Biology subjects

Battenberg, K.

Publications and source records attributed to Battenberg, K..

3 recordsLinked to original sources

bioRxiv2024

snRNA-seq analysis of the moss Physcomitrium patens reveals a conserved cytokinin-ESR module promoting pluripotent stem cell identity

The shoot apical meristem (SAM), which contains pluripotent stem cells, serves as the source of the entire shoot system in land plants. To uncover the mechanisms underlying SAM development and its orign, we employed single-nucleus RNA sequencing technology in Physcomitrium patens, which contains a single stem cell known as the gametophore apical cell. We identified distinct cell clusters representing major cell types of the P. patens gametophyte, including the gametophore apical cells. We revealed dynamic gene expression changes during cell fate progression in the gametophore apical cell and found upregulation of cytokinin biosynthesis genes in this cell. We also identified ENHANCER OF SHOOT REGENERATION 1 (ESR1) orthologs as key regulators of gametophore apical cells downstream of cytokinin. Given that ESRs promote SAM formation under cytokinin in angiosperms, we propose that the cytokinin-ESR module represents a conserved mechanism promoting stem cell identity that evolved in the common ancestor of land plants.

plant biology↗

bioRxiv2022

Gene losses resulting in specialized metabolism in the earliest divergent symbiotic Frankia clade can be linked to its low saprotrophic capabilities

Frankia cluster-2 are diazotrophs that engage in root nodule symbiosis with host plants of the Cucurbitales and the Rosales. They are rarely found in the soil in the absence of their hosts. Previous studies have shown that an assimilated nitrogen source, presumable arginine, is exported to the host in nodules of Datisca glomerata (Cucurbitales), but not in the nodules of Ceanothus thyrsiflorus (Rosales). To investigate if an assimilated nitrogen form is commonly exported by cluster-2 strains, and which nitrogen source would then be exported to C. thyrsiflorus, gene expression levels, metabolite profiles and enzyme activities were analysed. We found that the export of assimilated nitrogen in symbiosis is a common feature for Frankia cluster-2 strains, but which source is host-plant dependent. We also identified several gene losses. The ammonium assimilation via the GS/GOGAT cycle for export to the host, entails a high demand of 2-oxoglutarate from the TCA cycle. This specialised metabolism seems to have led to genome reduction: we show that Frankia cluster-2 strains have lost the glyoxylate shunt and succinate semialdehyde dehydrogenase, leading to a linearization of the TCA cycle. This could explain the low saprotrophic potential of Frankia cluster-2.

plant biology↗

bioRxiv2021

UniverSC: a flexible cross-platform single-cell data processing pipeline

Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.

bioinformatics↗