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1. The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation

   https://doi.org/10.1093/plcell/koaa042  

   Yokoyama, Ryo; de Oliveira, Marcos V; Kleven, Bailey; Maeda, Hiroshi A (January 2021, The Plant Cell)

   null (Ed.)

   Abstract The plant shikimate pathway directs bulk carbon flow toward biosynthesis of aromatic amino acids (AAAs, i.e. tyrosine, phenylalanine, and tryptophan) and numerous aromatic phytochemicals. The microbial shikimate pathway is feedback inhibited by AAAs at the first enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DHS). However, AAAs generally do not inhibit DHS activities from plant extracts and how plants regulate the shikimate pathway remains elusive. Here, we characterized recombinant Arabidopsis thaliana DHSs (AthDHSs) and found that tyrosine and tryptophan inhibit AthDHS2, but not AthDHS1 or AthDHS3. Mixing AthDHS2 with AthDHS1 or 3 attenuated its inhibition. The AAA and phenylpropanoid pathway intermediates chorismate and caffeate, respectively, strongly inhibited all AthDHSs, while the arogenate intermediate counteracted the AthDHS1 or 3 inhibition by chorismate. AAAs inhibited DHS activity in young seedlings, where AthDHS2 is highly expressed, but not in mature leaves, where AthDHS1 is predominantly expressed. Arabidopsis dhs1 and dhs3 knockout mutants were hypersensitive to tyrosine and tryptophan, respectively, while dhs2 was resistant to tyrosine-mediated growth inhibition. dhs1 and dhs3 also had reduced anthocyanin accumulation under high light stress. These findings reveal the highly complex regulation of the entry reaction of the plant shikimate pathway and lay the foundation for efforts to control the production of AAAs and diverse aromatic natural products in plants. 

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2. Xylose and shikimate transporters facilitates microbial consortium as a chassis for benzylisoquinoline alkaloid production

   https://doi.org/10.1038/s41467-023-43049-w  

   Gao, Meirong; Zhao, Yuxin; Yao, Zhanyi; Su, Qianhe; Van Beek, Payton; Shao, Zengyi (December 2023, Nature Communications)

   Abstract Plant-sourced aromatic amino acid (AAA) derivatives are a vast group of compounds with broad applications. Here, we present the development of a yeast consortium for efficient production of (S)-norcoclaurine, the key precursor for benzylisoquinoline alkaloid biosynthesis. A xylose transporter enables the concurrent mixed-sugar utilization inScheffersomyces stipitis, which plays a crucial role in enhancing the flux entering the highly regulated shikimate pathway located upstream of AAA biosynthesis. Two quinate permeases isolated fromAspergillus nigerfacilitates shikimate translocation to the co-culturedSaccharomyces cerevisiaethat converts shikimate to (S)-norcoclaurine, resulting in the maximal titer (11.5 mg/L), nearly 110-fold higher than the titer reported for anS. cerevisiaemonoculture. Our findings magnify the potential of microbial consortium platforms for the economical de novo synthesis of complex compounds, where pathway modularization and compartmentalization in distinct specialty strains enable effective fine-tuning of long biosynthetic pathways and diminish intermediate buildup, thereby leading to increases in production. 

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3. A simplified liquid chromatography‐mass spectrometry methodology to probe the shikimate and aromatic amino acid biosynthetic pathways in plants

   https://doi.org/10.1111/tpj.17105  

   El‐Azaz, Jorge; Maeda, Hiroshi A (December 2024, The Plant Journal)

   SUMMARY Plants direct substantial amounts of carbon toward the biosynthesis of aromatic amino acids (AAAs), particularly phenylalanine to produce lignin and other phenylpropanoids. Yet, we have a limited understanding of how plants regulate AAA metabolism, partially because of a scarcity of robust analytical methods. Here, we established a simplified workflow for simultaneous quantification of AAAs and their pathway intermediates from plant tissues, based on extraction at two alternative pH and analysis by Zwitterionic hydrophilic interaction liquid chromatography coupled to mass spectrometry. This workflow was then used to analyze metabolic responses to elevated or reduced carbon flow through the shikimate pathway in plants. Increased flow upon expression of a feedback‐insensitive isoform of the first shikimate pathway enzyme elevated all AAAs and pathway intermediates, especially arogenate, the last common precursor within the post‐chorismate pathway of tyrosine and phenylalanine biosynthesis. Additional overexpression of an arogenate dehydrogenase enzyme increased tyrosine levels and depleted phenylalanine and arogenate pools; however, the upstream shikimate pathway intermediates remained accumulated at high levels. Glyphosate treatment, which restricts carbon flow through the shikimate pathway by inhibiting its penultimate step, led to a predictable accumulation of shikimate and other precursors upstream of its target enzyme but also caused an unexpected accumulation of downstream metabolites, including arogenate. These findings highlight that the shikimate pathway and the downstream post‐chorismate AAA pathways function as independently regulated modules in plants. The method developed here paves the way for a deeper understanding of the shikimate and AAA biosynthetic pathways in plants. 

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4. AXR1 modulates trichome morphogenesis through mediating ROP2 stability in Arabidopsis

   https://doi.org/10.1111/tpj.16403  

   Liu, Lu; Niu, Linyu; Ji, Ke; Wang, Yali; Zhang, Chi; Pan, Mi; Wang, Wenjia; Schiefelbein, John; Yu, Fei; An, Lijun (November 2023, The Plant Journal)

   SUMMARY Cell differentiation and morphogenesis are crucial for the establishment of diverse cell types and organs in multicellular organisms. Trichome cells offer an excellent paradigm for dissecting the regulatory mechanisms of plant cell differentiation and morphogenesis due to their unique growth characteristics. Here, we report the isolation of an Arabidopsis mutant,aberrantlybranchedtrichome 3–1(abt3‐1), with a reduced trichome branching phenotype. Positional cloning and molecular complementation experiments confirmed thatabt3‐1is a new mutant allele ofAuxin resistant 1(AXR1), which encodes the N‐terminal half of ubiquitin‐activating enzyme E1 and functions in auxin signaling pathway. Meanwhile, we found that transgenic plants expressing constitutively active version ofROP2(CA‐ROP2) caused a reduction of trichome branches, resembling that ofabt3‐1. ROP2 is a member of Rho GTPase of plants (ROP) family, serving as versatile signaling switches involved in a range of cellular and developmental processes. Our genetic and biochemical analyses showedAXR1genetically interacted withROP2and mediated ROP2 protein stability. The loss ofAXR1aggravated the trichome defects ofCA‐ROP2and induced the accumulation of steady‐state ROP2. Consistently, elevatedAXR1expression levels suppressedROP2expression and partially rescued trichome branching defects inCA‐ROP2plants. Together, our results presented a new mutant allele ofAXR1, uncovered the effects ofAXR1andROP2during trichome development, and revealed a pathway ofROP2‐mediated regulation of plant cell morphogenesis in Arabidopsis. 

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5. Stronger increase of methane emissions from coastal wetlands by non‐native Spartina alterniflora than non‐native Phragmites australis

   https://doi.org/10.1002/ppp3.10578  

   Fuchs, Andrea; Davidson, Ian C; Megonigal, J Patrick; Devaney, John L; Simkanin, Christina; Noyce, Genevieve L; Lu, Meng; Cott, Grace M (January 2025, PLANTS, PEOPLE, PLANET)

   Societal Impact StatementThe invasive speciesS. alternifloraandP. australisare fast growing coastal wetland plants sequestering large amounts of carbon in the soil and protect coastlines against erosion and storm surges. In this global analysis, we found thatSpartinaandPhragmitesincrease methane but not nitrous oxide emissions, withPhragmiteshaving a lesser effect. The impact of the invasive species on emissions differed greatly among different types of native plant groups, providing valuable information to managers and policymakers during coastal wetland planning and restoration efforts. Further, our estimated net emissions per wetland plant group facilitate regional and national blue carbon estimates. SummaryGlobally,Spartina alternifloraandPhragmites australisare among the most pervasive invasive plants in coastal wetland ecosystems. Both species sequester large amounts of atmospheric carbon dioxide (CO₂) and biogenic carbon in soils but also support production and emission of methane (CH₄). In this study, we investigated the magnitude of their net greenhouse gas (GHG) release from invaded and non‐invaded habitats.We conducted a meta‐analysis of GHG fluxes associated with these two species and related soil carbon content and plant biomass in invaded coastal wetlands.Our results show that both invasive species increase CH₄fluxes compared to uninvaded coastal wetlands, but they do not significantly affect CO₂and N₂O fluxes. The magnitude of emissions fromSpartinaandPhragmitesdiffers among native habitats. GHG fluxes, soil carbon and plant biomass ofSpartina‐invaded habitats were highest compared to uninvaded mudflats and succulent forb‐dominated wetlands, while being lower compared to uninvaded mangroves (except for CH₄).This meta‐analysis highlights the important role of individual plant traits as drivers of change by invasive species on plant‐mediated carbon cycles. 

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