RESULTS Positional Cloning of the EMF1 Locus The EMF1 locus has been mapped to the upper part of chromosome V ( Yang et al., 1995). Figure 1A diagrams the positional cloning experiments. By using restriction fragment length polymorphism (RFLP) markers and a segregating population representing ~1200 meiotic events, EMF1 was fine mapped between markers 9G2-R and 18G5-R, which were derived from the ends of yeast artificial chromosome (YAC) clones included in a large contig covering that region. P1 and transformation-competent bacterial artificial chromosome (TAC) clones were anchored to these markers, and a contig was assembled based on information available at www.kazusa.or.jp/kaos/kazusa/chr5/pmap/P1_map_3.html. The 9G2-R and 18G5-R ends were used as probes to initiate a chromosome walk. Cosmid clones were isolated from binary cosmid libraries. Internal fragments of cosmid or P1 clones were converted into RFLP markers and used to delimit the EMF1 locus on cosmid clone CD82. | Figure 1. Map-Based Cloning and Gene Structure of EMF1. |
Sequence analysis of the 17,341-bp CD82 clone and sequence data from bacterial artificial chromosome clone F15N18 revealed the presence of four open reading frames (ORFs) on cosmid clone CD82 ( Figure 1A). RFLP mapping localized the EMF1 locus to a fragment common to P1 clone MZH1, TAC K22P7, and cosmid CD82 ( Figure 1A). We subcloned a SpeI–Asp718 fragment from the genomic DNA of TAC K22P7 and transformed emf1-1 and emf1-2 segregating plants. T2 seed from T1 lines carrying the emf1 alleles were sown on kanamycin (Km) medium, and Km resistance and the emf mutant phenotype were scored in progeny of four emf1-1 T1 lines totaling 231 plants and six emf1-2 T1 lines totaling 884 plants ( Table 1). The absence of any Km-resistant emf mutants showed that this region contained a functional EMF1 gene that complements the emf1 phenotypes. The complementing fragment has two ORFs ( Figure 1A). One ORF has sequence homology with l-gulono-lactone oxidase (GLOxidase) and encodes a GLOxidase-like protein ( Koshizaka et al., 1988). The second ORF has homology with two expressed sequence tags (ESTs) from Arabidopsis encoding putative polypeptides of unknown function and a hypothetical protein from the rice genomic sequencing project. | Table 1. Complementation of emf1 Mutant Alleles by the SpeI–Asp718 Genomic DNA |
We sequenced these two candidate genes from genomic DNA isolated from the emf1 mutants and corresponding wild-type plants. All three emf1 mutant alleles ( emf1-1, emf1-2, and emf1-3) have a single base pair mutation in the second ORF: each mutation creates a stop codon interrupting the predicted ORF ( Figure 1B). The emf1-1 and emf1-2 mutations generate allele-specific RFLPs that were detected using a polymerase chain reaction (PCR)-based method derived from the cleaved amplified polymorphic sequence marker ( Konieczny and Ausubel, 1993; Michaels and Amasino, 1998). A G-to-A change in emf1-1 and a deleted C in emf1-2 changed a HaeIII restriction site to HincII in emf1-1 and deleted a MaeIII site in emf1-2. The PCR products obtained from wild type, emf1-1, and emf1-2 and digested with the relevant restriction enzymes had the predicted fragment length polymorphisms ( Figure 1C). Based on the complementation experiment and the presence of mutations in all three mutant alleles, we concluded that we had identified the EMF1 gene. EMF1 and OsEMF1: A Novel Class of Putative Transcriptional Regulators Using reverse transcription (RT)-PCR, we generated a 3.8-kb cDNA (see Methods) that is likely the full-length EMF1 cDNA because the first ATG initiating a 1096–amino acid polypeptide is preceded by one or more stop codons in all frames. This cDNA detected a single low-abundance transcript of ~4 kb on poly(A) + RNA gel blots (see below). Sequence comparison between Arabidopsis genomic DNA and this cDNA product revealed seven introns ( Figure 1B), all of which display the consensus border sequence GT/AG ( Hanley and Schuler, 1988). The first and last introns are located in the untranslated transcribed regions; the other five introns are located within the coding region ( Figure 1B). The EMF1 gene encodes a predicted 121.7-kD protein ( Figure 2A) with similarity to two ESTs from Arabidopsis and a rice sequence, as mentioned above. The two EST clones are identical to the cDNA clone amplified by RT-PCR. Analysis of the size of the two ESTs showed that they are partial cDNA clones. Furthermore, analysis of the Arabidopsis genome sequence did not reveal any other sequence closely related to the EMF1 gene. Thus, we conclude that the EMF1 gene is a single- copy gene in the Arabidopsis genome. | Figure 2. Alignment between Predicted EMF1 and OsEMF1 Amino Acid Sequences and Protein Structures. |
To better characterize the rice EMF1 homolog ( OsEMF1), we isolated the corresponding cDNA clone by the rapid amplification of cDNA ends technique (see Methods). The OsEMF1 cDNA of 3896 nucleotides predicts a 1057–amino acid polypeptide (estimated molecular mass, 116.4 kD) that is 328 amino acids shorter than the predicted protein in BAA94774.1. The organization of introns and exons predicted at the 5′ end in BAA94774.1 was not confirmed by the sequence of the OsEMF1 cDNA ( Figure 2A). The OsEMF1 cDNA likely includes a complete ORF because several stop codons are found in all three possible reading frames upstream of the first ATG initiating the 1057–amino acid polypeptide. The Arabidopsis and rice predicted protein sequences display 37% similarity and 20% identity over their entire lengths. Neither EMF1 nor OsEMF1 displays significant homology with proteins of known function from any organism. Nevertheless, several domains could be identified in the predicted EMF1 and OsEMF1 polypeptides ( Figure 2B), including nuclear localization signals ( Raikhel, 1992), phosphorylation sites, an ATP/GTP binding motif (P-loop) ( Walker et al., 1982), and an LXXLL motif. The LXXLL motif has been demonstrated to mediate the binding of steroid receptor coactivator complexes to a nuclear receptor ( Heery et al., 1997; Torchia et al., 1997). In plants, it has been identified in the RGA and GAI proteins, two putative transcriptional regulators in the gibberellic acid signal transduction pathway ( Peng et al., 1997; Silverstone et al., 1998). A PSI-BLAST homology search ( Altschul et al., 1997) revealed a region of the EMF1 protein between amino acids 901 and 1034 that displays similarity (identity, 23%; positive, 37%) with two members of a nuclear receptor gene family. This gene family comprises one of the most abundant groups of transcriptional regulators in mammals, with members involved in various developmental processes ( Sluder et al., 1999). Furthermore, the EMF1 protein displays homopolymeric stretches of serine residues, as do the two putative transcriptional regulators RGA and GAI ( Silverstone et al., 1998). The identification of these motifs indicates that EMF1 and OsEMF1 could represent a new class of molecules that could function as transcriptional regulators during shoot development in higher plants. Ubiquitous Expression of EMF1 To investigate the molecular mechanism of EMF1-regulated shoot development, we studied the spatial and temporal expression of EMF1. RNA gel blot analysis found EMF1 mRNA in all organs examined: roots, rosette leaves, stems, cauline leaves, and flower clusters ( Figure 3A). Using the glyceraldehyde 3-phosphate dehydrogenase c ( GAPc) gene as a loading control, we found that EMF1 was expressed in all vegetative organs and was more abundant (~20 to 30%) in flower clusters, which contain the inflorescence meristem, many flower meristems, and flowers of all stages. Thus, EMF1 RNA appeared to be expressed constitutively. Figure 3B shows that EMF1 RNA levels remained constant throughout the development of wild-type Arabidopsis plants grown under short-day conditions. Although EMF1 RNA expression did not decrease during Arabidopsis development, as proposed previously ( Chen et al., 1997), EMF1 protein activity may be modulated during development by protein modification via phosphorylation, nuclear localization, or other means. | Figure 3. Expression of EMF1 RNA in Wild-Type Arabidopsis. |
Modulation of the EMF1 Level Alters Flowering Time and Shoot Determinacy To study the function of EMF1, we attempted to decrease EMF1 expression in wild-type plants. Three constructs containing the EMF1 coding sequence extending 0.6, 2.4, and 3.3 kb from the translation initiation codon in the antisense orientation under the control of the 35S cauliflower mosaic virus promoter (35S) (see Methods) were introduced into wild-type Arabidopsis ( Bechtold et al., 1993). The 2226 T1 transgenic plants carrying the three different antisense constructs displayed a spectrum of emf1-like, early-flowering, and wild-type–like phenotypes ( Figures 4A and 4B). The emf1-like plants were sterile, whereas the early-flowering plants were fertile and could grow in soil. The proportion of the three phenotypic categories observed varied among the constructs ( Table 2). The two longer antisense constructs (2.4 and 3.3 kb) gave higher proportions of emf1-like transgenic plants and lower proportions of early-flowering plants than the shortest construct. The emf1-like transgenic plants, like emf1 mutants ( Figure 4C), lacked rosette leaves and flowered at 14 to 16 days after sowing. Early-flowering transgenic plants produced two to eight normal petiolated rosette leaves and flowered at 16 to 20 days after sowing ( Figure 4A); in the same growth conditions, wild-type–like plants produced 10 to 13 rosette leaves and flowered at ~25 days after sowing. The endogenous EMF1 transcript levels of the early-flowering and emf1-like antisense plants were decreased greatly relative to those of wild-type–like antisense plants and wild-type plants ( Figure 4E). | Figure 4. Phenotypes and EMF1 mRNA Levels of 35S::Antisense EMF1 Transgenic Plants. |
| Table 2. Phenotypes of 35S::Antisense EMF1 T1 Transgenic Plants |
All of the emf1-like and early-flowering antisense plants made the shift from indeterminate to determinate growth by producing terminal flowers ( Figures 4A and 4B). Additionally, some early-flowering plants showed a sympodial branching phenotype during shoot development, a phenotype that is seen in nature ( Foster and Gifford, 1974) but that is never observed in wild-type Arabidopsis. We also found evidence of the sensitivity of flower organ differentiation to EMF1 level. Some emf1-like and early-flowering antisense plants with three or four rosette leaves produced stigmatic papillae and ovule-like structures on stamens or sepals ( Figure 4D). To study the effect of ectopic EMF1 expression on shoot development, we generated 35S::sense EMF1 transgenic plants (see Methods). Approximately 400 T1 plants and 3000 T2 plants were analyzed. The sense transgenic plants displayed the same flowering time phenotypes as the antisense transgenic plants: emf1-like, early-flowering, and wild-type–like plants. None of the 35S::sense EMF1 transgenic plants were late flowering. In the emf1-like sense transgenic plants, no EMF1 RNA was detected by RT-PCR and RNA gel blot analyses (data not shown). Thus, the emf1-like sense transgenic plant phenotypes are best explained by the occurrence of post-transcriptional gene silencing in response to the level of overexpression of EMF1 RNA ( Hamilton and Baulcombe, 1999). Transgenic plants that were verified to overexpress EMF1 RNA by RNA gel blot analysis had wild-type–like phenotypes (data not shown). |
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