Transcriptional profiling of high pigment-2dg tomato mutant links early fruit plastid biogenesis with its overproduction of phytonutrients

Comparative transcripts profiling reveals new insight into molecular processes regulating lycopene accumulation in a sweet orange (Citrus sinensis) red-flesh mutant

Background

Interest in lycopene metabolism and regulation is growing rapidly because accumulative studies have suggested an important role for lycopene in human health promotion. However, little is known about the molecular processes regulating lycopene accumulation in fruits other than tomato so far.

Results

On a spontaneous sweet orange bud mutant with abnormal lycopene accumulation in fruits and its wild type, comparative transcripts profiling was performed using Massively Parallel Signature Sequencing (MPSS). A total of 6,877,027 and 6,275,309 reliable signatures were obtained for the wild type (WT) and the mutant (MT), respectively. Interpretation of the MPSS signatures revealed that the total number of transcribed gene in MT is 18,106, larger than that in WT 17,670, suggesting that newly initiated transcription occurs in the MT. Further comparison of the transcripts abundance between MT and WT revealed that 3,738 genes show more than two fold expression difference, and 582 genes are up- or down-regulated at 0.05% significance level by more than three fold difference. Functional assignments of the differentially expressed genes indicated that 26 reliable metabolic pathways are altered in the mutant; the most noticeable ones are carotenoid biosynthesis, photosynthesis, and citrate cycle. These data suggest that enhanced photosynthesis and partial impairment of lycopene downstream flux are critical for the formation of lycopene accumulation trait in the mutant.

Conclusion

This study provided a global picture of the gene expression changes in a sweet orange red-flesh mutant as compared to the wild type. Interpretation of the differentially expressed genes revealed new insight into the molecular processes regulating lycopene accumulation in the sweet orange red-flesh mutant.

Genome analysis and genetic enhancement of tomato

The Solanaceae is an important family of vegetable crops, ornamentals and medicinal plants. Tomato has served as a model member of this family largely because of its enriched cytogenetic, genetic, as well as physical, maps. Mapping has helped in cloning several genes of importance such as Pto, responsible for resistance against bacterial speck disease, Mi-1.2 for resistance against nematodes, and fw2.2 QTL for fruit weight. A high-throughput genome-sequencing program has been initiated by an international consortium of 10 countries. Since heterochromatin has been found to be concentrated near centromeres, the consortium is focusing on sequencing only the gene-rich euchromatic region. Genomes of the members of Solanaceae show a significant degree of synteny, suggesting that the tomato genome sequence would help in the cloning of genes for important traits from other Solanaceae members as well. ESTs from a large number of cDNA libraries have been sequenced, and microarray chips, in conjunction with wide array of ripening mutants, have contributed immensely to the understanding of the fruit-ripening phenomenon. Work on the analysis of the tomato proteome has also been initiated. Transgenic tomato plants with improved abiotic stress tolerance, disease resistance and insect resistance, have been developed. Attempts have also been made to develop tomato as a bioreactor for various pharmaceutical proteins. However, control of fruit quality and ripening remains an active and challenging area of research. Such efforts should pave the way to improve not only tomato, but also other solanaceous crops.

Characterization of the intense pigment tomato genotype emphasizing targeted fruit metabolites and chloroplast biogenesis

The tomato INTENSE PIGMENT (IP) genotype is characterized by intense visual pigmentation of unripe and ripe fruits, not thoroughly analyzed thus far. This study was therefore designed to analyze key morphologic, metabolomic, and photomorphogenic phenotypes of this genotype in comparison to its near-isogenic normal counterpart and to evaluate its significance relative to other tomato mutants known for increased fruit pigmentation. The IP genotype produced smaller and darker red fruits, and a substantially increased chloroplast biogenesis was found in its green fruit and leaf tissues. Ripe-red fruits of the IP genotype produced 34-38% more soluble solids and up to 62.6% more carotenoids, but no differences were found in the concentration of flavonoid compounds in its peel tissue. The IP genotype was found to display a greater hypocotyl inhibition response to blue and yellow light, but a more prominent and novel response to total darkness. As a whole, the IP genotype exhibited highly desirable traits, making it a valuable genotype for tomato breeders attempting to introduce functional and taste qualities into tomato fruits.

Regulatory features underlying pollination-dependent and -independent tomato fruit set revealed by transcript and primary metabolite profiling

Indole Acetic Acid 9 (IAA9) is a negative auxin response regulator belonging to the Aux/IAA transcription factor gene family whose downregulation triggers fruit set before pollination, thus giving rise to parthenocarpy. In situ hybridization experiments revealed that a tissue-specific gradient of IAA9 expression is established during flower development, the release of which upon pollination triggers the initiation of fruit development. Comparative transcriptome and targeted metabolome analysis uncovered important features of the molecular events underlying pollination-induced and pollination-independent fruit set. Comprehensive transcriptomic profiling identified a high number of genes common to both types of fruit set, among which only a small subset are dependent on IAA9 regulation. The fine-tuning of Aux/IAA and ARF genes and the downregulation of TAG1 and TAGL6 MADS box genes are instrumental in triggering the fruit set program. Auxin and ethylene emerged as the most active signaling hormones involved in the flower-to-fruit transition. However, while these hormones affected only a small number of transcriptional events, dramatic shifts were observed at the metabolic and developmental levels. The activation of photosynthesis and sucrose metabolism-related genes is an integral regulatory component of fruit set process. The combined results allow a far greater comprehension of the regulatory and metabolic events controlling early fruit development both in the presence and absence of pollination/fertilization.

Effect of tomato pleiotropic ripening mutations on flavour volatile biosynthesis

Ripening is a tightly controlled and developmentally regulated process involving networks of genes, and metabolites that result in dramatic changes in fruit colour, texture and flavour. Molecular and genetic analysis in tomato has revealed a series of regulatory genes involved in fruit development and ripening, including MADS box and SPB box transcription factors and genes involved in ethylene synthesis, signalling and response. Volatile metabolites represent a significant part of the plant metabolome, playing an important role in plant signalling, defence strategies and probably in regulatory mechanisms. They also play an important role in fruit quality. In order to acquire a better insight into the biochemical and genetic control of flavour compound generation and links between these metabolites and the central regulators of ripening, five pleiotropic mutant tomato lines were subjected to volatile metabolite profiling in comparison with wild-type Ailsa Craig. One hundred and seventeen volatile compounds were identified and quantified using SPME (Solid Phase Microextraction) headspace extraction followed by Gas Chromatography-Mass Spectrometry (GC-MS) and the data were subjected to multivariate comparative analysis. We find that the different mutants each produce distinct volatile profiles during ripening. Through principal component analysis the volatiles most dramatically affected are those derived from fatty-acids. The results are consistent with the suggestion that specific isoforms of lipoxygenase located in the plastids and the enzymes that provide precursors and downstream metabolites play a key role in determining volatile composition.

A mutation in the tomato DDB1 gene affects cell and chloroplast compartment size and CDT1 transcript

Fruits harvested from tomato (Solanum lycopersicum) plants carrying mutations at the DAMAGED DNA BINDING PROTEIN 1 gene (SlDDB1; hp-1 and hp-1(w)) are characterized by significantly elevated levels of lycopene and several other phytonutrients. We hypothesize that the pleotropic effect on mutant Slddb1 are some general function of DDB1 protein on cell growth. The main objective of this research was to carry out functional analysis of the mutant SlDDB1 alleles both in-planta and ex-planta in comparison to their normal counterparts. Our major results indicate that: mutant Slddb1 seedlings exhibited delayed growth and smaller cell size, greater chloroplast density, smaller chloroplasts and higher concentration of chlorophyll.Cotyledons cells of Slddb1 mutant also displayed abnormal stomatal pattern, reduced content of CDT1 transcript and altered response to cytokinin. Some of these observations were previously described to be connected to defects in cell cycle control. Our results, coupled with former studies, also suggest that the CDD complex (composed of DDB1, DET1 and COP10) mediate the effect of light and cytokinin activity by possibly regulating the replication licensing factor CDT1 thus affecting both cell size and plastid multiplication.

Exploring and exploiting carotenoid accumulation in Dunaliella salina for cell-factory applications

The unicellular alga Dunaliella salina is the most interesting cell factory for the commercial production of beta-carotene because this species accumulates carotenoids to high concentrations. Nevertheless, little is known about the underlying mechanisms of carotenoid accumulation. Here, we review the regulatory mechanisms involved in beta-carotene overproduction in D. salina. The potential roles of reactive oxygen species and the plastoquinone redox state in signal sensing are discussed, together with available evidence on transcriptional and (post)translational regulation. Moreover, future directions that might further our knowledge in this area are given. Ultimately, a better understanding of the regulatory mechanisms involved in beta-carotene overproduction will facilitate innovative production of specific carotenoids and other products in D. salina and in related organisms.

Susceptibility of the tomato mutant high pigment-2dg (hp-2dg) to Orobanche spp. infection

The consumption of natural products with potential health benefits has been continuously growing, and enhanced pigmentation is of major economic importance in fruits and vegetables. The tomato hp-2 ( dg ) is an important mutant line that has been introgressed into commercial tomato cultivars marketed as lycopene rich tomatoes (LRT) because of their enhanced fruit pigmentation, attributed to higher levels of carotenoids, including lycopene. Strigolactones are signaling compounds that mediate host finding in root parasitic plants and are biosynthetically derived from carotenoids. Considering the high carotenoid content of the hp-2 ( dg ) mutant, we studied its susceptibility to the root parasite Orobanche. In a field experiment, the average number of Orobanche aegyptiaca plants growing on hp-2 ( dg ) was surprisingly significantly reduced compared with its isogenic wild-type counterpart. In vitro assays and LC-MS/MS analysis showed that this reduction was associated with a lower production of strigolactones, which apparently renders the high-carotenoid hp-2 ( dg ) mutant less susceptible to Orobanche.

Carotenoid metabolism: biosynthesis, regulation, and beyond

Carotenoids are indispensable to plants and play a critical role in human nutrition and health. Significant progress has been made in our understanding of carotenoid metabolism in plants. The biosynthetic pathway has been extensively studied. Nearly all the genes encoding the biosynthetic enzymes have been isolated and characterized from various organisms. In recent years, there is an increasing body of work on the signaling pathways and plastid development, which might provide global control of carotenoid biosynthesis and accumulation. Herein, we will highlight recent progress on the biosynthesis, regulation, and metabolic engineering of carotenoids in plants, as well as the future research towards elucidating the regulatory mechanisms and metabolic network that control carotenoid metabolism.

Using metabolomics to estimate unintended effects in transgenic crop plants: problems, promises, and opportunities

Transgenic crops are widespread in some countries and sectors of the agro-economy, but are also highly contentious. Proponents of transgenic crop improvement often cite the "substantial equivalence" of transgenic crops to the their nontransgenic parents and sibling varieties. Opponents of transgenic crop improvement dismiss the substantial equivalence standard as being without statistical basis and emphasize the possible unintended effects to food quality and composition due to genetic transformation. Systems biology approaches should help consumers, regulators, and other stakeholders make better decisions regarding transgenic crop improvement by characterizing the composition of conventional and transgenically improved crop species and products. In particular, metabolomic profiling via mass spectrometry and nuclear magnetic resonance can make broad and deep assessments of food quality and content. The metabolome observed in a transgenic variety can then be assessed relative to the consumer and regulator accepted phenotypic range observed among conventional varieties. I briefly discuss both targeted (closed architecture) and nontargeted (open architecture) metabolomics with respect to the transgenic crop debate and highlight several challenges to the field. While most experimental examples come from tomato (Solanum lycoperiscum), analytical methods from all of systems biology are discussed.

Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1-interacting protein CUL4

Fruits are a major source of nutrition in human diets, providing carbohydrates, fiber, vitamins and phytonutrients. Carotenoids are a principal class of compounds found in many fruits, providing nutritional benefits both as precursors to essential vitamins and as antioxidants. Molecular characterization revealed that the tomato high pigment mutant genes (hp1 and hp2) encode UV-DAMAGED DNA BINDING PROTEIN-1 (DDB1) and DE-ETIOLATED-1 (DET1) homologs, respectively, and both are essential components of the recently identified CUL4-based E3 ligase complex. Here we have isolated a tomato CUL4 homolog and performed yeast two-hybrid assays to suggest possible association of tomato DDB1 with CUL4 and DET1. Real-time RT-PCR analysis indicated that both HP1 and CUL4 are expressed constitutively. Abscisic acid is implicated in plastid division control and its application substantially enhances HP1/DDB1 mRNA accumulation. Transformation of constructs expressing CUL4-YFP and DDB1-YFP fusion proteins driven by the CaMV 35S promoter reveals that both CUL4 and DDB1 are targeted to tomato plastids and nuclei simultaneously. Using fruit-specific promoters combined with RNAi technology, we show that downregulated DDB1 expression in transgenic fruits results in a significant increase in the number of plastids and corresponding enhanced pigment accumulation. CUL4-RNAi repression lines provide insight regarding CUL4 function during tomato development, and reveal that this tomato cullin is important in the regulation of plastid number and pigmentation, which in turn have a direct impact on fruit nutrient quality.

Transcriptional profiling of aluminum toxicity and tolerance responses in maize roots

Aluminum (Al) toxicity is a major factor limiting crop yields on acid soils. There is considerable genotypic variation for Al tolerance in most common plant species. In maize (Zea mays), Al tolerance is a complex phenomenon involving multiple genes and physiological mechanisms yet uncharacterized. To begin elucidating the molecular basis of maize Al toxicity and tolerance, a detailed temporal analysis of root gene expression under Al stress was performed using microarrays with Al-tolerant and Al-sensitive genotypes. Al altered the expression of significantly more genes in the Al-sensitive genotype, presumably as a result of more severe Al toxicity. Nevertheless, several Al-regulated genes exhibited higher expression in the Al-tolerant genotype. Cell wall-related genes, as well as low phosphate-responsive genes, were found to be regulated by Al. In addition, the expression patterns of genes related to Al-activated citrate release indicated that in maize this mechanism is probably regulated by the expression level and/or function of the citrate transporter. This study is the first comprehensive survey of global transcriptional regulation under Al stress. The results described here will help to further our understanding of how mechanisms of Al toxicity and tolerance in maize are regulated at the transcriptional level.