New paper in Plant Cell

Our paper "Arabidopsis NPCC6/NaKR1 Is a Phloem Mobile Metal Binding Protein Necessary for Phloem Function and Root Meristem Maintenance" was just published in Plant Cell.  This paper was mainly the result of the hard work of newly minted Ph.D Hui Tian from John Ward's Lab at UMN.  She worked with me to clone the gene, finally finding it when the causal deletion of only 7 bp disrupted a single oligo on the Arabidopsis tiling array. It's a fascinating gene, encoding a protein that moves through the phloem, the part of the plants vasculature responsible for moving solutes away from leaves.

Here is the abstract:

SODIUM POTASSIUM ROOT DEFECTIVE1 (NaKR1; previously called NPCC6)encodes a soluble metal binding protein that is specificallyexpressed in companion cells of the phloem. The nakr1-1 mutantphenotype includes high Na⁺, K⁺, Rb⁺, and starch accumulationin leaves, short roots, late flowering, and decreased long-distancetransport of sucrose. Using traditional and DNA microarray-baseddeletion mapping, a 7-bp deletion was found in an exon of NaKR1that introduced a premature stop codon. The mutant phenotypeswere complemented by transformation with the native gene orNaKR1-GFP (green fluorescent protein) and NaKR1-β-glucuronidasefusions driven by the native promoter. NAKR1-GFP was mobilein the phloem; it moved from companion cells into sieve elementsand into a previously undiscovered symplasmic domain in theroot meristem. Grafting experiments revealed that the high Na⁺accumulation was due mainly to loss of NaKR1 function in theleaves. This supports a role for the phloem in recirculatingNa⁺ to the roots to limit Na⁺ accumulation in leaves. The onsetof root phenotypes coincided with NaKR1 expression after germination.The nakr1-1 short root phenotype was due primarily to a decreasedcell division rate in the root meristem, indicating a role inroot meristem maintenance for NaKR1 expression in the phloem.

And here is a non-technical summary:

A major problem for world agriculture is the growing decrease in avaialable arable land. More and more we are working in solils that impart a stress on the plants that make up the crops we depend on. In order for plants to survive without being able to move out of unfavorable soil environments, they adjust the biochemical composition of their tissues through a wide variety of mechanisms.  One of these mechanisms is to move  elements such as sodium (Na) and potassium (K) from tissue to tissue, including from the root to the shoot and back again.  Understanding the molecular basis of these mechanisms will enable the production of crops that are better able to respond to the changing environment  and increase yields with fewer inputs.  In this study, we identified and characterized a gene which is important for loading Na  into the phloem, the 'veins' of the plant responsible for moving molecules out of the leaves to the seeds and roots. The protein also moves into the  phloem. Plants without a functional form of this gene, called NAKR1, have altered levels of Na, K and starch in the leaves, have shorter roots and flower later than plants with a functional copy of NAKR1.  These results will lead to a better understanding of how plants distribute elements between tissues and ultimately will allow for crop improvement strategies that deal with poor soil quality.

New lab members

 

A belated welcome to our new lab members:

Jennie Hard is working on the algae project, and has already made a great impact. Appropriately for a member of an ionomics lab, in her spare time, Jennie plays in a (folk) Metal band.

Greg Ziegler has joined the ionomics team as a jack of all trades. A recent St. Louis transplant, Greg is working with us while finishing up his Ph.D in Computational Biology from Purdue.

New paper in PLoS Genetics!

Our paper "A Coastal Cline in Sodium Accumulation in Arabidopsis thaliana Is Driven by Natural Variation of the Sodium Transporter AtHKT1;1" has just been published in PLoS Genetics. There is an accompanying perspective, "Beyond QTL Cloning", by Jill Anderson and Thomas Mitchell-Olds which says (among other nice things):

In this issue of PLoS Genetics, Baxter et al. [9] present an elegant study of the geographic variation in salinity tolerance, and allelic variation at the sodium transport gene AtHKT1;1 in European populations of A. thaliana.

As always, it was great team effort and many thanks go out to my collaborators at Purdue, UChicago, and USC. Here is the non-technical summary of the paper:

The unusual geographical distribution of certain animal and plant species has provided puzzling questions to the scientific community regarding the interrelationship of evolutionary and geographic histories for generations. With DNA sequencing, such puzzles have now extended to the geographical distribution of genetic variation within a species. Here, we explain one such puzzle in the European population of Arabidopsis thaliana, where we find that a version of a gene encoding for a sodium-transporter with reduced function is almost uniquely found in populations of this plant growing close to the coast or on known saline soils. This version of the gene has previously been linked with elevated salinity tolerance, and its unusual distribution in populations of plants growing in coastal regions and on saline soils suggests that it is playing a role in adapting these plants to the elevated salinity of their local environment.

and here is the technical abstract:

The genetic model plant Arabidopsis thaliana, like many plant species, experiences a range of edaphic conditions across its natural habitat. Such heterogeneity may drive local adaptation, though the molecular genetic basis remains elusive. Here, we describe a study in which we used genome-wide association mapping, genetic complementation, and gene expression studies to identify cis-regulatory expression level polymorphisms at the AtHKT1;1 locus, encoding a known sodium (Na+) transporter, as being a major factor controlling natural variation in leaf Na+ accumulation capacity across the global A. thaliana population. A weak allele of AtHKT1;1 that drives elevated leaf Na+ in this population has been previously linked to elevated salinity tolerance. Inspection of the geographical distribution of this allele revealed its significant enrichment in populations associated with the coast and saline soils in Europe. The fixation of this weak AtHKT1;1 allele in these populations is genetic evidence supporting local adaptation to these potentially saline impacted environments.

Welcome Aimee!

I am happy to introduce the labs newest researcher, Aimee Terauchi. Aimee got
her BA from UC-Berkeley and her Ph.D from UCLA. As you can see from the picture, she is a Californian at heart, but she is really looking forward to her first midwestern winter. :)

For her Ph.D Aimee did some fantastic work on Fe homeostasis and it's relation to phonotsynthesis in Chlamydomonas. She will continue her work in the Baxter lab as part of the NAABB project.

Welcome Aimee!

Technician Position available.

There is a technician position available in the lab as part of the NAABB project. The announcement is below, please spread the word to all interested parties.....




The USDA, ARS, Plant Genetics Research Unit in St. Louis, MO, is seeking applications for a Biological Science Laboratory Technician, GS-0404-4/5, to work on an algal biofuels project. Salary range is $27,990 to $40,706 per annum, plus benefits. This is a Term appointment NTE 13 months which may be extended up to 4 years without further competition. U.S Citizenship is required. For information on application procedures visit full vacancy announcement ARS-D10W-0255R at http://www.afm.ars.usda.gov/divisions/hrd/vacancy/VAC2.HTM. Candidates must submit specific information as outlined in the vacancy announcement. Applications must be received by September 24, 2010. Contact JoAnne Kniptash at 573-875-5293 with questions on application process. USDA/ARS is an equal opportunity provider and employer.

Postdoctoral position available in the Baxter Lab

I am looking for a post-doc for the NAABB project in the lab. The announcement is below, please spread the word to all interested parties.....

The USDA-ARS Plant Genetics Research Unit at the Danforth Plant Sciences Center in St Louis, MO is seeking a Postdoctoral Research Associate, for a two year appointment with possibility for extension. Ph.D. in plant sciences, genetics, molecular biology or related field is required. Salary is commensurate with experience ($57,408-$74,628) plus benefits. Citizenship restrictions apply. The incumbent will conduct research studying the systems biology of algal mineral nutrition. A successful candidate will combine bioinformatics, microbiology and genetics to understand how interactions between elements and gene-element interactions affect the growth of biofuel-relevant strains of Algae. Send application materials and references to Dr. Ivan Baxter at ivan.baxter@ars.usda.gov . The position is open until filled. USDA/ARS is an equal opportunity employer and provider.

Arabidopsis RILs paper is published

Our paper on "Natural Genetic Variation in Selected Populations of Arabidopsis thaliana Is Associated with Ionomic Differences" has just been published in PLoS ONE. I'm really happy that this paper is out because it demonstrates something that we have been talking about for several years now: that the ionome is dynamic and interconnected, and the relationships between elements are dependent on both genetics and the environment. The first three figures in this paper describe experiments which were the basis for three other papers that we have already published. Here is the abstract and none technical summary:

Abstract:
Controlling elemental composition is critical for plant growth and development as well as the nutrition of humans who utilize plants for food. Uncovering the genetic architecture underlying mineral ion homeostasis in plants is a critical first step towards understanding the biochemical networks that regulate a plant's elemental composition (ionome). Natural accessions of Arabidopsis thaliana provide a rich source of genetic diversity that leads to phenotypic differences. We analyzed the concentrations of 17 different elements in 12 A. thaliana accessions and three recombinant inbred line (RIL) populations grown in several different environments using high-throughput inductively coupled plasma- mass spectroscopy (ICP-MS). Significant differences were detected between the accessions for most elements and we identified over a hundred QTLs for elemental accumulation in the RIL populations. Altering the environment the plants were grown in had a strong effect on the correlations between different elements and the QTLs controlling elemental accumulation. All ionomic data presented is publicly available at www.ionomicshub.org.

Non-technical Summary:
Understanding how plants regulate element composition of tissues is critical for agriculture, the environment, and human health. Sustainably meeting the increasing food and biofuel demands of the planet will require growing crops with fewer inputs such as the primary macronutrients phosphorus (P) and potassium (K). Ionomics is the study of elemental accumulation in living systems using high-throughput elemental profiling. With this technique, we can rapidly generate large quantities of data on thousands of samples, allowing for the profiling of large genetic mapping populations and the discovery of hundreds of loci important for elemental accumulation. We have used this approach to sample the natural diversity present in collections of a model plant, the wild mustard Arabidopsis, and mapping populations derived from those collections. We find that when the soil environment changes, the identity of the genes important for elemental accumulation changes as well. We also find that elements will have different relationships between them depending on the environment and the lines under study. This suggests that crop varieties developed for improved elemental uptake and accumulation will be highly environment specific.