Biology subjects

Maeda, H. A.

Publications and source records attributed to Maeda, H. A..

8 recordsLinked to original sources

bioRxiv2026

AATRhg1 is a tonoplast protein that alters amino acid, metabolic and defense responses and nematode resistance

Soybean cyst nematode (SCN, Heterodera glycines) causes significant soybean yield losses. The Rhg1 locus is a major contributor to SCN resistance and contains three genes that mediate this trait including Rhg1-GmAAT (Glyma.18G022400), which encodes putative amino acid transporter AATRhg1. The molecular function of AATRhg1 in SCN resistance is not understood. In this study, rhg1-b soybean lines with Rhg1-GmAAT silencing demonstrated that Rhg1-GmAAT can contribute resistance against HG 0 SCN and also against problematic HG 2.5.7 populations that partially overcome rhg1-b-mediated resistance. An AATRhg1 Y268L mutant complemented SCN resistance in Rhg1-GmAAT-silenced plants while an AATRhg1 D122A mutant did not. Overexpression of Rhg1-GmAAT was not sufficient to enhance SCN resistance, suggesting that AATRhg1 requires coordinated activity with other proteins or pathways. Confocal microscopy demonstrated that AATRhg1 localizes to the tonoplast in soybean root cells. Amino acid, transcriptomic and metabolomic profiles were determined for SCN-infected root segments 3 days after SCN inoculation. In Rhg1-GmAAT-silenced plants relative to fully resistant (non-silenced) rhg1-b plants, levels of leucine, isoleucine, and tyrosine were significantly elevated. Rhg1-GmAAT silencing reduced SCN-responsive transcript abundances for multiple processes, significantly including genes for MAPK signaling, ethylene responses and starch and sucrose metabolism. The most common identified metabolomic changes were in amino acid derivatives, shikimate/phenylpropanoid/isoflavonoid compounds, terpenoids, and especially fatty acids. These findings can guide further investigation into the mechanisms by which AATRhg1 contributes to SCN resistance.

plant biology↗

bioRxiv2026

Enhanced phenylalanine biosynthesis amplifies light-stress-driven phenylpropanoid production in Arabidopsis

Phenylpropanoids are L-phenylalanine (Phe)-derived specialized metabolites with crucial roles in plant stress adaptation. Among various abiotic stresses, high-light (HL) is a major threat that leads to oxidative damage and therefore upregulates the biosynthesis of antioxidant phenylpropanoids, including anthocyanins, in plants. Phenylpropanoid production is initiated by the conversion of Phe by phenylalanine ammonia-lyase (PAL) enzyme, which acts as the key gatekeeper controlling carbon influx from the Phe pool into phenylpropanoid biosynthesis. Despite the importance of Phe as a precursor for phenylpropanoid production, we have limited knowledge of how Phe precursor availability influences downstream pathways, particularly in the context of stress adaptation. To tackle this question, Arabidopsis thaliana wild-type and production of anthocyanin pigment 1 dominant (pap1D) mutant, a line genetically enhanced for anthocyanin production, were subjected to HL treatment, followed by proteome and metabolome analyses. Our multi-omics data indicated that Phe biosynthesis was insufficiently responsive to meet the increased precursor demand from the downstream phenylpropanoid pathway, likely making Phe availability a rate-limiting factor for HL-induced phenylpropanoid production. We then generated pap1D double mutants with Phe-overaccumulating mutants. Untargeted metabolomics revealed that enhanced Phe availability had little impact on phenylpropanoid accumulation under standard growth conditions but additively promoted the accumulation of specific phenylpropanoid intermediates and anthocyanin species under HL stress. This metabolic difference between light treatment and genotypes was correlated with the activation of PAL enzymatic activity. This study demonstrates that enhanced Phe biosynthesis amplifies HL-induced phenylpropanoid biosynthesis.

plant biology↗

bioRxiv2025

Dynamic Retuning of Precursor Supply Before and After the Evolution of the Dual Lignin Pathway in Poales

ABSTRACTPlants produce diverse and abundant natural products, critical for plant adaptation and human society. While tremendous diversification of plant natural product pathways is well documented, how the upstream primary metabolism evolved in coordination with the lineage-specific pathways remain poorly understood. Here we studied the evolution of aromatic amino acid (AAA) biosynthesis during the emergence of tyrosine-derived lignin pathway uniquely found in grasses and closely related Poales. Phylogeny-guided in vitro and in planta functional analyses were conducted on two key regulatory enzymes--3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DHS) and arogenate dehydrogenase (TyrA)--catalyzing the first and last steps of AAA and tyrosine biosynthesis, respectively. Deregulated TyrAs were broadly present across Poales, with PACMAD grasses exhibiting stronger deregulation, suggesting that the active tyrosine biosynthesis likely emerged before, but were also selected upon, the evolution of tyrosine-lignin pathway. Conversely, DHS deregulation occurred more recently within BOP grasses after the emergence of tyrosine-lignin pathway, via multiple mutations that acted synergistically in the enzymes allosteric regulatory domain. The study highlights how the regulation of upstream primary metabolism is dynamically tuned both before and after the evolution of emerging natural product pathways. These findings underscore the importance of coordinating primary and secondary metabolism for efficient production of natural products in plants.

plant biology↗

bioRxiv2024

Genomes of Poaceae sisters reveal key metabolic innovations preceding the emergence of grasses

The grass family (Poaceae, Poales) holds immense economic and ecological significance, exhibiting unique metabolic traits, including dual starch and lignin biosynthetic pathways. To investigate when and how the metabolic innovations known in grasses evolved, we sequenced the genomes of four Poales species, including Joinvillea ascendens and Ecdeiocolea monostachya representing the sister clade to Poaceae. The rho whole genome duplication ({rho}WGD) in the ancestral lineage for all grasses contributed to the gene family expansions underlying cytosolic starch biosynthesis, whereas an earlier tandem duplication of phenylalanine ammonia lyase (PAL) gave rise to phenylalanine/tyrosine ammonia lyase (PTAL) responsible for the dual lignin biosynthesis. Integrated functional genomic and biochemical analyses of grass relatives further revealed the molecular basis of key metabolic innovations predating the evolution of grasses. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/622220v2_ufig1.gif" ALT="Figure 1"> View larger version (108K): org.highwire.dtl.DTLVardef@117dd71org.highwire.dtl.DTLVardef@1cb5daborg.highwire.dtl.DTLVardef@72a331org.highwire.dtl.DTLVardef@38124e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Arabidopsis 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthases of the shikimate pathway display both manganese- and cobalt-dependent activities

The plant shikimate pathway directs a significant portion of photosynthetically assimilated carbon into the downstream biosynthetic pathways of aromatic amino acids (AAA) and aromatic natural products. 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase (DHS) catalyzes the first step of the shikimate pathway, playing a critical role in controlling the carbon flux from central carbon metabolism into the AAA biosynthesis. Previous biochemical studies suggested the presence of manganese- and cobalt-dependent DHS enzymes (DHS-Mn and DHS-Co, respectively) in various plant species. Unlike well-studied DHS-Mn, however, the identity of DHS-Co is still unknown. Here, we show that all three DHS isoforms of Arabidopsis thaliana exhibit both DHS-Mn and DHS-Co activities in vitro. A phylogenetic analysis of various DHS orthologs and related sequences showed that Arabidopsis 3-deoxy-D-manno-octulosonate-8-phosphate synthase (KDOPS) proteins were closely related to microbial Type I DHSs. Despite their sequence similarity, these Arabidopsis KDOPS proteins showed no DHS activity. Meanwhile, optimization of the DHS assay conditions led to the successful detection of DHS-Co activity from Arabidopsis DHS recombinant proteins. Compared to DHS-Mn, DHS-Co activity displayed the same redox dependency but distinct optimal pH and cofactor sensitivity. Our work provides biochemical evidence that the DHS isoforms of Arabidopsis possess DHS-Co activity.

plant biology↗

bioRxiv2024

Multi-substrate specificity shaped the complex evolution of the aminotransferase family across the tree of life

Aminotransferases (ATs) are an ancient enzyme family that play central roles in core nitrogen metabolism essential to all organisms. However, many of the AT enzyme functions remain poorly defined, limiting our fundamental understanding of the nitrogen metabolic networks that exist in different organisms. Here we traced the deep evolutionary history of the AT family by analyzing AT enzymes from 90 species spanning the tree of life (ToL). We found that each organism has maintained a relatively small and constant number of ATs. Mapping the distribution of ATs across the ToL uncovered that many essential AT reactions are carried out by taxon-specific AT enzymes due to wide-spread non-orthologous gene displacements. This complex evolutionary history explains the difficulty of homology-based AT functional prediction. Biochemical characterizations of diverse aromatic ATs further revealed their broad substrate specificity, unlike other core metabolic enzymes that evolved to catalyze specific reactions today. Interestingly, however, we found that these AT enzymes that diverged over billion years share common signatures of multi-substrate specificity by employing different non-conserved active site residues. These findings illustrate that AT evolution had leveraged their inherent substrate promiscuity to maintain a small yet distinct set of multi-functional AT enzymes in different taxa. This evolutionary history of versatile ATs likely contributed to the establishment of robust and diverse nitrogen metabolic networks that exist throughout the ToL. The study provides a critical foundation to systematically determine diverse AT functions and underlying nitrogen metabolic networks across the ToL. Significance StatementThe ToL-wide analyses of the ubiquitous aminotransferases (AT) family revealed that the broad substrate promiscuity of ATs, which is unusual for core metabolic enzymes, allowed recruitment of distinct, non-orthologous ATs to carry out essential AT reactions in different taxa but without increasing their copy numbers. Some distantly related ATs were also found to exhibit a common signature of multi-substrate specificity by employing different non-conserved active site residues. The versatile evolutionary trajectory of the promiscuous AT enzyme family likely led to biochemical diversity of the robust nitrogen metabolic networks that exist among various extant organisms.

biochemistry↗

bioRxiv2020

Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily

The emergence of type III polyketide synthases (PKSs) was a pre-requisite for the conquest of land by the green lineage. To study the deep evolutionary history of this key family, we used phylogenomic synteny network and phylogenetic analyses of whole-genome data from 126 species spanning the green lineage. This study thereby combined study of genomic location and context with changes in gene sequences. We found that two major clades, CHS and LAP5/6 homologs, evolved early by a segmental duplication event prior to the divergence of Bryophytes and Tracheophytes. We propose that the macroevolution of the type III PKS superfamily is governed by whole-genome duplications and triplications. Intriguingly, the combined phylogenetic and synteny analyses in this study shed new insights into changes in the genomic location and context that are retained for a longer time scale with more recent functional divergence captured by gene sequence alterations.

plant biology↗

bioRxiv2019

Role of Cytosolic, Tyrosine-Insensitive Prephenate Dehydrogenase in Medicago truncatula

L-Tyrosine (Tyr) is an aromatic amino acid synthesized de novo in plants and microbes downstream of the shikimate pathway. In plants, Tyr and a Tyr pathway intermediate, 4-hydroxyphenylpyruvate (HPP), are precursors to numerous specialized metabolites, which are crucial for plant and human health. Tyr is synthesized in the plastids by a TyrA family enzyme, arogenate dehydrogenase (ADH/TyrAa), which is feedback inhibited by Tyr. In addition to ADH enzymes, many legumes possess prephenate dehydrogenases (PDH/TyrAp), which are insensitive to Tyr and localized to the cytosol. Yet the role of PDH in legumes is currently unknown. This study isolated and characterized Tnt1-transposon mutants of MtPDH1 (pdh1) in Medicago truncatula to investigate PDH function. The pdh1 mutants lacked PDH transcript, PDH activity, and displayed little aberrant morphological phenotypes under standard growth conditions providing genetic evidence that MtPDH1 is responsible for the PDH activity detected in M. truncatula. Though plant PDH enzymes and activity have been specifically found in legumes, nodule number and nitrogenase activity of pdh1 mutants were not significantly reduced compared to wild-type (Wt) during symbiosis with nitrogen-fixing bacteria. Although Tyr levels were not significantly different between Wt and mutants under standard conditions, when carbon flux was increased by shikimate precursor feeding, mutants accumulated significantly less Tyr than Wt. These data suggest that MtPDH1 is involved in Tyr biosynthesis when the shikimate pathway is stimulated, and possibly linked to unidentified legume-specific specialized metabolism.

plant biology↗