Biology subjects

Widhalm, J. R.

Publications and source records attributed to Widhalm, J. R..

6 recordsLinked to original sources

bioRxiv2026

Thiol depletion and disruption of proteostasis contribute to the phytotoxicity of juglone

O_LIJuglone is the phytotoxic 1,4-naphthoquinone responsible for the allelopathic effects of black walnut (Juglans nigra), yet how plants perceive and respond to juglone remain poorly understood. C_LIO_LIWe conducted transcriptome profiling of rosettes and roots of Arabidopsis thaliana exposed to juglone from 30 min to 5 d, along with targeted metabolic profiling, biochemical assays, and untargeted proteomics to gain a systems-level understanding of how plants respond to juglone and to test hypotheses underlying its phytotoxicity. C_LIO_LIJuglone exposure induced expression of genes involved in glutathione, cysteine, and sulfur metabolism pathways, and in protein homeostasis. We found that juglone depletes the pool of reduced glutathione (GSH) in roots, in part, through conjugation. We demonstrate that via upregulation of transcription factors (NAC53 and NAC78), the response to juglone activates components of the proteasome stress regulon and triggers extensive proteome remodeling with engagement of the autophagy pathway when proteasome capacity is limited. C_LIO_LIOur findings (i) indicate that thiol depletion and disruption of proteostasis through juglones dual redox cycling and alkylation activities are central to its phytotoxicity, (ii) cast doubt on previous reports that juglone targets a specific enzyme in plants or other organisms, and (iii) provide insight into how the chemical properties of allelopathic quinones shape their ecological roles. C_LI

plant biology↗

bioRxiv2024

Transcriptional repression of GTL1 under water-deficit stress promotes anthocyanin biosynthesis to enhance drought tolerance

The transcription factor GT2-LIKE 1 (GTL1) has been implicated in orchestrating a transcriptional network of diverse physiological, biochemical, and developmental processes. In response to water-limiting conditions, GTL1 is a negative regulator of stomatal development, but its potential role in other water-deficit responses is unknown. We hypothesized that GTL1 regulates transcriptome changes associated with drought tolerance over leaf developmental stages. To test the hypothesis, gene expression was profiled by RNA-seq analysis in emerging and expanding leaves of wild-type and a drought-tolerant gtl1-4 knockout mutant under well-watered and water-deficit conditions. Our comparative analysis of genotype-treatment combinations within leaf developmental age identified 459 and 1073 differentially expressed genes in emerging and expanding leaves, respectively, as water-deficit responsive GTL1-regulated genes. Transcriptional profiling identified a potential role of GTL1 in two important pathways previously linked to drought tolerance: flavonoid and polyamine biosynthesis. In expanding leaves, negative regulation of GTL1 under water-deficit conditions promotes biosynthesis of flavonoids and anthocyanins that may contribute to drought tolerance. Quantification of polyamines did not support a role for GTL1 in these drought-responsive pathways, but this is likely due to the complex nature of synthesis and turnover. Our global transcriptome analysis suggests that transcriptional repression of GTL1 by water deficit allows plants to activate diverse pathways that collectively contribute to drought tolerance.

plant biology↗

bioRxiv2023

A reference genome for the long-term kleptoplast-retaining sea slug Elysia crispata morphotype clarki

Several species of sacoglossan sea slugs possess the incredible ability to sequester chloroplasts from the algae they consume. These photosynthetic animals incorporate stolen chloroplasts, called kleptoplasts, into the epithelial cells of tubules that extend from their digestive tracts throughout their bodies. The mechanism by which these slugs maintain functioning kleptoplasts in the absence of an algal nuclear genome is unknown. Here, we report a draft genome of the saccoglossan slug Elysia crispata morphotype clarki, a morphotype native to the Florida Keys that can retain photosynthetically active kleptoplasts for several months without feeding. We used a combination of Oxford Nanopore Technologies long reads and Illumina short reads to produce a 786 Mbp assembly containing 68,514 predicted protein-coding genes. A phylogenetic analysis found no evidence of horizontal acquisition of genes from algae. We performed gene family and gene expression analyses to identify E. crispata genes unique to kleptoplast-containing slugs that were more highly expressed in fed versus unfed developmental life stages. Consistent with analyses in other kleptoplastic slugs, our investigation suggests that genes encoding lectin carbohydrate-binding proteins and those involved in regulation of reactive oxygen species and immunity may play a role in kleptoplast retention. Lastly, we identified four polyketide synthase genes that could potentially encode proteins producing UV- and oxidation-blocking compounds in slug cell membranes. The genome of E. crispata is a quality resource that provides potential targets for functional analyses and enables further investigation into the evolution and mechanisms of kleptoplasty in animals.

genomics↗

bioRxiv2022

Disruption of Zea mays isochorismate synthase1 decreases PHENYLALANINE AMMONIA LYASE activity and suppresses hypersensitive response-induced metabolism

ISOCHORISMATE SYNTHASE (ICS) catalyzes the isomerization of chorismate to isochorismate, an essential precursor in the biosynthesis of the Photosystem I electron carrier phylloquinone and of one of two pathways for the biosynthesis of the defense response hormone salicylic acid (SA). We characterized a Zea mays ics1 mutant for impacts on metabolism, photosynthesis, and immune signaling. Phylloquinone was reduced in the mutant resulting in low electron transfer rates and high electron backflow rates. SA accumulation induced by autoactive alleles of the nucleotide-binding leucine-rich repeat (NLR) gene Resistance to Puccinia sorgi1 (Rp1) required ics1. Induced accumulation of SA was not required for lesion formation by the autoactive Rp1-D21#4 allele. Metabolomic analyses and SA supplementation of Rp1-D21#4 mutants, ics1-1 mutants and Rp1-D21#4; ics1-1 double mutants demonstrated that most hypersensitive response-induced metabolism required ics1 but this was independent of SA accumulation. Both the PAL and ICS pathways contributed to SA biosynthesis in maize as labeled phenylalanine was incorporated into SA glucoside. Maize ics1-1 mutants had low PHENYLALANINE AMMONIA LYASE activity, accumulated phenylalanine, and decreased abundance of phenylalanine derived metabolites. This demonstrates that the ICS and PAL pathways interact by a yet unknown mechanism complicating the interpretation of SA biosynthesis in plants from genetics alone.

plant biology↗

bioRxiv2021

Integrative analysis of the shikonin metabolic network identifies new gene connections and reveals evolutionary insight into shikonin biosynthesis

Plant specialized 1,4-naphthoquinones present a remarkable case of convergent evolution. Species across multiple discrete orders of vascular plants produce diverse 1,4-naphthoquinones via one of several pathways using different metabolic precursors. Evolution of these pathways was preceded by events of metabolic innovation and many appear to share connections with biosynthesis of photosynthetic or respiratory quinones. Here, we sought to shed light on the metabolic connections linking shikonin biosynthesis with its precursor pathways and on the origins of shiknoin metabolic genes. Downregulation of Lithospermum erythrorhizon geranyl diphosphate synthase (LeGPPS), recently shown to have been recruited from a cytoplasmic farnesyl diphosphate synthase (FPPS), resulted in reduced shikonin production and a decrease in expression of mevalonic acid and phenylpropanoid pathway genes. Next, we used LeGPPS and other known shikonin pathway genes to build a coexpression network model for identifying new gene connections to shikonin metabolism. Integrative in silico analyses of network genes revealed candidates for biochemical steps in the shikonin pathway arising from Boraginales-specific gene family expansion. Multiple genes in the shikonin coexpression network were also discovered to have originated from duplication of ubiquinone pathway genes. Taken together, our study provides evidence for transcriptional crosstalk between shikonin biosynthesis and its precursor pathways, identifies several shikonin pathway gene candidates and their evolutionary histories, and establishes additional evolutionary links between shikonin and ubiquinone metabolism. Moreover, we demonstrate that global coexpression analysis using limited transcriptomic data obtained from targeted experiments is effective for identifying gene connections within a defined metabolic network.

plant biology↗

bioRxiv2019

Defense hormones modulate root microbiome diversity and composition in tomato

Plant roots live closely associated with soil microbes. Understanding how roots defend against pathogenic microbes while associating with non-pathogenic microbes is critical to using root microbiomes for successful outcomes. The aim of this study was to determine the contribution of the plant defense hormones ethylene (ET), jasmonic acid (JA), and salicylic acid (SA) to the tomato root microbiome. We used 16S rRNA amplicon sequencing to examine the root microbiome of four tomato genotypes defective in three hormone pathways. We found that ET and SA pathways, but not JA, were critical for root endosphere microbial alpha ()-diversity. Root endosphere communities of ACD, deficient in a precursor of ET, and the SA-deficient NahG transgenic, had significantly less -diversity than wild-type tomatoes. NahG and ACD root endosphere enrichment profiles were similar and driven by two taxa. In NahG, ACD, and in a panel of 24 wild-type tomatoes, the abundance of these two taxa was correlated with lower root endosphere -diversity. The abundance of these taxa was also moderately negatively correlated with the level of SA in roots. Our results suggest that SA and ET pathways contribute to tomato root endosphere diversity by modulating the abundance of specific bacterial taxa.

plant biology↗