Guenther, J. | bioRxiv Science

bioRxiv2023

JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations

Image-based profiling has emerged as a powerful technology for various steps in basic biological and pharmaceutical discovery, but the community has lacked a large, public reference set of data from chemical and genetic perturbations. Here we present data generated by the Joint Undertaking for Morphological Profiling (JUMP)-Cell Painting Consortium, a collaboration between 10 pharmaceutical companies, six supporting technology companies, and two non-profit partners. When completed, the dataset will contain images and profiles from the Cell Painting assay for over 116,750 unique compounds, over-expression of 12,602 genes, and knockout of 7,975 genes using CRISPR-Cas9, all in human osteosarcoma cells (U2OS). The dataset is estimated to be 115 TB in size and capturing 1.6 billion cells and their single-cell profiles. File quality control and upload is underway and will be completed over the coming months at the Cell Painting Gallery: https://registry.opendata.aws/cellpainting-gallery. A portal to visualize a subset of the data is available at https://phenaid.ardigen.com/jumpcpexplorer/.

bioinformatics↗

bioRxiv2022

Heterologous expression of PtAAS1 reveals the metabolic potential of the common plant metabolite phenylacetaldehyde for auxin synthesis in planta

Aromatic aldehydes and amines are common plant metabolites involved in several specialized metabolite biosynthesis pathways. Recently, we showed that the aromatic aldehyde synthase PtAAS1 and the aromatic amino acid decarboxylase PtAADC1 contribute to the herbivory-induced formation of volatile 2-phenylethanol and its glucoside 2-phenylethyl-{beta}-D-glucopyranoside in Populus trichocarpa. To gain insights into alternative metabolic fates of phenylacetaldehyde and 2-phenylethylamine beyond alcohol and alcohol glucoside formation, we expressed PtAAS1 and PtAADC1 heterologously in Nicotiana benthamiana and analyzed plant extracts using untargeted LC-qTOF-MS analysis. While the metabolomes of PtAADC1-expressing plants did not significantly differ from those of control plants, expression of PtAAS1 resulted in the accumulation of phenylacetic acid (PAA) and PAA-amino acid conjugates, identified as PAA-aspartate and PAA-glutamate. Moreover, targeted LC-MS/MS analysis showed that PtAAS1-expressing plants accumulated significant amounts of free PAA. The measurement of PAA and PAA-Asp in undamaged and herbivory-damaged poplar leaves revealed significantly induced accumulation of PAA-Asp while levels of free PAA remained unaltered by herbivore treatment. Sequence comparisons and transcriptome analysis showed that members of a small gene family comprising five putative auxin-amido synthetase GH3 genes potentially involved in the conjugation of auxins like PAA with amino acids were significantly upregulated upon herbivory in P. trichocarpa leaves. Overall, our data indicates that phenylacetaldehyde generated by poplar PtAAS1 serves as a hub metabolite linking the biosynthesis of volatile, non-volatile herbivory-induced specialized metabolites, and phytohormones, suggesting that growth and defense are balanced on a metabolic level.

plant biology↗