The latest news about the ionomics project and thoughts from team members.

Monday, September 9, 2013

Ionomics reveals as role for dirigent proteins in lignin deposition

New research into the function of ESB1 (Enhanced Suberin 1) has revealed that this dirigent protein plays an essential role in building lignin-based Casparian strips in cell walls of endodermal cells. These discoveries recently published in PNAS start to dissect the molecular mechanisms involved in endodermal control of solute entry into plants. Further, they provide in vivo evidence for proteins in the dirigent family functioning as part of the machinery that builds extracellular lignin-based structures, opening a new avenue to determine the elusive role of this protein family in planta.

Hosmani PS, Kamiya T, Danku J, Naseer S, Geldner N, Guerinot ML, Salt DE. Dirigent domain-containing protein is part of the machinery required for formation of the lignin-based Casparian strip in the root. Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14498-503. doi: 10.1073/pnas.1308412110. Epub 2013 Aug 12. PubMed PMID: 23940370.

Abstract: The endodermis acts as a “second skin” in plant roots by providing the cellular control necessary for the selective entry of water and solutes into the vascular system. To enable such control, Casparian
strips span the cell wall of adjacent endodermal cells to form a tight junction that blocks extracellular diffusion across the endodermis. This junction is composed of lignin that is polymerized by oxidative coupling of monolignols through the action of a NADPH oxidase and peroxidases. Casparian strip domain proteins
(CASPs) correctly position this biosynthetic machinery by forming a protein scaffold in the plasma membrane at the site where the Casparian strip forms. Here, we show that the dirigent-domain containing protein, enhanced suberin1 (ESB1), is part of thismachinery, playing an essential role in the correct formation of Casparian strips. ESB1 is localized to Casparian strips in a CASP-dependent manner, and in the absence of ESB1, disordered and defective Casparian strips are formed. In addition, loss of ESB1 disrupts the localization of the CASP1 protein at the casparian strip domain, suggesting a reciprocal requirement for both ESB1 and CASPs in forming the Casparian Strip Domain.

Ionomics sheds new light on evolution

A new paper in Science from the Salt lab describes how polyploidy enhances leaf concentration of potassium and fitness in saline soils, supporting the notion that genome duplication is important in the evolutionary history of plants.

Chao DY, Dilkes B, Luo H, Douglas A, Yakubova E, Lahner B, Salt DE. Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science. 2013 Aug 9;341(6146):658-9. doi: 10.1126/science.1240561. Epub 2013 Jul 25.
PubMed PMID: 23887874.

Abstract: Genome duplication (or polyploidization) has occurred throughout plant evolutionary history, and is thought to have driven the adaptive radiation of plants. We found that the cytotype of the root, and not the genotype, determined the majority of heritable natural variation in the concentration of leaf potassium (K) in Arabidopsis thaliana. Autopolyploidy also provided resistance to salinity and may represent an adaptive outcome of the enhanced K accumulation of plants with higher ploidy.

Thursday, March 14, 2013

GWAS paper on Cd accumulation

The Salt lab recently published a paper in PLoS Genetics in which we describe the use of GWA mapping to identify HMA3 as the primary locus controlling natural variation in foliar accumulation of Cd in Arabidopsis thaliana. The paper can be read at and the abstract can be seen below.

Abstract: Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5-2 µg Cd g(-1) dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids.