Armstrong, E. A. | bioRxiv Science

bioRxiv2022

Cell-type specific transcriptional networks in root xylem adjacent cell layers

Transport of water, ions and signals from roots to leaves via the xylem vessels is essential for plant life and needs to be tightly regulated. The final composition of the transpiration stream before passage into the shoots is controlled by the xylem-adjacent cell layers, namely xylem parenchyma and pericycle, in the upper part of the root. To unravel regulatory networks in this strategically important location, we generated Arabidopsis lines expressing a nuclear tag under the control of the HKT1 promoter. HKT1 retrieves sodium from the xylem to prevent toxic levels in the shoot, and this function depends on its specific expression in upper root xylem-adjacent tissues. Based on FACS RNA-sequencing and INTACT ChIP-sequencing, we identified the gene repertoire that is preferentially expressed in the tagged cell types and discovered transcription factors experiencing cell-type specific loss of H3K27me3 demethylation. For one of these, ZAT6, we show that H3K27me3-demethylase REF6 is required for de-repression. Analysis of zat6 mutants revealed that ZAT6 activates a suite of cell-type specific downstream genes and restricts Na+ accumulation in the shoots. The combined Files open novel opportunities for bottom-up causal dissection of cell-type specific regulatory networks that control root-to-shoot communication under environmental challenge.

plant biology↗

bioRxiv2018

Bacterial analogs of plant piperidine alkaloids mediate microbial interactions in a rhizosphere model system

Plants expend significant resources to select and maintain rhizosphere communities that benefit their growth and protect them from pathogens. A better understanding of assembly and function of rhizosphere microbial communities will provide new avenues for improving crop production. Secretion of antibiotics is one means by which bacteria interact with neighboring microbes and sometimes change community composition. In our analysis of a taxonomically diverse consortium from the soybean rhizosphere, we found that Pseudomonas koreensis selectively inhibits growth of Flavobacterium johnsoniae and other members of the Bacteroidetes grown in soybean root exudate. A genetic screen in P. koreensis identified a previously uncharacterized biosynthetic gene cluster responsible for the inhibitory activity. The metabolites were isolated based on biological activity and were characterized using tandem-mass spectrometry, multidimensional NMR, and Mosher ester analysis, leading to the discovery of a new family of bacterial piperidine alkaloids, koreenceine A-D (1-4). Three of these metabolites are analogs of the plant alkaloid {gamma}-coniceine. Comparative analysis of the koreenceine cluster with the {gamma}-coniceine pathway revealed distinct polyketide synthase (PKS) routes to the defining piperidine scaffold, suggesting convergent evolution. Koreenceine-type pathways are widely distributed among Pseudomonas species, and koreenceine C was detected in another Pseudomonas sp. from a distantly related cluster. This work suggests that Pseudomonas and plants convergently evolved the ability to produce similar alkaloid metabolites that can mediate inter-bacterial competition in the rhizosphere.\n\nIMPORTANCEThe microbiomes of plants are critical to host physiology and development. Microbes are attracted to the rhizosphere due to massive secretion of plant photosynthates from roots. Microorganisms that successfully join the rhizosphere community from bulk soil have access to more abundant and diverse molecules, producing a highly competitive and selective environment. In the rhizosphere, as in other microbiomes, there is little known about the genetic basis for individual species behaviors within the community. In this study, we characterized competition between Pseudomonas koreensis and Flavobacterium johnsoniae, two common rhizosphere inhabitants. We identified a widespread gene cluster in several Pseudomonas spp., which is necessary for the production of a novel family of piperidine alkaloids that are structural analogs of plant alkaloids. We expand the known repertoire of antibiotics produced from Pseudomonas in the rhizosphere and demonstrate the role of the metabolites in interactions with other bacteria of the rhizosphere.

microbiology↗