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Current Research
Daniel Schachtman, Ph.D.
Member and Principal Investigator
Roots, Roots, Roots
Lab Theme
Song (Unbound, by
Suzanne Vega)
We study roots and what's going
on underground so we see the world differently from most other plant
scientists who study above ground activities such as leaves, flowers and
fruits. Unbound
in our thinking we seek to be creative in our science in order to
contribute new ideas and directions to the scientific thought in our
field.
The
research focus of the lab is aimed at identifying the key mechanisms by
which roots regulate mineral uptake and adapt to changing soil
conditions such as drought and nutrient deficiencies
Root
Potassium and Nitrogen Sensing and Signaling
in Arabidopsis and Corn
(Funded by Monsanto Company and originally by Danforth
Startup Funds)
| 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.
Therefore we seek to elucidate how
roots sense changes in soils nutrient status and how that is
translated into adaptations that are important for survival and
growth |
(click to expand) |
We studied the global
regulation of
gene expression under nutrient deficiency in both Arabidopsis
and corn roots. Using microarrays 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 Arabidopsis roots. Two genes in Arabidopsis that
are downregulated by potassium deprivation were studied in
detail.
We showed that the SnRK2.8 kinase was linked
to decreased growth through the regulation of metabolism.
We also
found that MYB77 regulates lateral root
growth by modulating auxin signal
transduction. See figure above for current working model.
Our work to elucidate
nutrient signal transduction pathways continues with studies on
factors that are regulated by SnRK2.8 phosphorylation and through screening a
promoter luciferase fusion
activation tagged library.
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.Publications related to this project:
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Schachtman,
DP and Shin, R (2007) Nutrient Sensing and Signaling: NPKS,
Annual Review of Plant Biology
58:47 - 69
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Shin,
R, Alvarez, S., Burch, AY, Jez, JM,
Schachtman, DP (2007)
Phosphoproteomic identification of Targets of the Arabidopsis
SNF-like protein kinase SnRK2.8 reveals a connection to metabolic
Processes
Proceedings National Academy
Science USA
104:6460 - 6465
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Shin,
R,
Burch, AY,
Huppert, KA, Tiwari, SB, Murphy, AS, Guilfoyle, TJ,
Schachtman,
DP (2007)
The Arabidopsis transcription factor
MYB77 modulates auxin signal transduction
The Plant Cell
19:2440 - 2453
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Shin R, Schachtman DP (2004) Hydrogen peroxide mediates
plant root response to nutrient deprivation. Proc Natl Acad Sci U S
A 101: 8827-8832
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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
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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
Protocol for Imaging Reactive
Oxygen Species in Arabidopsis Roots
Protocol for quantification of
ROS in plant tissues using Amplex Red
Increasing
bioavailable zinc in cassava
(Funded
by Bill and Melinda Gates Foundation)
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The aim of this project is to
increase the zinc content of cassava roots to enhance human nutrition.
We have overexpressed specific plant zinc transport proteins to increase
the zinc content in the tubers, which are the edible part of the plant.
Our strategies are shown below.
Related link:
http://biocassavaplus.org/ |
Progress: We currently have
generated over 150 transgenic lines and analyzed the zinc content of the
fleshy edible part of the tuber in 60 transgenic lines.
We identified three lines with over 600%
higher and ten lines with between 150 - 350% higher zinc content.
These lines either express ZAT1 which is a
vacuolar zinc transporter or ZIP1 which is a plasma membrane zinc
transporter whose expression is driven by the patatin promoter.
Lines that simultaneously express both of
these genes are also being generated and will be tested.
Publications related to this project:
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Ramesh,
S., Choimes, S. and Schachtman,
D.P. (2004)
Overexpression of an Arabidopsis zinc
transporter in Hordeum vulgare
increases short-term zinc uptake after zinc deprivation and seed
zinc content
Plant Molecular Biology
54:373-385.
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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
Strategies to increase the zinc content of cassava
tuberous roots.
Gene
discovery in grapevine species
(Funded by USDA and
Missouri
Life Sciences Foundation)
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Missouri
is a center of diversity for grapevine species.
In particular the vines that are endemic to
Missouri
have a higher degree of resistance to fungal diseases than the
commonly grown Vitis
vinifera vines that originate from less humid climates.
In order to reduce the use of fungicides and
to increase the geographical area for grapevine cultivation it
would be useful to understand the molecular basis of powdery
mildew resistance in native American grapevines.
This knowledge could be applied to
increasing the disease resistance of the
V. vinifera cultivars. |
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This
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 have used microarrays to discover
the differences in gene expression in leaves that have been
infected with the fungal pathogen--"powdery mildew". This work
provides clues as to why Norton is more resistant than Cabernet
Sauvignon to powdery mildew. We are also using a differential
proteomic approach called iTRAQ to identify changes in protein
abundance in powdery mildew infected leaves of Cabernet
Sauvignon.
In the near future we will embark on
studying poly phenol production in response to pathogen
infection and how these compounds increase disease resistance.
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Publications related to this project:
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Fung, RWM, Gonzalo, M,
Fekete, C, Kovacs, LG, He, Y, Marsh, E, McIntyre, LM,
Schachtman,
DP, Qiu, W,
(2008) Transcriptional profiling
reveals novel insights Into powdery mildew-induced defense response
in grapevine. Plant Physiology
146:236-249
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Fung, RWM, Qiu, W., Su,
Y., Schachtman,
DP, Huppert, K., Fekete, C., Kovacs, LG (2007)
Gene
Expression Variation in Grapevine Species
Vitis
vinifera L. and
Vitis
aestivalis Michx.
Genetic Resources and Crop Evolution
54:1541-1553.
A genomic and physiology
approach to understanding the impact of mycorrhizal fungal colonization
on root metabolism and nutrient acquisition from nutrient patches
(Funded by NSF for three years - Environmental
Genomic Program)
Broad aim:
To gain a comprehensive understanding of how root metabolism and
nutrient uptake change in mycorrhizal and non-mycorrhizal roots in the
field and in the greenhouse when patches of nutrients are encountered.
This project brings together the
disciplines of plant genomics, physiology
and ecology.
The grant to study soil fertility and plant
uptake of essential nutrients is a collaboration between Drs. Daniel
Schachtman (Danforth
Center)
and
Brad Barbazuk (http://www.danforthcenter.org/barbazuk/),
and
Louise Jackson (University
of California,
Davis http://groups.ucanr.org/jacksonlab/).
Our team will use the most modern genomics
tools to learn more about how roots function to take up essential
minerals from soils.
This research will also elucidate the
molecular details of the symbiotic relationships that are established
between fungi and roots, and how this relationship aids plants in the
acquisition of essential mineral nutrients.
We will use tomato as a model plant in the
research to study how mycorrhizal fungi impact root function in the
uptake of nitrate, ammonium, zinc and phosphorus from the soil.
We will use both standard microarray
analysis and ultra-high throughput sequencing for studying genome-wide
changes in gene expression. The results of this work will yield a better
understanding of potential strategies that may be used for agricultural
management and crop breeding to achieve greater benefits from
mycorrhizal symbiosis and to increase nutrient use efficiency.
Providing
Drought Tolerance to Crop Plants Through Modification of Suberin
Deposition in Roots
(Funded by the Lubin Foundation)
Special thanks to
Sara Lee Schupf
(http://www.cnn.com/ALLPOLITICS/time/1999/05/10/charity.html)
and her family for their support
Press Release
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http://www.danforthcenter.org/newsmedia/NewsCoverageDetail.asp?nid=149
As water resources in the world
become increasingly scarce in the next 50 years and as agriculture is
forced to use more marginal land for food and biofuel production, it is
essential that we create new types of crop plants that are more tolerant
of dry conditions. In many arid regions such as the
Middle East
water resources are already scarce and so the need for agricultural
crops that use less water is critical for political and economic
stability of these regions. The shift in agriculture to biofuel crops
must be done carefully, since world populations are increasing and
therefore food supplies should not decrease as crops are shifted to
biofuel production. Therefore it will be essential to both increase
yields of existing crops and use more marginal land for production of
biofuels. Drought tolerance is a trait that will both increase existing
yields and will allow for crop production on more marginal lands.
Modifications that affect root structure and
function could potentially reduce plant water usage thereby increasing
water use efficiency; alternatively modifications may reduce the uptake
of toxic ions to increase tolerance to saline conditions.
This is a
collaborative project with
Dr. Asaph Aharoni (http://www.weizmann.ac.il/plants/aharoni/index.html)
at the Weizmann
Institute in
Israel.
Our aim is to create plants with modified
suberin in roots and then test for drought tolerance and root hydraulic
conductance.
Identification and cloning
of drought related genes in wheat (T.
aestivum)
(Funded by
USA
National
Academy
of Science)
Wheat is
the staple food of millions of people around the world, in
Pakistan
and USA.
Drought is the major limiting factor in crop production. This is a joint
project between Dr. Schachtman and Dr. Naseer Saeed who is located at
the
National
Institute for Biotechnology and Genetic Engineering in
Faisalabad,
Pakistan
(http://www.nibge.org/).
This collaborative project is aimed at
providing crops for
Pakistan
with increased drought tolerance using established technologies and
newly discovered genes.
Pakistan
is located in arid and semi arid regions of the world where annual rain
fall is 240 mm which is quite low. The population of
Pakistan
is about 165 million, of which 67 % live in rural areas.
Wheat is widely grown but irrigation water
is limited and so there is a need develop drought tolerant crops that
can grow with limited water.
Recent Past Projects
Functional Genomics of Root to Shoot
Signaling Under Drought
(Funded by
NSF-USA Plant Genome Program)
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.
This
project aimed 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
embarked on a collaborative genomics project with groups at the
Universities of Illinois and
Missouri
(http://rootgenomics.missouri.edu/). We 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 have
written several papers
characterizing
the changes in sap composition that occurs under mild and extended water
stress.
In addition, our group
collaborated with Dr. Robert Sharp's at the
University
of Missouri,
Columbia.
In that collaboration we studied 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.
This project was funded from
2002 - 2007.
We are still writing two manuscripts from
this project, but the experimental phase of the project has ended.
Related Links
Database containing proteomic data on maize xylem sap
proteins and root cell wall proteins:
http://protic.danforthcenter.org/SmallMoleculeDB/molecule_search.php
Small Molecular Database for LCMS users with MRM
functionality:
http://protic.danforthcenter.org/proticdb-1.2.1/Protic/home/index.php
Publications
related to this project:
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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
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Zhu, J, Chen, S, Alvarez,
S., Asirvatham, VS,
Schachtman,
DP, Wu, Y. Sharp, RE (2006) Cell Wall Proteome in the Maize Primary
Root Elongation Zone. I. Extraction and Identification of Water
Soluble and Lightly Ionically-Bound Proteins
Plant
Physiology 140:311-325
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Alvarez, S, Goodger, JQD,
Marsh, EL, Chen, S, Asirvatham, VS,
Schachtman, DP, (2006)
Characterization of the maize xylem sap proteome.
Journal
of Proteome Research 5:963-972
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Zhu, J.,
Alvarez, S., Marsh, E.L.,
LeNoble,
M.E.,
Cho, I.J., Sivaguru, M., Chen, S., Nguyen, H.T., Wu, Y.,
Schachtman, D.P.,
Sharp, R.E. (2007) Cell wall proteome in the maize primary root
elongation zone.
Region-specific changes in water
soluble and lightly ionically-bound proteins under water deficit.
Plant Physiology
145:1533-48
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Schachtman,
D.P., Goodger, J.Q.D. (2008) Chemical root to shoot signaling under
drought Trends in Plant Science
577: 1360-1385.
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Alvarez, S, Marsh, EL, Schroeder, SG,
Schachtman, DP, (2008) Metabolomic and
proteomic changes in the xylem sap of maize under drought.
Plant Cell and Environment
31:
325-40.
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Spollen, W.G., Tao, W., Balliyodan, B., Chen,
K., Hejlek, L.G., Kim, J.J., LeNoble, M.E., Zhu, J., Bohnert, H.J.,
Henderson, D., Schachtman,
D.P., Davis, G.E., Springer, G.K., Sharp, R.E., Nguyen, H.T. (2008)
Spatial distribution of transcript changes in the maize primary root
elongation zone at low water potential
BMC Plant Biology 8:32.
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Goodger, JQD and
Schachtman, DP (2008) Nitrogen Source
Influences Root to Shoot Signaling Under Drought.
In:
Abiotic Stress Adaptation in Plants: Physiological, Molecular and
Genomic Foundation Editors: Ashwani Pareek, Sudhir K. Sopory, Hans
J. Bohnert, Govindjee; Springer (Dordrecht, The
Netherlands).
Identification,
characterization, and functional analysis of transport proteins involved
in Arabidopsis root-knot nematode-induced feeding sites
(Funded
by NSF Integrated Plant Biology Program)
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 worked to understand which transport processes are important in
nematode induced giant cells. We are studied 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.
A unique amino acid transporter was
identify and characterized as preferentially transporting the amino
acids that are essential for animal nutrition.
Most recently we have shown that two amino
acid transporters are involved in nematode infestation.
Publications related to this
project:
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Hammes U,
Schachtman DP, 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
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Hammes, UZ, Nielsen, E,
Honaas, L, Taylor, CG,
Schachtman, DP, (2006) AtCAT6, a
sink tissue localized amino acid transporter for essential amino
acids in Arabidopsis
Plant Journal
48:414-426
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Yang, Y. Hammes, UZ,
Taylor,
CG,
Schachtman,
DP, Nielsen, E (2006) High-affinity auxin transport by the AUX1
influx carrier protein
Current
Biology 11: 1123 - 112
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Marella, HH, Nielsen, E,
Schachtman,
DP, Taylor, CG (2008)
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Two amino acid permeases are involved in
root-knot nematode parasitism of Arabidopsis, submitted to MPMI
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Swarup, K., Benkova, E., Swarup, R.,
Casimiro, I, PĂ©ret. B, Yang, Y., Parry, G., Nielsen, E., De Smet,
I., Vaneste, S., Levesque, M.P., Carrier, D., James, N., Calvo, V.,
Ljung, K., Kramer, E.M., Roberts, R., Graham, N., Marillonnet, S.,
Patel, K., Jones, J.D.G., Taylor, C.G., Schachtman, D.P.,
May, S.T., Sandberg, G., Benfey, P., Friml, J., Kerr, I., Beeckman,
T., Laplaze, L. and Bennett, M.J. (2008) The auxin influx carrier
LAX3 facilitates lateral root emergence in Arabidopsis,
Nature Cell Biology
10:946-954.
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