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Biology subjects

Kocaoglan, E. G.

Publications and source records attributed to Kocaoglan, E. G..

2 recordsLinked to original sources

Spatial and developmental reprogramming enables root growth under high salinity in the extremophyte Schrenkiella parvula

High salinity severely restricts root growth in most plants, yet the extremophyte model Schrenkiella parvula maintains growth under otherwise inhibitory conditions through a previously unrecognized developmental reorganization of the primary root. Under high salinity, the elongation zone rapidly reorganizes into two distinct states: the bulged and gap zones. These zones form in response to ionic stress and emerge during a transient growth pause followed by resumed tip growth and localized lateral root emergence from the gap zone. Jasmonic acid (JA) is necessary to initiate this developmental transition, while cell-layer-resolved hormone profiling revealed spatiotemporally coordinated JA and auxin accompanying the maintenance of the distinct zones. The zone-specific expression profiling resolved transcriptomic networks spanning core development and broad or zone-specific stress responses, revealing spatial regulation of hormone signaling, cell-wall remodeling, and osmotic and oxidative stress pathways. Raman spectroscopy, metabolite profiling, and cellular imaging supported localized regulation of water availability, ionic balance, and suppression of ROS accumulation and cell death. These networks also identified orthologous genes co-opted for novel functions potentially used to sustain growth. Together, these findings reveal a spatially coordinated mechanism for maintaining root growth under salt stress and provide a framework for discovering genetic mechanisms that optimize growth under stress.

plant biology↗

Mobius Assembly for Plant Systems uncovers combinatorial interactions among promoters, coding sequences, and terminators in gene regulation

Plants are the primary biological platforms for producing food, energy, and materials in agriculture; however, they remain a minor player in the recent synthetic biology-driven transformation in bioproduction. Molecular tools and technologies for complex, multigene engineering in plants are as yet limited, with the challenge to enhance their stability and predictivity. Here, we present a new standardized and streamlined toolkit for plant synthetic biology, Mobius Assembly for Plant Systems (MAPS). It is based on small plant binary vectors pMAPs, which contain a fusion origin of replication that enhances plasmid yield in both Escherichia coli and Rhizobium radiobacter. MAPS includes a new library of promoters and terminators with different activity levels; part sizes were minimized to improve construct stability and transformation efficiency. These promoters and terminators were characterized using a high-throughput protoplast expression assay. We observed a significant influence of terminators on gene expression, as the strength of a single promoter can change more than seven-folds in combination with different terminators. Changing the coding sequence changed the relative strength of promoter and terminator pairs, thus uncovering combinatorial gene regulation among all parts of a transcriptional unit. We further gained insights into the mechanisms of such interactions by analyzing RNA folding, with which we suggest a design principle for more predictive and context-independent genetic parts in synthetic biology of plant systems and beyond.

synthetic biology↗