Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

Torrens-Spence, Michael P.; Chiang, Ying‐Chih; Smith, Tyler A.; Vicent, Maria A.; Wang, Yi; Weng, Jing‐Ke

doi:10.1101/404970

Cited by 12 publications

(19 citation statements)

References 98 publications

(86 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…4HPAAS belongs to the plant aromatic amino acid decarboxylase (AAAD) family (Facchini et al 2000), of which other members include TYDC, tryptophan decarboxylase (TDC), and phenylacetaldehyde synthase (PAAS) (Torrens-Spence et al 2018b). A single amino acid substitution of plant AAADs is capable of impacting substrate selectivity or altering catalytic reactions (Torrens-Spence et al 2013, 2018b.…”

Section: Biosynthesis Of Tyrosine-derived Specialized Metabolitesmentioning

confidence: 99%

General and specialized tyrosine metabolism pathways in plants

Fang

et al. 2019

aBIOTECH

View full text Add to dashboard Cite

The tyrosine metabolism pathway serves as a starting point for the production of a variety of structurally diverse natural compounds in plants, such as tocopherols, plastoquinone, ubiquinone, betalains, salidroside, benzylisoquinoline alkaloids, and so on. Among these, tyrosine-derived metabolites, tocopherols, plastoquinone, and ubiquinone are essential to plant survival. In addition, this pathway provides us essential micronutrients (e.g., vitamin E and ubiquinone) and medicine (e.g., morphine, salidroside, and salvianolic acid B). However, our knowledge of the plant tyrosine metabolism pathway remains rudimentary, and genes encoding the pathway enzymes have not been fully defined. In this review, we summarize and discuss recent advances in the tyrosine metabolism pathway, key enzymes, and important tyrosine-derived metabolites in plants.

show abstract

Section: Biosynthesis Of Tyrosine-derived Specialized Metabolitesmentioning

confidence: 99%

General and specialized tyrosine metabolism pathways in plants

Fang

et al. 2019

aBIOTECH

View full text Add to dashboard Cite

show abstract

“…The latter situation is amplified for plant genomes where local and whole genome duplications are common, resulting in complex evolutionary relationships between genes (such as orthologs from speciation, paralogs from gene duplication, and homoeologs from successive speciation and allopolyploidization events). These related genes can have similar sequences but divergent functions (Jiang et al., 2016; Karunanithi & Zerbe, 2019; Li et al., 2019; Torrens‐Spence et al., 2020; Xu et al., 2007). As a result, analyses relying solely on sequence similarity to guide functional inference may produce false functional predictions.…”

Section: Introductionmentioning

confidence: 99%

PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference

et al. 2020

View full text Add to dashboard Cite

We aim to enable the accurate and efficient transfer of knowledge about gene function gained from Arabidopsis thaliana and other model organisms to other plant species. This knowledge transfer is frequently challenging in plants due to duplications of individual genes and whole genomes in plant lineages. Such duplications result in complex evolutionary relationships between related genes, which may have similar sequences but highly divergent functions. In such cases, functional inference requires more than a simple sequence similarity calculation. We have developed an online resource, PhyloGenes (phylogenes.org), that displays precomputed phylogenetic trees for plant gene families along with experimentally validated function information for individual genes within the families. A total of 40 plant genomes and 10 non‐plant model organisms are represented in over 8,000 gene families. Evolutionary events such as speciation and duplication are clearly labeled on gene trees to distinguish orthologs from paralogs. Nearly 6,000 families have at least one member with an experimentally supported annotation to a Gene Ontology (GO) molecular function or biological process term. By displaying experimentally validated gene functions associated to individual genes within a tree, PhyloGenes enables functional inference for genes of uncharacterized function, based on their evolutionary relationships to experimentally studied genes, in a visually traceable manner. For the many families containing genes that have evolved to perform different functions, PhyloGenes facilitates the use of evolutionary history to determine the most likely function of genes that have not been experimentally characterized. Future work will enrich the resource by incorporating additional gene function datasets such as plant gene expression atlas data.

show abstract

“…AADC and AAS both belong to group II pyridoxal-59-phosphate (PLP)-dependent enzymes that encompass a large family referred to as the plant aromatic amino acid decarboxylase family (AAAD; Facchini et al, 2000;Torrens-Spence et al, 2018a). AAADs can be assigned to three major groups depending on their substrate specificity for Trp, Tyr, or Phe, respectively.…”

mentioning

confidence: 99%

Separate Pathways Contribute to the Herbivore-Induced Formation of 2-Phenylethanol in Poplar

et al. 2019

View full text Add to dashboard Cite

Upon herbivory, the tree species western balsam poplar (Populus trichocarpa) produces a variety of Phe-derived metabolites, including 2-phenylethylamine, 2-phenylethanol, and 2-phenylethyl-b-D-glucopyranoside. To investigate the formation of these potential defense compounds, we functionally characterized aromatic L-amino acid decarboxylases (AADCs) and aromatic aldehyde synthases (AASs), which play important roles in the biosynthesis of specialized aromatic metabolites in other plants. Heterologous expression in Escherichia coli and Nicotiana benthamiana showed that all five AADC/AAS genes identified in the P. trichocarpa genome encode active enzymes. However, only two genes, PtAADC1 and PtAAS1, were significantly upregulated after leaf herbivory. Despite a sequence similarity of ;96%, PtAADC1 and PtAAS1 showed different enzymatic functions and converted Phe into 2-phenylethylamine and 2-phenylacetaldehyde, respectively. The activities of both enzymes were interconvertible by switching a single amino acid residue in their active sites. A survey of putative AADC/AAS gene pairs in the genomes of other plants suggests an independent evolution of this function-determining residue in different plant families. RNA interference-mediated-downregulation of AADC1 in gray poplar (Populus 3 canescens) resulted in decreased accumulation of 2-phenylethylamine and 2-phenylethyl-b-D-glucopyranoside, whereas the emission of 2-phenylethanol was not influenced. To investigate the last step of 2-phenylethanol formation, we identified and characterized two P. trichocarpa short-chain dehydrogenases, PtPAR1 and PtPAR2, which were able to reduce 2-phenylacetaldehyde to 2-phenylethanol in vitro. In summary, 2-phenylethanol and its glucoside may be formed in multiple ways in poplar. Our data indicate that PtAADC1 controls the herbivore-induced formation of 2-phenylethylamine and 2-phenylethyl-b-D-glucopyranoside in planta, whereas PtAAS1 likely contributes to the herbivore-induced emission of 2-phenylethanol.

show abstract

Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

Cited by 12 publications

References 98 publications

General and specialized tyrosine metabolism pathways in plants

General and specialized tyrosine metabolism pathways in plants

PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference

Separate Pathways Contribute to the Herbivore-Induced Formation of 2-Phenylethanol in Poplar

Contact Info

Product

Resources

About