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• W2023934400 abstract "Although normally termed “plant secondary metabolism”, the phrase “plant specialized metabolism” has become accepted in recent years, since the boundary between plant primary and secondary metabolism for plant natural products is indistinct (Gang 2005). The early studies of plant natural products can be traced back thousands of years ago to the utilization of herbs for pharmaceutical and cosmetic purposes. Since the nineteenth century, with the development of chemical analysis, more and more plant natural products have been isolated and their chemical structures identified. This research field has grown tremendously in the past decades with modern analytical instruments, such as gas chromatography, high performance liquid chromatography, mass spectrometry and nuclear magnetic resonance. Molecular biology provides new opportunities for plant metabolic studies. It has become possible to isolate genes accounting for different metabolic steps and to manipulate plant metabolic pathways by gene transformation. With the accumulation of sequence information for genes on different metabolic pathways in various plants, and the accomplishment of the genome sequencing projects for Arabidopsis (Arabidopsis Genome Initiative 2000) and other organisms, it is now feasible to predict the function of some genes based on sequence homology. In addition to this, there is also an increasing amount of microarray/DNA chip data on gene expression and co-expression, contributed by research laboratories worldwide. This provides the advantage of knowing the expression and the regulation of a gene before functional characterization. Among the various plant specialized metabolic pathways, the biosynthesis of terpenoids has been very well studied in the past 20 years. Because most terpene synthases share the common conserved domains (Bohlmann et al. 1998), it is relatively easy to isolate a putative terpene synthase gene by homology cloning, and it is also possible to predict the gene as a mono-, sesqui- or diterpene synthase from its deduced amino acid sequence. Based on the availability of a large number of plant terpene synthase genes, genetic engineering, such as in chemical ecology research, has achieved good progress, which has been reviewed in an earlier issue of this Journal (Zulak and Bohlmann 2010). However, terpenes are usually modified by oxidation, hydroxylation, glycosylation and so on. It is still difficult to isolate and characterize P450s and glycosyltransferases for terpene derivates. The difficulty lies in two aspects. The first is that the sequence similarity among different members in the same gene family/subfamily is low. And the second is that there is almost no way to predict what the substrate of the enzyme could be. An example could be found in this issue where Nong et al. (2010) characterized a novel β-thioglucosidase from papaya. Carotenoids are synthesized from the terpenoid metabolic pathway. Genes for their metabolism have also been isolated and characterized from various organisms, and there have been successful transgenic practices in bacteria (Cunningham and Gantt 1998), microalgae (Steinbrenner and Sandmann 2006) and higher plants (Ye et al. 2000). Golden rice has been one of the most successful examples of plant metabolic engineering studies (Ye et al. 2000). In spite of these progresses, there are other reports on how plant carotenoid metabolism is regulated (Lu and Li 2008). Both phytoene synthase (PSY) and phytoene desaturase (PDS) were proposed as the key enzymes for carotenoid biosynthesis. However, a recent metabolic flux analysis showed that the controlling point could shift from PSY to PDS (Rios-Estepa and Lange 2007), which suggested an integrated regulation. In this issue, Sun et al. (2010) reported the coordinated regulation at the transcriptional level of carotenoid biosynthesis in Chlamydomonas reinhardtii, the unicellular green algae with a single methylerythritol pathway for carotenoid biosynthesis. Because Chlamydomonas has fewer copy numbers of genes encoding enzymes for carotenoid pathway (e.g. only one copy of ggps for geranylgeranyl diphosphate synthase instead of 12 putative ggps in Arabidopsis thaliana), it would be relatively easy to quantitatively analyze gene expression, enzyme activity and metabolic flux under different regulatory mechanisms. Besides terpenoid/carotenoid metabolism, flavonoid biosynthesis also received much attention in the past decades (Harborne 1993; Lepiniec et al. 2006). Different from terpene research, which mainly focuses on characterization of new terpene synthase and their chemical ecological functions, molecular studies of plant flavonoid metabolism made attractive progresses in identifying new transcription factors, such as MYB and bHLH (Vom Endt et al. 2002). The key enzymes for flavonoid metabolism, such as chalcone synthase, were also studied for rhythmic expression and epigenetic regulation (Peter et al. 1991; Metzlaff et al. 1997). Along with these advances, biosynthesis and its regulation of some plant flavonoids, such as lignin and proanthocyanins are yet to be understood (Buer et al. 2010; Karkonen and Koutaniemi 2010; Moura et al. 2010). Cloning and identifying novel glycosyltransferase genes for the production of flavonoid glycosides remains an enigma. In this issue, Ye et al. (2010) reported the comparison of expressed sequence tags (ESTs) from the mutant oranges in red and the wild type. The study clearly showed a difference in the expression of a large number of transcription factors and the presence of genes encoding chalcone synthase and isopentenyl diphosphate isomerase, which are the enzymes for the biosynthesis of flavonoids and carotenoids, the two large families of plant pigments. It would help us to understand how plant pigmentation is regulated if we could link the functions of those transcription factors and enzymes to plant development and biotic/abiotic responses. Although it is not a common problem in isolating novel genes for enzymes, functional characterization could still be tough for some families of enzyme. It would provide greater contribution if more work could be carried out on quantitative metabolic flux analyses, integrative regulation among different metabolic branches and the identification of new regulatory mechanisms (e.g., transcription factors, epigenetics and source-sink relationship)." @default.
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• W2023934400 title "Plant Specialized Metabolism: the Easy and the Hard" @default.
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• W2023934400 doi "https://doi.org/10.1111/j.1744-7909.2010.00997.x" @default.
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