40, and Table 1).…”

“…The poly(A) binding mechanism of Hfq also differs entirely from that used by the human poly(A) binding protein (hPABP), 6 160 Ϯ 30 A 16 1.4 Ϯ 0.9 A 27 1.6 Ϯ 0.9 (GGA) 2 88 Ϯ 28 (GGA) 9 16 Ϯ 1 (GCA) 9 70 Ϯ 4 (GCCA) 9 42 Ϯ 4 AU 5G 6 4 Ϯ 10 G 6 14,900 Ϯ 1,000 C 6 6,200 Ϯ 600 DNA-A 6 9,500 Ϯ 2,800 AAYAA element † 7.7 Ϯ 1 *Binding constants and errors are the average and standard deviation of at least 5 measurements. † The affinity of the AAYAA element has been measured only once, and the error is associated with the fit of the curve to the polarization data.…”

“…The extent of poly(A) tailing of Ec mRNAs by PAP I has been estimated recently to be greater than 90% of all ORFs of bacteria that are growing exponentially (31). Intriguingly, Hfq switches PAP I from a distributive to a processive catalytic mode, allowing for the more extensive adenylation of mRNAs (27). How Hfq causes this switch is unknown.…”

“…Beyond its role as an RNA chaperone, Escherichia coli (Ec) Hfq also functions in RNA stability by binding with nanomolar to subnanomolar affinities to polyadenylate [poly(A)] tails that have been added to the 3Ј ends of RNAs by poly(A) polymerase (PAP I) (27)(28)(29). Unlike cytosolic eukaryotic mRNA, the addition of adenosine nucleotides to bacterial mRNAs enhances their degradation (30).…”

“…The latter two enzymes are members of the degradosome, a multicomponent assembly that is responsible for RNA decay in bacteria (32). Hfq has been shown to interact with polynucleotide phosphorylase (PNPase), which adds AG-rich polynucleotide tails to the 3Ј ends of mRNAs that are terminated in a Rho-independent fashion, and RNase E, the key endoribonuclease involved in RNA destruction (27)(28)(29)-both presumably via protein-RNA-protein interactions (33).…”