Plant Mol Biol (2007) 63:519–532 DOI 10.1007/s11103-006-9106-y Isolation and characterization of the cytoplasmic male sterilityassociated orf456 gene of chili pepper (Capsicum annuum L.) Dong Hwan Kim Æ Jeong Gu Kang Æ Byung-Dong Kim Received: 21 April 2006 / Accepted: 30 October 2006 / Published online: 21 January 2007 Springer Science+Business Media B.V. 2007 Abstract Cytoplasmic male sterility (CMS) in plants is known to be associated with novel open reading frames (ORFs) that result from recombination events in the mitochondrial genome. In this study Southern and Northern blot analyses using several mitochondrial DNA probes were conducted to detect the presence of differing band patterns between male fertile and CMS lines of chili pepper (Capsicum annuum L.). In the CMS pepper, a novel ORF, termed orf456, was found at the 3¢-end of the coxII gene. Western blot analysis revealed the expression of an approximately 17-kDa product in the CMS line, and the intensity of expression of this protein was severely reduced in the restorer pepper line. To investigate the functional role of the ORF456 protein in plant mitochondria, we carried out two independent experiments to transform Arabidopsis with a mitochondrion-targeted orf456 gene construct by Agrobacterium-mediated transformation. About 45% of the T1 transgenic population showed the male-sterile phenotype and no seed set. Pollen grains from semi-sterile T1 plants were observed to have defects on the exine layer and vacuolated pollen phenotypes. It is concluded that this newly discovered orf456 may represent a strong candidate gene – from among GenBank accession number DQ116040 (orf456 genomic sequence), DQ126683 (pepper coxII genomic sequence) D. H. Kim J. G. Kang B.-D. Kim (&) Department of Plant Science, College of Agriculture and Life Sciences, and Center for Plant Molecular Genetics and Breeding Research, Seoul National University, Seoul 151921, Korea e-mail: [email protected] the many CMS-associated mitochondrial genes – for determining the male-sterile phenotype of CMS in chili pepper. Keywords Arabidopsis thaliana Capsicum annuum L. Cytoplasmic male sterility (CMS) Mitochondrial mutant Mitochondrial targeting signal orf456 Introduction Cytoplasmic male sterility (CMS) is a maternally inherited trait that leads to the failure to produce functional pollens. The gene associated with the CMS trait has been identified in the mitochondrial genome (Schnable and Wise 1998). Specific genes implicated in CMS have been reported for maize (Dewey et al. 1986), petunia (Young and Hanson 1987), bean (Johns et al. 1992), Brassica (Bonhomme 1992; Grelon et al. 1994), radish (Makaroff et al. 1990), sunflower (Moneger et al. 1994), rice (Akagi 1995), carrot (Kanzaki et al. 1991), sorghum (Tang et al. 1996) and many others. Although these CMS-associated genes are usually generated by intra-molecular rearrangement of mitochondrial DNA (mtDNA) (Hanson 1991), the open reading frames (ORFs) share no significant sequence homology, and it is still not clear just how these genes act in CMS plants to produce mitochondrial dysfunction (Hanson and Bentolila 2004). Several attempts have been made to transform these CMS-associated genes into fertile plants. The orf239, which is the CMS-associated mtDNA sequence of common bean (Abad et al. 1995), has been transformed into tobacco, with or without mitochondrial 123 520 targeting sequences. The transformed tobacco plants exhibited a semi-sterile or male-sterile phenotype, despite the fact that the protein may not have been targeted to the mitochondria (He et al. 1996). Another CMS-associated gene, the urfS sequence of the pcf gene that encodes a 25-kDa protein in petunia, has been transformed into petunia and tobacco plants with constructs that contain mitochondrial targeting sequences. The expression of the PCF protein was detected in the mitochondria of transgenic petunia and tobacco plants, although plant fertility was not affected (Wintz et al. 1995). In chili pepper (Capsicum annuum L.), CMS was first documented in the PI 164835 line from India (Peterson 1958). CMS pepper has subsequently been utilized for the production of F1 hybrids in South Korea and world wide. This so-called Peterson’s CMS line is the only source of hybrid F1 pepper seeds. Despite the agricultural importance of CMS pepper, not a great deal of attention has been paid to the molecular analysis of the CMS genes in pepper. Based on the results of a restriction fragment length polymorphism analysis of male-fertile and CMS pepper, we recently reported that the coxII and atp6-2 regions of these two lines have different DNA structures (Kim et al. 2001). We subsequently developed CMSspecific SCAR (sequence-characterized amplified region) markers on the basis of the sequence data (Kim and Kim 2005). The CMS trait can be suppressed by the action of the Rf gene in nucleus (Hanson and Bentolila 2004). Genetic studies between CMS mitochondrial factors and nuclear Rf genes in pepper have been reported by several groups. However, just how many Rf genes actually affect the CMS trait in pepper has not yet been clearly determined. Suggestions to date include the existence of the Rf gene as one or two major Rf genes or, alternatively, as a major dominant gene with several modifier genes (Peterson 1958; Novak et al. 1971; Wang et al. 2004). In a study on fertility restoration in CMS pepper, Wang et al. (2004) recently detected one major quantitative trait locus (QTL) and four additional minor QTLs. Based on these reports, we hypothesized that there may be more than one CMSinducing factor in pepper mitochondria. Despite the fact that we had already detected transcriptional differences in the atp6 gene between the CMS and restorer line (Kim and Kim 2006a), we focused on investigating a second CMS-associated gene in pepper. We report here our detection of a CMS-associated gene in pepper, orf456, and present evidence that it generates the male-sterile phenotype in transformed Arabidopsis when introduced together with mito- 123 Plant Mol Biol (2007) 63:519–532 chondrion-targeting sequences. Based on this evidence, we propose that orf456 is a strong candidate gene for determining the male-sterile phenotype of CMS in chili pepper. Results Southern blot analysis was performed using eight mitochondrial gene-specific probes which had been reported to be associated to CMS in other higher plants (Table 2). Of these, four probes, namely, atpA, atp6, coxI, and coxII revealed RFLPs between malefertile and CMS pepper lines (Fig. 1a). Northern blot analysis between the male-fertile and CMS mtDNAs revealed an absence of differences with the atpA, atp6, and coxI probes but the coxII transcripts showed different band patterns (the uppermost bands indicated by arrows in Fig. 1b). We therefore subjected the coxII gene region to analysis by inverse PCR. The ORF FINDER program (http://www.ncbi.nlm.nih.gov/gorf/) predicted a new ORF, which we termed orf456, in the 3¢-end region of the coxII gene in the CMS line (Fig. 1c). Differences in the nucleotide sequences of the fertile and CMS coxII flanking regions were apparent in the 3¢-end non-coding region, which lies 41 nt in the 3¢-direction from the stop codon of the coxII gene (Fig. 2). In the case of rice, incomplete RNA editing events, which produce malfunctional proteins, have been associated with fertility restoration (Iwabuchi et al. 1993). To test this possibility we amplified DNA complementary to orf456 from both CMS (S/rf/rf) pepper and restorer (S/Rf/Rf) pepper lines and compared these samples for the occurrence of RNA editing. All of the orf456 clones from the CMS and restorer lines shared the same single editing site at 150 nt downstream from the start codon. The RNA editing from C to U would result in a silent mutation (Leu fi Leu) (Fig. 2). The RT-PCR and Northern blot analyses confirmed that orf456 was transcribed in sterile and restorer lines as both of these carried the S-cytoplasm that induces the CMS phenotype in chili peppers (Fig. 3a, b). The primer region and sequences spanning the orf456 coding sequence for the RT-PCR experiments are shown in Fig. 1c and Table 1, respectively. RT-PCR with the primer pair of (1) and (3) revealed that the 456-bp orf456 gene was transcribed exclusively in the S-cytoplasm of the pepper. RT-PCR with the primer pairs of (2) and (3) generated an 804-bp product exclusively in the S-cytoplasm, which indicated that the orf456 gene is co-transcribed with the coxII gene Plant Mol Biol (2007) 63:519–532 521 Fig. 1 Southern and Northern blot analysis of male-fertile and cytoplasmic male-sterile (CMS) mitochondrial (mt)DNAs.a Southern blot analysis of mtDNAs digested with EcoRI, HindIII, and BamHI hybridized with eight mitochondrial probes (coxI, coxII, coxIII, atpA, atp6, atp9, cob, and nad9 genes) to compare male-fertile (F) and CMS (S) lines in Capsicum annuum L. Polymorphic bands between the male-fertile and CMS line are indicated by arrows. b Northern blot analysis of mtRNAs with four mitochondrial probes (atpA, atp6, coxI, and coxII). The coxII gene showed polymorphic band patterns of RNA tran- scripts (indicated by arrow). c Schematic structure of the malefertile and CMS coxII 5¢ and 3¢ flanking regions determined by inverse PCR. The horizontal arrowheads indicate the primer region used for inverse PCR and the reverse transcription (RT)PCR experiments. Primers a, b, c, and d were used for the inverse PCR experiment. Primers (1), (2), and (3) were used for the RT-PCR experiment. The oligonucleotide sequences are listed in the Table 1. The length of the nucleotide sequence of each region is represented above that region. F Male fertile, S CMS pepper upstream (Fig. 3a). Northern blot data on male-fertile and CMS total RNAs also showed that orf456 was transcribed exclusively in the sterile S-cytoplasm. Northern blot analysis was carried out to determine the difference between orf456 transcription in the restorer and CMS lines. The electrophoresis of the RNA shown in Fig. 3b was run for a longer time than that depicted in Fig. 1b in order to obtaine more distinct RNA bands. Although less intensive bands were obtained for the CMS line (which seemed to result from an inequality of RNA transfer to membrane) than for the restorer line, there was little difference in the RNA banding patterns (Fig. 3b). The BLAST search of the nucleotide databases revealed no significant homology with orf456, with the exception that the 5¢-region (40–91 nt) of orf456 showed 90% homology with the 5¢-non-coding region of the mitochondrial atp6 gene of Helianthus annuus (GenBank number X82388; Spassova et al. 1994). The transmembrane region is a common feature of proteins 123 522 Fig. 2 Comparison of nucleotide sequences of coxII 3’ flanking region between male fertile (upper) and CMS (lower) lines. The coxII 5’ flanking and coding sequences (7- 2792) were omitted. The coxII coding sequence can be found in the GenBank by the accession number of DQ126683. The 5’ nucleotide sequences common to male fertile and CMS were shown in gray characters. Asterisks indicated the start sites of sequence divergence. The orf456, a new-made open reading frame (456-bp) at CMS coxII downstream region, underlined between the start (ATG) and stop (TAA) codons in bold characters, was found by the program ‘ORF finder’ in NCBI homepage. EcoRI enzyme sites were indicated by parentheses. The sequence homologous to the 5’-non-coding region of the mitochondrial atp6 gene of H. annuus was indicated by upper dots. The C to T editing site 159 bp downstream from the start codon was indicated by a small character Plant Mol Biol (2007) 63:519–532 Fertile TAA 2795 1 (GAATTC) 2796 AGCGCGGAAGCTTAAGCGGAAATGAAAGAGGAGGTTGAGG GAAGCCACT AAATTGAGGGCTTCGCTCGCTCGCTCTAACGCTCGTTTAGTAGACAGCGA GTGGAGTGCATAAGCCCCTTTAGAGATAGGGGTGAGTACTACACGAGCT CGTAAGTAAAGTACGGAACGAGCCTTGTCTACGAAGCAGAGCGACCTCAT 3040 CTTGCTTGCTTCTGGCGAAGCTTCTAGCTCTAAATAATAGG(GAATTC) * CM S TAA 2795 1 (GAATTC) 2796 AGCGCGGAAGCTTAAGCGGAAATGAAAGAGGAGGTTGAGG TTATGAAGTC ACTTAGCCGTATACTATACAAAGGGAAAGGCGTCGGTACGGAGTCACGTC AGCTGTGGATATAGACTAGGCTATAAGGAACGGAGTCTTAAACTATGGACC •••••••••••••••••••••• GAGACAGATATATAGAAAGTGTGCAGTGAGGGTGCTTGTAAATCACTAGGT ••••••••••••••••••••••• AGCCTAGCTCGACCCAAGCAATGCCCAAAAGTCCCATGTATTTCTGGTTAA ACAAACCAGCAATTTCCGACAAGTCTTTCTTCATTGGAAGAGCAAGAAGCG GAACTACAACATTTACATGCAATTTCACCATGAATTTTATTGATTATGGCACA TTGTTTACTTTTTCTTTTTATCTcGGTATTTCAATCGGCATTTTTGCGGGCCG GTTTTTTGAGCGAAGTGAAGTTTTACAGGAATTGGAGAACTTCCAGCTAGA AAAAATAAAACTGAAAACGGAAGCAGAACTGCAATTTCTTTGTAGAGAGCA CTTGAGAATGAATGAAGAATTACAATTACCTGTTCCAGATGGAACGAGTAT GCACATCTCCGACTTTTTAGGGAAAGCCTTTTTGGTCGACGAGACTGTGAG GGAACGAATATTAGGGCTGACTCAAATTTATATGGATCTAAAAAACAATGGA GCAACCGAGTAACTTTTTTCTTTTATTTTTAGACTATTATAGCAATTTGTTTA GCGCTTTTTAATATATTCGTCTGTCGCCGTTGCAGCTAAAATAACGGAGGA TGGAGGCGGGGAGGGGAGGGGGACATCAAATGGATTCAAGTTTGAACAAA ACAGGAAGAGGTTCGATTCCTCTTTGATGTTGTTAAGCCAAGAGCGCCAAG CGCATGCGCGAAATGAGAGCGTCAGGAATGGAAAGGCAAAACCTACTATG CACCAAGTCCAGGAACCCGAGTCCGAGTACAGTGAATCAAGGAAGAGACT GCAGCTTCATCAGCTCAATGCAAGGTCCGTCGAAATCTTCCGGAGGGGTC TAGCATCCCGTAGGTCAGTTACTCCAGCGCCACAGTTCGACAGCTCGGGA AATACCTCTCACGCCCACGGTCGTCTTTTGACCACGCAATGACCTTCCCAG AATGGGTTGCAGAAAGCAGAATCTCAAAGGGGGAACCCCATCCAGGGGAT 4385 ATGCAGATAGAGCGCCCAAGACTTGGCAGGGAACGGGACCGTGATTCTGA AGAGGAACAGACAAGAGGAAAGCAAGGCCAAGAAGCCTCCGGGATAGACT CCTCCCTCTATACGTGGGAGCAACATAGACAGTTCCTCTTCCCTGAAGCCG AGGCCAAACTAACATATCCTGTTTCTCCCGAAACAACGGATTCCTCACCCT CAGGAGCCCCAAGTAACGAATCCGAATGCCTATCTCCCGTTTAATAAGACT TATTGGAATGGAAGAAGGAGAGTAGTCCTCTGGTCATCAGTTAGTAGTTCA ATAATCCCAGTAGTTGTCCTCTTGCCTAAAAAAAGGAGTCAGCCCAACATG GACAATGATAGGCAGACCAAAGATTTACGCAGTCCTTGCGTGCTTGCTTTG CGCACC(GAATTC) encoded by CMS-associated genes in plants (data not shown). This gene was also predicted to encode a transmembrane protein with a molecular mass of 17 kDa. To verify that the orf456 transcript was really translated into a protein, the orf456 cDNA was cloned into the pTrcHis2-TOPO expression vector. An IPTGinduced band of the expected size (approximately 21 kDa; i.e., the 17-kDa ORF456 plus the 4-kDa His tag) was detected by 12% SDS-PAGE in the insoluble fraction of the E. coli extracts (Fig. 3c). The identity of this band was confirmed by Western blot analysis using the anti-His tag antibody (Fig. 3d). The induced ORF456 polypeptide (2.5 mg) was eluted for injection into a rabbit. When the anti-ORF456 antibodies were tested against protein extracts from fertile and CMS mitochondria, a single band of about 17 kDa was detected exclusively in the CMS line (Fig. 3e). Furthermore, the band intensity of the ORF456 product was 123 * severely diminished in the restorer line that carried the Rf gene with S cytoplasm background (Fig. 3f). The presence of the nuclear Rf gene in the restorer line is known to suppress expression of the CMS trait and, consequently, to restore pollen fertility in CMS plants. To further ascertain the association between the orf456 gene and the CMS trait in pepper, we designed constructs for Arabidopsis transformation. The detailed structure of the orf456 and egfp genes with restriction sites that were used in the insert construction is shown in Fig. 4a. In the first construct (referred to as coxIV-orf456), the orf456 sequence was fused to the mitochondrial transit peptide sequence of the presequence (54 codons) of the nuclear coxIV gene of yeast for mitochondrial targeting of the protein. The second construct (referred to as nontargeting-orf456) did not contain the mitochondrion-targeting peptide sequence. A third construct (coxIV-gfp) was designed using the coxIV presequence and egfp (720 bp) in Plant Mol Biol (2007) 63:519–532 Fig. 3 RNA and protein expression analysis of orf456 gene. a RT-PCR analysisof orf456, which is located in the 3’ region of the coxII gene in the CMS line. RT-PCR with primer (1) and (3) pair was performed to detect whether newly-made orf456 is really and uniquely transcribed in the CMS line. RT-PCR with the primer (2) and (3) pair was performed to detect whether the orf456 gene is co-transcribed with coxII located on the upstream region. b Northern blot analysis of total RNAs extracted from each tissue of the male-fertile, CMS, and restorer line with the orf456 cDNA probe. About 20 lg/lane RNA from each tissue was loaded onto a 1.2% agarose gel and transferred to a N+ nylon membrane. The bands which showed polymorphism in Fig. 1b are indicated by arrows. F Fertile, S CMS, R restorer line. c Induction of the ORF456-His recombinant fusion protein by isopropyl-beta-D-thiogalactopyranoside (IPTG). Each Escherichia coli protein extract (15 lg) separated into a soluble (S) and insoluble (I) fraction was loaded onto a 12% sodium dodecyl sulfate-polyacrylamide electrophoresis gel (SDS-PAGE). The induced ORF456-His recombinant protein is indicated by an 523 arrow. d Western blot analysis of the ORF456-His recombinant protein using the His-tag antibody. The IPTG-induced ORF456His recombinant protein was detectedin the insoluble fraction (arrow indicated). Weak expression of the ORF456-His recombinant protein was also detected in the insoluble fraction even at no addition of IPTG. e Western blot analysis using the anti-ORF456 antibody on mitochondrial proteins from malefertile and CMS pepper. The analysis was performed on about 30 lg of purified mitochondrial protein from male-fertile (F) and CMS (S) pepper. Protein extracts from the insoluble fraction of E. coli containing ORF456-His recombinant protein were used as positive control (I). Molecular mass markers in kiloDaltons (kDa) are shown to the left. f Western blot analysis using antiORF456 antibody on mitochondrial proteins from CMS (S) and restorer (R) pepper. Purified mitochondrial proteins from CMS and restorer were loaded on the SDS-PAGE gel. The antimitochondrial ATPase subunit a (ATPa) antibody was used as a control. Molecular mass markers in kiloDaltons are shown to the left. M Western view size marker (Elpisbio, Korea) 123 524 Plant Mol Biol (2007) 63:519–532 order to investigate whether the coxIV presequence was capable of transporting a protein of interest into plant mitochondria. The primer pairs used for constructing the insert are listed in Table 1. The EGFP fusion construct was transiently expressed in onion epidermal cells following particle bombardment. The Mitotracker CMSRox dye was used to detect mitochondria. The GFP fluorescence image and the Mitotracker dye image matched perfectly (Fig. 4b), indicating that the coxIV presequence from yeast could target a translation product of interest in plant cell mitochondria. The first (coxIV-orf456) and the second (non-targeting-orf456) constructs were used to transform Arabidopsis using the floral dip method (Clough and Bent 1998). The flower phenotype of the non-targetingorf456 transformants was normal and similar to that of the wild-type plant. However, the anthers of coxIVorf456 T1 plants exhibited a male-sterile phenotype (Fig. 5). At the early stage of development, the anthers of coxIV-orf456 transformants developed normally. However, the coxIV-orf456 transformants at the dehiscent stage did not produce any pollen grains and Table 1 Oligonucleotides used in this study. The restriction enzyme sequences for cloning were indicated by underline 123 normal siliques (Fig. 5j). To confirm the function of orf456 in producing the male-sterile phenotype, two independent transformation tests were conducted. About 45% of the total transgenic Arabidopsis T1 plants that contained coxIV-orf456 exhibited the malesterile phenotype (Fig. 6a). RNA gel blot analysis with nine kanamycin-resistant T1 plants revealed that malesterile T1 plants (nos. 1, 2, and 3 in Fig. 6c) strongly expressed the orf456 gene. Several plants (nos. 4, 5, 7, and 9) that were kanamycin resistant but did not, or only slightly, express the targeted orf456 gene had a fertile phenotype indistinguishable from that of the wild type. Interestingly, two T1 plants (nos. 8 and 11) showing some expression were revealed to have a semi-fertile phenotype and poor seed setting when compared to the wild-type or other fertile transformants. In the first transformation experiment, three T1 plants (nos. 8, 11, and 15) out of 51 transgenic T1 plants had the semi-fertile phenotype. Therefore, T2 progenies from two semi-fertile T1 transformants (nos. 8 and 15) were grown under the same conditions, and the fertility of the T2 plants was evaluated. More than 60% of the T2 progenies of T1 lines nos. 8 and 15 had the Oligonucleotide name Sequence (5¢-3¢) Application cob-F cob-R nad9-F nad9-R atpA-F atpA-R atp6-F atp6-R atp9-F atp9-R coxI-F coxI-R coxII-F coxII-R coxIII-F coxIII-R Primer a Primer b Primer c Primer d Primer (1) Primer (2) Primer (3) BamHI-coxIVF SmaI-coxIVR SmaI-DcoxIVR orf456-F SacI-orf456R egfp-F SacI-egfpR AGCATTTGATAGATTATCCAACCCC GAATGGGCGTTATGGCAAAGAA CATGGGAATAGATCTGATACCAAT GCAAAATCGAAATAGCGAAATTCTT ATTTTCAAGTGGATGAGATCGGT GATCACAGAATCCATTGACAGCT TATTTCTCATTCACAAATCCC AGCATCATTCAAGTAAATACAGAT ATGTTAGAAGGTGCAAAATCA GAAAACGAATGAGATCAGAAAGGC TAACCACAAGGATATAGGGACTC GATTGTTACGACCACGAAGAAAC GATGCAGCGGAACCATGGCAATTA ACTGCACTGACCATAGTAAACTCC ATGATTGAATCTCAGAGGCAC ACCACCCCACCAATAGATAGA GCCATAAAGCGCGACCCAAGATCCATGATACGAA GAGAATTGACCTATTCATAGAGTGATCCTATGATC CTTGGCTGGTAGAACCACTCTATTG GAAGGAGTTTACTATGGTCAGTGCAG ATGCCCAAAAGTCCCATGTAT GAAGGAGTTTACTATGGTCAGTGCAG TTACTCGGTTGCTCCATTGT GGATCCATGTTGTCACTACGTCAATCTATAAGA CCCGGGACCCTCTTTAGCACCAGGACC CCCGGGTTTTTGCTGAAGCAGATATCT ATGCCCAAAAGTCCCATGTATTT GAGCTCTTACTCGGTTGCTCCATTGTT ATGGTGAGCAAGGGCGAGGAGC GAGCTCTTACTTGTACAGCTCGTC Probe Probe Probe Probe Probe Probe Probe Probe Probe Probe Probe Probe Probe Probe Probe Probe Inverse PCR Inverse PCR Inverse PCR Inverse PCR RT-PCR RT-PCR RT-PCR pCAMBIA2300 pCAMBIA2300 pCAMBIA2300 pCAMBIA2300 pCAMBIA2300 pCAMBIA2300 pCAMBIA2300 Plant Mol Biol (2007) 63:519–532 525 Fig. 4 a Construction of orf456 and egfp-1 transgene for Arabidopsis transformation. The diagram shows the strategy for cloning each gene construct into the modified pCAMBIA2300 plant transformation vector. The egfp indicates the green fluorescent protein (GFP) variants purchased from Clontech (Palo Alto, Calif.). Amino acid sequences of the cox4 presequence (mitochondria-targeting sequence) are shown below the cox4’ gray box. NPTII Neomycin phosphotransferase II gene, MCS multi-cloning site, NOS ter NOS terminator site, LB left border, RB right border, Kmr kanamycin resistance gene. b Images of GFP fluorescence in the onion transient expression assay. The left image depicts the mitochondrial-targeting GFP fluorescence, the right image shows staining with the Mitotracker CMXRox red dye (Molecular Probes, Eugene, Ore.) The merged picture is shown below Fig. 5 Phenotype of non-targeting-orf456 and mitochondriatargeting coxIV-orf456 transgenic T1 Arabidopsis plant. a Feature of non-targeting-orf456 Arabidopsis T1 transformant. b Feature of mitochondria-targeting coxIV-orf456 Arabidopsis T1 transformant. c Flower of non-targeting-orf456 T1 transformant; normal pollen grains were observed (inset). d Flower of mitochondria-targeting coxIV-orf456 Arabidopsis T1 transformant; male-sterile phenotype with no pollen grains was observed (inset). e Anther morphology of non-targeting-orf456 T1 transformant; enlarged photograph from inset within c. Normal pollen grains are shown. f Pistil morphology of non-targeting-orf456 T1 transformant. g Anther morphology of mitochondria-targeting coxIV-orf456 T1 transformant. Enlarged photograph from inset within d. No pollen grains were observed (arrow). h Pistil morphology of mitochondria-targeting coxIV-orf456 T1 transformant. I Silique formation of non-targeted-orf456 transformant along the developmental stage. Normal silique was produced. j Silique formation of mitochondria-targeting coxIV-orf456 transformant along the development stages. Normal silique was not produced male-sterile phenotype (Fig. 6b). Three male-fertile (nos. 1, 2, 7) and three male-sterile (nos. 4, 10, 14) T2 plants from the T1 line no. 8 transformant were used for Northern blot analysis (Fig. 6d). The transgenic plants showing the male-sterile phenotype were detected to have strong orf456 expression levels. 123 526 Plant Mol Biol (2007) 63:519–532 b Fig. 6 Fertility evaluation on transgenic Arabidopsis plants from two independent transformation experiments. Three T1 plants (#8, #11, #15) showing semi-sterile phenotype are indicated by asterisk. This classification was based on anther morphology at the dehiscent stage and seed sets. Double-hatched bar indicates the number of total plants used for each transformation experiment. Single-hatched bar indicates the number of male fertile T2 transformants. White bar indicates the number of male sterile T1 transformants. 35S-GFP CaMV35S::egfp construct (positive control), 35S-ORF CaMV35S::orf456 construct (nontargeting), 35S-CXORF CaMV35S::coxIV::orf456 construct (mitochondria-targeting). b Result of fertility evaluation on transgenic T2 Arabidopsis progenies (T2 from T1 nos. 8 and 15 showing the semi-sterile phenotype). Double-hatched bar indicates the number of total plants used for each transformation experiment, single-hatched bar indicates the number of malefertile T2 transformants, white bar indicates the number of malesterile T2 transformants. The observed plant number of each transformant is shown above each bar. WT Wild type (ecotype Columbia), 35S-GFP CaMV35S::egfp construct (positive control), 35S-ORF CaMV35S::orf456 construct (non-targeting), 35S-CXORF CaMV35S::coxIV::orf456 construct (mitochondriatargeting). This classification was based on anther morphology at the dehiscent stage and seed sets. c PCR and Northern blot analysis on T1 Arabidopsis transgenic plants. Wild-type plant and nine coxIV-orf456 T1 transgenic plants were used for the analysis. For the PCR analysis, Primer (1) and (3) in Table 1 was used. Full-length orf456 cDNA was used for the Northern blot analysis. Total RNA (15 lg) was loaded onto a 1.2% formaldehyde gel. Fertility evaluation was carried out under a stereo-microscope at least three times at different flowering periods. T1 nos. 8 and 11 plants showing the semi-sterile phenotype are indicated with asterisks. d Northern blot analysis of T2 Arabidopsis transgenic plants. Three male-fertile and three male-sterile T2 transgenic plants from T1 no. 8 plant were selected and used for analysis. WT Wild type Light microscopy examination was unable to find pollen grains in the anther epidermis of coxIV-orf456 transformants (Fig. 5g). However, pollen-like grains were observed within the anther locules following aceto-carmine staining (data not shown). The plasmolysis test was performed to check the intactness of pollen-like grains. When placed in hypertonic (25% glycerol) solution, the pollen-like grains burst within 10 min (Fig. 7b), while the wild-type pollen grains remained intact even after 24 h (Fig. 7a). Each anther of the coxIV-orf456 transformants and wild-type plants were collected at the dehiscent stage and fixed for light microscopy (LM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Pollen grains within the anther locules were squeezed out and observed under SEM. While the pollen from the wild-type plants had the normal phenotype (Fig. 7c, d), most of the pollen from the coxIV-orf456 transformants had abnormal exine surfaces (Fig. 7e and f, arrows). Wild-type anthers contained many dehiscent pollen grains in the anther sac 123 (Fig. 7g, h). However, the coxIV-orf456 anthers did not dehiscence and there was no pollen in the anther sac (Fig. 7I, j). Anthers at the dehiscent stage were cross-sectioned and observed by LM and TEM. Under LM, the coxIVorf456 anthers were found to contain vacuolated pollen grains (Fig. 7l), while the wild-type anthers showed normal features (Fig. 7k) (Bowman 1993). More detailed features of the pollen grains were obtained by TEM. The wild-type pollen grains were filled with normal cytoplasmic components (Fig. 7m and n), while the coxIV-orf456 male-sterile anthers contained abnormally vacuolated pollen grains, even at the dehiscent stage (Fig. 7o, p). Discussion In all CMS systems investigated up to date, the CMS has resulted from changes in the organization of mitochondrial genes. RFLP analysis has been used in Plant Mol Biol (2007) 63:519–532 527 Fig. 7 Light microscopy (LM) and electron microscopy photographs of anther and pollen of wild-type and mitochondriatargeting coxIV-orf456 T1 plants. a Pollen grain of wild-type Arabidopsis plant stored in a 25% glycerol hypertonic solution for 24 h. b Pollen grain of mitochondria-targeting coxIV-orf456 T1 Arabidopsis plant stored with 25% glycerol hypertonic solution for 10 min. c Scanning electron microscope (SEM) picture of pollen grains of wild-type A. thaliana. Bar: 10 um. d SEM picture on pollen grain of wild type A. thaliana. Bar: 5 um. e SEM picture on pollen grains of mitochondria-targeting coxIVorf456 T1 plant. Bar: 10 um. f SEM picture on pollen grain of mitochondria-targeting coxIV-orf456 T1 plant. The abnormal exine layer of the pollen grain is shown and indicated by arrows. Bar: 5 lm. g SEM picture of the anther at the dehiscent stage from wild-type A. thaliana. Bar: 50 lm. h SEM picture enlarged from the inset within g. Bar: 10 lm. I SEM picture on anther at dehiscent stage from mitochondria-targeting coxIV-orf456 T1 plant. Bar: 50 lm. j SEM picture enlarged from the inset within I. Bar: 10 lm. k LM picture of cross-sectioned anther at dehiscent stage from wild type A. thaliana. l LM picture of cross-sectioned anther at dehiscent stage from wild-type A. thaliana. Vacuolated pollen grains are indicated by arrows. m Transmission electron microscopy (TEM) picture of crosssectioned pollen grains of wild-type A. thaliana. Bar: 5 lm. n Enlarged view of inset within picture m of wild-type A. thaliana. Bar: 2 lm. o TEM picture of cross-sectioned pollen grains of the mitochondria-targeting coxIV-orf456 T1 plant. Bar: 5 lm. p Enlarged view of inset within picture o of the mitochondriatargeting coxIV-orf456 T1 plant. Abnormal vacuoles within the pollen grain were observed and are indicated by arrows. Bar: 2 lm several plant species to detect differences in mtDNA structure between male-fertile and CMS lines, resulting in the successful identification of CMS-associated genes (rice, Akagi et al. 1994; rye, Dohmen et al. 1994; sorghum, Sane et al. 1994; sunflower, Spassova et al. 1994). In the present study, four of the eight mitochondrial genes used as probes resulted in RFLP polymorphisms. The Northern blot analysis of these polymorphisms in the male-fertile and CMS lines revealed that only one of these genes (coxII) showed different banding patterns. Based on these results from the RFLP and Northern analyses (Fig. 1a, b), we postulated that the flanking region of the coxII gene may have undergone some degree of alteration to its structure. To date, more than 50 genes, however, have been identified in several plant mitochondria (Kubo et al. 2000; Notsu et al. 2002; Sugiyama et al. 2005; Unseld et al. 1997). For our RFLP analysis, we used eight highly likely candidate genes as probes that had been reported to be associated to CMS in other higher plants (Table 2); nevertheless, we cannot eliminate the possibility that other polymorphic bands could be present since we did not use all of the known mitochondrial genes as probes in this study. In a similar fashion, it is possible that more transcriptional aber- rations (CMS-associated or not) could have been detected if the Northern analysis had been carried out with more gene probes. Therefore, there is a definite possibility that other CMS-associated factors may be present in addition to orf456 and atp6. Northern blot analysis revealed the presence of multi-banding transcripts, among which coxII in particular showed one polymorphic band. This multibanding pattern of mitochondrial genes has been reported in other higher plants and is considered to result from various RNA processing events, such as RNA splicing, multiple 5¢ initiation or 3¢ termination sites, dicistronic transcription, and polyadenylation in plant mitochondria (Cooper et al. 1990; Kuhn et al. 2001; Kuhn and Binder 2002; Menassa et al. 1999; Pruitt and Hanson 1989). To obtain more detailed information on the coxII multi-banding transcripts, it will be necessary to investigate the transcript extremities using the methods like circular RT-PCR, RACE-PCR, or primer extension, among others. The results from such studies will help exclude any differences in transcriptional regulation between CMS and restorer lines. A novel ORF, orf456, was detected in the 3¢-noncoding region of the mitochondrial coxII in the CMS 123 528 Plant Mol Biol (2007) 63:519–532 Table 2 Mitochondrial genes associated with the CMS phenotype in several higher plants Mt probes used in this Plant Species study References atpA Radish atp6 Sunflower Brassica napus Rice Makaroff et al. (1990) Köhler et al. (1991) Singh et al. (1996) Iwabuchi et al. (1993) Levings III (1990) Mohr et al. (1993) atp9 T-Maize Triticum timopheevi T-Maize Sunflower Petunia CoxI coxII Sorghum Teosinte Petunia CoxIII Rice cob nad9 Sunflower Beet Levings III (1990) Köhler et al. (1991) Prutt and Hanson (1989) Tang et al. (1996) Cooper et al. (1990) Prutt and Hanson (1989) Iwabuchi et al. (1993) Köhler et al. (1991) Ducos et al. (2001) line but not in the male-fertile cytoplasm of the pepper (C. annuum L.). Transcripts of orf456 were detected in the CMS and restorer lines that carried the CMSinducing S cytoplasm, but not in the fertile N line (Fig. 2). There was very little difference in the banding patterns of the orf456 transcripts between the CMS and the restorer lines (Fig. 2c), indirectly indicating that nuclear restoration by the restorer gene (Rf) may be mediated by regulation at the post-transcriptional or translational level rather than at the transcriptional level. Indeed, Western blot analysis did detect a severely reduced level of ORF456 protein band in the restorer line relative to the CMS line (Fig. 3d), indicating that the expression of orf456 is modulated at the translational level by the nuclear encoded Rf gene. When we investigated an RNA editing event between CMS and restorer orf456 cDNA, only one C to U editing site was detected at +150 nt from the start codon and this was a silent mutation (ctc fi ctt; Leu fi Leu) (Fig. 2). We conclude that although an RNA editing event does occur, it has no consequence on CMS restoration in chili peppers. To investigate the biological function of the orf456 gene, we adopted an Arabidopsis transformation method in which mitochondrion-targeting sequences (coxIV presequence of the yeast nuclear origin) were used to localize the orf456 gene product into plant mitochondria. The coxIV presequence for mitochondria localization has been used previously by the group 123 of M.R. Hanson (Cornell University) to successfully target proteins (Köhler et al. 1997). While the Hanson lab used a partial 5¢-region (87 bp), we used a full (162bp) targeting signal sequence (Fig. 4a). The coxIV presequence (partial or full) is expected to be utilized for mitochondrial targeted vector construction in plant biotechnology. Transgenic experiments with other CMS-associated sequences, such as the pcf (petunia) and T-urf13 (Tmaize) genes, have been attempted by several researchers (Chaumont et al. 1995; Wintz et al. 1995). However, these experiments failed to generate any male-sterile transgenic plants, probably due to the improper localization of the CMS-associated protein in plant cells or the weak promotion of the CaMV35S promoter in anther tissues. In the present study of the coxIV-orf456 transformants, approximately 45% of the Arabidopsis plants showed the male-sterile phenotype in the T1 generation. This successful transformation of Arabidopsis with the pepper orf456 gene which resulted in male sterility is an important finding in terms of research on the CMS mechanism – even though we did not observe a fully male-sterile phenotype in neither the T1 nor the T2 generation in all of the transgenic populations. This incomplete penetrance may be the consequence of transgene inactivation. The precise molecular mechanism of CMS in pepper has not been resolved to date. On the basis of the microscopy data, however, we could observe that pollen maturation might be disturbed and, therefore, incomplete. Two representative male-sterile features were detected in the CMS pepper line: (1) defects in the exine layer and (2) vacuolated pollen grains. With respect to defects in exine layer, the coxIV-orf456 sterile anthers did not shed any pollen grains and failed to produce any siliques during the microspore developmental stage (Fig. 5g, I). Although pollen-like grains were detected within the coxIV-orf456 anther locules, the pollen grains themselves had defects on the exine surface, as evidenced by their easy rupturing in a hypertonic solution (Fig. 7b, e, f). In a recent investigation, Luo et al. (2006) studied CMS pollen grains by microscopy and reported features similar to our results. In the CMS line, they detected several defects in mitochondria within the tapetum, which plays an important role in providing nutrition, such as lipids and protein components, to the developing pollen walls (Piffanelli et al. 1998). These mitochondrial defects may result in premature cellular degradation of the tapetum and suppress viable pollen grain development, particularly in parts of the pollen cell wall such as the exine layer. The exine layers of the CMS pollen grains were poorly visible, and the cell walls appeared to be thin when compared to those of the fertile Plant Mol Biol (2007) 63:519–532 pollen grain. These defects resulted in the cellular components of the pollen grains being released into the locular space and the pollen grains collapsing within a relatively short time (Luo et al. 2006). In the vacuolated pollen grains, subsequent observations using TEM showed abnormally vacuolated pollen grains (Fig. 7l, o, p). In fact, vacuolated pollen grains appear in the middle stage of the normal developmental process of pollen grains (Bowman 1993). These results indicate that the maturation of pollen grains has not been completed, and that this immaturity could be the cause of male sterility. In an earlier report, we suggested that the atp6 genes may be one candidate for causing the CMS condition. Our results indicate that the expression of the orf456 gene is controlled at the post-transcriptional or translational level. Conversely, atp6 genes are regulated by the Rf gene at the transcriptional level (Kim and Kim 2006a). This leaves one major question: ‘‘Which one of these genes can be considered to be the major CMS-associated gene?’’ Clarification of this question will require further experimental approaches, such as map-based Rf gene cloning, and yeast two hybrid screening of ORF456 (in this study) or YATP6-2 (Kim and Kim 2006a) will help resolve the question. We recently developed a pepper line with a major Rf gene-linked cleaved amplified polymorphic sequence (CAPS) marker by amplified AFLP analysis (Kim et al. 2006) and mapped into SNU2 pepper linkage map (Lee et al. 2004). The identification of Rf genes in pepper by means of a map-based cloning strategy will accelerate the characterization of major and minor CMS genes and their Rf-CMS interacting mechanism. In conclusion, the orf456 gene may represent one candidate from among the CMS-associated mitochondrial genes in chili pepper (Capsicum annuum L.).The transgenic Arabidopsis line developed here will be helpful for gaining insights into the molecular mechanisms of CMS in pepper (Capsicum annuum L.). Experimental procedures Plant materials The near-isogenic male fertile (N/rf/rf genotype), male-sterile (S/rf/rf), and restorer (S/Rf/Rf) lines of chili pepper (Capsicum annuum) cv. Milyang were used in this study. These plants were provided by J.H. Yoo of Hungnong Seed Co. in Korea. Arabidopsis thaliana ecotype Columbia plants were used for the transformation experiments. 529 RFLP and Northern blot analyses The extraction of mtDNA and subsequent membrane transfer were performed as previously described (Kim et al. 2005). Total anther RNA was extracted using a Nucleospin kit (Macherey-Nagel Co, Germany). For the Northern blot analysis, total RNA samples (20 lg) from the flowers, leaves, and anther tissues of sterile, fertile, and restorer lines were fractionated and transferred to a Hybond N+ nylon membrane (Amersham Pharmacia Biotech, Piscataway, N.J.) by capillary blotting (Sambrook et al. 1989). The blots were hybridized with the radioactively labeled orf456 DNA probe at 60C for 16 h, with a final wash in 0.5· SSC, 0.1% SDS. Inverse PCR for the flanking and coding sequences of the coxII gene Inverse PCR was carried out as previously described (Kim et al. 2005). The primer sequences (primers a and b for the 5¢-flanking region; primers c and d for the 3¢flanking region) used in the inverse PCR experiments are listed in Table 1. A new ORF was identified using the ORF FINDER program on the NCBI website. RT-PCR and Northern blot analysis Total anther RNA (3 lg) was used for first-strand cDNA synthesis using M-MLV reverse transcriptase (Invitrogen). The PCR reaction was performed with specific primer pairs (10 pM) listed in Table 1. Extraction of mitochondrial proteins Approximately 500 fertile (N/rf/rf), CMS (S/rf/rf), and restorer (S/Rf/Rf) pepper seeds were germinated in two rolls of germination paper in the dark at room temperature. Seven-day-old etiolated shoots of pepper were homogenized in five volumes of buffer I [0.3 M mannitol, 50 mM Tris-HCl, 3 mM EDTA, 1 mM 2mercaptoethanol, 0.1% BSA, 1% PVP-40, 1 tablet per 50 ml of proteinase inhibitor mixture (Roche, Germany); pH adjusted to 7.5 with KOH]. Additional steps were performed as described by Millar et al. (2001), with the exception that we used 28% Percoll centrifugation. Antibody generation and Western blotting The 456-bp orf456 cDNA (151 amino acids, predicted molecular weight of 17 kDa) was cloned into the pTrcHis2-TOPO expression vector (Invitrogen), 123 530 thereby creating a translational fusion with the His tag epitope (approximately 4 kDa), and introduced into the Top10 strain of E. coli. For antibody production, the His tag-fused recombinant protein was purified from the SDS-PAGE gel. Polyclonal antibodies against the purified recombinant ORF456 (2.5 mg) were raised in rabbits (LabFrontier, Seoul, Korea). Fertile and CMS mitochondrial proteins (30 lg) were separated on a 12% SDS-PAGE system and transferred to a nitrocellulose membrane. The membrane was blocked with 5% skim milk in buffer solution [10 mM Tris-HCl (pH 7.5), 150 mM NaCl, 0.1% Tween-20] for 1 h at 25C, followed by incubation first in primary antibody for 1 h at 25C and then in secondary antibody for 1 h at 25C. The primary antibody was a rabbit anti-His tag antibody (Invitrogen), which was diluted 1:1000. The secondary antibody was peroxidase-labeled anti-rabbit antibody (Pierce, Rockford, Ill.), which was diluted 1:10000. The blots were developed in the WEST-ZOL plus solution (iNtRON Biotechnology, Korea). For antibody production, the His tag-fused recombinant protein was purified from the SDS-PAGE gel. Polyclonal antibodies against purified recombinant ORF456 (2.5 mg) were raised in rabbits (LabFrontier). Fertile and CMS mitochondrial proteins (30 lg) were separated on 12% SDS-PAGE gels and transferred to a nitrocellulose membrane. Western blot analysis using anti-ORF456 antibodies was performed as described above. Transient expression in onions The egfp sequence was amplified from the pEGFP-1 vector (Clontech). The presequence (54 codons) of the nuclear coxIV gene of yeast (strain Y187) was used as the mitochondrial transit peptide sequence. This was amplified by PCR and used for mitochondria-targeting the ORF456 protein. The amplified coxIV target sequence and egfp sequence were ligated using T4 DNA ligase (Promega, Madison, Wis.) and then cloned into the pCAMBIA2300 vector (MRC, Cambridge, UK). The fusion constructs in the pCAMBIA2300 vector were transiently expressed in onion epidermal cells after transfection. Mitochondrial localization was examined by confocal laser scanning microscopy using the Radiance 2000 MultiPhoton Imaging System (Bio-Rad, Hercules, Calif.) at the National Instrumentation Center for Environmental Management (NICEM, Seoul, Korea). The Mitotracker Red CMXRox dye (Molecular Probes) was used for the detection of mitochondria in the onion epidermal cells. 123 Plant Mol Biol (2007) 63:519–532 Expression of orf456 in E. coli and Arabidopsis The cDNA fragment of orf456 was amplified from the CMS pepper. The expression of orf456 in E. coli TOP10 cells was induced by adding 1 mM IPTG. The plasmids, which contained the coxIV presequence plus orf456 or egfp, were digested with BamHI and SacI for cloning into the plant transformation vector pCAMBIA2300. A non-targeting construct, which contained truncated coxIV plus orf456, was made using the following strategy. Since the non-targeting-coxIV construct contains an XbaI site (+61 bp) within itself, following ligation to the orf456 gene, the fusion constructs were digested with XbaI. In the case of the nontargeting-orf456 insert, only 16 bp of the coxIV presequence was fused to the 5¢-region of the orf456 inserts. Each insert was confirmed by restriction enzyme digestion and sequencing. Detailed primer sequences for transgene constructs are shown in Table 1. The Agrobacterium tumefaciens-mediated transformation was performed according to the modified floral-dip method (Clough and Bent 1998). Pollen staining and plasmolysis For the pollen plasmolysis test, the anthers were pressed open (by gently pressing the cover glass to release the pollen grains) in 20 ll of hypertonic solution (20% glycerol) on glass slides. After 10 min of incubation at room temperature, the solution was covered with a glass coverslip and photographed under light microscopy. Light microscopy (LM) and electron microscopy (SEM and TEM) For microscopic observation, the anthers were collected from flowers of wild-type and coxIV-orf456 male-sterile transformants. Prepared samples were observed by LM (Axiophoto; Zeiss, Germany) after staining with a 0.01% aniline blue solution (Sigma, St. Louis, Mo.). For SEM, dried samples were mounted on aluminum stubs with carbon tape and sputter coated with gold/palladium. The samples were viewed in an Amray 1000 SEM (JSM-5410LV) with an accelerating voltage of 5 kV and an emission of 40 M. For TEM, thin sections (40–50 nm in thickness) were prepared with an ultramicrotome (MTX, RMC Industries, Tucson, Ariz.). The thin sections were collected on nickel grids (1-GN, 150 mesh) and stained with 2.5% uranyl acetate for 20 min. After the grids had been washed with pure water, the specimen was stained with lead citrate for 7 min at room temperature. After double- Plant Mol Biol (2007) 63:519–532 staining, observations were made under a TEM (JEM1-1; JEOL, Tokyo, Japan). Acknowledgements This research was supported by a grant from the Center for Plant Molecular Genetics and Breeding Research (CPMGBR) via the Korea Science and Engineering Foundation (KOSEF) and the Korea Ministry of Science and Technology (MOST). 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