Current Research

Daniel Schachtman, Ph.D.

Associate Member and Principal Investigator

FUNCTIONAL GENOMICS OF ROOT-TO-SHOOT SIGNALING UNDER DROUGHT:

When soils begin to dry, roots transmit signals to leaves which reduce their water usage and growth. Signals from roots are an important early warning system that allows plants to adapt to drought. (For review see: Wilkinson S, Davies WJ (2002) ABA-based chemical signaling: the co-ordination of responses to stress in plants. Plant Cell Environ 25: 195-210.)

This project aims to provide new insights into how corn roots signal to the above ground parts of the plant when dry soil has been encountered. To understand more about the identity and transport of root signals, we have embarked on a collaborative genomics project with groups at the Universities of Illinois and Missouri (http://rootgenomics.missouri.edu/). We have developed methods for extracting and profiling important chemical constituents in xylem sap of well-watered and water-stressed corn plants. We also developed methods to isolate proteins and peptides from xylem sap, determined changes in protein abundance under drought; and recently this has led to the identification of over 100 proteins found in maize xylem sap. We are now characterizing the changes that occur under mild and extended water stress.

In addition, our group collaborates with Dr. Robert Sharp's at the University of Missouri, Columbia. In that collaboration we are studying the changes in the root cell wall proteome to identify changes in protein abundance that lead to the maintenance of root growth under severe water stress.

Selected Publications

Goodger JQ, Sharp RE, Marsh EL, Schachtman DP (2005) Relationships between xylem sap constituents and leaf conductance of well-watered and water-stressed maize across three xylem sap sampling techniques. J Exp Bot 56: 2389-2400

Zhu J, Chen S, Asirvatham VS, Schachtman DP, Wu Y, Sharp RE (2005) Cell wall proteome in the maize primary root elongation zone. I. extraction and identification of water soluble and lightly ionically-bound proteins. Plant Physiol.

Alvarez S, Goodger J, Marsh E, Chen S, Asirvatham V, Schachtman DP (2006) Characterization of the maize xylem sap proteome. Journal of Proteome Research in press

Other related publications from this project:

Poroyko V, Hejlek LG, Spollen WG, Springer GK, Nguyen HT, Sharp RE, Bohnert HJ (2005) The maize root transcriptome by serial analysis of gene expression. Plant Physiol 138: 1700-1710

Sharp RE, Poroyko V, Hejlek LG, Spollen WG, Springer GK, Bohnert HJ, Nguyen HT (2004) Root growth maintenance during water deficits: physiology to functional genomics. J Exp Bot 55: 2343-2351

ROOT POTASSIUM AND NITROGEN SENSING AND SIGNALING IN ARABIDOPSIS AND CORN

Adaptation to short- and long-term changes in soil fertility is critical for crop productivity and nutrient capture. Improved nutrient capture reduces the need for fertilizer inputs, leading to reduced fertilizer runoff, decreased water contamination, and increased yield when soil fertility is low. Potassium and nitrogen are essential nutrients required in large quantities by plants. When nutrients are deficient in the soil, roots employ specialized strategies to ensure that plants obtain sufficient amounts of minerals for growth. It is not known how plant root cells sense or signal the changes that occur at the onset of nutrient deficiency. To elucidate the signal transduction pathways and the regulation of gene expression under nutrient deficiency, we have conducted microarray analyses. Using GeneChips to assay expression of the entire Arabidopsis genome, we identified genes and biochemical processes involved in the response to deficiency. This work led to the discovery that the signaling molecule hydrogen peroxide plays a role in response to nutrient deprivation in plant roots. We have also identified and characterized the expression of a high affinity K+ transporter.  Through our studies we have identified key regulatory genes that may be important for plant adaptation to nutrient deficiencies. This understanding of how plant roots adapt to nutrient deficiencies will potentially lead to new strategies for increasing nutrient capture and for increasing growth in nutrient depleted soils.

Shin R, Berg RH, Schachtman DP (2005) Reactive oxygen species and root hairs in Arabidopsis root response to nitrogen, phosphorus and potassium deficiency. Plant Cell Physiol 46: 1350-1357

Shin R, Schachtman DP (2004) Hydrogen peroxide mediates plant root response to nutrient deprivation. Proc Natl Acad Sci U S A 101: 8827-8832

Ahn SJ, Shin R, Schachtman DP (2004) Expression of KT/KUP genes in Arabidopsis and the role of root hairs in K+ uptake. Plant Physiol 134: 1135-1145

Identification, characterization, and functional analysis of transport proteins involved in Arabidopsis root-knot nematode-induced feeding sites

Root-knot nematodes (Meloidogyne spp.) colonize Arabidopsis roots and form giant cells, which act as a feeding site for this destructive parasite. In a collaborative project with other labs at the Danforth Center we are working to understand which transport processes are important in nematode induced giant cells. We are currently studying several amino acid transporters whose genes are up-regulated during the formation of giant cells to determine how amino acid transport is involved in nematode nutrition and giant cell formation. Two auxin transporters are upregulated by nematode infestation and one of them has now been fully characterized.

Hammes U, Schachtman D, Berg R, Nielsen E, Koch W, McIntyre L, Taylor C (2005) Nematode induced changes of transporter gene expression in Arabidopsis roots MPMI 18: 1247-1257

Increasing bioavailable zinc in cassava

We have recently embarked on a project to increase the zinc content of cassava roots to enhance human nutrition which is funded by the Gates Foundation. We will overexpress specific plant zinc transport proteins to increase the zinc content in the tubers, which are the edible part of the plant.

Related link: http://biocassavaplus.org/

Previous publications related to this project:

Ramesh S, Choimes S, Schachtman DP (2004) Overexpression of an Arabidopsis zinc transporter in Hordeum vulgare increases short-term zinc uptake after zinc deprivation and seed zinc content. Plant Mol. Biol. In press

Ramesh SA, Shin R, Eide DJ, Schachtman DP (2003) Differential metal selectivity and gene expression of two zinc transporters from rice. Plant Physiol 133: 126-134

Gene discovery in grapevine species

We are involved in a joint research project with Missouri State University and University of Missouri, Columbia. The purpose of the project is to identify and characterize genes that increase resistance to fungal pathogens. We are working with two different grapevine species, Vitis aestivalis, commonly known as Norton, and the Vitis vinifera variety Cabernet Sauvignon. We are currently using microarrays to discover the differences in gene expression in leaves that have been infected with the fungal pathogen--"powdery mildew". This will provide clues as to why Norton is more resistant than Cabernet Sauvignon to powdery mildew. Next year we will be using proteomics tools to identify changes in protein profiles in grapevine leaves infected with powdery mildew.

The role of the Arabidopsis KUP transporters in cell expansion, plant development and potassium uptake

One manuscript has been published from this work:
Ahn, S.J., Shin, R. and Schachtman, D.P. (2004) Analysis of the expression of genes expressing KUP transporters in Arabidopsis Plant Physiology 134:1135-45