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Received by W. Martin
Abstract
Myo-inositol (inositol) monophosphatase (IMP), an enzyme which catalyzes the synthesis of free inositol from various inositol
monophosphates, is encoded by a small multigene family in many organisms. The tomato IMP gene family encodes three IMP isoforms with
identical in vitro biochemical properties. To determine the role of each tomato LeIMP gene in plant growth, we isolated the genomic DNA
copies of the LeIMP-1 and LeIMP-2 genes. The LeIMP-1 gene spans approximately 5.8 kb and consists of 12 exons, whereas the LeIMP-2
gene consists of an uninterrupted, single open reading frame (ORF). We have previously shown that steady-state levels of LeIMP-2 mRNA
were very low in comparison to LeIMP-1 and LeIMP-3 mRNA levels. To determine whether LeIMP-2 gene expression was spatially
restricted to a discreet domain within the plant we constructed transgenic plants containing an LeIMP-2 promoter::uidA gene fusion. Analysis
of transgenic seedlings revealed that the LeIMP-2 promoter directed gene expression within epidermal and cortex cells of specific stem/leaf
junctions in an abaxial-specific pattern and in the shoot apical meristem. Further, inositol, the product of IMP catalysis, and Li+, an inhibitor
of IMP catalysis, decreased expression of the LeIMP-2 promoter as measured by a decrease in h-glucuronidase activity after treatment.
D 2003 Elsevier B.V. All rights reserved.
0378-1119/$ - see front matter D 2003 Elsevier B.V. All rights reserved.
doi:10.1016/j.gene.2003.09.048
36 J.C. Styer et al. / Gene 326 (2004) 35–41
These data give us information on the average expression heuristic search of tree-bisection-reconnection branch swap-
level of IMPs within tissues, but do not give us any ping. The gaps were treated as missing data. The initial
information on the spatial regulation of the genes within MaxTrees were set as 100 starting trees obtained via
tissues. Therefore, to test whether specific IMP genes are stepwise addition. The number of trees held at each step
spatially regulated in their expression, we isolated and during stepwise addition was 5. Confidence of the group-
analyzed genomic DNA corresponding to two of the three ings was estimated using 500 bootstrap replications.
tomato IMP genes (LeIMP-1 and LeIMP-2). The data pre-
sented here show that the LeIMP-1 and LeIMP-2 genes differ 2.3. Transgenic plant construction
in their exon – intron organization. The analysis of the regu-
lation of the LeIMP-2 promoter indicates that the LeIMP-2 Transgenic tomato plants were constructed in the follow-
promoter is active in a spatially restricted subset of cells in ing manner: a 1.2-kb fragment containing the putative
tomato seedlings. This suggests that LeIMP-2 plays a unique promoter region of LeIMP-2 (LeIMP-2p) was amplified by
role in inositol metabolism and recycling in tomato. high-fidelity PCR utilizing oligonucleotide primers contain-
ing NcoI restriction enzyme sites. The resulting PCR frag-
ment was digested with NcoI and cloned into the NcoI site
2. Materials and methods of plasmid pSLJ4K1 which contains the open reading frame
(ORF) of the uidA (GUS) gene and nopaline synthase 3V
2.1. Plant materials and treatments processing sequences (nos 3V) (Jones et al., 1992). The
position of the LeIMP-2 ( + 1) site relative to its initiating
Tomato Lycopersicon esculentum (cv. Ailsa Craig) seeds methionine codon (ATG) was kept intact. The LeIMP-2p-
were surface sterilized for 10 minutes using 30% Clorox, GUS-nos 3V region was removed by digestion with SstI and
rinsed with sterile water three times and germinated on BamH1 enzymes and subcloned into the binary vector
0.5 Murashige and Skoog Basal Salt Mixture media (MS pSLJ7292 (Jones et al., 1992). This construct was trans-
salts) (Sigma) in magenta boxes or soil (Sunshine Mix). For ferred to Agrobacterium tumefaciens strain LBA4404 by
Li+ and inositol treatment of plants, LiCl or inositol (Sigma) triparental mating, and leaf disc transformation was per-
was added to the media at 10 and 50 mM final concen- formed using methods previously described (An et al.,
trations, respectively. Transgenic seed were selected on the 1986). Putative transformants were isolated on kanamycin
ability to germinate in the presence of media containing 50 selective media and analyzed for the presence of LeIMP-2p-
Ag/ml of kanamycin sulfate (Sigma). Plants were grown uidA insertions by PCR. Transgenic plants were transferred
either in magenta boxes at 22 jC under continuous light in a to soil, maintained in greenhouses and allowed to self-
growth chamber (Percival Scientific) or to maturity in soil in fertilize. Subsequent generations of plants were obtained
a greenhouse. from transgenic seed and maintained under standard green-
house conditions. Construction and analysis of transgenic
2.2. Gene cloning and sequence analyses hydroxymethylglutaryl reductase (HMGR) plants has been
described (Jelesko et al., 1999).
Fragments of the LeIMP-1 and LeIMP-2 genes were used
to screen a Egt11 genomic library constructed from tomato 2.4. h-Glucuronidase (GUS) assays
DNA (Narita and Gruissem, 1989). DNA from hybridizing
plaques was purified, cloned and sequenced as previously Seedling tissues were dissected using a sterilized double-
described (Narita and Gruissem, 1989). The genomic edged razor blade, immersed in GUS assay solution (0.025
sequences of LeIMP-1 and LeIMP-2 have been deposited AM ferrocyanide, 0.025 AM ferrous cyanide, 0.1 mM
into Genbank (accession numbers AY227666 and sodium phosphate buffer pH 7.0, 0.01% Triton X-100, 0.5
AY227667, respectively). Genomic sequences were com- Ag/ml 5-bromo-4-chloro-3-indoyl-D-glucuronic acid), vacu-
pared to the previously published cDNA sequences of um infiltrated for 30 min and incubated at 37 jC overnight.
LeIMP-1 and LeIMP-2 (Gillaspy et al., 1995) to predict After incubation, the assay solution was replaced by forma-
exon – intron organization boundaries using ClustalW soft- lin – acid – alcohol (FAA: 50% (v/v) ethanol, 10% (v/v) 37%
ware (Thompson et al., 1994). Putative regulatory elements formaldehyde, 5% (v/v) glacial acetic acid) to preserve
were analyzed using the Plant Cis-Acting Regulatory Ele- tissue morphology. Control transformed seedlings contain-
ment (Plant CARE) website (Lescot et al., 2002). Genomic ing an empty pSLJ7292 vector and wildtype tomato seed-
DNA from tomato plants was prepared and analyzed by lings were similarly treated and served as negative controls
southern blotting as described (Berdy et al., 2001). IMP in GUS assays.
amino acid sequences were aligned with ClustalW software
(gap weight = 4, gap extension weight = 0.05). Unrooted 2.5. Imaging and histology
phylogenetic trees were created with PAUP 4.0 b10 (Swof-
ford, 2002) using a parsimony algorithm based on the full Tissue was examined using a stereomicroscope (Stemi
alignment. A parsimony analysis was performed with a SVII Apo, Ziess). Results were recorded using a digital
J.C. Styer et al. / Gene 326 (2004) 35–41 37
Fig. 2. Genomic organization of the LeIMP-1 and LeIMP-2 genes. (A) The LeIMP-1 gene. Black boxes represent exons; sizes (in bp) are in black below the
boxes. Intron sizes (bp) are indicated in gray. Start and stop refer to the positions of the start and stop codons, respectively. (B) The LeIMP-2 promoter and gene.
The large black box represents the single exon. Positions of the TATA box, transcriptional start site ( + 1), start and stop codons are indicated by arrows. Patterned
boxes (I – IV) represent putative transcriptional regulatory regions. Regions I, III and IV: light-responsive elements, region II: cold responsive element.
38 J.C. Styer et al. / Gene 326 (2004) 35–41
protein levels increase in seedlings exposed to light genes. ClustalW alignments and PAUP* phylogenetic anal-
(Gillaspy et al., 1995). yses revealed that At1g31190 and At4g39120 are more
similar to the SuhB gene (Chen and Roberts, 2000; Matsu-
3.2. Isolation and analysis of the genomic structure of the hisa et al., 1995) found in both prokaryotes and eukaryotes
LeIMP-2 gene than to IMP genes. In comparing the plant IMP genes with
the mouse and human IMP genes, we found that both types
To characterize the genomic structure of the LeIMP-2 gene, of animal genes exhibit identical exon– intron organization
we screened our tomato genomic DNA library with the and this structure differs from that of the plant IMP genes.
LeIMP-2 cDNA probe which we had also used in a Southern To address whether multiple IMP genes are likely to have
blot of tomato genomic DNA (Fig. 1). Sequencing of a evolved through a gene duplication event, we constructed a
positive clone revealed congruity between the observed pat- phylogenetic tree of tomato, Arabidopsis, mouse, human,
tern of hybridization in the Southern blot and the genomic dictyostelium and yeast IMP proteins (Fig. 3). The branch-
clone. We aligned the LeIMP-2 genomic DNA sequence ing pattern of human and mouse IMP sequences indicates
(2726 bp, Genbank accession number AAY227667) with that the two animal IMP genes arose through a gene
the LeIMP-2 cDNA (Genbank accession number U39443). duplication of an ancestral gene. In contrast, both the yeast
This alignment revealed that the LeIMP-2 gene contains a and plant IMP gene families are most likely a result of
single, uninterrupted ORF of 798 bp (Fig. 2B). The absence of separate gene duplication events. In particular, plant IMP
introns is unique to LeIMP-2, as PCR amplification using gene duplication events occurred after the divergence of
LeIMP-3-specific oligonucleotide primers with tomato ge- Arabidopsis and tomato, one of which produced an intron-
nomic DNA confirmed the presence of introns in parts of the less copy (LeIMP-2).
LeIMP-3 gene (data not shown). The absence of introns is rare
in plant genes; however, intron-less genes have been docu- 3.4. Spatial regulation of the LeIMP-2 promoter
mented (Hossain et al., 1996; Lui et al., 1997). Many chloro-
plastic and mitochondrial genes have few or no introns, We previously reported that LeIMP-2 mRNA expression
possibly due to their prokaryotic origins. It is possible that was very low in all tomato tissues examined by RNAse
transposon insertions into the tomato genome may have protection assays (Gillaspy et al., 1995). Since RNAse
provided the organism with an intron-less copy of one of the protection analysis gives information on the average expres-
LeIMP genes. Within the 2726 bp of DNA obtained at the sion level in tissues and does not provide spatial information,
LeIMP-2 locus, we also identified 338 bp of DNA that is we determined whether the LeIMP-2 gene was expressed in a
identical to the 3V end of a tomato calmodulin-like gene subset of cells. The 1.2-kb LeIMP-2 promoter (LeIMP-2p)
(Genbank accession number BG130697). Calmodulin, a
148-amino acid protein, binds calcium and functions to
activate regulatory subunits of other enzymes such as calmod-
ulin-dependent protein kinases (Luan et al., 2002). Down-
stream of the calmodulin-like gene, we identified 1,205 bp of
DNA of the putative LeIMP-2 promoter. Analysis of this DNA
revealed the presence of a putative TATA box at ( 30) and a
predicted start site of transcription 114 bp upstream from the
start site of translation and four putative regulatory elements
were found in this promoter sequence (I through IVin Fig. 2B).
We previously reported that light stimulated an increase in
LeIMP-2 mRNA expression, so it is likely that these elements
I, III and IV are functional (Gillaspy et al., 1995).
was fused to the uidA gene encoding GUS and transferred The significance of the LeIMP-2p:GUS expression pat-
into tomato plants by A. tumefaciens-mediated transforma- tern is not immediately obvious. One can speculate that
tion (An et al., 1986). Analysis of homozygous T2 transgenic genes exclusively expressed at stem/leaf junctions might be
seedlings from four independent lines indicated that the regulated by a type of ‘‘nutrient eddy’’ present at this
LeIMP-2 promoter directed expression of GUS predomi- location. For example, the hydroxymethylglutaryl Co-A
nantly in the stem/leaf junction of the seedling stem (Fig. 4). enzyme reductase 1 (HMGR-1) gene from tomato is
The most intense deposition of GUS product was found expressed in a similar location, although the abaxial
below the shoot apex and extended on the abaxial side of the ‘‘stripes’’ of LeIMP-2 expression are unique (compare Figs.
petiole of the first 1 – 2 sets of expanded leaflets into two 4B and 5D). Since a role for IMP in regulating dorsal –
abaxial ‘‘stripes’’ (Fig. 4B,C). In addition, other tissues (i.e. ventral specification in Xenopus laevis has been studied
stems, leaves, flowers) from mature plants and plants trans- (Busa and Gimlich, 1989; Maslanski et al., 1992), it is
formed with an empty vector did not contain appreciable intriguing to speculate that the LeIMP-2 gene in tomato
amounts of GUS activity. To determine specific cell types in might play a similar role in stem/leaf abaxial specification.
which the LeIMP-2 promoter was active, we examined
preserved sections of 21 day old transgenic LeIMP- 3.5. Regulation of the LeIMP-2 promoter by inositol and
2p:GUS seedlings stained for GUS activity (Fig. 4G,H). Li+
From these sections, we conclude that LeIMP-2 expression is
strongest in the epidermal and first few cortex cell layers of We were interested in whether the product of IMP
the stem and petiole (Fig. 4G – H). Surprisingly, cells within catalysis, inositol or an inhibitor of IMP catalysis, Li+,
the shoot apical meristem and developing leaf primordia also regulate the LeIMP-2 promoter. To address this, we grew
showed LeIMP-2p:GUS expression (Fig. 4G). LeIMP-2p:GUS seedlings for 21 days in the presence of
Fig. 4. Spatial regulation of the LeIMP-2 Promoter. The LeIMP-2 promoter was fused to the uidA reporter gene and transformed into tomato. Twenty-one-day-
old transgenic seedlings were assayed for GUS activity as described in Section 2. (A) Control, non-transformed seedling shoot apex, compound leaf and stem.
Bar = 1 mm. (B – H) LeIMP-2p:GUS seedlings. (B) Shoot apex, compound leaf and stem. Bar = 0.5 mm. (C) Close-up of stem and leaf. Bar = 2 mm. (D)
Adaxial internode surface. Bar = 2 mm. (E) Side surface of internode. Bar = 2 mm. (F) Abaxial surface of internode. Bar = 2 mm. (G) Dark-field microscopy of
a longitudinal section of the shoot apical meristem and leaf primordia. Bar = 0.14 mm. (H) Dark-field microscopy of a close-up of a transverse section of the
base of the shoot apex. Bar = 0.10 mm.
40 J.C. Styer et al. / Gene 326 (2004) 35–41
Fig. 5. Regulation of the LeIMP-2 promoter by inositol and Li+. (A – C) Twenty-one-day-old LeIMP-2p:GUS seedlings were grown on media alone (A), media
plus 50 mM inositol (B), or 10 mM LiCl (C), and assayed for GUS activity as described in Section 2. (D – F) Twenty-one-day-old HMGR-1p:GUS seedlings
were grown on media alone (D), media plus 50 mM inositol (E), or 10 mM LiCl (F), and assayed for GUS activity as described. Bar = 1.4 mm.
control media, media supplemented with 50 mM inositol, or The yeast Saccharomyces cerevisiae contains two IMP
media containing 10 mM LiCl. We have previously char- genes (INM1 and INM2); the INM1 gene has been shown to
acterized the effect of LiCl on tomato seedling development. be upregulated by inositol and downregulated by Li+ (Mur-
Our results indicated that LiCl takes 42 days to disrupt ray and Greenberg, 1997, 2000). The authors of this study
development of the stems and leaves (Gillaspy and Gruis- speculate that INM1 expression is tied to the need for
sem, 2001). Therefore, growth for 21 days in the presence of recycling inositol, which is a breakdown product of PIP
either LiCl or inositol does not outwardly affect develop- signaling molecules. Thus, when cellular synthesis of PIP is
ment. These treatments do, however, affect LeIMP-2 ex- high, the concentration of its breakdown product, inositol,
pression (Fig. 5). Inositol supplementation decreased overall will be increased. Conversely, since Li+ inhibits IMP and
GUS staining in both the stem/leaf junction and in the decreases the amount of inositol in yeast (Murray and
abaxial ‘‘stripes’’ that were present in untreated seedlings Greenberg, 2000), Li+ treatment could decrease INM1 ex-
(Fig. 5A,B). Addition of LiCl reduced almost all visible pression because of a decreased need for inositol recycling.
GUS staining (Fig. 5C). To determine if the effects of We found a similar decrease in LeIMP-2 expression in the
inositol and LiCl were specific to the LeIMP-2 promoter, presence of Li+. However, our results showing inositol also
we also examined HMGR-1p:GUS plants grown under decreases LeIMP-2 expression indicates a difference in IMP
similar conditions. Neither inositol nor LiCl treatment gene regulation between yeast and plants. We speculate that
decreased expression of the HMGR-1 promoter (Fig. 5D – inositol inhibition of LeIMP-2 expression in plants may
F). Therefore, we conclude that inositol and LiCl act indicate that this specific IMP isoform is regulated by
specifically to reduce LeIMP-2 expression. metabolic feedback from its product, inositol. We further
J.C. Styer et al. / Gene 326 (2004) 35–41 41
speculate that plants, which channel inositol and its break- Gillaspy, G., Gruissem, W., 2001. Li+ induces hypertrophic growth and
downregulation of IMP activity in tomato. J. Plant Growth Regul. 20,
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Acknowledgements
inositol monophosphatase: expression and characterization of the hu-
man recombinant enzyme. Biochem. J. 284, 749 – 754.
The authors would like to thank Susan Jenkins for help in Mitchell, R.H., 1986. Inositol lipids and their role in receptor function:
construction of transgenic plants, JinRi Shi and John Jelesko history and general principles. Journal, 1 – 24.
for preliminary characterization of transgenic plants, Jake Murray, M., Greenberg, M.L., 1997. Regulation of inositol monophospha-
tase in Saccharomyces cerevisiae. Mol. Microbiol. 25, 541 – 546.
Tu and Hongguang Shao for help in the phylogenetic
Murray, M., Greenberg, M.L., 2000. Expression of yeast INM1 encoding
analysis, and Bhadra Gunesekera for comments on the inositol monophosphatase is regulated by inositol, carbon source and
manuscript. This work was supported by a Jeffress growth stage and is decreased by lithium and valproate. Mol. Microbiol.
Memorial Trust award and the Commonwealth Health 36, 651 – 661.
Research Board of Virginia. Narita, J.O., Gruissem, W., 1989. Tomato hydroxymethylglutaryl-CoA
reductase is required early in fruit development but not during ripen-
ing. Plant Cell 1, 181 – 190.
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