Biology subjects

Vatamaniuk, O. K.

Publications and source records attributed to Vatamaniuk, O. K..

6 recordsLinked to original sources

bioRxiv2022

Characterization and visualization of global metabolomic responses of Brachypodium distachyon to environmental changes

Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from tandem liquid chromatography mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how different metabolite classes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots and other organs of Brachypodium distachyon, a model Poaceae species, under 17 different organ-condition combinations, including copper deficiency, heat stress, low phosphate and arbuscular mycorrhizal symbiosis (AMS). We used a combination of information theory-based metrics and machine learning-based identification of metabolite structural classes to assess metabolomic changes. Both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We also found that one week of copper deficiency shielded the root metabolome, but not the leaf metabolome, from perturbation due to heat stress. Using a recently published deep learning based method for metabolite class predictions, we analyzed the responsiveness of each metabolite class to environmental change, which revealed significant perturbations of various lipid classes and phenylpropanoids such as cinnamic acids and flavonoids. Co-accumulation analysis further identified condition-specific metabolic biomarkers. Finally, to make these results publicly accessible, we developed a novel visualization platform on the Bioanalytical Resource website, where significantly perturbed metabolic classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and plant stress adaptation.

plant biology↗

bioRxiv2021

OPT3 plays a central role in both copper and iron homeostasis and signaling due to its ability to deliver copper as well as iron to the phloem in Arabidopsis

Copper and iron are essential micronutrients but are toxic when accumulating in cells in excess. Thus, their uptake by roots is tightly regulated. While plants sense and respond to local copper availability, the systemic regulation of copper uptake has not been documented. By contrast, both local and systemic control for iron uptake has been reported. Iron abundance in the phloem has been suggested to act systemically, regulating the expression of iron uptake genes in the root. Consistently, shoot-to-root iron signaling is disrupted in A. thaliana mutants lacking the phloem companion cell-localized iron transporter, AtOPT3: opt3 mutants overaccumulate iron in leaves while constitutively upregulating iron deficiency-responsive genes in roots. We report that AtOPT3 transports copper and mediates its delivery from source leaves to sinks including young leaves and developing embryos. Consequently, the opt3 mutant accumulates less copper in the phloem, is sensitive to copper deficiency, and mounts transcriptional copper deficiency response in roots. Copper rescues these defects. Notably, feeding the opt3 mutant with copper or iron via the phloem in leaves downregulates the expression of both copper and iron-deficiency marker genes in roots, suggesting that copper and iron can substitute each others function in the phloem in shoot-to-root communication. One-sentence summaryAtOPT3 loads copper and iron into the phloem companion cells, for subsequent distribution to sink tissues and systemic signaling of copper and iron deficiency.

plant biology↗

bioRxiv2021

Genome-wide association study reveals an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels

Despite being one of the most consumed vegetables in the United States, the elemental profile of sweet corn (Zea mays L.) is limited in its dietary contributions. To address this through genetic improvement, a genome-wide association study was conducted for the concentrations of 15 elements in fresh kernels of a sweet corn association panel. In concordance with mapping results from mature maize kernels, we detected a probable pleiotropic association of zinc and iron concentrations with nicotianamine synthase5 (nas5), which purportedly encodes an enzyme involved in synthesis of the metal chelator nicotianamine. Additionally, a pervasive association signal was identified for cadmium concentration within a recombination suppressed region on chromosome 2. The likely causal gene underlying this signal was heavy metal ATPase3 (hma3), whose counterpart in rice, OsHMA3, mediates vacuolar sequestration of cadmium and zinc in roots, whereby regulating zinc homeostasis and cadmium accumulation in grains. In our association panel, hma3 associated with cadmium but not zinc accumulation in fresh kernels. This finding implies that selection for low cadmium will not affect zinc levels in fresh kernels. Although less resolved association signals were detected for boron, nickel, and calcium, all 15 elements were shown to have moderate predictive abilities via whole-genome prediction. Collectively, these results help enhance our genomics-assisted breeding efforts centered on improving the elemental profile of fresh sweet corn kernels.

genetics↗

bioRxiv2020

Ferroportin 3 is a dual-targeted mitochondrial/chloroplast iron exporter necessary for iron homeostasis in Arabidopsis

Mitochondria and chloroplasts are organelles with high iron demand that are particularly susceptible to iron-induced oxidative stress. Despite the necessity of strict iron regulation in these organelles, much remains unknown about mitochondrial and chloroplast iron transport in plants. Here, we propose that Arabidopsis Ferroportin 3 (FPN3) is an iron exporter dual-targeted to mitochondria and chloroplasts. FPN3 is expressed in shoots regardless of iron conditions, but its transcripts accumulate under iron deficiency in roots. fpn3 mutants cannot grow as well as wild type under iron-deficient conditions and shoot iron levels are reduced in fpn3 mutants compared to wild type. ICP-MS measurements show that iron levels in the mitochondria and chloroplasts are increased relative to wild type, consistent with the proposed role of FPN3 as a mitochondrial/plastid iron exporter. In iron deficient fpn3 mutants, abnormal mitochondrial ultrastructure was observed, whereas chloroplast ultrastructure was not affected, implying that FPN3 plays a critical role in the mitochondria. Overall, our study suggests that FPN3 is essential for optimal iron homeostasis. Significance statementIron homeostasis must be tightly controlled in the mitochondria and chloroplasts, but iron trafficking in these organelles is not fully understood. Our work suggests that FPN3 is an iron exporter required for maintaining proper iron levels in mitochondria and chloroplasts. Furthermore, FPN3 is necessary for the optimal growth and normal mitochondrial ultrastructure under iron deficiency. This study reveals the physiological role of FPN3 and advances our understanding of iron regulation in mitochondria and chloroplasts.

plant biology↗

bioRxiv2020

Copper deficiency alters shoot architecture and reduces fertility of both gynoecium and androecium in Arabidopsis thaliana

Copper deficiency reduces plant growth, male fertility and seed set. The contribution of copper to female fertility and the underlying molecular aspects of copper deficiency-caused phenotypes are not well-known. We show that among copper deficiency-caused defects in Arabidopsis thaliana were the increased shoot branching, delayed flowering and senescence, and entirely abolished gynoecium fertility. The increased shoot branching of copper-deficient plants was rescued by the exogenous application of auxin or copper. The delayed flowering was associated with the decreased expression of the floral activator, FT. Copper deficiency also decreased the expression of senescence-associated genes, WRKY53 and SAG13, but increased the expression of SAG12. The reduced fertility of copper-deficient plants stemmed from multiple factors including the abnormal stigma papillae development, the abolished gynoecium fertility, and the failure of anthers to dehisce. The latter defect was associated with reduced lignification, the upregulation of copper microRNAs and the downregulation of their targets, laccases, implicated in lignin synthesis. Copper-deficient plants accumulated ROS in pollen and had reduced cytochrome c oxidase activity in leaves. This study opens new avenues for the investigation into the relationship between copper homeostasis, hormone-mediated shoot architecture, gynoecium fertility and copper deficiency-derived nutritional signals leading to the delay in flowering and senescence. HighlightCopper deficiency alters shoot architecture, delays flowering and senescence, and compromises fertility by altering stigma morphology, disrupting anther lignification and dehiscence, and pollen redox status in Arabidopsis thaliana.

plant biology↗

bioRxiv2019

YSL3-mediated copper distribution is required for fertility, grain yield, and size in Brachypodium.

Addressing the looming global food security crisis requires the development of high yielding crops. In this regard, the deficiency for the micronutrient copper in agricultural soils decreases grain yield and significantly impacts a globally important crop, wheat. In cereals, grain yield is determined by inflorescence architecture, flower fertility, grain size and weight. Whether copper is involved in these processes and how it is delivered to the reproductive organs is not well understood. We show that copper deficiency alters not only the grain set but also flower development in both wheat and its recognized model, Brachypodium distachyon, We then show that a brachypodium yellow-stripe-like 3 (YSL3) transporter localizes to the phloem and mediates copper delivery to flag leaves, anthers and pistils. Failure to deliver copper to these structures in the ysl3 CRISPR/Cas9 mutant results in delayed flowering, altered inflorescence architecture, reduced floret fertility, grain number, size, and weight. These defects are rescued by copper supplementation and are complemented by the YSL3 cDNA. This new knowledge will help to devise sustainable approaches for improving grain yield in regions where soil quality is a major obstacle for crop production.

plant biology↗