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Plant Physiology 144:1235-1236 (2007) © 2007 American Society of Plant Biologists On the InsideHow Common Is Alternative Splicing in Plants?Alternative RNA processing enables genes to produce a variety of mRNA and protein products, thus expanding the potential informational content of eukaryotic genomes. Recent evidence indicates a high incidence (up to 60%) of alternative splicing (AS) in the human genome, predominantly in the form of exon skip, whereas a minor form is of the type called intron retention (5%–16%). Plants are thought to exhibit less AS, and analyses of AS in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) indicate that intron retention is the most common type of AS in these species. Comparison of AS between different species can provide information about the evolution of AS, the conservation of mechanisms that control AS, and its biological consequences for a species. At the gene level, conservation of AS can provide insights into gene function and the evolutionary history of particular genes and their families. Ner-Gaon et al. (pp. 1632–1641) have developed an algorithm (based on EST pairs gapped alignment) that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ESTs to search for AS. EST pairs gapped alignment was first evaluated in Arabidopsis, rice, and tomato (Solanum lycopersicum), for which annotated genome sequences are available, and was shown to accurately predict splicing events. The method was then applied to 11 plant species that include 17 cultivars for which enough ESTs are available. The results show a large, 3.7-fold difference in AS frequencies between plant species, with Arabidopsis and rice in the lower range and lettuce (Lactuca sativa) and sorghum (Sorghum bicolor) in the upper range. Hence, compared to higher animals, plants show a much greater degree of variety in the frequency of alternatively spliced genes. In eudicots but not monocots, a correlation between genome size and AS frequency was detected, implying that in eudicots the mechanisms that lead to larger genomes are a driving force for the evolution of AS. Loss of Flavonoid Production Causes Seedless Tomatoes Flavonoids, of which more than 6,000 have been identified, are plant secondary metabolites that are widespread throughout the plant kingdom. In nature, flavonoids act as UV light scavengers to protect against oxidative damage, as antimicrobial compounds to defend against pathogens, and as pigments in fruits, flowers, and seeds, where they have a function in attracting pollinators and seed dispersers to facilitate reproduction. Flavonoids are also present in pollen and pistils of many plant species, and there is increasing evidence that flavonoids may play a crucial role in fertility and sexual reproduction. For example, pollination experiments revealed that flavonoids in either the anther or pistil are essential for pollen tube growth, fertilization, and subsequent seed set. To obtain more insight into the role of flavonoids in reproduction and fruit development, Schijlen et al. (pp. 1520–1530) have blocked flavonoid biosynthesis in tomato by RNA interference (RNAi) suppression of the gene encoding chalcone synthase. The resulting transgenic fruits showed a strong decrease of total flavonoid levels and displayed an altered color. More importantly, the fruits were devoid of seeds. The observed parthenocarpic fruit development appeared to be pollination dependent. Fertilization, however, did not occur because chalcone synthase RNAi fruits displayed impaired pollen tube growth. Such seedless fruit phenotypes may prove to be of potential interest to consumers, processing industries, and breeding companies. Nuclear Pore Complex Protein Affects Floral Induction Because the sites of transcription and translation are physically separated by the nuclear membrane, transcripts must be exported from the nucleus to the cytoplasm through the nuclear pore. The nuclear pore complex (NPC) is constructed from subcomplexes composed of approximately 30 proteins. A major ultrastructural feature of the NPC is the nuclear basket, a filamentous network of proteins that extends from the NPC into the nuclear matrix. The nuclear basket is thought to act as a scaffold for the assembly of various molecules involved in nuclear export. A component of the nuclear basket in vertebrates is TRANSLOCATED PROMOTER REGION (TPR), a large coiled-coil protein associated with inner basket filaments. In a screen for Arabidopsis mutants that suppress the expression of the floral inhibitor FLOWERING LOCUS C, Jacob et al. (pp. 1383–1390) have identified lesions in the Arabidopsis homolog of TPR (AtTPR). In addition to their early-flowering phenotype, attpr mutants display a number of other developmental abnormalities, including reduced size and fertility, occurrence of terminal flowers, and a disorganized cell morphology. A striking molecular phenotype of attpr mutants is the accumulation of polyadenylated (polyA) transcripts in the nucleus. A similar nuclear accumulation of polyA RNA has been reported for mutants in two other Arabidopsis NPC proteins, called SUPPRESSOR OF AUXIN RESISTANCE1 and 3 (SAR1 and SAR3). The nuclear accumulation of polyA RNA suggests that AtTPR is required for the efficient export of RNA from the nucleus. The authors also show that the effects of AtTPR on small RNA abundance and auxin signaling are similar to that of two other NPC-associated proteins, HASTY (HST) and SAR3. These data indicate that attpr, sar3, and hst have similar effects on development, and that early flowering, alterations in auxin sensitivity, and RNA levels may be general phenotypes associated with impaired nuclear pore function. Salicylic Acid and Phospholipid Signaling Salicylic acid (SA) has been implicated as a key player in the responses of plants to a wide array of biotic and abiotic stress responses, including systemic acquired resistance. SA has also been demonstrated to reduce plant reproductive fitness, improve seed vigor under stress conditions, induce earlier flowering, and enhance senescence. Despite the apparent involvement of SA in these myriad plant responses, our knowledge of the signal transduction pathways activated by SA is fragmentary. Krinke et al. (pp. 1347–1359) now present evidence that phospholipid signaling may be involved in SA signal transduction. By means of radiolabeled phospholipids, the authors demonstrated that the addition of SA induced a rapid and early (in a few minutes) decrease in a pool of phosphatidylinositol (PI). This decrease paralleled an increase in PI 4-phosphate and PI 4,5-bisphosphate. These changes were inhibited by wortmannin, an inhibitor of type III PI 4-kinases, suggesting that PI 4-kinase is rapidly and transiently activated in response to SA in Arabidopsis suspension cells. The authors also examined the effects of wortmannin on the SA-induced transcriptome. A total of 774 genes were differentially expressed upon SA treatment. The response to SA of 112 of them was inhibited by concentrations of wortmannin sufficient to inhibit PI 4-kinase activity. Ethylene Insensitivity and Photosynthesis Seedlings grown at high sugar concentrations show impaired development. This developmental arrest can be overcome by applying the ethylene precursor 1-aminocyclopropane-1-carboxylic acid. In keeping with these results, ethylene-insensitive seedlings are found to be more strongly inhibited by Glc in their development than wild-type plants. Moreover, previous studies of Arabidopsis have shown that high abscisic acid (ABA) levels enhance the sensitivity of seedling growth to Glc, and a light-responsive element of a Rubisco promoter responds negatively to both ABA and sugars. Based on the observed cross talk between ethylene, ABA, and sugar signaling in seedling development, Tholen et al. (pp. 1305–1315) have hypothesized that ethylene reduces the negative feedback of carbohydrates on photosynthetic gene expression. Previously, the authors observed a lower rate of whole-plant photosynthesis in ethylene-insensitive Arabidopsis plants containing a dominant-negative mutant allele of the ethylene receptor gene ETHYLENE RESPONSE1. In this study, they switched to a similar ethylene-insensitive version of tobacco (Nicotiana tabacum) because gas exchange can be measured more accurately due to its greater leaf size. They conclude that the inability to perceive ethylene results in an increased sensitivity to Glc, which may be mediated by a higher ABA concentration. This increased sensitivity to endogenous Glc has negative consequences for the Rubisco content and the photosynthetic capacity of these plants. A Histone Deacetylase That Limits Chromosome Damage Histone acetylation involves the transfer of acetyl groups from acetyl-CoA to the Lys residues of histones. The hyperacetylation of histones leads to a relaxation of chromatin structure and is associated with transcriptional activation, whereas hypoacetylation of histones induces chromatin compaction and gene repression. The SILENT INFORMATION REGULATOR2 (SIR2) family proteins, also known also as sirtuins, are NAD+-dependent histone deacetylases. Sir2 is involved in chromatin silencing in yeast and is associated with lifespan extension in yeast, worms, and flies. In this issue, Huang et al. (pp. 1508–1519) provide insights into the role of OsSRT1, one of the two SIR2-related genes found in rice. They demonstrate that OsSRT1 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues. Phenotypic and molecular analyses of RNAi transgenic plants suggest that OsSRT1 is involved in the deacetylation of the histone H3 Lys-9 (H3K9) and that it is required for the transcriptional repression of transposable elements and apoptosis-related genes. TUNEL assays and molecular marker gene analysis demonstrated that cell death was induced in OsSRT1 RNAi plants. The TUNEL-positive signals detected in the nuclei of the RNAi leaf cells were indicative of DNA fragmentation similar to that which occurs during programmed cell death and the plant hypersensitive response. The overexpression of OsSRT1 enhanced tolerance to oxidative stress. To study whether the down-regulation of OsSRT1 affected gene expression, the authors compared the transcripts of the RNAi to the wild-type plants by microarray analysis. Such analyses revealed that the transcription of many transposons and retrotransposons as well as genes related to hypersensitive response and/or programmed cell death was activated in OsSRT1 RNAi plants. These findings suggest that OsSRT1 may function in safeguarding plants against genome instability and DNA damage.
Department of Natural Sciences, Mercy College, Dobbs Ferry, New York 1052 FOOTNOTES www.plantphysiol.org/cgi/doi/10.1104/pp.104.900230 Related articles in Plant Physiol.:
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