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First published online October 19, 2007; 10.1104/pp.107.108076 Plant Physiology 145:1637-1646 (2007) © 2007 American Society of Plant Biologists Two DEAD-Box Proteins May Be Part of RNA-Dependent High-Molecular-Mass Protein Complexes in Arabidopsis Mitochondria1,[W]Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany (A.M., S.S.-G., D.K., J.F., S.W., S.B.); and Max-Planck-Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry Group, D–37077 Goettingen, Germany (M.R., H.U.)
Posttranscriptional processes are important for regulation of gene expression in plant mitochondria. DEAD-box proteins, which form a huge protein family with members from all kingdoms, are fundamental components in virtually all types of processes in RNA metabolism. Two members of this protein family, designated PMH1 and PMH2 (for PUTATIVE MITOCHONDRIAL RNA HELICASE), were analyzed and characterized in mitochondria of Arabidopsis (Arabidopsis thaliana). Green fluorescent protein tagging with N-terminal PMH1 and PMH2 sequences supports the mitochondrial localization of these proteins. Northern experiments, as well as histochemical β-glucuronidase staining of transgenic plants carrying respective promoter:β-glucuronidase fusion constructs, revealed differing transcription patterns for the two genes. In response to cold, however, transcript levels of both genes increased. Immunodetection analyses of mitochondrial protein complexes after two-dimensional blue native/urea SDS-PAGE and after fractionation on sucrose gradients strongly suggest that one or both proteins are part of RNA-dependent complexes. Cold treatment of cell cultures or solubilization of mitochondria in the presence of MgCl2 favored the detection of high-molecular-mass complexes. This study paves the way for detailed analysis of high-molecular-mass complexes in mitochondria of higher plants.
Various posttranscriptional processes so far described in plant mitochondria have been suggested to be important for regulation of gene expression in this subcellular compartment (Hoffmann and Binder, 2002
DEAD-box proteins form a large gene family and are present in almost all organisms from all kingdoms (Linder, 2006 To identify proteins involved in the RNA metabolism in higher plant mitochondria, we have now analyzed two DEAD-box proteins in Arabidopsis. We determined their subcellular localization and investigated transcript levels as well as the promoter activities of these two genes. We find that these proteins are integrated in RNA-dependent high-molecular-mass complexes.
Posttranscriptional processes play a key role in gene expression in plant mitochondria (Gagliardi and Binder, 2007
PMH2 has previously been found in proteome analyses of plant mitochondria indicating that this protein is located in this organelle (Millar et al., 2001
PMH1 and PMH2 Show Differing Expression Patterns, But Both Are Induced by Cold Treatment
The high similarity of these proteins suggests that they might have similar functions, which can complement each other. As a first step, we investigated whether they are expressed in different tissues and developmental stages. In northern analyses, performed with gene-specific probes covering the 5'-untranslated regions as well as the unique regions of the mitochondrial targeting sequences, PMH1 steady-state transcripts are mainly found in flowers, at very low levels in roots and seedlings, but are hardly detectable in leaves (Fig. 2
, left). Because many RNA helicases from bacteria and various eukaryotic organisms show enhanced expression at low temperatures (Owttrim, 2006
Enhanced PMH1 transcription after cold treatment was further analyzed and quantitatively resolved over time. Approximately a 7-fold induction is seen 12 h after transfer of the seedlings to 4°C. A 3-fold increased mRNA level is still detectable after 48 h. Maximal induction is observed after 36 h with approximately a 10-fold higher amount of PMH1 mRNAs in comparison to the control plants grown under identical conditions at 23°C (data not shown). Transcriptional activity was studied in more detail using the GUS reporter gene. To this end, 2.0 kb upstream of the ATG containing potential promoter sequences of both genes were fused to the GUS reading frame. This region upstream of PMH1 includes the preceding gene At3g22300 and 331 bp of its promoter. The PMH2 upstream region comprises the gene At3g22320, which is encoded on the opposite strand. After transformation of the respective constructs into Arabidopsis, five different plant lines originating from five individual integration events per construct were examined by histochemical GUS staining. Substantial staining is consistently observed in transgenic plants expressing GUS under the control of the PMH2 promoter. Strong promoter activities are indicated in cotyledons, emerging leaves, expanded leaves, as well as root tips of 6-, 9-, and 16-d-old seedlings grown on Murashige and Skoog medium (Fig. 3 ) or soil (data not shown). Transcriptional activity is also observed in roots, anthers, and the basal parts of siliques of adult plants. In addition, pronounced staining is found in tissue parts close to the cut sites of detached leaves and siliques, as well as of parts of flowering stalks, suggesting that transcription of PMH2 is triggered by wounding (Fig. 3). This is confirmed by experiments in which the leaf blades were mechanically wounded by a cut or a pin prick. All of these mechanical injuries consistently trigger promoter activity in tissues adjacent to the site of treatment (Supplemental Fig. S2).
A different pattern of activity was found in plants expressing GUS governed by the PMH1 promoter. Whereas no staining at all is detectable in seedlings grown on soil (data not shown), very weak promoter activity is indicated in the root tips of seedlings cultivated on Murashige and Skoog medium under otherwise identical conditions (Fig. 3, top, indicated by an arrow). GUS activity is not seen in any part of the adult plants, except for substantial promoter activity restricted to anthers. In contrast to PMH2, no induction by mechanical treatment is observed for PMH1, indicating that both genes respond differently to this external stimulus. All in all, the results of northern analysis are consistent with the observations in the histochemical analyses, both indicating different expression patterns for each gene, suggesting that the two proteins have partially different roles in the plant.
For further analysis of the PMH proteins, two PMH1-derived peptides were synthesized and used for antibody production in rabbits (Supplemental Fig. S1). The antiserum should detect both proteins and indeed also binds to recombinant PMH2 (data not shown).
To investigate whether both proteins are expressed in an Arabidopsis cell suspension culture, mitochondria were isolated and purified from this tissue. Proteins from these organelles were separated by isoelectric focusing (IEF) on immobilized nonlinear pH gradients ranging from pH 3 to 11 followed by standard SDS-PAGE. Staining with Coomassie Blue revealed a protein pattern similar to those observed in previous proteome analyses of mitochondria (Kruft et al., 2001
Taken together, this analysis shows that PMH1 as well as PMH2 are expressed in this Arabidopsis cell suspension culture. In addition, these experiments confirm that the antiserum recognizes the PMH proteins and can be used for selective detection of these proteins in mitochondrial lysates.
PMH1/PMH2 antiserum was then used to examine whether these DEAD-box proteins are associated with other proteins. To follow this issue, 1 mg of total mitochondrial protein isolated from the cell suspension culture was solubilized with dodecylmaltoside (DDM) and separated by two-dimensional blue native (BN)/urea SDS-PAGE. Coomassie staining of proteins after the separation revealed a pattern in which distinct complexes can be identified by comparison with the results of analogous separations (Fig. 5A
; Eubel et al., 2003
DEAD-box proteins are involved in multiple processes that require interaction of these proteins with RNA. We thus tested whether the integrity of the PMH1/PMH2-containing complexes depends on the presence of RNA. To this end, solubilized total mitochondrial protein was treated with RNase A prior to separation by two-dimensional BN/urea SDS-PAGE. Digestion of the RNA almost completely disassembled the high-molecular-mass complexes (Fig. 5C). Beside a weak signal corresponding to a size of about 580 kD (ATP synthase), only the signal most likely representing the monomeric protein can now be detected (Fig. 5C). This strongly suggests that the stability or maintenance of the detected complexes or at least the association of PMH1 or PMH2 with the complexes depends on the presence of RNA. Because cold treatment enhanced the steady-state transcript levels of both PMH proteins, we also examined the influence of cold on complex composition and/or size. The cell suspension culture was grown under normal conditions and then incubated for 18 h at 4°C under otherwise identical conditions. Mitochondria were isolated and proteins were investigated as in the previous experiments. This treatment decreased the abundance of the complexes with sizes below 480 kD (corresponding to the size of complex III; Fig. 5D). In contrast, substantially more complexes are detectable that are even larger than those observed in mitochondria from normally grown cultures (Fig. 5D). A similar complex pattern is apparent when the mitochondrial protein is solubilized in the presence of 10 mM MgCl2, which can stabilize ribonucleoprotein particles (Fig. 5E). Again, a shift toward higher molecular masses is seen under these conditions. In summary, our analysis suggests that PMH1 and/or PMH2 is part of RNA-dependent high-molecular-mass complexes. The size of the protein complexes or at least the interaction of the PMH proteins with complexes of higher molecular masses increases upon cultivation of the cells at 4°C or by the presence of MgCl2 during solubilization.
To investigate the complex association of the PMH proteins by an independent experimental procedure, DDM-solubilized mitochondrial protein was fractionated in discontinuous Suc gradients. In addition, this experiment will allow conclusions about potential interaction of the PMH proteins with ribosomes. Thus, 100 mg of mitochondria were solubilized with DDM under conditions optimized for the enrichment of intact mitochondrial ribosomes and polysomes (Raczynska et al., 2006 Proteins were investigated by immunodetection analysis with the PMH1/PMH2 antiserum after SDS-PAGE of 50 µL of each fraction. PMH1 and/or PMH2 is detected in fractions 1 to 7 and a slightly larger protein is found mainly in fractions 1 and 2 (Fig. 6A , top). This protein has also been detected in BN/SDS-PAGE, but had not been seen in the IEF/SDS-PAGE analysis, which might be attributed to conditions during IEF.
To determine the localization of ribosomes or polysomes in the gradient, total RNA was extracted from 800 µL of each Suc gradient fraction and inspected by agarose gel electrophoresis. The rRNAs were found predominantly in fractions 3 to 5, but only found in minor amounts in fraction 2, where the PMH proteins are highly abundant (Fig. 6A). This experiment demonstrates that a large portion of the PMH proteins does not cofractionate with ribosomes. When mitochondria are lysed in the presence of 300 mM KCl (Fig. 6B), the ribosomal RNA is again found in the same fractions, indicating that they remained intact as expected from a previous analysis (Fig. 6B, top; Raczynska et al., 2006
PMH1 and PMH2 Are Mitochondrial Proteins
In this study, we analyze two DEAD-box proteins encoded in the nuclear genome of Arabidopsis. We provide evidence for localization of the two proteins in mitochondria (Fig. 1). Fusion proteins consisting of different N-terminal parts of these polypeptides and GFP were consistently transported into these organelles. In addition, the putative RNA helicases were repeatedly detected in mitochondrial protein fractions (Figs. 4–6 In the mitochondrial lysate, several spots are detected after IEF and SDS-PAGE. Presently, we can only speculate about the appearance of different protein spots, which were observed in all experiments performed. These might be experimental artifacts, such as protein carbamylation or oxidation, even though IEF conditions were chosen to avoid such effects. In addition, the differential presence of PMH proteins in these spots suggests that they represent PMH proteins with differing posttranslational modifications. However, further experiments are required to clarify this issue.
PMH1 and PMH2 share 77% identical amino acids and thus are very similar to each other. In addition, each protein contains a characteristic C terminus, which is in both proteins predominantly composed of Ser and Gly. These similarities suggest similar functions of both proteins; however, there are clear differences in terms of the spatiotemporal transcription patterns of each gene. Also, the response of PMH1 expression to cold is stronger than the induction of PMH2 and only PMH2 promoter activity is induced by wounding. From these experiments, it can be concluded that, despite the high similarity of the two proteins, the polypeptides might fulfill different roles in plant mitochondria. PMH1 is expressed only in certain situations and might support PMH2 in its function. For instance, during flowering, which is an energy-consuming process, elevated mitochondrial activity is required. Likewise, cold stress might be a situation in which PMH2 activity is needed and in which it is supported by PMH1, which is more strongly induced under this environmental condition than PMH2. Although the Genevestigator expression analysis tool (https://www.genevestigator.ethz.ch) cannot discriminate between PMH1 and PMH2 genes (both genes are represented by a single oligonucleotide on the ATH1 gene chip), cold induction is confirmed by a meta-profile analysis. This investigation also reveals enhanced expression after heat stress in seeds, particularly 3 h after imbibition, and in stems, conditions, and tissues not inspected in our expression studies. In contrast to our northern and histochemical GUS-staining analyses, strong expression in flowers or parts of them is not indicated by the meta-profile analysis. Likewise, no response to wounding is found by this gene expression analysis, although enhanced PMH mRNA levels are found upon biotic stress caused by different pathogens. However, nothing is known about a function of a DEAD-box protein in response to wounding or pathogen attack.
Both PMH proteins contain approximately 100-amino-acid-long C termini rich in Arg, Gly, and Ser. Such termini, although in different lengths, are widespread among RNA-binding proteins (Lorkovic and Barta, 2002
As indicated by two-dimensional BN/SDS-PAGE and discontinuous Suc gradient centrifugation, both, or at least one, of the PMH proteins are part of large protein complexes. The exact composition of these complexes is presently unclear, but extrapolating from other DEAD-box protein-containing complexes, it can be assumed that several different proteins are present in these complexes. Certainly, RNA is a component of the complexes as clearly indicated by the observation that RNase digestion disrupts the complexes themselves or at least prevents the interaction of the PMH proteins with the complexes. In the latter case, the DEAD-box proteins would directly interact with the RNA, which would be possible through the Gly-rich C termini as mentioned above, whereas the former would indicate a central role of RNA in the architecture of the complex. Recently, another RNA-dependent protein complex has been observed in plant mitochondria, which contains a FLAG-tagged version of the PPR protein RF592, the restorer of the pcf-associated CMS in petunia (Petunia hybrida; Gillman et al., 2007
The dependence of complex formation on RNA might also explain the size variability of the complex, which ranges from the monomeric form up to 1,500 kD as estimated from BN/SDS-PAGE. Within this size range, distinct intermediate complexes are reproducibly observed. In addition, size variability is also indicated by the presence of the PMH proteins in different fractions of the Suc gradients, suggesting that size variation is not the result of a particular preparative procedure. This distribution is highly reproducible and independent from the presence of aminocaproate, which can destabilize protein complexes (data not shown; Novakova et al., 2006
Several explanations are possible for this size variation. First, the different complexes could represent different degradation intermediates, but the high reproducibility and the influences of MgCl2 and cold do not support this explanation. Second, the pattern might be attributed to assembly intermediates, but such intermediates are typically rather low in abundance and should not be detectable at such high levels. Third, this pattern might indicate the presence of mature complexes with varying associated components, different RNA molecules, different proteins, or both. This has, for instance, been observed for p53. This multifunctional protein is present in different complexes as indicated by a western-blot analysis of whole-cell extracts also separated by two-dimensional BN/SDS-PAGE (Camacho-Carvajal et al., 2004
The functions of PMH1 and PMH2 remain unclear. Distribution of these proteins and of the rRNAs in the discontinuous Suc gradients is too different to reflect stable association with mature ribosomes, although weak interaction of PMH1 and PMH2 is possible (Fig. 6). Thus, a function of these proteins in translation initiation cannot be excluded. To obtain more information about the functional role of these proteins, we established the respective knockout mutants. However, preliminary characterization of these plants grown under normal conditions as well as under different temperatures did not reveal any obvious phenotype (data not shown). Thus, further detailed studies are required to uncover the physiological function of these PMH proteins.
Maybe PMH proteins are involved in RNA secondary structure rearrangements, which are required for maintenance of cellular functions at reduced and elevated temperatures, as has been suggested for prokaryotic DEAD-box RNA helicases (Owttrim, 2006
Subcellular Localization Studies
DNA fragments representing the N-terminal parts of PMH1 and PMH2, respectively, were amplified with the following primer pairs: pmh1GFP1.5 (5'-CACTCTCTGGGATCCGAAAATG)/pmh1GFP1.3 (5'-GCGGATCCTAACATGAAAGTCTCTCAC), pmh1GFP1.5/pmh1GFP2.3 (5'-CGAATCTCGGATCCCTCCATCG), pmh2GFP1.5 (5'-CACCTGGATCCGAAAATGATCAC)/pmh2GFP1.3 (5'-ATGGATCCCTTTCGCTTCAACACC), and pmh2GFP1.5/pmh2GFP2.3 (5'-GCGGATCCCAAGCCCATCACCACCAAC). PCR was performed using oligo(dT)-primed cDNA from Arabidopsis (Arabidopsis thaliana) total RNA as template and BD Advantage 2 polymerase following the instructions given by the manual (TaKaRa). The cDNA products, which code for 69 and 100 amino acids of the PMH1 protein and 62 and 104 amino acids of the PMH2 polypeptide, respectively, were digested with BamHI and ligated into the corresponding site in the psmGFP4 vector (Davis and Vierstra, 1998
Arabidopsis ecotype Col-0 was grown on standard soil supplemented with Osmocote Exact Mini (Scotts) or on Murashige and Skoog medium in a growth chamber under a 16-h-light (160–200 µmol m–2 s–1, 23°C)/8-h-dark (21°C) regime. Tissues from adult plants were harvested from 3- to 4-week-old plants. Seedlings were grown for 7 d and then transferred to cold or kept at 23°C as control. RNA was isolated using an RNeasy plant mini kit following the manual given by the manufacturer (Qiagen). For northern analysis, about 10 µg of total RNA were denatured with glyoxale, separated on agarose gels, transferred to Hybond N nylon membranes, and hybridized according to standard protocols or to a protocol provided by the manufacturer (GE Healthcare). Probes used for hybridizations correspond to the long cDNA fragments used for studying subcellular targeting. Loading of the gels was monitored by hybridization with oligonucleotide P18SrRNA (5'-AAGCATATGACTACTGGCAGG) complementary to nuclear/cytoplasmic 18S rRNA sequences.
To study in vivo promoter activities, potential promoter regions corresponding to sequences from –1,981 to +14 (PMH1) and –2,067 to +3 (PMH2) with respect to the ATG (+1) were amplified with primer pairs pmh1prom5' (5'-ATAGTCGACTCAGAAACTCTAGAATCC)/pmh1prom3' (5'-ATAGTCGACTGTGCTAATCATTTTCAG) and pmh2prom5'Xba2 (5'-ACTCTAGAATGGTAGCCATCTCAACACC)/pmh1prom3'Xba (5'-TATCTAGACATTTTCAGATTCAGGTGTTC) on total DNA extracted with a DNeasy plant mini kit as outlined by the manufacturer (Qiagen). After amplification, PCR fragments were cloned upstream of the GUS genes into vector pBecks19/101, transformed into Arabidopsis plants by floral dip, and selected on kanamycin-containing Murashige and Skoog medium (Clough and Bent, 1998
Mitochondria were isolated and purified from an Arabidopsis Col-0 cell suspension culture as described before (Klein et al., 1998
IEF was performed with the IPGphor system following the manufacturer's instructions (GE Healthcare). About 20 mg of mitochondria were resolved in 200 µL lysis buffer (2 M thiourea, 5 M urea, 2% CHAPS, 2% SB 3–10, 40 mM Tris base, 2 mM Tris-bicarbonate-phosphate, 0.2 mM phenylmethylsulfonyl fluoride) for 1 h and insoluble constituents were removed by centrifugation at 18,400g for 20 min. Prior to separation by IEF, proteins were precipitated by adding 3 volumes of precipitation solution (90% [v/v] acetone, 10% [v/v] methanol, 10 mM dithiothreitol [DTT]), incubated overnight, and centrifuged for 15 min at 20,000g. Proteins were resuspended in rehydration solution (2 M thiourea, 5 M urea, 1% [w/v] CHAPS, 1% [w/v] SB 3–10, a trace of bromphenol blue, 2 mM Tris-bicarbonate-phosphate, 0.5% immobilized pH gradient buffer). Separation was done on immobiline nonlinear DryStrip gels, pH 3 to 11 and 7 to 11, respectively, under the following conditions: 50 µA per strip at 21°C. For pH 3 to 11 gradients, rehydration 12 h, step 1: step and hold, 200 V, 3 h; step 2: step and hold, 500 V, 3 h; step 3: gradient 1,000 V, 3 h; step 4: gradient, 8,000 V, 6 h; and step 5: step and hold, 8,000 V, 7 h. pH gradient 7 to 11: rehydration 24 h, step 1: step and hold, 200 V, 2 h; step 2: step and hold, 500 V, 2 h; step 3: gradient, 4,000 V, 4 h; step 4: gradient, 8,000 V, 5 h; and step 5: step and hold, 8,000 V 7 h. After focusing, gel strips were equilibrated in buffer A (50 mM Tris-HCl, pH 8.8, 6 M urea, 30% [v/v] glycerol, 2% [w/v] SDS, a trace of bromphenol blue, 1% [w/v] DTT) or buffer B, which is identical to buffer A except that DTT is replaced by 2.5% indole acetic acid. Subsequently, Tris-Tricine PAGE was carried out according to a previously described protocol (Schagger and von Jagow, 1987
For MS, visible protein spots were excised from the gel and digested with trypsin as described previously (Shevchenko et al., 1996
For subfractionation of mitochondrial protein complexes, 100 mg of purified organelles were dissolved in solubilization buffer (see above) in the presence of 200 mM Tris-HCl, pH 8.0, 35 mM MgCl2, 25 mM EGTA, 200 mM Suc, 40 mM EDTA, 2% (w/v) DDM, 0.5 mg/mL heparin, 10 mM β-mercaptoethanol, 500 mM chloramphenicol, and optional 300 mM KCl (Raczynska et al., 2006
The following materials are available in the online version of this article.
We thank Friedrich Ossenbühl, Jesco Heinemeyer, and Hans-Peter Braun for their technical advice in BN-PAGE. We are also very grateful to Bärbel Weber for excellent technical assistance. Received August 24, 2007; accepted October 5, 2007; published October 19, 2007.
1 This work was supported by the Deutsche Forschungsgemeinschaft (grant nos. Bi 590/7–1 and 7–2) and the Studienstiftung des deutschen Volkes (fellowship to J.F.). The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Stefan Binder (stefan.binder{at}uni-ulm.de).
[W] The online version of this article contains Web-only data. www.plantphysiol.org/cgi/doi/10.1104/pp.107.108076 * Corresponding author; e-mail stefan.binder{at}uni-ulm.de.
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