A plant poly(A) polymerase requires a novel RNA-binding protein for activity

Transcriptome and Small RNA Profiling of Potato Virus Y Infected Potato Cultivars, Including Systemically Infected Russet Burbank

Potatoes are the world’s most produced non-grain crops and an important food source for billions of people. Potatoes are susceptible to numerous pathogens that reduce yield, including Potato virus Y (PVY). Genetic resistance to PVY is a sustainable way to limit yield and quality losses due to PVY infection. Potato cultivars vary in their susceptibility to PVY and include susceptible varieties such as Russet Burbank, and resistant varieties such as Payette Russet. Although the loci and genes associated with PVY-resistance have been identified, the genes and mechanisms involved in limiting PVY during the development of systemic infections have yet to be fully elucidated. To increase our understanding of PVY infection, potato antiviral responses, and resistance, we utilized RNA sequencing to characterize the transcriptomes of two potato cultivars. Since transcriptional responses associated with the extreme resistance response occur soon after PVY contact, we analyzed the transcriptome and small RNA profile of both the PVY-resistant Payette Russet cultivar and PVY-susceptible Russet Burbank cultivar 24 h post-inoculation. While hundreds of genes, including terpene synthase and protein kinase encoding genes, exhibited increased expression, the majority, including numerous genes involved in plant pathogen interactions, were downregulated. To gain greater understanding of the transcriptional changes that occur during the development of systemic PVY-infection, we analyzed Russet Burbank leaf samples one week and four weeks post-inoculation and identified similarities and differences, including higher expression of genes involved in chloroplast function, photosynthesis, and secondary metabolite production, and lower expression of defense response genes at those time points. Small RNA sequencing identified different populations of 21- and 24-nucleotide RNAs and revealed that the miRNA profiles in PVY-infected Russet Burbank plants were similar to those observed in other PVY-tolerant cultivars and that during systemic infection ~32% of the NLR-type disease resistance genes were targeted by 21-nt small RNAs. Analysis of alternative splicing in PVY-infected potato plants identified splice variants of several hundred genes, including isoforms that were more dominant in PVY-infected plants. The description of the PVYN-Wi-associated transcriptome and small RNA profiles of two potato cultivars described herein adds to the body of knowledge regarding differential outcomes of infection for specific PVY strain and host cultivar pairs, which will help further understanding of the mechanisms governing genetic resistance and/or virus-limiting responses in potato plants.

Cooperation of Endo- and Exoribonucleases in Chloroplast mRNA Turnover

Chloroplasts were acquired by eukaryotic cells through endosymbiosis and have retained their own gene expression machinery. One hallmark of chloroplast gene regulation is the predominance of posttranscriptional control, which is exerted both at the gene-specific and global levels. This review focuses on how chloroplast mRNA stability is regulated, through an examination of poly(A)-dependent and independent pathways. The poly(A)-dependent pathway is catalyzed by polynucleotide phosphorylase (PNPase), which both adds and degrades destabilizing poly(A) tails, whereas RNase II and PNPase may both participate in the poly(A)-independent pathway. Each system is initiated through endonucleolytic cleavages that remove 3' stem-loop structures, which are catalyzed by the related proteins CSP41a and CSP41b and possibly an RNase E-like enzyme. Overall, chloroplasts have retained the prokaryotic endonuclease-exonuclease RNA degradation system despite evolution in the number and character of the enzymes involved. This reflects the presence of the chloroplast within a eukaryotic host and the complex responses that occur to environmental and developmental cues.

Polynucleotide phosphorylase functions as both an exonuclease and a poly(A) polymerase in spinach chloroplasts

The molecular mechanism of mRNA degradation in the chloroplast consists of sequential events including endonucleolytic cleavage, the addition of poly(A)-rich sequences to the endonucleolytic cleavage products, and exonucleolytic degradation by polynucleotide phosphorylase (PNPase). In Escherichia coli, polyadenylation is performed mainly by poly(A)-polymerase (PAP) I or by PNPase in its absence. While trying to purify the chloroplast PAP by following in vitro polyadenylation activity, it was found to copurify with PNPase and indeed could not be separated from it. Purified PNPase was able to polyadenylate RNA molecules with an activity similar to that of lysed chloroplasts. Both activities use ADP much more effectively than ATP and are inhibited by stem-loop structures. The activity of PNPase was directed to RNA degradation or polymerization by manipulating physiologically relevant concentrations of P(i) and ADP. As expected of a phosphorylase, P(i) enhanced degradation, whereas ADP inhibited degradation and enhanced polymerization. In addition, searching the complete Arabidopsis genome revealed several putative PAPs, none of which were preceded by a typical chloroplast transit peptide. These results suggest that there is no enzyme similar to E. coli PAP I in spinach chloroplasts and that polyadenylation and exonucleolytic degradation of RNA in spinach chloroplasts are performed by one enzyme, PNPase.

Exoribonucleases and their multiple roles in RNA metabolism

In recent years there has been a dramatic shift in our thinking about ribonucleases (RNases). Although they were once considered to be nonspecific, degradative enzymes, it is now clear that RNases play a central role in every aspect of cellular RNA metabolism, including decay of mRNA, conversion of RNA precursors to their mature forms, and end-turnover of certain RNAs. Recognition of the importance of this class of enzymes has led to an explosion of work and the establishment of significant new concepts. Thus, we now realize that RNases, both endoribonucleases and exoribonucleases, can be highly specific for particular sequences or structures. It has also become apparent that a single cell can contain a large number of distinct RNases, approaching as many as 20 members, often with overlapping specificities. Some RNases also have been found to be components of supramolecular complexes and to function in concert with other enzymes to carry out their role in RNA metabolism. This review focuses on the exoribonucleases, both prokaryotic and eukaryotic, and details their structure, catalytic properties, and physiological function.

Nuclear and chloroplast poly(A) polymerases from plants share a novel biochemical property

Poly(A) polymerases are centrally involved in the process of mRNA 3' end formation in eukaryotes. In animals and yeast, this enzyme works as part of a large multimeric complex to add polyadenylate tracts to the 3' ends of precursor RNAs in the nucleus. Plant nuclear enzymes remain largely uncharacterized. In this report, we describe an initial analysis of plant nuclear poly(A) polymerases (nPAPs). An enzyme purified from pea nuclear extracts possesses many features that are seen with the enzymes from yeast and mammals. However, the pea enzyme possesses the ability to polyadenylate RNAs that are associated with polynucleotide phosphorylase (PNP), a chloroplast-localized enzyme involved in RNA turnover. Similar behavior is not seen with the yeast poly(A) polymerase (PAP). A fusion protein consisting of glutathione-S-transferase and the active domain of an Arabidopsis-encoded nuclear poly(A) polymerase was also able to utilize PNP, indicating that the activity of the pea enzyme was due to an interaction between the pea nPAP and PNP, and not to other factors that might copurify with the pea enzyme. These results suggest the existence, in plant nuclei, of factors related to PNP, and an interaction between such factors and poly(A) polymerases.

Polynucleotide phosphorylase is a component of a novel plant poly(A) polymerase

We have isolated cDNA clones encoding a novel RNA-binding protein that is a component of a multisubunit poly(A) polymerase from pea seedlings. The encoded protein bears a significant resemblance to polynucleotide phosphorylases (PNPases) from bacteria and chloroplasts. More significantly, this RNA-binding protein is able to degrade RNAs with the resultant production of nucleotide diphosphates, and it can add extended polyadenylate tracts to RNAs using ADP as a donor for adenylate moieties. These activities are characteristic of PNPase. Antibodies raised against the cloned protein simultaneously immunoprecipitate both poly(A) polymerase and PNPase activity. We conclude from these studies that PNPase is the RNA-binding cofactor for this poly(A) polymerase and is an integral player in the reaction catalyzed by this enzyme. The identification of this RNA-binding protein as PNPase, which is a chloroplast-localized enzyme known to be involved in mRNA 3'-end determination and turnover (Hayes, R., Kudla, J., Schuster, G., Gabay, L., Maliga, P., and Gruissem, W. (1996) EMBO J. 15, 1132-1141), raises interesting questions regarding the subcellular location of the poly(A) polymerase under study. We have reexamined this issue, and we find that this enzyme can be detected in chloroplast extracts. The involvement of PNPase in polyadenylation in vitro provides a biochemical rationale for the link between chloroplast RNA polyadenylation and RNA turnover which has been noted by others (Lisitsky, I., Klaff, P., and Schuster, G. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 13398-13403).

The mechanism of preferential degradation of polyadenylated RNA in the chloroplast. The exoribonuclease 100RNP/polynucleotide phosphorylase displays high binding affinity for poly(A) sequence

Polyadenylation of mRNA in the chloroplast has recently been shown to target the RNA molecule for rapid exonucleolytic degradation. A model has been suggested in which the degradation of chloroplast mRNA is initiated by endonucleolytic cleavage(s) followed by the addition of poly(A)-rich sequences and rapid exonucleolytic degradation. When in vitro transcribed RNAs were incubated with chloroplast protein extract, competition between polyadenylated and non-polyadenylated RNAs for degradation resulted in the rapid degradation of the polyadenylated molecules and stabilization of their non-polyadenylated counterparts. To elucidate the molecular mechanism governing this effect, we determined whether the chloroplast exoribonuclease 100RNP/polynucleotide phosphorylase (PNPase) preferably degrades polyadenylated RNA. When separately incubated with each molecule, isolated 100RNP/PNPase degraded polyadenylated and non-polyadenylated RNAs at the same rate. However, when both molecules were mixed together, the polyadenylated RNA was degraded, whereas the non-polyadenylated RNA was stabilized. In RNA binding experiments, 100RNP/PNPase bound the poly(A) sequence with much higher affinity than other RNA molecules, thereby defining the poly(A)-rich RNA as a preferential substrate for the enzyme. 100RNP/PNPase may therefore be involved in a mechanism in which post-transcriptional addition of poly(A)-rich sequence targets the chloroplast RNA for rapid exonucleolytic degradation.

Polyadenylation of mRNA in prokaryotes

The 3'-ends of both prokaryotic and eukaryotic mRNA are polyadenylated, but the poly(A) tracts of prokaryotic mRNA are generally shorter, ranging from 15 to 60 adenylate residues and associated with only 2-60% of the molecules of a given mRNA species. The sites of polyadenylation of bacterial mRNA are diverse and include the 3'-ends of primary transcripts, the sites of endonucleolytic processing in the 3' untranslated and intercistronic regions, and sites within the coding regions of mRNA degradation products. The diversity of polyadenylation sites suggests that mRNA polyadenylation in prokaryotes is a relatively indiscriminate process that can occur at all mRNA's 3'-ends and does not require specific consensus sequences as in eukaryotes. Two poly(A) polymerases have been identified in Escherichia coli. They are encoded by unlinked genes, neither of which is essential for growth, suggesting significant functional overlap. Polyadenylation promotes the degradation of a regulatory RNA that inhibits the replication of bacterial plasmids and may play a similar role in the degradation of mRNA. However, under certain conditions, poly(A) tracts may lead to mRNA stabilization. Their ability to bind S1 ribosomal protein suggests that poly(A) tracts may also play a role in mRNA translation.