Evidence for in vivo modulation of chloroplast RNA stability by 3؅-UTR homopolymeric tails in Chlamydomonas reinhardtii Yutaka Komine*, Elise Kikis*, Gadi Schuster†, and David Stern*‡ *Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853; and †Department of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel Edited by Lawrence Bogorad, Harvard University, Cambridge, MA, and approved January 8, 2002 (received for review June 27, 2001) Polyadenylation of synthetic RNAs stimulates rapid degradation in synthesizes and degrades poly(A) tails (13). E. coli, by contrast, vitro by using either Chlamydomonas or spinach chloroplast extracts. encodes a poly(A) polymerase. These differences may reflect the Here, we used Chlamydomonas chloroplast transformation to test the evolution of the chloroplast to a compartment whose gene effects of mRNA homopolymer tails in vivo, with either the endog- regulation is controlled by the nucleus. enous atpB gene or a version of green fluorescent protein developed Unlike eukaryotic poly(A) tails, the roles of 3Ј-UTR tails in for chloroplast expression as reporters. Strains were created in which, prokaryotic gene expression are largely unexplored, although after transcription of atpB or gfp, RNase P cleavage occurred upstream they are widely distributed in microorganisms including cya- Glu of an ectopic tRNA moiety, thereby exposing A28,U25A3,[A؉U]26, nobacteria (14). Polyadenylated mRNAs have also been found in or A3 tails. Analysis of these strains showed that, as expected, both plant (15, 16) and animal mitochondria (17). The functions polyadenylated transcripts failed to accumulate, with RNA being of these tails have mostly been tested in vitro, which has undetectable either by filter hybridization or reverse transcriptase– highlighted RNA degradation but not interactions with other PCR. In accordance, neither the ATPase ␤-subunit nor green fluores- RNA processing or expression pathways. In particular, the site cent protein could be detected. However, a U25A3 tail also strongly and composition of the 3Ј-UTR tail has not been manipulated in .reduced RNA accumulation relative to a control, whereas the [A؉U] vivo, which might reveal important mechanisms tail did not, which is suggestive of a degradation mechanism that Our studies with Chlamydomonas have detected polyadenylated does not specifically recognize poly(A), or that multiple mechanisms forms of mRNA, tRNA, and rRNA by RT-PCR, and shown that an exist. With an A3 tail, RNA levels decreased relative to a control with A25 tail is sufficient to confer marked instability in vitro (9). Here, no added tail, but some RNA and protein accumulation was observed. we have manipulated the endogenous atpB gene, which encodes the We took advantage of the fact that the strain carrying a modified atpB ␤-subunit of ATP synthase, and a green fluorescent protein (GFP) gene producing an A28 tail is an obligate heterotroph to obtain reporter gene, to examine the consequences of adding specific 3Ј photoautotrophic revertants. Each revertant exhibited restored atpB end tails in vivo. Our data suggest that both poly(A) and poly(U) mRNA accumulation and translation, and seemed to act by preventing destabilize the upstream mRNA. We also demonstrate a genetic PLANT BIOLOGY poly(A) tail exposure. This suggests that the poly(A) tail is only approach to identifying nuclear factors involved in RNA processing .recognized as an instability determinant when exposed at the 3؅ end and the polyadenylation͞degradation pathways of a message. Materials and Methods odulation of RNA stability plays a variety of roles in gene Strains and Culture Conditions. Extracts for in vitro assays were Mregulation during organism development and environmental obtained from strain CC406. Strain CC373 (ac-u-c-2–25), which responses. Moreover, mRNA turnover can eliminate aberrant carries a deletion in the atpB gene and downstream region (18), transcripts and thereby contribute to accurate translation (1, 2). was used for chloroplast transformations. Cells were grown Studies in yeast have defined the major steps for turnover of under constant light in Tris-acetate-phosphate medium (19). nucleus-encoded mRNAs, which initiates with 3Ј end deadenyla- tion followed by 5Ј end decapping (3). These products are then Plasmids, DNA Constructs, and Chloroplast Transformation. The in- degraded by a 5Ј-to3Ј-exoribonuclease, or by the exosome complex sert of the atpX-AAD selectable marker cassette (20) was of 3Ј-to5Ј-exonucleases (4). A multiprotein complex may also be amplified by PCR and inserted into pGEM-T (Promega) after Ј involved in RNA degradation in Escherichia coli. This complex, adding a BglII site to the 5 primer. The cassette was excised as termed the degradosome, consists of polynucleotide phosphorylase a BglII-BamHI fragment, and inserted into the BglII sites of ⌬ ⌬ ⌬ (PNPase), a DEAD-box RNA helicase, RNase E, enolase, and plasmids atpB 19, atpB 21, and atpB 26; these sites lie imme- possibly other proteins. In contrast to eukaryotic mRNA degrada- diately downstream of deletion endpoints ranging from several Ј tion, however, 3Ј-polyadenylation stimulates decay in E. coli base pairs after the stop codon to within the 3 -UTR stem-loop through its recognition by PNPase (5, 6). Thus, although both structure (21) (see Fig. 2). Clones were identified in which the prokaryotic and eukaryotic cells have exonuclease-containing deg- cassette was transcribed in tandem with atpB (Fig. 1A), yielding ⌬ ⌬ ⌬ radation complexes, one prefers polyadenylated substrates and the constructs atpB 19AD, atpB 21AD, and atpB 26AD; these other acts on deadenylated molecules. retained a BglII site between the modified atpB gene and the The chloroplast, an endosymbiotic organelle, can be viewed as aadA cassette. The trnE gene was cloned by using PCR, with the a prokaryotic compartment in a eukaryotic cell. In the chloro- plast, polyadenylated mRNAs have been found by using reverse This paper was submitted directly (Track II) to the PNAS office. transcriptase–PCR (RT-PCR), and their incubation in soluble Abbreviations: RT-PCR, reverse transcriptase–PCR; UTR, untranslated region; GFP, protein extracts results in rapid degradation (7–9). Chloroplasts green fluorescent protein; ECS, endonuclease cleavage site; PNPase, polynucleotide contain a nucleus-encoded form of PNPase (10), which has a phosphorylase. strong affinity for poly(A) (11), and likely recognizes poly(A) ‡To whom reprint requests should be addressed. E-mail: [email protected]. tails in vivo. Although the existence of a chloroplast degrado- The publication costs of this article were defrayed in part by page charge payment. This some was reported (10), it now seems that chloroplast PNPase article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. is not part of a multiprotein complex (12), and that it both §1734 solely to indicate this fact. www.pnas.org͞cgi͞doi͞10.1073͞pnas.052327599 PNAS ͉ March 19, 2002 ͉ vol. 99 ͉ no. 6 ͉ 4085–4090 Downloaded by guest on September 28, 2021 atpB⌬21AD]. For GFP constructs, plasmid MR220 containing cpgfp1 (GenBank accession no. AF303131), which is optimized for tobacco chloroplast expression, was obtained from M. Han- son (Cornell University). The gfp gene was excised with NcoI and XbaI, and inserted into NcoI- and XbaI-digested pDAAD (22), creating plasmid pDGFP. pDAAD contains the cassette petD promoter-aadA-coding region-rbcL 3Ј-UTR, inserted down- stream of the atpB gene, and in pDGFP the aadA-coding region is replaced by that of gfp. Modified trnE genes were created as above, except both PCR primers contained SpeI sites, because the trnE gene contains compatible XbaI sites. Modified trnE gene fragments were digested with SpeI and inserted into XbaI-digested pDGFP, placing the tRNA and flanking se- quences between the gfp-coding region and the rbcL 3Ј-UTR, as shown in Fig. 1C. Each construct was verified by DNA sequence analysis. Chloroplast transformation was performed as described (21). The cpDNA configuration in the spa revertants (Fig. 6) was determined by sequence analysis with PCR amplification from total DNA with primers YK03 and atpX-3Ј. YK03 anneals 60 bp upstream of the atpB stop codon, and atpX-3Ј anneals immediately upstream of the atpA translation initiation codon fused to the aadA-coding region. When used to amplify DNA from ⌬26pAtE, the product obtained is 984 bp, which was also the case for each spa mutant except spa2. In spa2, a deletion begins 37 bp into the trnE cassette, within the mature tRNA-coding region, and ends 74 bp upstream of the atpA translation initiation codon, a total of 765 bp. RNA and Protein Analysis. Total RNA and protein were isolated from early-log-phase cultures (1–2 ϫ 106 cells per ml). Each assay involved at least three independent preparations, and results were averaged. The data shown here are representative Fig. 1. Gene organization in chloroplast transformants to test 3Ј-UTR mod- of the averaged results. RNA filter hybridizations were per- ifications. (A) Addition of a poly(A) sequence downstream of different ver- formed as described (23). sions of atpB. The gray box represents the atpB-coding region, which in strain For RT-PCR, total RNA was precipitated with 2 M LiCl, and ⌬26 is followed by a BglII site (B) in lieu of the normal stem-loop-forming 25-␮g aliquots were treated with 10 units RQ1 DNase (Promega) inverted repeat (IR). The hatched box represents a sequence of 25 adenosines 2 for 1 h and purified by using the RNeasy Plant Mini Kit (Qiagen, immediately followed by an RNase P cleavage site (AAA GC), and then the Chatsworth, CA). Negative controls were identical reactions sequence corresponding to mature trnE and some downstream sequences (see Materials and Methods). In ⌬21 and ⌬19, most or all, respectively, of the atpB except reverse transcriptase was omitted, and no product was 3Ј IR remains, as indicated by the horizontal arrows. The aadA selectable generated (data not shown). For the competitive RT-PCR shown marker cassette, transcribed in the same orientation as atpB, is shown as a in Figs.