Flavonoids are widely distributed among mosses, liverworts, and vascular plants, but are not found in hornworts. Algae generally contain no flavonoids Rausher, , but they have been found in a few evolutionary divergent lineages of microalgae Goiris et al. These observations suggest that the ability to produce flavonoids may have evolved multiple times, or that the ability was widely lost during evolutionary processes.
The upstream genes may be evolutionarily constrained due to their profound effects on the pathways. In addition, the genes encoding transcription factors that regulate anthocyanin biosynthesis have evolved more rapidly than the structural genes Rausher et al. The CHS genes are widely distributed in plants, from bryophytes to angiosperms Jiang et al. Every land plant species with available genomic data has at least one putative CHS gene Shimizu et al. They are found in land plants, microalgae, fungi, and bacteria, but are not found in animals or archaea Shimizu et al.
The number of land plant type III PKS genes is highly variable among species in the same taxa; for instance, eudicot species have two to 42 genes, whereas the numbers in fungi and bacteria are relatively low less than five Shimizu et al. Figure 3. The functional diversity of the type III PKSs is generally derived from differences in the starter molecules, the numbers of chain elongation steps, and the mechanisms of the cyclization reactions Austin and Noel, ; Abe and Morita, CHSs and STSs generate the same intermediates from the same starter molecules using the same chain elongation steps, but they catalyze different intra-molecular cyclizations and produce different products Austin et al.
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Data from angiosperms Vitis vinifera, Arachis hypogaea , and Sorghum bicolor , gymnosperms P. Five of the moss CHS family genes were derived from a whole genome duplication, and four are suggested to be derived from segmental duplication and transposition Wolf et al. Four of the genes are upregulated by broad-band UV-B irradiation, and the moss plants show increased levels of a flavonol derivative under UV-B illumination.
These observations support the hypothesis that the genes and enzymes involved in the UV stress response evolved with the water-to-land transition, when early plants were exposed to increased levels of sunlight Wolf et al. In the bryophyte liverwort M. Furthermore, transgenic Marchantia plants overexpressing a MpMyb14 transcription factor gene showed increased expression levels of the same CHS gene under normal growth conditions Albert et al.
Knockout Mpmyb14 mutants were partially impaired by an increase in CHS expression levels under nitrogen deficient conditions Kubo et al. The results suggest that these liverwort species have at least one CHS gene that is activated by the UVR8 signal transduction pathway. The non-CHS group includes many enzymes involved in the biosynthesis of secondary metabolites, such as acridone synthases, pyrone synthases, bibenzyl synthases, and p -coumaroyltriacetic acid synthases Winkel-Shirley, These non-CHS PKS enzymes evolved through repeated gene duplication, mutation, and functional diversification from their ancestral plant enzymes.
Ectopic expression of a CHS gene from either the bryophyte P. Crystal structures of CHSs from P. The Cys residues in the three recent lineages monilophytes, gymnosperms, and angiosperms are present in the thiolate anion form, which gives them stronger nucleophilic power Liou et al. CHSs do not accept bulky substrates, but the lycophyte Huperzia serrata HsPKS1 exhibits remarkable substrate tolerance and catalytic potential Wanibuchi et al. In vitro , HsPKS1 produces naringenin chalcone and other polyketides, including aromatic tricyclic pyridoisoindole compounds, which are not found in natural products.
A single amino acid replacement in HsPKS1 increases its active-site cavity volume and alters the product chain length and the mechanism of the cyclization reaction. This substrate promiscuity in the type III PKSs provides diverse polyketide scaffolds for the subsequent biosynthesis of secondary metabolites in land plants. Alkylresorcinols in grain crop species show anti-fungal and allelopathic activities.
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The pksa pksb double mutant plants are male sterile. Bacteria, fungi, and mosses also have genes encoding type III PKSs that produce these long-chain fatty acyl containing-polyketides Colpitts et al. These proteins share a common folded three-dimensional structure Jez et al. The FAP family is distributed in many bacteria, fungi, and plant species. The moss P. The liverwort M. There are two types of CHI. Type I CHIs are ubiquitous in vascular plants, whereas type II CHIs are specific to legumes and are involved in flavonoid synthesis during nitrogen-fixing root nodule symbioses Shimada et al.
These four CHI genes form a tandem cluster within a kb region of the genome. In soybean, a type I and two type II CHI genes are organized in a gene cluster on chromosome 20 Dastmalchi and Dhaubhadel, , and are probably derived from tandem gene duplications. The role of the CHIs in legume symbiosis remains unclear.
Nitrogen-fixing root nodule symbioses are found in four angiosperm orders: Fabales, Fagales, Cucurbitales, and Rosales the latter three are known as actinorhizal plants. The expression of a CHI gene is upregulated in nodules of the actinorhizal plant Datisca glomerata Gifford et al. The A. This phenotype is largely complemented by ectopic expression of a CHI gene from either the liverwort M. These chi mutants are highly sensitive to UV-B stress treatment.
These results indicate that this basal plant species already has a gene encoding a bona fide CHI to catalyze the cyclization of naringenin chalcone in the flavonoid biosynthetic pathway. CHILs are categorized as type IV CHI-fold proteins and are found in basal and higher plant species including mosses, liverworts, lycophytes, ferns, gymnosperms, and angiosperms.
Three independent Ipomoea nil Japanese morning glory mutants with alterations in enhancer of flavonoid production a CHIL gene showed pale-colored flower phenotypes Morita et al. CHIL loss-of-function mutants in A. However, the A. The common ancestral proteins of the CHIs and CHILs were inferred in an extensive phylogenic analysis, and it appears that all three key catalytic residues were conserved in the ancestral proteins but were inactive Kaltenbach et al. The authors performed a stepwise, activity-based screening of recombinant ancestral proteins using an E.
The results indicated that mutations in amino acid residues other than the catalytic residues were required to initiate CHI evolution, and to acquire CHI catalytic activity. The 2OGD superfamily is one of the largest protein families in the plant kingdom. Its members are widely distributed in bacteria, fungi, plants, vertebrates, and even viruses van den Born et al. The 2OGDs are non-heme iron containing enzymes that are localized in the cytosol. In plants, 2OGDs are involved in histone demethylation, iron sensing, phytohormone metabolism, and the biosynthesis of secondary metabolites reviewed in Farrow and Facchini, Each class contains proteins from all six species.
The DOXB class contains prolyl 4-hydroxylases that catalyze the hydroxylation of proline residues in plant cell wall proteins Hieta and Myllyharju, Proteins in the DOXC class are involved in phytohormone metabolism and the biosynthesis of secondary metabolites including flavonoids, terpenoids, alkaloids, and glucosinolates. A phylogenetic analysis showed that the genes in the DOXC class can be classified into over 50 clades Kawai et al. Among the flavonoid biosynthetic genes in the 2OGD superfamily, it has been proposed that F3H was the first to appear Rausher, The common horsetail E.
Further research in the 2OGD genes of bryophytes, lycophytes, and ferns will help to clarify their evolutionary processes.
The CYPs are widely distributed in viruses, archeae, bacteria, and eukaryotes. In eukaryotes, the CYPs are heme-containing membrane proteins localized on the cytosolic surface of the endoplasmic reticulum. The land plant CYPs form 11 clans and seven of these clans 51, 74, 97, , , , and consist of single CYP families, while the remaining four clans 71, 72, 85, and 86 include proteins in multiple CYP families Nelson and Werck-Reichhart, Green algae contain CYPs in five single family clans clans 51, 97, , , and , and members of these clans are involved in fundamental biological processes such as biosynthesis of sterols, xanthophylls, and phytohormones Nelson, ; Nelson and Werck-Reichhart, Therefore, it is likely that these clans include the ancestral CYPs.
Additional novel CYP families were gained in stepwise processes following the evolution of vascular plants. However, there are some exceptions. However, the CYP family is distributed among bryophytes and vascular plants while the CYP75 family is found in gymnosperms and angiosperms. Such inconsistencies in the relationships between metabolites and genes are also observed in phenylpropanoid metabolism.
However, the syringyl lignin units from the phenylpropanoid pathway are distributed in land plants Bowman et al. A genome-wide analysis of the CYP93 family genes from 60 green plants indicated that the CYP93 family is found only in angiosperms Du et al. Thus, the CYP93 family shows plant lineage-specific evolution.
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Therefore, phylogenetic analyses suggest that the functions of the FNSII and F2H enzymes were established after the divergence of monocots and dicots. As with the CYP75 family, there are inconsistencies in the relationships between metabolites and genes in the CYP93 family.
The CYP93 family genes are found only in angiosperms Nelson and Werck-Reichhart, , but flavones are widely distributed in plants, from bryophytes to angiosperms Figure 1. Isoflavonoids are the typical flavonoids found in legumes, and isoflavone biosynthetic genes are found only in legumes.
However, isoflavonoids are also found in non-legume plants including Iris , which contains a wide variety of isoflavones, some mosses e. The SDRs constitute one of the largest NAD P H dependent oxidoreductase families and are involved in the primary metabolism of lipids, carbohydrates, and hormones, and the secondary metabolism of molecules such as terpenoids, alkaloids, and phenolic compounds Jornvall et al.
A genome sequence analysis using 10 species including C. Compared to other families that contain a few genes per species, the SDRE family contains the largest number of SDR genes; for example, this family includes 24 genes in A. The distribution of SDRE family genes in 10 species indicates that this family has expanded significantly in vascular plants. Furthermore, enzymes involved in phytohormone metabolism, such as phaseic acid reductase for abscisic acid catabolism Weng et al.
Each enzyme type forms a distinct cluster in the phylogenetic tree. The CCR and phenylacetaldehyde reductase clusters contain enzymes from P. SDR families that are less diversified contain genes involved in primary metabolism, such as lipid and chlorophyll biosynthesis Moummou et al. The SDRA family is also referred to as the PIP family, named after the first three enzymes pinoresinol-laricirecinol reductase, isoflavone reductase, and phenylcoumaran benzylic ether reductase that were discovered to belong to this family Gang et al.
In addition, vestitone reductase, eugenol synthase, and isoeugenol synthase also belong to this family Koeduka et al. Pinoresinol-laricirecinol reductase and phenylcoumaran benzylic ether reductase function in the lignan biosynthetic pathway; isoflavone reductase and vestitone reductase are involved in isoflavonoid biosynthesis; and eugenol synthase and isoeugenol synthase are involved in the biosynthesis of volatile phenylpropenes. Thus, the SDRA family members are involved in the biosynthesis of various phenolic compounds.
A phylogenetic analysis of LARs from various plants revealed that the plant LARs can be classified into two clusters: proteins from dicotyledons, and proteins from monocotyledons and gymnosperms Wang et al.
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