RNA Polyadenylation and Degradation in Cyanobacteria Are Similar to the Chloroplast but Different from Escherichia coli

Abstract

The mechanism of RNA degradation in Escherichia coli involves endonucleolytic cleavage, polyadenylation of the cleavage product by poly(A) polymerase, and exonucleolytic degradation by the exoribonucleases, polynucleotide phosphorylase (PNPase) and RNase II. The poly(A) tails are homogenous, containing only adenosines in most of the growth conditions. In the chloroplast, however, the same enzyme, PNPase, polyadenylates and degrades the RNA molecule; there is no equivalent for the E. coli poly(A) polymerase enzyme. Because cyanobacteria is a prokaryote believed to be related to the evolutionary ancestor of the chloroplast, we asked whether the molecular mechanism of RNA polyadenylation in the Synechocystis PCC6803 cyanobacteria is similar to that in E. coli or the chloroplast. We found that RNA polyadenylation in Synechocystis is similar to that in the chloroplast but different from E. coli. No poly(A) polymerase enzyme exists, and polyadenylation is performed by PNPase, resulting in heterogeneous poly(A)-rich tails. These heterogeneous tails were found in the amino acid coding region, the 5 and 3 untranslated regions of mRNAs, as well as in rRNA and the single intron located at the tRNA fmet . Furthermore, unlike E. coli, the inactivation of PNPase or RNase II genes caused lethality. Together, our results show that the RNA polyadenylation and degradation mechanisms in cyanobacteria and chloroplast are very similar to each other but different from E. coli.The molecular mechanism of RNA degradation in prokaryotes and organelles includes a series of sequential steps. The degradation starts with the initial endonucleolytic cleavage carried out primarily by the endoribonuclease E (RNase E). The cleavage products are then polyadenylated at their 3Ј ends by the poly(A) polymerase (PAP) 1 enzyme in Escherichia coli and the polynucleotide phosphorylase (PNPase) in the chloroplast. The polyadenylated molecules are then rapidly degraded exonucleolytically by PNPase and ribonuclease II (RNase II) (1-3). Finally, the remaining short oligoribonucleotides are degraded by the oligoribonuclease enzyme (4). Although the inhibition of polyadenylation in the chloroplast inhibited exonucleolytic degradation, implying that this is the only mechanism in the RNA degradation process, two RNA degradation mechanisms, a polyadenylation-dependent and a polyadenylation-independent one, were suggested to take place in E. coli (5, 6). Polyadenylation in E. coli is carried out primarily by PAP (7). Also in this bacterium, the RNase E enzyme, part of the PNPase population, an RNA helicase, some RNA molecules, and the glycolytic enzyme enolase are associated in a high molecular weight complex called a degradosome (8).In the chloroplast, the photosynthetic organelle of the plant cell is believed to have an evolutionary prokaryotic origin; many characteristics of the gene expression system resemble those of bacteria. When the RNA degradation mechanism was analyzed in the chloroplast, it was found to be very similar to that of E. coli (1-3). However...

RNA 3′-tail synthesis in Streptomyces: in vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase

“…We argue, as do Sohlberg et al (2003), that the enzyme responsible for the synthesis of those tails is PNPase. This conclusion is consistent with the observation that spinach chloroplasts and a Synechocystis species, like S. coelicolor, do not encode a dedicated PAP (Rott et al, 2003;Yehudai-Resheff et al, 2001). In the two former systems, and in pcnB mutants of E. coli, the RNA 39-polyribonucleotide polymerase is PNPase and as in S. coelicolor, the 3-tails of RNAs in spinach chloroplasts, in the Synechocystis sp.…”

Targeted depletion of a mitochondrial nucleotidyltransferase suggests the presence of multiple enzymes that polymerize mRNA 3′ tails in Trypanosoma brucei mitochondria

“…The canonical PAP, represented by bacterial class II (24) or eukaryotic class I (25) PAPs, mainly synthesizes homopolymeric adenosine tails. Another enzyme, polynucleotide phosphorylase, which is primarily a degradative enzyme in vivo, has been shown to possess polyadenylation activity and create heteropolymeric tails in prokaryotes, cyanobacteria, and chloroplasts of higher plants (26)(27)(28). Recently, a new class of PAPs was described in several eukaryotes.…”

Sequence motifs that distinguish ATP(CTP):tRNA nucleotidyl transferases from eubacterial poly(A) polymerases

“…In Escherichia coli, eubPAP (Cao and Sarkar 1992) is a nonessential enzyme and its function can be replaced by polynucleotide phosphorylase (PNP; Mohanty and Kushner 2000), an enzyme which can both synthesize and degrade poly(A). PNP was also found to be responsible for poly(A) addition to mRNAs in spinach chloroplasts and cyanobacteria (Yehudai-Resheff et al 2001;Rott et al 2003).…”

“…Some bacterial species or entire groups, such as the ␣-and -proteobacteria, eventually lost eubPAP. If loss of eubPAP is "easy" for the cell, then many losses can be accepted on parsimony grounds, considering the fact that other enzymes, such as polynucleotide phosphorylase (PNP), take over the function of eubPAP (Yehudai-Resheff et al 2001;Rott et al 2003). In a second event, eubPAPs and CCA-adding enzymes were transmitted from eubacteria to an early eukaryote by endosymbiosis.…”