Ionomics Blog

PLoS one paper on CPR5 and potassium

2011-11-04T01:26:00.000-07:00

The Salt group has published a new paper on a novel role of CPR5 in the regulation of potassium in A. thaliana.

Borghi M, Rus A, Salt DE (2011) Loss-of-Function of Constitutive Expresser of Pathogenesis Related Genes5 Affects Potassium Homeostasis in Arabidopsis thaliana. PLoS ONE 6(10): e26360. doi:10.1371/journal.pone.0026360

Here is the Abstract
Here, we demonstrate that the reduction in leaf K⁺ observed in a mutant previously identified in an ionomic screen of fast neutron mutagenized Arabidopsis thaliana is caused by a loss-of-function allele of CPR5, which we name cpr5-3. This observation establishes low leaf K⁺ as a new phenotype for loss-of-function alleles of CPR5. We investigate the factors affecting this low leaf K⁺ in cpr5 using double mutants defective in salicylic acid (SA) and jasmonic acid (JA) signalling, and by gene expression analysis of various channels and transporters. Reciprocal grafting between cpr5 and Col-0 was used to determine the relative importance of the shoot and root in causing the low leaf K⁺ phenotype of cpr5. Our data show that loss-of-function of CPR5 in shoots primarily determines the low leaf K⁺ phenotype of cpr5, though the roots also contribute to a lesser degree. The low leaf K⁺ phenotype of cpr5 is independent of the elevated SA and JA known to occur in cpr5. In cpr5 expression of genes encoding various Cyclic Nucleotide Gated Channels (CNGCs) are uniquely elevated in leaves. Further, expression of HAK5, encoding the high affinity K⁺ uptake transporter, is reduced in roots of cpr5 grown with high or low K⁺ supply. We suggest a model in which low leaf K⁺ in cpr5 is driven primarily by enhanced shoot-to-root K⁺ export caused by a constitutive activation of the expression of various CNGCs. This activation may enhance K⁺ efflux, either indirectly via enhanced cytosolic Ca²⁺ and/or directly by increased K⁺ transport activity. Enhanced shoot-to-root K⁺ export may also cause the reduced expression of HAK5 observed in roots of cpr5, leading to a reduction in uptake of K⁺. All ionomic data presented is publically available at www.ionomicshub.org.

Two new Plant Cell Papers

2011-04-26T09:05:00.001-07:00

Two new papers have been published in Plant Cell in the last month describing genes that we cloned from the original Lahner et al. ionomics screen:

The first is "Arabidopsis NPCC6/NaKR1 Is a Phloem Mobile Metal Binding Protein Necessary for Phloem Function and Root Meristem Maintenance". 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 us 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.

The second is "Sphingolipids in the Root Play an Important Role in Regulating the Leaf Ionome in Arabidopsis thaliana". A great collaboration between our group and several groups working on sphingolipids resulted when we landed on a gene in the sphingolipid pathway. Subtly altering the sphingolipid pathway results in what appears to be two different ionomics associated phenotypes: altered suberin and Fe homeostasis.

Here is the abstract of the first paper:

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 summary intended for lay audiences:

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.

And here is the abstract of the second paper:

Sphingolipid synthesis is initiated by condensation of Ser with palmitoyl-CoA producing 3-ketodihydrosphinganine (3-KDS), which is reduced by a 3-KDS reductase to dihydrosphinganine. Ser palmitoyltransferase is essential for plant viability. Arabidopsis thaliana contains two genes (At3g06060/TSC10A and At5g19200/TSC10B) encoding proteins with significant similarity to the yeast 3-KDS reductase, Tsc10p. Heterologous expression in yeast of either Arabidopsis gene restored 3-KDS reductase activity to the yeast tsc10Δ mutant, confirming both as bona fide 3-KDS reductase genes. Consistent with sphingolipids having essential functions in plants, double mutant progeny lacking both genes were not recovered from crosses of single tsc10A and tsc10B mutants. Although the 3-KDS reductase genes are functionally redundant and ubiquitously expressed in Arabidopsis, 3-KDS reductase activity was reduced to 10% of wild-type levels in the loss-of-function tsc10a mutant, leading to an altered sphingolipid profile. This perturbation of sphingolipid biosynthesis in the Arabidopsis tsc10a mutant leads an altered leaf ionome, including increases in Na, K, and Rb and decreases in Mg, Ca, Fe, and Mo. Reciprocal grafting revealed that these changes in the leaf ionome are driven by the root and are associated with increases in root suberin and alterations in Fe homeostasis.

And here is a summary intended for lay audiences:

Sphingolipids, a class of membrane lipids with essential functions in all Eukaryotes, are thought to make up a large percentage of some plant membranes and have specific roles in cell processes through the formation of small microdomains. Here we discuss the role of two genes in the sphigolipid biosynthesis pathway in the model plant Arabidopsis Thaliana. When both genes are disrupted, the plants are not viable. However, when the higer expressed gene is disrupted, the plants look normal but elemental profiling reveals that they have significantly altered elemental accumulation in their leaves. Several of the changes appear to be the result of altering the the amount of suberin, a polymer which forms a barrier to water and ion movement in the root, is altered. We also observed alterations in the plants Fe homestasis mechanisms, the cause of which is still unknown. Understanding these processes will enable the prodcution of crops that are more efficient in their water and nutrient uptake effficiency.

New paper in PLoS Genetics!

2010-11-12T14:38:00.001-08:00

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 our 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.

Prof Salt accepts new position at University of Aberdeen

2010-10-21T09:56:00.000-07:00

Professor David Salt accepts new position as 6th Century Chair in the School of Biological Sciences at the University of Aberdeen starting May 2011. Professor Salt will continue his ionomic's projects and development of the ionomicsHUB (iHUB)

Arabidopsis RILs paper is published

2010-06-17T08:12:00.001-07:00

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.

Arabidopsis Association Paper published in Nature

2010-04-25T19:39:00.001-07:00

The big Nature paper, to which we contributed phenotype data, is now out. Its a great example of the power of plant genetics, many different phenotypes evaluated on a common population resulting in a wealth of really interesting associations. Its way cool, but the bigger populations that we have analyzed are even better and soon we will be submitting some really cool new results for publication.

David Salt Wins McCoy Award

2010-03-05T08:27:00.001-08:00

Congratulations to David for this well deserved honor!!!

"David Salt, professor of horticulture and landscape architecture in the College of Agriculture, is the winner of the 2010 Herbert Newby McCoy Award, the most prestigious research award given by Purdue. The award is in recognition of Salt’s pioneering and innovative efforts in the use of genome-scale biological approaches and information technologies to define and drive the field of ionomics. He is an international leader in the field of plant nutrition and has made significant impacts on environmental sustainability, agriculture and human health."

Ferroportin Paper published in Plant Cell

2009-11-03T15:05:00.001-08:00

Our paper describing the function of the two Ferroportin genes in Arabidopsis has just been published in the early access feed of Plant Cell!

The pdf is here (also available from our publications page)

here is the abstract......

Relatively little is known about how metals such as iron are effluxed from cells, a necessary step for transport from the root to the shoot. Ferroportin (FPN) is the sole iron efflux transporter identified to date in animals, and there are two closely related orthologs in Arabidopsis thaliana, IRON REGULATED1 (IREG1/FPN1) and IREG2/FPN2. FPN1 localizes to the plasma membrane and is expressed in the stele, suggesting a role in vascular loading; FPN2 localizes to the vacuole and is expressed in the two outermost layers of the root in response to iron deficiency, suggesting a role in buffering metal influx. Consistent with these roles, fpn2 has a diminished iron deficiency response, whereas fpn1 fpn2 has an elevated iron deficiency response. Ferroportins also play a role in cobalt homeostasis; a survey of Arabidopsis accessions for ionomic phenotypes showed that truncation of FPN2 results in elevated shoot cobalt levels and leads to increased sensitivity to the metal. Conversely, loss of FPN1 abolishes shoot cobalt accumulation, even in the cobalt accumulating mutant frd3. Consequently, in the fpn1 fpn2 double mutant, cobalt cannot move to the shoot via FPN1 and is not sequestered in the root vacuoles via FPN2; instead, cobalt likely accumulates in the root cytoplasm causing fpn1 fpn2 to be even more sensitive to cobalt than fpn2 mutants.

Review publications

2009-10-08T13:00:00.001-07:00

We have added a new publications page to hold review papers produced by the ionomics team. You can find it here or follow the link from the top of the main publications page.

Database repairs Oct 9

2009-09-24T13:26:00.000-07:00

The ionomicshub will be down for a few essential security patches on Friday, October 9th. These updates will start at 11:00am and be complete by 1:00pm (ET) (may be before).

Yeast database goes live

2009-09-24T09:54:00.001-07:00

The Beta version of our yeast database is now live. This database holds over 50,000 samples worth of ionomic data on all viable yeast strains from both the full genome knockout and over expression collections. A description of how the data was collected has been published in Danku et al., J Anal. At. Spectrom. 2009, 24, 103-107. The database supports searches for specific genes, data display and download. We have also included features that allow the re-upload of downloaded data sets after user-defined manipulations have been performed. These new up-loaded user-defined data sets then become searchable by the community. We are currently working on a paper in which we describe the statistical analysis of the data and its biological implications. Please report bugs or suggestions to dsalt@purdue.edu or IBaxter@danforthcenter.org.

iHUB proposal submitted to NSF

2009-07-21T10:35:00.000-07:00

The Salt lab has just submitted a proposal to the US NSF Research Coorodination Network in Biological Science (RCN) program titled "The iHUB: A Collaborative International Network for Ionomics". If funded we will add various new tools to the ionomicsHUB including:

1. Tools to allow the easy sharing and annotation of data.

2. Literature Cloud: A tool to allow the easy filtering and sharing of literature.

3. Tools to allow the coordinated collection of ICP data from distributed sites.

4. Tools to allow the easy sharing of presentations and lectures.

5. Tools to allow the self formation of online work groups and online communication.

6. iHUB interaction map – The iHUB interactome.

7. On-line Help tools.

8. iHUB Annual Meeting.

9. Student and facility scientific exchange between collaborating laboratories.

esb1 paper is out!

2009-06-05T12:03:00.001-07:00

Our paper on the esb1 mutant is now available at Plos Genetics. You can find it here

Arabidopsis Piims data download error fixed

2009-04-16T21:48:00.003-07:00

We just fixed a bug in the csv download code of the Arabidopsis Piims which was causing incorrect data to be produced for some samples. The error was introduced around November 13th, 2008. If you downloaded a csv file during the intervening time, you should re-download the data.

We apologize for the inconvenience.

esb1 paper accepted at Plos Genetics

2009-04-16T21:48:00.001-07:00

Our paper entitled 'Root suberin forms an extracellular barrier that affects water relations and mineral nutrition in Arabidopsis' has just been accepted for publication at PLoS Genetics. Here is the abstract:

Background: Though central to our understanding of how roots perform their vital function of scavenging water and solutes from the soil, no direct genetic evidence currently exists to support the foundational model that suberin acts to form a chemical barrier limiting the extracellular, or apoplastic, transport of water and solutes in plant roots.

Methodologies/Principle Findings: Using the newly characterized enhanced suberin1 (esb1) mutant, we established a connection in Arabidopsis thaliana between suberin in the root, and both water movement through the plant, and solute accumulation in the shoot. Esb1 mutants, characterized by increased root suberin, were found to have reduced day time transpiration rates, and increased water use efficiency during their vegetative growth period. Furthermore, these changes in suberin and water transport were associated with decreases in the accumulation of Ca, Mn and Zn, and increases in the accumulation of Na, S, K, As, Se and Mo in the shoot.

Conclusions/Significance: Here we present direct genetic evidence establishing that suberin in the roots plays a critical role in controlling both water and mineral ion uptake and transport to the leaves. The changes observed in the elemental accumulation in leaves are also interpreted as evidence that a significant component of the radial root transport of Ca, Mn and Zn occurs in the apoplast.

Open science helps reviewers!

2009-04-03T07:55:00.001-07:00

We just got the reviews back from Plos Genetics for our esb1 paper. There were many constructive suggestions and helpful suggestions, which is what we have come to expect from Plos Genetics (and why we submit many of our manuscripts there).

One of the reviewers actually came to Piims and retrieved some of the data that went into the paper to make the point that we should comment on the Mg effect of the mutation. Specifically, the reviewer pointed out that the mutation doesn't affect Mg, even though it affects Ca. They even included a figure of the data! I am posting the figure here, Blue is the mutant, and pink is the wild-type.

Just another reason to put all your data out there. We thank the reviewer for the helpful suggestions.

ps: Though we are collecting data about who visits our website, we don't collect data about what they search, so the kind reviewer is still anonymous to us.

Rice Piims is up and running!

2009-03-24T13:28:00.001-07:00

We have now deployed a working prototype of Piims to manage the pipeline and data for our NSF funded Rice project. This represents a substantial redesign of the Piims system. Some of the major changes are listed below. We are releasing the data as soon as it enters the database. We are in the process of uploading all of the ~7000 samples that we have already run into the database.

New features:
The biggest change is that for Rice, we have incorporated features allowing us to track samples that were grown in fields by collaborators. Piims will now allow us to keep track of Packets of seed that get sent to us.

Piims will track information like field location and weather data for fields.

Piims will now allow for the flexible construction of analysis runs, so packets from different fields and years can be analyzed to together.

New seed grant to develop collaborative tools

2009-01-08T12:10:00.001-08:00

We are please to announce that along with our support from NSF and NIH for ionomicsHUB, we have recently been awarded a seed grant from the Purdue University Cyber center to develop collaborative work space and literature sharing tools for the ionomicsHUB. Look out for these new tools in 2009

Sorry for loss of PiiMS service over the last 5-day

2008-10-20T10:06:00.000-07:00

Over the last 5-days system administrators have been trying to upgrade the PiiMS system kernel from 32 to 64 bits. We expected that this would increase the performance of PiiMS. Unfortunately, the system administration team ran into some technical problems and was unable to perform the upgrade. We will try again in the near future and would hope to have much less system down time.

The Figure Reviewers Didn't Like

2008-08-24T22:32:00.001-07:00

In our previous attempts to get the Fe model published, we included the figure below. It shows how the Fe model predicts that the Fe status of the soil varied greatly across the many trays that we have run. We like it because it shows that even though the environment is changing (despite our best efforts to keep it constant) this model and others like it will allow us to account for this variation when we look at data.

The reviewers didn't like it for reasons I disagree with so vociferously I shall not repeat them here. So we left it out of the version that was submitted to PNAS.

You can see how changing the soil batch had a major effect on the Fe status of the plants. We were only able to grow plants in Fe sufficient conditions once we started watering with the Fe specific chelator HBED.

Piims is now all open source.

2008-08-13T10:36:00.001-07:00

We have just rolled out the new version of Piims which is based on all open souce software:
the database is Postgres and the front end is run on Tomcat.

We have also added a bunch of functionalities to the lab side of the database and have fixed a large (really large) number of bugs.

Users are now able to see more of the meta-data and pictures of the trays have been visible for awhile now.

The yeast and rice versions of Piims are based on this format and should be publically available soon.

A huge thanks to all the people who worked on this:
Gemez Marshall did the bulk of the work but he had a lot of help from Mourad Ouzzani, Brad Kennedy and Maged Zereba.

Fe&P model paper is online!

2008-08-13T10:29:00.001-07:00

Our paper showing how we can use the ionome to detect plants responding to Fe and P deficient conditions is now online at PNAS

Fe Model is accepted in PNAS

2008-06-22T23:11:00.001-07:00

Our paper describing how the ionome can be used to determine the physiological status of a plant has just been accepted for publication in PNAS.

Ionomics blog is live!

2008-04-15T21:18:00.000-07:00

Welcome to the Ioniomics blog-

This will be your source for timely and topical news about what is going on with the Ionomics project.

Ivan