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First published online July 6, 2007; 10.1104/pp.107.104000 Plant Physiology 145:41-48 (2007) © 2007 American Society of Plant Biologists OPEN ACCESS ARTICLE
Mitochondrial Protein Lipoylation Does Not Exclusively Depend on the mtKAS Pathway of de Novo Fatty Acid Synthesis in Arabidopsis1,[W],[OA]Department of Plant Physiology, University of Rostock, D–18059 Rostock, Germany (R.E., Ü.K., U.B., H.B.); and Core Facility Proteome Analytics, Medical Faculty, University of Rostock, D–18057 Rostock, Germany (S.M.)
The photorespiratory Arabidopsis (Arabidopsis thaliana) mutant gld1 (now designated mtkas-1) is deficient in glycine decarboxylase (GDC) activity, but the exact nature of the genetic defect was not known. We have identified the mtkas-1 locus as gene At2g04540, which encodes -ketoacyl-[acyl carrier protein (ACP)] synthase (mtKAS), a key enzyme of the mitochondrial fatty acid synthetic system. One of its major products, octanoyl-ACP, is regarded as essential for the intramitochondrial lipoylation of several proteins including the H-protein subunit of GDC and the dihydrolipoamide acyltransferase (E2) subunits of two other essential multienzyme complexes, pyruvate dehydrogenase and -ketoglutarate dehydrogenase. This view is in conflict with the fact that the mtkas-1 mutant and two allelic T-DNA knockout mutants grow well under nonphotorespiratory conditions. Although on a very low level, the mutants show residual lipoylation of H protein, indicating that the mutation does not lead to a full functional knockout of GDC. Lipoylation of the pyruvate dehydrogenase and -ketoglutarate dehydrogenase E2 subunits is distinctly less reduced than that of H protein in leaves and remains unaffected from the mtKAS knockout in roots. These data suggest that mitochondrial protein lipoylation does not exclusively depend on the mtKAS pathway of lipoate biosynthesis in leaves and may occur independently of this pathway in roots.
Research on the photorespiratory pathway has triggered progress in many other fields of plant research and helped in the establishment of Arabidopsis (Arabidopsis thaliana) as an important model organism (Somerville, 2001
Here, we report on the identification of the gld1 locus (now designated mtkas-1) and show that it resides on gene At2g04540 encoding
mtkas-1 Is Defective in the Mitochondrial -Ketoacyl-[ACP] Synthase, mtKAS
The recessive mutation of mtkas-1 was originally mapped to chromosome II at a distance of about ±40 cM from the er-py visible marker region (Artus et al., 1994
To identify the defective gene, we chose to analyze T-DNA insertion lines for a variety of genes in this region. Among these lines, only seedlings of a population of a T-DNA insertion mutant for gene At2g04540 (SALK 022295; mtkas-2) segregated with a phenotype very similar to that of mtkas-1 (Fig. 1). Preliminary analysis of soluble amino acids revealed a highly elevated leaf Gly content, which corresponds with published labeling data for mtkas-1 plants (Somerville and Ogren, 1982
In contrast to the knockout T-DNA lines mtkas-2 and mtkas-3, significant amounts of mtKAS transcripts are detectable in mtkas-1 plants (Fig. 3). To further support our notion that the mutation in mtkas-1 affects the mtKAS locus, we therefore crossed emasculated plants of the mtkas-1 genotype to homozygous mtkas-2 and mtkas-3 plants. The F1 progenies, which were hybrid hemizygous for both the mtkas-1 and the respective mtkas-2 or mtkas-3 allele, should lack intact mtKAS alleles and the wild-type phenotype should not be restored. Indeed, these hybrid plants showed slow growth with pale-green to yellow leaves in normal air and were indistinguishable from the homozygous parents' photorespiratory phenotype (Supplemental Fig. S1). This lack of complementation provides direct genetic evidence that the photorespiratory phenotype of mtkas-1 is caused by a defect in the single-copy mtKAS gene, At2g04540. To exactly identify the mutation in the mtKAS gene of mtkas-1 plants, we then used two experimental strategies. First, sequencing of mtkas-1 cDNA obtained by RT-PCR with primers specific for mtKAS revealed a 1-bp deletion, which leads to a frameshift in the open reading frame and a truncated protein. Second, we isolated genomic DNA from mtkas-1 plants and amplified a 3.1 kb fragment by PCR. Sequencing of this genomic fragment revealed a G-to-A transition at the 3' splice site of the seventh intron, which results in the out splicing of one additional nucleotide (corresponding to the 1-bp deletion in the cDNA) in combination with a premature stop codon (Fig. 2B). Therefore, translation of the mtkas-1 mRNA stops at a position corresponding to Ile-277 with consequential loss of 185 C-terminal amino acids, i.e. about 40% of the native full-length protein. Importantly, none of the analyses to be discussed in the following paragraphs revealed any notable differences between mtkas-1 and the two T-DNA insertion lines, which confirms that all three lines are true knockout mutants.
These four lines of evidence, recombination mapping, phenotype analysis of T-DNA insertion lines, complementation analysis, and sequencing, evidently show that the gld1 (mtkas-1) locus is identical with the single-copy gene encoding the recently predicted (Mekhedov et al., 2000
To more exactly determine photosynthetic properties of mtKAS-deficient mutants, we measured the photosynthetic performance of plants grown under elevated CO2. Photosynthetic rates of mtkas-2 plants (7.2 ± 0.2 µmol m–2 s–1) were about 65% of wild-type rates (11.2 ± 0.8 µmol m–2 s–1) at 21% O2 and did not significantly deteriorate during the measurements. We also examined effects of photorespiratory conditions (normal air) on the steady-state levels of soluble amino acids in leaves of all three allelic mtkas mutants over a 24-h cycle (Fig. 4 ). In comparison with wild-type plants, Gly concentrations were 40- to 50-fold elevated in the mutants during illumination and become reduced by about 20% to 30% during the following dark period. Levels of Ser, Gln, Glu, and Ala changed into the opposite direction, i.e. about wild-type levels were found in the second half of the light phase and increased concentrations during the dark. No or only moderate changes were observed in the content of other amino acids (data not shown).
Both the recovery of the mtkas mutants by elevated CO2 and these two sets of more quantitative data correspond well with earlier findings (Somerville and Ogren, 1982 -ketoacid dehydrogenase complexes PDH and KGDH, also require lipoylation for their activity (Mooney et al., 2002
To more directly assess effects of mtKAS deficiency on mitochondrial metabolism, we next examined the efficiency of Gly decarboxylation by intact mitochondria (Table I
; Supplemental Fig. S2 for details). Good quality of the mitochondrial preparations was indicated by high rates of O2 consumption with malate or NADH and normal respiratory coupling levels (Keech et al., 2005
Activities of PDH and KGDH Are Reduced in mtkas Mitochondria
External pyruvate and
To further examine the possibility that the functional loss of mtKAS might affect subunit lipoylation in the three multienzyme complexes, GDC, PDH, and KGDH, to different extents, we performed western analyses with antisera specific for H protein and lipoic acid (LA), respectively. Lipoylation, within the restrictions of this method, means antigenic reactivity. This definition is important because protein-bound LA can react with the lipid peroxidation product 4-hydroxy-2-nonenal (HNE), which leads to loss of antigenicity of the respective protein domains. It has been shown that H protein is more susceptible to such modification than the E2 subunits of PDH and KGDH (Millar and Leaver, 2000
While GDC is an exclusively mitochondrial enzyme, PDH and KGDH are also present in plastids. To obtain additional evidence for H protein and also examine lipoylation of the E2 subunits of PDH and KGDH, we therefore performed similar experiments with mitochondria isolated from wild-type and mutant plants. Again, lipoylation of H protein in the mutant plants was detectable only after strong overexposure of the films (about 1% relative to wild type, Fig. 6, A and B ), while the level of H apoprotein remains unchanged (Fig. 6C). In contrast, we observed distinctly higher lipoylation levels for the PDH and KGDH E2 subunits (about 30% relative to wild type, Fig. 6A), which were identified according to antigenicity and apparent molecular masses (Taylor et al., 2004
By matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of peptides obtained from H-protein bands excised from a Coomassie-stained gel run in parallel, signals for the respective lipoylated H-protein peptide were detected for wild-type mitochondria, but below detection limit in mitochondria isolated from mtkas-1 and mtkas-2 plants. In the mutants, only signals corresponding to the respective unlipoylated peptide, but not to HNE-modified lipoylated peptides, could be detected (Supplemental Fig. S3). It shall be noted that modifications can reduce the signal intensity of peptides. While we cannot entirely exclude the possible presence of a small fraction of HNE-modified peptides in our preparations, limited bias caused by HNE would not weaken but even strengthen our argumentation.
H protein of GDC is the dominant lipoylated protein in photosynthesizing plant cells and occurs in large amounts in green leaf mitochondria, representing the major sink for octanoyl chains in these organelles (Wada et al., 1997
The existence of an mtKAS-independent pathway for mitochondrial octanoyl-ACP biosynthesis is not supported by the literature. Therefore, the import of free or protein-bound lipoate or octanoate from extramitochondrial compartments appears as more likely. Plastidal de novo synthesis and export of fatty acids (Koo et al., 2004
In this report, we identify the genetic lesion in the GDC-deficient mtkas-1 (gld1) mutant (Somerville and Ogren, 1982
Plants and Growth Conditions
Arabidopsis (Arabidopsis thaliana) L. Heynh., ecotype Columbia-0, was used as wild-type reference and ecotype Ler-0 was used for recombination mapping. Seeds of the mtkas-1 mutant (CS8012, Columbia ecotype) were obtained from Jitao Zou and T-DNA insertion lines SALK 022295 and SALK 087186 (Alonso et al., 2003
To map the mtkas-1 locus, homozygous mtkas-1 plants were crossed to wild-type plants of the Ler-0 background. The segregating F2 generation was grown in normal air and screened for the mutant phenotype. A total of 415 individuals of the pale-green and slow-growing mtkas-1 phenotype were selected, and DNA was extracted individually. PCR analysis was performed with primer combinations listed in Supplemental Table S1, and resulting PCR fragments were differentiated according to size or different restriction sites. For the initial mapping steps, framework markers (http://Arabidopsis.info/new_ri_map.html) were used and, to narrow the region of the mtkas-1 locus, further markers were designed using information from the Monsanto LER sequence collection (Jander et al., 2002
Genomic DNA of T-DNA lines SALK 022295 (mtkas-2) and SALK 087186 (mtkas-3) was subjected to standard PCR (Master Mix, Quiagen) with primers specific for the left (R741, mLB1) or right (R409, SALK-RB1) border, respectively, and gene-specific primers 04540-A1 (R759 for SALK 022295) and mtKAS-2A (R833 for SALK 087186). All primer sequences are shown in Supplemental Table S2. The obtained fragments were directly sequenced to verify the insertion sites. Homozygous plants were identified by PCR with genomic DNA using a combination of two gene-specific primers (R759 and R726 for SALK 022295, R833 and R795 for SALK 087186) encompassing the respective T-DNA insertion. The knockout of mtKAS in homozygous plants of both mutant lines was verified by RT-PCR using 2.5 µg of leaf RNA (Nucleospin RNA plant kit, Macherey-Nagel) for cDNA synthesis (RevertAid cDNA synthesis kit, MBI Fermentas) and the primer combination R795 and R758. Prior to PCR analysis, cDNA amounts were calibrated according to signals from the constitutively expressed At2g09990 gene encoding the 40S ribosomal protein S16 (primers R176 and R177).
Photosynthetic rates were measured with fully expanded leaves of plants grown in air enriched to 5.000 µL L–1 CO2 using a Licor-6400 gas-exchange system (LI-COR). Measurements were performed at a photosynthetic photon flux density of 500 µE m–2 s–1 supplied by an in-built red/blue LED light source, 380 µL L–1 CO2, 21% (v/v) O2, and a leaf temperature of 25°C.
Amino acids were extracted in 1.8 mL 80% (v/v) ethanol from 100 mg leaf material powdered in liquid nitrogen. After centrifugation, the supernatants were dried by lyophilization and redissolved in 8 mM Na2PO4 (pH 6.8) and 0.4% (v/v) tetrahydrofurane. Individual amino acids were quantified after derivatization with o-phthaldialdehyde as described elsewhere (Eisenhut et al., 2006
All plants for these experiments were grown at elevated CO2. Mitochondria were isolated from wild-type and mutant leaves according to Keech et al. (2005)
Respiratory rates were determined from three (wild type), two (mtkas-2), or one (mtkas-1) independent mitochondria preparations using about 100 µg protein per measurement. The Oxygraph oxygen electrode chambers (Hansatech) contained, in a total volume of 1 mL at 25°C, 0.3 M Suc, 10 mM TES (pH 7.5 with KOH), 10 mM KCl, 2 mM MgSO4, 5 mM KH2PO4, 0.1% (w/v) bovine serum albumin, and mitochondria equivalent to about 100 µg protein (Bradford, 1976
PDH and KGDH activities were measured in triplicate from three independent mitochondrial preparations (n = 9) for each genotype (wild type and mtkas-2). Assays contained, in 1 mL at 25°C, 50 mM TES-KOH, pH 7.5, 2% (v/v) Triton X-100, 3.3 mM MgCl2, 3 mM Cys, 2.5 mM NAD+, 0.2 mM thiamine pyrophosphate, 1.5 mM pyruvate, or Whole organ extracts were prepared by grinding 500 mg leaf material or 2 g washed roots in liquid nitrogen with subsequent extraction in a 4-fold volume of ice-cold extraction buffer (50 mM HEPES-NaOH, pH 7.6, 1 mM sodium EDTA, 5 mM MgCl2, 10 mM NaCl, 100 mM sorbitol, and 1 mM phenylmethanesulfonyl fluoride) followed by centrifugation at 20,000g for 10 min.
Mitochondrial and whole leaf proteins were separated in 12% (w/v) Tricine-SDS-polyacrylamide gels (Schägger, 2006
Mitochondrial proteins of wild-type and mtkas1-1 plants were separated in a 12% (w/v) Tricine-SDS-polyacrylamide gels and stained with Coomassie. Excised H-protein bands were reduced and alkylated with tributylphosphine and iodoacetamide, respectively, and digested with trypsin. The resulting peptide mixtures were analyzed by MALDI-TOF MS using a Reflex III mass spectrometer (Bruker Daltonik) as described (Fulda et al., 2006
The following materials are available in the online version of this article.
We gratefully acknowledge the helpful discussions and support received from Dr. Murray Badger as well as the photosynthesis measurements by Dr. Susanne von Caemmerer (Australian National University, Canberra, Australia). We are grateful to Kirsten van den Daele for initial experiments, Klaudia Michl for performing amino acid analyses, and Dr. Martin Hagemann for critical discussions (all at University of Rostock, Germany), and unknown reviewers for helpful suggestions. This work would not have been possible without the mutant lines obtained from the Nottingham Arabidopsis Stock Centre and seeds of the mtkas-1 mutant (CS8012) kindly provided by Dr. Jitao Zou (Plant Biotechnology Institute, Saskatoon, Canada). Received June 14, 2007; accepted June 27, 2007; published July 6, 2007.
1 This work was supported by a grant from the Deutsche Forschungsgemeinschaft (to H.B.).
2 Present address: Center for Life Science Automation, F.-Barnewitz-Str. 8, D–18119 Rostock, Germany. 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: Hermann Bauwe (hermann.bauwe{at}uni-rostock.de).
[W] The online version of this article contains Web-only data.
[OA] Open Access articles can be viewed online without a subscription. www.plantphysiol.org/cgi/doi/10.1104/pp.107.104000 * Corresponding author; e-mail hermann.bauwe{at}uni-rostock.de.
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