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First published online September 26, 2003; 10.1105/tpc.013821
American Society of Plant Biologists Dual Regulated RNA Transport Pathways to the Cortical Region in Developing Rice Endosperm
a Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340 7 To whom correspondence should be addressed. E-mail okita{at}wsu.edu; fax 509-335-7643
Prolamine and glutelin RNAs are localized to two subdomains of the cortical endoplasmic reticulum (ER), the protein body ER and the cisternal ER, in developing rice seeds. The addition of nearly full-length prolamine sequences at the 3' untranslated region of a reporter RNA redirects its localization from the cisternal ER to the protein body ER. Deletion analysis of prolamine RNA sequences indicates the presence of two partially redundant cis elements required for protein body ER targeting. The addition of glutelin 3' untranslated region to protein body ER cis sequences, however, redirects RNA localization to the cisternal ER. These results indicate that there are at least two regulated RNA transport pathways as well as a constitutive pathway to the cortical ER.
The targeting of proteins to specific subcellular locations (e.g., vacuole, chloroplast, etc.) is directed by a variety of signal determinants. Many of these signals consist of amino acids arranged linearly, whereas others are arranged noncontiguously and constitute three-dimensional motifs. In addition to peptide-sorting signals, it is well established that the mRNA itself may have signals that direct it to discrete locations within the cell (Singer, 1993
RNA localization to the ER is a conspicuous feature in developing rice endosperm. This seed storage organ accumulates two major types of storage proteins, prolamines and glutelins, which are sequestered in separate endomembrane compartments. Prolamines accumulate and assemble to form a spherical intracisternal inclusion granule, 1 to 2 µm in diameter, within the ER lumen. Although glutelins are translocated initially to the ER lumen by a cotranslational import process, these proteins are transported to the Golgi and later to small storage vacuoles to form irregularly shaped, electron-dense protein bodies 2 to 3 µm in diameter. Li et al. (1993)
The segregation of these storage protein RNAs to specific cortical ER subdomains was confirmed and extended by a recent study (Choi et al., 2000 Here, we defined the prolamine RNA sorting signals by studying the localization of RNAs coded by a series of green fluorescent protein (GFP)prolamine cDNA genes. GFP RNAs, which normally are localized to the cisternal ER, are redirected to the PB-ER when prolamine RNA sequences are attached to the 3' end. These results indicate the existence of a regulated prolamine RNA transport pathway to the PB-ER as well as a constitutive pathway to the cisternal ER. Deletion analysis showed that the regulated prolamine RNA transport pathway to the PB-ER requires two partially redundant cis elements, one located in the coding sequence and a second residing in the 3' UTR. In addition, we provide evidence that glutelin RNAs are transported by a second regulated RNA transport pathway to the cisternal ER by a process that is dominant over the prolamine-regulated pathway.
Prolamine RNA Placed at the 3' UTR Maintains Targeting Specificity We demonstrated previously by in situ hybridization at the electron microscopy level (Li et al., 1993 -glucuronidase RNA containing prolamine RNA sequences positioned at the 3' UTR (Choi et al., 2000
Before this study was initiated, we studied the expression and localization of a series of GFP storage protein RNAs (nearly full-length prolamine and glutelin RNA)3' nopaline synthase (nos) RNAs (Figure 1A) in developing rice endosperm to verify that the hybrid RNAs would be targeted to the same cortical ER subdomains as the native storage protein RNA species. RNAs containing prolamine and glutelin RNA sequences were
Prolamine RNAs Contain Two cis Elements for PB-ER Targeting To identify the cis-acting signal determinants of the prolamine mRNA, a series of 5' and 3' deletions of the prolamine transcribed gene sequences were constructed. Deletions were made by dividing the coding sequence, which spans nucleotides 205 to 689, into four segments; the 3' UTR was divided into two segments for deletion (Figure 2). These various 5' and 3' deletions of the prolamine transcribed gene sequences then were cloned between the GFP reporter and 3' nos UTR plus terminator sequences and expressed in developing endosperm in transgenic rice plants.
Confocal microscopic observation of endosperm sections expressing these gene constructs showed that hybrid RNAs lacking the prolamine 5' UTR sequences remained restricted to the prolamine PBs (Figure 2, constructs 1 and 2) in a distribution pattern identical to that observed for wild-type prolamine mRNAs. Hence, cis-acting sorting determinants required for prolamine PB localization are located in the coding sequence and/or 3' UTR. Removal of the signal peptide and coding sequence region 1 (CDS1; nucleotides 205 to 317) resulted in a change in RNA distribution pattern. Although the hybrid RNAs were observed on the prolamine PBs, they also were distributed on the cisternal ER as well. This distribution of RNAs to both the PB-ER and the cisternal ER also was observed for other prolamine 5' deletions (constructs 4 to 6). The smallest 5' deletion fragment containing only the 3' UTR (construct 6; nucleotides 651 to 766) was sufficient for this dual RNA localization pattern. These observations suggest that the 3' UTR contains one or more sorting signal determinants required for RNA localization to the PB-ER. 3' deletion analysis confirmed the presence of a cis element in the prolamine 3' UTR. Removal of the distal half of the 3' UTR (construct 10) had no effect on the RNA distribution to both the PB-ER and the cisternal ER. By contrast, removal of the proximal 3' UTR end (constructs 11 to 13) resulted in the total loss of RNA localization to the PB-ER. Hence, the proximal half of the prolamine 3' UTR contains at least one cis element required for PB-ER localization.
As described above, 5' deletion of the signal peptide and CDS1 (construct 3) resulted in only a partial localization of RNAs to the PB-ER, suggesting the presence of a cis element in this region. Because we had demonstrated previously that the removal of the signal peptide sequences had no effect on prolamine RNA targeting to the PB-ER (Choi et al., 2000 To confirm the presence of cis elements in CDS1 and UA, a series of internal deletions of the prolamine gene sequences were obtained (Figure 3A) and expressed as described above. All internal deleted mRNAs containing CDS1 and UA were targeted to the PB-ER (Figure 3B). These results demonstrate that CDS1 and UA are sufficient to direct RNA targeting to the prolamine protein body. A direct comparison of the RNA sequences within CDS1 and UA indicates considerable sequence similarity, especially when gaps are introduced to maximize alignment (Figure 4).
Glutelin RNAs Are Transported to the Cisternal ER by a Regulated Pathway The deletion studies demonstrate that PB-ER targeting of prolamine RNAs requires two partially redundant cis elements and that the removal of one of these elements (e.g., the 3' UTR) results in a reduction in RNA localization to the PB-ER. However, results from a previous study (Choi et al., 2000
To test for the presence of a glutelin signal determinant, the localization of a maize 10-kD zein RNA in developing rice endosperm was studied. A hybrid RNA containing the 10-kD zein coding sequence and the nos 3' UTR was targeted to the PB-ER, indicating that the coding sequence of this maize storage protein RNA contains one or more cis elements functionally equivalent to those present in the prolamine RNA. Replacement of the nos 3' UTR with the glutelin 3' UTR, however, redirected the location of the RNAs mainly to the cisternal ER (Figure 5). Overall, the results described here (Figures 2 and 5) and those from a previous study (Choi et al., 2000
We had demonstrated previously that prolamine RNAs were sorted to the PB-ER by an RNA-based mechanism (Choi et al., 2000
The results described here also show that there is a second regulated RNA transport pathway from the nucleus to the cortical region of the developing rice endosperm cell. The glutelin RNA transport pathway is evident by its apparent dominance over the prolamine pathway when the glutelin 3' UTR is present (Choi et al., 2000
The prolamine targeting domains, CDS1 and UA, share two small conserved sequences of
RNA localization signals can be both sequence and/or structural in nature (Serano and Cohen, 1995 A question that arises from this study is why the storage protein RNAs are transported and localized to the cortical ER. In plant cells that have a large central vacuole, the transport, localization, and translation of RNAs to the cortical region would be expected, because the large vacuole would displace the cytoplasm to the peripheral regions of the cell. However, the young subaleurone cells of developing rice endosperm studied here lack large vacuoles. Instead, they have a dense cytoplasm containing small vacuoles (one type is the glutelin PBs) dispersed throughout the cell. Although the ER-associated nuclear envelope and the ER distributed throughout the cytoplasm are potential sites for the localization and translation of storage protein RNAs, they appear to be underused for protein synthesis, because our in situ RT-PCR analysis showed that these RNAs are restricted to the cortical ER. Hence, the transport and targeting of RNAs to the cortical region is not caused by a trivial condition but likely is a requisite step for efficient gene expression.
Closely associated with this ER domain is a prominent cytoskeleton network (Muench et al., 2000
RNAs that code for protein reporters such as GFP (this study) and
In addition to these RNA transport pathways to the cortical region of the cell, others are likely to exist. Viral and plant RNAs are able to move intercellularly and even long distances between tissues. The entry point for this transport is the plasmodesmata, channels that connect the cytoplasm of neighboring cells (Lucas and Gilbertson, 1994
The segregation of prolamine and glutelin RNAs to the PB-ER and the cisternal ER, respectively, likely facilitates the targeting of the coded proteins to their respective intracellular protein bodies (Okita et al., 1994 Our results support the existence of two RNA pathways to the cisternal ER: a regulated glutelin RNA transport pathway and a constitutive RNA pathway. The redundancy of multiple pathways to the cisternal ER raises the possibility that the regulated pathway targets RNAs to a destination site on the cortical ER that is not identical to those of RNAs engaged along the constitutive pathway. Efforts are under way to determine whether the cisternal ER is composed of subdomains that harbor unique RNAs.
T-DNA Vector Construction and Rice Transformation The T-DNA vector pCAMBIA 1301 was used for all expression studies in transgenic rice (Oryza sativa). The core vector (pYW502) contained a rice glutelin Gt1 2.5-kb promoter (Choi et al., 2000 Various prolamine cDNA sequences were obtained by PCR using the primers listed in Table 1. For plasmid constructs 1 to 13 (Figure 2), the sense primers contained a SacI site at the 5' end and the downstream antisense primers contained BamHI-SacI sites at the 3' end. Amplified prolamine cDNA sequences were purified, digested with SacI, and cloned 3' to the chitinase signal peptideGFP reporter sequences contained in pYW100R. The GFP-prolamine DNA sequences then were obtained by BamHI digestion and subsequently cloned into the corresponding site of pYW502. Plasmid DNAs containing correctly oriented chitinase signal peptideGFPprolamine cDNA sequences were identified by restriction enzyme mapping.
Plasmid constructs 14 and 15 containing internal deletions of the prolamine cDNA sequences were obtained by PCR amplification of individual DNA fragments that flanked the 5' and 3' ends of the deleted DNA segment and subsequent ligation. Both plasmid constructs 14 and 15 contained the proximal half (nucleotides 651 to 691) of the 3' untranslated region (UTR), which was amplified using PF11-Xba and PR4-Bam primers for PCR amplification. The amplified 3' UTR fragment was digested with XbaI and BamHI and then cloned into the complementary sites of pBluescript II KS- (Stratagene) to give pSB33. The upstream regions were amplified with PF1 in combination with PR12-Xba or PF11-Xba. The resulting DNA fragments then were digested with SacI and XbaI and cloned into the corresponding sites of pSB33 to give pSB36 and pSB37, respectively. These prolamine DNA sequences were digested with SacI and HindIII and inserted into the corresponding sites of pYW100R, which places the prolamine sequences 3' to the chitinase signal peptideGFP reporter gene to give pSB36-1 (construct 15) and SB37-1 (construct 14). These DNAs then were digested with BamHI, and the chitinase signal peptideGFPprolamine sequences were cloned into pYW502. Plasmid construct 16 was prepared as follows. pYW103, which contains the chitinase signal peptideGFPprolamine sequences (construct 1) cloned in pBluescript II KS- was digested with SalI, filled in with Klenow, and ligated to remove the SalI site in the polylinker region. The resulting plasmid was used in PCR to remove prolamine sequence 313 to 654 using primers PFM and PRM. The resulting DNA then was digested with SalI and ligated to give pCW78. This plasmid was used as a template for PCR amplification using PF3-Bgl and PR4-Bam or PF4-Bgl and PR4-Bam. These amplified DNA fragments were cloned into the filled-in SacI site of pYW500R to form pCW79. pYW500R contains the chitinase signal peptideGFP sequences cloned in the BamHI and SacI sites of pYW502.
T-DNA vectors containing the 10-kD
The various T-DNA vectors were transferred to Agrobacterium tumefaciens strain AgL1, which was used to transform rice as described previously (Choi et al., 2000
RNA and Protein Gel Blot Analysis
In Situ Reverse TranscriptaseMediated PCR and Microscopy Confocal microscopy was performed on a Zeiss 410 series laser scanning confocal microscope (Jena, Germany) and a Bio-Rad View Scan DVC-250 laser scanning confocal microscope using the fluorescein and rhodamine filter sets. Image processing was performed using Adobe Photoshop (Mountain View, CA), NIH Image, or Microsoft Powerpoint (Redmond, WA). Upon request, materials integral to the findings presented in this publication will be made available in a timely manner to all investigators on similar terms for noncommercial research purposes. To obtain materials, please contact T.W. Okita, okita{at}mail.wsu.edu.
This work was supported by grants from the National Science Foundation awarded to T.W.O. and by Department of Energy Grant DOE DE-FG05-95ER20194 to J.M.
Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.013821.
1 These authors contributed equally to this work.
2 Current address: RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan.
3 Current address: Department of Biology, Maejo University, Sunsai, Chiang Mai 50290, Thailand.
4 Current address: Department of Biological Sciences, Myongji University, Yongin Kyunggido 449-728, Korea.
5 Current address: Amplicon Express, 1610 NE Eastgate Boulevard, Suite 880, Pullman, WA 99163.
6 Current address: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, Assam, India. Received May 19, 2003; accepted August 18, 2003.
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