Addition of Poly(A) and Heteropolymeric 3′ Ends inBacillus subtilisWild-Type and Polynucleotide Phosphorylase-Deficient Strains

Abstract

Polyadenylation plays a role in decay of some bacterial mRNAs, as well as in the quality control of stable RNA. In Escherichia coli, poly(A) polymerase I (PAP I) is the main polyadenylating enzyme, but the addition of 3 tails also occurs in the absence of PAP I via the synthetic activity of polynucleotide phosphorylase (PNPase). The nature of 3-tail addition in Bacillus subtilis, which lacks an identifiable PAP I homologue, was studied. Sizing of poly(A) sequences revealed a similar pattern in wild-type and PNPase-deficient strains. Sequencing of 152 cloned cDNAs, representing 3-end sequences of nontranslated and translated RNAs, revealed modified ends mostly on incomplete transcripts, which are likely to be decay intermediates. The 3-end additions consisted of either short poly(A) sequences or longer heteropolymeric ends with a mean size of about 40 nucleotides. Interestingly, multiple independent clones exhibited complex heteropolymeric ends of very similar but not identical nucleotide sequences. Similar polyadenylated and heteropolymeric ends were observed at 3 ends of RNA isolated from wild-type and pnpA mutant strains. These data demonstrated that, unlike the case of some other bacterial species and chloroplasts, PNPase of Bacillus subtilis is not the major enzyme responsible for the addition of nucleotides to RNA 3 ends.Polyadenylation is an important posttranscriptional modification of prokaryotic, eukaryotic, and organellar RNA. In Escherichia coli, polyadenylation has been shown to play a role in the process of decay, and the enzymes responsible for both polyadenylation and degradation are known (reviewed by ). Poly(A) polymerase I (PAP I), an enzyme belonging to the nucleotidyltransferase family, adds poly(A) extensions to the 3Ј ends of mRNAs, as well as to tRNA and rRNA (22). It has been shown that such extensions aid in the 3Ј-to-5Ј exoribonucleolytic degradation of RNAs, particularly for the degradation by polynucleotide phosphorylase (PNPase) of RNAs containing structured ends, such as transcription terminators (1,9,13,16,20,35). Coordination of endo-and exonucleolytic activities is thought to occur through the physical interaction of RNase E and PNPase, which, together with RNA helicase RhlB and enolase, form the degradosome (reviewed in reference 8). Physical interaction between PAP I and RNase E has also been observed (28), suggesting that polyadenylation may also be a part of the coordinated decay process.PNPase can act as a 3Ј-to-5Ј phosphorolytic exoribonuclease or as an RNA polymerase, depending on the availability of phosphate and ribonucleoside diphosphates. The possibility of in vivo polymerase activity of PNPase has gained more attention recently. In an E. coli strain deficient for PAP

Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets

“…In contrast to the other rli genes, rliD , rliE and rliH partially overlap with and are transcribed divergently to the ORFs of their flanking genes pnpA , comC and lmo1150 , respectively, indicating that these ncRNAs may act as antisense (Figure 2B). pnpA encodes the polynucleotide phosphorylase (PNPase) (39), comC encodes a putative type IV prepilin peptidase analogous to the comC gene of Bacillus subtilis (40), and lmo1150 encodes a putative transcription regulator similar to Salmonella typhimurium PocR (41), (Figure 2B). rliD , E and H are also present in L. innocua and L. ivanovii species (Table 1).…”

Ribosomes initiating translation of the hbs mRNA protect it from 5′‐to‐3′ exoribonucleolytic degradation by RNase J1

“…In E. coli , this task is performed by the 3′‐to‐5′ exoribonucleases with the help of poly(A) polymerase, which synthesizes poly(A) tails to provide the exonucleases with a toe‐hold (Hajnsdorf et al ., 1995; Mohanty and Kushner, 2006). Although poly(A) tails have been described in B. subtilis , it is not clear what enzyme catalyses their addition (Campos‐Guillen et al ., 2005). Regardless of the identity or level of activity of this enzyme, the accumulation of 3′ terminal fragments under RNase J1 depletion conditions rather than in strains lacking 3′‐to‐5′ exonucleases shows that the 5′‐to‐3′ pathway is clearly more efficient than the reverse orientation for 3′ terminal fragment removal in B. subtilis .…”

Importance and key events of prokaryotic RNA decay: the ultimate fate of an RNA molecule

“…B. subtilis, in which as much as 15–25% of total RNA was estimated to be polyadenylated,112 lacks an identifiable PAP I homologue. Nonetheless, similar polyadenylated and heteropolymeric ends have been observed at the 3′‐ends of RNA isolated from wild‐type and PNPase mutant strains, indicating that PNPase is not the only enzyme responsible for the addition of nucleotides to the 3′‐end of RNAs in this organism 113…”