Biology subjects

Fish, T.

Publications and source records attributed to Fish, T..

4 recordsLinked to original sources

bioRxiv2026

Gene-metabolite networks reveal physiological trade-offs but not transcriptional co-regulation between carotenoids and dry matter in cassava (Manihot esculenta) roots

Provitamin A biofortification of cassava (Manihot esculenta) is constrained by a negative genetic correlation between total carotenoid (TC) and dry matter (DM) contents, but its underlying biological mechanism remains unclear. We examined this relationship in 24 African, Latin American, and hybrid cassava genotypes by measuring gene expression and metabolites in inner and outer storage root layers that varied spatially in carotenoid accumulation, enabling comparisons across and within genotypes. TC, and particularly upstream cis-carotenes, were negatively associated with DM after accounting for genotype, and this relationship strengthened across developmental timepoints, consistent with a physiological component of the trade-off. Gene-metabolite co-expression networks constructed from genetic, non-genetic, and overall phenotypic trait components showed no significant topological overlap between carotenoid- and starch-related gene sets, indicating that the TC/DM relationship is not driven by transcriptional co-regulation of the main pathways, although individual associations between carotenoids and carbohydrate-related genes suggested possible indirect metabolic links. Instead, TC accumulation was most strongly associated with regulatory, stress-, redox-, and plastid-related genes, enriched for heme-binding and oxidoreductase functions. These findings suggest that the TC/DM trade-off is not a fixed constraint, and identify candidate regulators of carotenoid content for future functional validation to support cassava provitamin A biofortification. HighlightGenetic, spatial, and developmental variation in cassava storage roots implicate cis-carotenes, but not direct transcriptional regulation of the carotenoid and starch pathways, in the trade-off between carotenoids and dry matter.

plant biology↗

bioRxiv2025

Phytoene synthase modulates seed longevity via the action of β-carotene derived metabolites

Seed longevity, the seeds ability to stay viable over time, is an important trait in agriculture. Despite extensive research, seed longevity remains one of the fundamental topics in plant biology. Here, we discovered the novel role of carotenoid metabolites in prolonging seed lifespan. We found that phytoene synthase (PSY), the gene encoding a major rate-limiting enzyme in carotenoid biosynthesis, modulated seed storability in Arabidopsis under both natural and artificial aging conditions. Seeds from the PSY overexpression (OE) lines exhibited significantly enhanced lifespan with low levels of reactive oxygen species (ROS), a major factor affecting longevity, whereas those from the psy mutants had decreased viability with high ROS levels. While lutein and {beta}-carotene were detected in seeds, only {beta}-carotene and its derived apocarotenoids, i.e. {beta}-cyclocitral and {beta}-ionone, were found to improve seed lifespan. Notably, the carotenoid cleavage dioxygenase 1 and 4 (ccd1 ccd4) double mutant and PSY ccd1 ccd4 seeds showed significantly reduced seed longevity, indicating that {beta}-carotene cleavage is necessary for or it is apocarotenoids playing the role in preserving seed lifespan. Comparative proteomic analysis identified TIP2;2, an aquaporin protein, which showed differential abundances in seeds of PSY OE and psy mutant vs wild type. The mutant tip2;2 had reduced seed longevity, and its promoter was transactivated by apocarotenoids. Collectively, this study uncovers a novel role of apocarotenoids in protecting seed longevity and highlights the importance of seed carotenoid production in strengthening agriculture. One Sentence SummaryPhytoene synthase, the gene encoding a major rate-limiting enzyme in carotenoid biosynthesis, modulates seed longevity via {beta}-carotene derived apocarotenoids and an aquaporin protein TIP2;2 identified is a new player that responds to apocarotenoid signaling and influences seed longevity.

plant biology↗

bioRxiv2022

Orchestration of Chlorophyll and Carotenoid Biosynthesis by ORANGE Family Proteins in Plant

Chlorophyll and carotenoid are essential photosynthetic pigments. Plants must spatiotemporally coordinate the needs of chlorophyll and carotenoid for optimal photosynthesis and plant fitness in response to diverse environmental and developmental cues. However, how these two biosynthesis pathways are orchestrated remains largely unknown. Here, we report that the highly conserved ORANGE (OR) family proteins are the common regulators of both pathways via posttranslationally regulating the first committed enzyme in each pathway. We demonstrate that OR family proteins physically interact with magnesium chelatase subunit I (CHLI) in addition to phytoene synthase (PSY) and concurrently regulate CHLI and PSY protein stability and activity. We show that loss of OR genes hinders both chlorophyll and carotenoid biosynthesis, limits light-harvesting complex assembly, and impairs thylakoid grana stacking in chloroplast. OR overexpression safeguards photosynthetic pigment biosynthesis and enhances thermotolerance in both Arabidopsis and tomato plants. Our findings establish a conserved mechanism of green plant to coordinate chlorophyll and carotenoid biosynthesis and provide a potential genetic target to generate climate-resilient crops.

plant biology↗

bioRxiv2020

Correlative cryo-structured illumination fluorescence microscopy and soft X-ray tomography elucidates reovirus intracellular release pathway

Imaging of biological matter across resolution scales presents the challenge of preserving the direct and unambiguous correlation of subject features from the macroscopic to the microscopic level. We present here a correlative imaging platform developed specifically for imaging cells in 3D, under cryogenic conditions. Rapid cryo-preservation of biological specimens is the current gold standard in sample preparation for ultrastructural analysis in X-ray imaging. However, cryogenic fluorescence localisation methods are by and large diffraction-limited and fail to deliver matching resolution. We addressed this technological gap by developing an integrated, user-friendly, platform for 3D correlative imaging of cells in cryo-preserved states using super-resolution structured illumination microscopy (SIM) in conjunction with soft X-ray tomography (SXT). The power of this new approach is demonstrated by studying the process of reovirus release from intracellular vesicles during the early stages of infection and identifying novel virus-induced structures.

cell biology↗