Biology subjects

Eroglu, S.

Publications and source records attributed to Eroglu, S..

4 recordsLinked to original sources

bioRxiv2026

Iron-Flavonoid-Peroxidase Signaling Triggers Seed-Coat Remodeling for Rapid Germination

Seed germination and survival depend on a sustained water supply. We previously observed that iron (Fe) supply accelerates germination in tomato. Using Arabidopsis thaliana, we show here that increased Fe in the spermosphere acts as an extrinsic signal that increases seed coat permeability. Fe triggers structural remodeling of the cuticle covering the endosperm, as evidenced by loss of Auramine O staining in the testa-ruptured seeds. Fe-triggered germination phenotypes are compromised in the flavonoid (tt4 and tt7) and prx17 mutants, and in peroxidase inhibitor-treated wild-type seeds. We hypothesize that PRX17-driven peroxidase activity is governed by a maternal repressor-derepressor mechanism in which seed coat flavonoids constitutively repress enzyme activity. This repression is relieved by chelation of Fe by flavonoids, allowing PRX17 to remodel the cuticle and accelerate germination. To test this model, we examined the interaction between Fe and peroxidases with quercetin, a major seed coat flavonoid. Upon imbibition, quercetin is deglycosylated and inhibits PRX17 activity. Formation of Fe-quercetin complexes at the chalaza reduces the level of active quercetin, thereby restoring PRX17 activity in a dose-dependent manner. This study suggests that elevated Fe levels in oxygen-deprived, submerged soils prime seeds for rapid germination, a novel control mechanism mediated by seed coat biochemistry.

plant biology↗

bioRxiv2025

Gene co-expression network reveals key hub genes associated with endometriosis using bulk RNA-seq

Endometriosis (EMs) is a complex and prevalent gynecological disorder with a significant genetic component, posing a major clinical challenge in reproductive medicine due to multifactorial inheritance patterns and the involvement of gene-environment interactions in pathophysiology. However, despite extensive research, reliable diagnostic biomarkers for EMs have yet to be identified. We utilized bulk transcriptome sequencing data obtained from the Gene Expression Omnibus to identify hub genes involved in EMs. This study was conducted using a system biology analysis, incorporating differential gene expression, meta-analysis of transcriptomic data, functional enrichment analysis, construction of gene co-expression networks, and comprehensive topological analysis to identify key regulatory genes. Bulk RNA-seq analysis revealed significant differential gene expression between healthy and EMs groups. Overall, 603 and 443 meta-genes were discovered using the Fisher and Invorm P-value combination methods, respectively. A total of 427 meta-genes were subjected to functional enrichment analysis, which revealed significant enrichment in several KEGG pathways related to EMs including "Adherens junction," "p53 signaling pathway," and "AMPK signaling pathway." Additionally, Gene Ontology analysis revealed key processes including "Regulation of Anatomical Structure Morphogenesis," Acetylglucosaminyltransferase Activity" and "Positive Regulation of Intracellular Signal". Co-expression network analysis identified the turquoise module as a critical functional module, within this significant module, the genes IGFBP7, IGFBP3, and NKAP were identified as EMs hub genes based on high connectivity and central roles in the network. The constructed protein-protein interaction network further highlighted STAR, PLCD3, RPAP2, MSI2, MAS1, TBX1, LIPT1, and SVIL, as key genes. These genes represented high centrality within the network, suggesting potential regulatory and functional significance in the molecular mechanisms underlying EMs. Notably, miR-143-3p, miR-340-5p, miR-410-3p, and miR-302b-5p were implicated in EMs-associated regulatory networks. This integrative approach significantly enhances our understanding of the molecular mechanisms underlying EMs and provides a robust foundation for the development of diagnostic biomarkers.

bioinformatics↗

bioRxiv2023

Improved sample preparation for fruits allowed histochemistry and X-ray microscopy to reveal conserved iron hotspots

Global fruit production suffers from pre- and post- harvest losses, part of which are related to metal deficiencies. Despite fruits being one of the most widely consumed plant parts, the spatial distribution of metals and their physiological significance remained largely unexplored. In this study, we investigated metal accumulation sites in fruits of 28 major crops by using X-ray and histochemical-based techniques. We found that calcium accumulated in the outermost hardened tissues, potassium in sugar accumulating fleshy tissues, and iron (Fe) in vascular tissues in a conserved manner. Vascular Fe pattern traced to the seed revealed an Fe reservoir at the fruit-seed juncture in tomato, which persisted in the seeds chalazal region upon dispersal. To determine the physiological function of these stored reserves, we manipulated Fe bioavailability. Two opposely acting chelators, desferoxamine, an Fe immobilizer, delayed germination, while nicotianamine, a mobilizer, accelerated it in wild-type plants but not in mutants with low chalazal Fe. Additionally, external Fe supplementation also increased germination speed in a dose-dependent manner. Collectively, these findings demonstrate that fruit vasculature serves as a critical delivery system to establish seed Fe pools, which are determinants of seed germination speed. This study provides the first comprehensive atlas of metal hotspots in fleshy fruits and links anatomical distribution to a defined physiological mechanism in seed biology.

plant biology↗

bioRxiv2018

VIT1-dependent Fe distribution in seeds is conserved in dicots

One third of the people suffer from iron (Fe) Fe deficiency. An underlying factor for this malnutrition is insufficient Fe intake from the diet. A major part of the human diet includes seeds of staple crops, which contain Fe that is poorly bioavailable. One reason for the low bioavailability is these seeds store Fe in cellular compartments that also contain antinutrients, such as phytate. Thus, several studies focused on decreasing phytate concentrations. As an alternative approach to increase bioavailable Fe, Fe reserves might be directed to cellular compartments such as plastids that are free of phytate. Previous studies indicated that Fe reserves can be relocalized inside the seed to the desired compartment by genetic modification, provided that a suitable iron transporter protein is used. However, to the best of our knowledge, a Fe transporter localizing to plastids have not been identified in seeds to date. To discover novel Fe transporters, we screened Fe patterns in seeds of distinct plant lineages, hypothesizing Fe hyperaccumulating sites would indicate Fe transporter presence. To this end, metal localizations in seeds of more than twenty species were investigated using histochemical or X-ray based techniques. Results showed that in Rosids, the largest clade of eudicots, Fe reserves were primarily confined in the embryo part of the seeds. Furthermore, inside the embryos, Fe was enriched in the endodermal cell layer, a well-known feature that is mediated by vacuolar Fe transporter, VIT1 in model plant Arabidopsis thaliana. This enrichment was well conserved in and beyond Rosid species. Finally, a few seeds showed novel Fe patterns, including Carica papaya which concentrated large Fe reserves exclusively in plastids called amyloplasts. Generally, Fe stored in amyloplast is considered bioavailable. Taken together, this study suggests dicot seeds store Fe mainly in the embryo, with a VIT1-dependent enrichment in its endodermal cell layer and indicate Carica papaya possess a strong Fe transporter at the plastid membrane. Once it is identified that might be useful in biofortification, as a novel tool to shift Fe to compartments where it is more bioavailable.

plant biology↗