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J. Biol. Chem., Vol. 281, Issue 4, 2177-2183, January 27, 2006
Mdv1 Interacts with Assembled Dnm1 to Promote Mitochondrial Division*
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| ABSTRACT |
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| INTRODUCTION |
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Existing experimental evidence indicates that the yeast dynamin-related protein, Dnm1, is the master regulator of mitochondrial division. Dnm1 self-assembles and in vivo exists at steady state in punctate structures associated with the outer mitochondrial membrane, often at points of membrane constriction and fission (3, 4, 11, 12). Recent biochemical and structural analysis of pure Dnm1 indicates that Dnm1 self-assembly functions to drive the membrane constriction and fission events associated with mitochondrial division (13). Specifically, Dnm1 forms extended spirals, which possess diameters greater than dynamin-1 spirals, but which are, remarkably, equal to diameters of mitochondrial constriction sites in vivo. Dnm1 self-assembly proceeds through a rate-limiting nucleation step and nucleotide hydrolysis by assembled Dnm1 structures is highly cooperative with respect to GTP (13). These kinetic features of Dnm1 suggest that the key rate-limiting event in division is the regulation of Dnm1 self-assembly.
In yeast, two additional components, Fis1 and Mdv1, are required and function together with Dnm1 in mitochondrial division (5). Fis1 is a highly conserved C-tail anchored outer membrane protein comprised largely of a cytosolic superhelical tetratricopeptide repeat domain (14). An interaction of the human ortholog, hFis1, with the human Dnm1 ortholog, Drp1, has been reported, but the role of this interaction in division is unknown (15). To date, however, no interaction between Fis1 and Dnm1 has been detected, raising the possibility it is labile or not essential in yeast. In yeast, the most well defined role of Fis1 is as a mitochondrial receptor for Mdv1, where the Fis1·Mdv1 complex functions to trigger division (16, 17).
Mdv1 is a multidomain protein containing three major regions, an N-terminal extension of unknown structure (NTE),3 a central predicted coiled-coil (C-C), and a C-terminal WD repeat (WD), predicted to form a seven-bladed propeller. Previous two-hybrid and cytological observations indicate that the Mdv1 NTE mediates an interaction with Fis1, the Mdv1WD mediates the interaction with Dnm1, and the central Mdv1 C-C mediates homo-oligomer formation (17). The WD is both necessary and sufficient for Mdv1 to interact with Dnm1 punctate structures (17, 18). Thus, Mdv1 functions as an adaptor linking Fis1 with Dnm1 during division.
Yeast cells possess a close Mdv1 structural homolog, Caf4, which also interacts and forms a complex with Fis1 (19). In the absence of Mdv1, a Fis1·Caf4 complex targets Dnm1 to the membrane; however, the Fis1·Caf4 complex only supports minimal division activity. Consistent with this, in cells lacking Caf4, mitochondrial morphology is reticular and indistinguishable from that of wild type. In cells lacking both Mdv1 and Caf4, Dnm1 is not stably targeted to mitochondria, an identical phenotype to fis1-
cells. Thus, Fis1 targets Dnm1 to mitochondria only through its ability to interact with either Mdv1 or Caf4. Analysis of Mdv1 indicating that it functions as a linker between Fis1 and Dnm1 supports this conclusion (17). The role of the Caf4·Fis1 complex in mitochondrial division is unknown at present, but it is clearly dispensable and most likely regulatory.
In this report, we further examine the role that Mdv1 plays in mitochondrial division subsequent to Dnm1 targeting. Our analysis suggests that Mdv1 interacts with Dnm1 only when it is self-assembled into GTP-dependent ring-like structures and not when it exists as extended filaments, which form in the absence of GTP. We also show that the Mdv1 WD domain plays both regulatory and structural roles in division via its interaction with Dnm1 and indicates that membrane division requires a dynamic Mdv1/Dnm1 interaction. We postulate that the critical activity of Mdv1 in division is to promote the assembly of Dnm1 into a division competent spiral-like structure.
| EXPERIMENTAL PROCEDURES |
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PlasmidsA plasmid containing GAL-regulated MDV1 was constructed by inserting the KpnI-SacI piece of p416GALL (American Type Culture Collection) containing the GALL promoter and MCS into pRS314 to create p414GALL. GFP-MDV1 was removed from p416GALL-MDV1 (17) by SpeI and XhoI digest and inserted in p414GALL resulting in p414GALL-GFP-MDV1.
p416GALL-dsRed/dimer2-MDV1 was created by ligating MDV1 into p416GALL (American Type Culture Collection) using BamHI and EcoRI sites. EcoRI and BamHI sites were introduced by PCR amplification of the MDV1 open reading frame and this construct was ligated into p416GALL resulting in p416GALLMDV1. XbaI and BamHI sites were introduced into the dsRed/dimer2 open reading frame by PCR amplification (22). This construct was ligated into p416GALL-MDV1 resulting in p416GALL-dsRed/dimer2-MDV1.
A mitochondrial targeted dsRedT1 was created by removing GFP from VT100U-mitoGFP (23) by KpnI-NotI digest, blunting the KpnI site in the vector backbone with Vent polymerase, dsRed.TI (24) was inserted creating a mitochondrially targeted dsRedT1. A mitochondrial targeted CFP was created by removing GFP from pYX223-mitoGFP (23) by SmaI digest and replacing it with CFP, which was PCR amplified from pDH3 obtained from the Yeast Resource Center, resulting in pYX223mitoCFP.
Generation of Mdv1 and Dnm1 MutantsSite-directed mutations were created using a complementary primer PCR method (QuikChange® kit, Invitrogen). Primers 40-60 bases in length were constructed with 20-30 nucleotides on either side of the altered nucleotide(s) and were purified by polyacrylamide gel as described (25). Whole plasmid amplification was performed and PCR products were digested with DpnI for 2 h at 37°C to remove template DNA. The amplified plasmid DNA was transformed into DH5
cells. Plasmid DNA was isolated from selected colonies and sequenced to confirm mutations. Expression of mutant proteins was determined by Western analysis using anti-Mdv1 and anti-Dnm1 antibodies (11, 16). All Mdv1 and Dnm1 mutant proteins used in this study were determined to be stable and expressed at levels similar to wild type protein. All mutants were analyzed under conditions where expression levels were similar to chromosomal wild type protein levels with the exception of Mdv1 mutants expressed under the GALL promoter, where levels were
10-20-fold higher (data not shown).
Random mutagenesis was performed using mutagenic PCR conditions to amplify nucleotides 1-687 of MDV1 and the resultant PCR products were used as megaprimers for whole plasmid amplification (26). Whole plasmid PCR products were transformed into DH5
cells to create a DNA library. Mdv1 mutants were screened and identified by their inability to rescue the glycerol growth defect in mdv1-
cells harboring the temperature-sensitive fusion mutant fzo1-1 (16). Potential mutants were tested for Mdv1 expression by Western analysis and sequenced before further analysis.
Dnm1 Purification and Electron MicroscopyBoth procedures were performed as previously described (13).
GTPase AssayA GTPase assay in which substrate was continuously regenerated and GTPase activity measured continuously was performed as previously described (13). Reactions were carried out in 25 mM HEPES, 25 mM PIPES, pH 7, 110 mM imidazole, pH 7.4, 7.5 mM KCl, 160 mM NaCl, 5 mM MgCl2, 1 mM phospho(enol)pyruvate, 20 units/ml pyruvate kinase/lactate dehydrogenase, 600 µM NADH, 5.5% Me2SO, and 250 µM GTP. In each reaction, the concentration of wild type Dnm1 was 0.048 mg/ml (0.55 µM). To assess the effect of mutants Dnm1K41A, Dnm1S42N, and Dnm1T62D/F on wild type Dnm1 GTPase activity, increasing amounts of each mutant were added to wild type Dnm1. Increasing concentrations of each of the mutant proteins, contained in a 40-µl volume of freezing buffer (20 mM HEPES, 20 mM PIPES, pH 7, 400 mM imidazole, pH 7.4, 400 mM NaCl, 20% Me2SO), were preincubated with 10 µg of wild type Dnm1. GTPase assay reactions were started by the addition of reaction buffer to the preincubated proteins.
All GTPase assay reactions were performed in 200-µl volumes, of which 150 µl was placed into wells of a 96-well plate. Depletion of NADH over time was measured for a duration of 40 min using a SpectraMAX 250 96-well plate reader (Molecular Devices). Spectrophotometric data were transferred to Excel and the measured depletion of NADH over time was converted to a protein activity.
GTP Binding AssayGTP binding assays were performed in 25 mM HEPES, 25 mM PIPES, pH 7, 90 mM NaCl, 60 mM imidazole, 0.5 µM [
-32P]GTP, 1 mM dithiothreitol, 5 mM MgCl2. Approximately 2.3 µg of protein was added to the GTP binding buffer in a 20-µl reaction volume. After incubating at room temperature for 5 min, the reactions were placed directly onto parafilm that was resting on top of the ice. The reactions were irradiated in a Spectrolinker XL-1500 (Spectrontics Corp.) at 254 nm for 300 s,
10 cm from the UV source. After cross-linking, 15 µl of each cross-linked reaction were placed into tubes containing 5 µl of 4x sample buffer, boiled for 5 min, and resolved on a 12% SDS-PAGE gel. The gel was stained with Coomassie, destained, dried onto Whatman paper, and wrapped in plastic. A phosphorscreen was exposed to the dried gel and scanned using a Storm system (Amersham Biosciences).
Two-hybrid AnalysisFull-length MDV1, 1-2142 nucleotides, or the WD region, 903-2142 nucleotides, were PCR amplified, introducing EcoRI and BamHI restriction sites, and ligated into pGAD and pGBDU to create pGAD-MDV1, pGAD-WD, pGBDU-MDV1, and pGBDU-WD (27). pGAD-FIS1tr and pGBDU-FIS1tr were created by ligation of PCR-amplified FIS11-381 nucleotides with introduced BamHI and SalI restriction sites into pGAD and pGBDU. pGADDNM1 and pGBDU-DNM1 were created by removing DNM1 from pRU23BD-DNM1 (28) and ligating it into pGAD and pGBDU using BamHI and SalI sites. For two-hybrid analysis, plasmids constructed as described above for pGBDU and pGAD were co-transformed into the yeast strain PJ69-4A and tested for interactions as previously described (27).
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strains expressing GFP-Mdv1 and GFPMdv1N544R. Mdv1 and Dnm1 mutants were determined to complement the respective null strains by the recovery of net-like mitochondria to reticular structures upon expression of Mdv1 and Dnm1 mutant alleles. Dominant negative phenotypes were determined by the interference of Mdv1 and Dnm1 mutants with wild type proteins as observed by the formation of nets upon the expression of the mutant alleles in an otherwise wild type background. | RESULTS |
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Mdv1 Interacts Specifically with Assembled Dnm1 Ring StructuresWe examined the effect of Dnm1 mutants predicted to affect both GTPase and self-assembly on the formation of the Mdv1·Dnm1 complex to determine its role during mitochondrial division. We mutated and analyzed three different residues within the GTPase domain of Dnm1, Dnm1K41A, Dnm1S42N, and Dnm1T62D/F, known from studies of orthologous dynamin mutations to be involved in nucleotide binding and hydrolysis. It has been shown by yeast two-hybrid assays that Dnm1 self-interacts through its GED and middle domains (28). Thus, in addition to the GTPase mutants, we also analyzed Dnm1G385D, a previously reported middle domain mutant, which blocks self-assembly in vivo and in vitro (13, 31).Asexpectedandconsistentwithpreviousobservations all four Dnm1 mutants block division as observed by the inability to rescue dnm1-
. Additionally they are dominant negative as indicated by net formation in wild type cells (data not shown) (18, 31).
We characterized this bank of Dnm1 mutants for GTPase activity, self-assembly, and in vivo behavior (Table 2). Recently we have characterized the kinetic and structural properties of Dnm1 (13). Our data indicate that, like dynamin, Dnm1 self-assembly stimulates its own GTPase activity
16-fold (wild type activity, 50 min-1) and that in the presence of GTP or non-hydrolyzable GTP analogs, Dnm1 self-assembles into spiral-like structures (13). In contrast, in the absence of nucleotides or the presence of GDP, Dnm1 forms extended slightly curved filaments. In addition, we have shown that Dnm1G385D cannot self-assemble and, as a consequence, exhibits lower GTPase activity (3 min-1) (13). Our studies have demonstrated that Dnm1G385D exists as a nucleotide-independent stable dimer, suggesting that dimeric Dnm1 is the building block for the formation of higher order Dnm1 structures (13). Using identical experimental conditions, we have characterized the activity of the Dnm1 GTPase domain mutants and observe that, in contrast to wild type, and as predicted, no GTPase activity can be detected (up to 2 mM GTP) for any of these GTPase mutants. Interestingly, although Dnm1K41A possessed no activity on its own, it uniquely stimulated wild type Dnm1 GTPase activity, suggesting that Dnm1K41A can promote the self-assembly of wild type Dnm1 into structures that are activated for GTP hydrolysis (Fig. 3A).
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Cytological analysis of these mutants also confirmed observations obtained from EM and two-hybrid analyses and uniquely placed them in the context of the division pathway in vivo. In vivo analysis of GFP-tagged Dnm1 GTPase mutants showed that in all cases mutant Dnm1 forms punctate-like structures consistent with self-assembly. However, more detailed time-lapse analysis revealed that Dnm1T62D/F and Dnm1S42N containing structures do not interact with mitochondria, are localized to the cytosol, and are structurally aberrant/larger as compared with wild type (Fig. 3D and Table 2). Previous analysis of Dnm1S42N and Dnm1T62F have also shown aberrant structures, however, these were reported to be associated with mitochondria (18). This difference in observations is possibly because of parental strain differences (18). Regardless, our observations, coupled with EM analysis of the Dnm1T62D/F and Dnm1S42N mutants showing that they cannot form GTP-dependent spirals, suggest that the observed aberrant in vivo structures are dead end aggregates. In contrast, in vivo analysis of the behavior of Dnm1K41A indicated that Dnm1K41A containing structures were exclusively localized to mitochondria and similar in morphology to wild type Dnm1 puncta (Fig. 3D and Table 2). These observations, together with EM analysis showing that Dnm1K41A can assemble into GTP-dependent rings suggest that the Dnm1K41A structures represent productive intermediates.
We examined the ability of Mdv1 to interact with this set of characterized Dnm1 mutants using cytological and two-hybrid analyses. Strikingly, based on both types of analysis, the ability of Mdv1 to interact with Dnm1 mutants was correlated with the ability of these Dnm1 mutants to self-assemble into ring and spiral-like structures. Specifically, as previously published, Mdv1 does not co-localize or interact in the two-hybrid assay with Dnm1T62F or Dnm1S42N (Table 2) (18). Additionally, Mdv1 does not co-localize or interact in the two-hybrid assay with Dnm1T62D or Dnm1G385D (Table 2). In contrast, Mdv1 does co-localize with mitochondrial associated Dnm1 and Dnm1K41A structures in vivo and interacts with Dnm1 and Dnm1K41A by two-hybrid analysis (Table 2). Taken together, our analysis suggests that Mdv1 interacts specifically with assembled GTP-dependent Dnm1 ring structures, which is consistent with a role for Mdv1 regulating Dnm1 assembly during division.
Structure Function Analysis of Mdv1 Confirms That the NTE Interacts with Fis1 and Indicates That the WD Region Functions as a Regulatory Domain via its Interaction with Dnm1To further understand the role of Mdv1 in division, we undertook a detailed structure-function analysis approach. We made a variety of mutations in both the NTE and WD regions of Mdv1, which, from deletional analysis, are known to mediate the interactions with Fis1 and Dnm1, respectively (17). Using random PCR mutagenesis, we identified the mutation L148P within the NTE that confirms ours previous findings that the NTE mediates the interaction between Mdv1 and Fis1 (Table 3). Specifically, Mdv1L148P failed to complement the mitochondrial morphological division defect in mdv1-
cells (Table 3).
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To analyze the role of the Mdv1 WD domain, we used site-directed mutagenesis of residues predicted to form the top and bottom loops between the
-sheets, which form each of the predicted seven blades of the propeller. The mutations are superimposed on the ribbon structure of the G
WD domain for clarity (Fig. 4A). The Mdv1 WD mutants segregated into three categories (Fig. 4 and Table 4). Class I mutations behaved as wild type Mdv1: they complemented mdv1-
cells, had no dominant negative effects on mitochondrial morphology, and formed puncta that co-localized with Dnm1 on the mitochondria (Table 4 and Fig. 4B, panel 1). Additionally, by two-hybrid analysis, class I mutants showed no alteration of interaction of Mdv1 with itself, Fis1, or Dnm1 (not shown). In contrast, class II mutants (H440E, H440N, H605E) behaved as loss of function mutants: they failed to complement the mitochondrial morphological defects of mdv1-
cells, had dominant negative effects, as defined by net formation in wild type cells, and colocalized with the mitochondria in a uniform pattern, indicating that they have lost their ability to interact with Dnm1 (Table 4 and Fig. 4B, panel 2). This conclusion is supported by two-hybrid analysis, which demonstrates that class II mutants lose their ability to interact with Dnm1, but maintain their interaction with Fis1 and Mdv1 (Table 5). An additional mutant, Mdv1R634E, was identified by its partial loss of function. Mdv1R634E only partially complements mdv1-
and is slightly dominant negative in wild type (Table 4) and interestingly it co-localizes with the mitochondria yet still forms a few puncta (data not shown). This suggests that Mdv1R634E has a partial loss of interaction with Dnm1 although no alteration of the interaction was detected by two-hybrid analysis (data not shown). As shown in Fig. 4A, these class II mutants are predicted to be on top of blades two and five, indicating that these regions mediate, either directly or indirectly, Mdv1/Dnm1 interactions. Cerveny and Jensen (18) previously reported that Mdv1R461A, which maps to blade two of the predicted Mdv1 WD, also disrupts the Mdv1/Dnm1 interaction by cytological and two-hybrid analyses (18).
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and when expressed in wild type cells displayed a dominant negative phenotype; it blocked division and caused small mitochondrial net-like structures to form like the class II mutants (Table 4). However, in contrast to the class II mutants, GFP-Mdv1N544R localized to Dnm1-dependent punctate structures based on cytological analysis (data not shown). In fact, time-lapse analysis of Mdv1N544R behavior indicated that a significant fraction of Mdv1N544R puncta were present in the cytosol, unlike wild type Mdv1 puncta (Fig. 4B, panel 4, arrows, and supplemental movies 1, A and B). Quantification of the behavior of Mdv1 and Mdv1N544R puncta over time revealed that 65 ± 15% of Mdv1N544R puncta are on the mitochondria compared with 93 ± 4% of wild type Mdv1, showing a significant mislocalization of Mdv1N544R puncta into the cytosol (5 cells were analyzed for each strain for a total of 200 time points, approximately 10 Mdv1 punctate structures were present/0.2-µm section). Additionally, analysis of Dnm1 in the presence of Mdv1N544R showed no alteration of the localization of Dnm1 to both cytosolic and mitochondrial pools (data not shown). Further analysis of Mdv1N544R using the two-hybrid approach confirmed that it interacts with Dnm1 and significantly, demonstrated that the interaction is more stable, as seen by robust growth of positive cells in 3 days, rather than the 1 week growing time to detect the wild type Mdv1/Dnm1 interaction (Table 5). Together two-hybrid analysis and cytological data are consistent with the interpretation that Mdv1N544R more stably interacts with Dnm1, causing the mislocalization of Mdv1 to the cytosol. To determine whether this more stable interaction caused by Mdv1N544R was capable of overcoming the inability of Dnm1S42N and Dnm1T62D/F to interact with Mdv1, we used both cytological and two-hybrid approaches to analyze the interaction between Mdv1N544R and Dnm1 GTPase mutants. The presence of the N544R mutation was not able to compensate for the loss of interaction of Mdv1 with Dnm1S42N and Dnm1T62D/F, although Mdv1N544R was capable of maintaining the interaction with Dnm1K41A as expected (data not shown). These findings emphasize the functional importance of the Mdv1/Dnm1 interaction and further suggest that during division this interaction is dynamic and that Mdv1 acts in a regulatory manner.
| DISCUSSION |
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| FOOTNOTES |
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The on-line version of this article (available at http://www.jbc.org) contains supplemental Movie 1. ![]()
1 Present address: Section of Molecular and Cellular Biology, University of California, Berkeley, CA. ![]()
2 To whom correspondence should be addressed. Tel.: 530-754-9774; Fax: 530-752-7522; E-mail: jmnunnari{at}ucdavis.edu.
3 The abbreviations used are: NTE, N-terminal extension; C-C, coiled-coil; WD, WD repeat
-propeller; SD, synthetic media with dextrose; S-Raf, synthetic media with raffinose; S-Gal, synthetic media with galactose; mito, mitochondrial targeting sequence; EM, electron microscopy; GMP-PCP, guanylyl 5'-(
,
-methylenediphosphonate); GFP, green fluorescent protein; CFP, cyan fluorescent protein; PIPES, 1,4-piperazinediethanesulfonic acid; dsRed, red fluorescent protein from Discoma sp. ![]()
4 Dnm1T62D and Dnm1T62F are phenotypically identical; all presented data are of Dnm1T62F unless noted. ![]()
| ACKNOWLEDGMENTS |
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| REFERENCES |
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