The Isolation and Characterization of the IronPhytosiderophore Transporter in Avena sativa
A thesis submitted to the School of Graduate Studies
of
Bloomsburg University

In Partial fulfillment of the Requirement
For the Degree of Master of Science

Program in Biology
Department of Biological and Allied Health Sciences
Bloomsburg University of Pennsylvania

By
Melissa L. Tomcavage

Bloomsburg,Pennsylvania
2009
Masters Candidate

This Thesis was accepted as meeting the research requirement for the master's degree.

APPROVED:

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Dr. Kristen D. Brubaker, Committee Member

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Dr. Kevin J. Williams, Committee Member

APPROVED:

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11

Abstract
Iron is a vital nutrient required for processes such as photosynthesis and respiration in
plants. Unfortunately, the mineral is found as an insoluble form in the rhizosphere. Plants have
evolved two different mechanisms for acquiring iron, a reduction based strategy and a chelation
based strategy. The chelation based strategy is restricted to grass species as they are the only
plants found to put out phytosiderophores. Until recently, the mechanisms for the uptake of the
phytosiderophore complexed to its ligand has been unknown. The discovery of the membrane
transporter gene used by the phytosiderophore in maize in 200 I has shed some light on the
mechanisms. A second transporter gene was discovered in 2006 in barley that moves ironphytosiderophore complexes into the root. This thesis presents the data for the sequence of a
putative iron-phytosiderophore transporter gene in oats that was compared to the sequences of
known phytosiderophore transporters, HvYS 1 from barley and ZmYS 1 from maize.

ll1

Table of Contents
Abstract

lll

Table of contents

lV

List of Figures

V

List of Tables

Vl

Acknowledgements

vu

Introduction

1

Iron Nutrition

1

Iron Nutrition in Plants

2

Iron Uptake Mechanisms of Plants

5

Phytosiderophores

7

Mugineic Acid

8

Phytosiderophore Secretion

11

Yellow Stripe 1

13

Experimental Approach

17

Results

21

Discussion

34

References

37

lV

List of Figures
Figure 1. Strategy I Uptake.

6

Figure 2. Strategy II Uptake

7

Figure 3. Oats grown hydroponically under iron deficient conditions.

17

Figure 4. Oat roots in iron deficient hydroponic solution.

17

Figure 5. Specificity Region of Agrostis stolonifera.

22

Figure 6. Nucleotide BLAST of A. stolonifera specificity region.

22-23

Figure 7. Nucleotide BLAST of A. stolonifera specificity region.

23

Figure 8: Amino Acid sequence of A. stolonifera specificity region.

24

Figure 9: Clustal Alignment of specificity regions and known transporters.

24

Figure 10. Full gene analysis, Nucleotide sequence.

27

Figure 11: Full gene nucleotide BLAST of Avena putative transporter.

28-30

Figure 12: Full gene protein analysis of putative Avena transporter.

30

Figure 13: Full Gene Protein BLAST of putative Avena transporter.

31

Figure 14. Clustal analysis between known transporter and putative Avena tranporter.

32-33

V

List of Tables
Table 1. Primers

20

VI

Acknowledgements
I would like to thank my thesis advisor, Dr. George Davis, for his guidance during the
course of this project. Input from Dr. Kristen Brubaker was highly appreciated as well. Thanks
to Dr. John Hranitz for his help with initial sequencing and to Dr. Carl Hansen for help with
bioinformatics analysis. In addition to the faculty, I thank several peers for assistance during
various parts of this project: Joshua Montgomery and Shirshendu Saha, assistance with the
benchwork; Andrew Troutman, assistance with initial sequencing; Essie Reed and Heather
Pursel, assistance in obtaining plant material.
I would also like to acknowledge Gene Wiz, Inc. for performing sequencing runs. This
project was funded by grants from the Department of Agriculture and the Internal Grant, ####,
from Bloomsburg University. The US Department of Agriculture, CS REES grant is as follows:
Project number: 2007-35318-18350
Project Title: Uptake Specificity of Snythetic Phytosiderophore Analogs by Graminaceous
Plants.

Vll

Introduction
Iron Nutrition
According to the World Health Organization, iron deficiency is the most common and widespread
nutritional disorder in the world (www.who.int). Humans depend mostly on plant foods for nutritional
health and plants are critical components of our diet in that they provide almost all essential mineral and
organic nutrients either directly or indirectly. A deficiency in the agricultural realm leads to reduced crop
yields as well (Astolfi et al., 2003; Grusak and DellaPenna 1999). Mammalian systems contain at least
four major classes of iron-containing proteins: iron containing enzymes which include hemoglobin,
myoglobin, and cytochromes; iron-sulfur enzymes such as flavoproteins and heme-flavoproteins; proteins
for iron storage and transport (ferritins); and other iron-containing or activated enzymes (Vasconcelos and
Grusak 2006).
Nutritional iron is divided into heme iron (easily absorbed) and non-heme iron (usually
considered "free" or "weak"). Heme iron intake is negligible for the majority of people in many
developing countries based on a more vegetarian type of diet. Therefore, non-heme iron is the main
source of dietary iron for most people in the world. Iron in any food has a particular bioavailability,
which is a function of its chemical form and the presence of other food components that either promote or
inhibit its absorption. The iron present in the human body is mostly in a stored form and losses are
usually minimal. However, dietary intake of iron is needed to replace the iron lost by passage of stool
and urine, shedding of skin, and sweating (Vasconcelos and Grusak 2006).
Plants contain almost all essential human nutrients, with cereal grains such as wheat, rice, and
maize providing about two-thirds of all energy in the human diet. However, not all plant sources provide
the same amount of iron, and the amount of iron ingested is directly proportional to the portion size that is
consumed (Vasconcelos and Grusak 2006; Cassman 1999). Iron acquisition is challenging due to the low
availability ofiron in soil. Although iron is the fourth most abundant element in the earth's crust, it is not
readily available to plants because it is found in most rocks as primary minerals in ferromagnesium
silicate forms like olivine, augite, hornblende, or biotite, which are considered unstable. One third of the

1

cultivated soils around the world are calcareous and therefore iron deficient (Kim and Guerinot 2007;
Brown and Jolley 1989; Briat 2008; Ma 2005). The total Fe2O3 content of soils varies from about 2-6%
in nonnal temperate soil to as much as 60% in tropical soils (Steward 1963). Other factors such as high
calcium and magnesium concentrations and high bicarbonate concentrations, soil carbonates, salinity, soil
iron composition nutrient interaction, soil moisture content, and soil bulk density also impact iron
bioavailability (Ma 2005; Murata et al., 2006; Hansen et al., 2006).
The Industrial Revolution caused an increase in food production which led to agricultural
practices involving application of chemical fertilizers, manures, pesticides, and other synthetic products to
maximize output. These practices caused an alteration in soil characteristics, such as soil pH, nutritional
conditions, and soil water conditions. The result is serious mineral imbalances and heavy metal
contamination in agricultural fields all over the world (Hiradate et al. 2007).
Iron Nutrition in Plants
If a continuous supply of iron from the soil is not available, the plant develops iron chlorosis - a
yellowing caused by low chlorophyll content in leaves that can be alleviated by supplying the plant with
iron (Astolfi et al. 2003; Brown and Jolley 1989; Briat 2008; Ma 2005; Thoiron et al. 1997). Chlorosis
occurs in the young leaves, with the other leaves frequently unaltered. Iron cannot be withdrawn from
mature leaves to support growth of new leaves and the veins of the leaves maintain their chlorophyll
while the interveinous regions lose theirs, giving the plant a characteristic appearance of iron deficiency.
The effects of iron deficiency are often associated with cytological alterations which mainly affect the
chloroplast ultrastructure. Thylakoids become disorganized and most of the mitochondria located in
chlorotic leaves display completely disorganized cristae (Briat 2008; Epstein 1972; Scott 2008; Thoiron et

al. 1997).
Iron is required in chlorophyll biosynthesis; iron deficiency impacts chlorophyll degradation by
increasing it - the quantity of carotenoids decreases when iron is in short supply, resulting in chlorophy 11
degradation (Briat 2008). Once total bleaching occurs in severe conditions of iron deficiency, leaf
margins collapse or whole leaves in general take on a "papery" attribute (Steward 1963). Problems

2

related to the low solubility of iron bearing mineral phases, slow dissolution kinetics, the transport of
soluble iron species to the root, the low bioavailability of certain soluble iron complexes, and slow iron
release from complexes in ligand or metal exchange reaction need to be overcome in order to supply iron
to plants (Kraemer et al. 2006).
Iron is one of the fourteen essential mineral elements for plants; it functions to accept and donate
electrons and plays important roles in the electron transport chains of photosynthesis and respiration as
well as involvement in chlorophyll synthesis. Other involvement includes nitrogen fixation and plant
hormone synthesis (Connolly and Guerinot, 2002; Kim and Guerinot 2007; Briat 2008; Charlson and
Shoemaker 2006; Hiradate et al. 2007). Iron is also one of three nutrients in addition to nitrogen and
phosphorus that most commonly limit plant growth (Guerinot, 2001).
Specifically for photosynthesis, iron is involved in electron transport through Photosystem II and
Photosystem I and in coordinating the flow of electrons from Photosystem II to Photosystem I. The
reaction center of photosystem II contains iron in the ionic form and that of photosystem I as three
molecules of 4Fe-4S type iron sulfur clusters. The iron-sulfur clusters function as redox signals for light
dark regulation of the Calvin cycle (Briate 2008; Shanna 2006). Photosystem I is affected by iron
deficiency to a larger extent than Photosystem II probably because it contains a very large number of iron
containing components (Sharma 2007).
The synthesis and metallation of chloroplast electron transport components slows down as the
electron transport system develops under the influence of iron deficiency and the seed stored iron is
exhausted. Under conditions of iron deficiency, the expression of genes encoding chlorophyll-binding
proteins would be downregulated, leading to the remodeling of the antenna components to adapt to the
potentially photoinhibitory conditions resulting from reduced electron transport capacity (Sharma 2007).
Iron is also forms a vital part of cytochromes, globins, various redox enzymes, and is a
constituent of nitrogenase; it is a component in haem proteins such as cytochromes, catalase, and Fe-S
proteins such as ferredoxin (Surridge 2001; Ma 2005; Epstein 1972; Curie and Briat 2003). In addition to

3

a decrease in the amount of chlorophylls from iron deficiency, there is also a decrease in the amount of
carotenoids, but this decrease is not as pronounced ( Abadia, J. and Abadia, A. 1993 ).
Iron exists in two valence states, ferric (Fe3J and ferrous (Fe2J. Ferrous iron is more easily taken
up and used by plants than ferric iron, although under the usually prevailing conditions in soils and
biological fluids, iron is predominantly in the ferric state. The soil pH strongly influences iron solubility
and therefore availability to plants. Iron is insoluble at neutral or basic pH levels in the soil and the iron
concentrations in solution decrease when the pH increases. Iron solubility is also influenced by several
soil properties such as the redox conditions and the presence of organic matter (bacterial siderophores for
example) (Briat 2008; Brown and Jolley 1989).
Water and oxygen liberate iron by weathering primary minerals. The weathering of iron bearing
primary minerals leads to formation of secondary iron oxides and the release of Fe2+ and Fe3+. In most
soils, iron oxides and hydroxides are the largest pool of iron. The low solubility of iron oxides in the
neutral pH range is responsible for low dissolved iron concentrations that induce iron deficiency
symptoms in many plant species (Briat 2008; Kraemer et al. 2006).
In the rhizosphere, plant-microorganism interactions can be described as a feedback loop during
which (1) plant roots secrete exudates that modify the rhizospheric environment; (2) these changes are
sensed by the resident microbial populations; (3) selection of adapted microbial population to the new
environment occurs, leading to a modification of the structure and activities of the microbial community;
(4) in turn, these variations will influence plant growth and physiology, leading to changes in plant root
exudates, and so on. To be more specific, microorganisms found in the soil may also enhance iron uptake
in plants (Briat 2008; Fodor 2006). The seed mineral content of iron depends on factors such as
mobilization from the soil, uptake by the roots, movement within the plant, and finally iron deposit in the
forming seeds (Chauhan 2006).
Iron is toxic at high levels and because of this potential, cells store iron with the specialized iron
storage protein, ferritin. While animal ferritins are found in the cytosol, plant ferritins contain transit
peptides for delivery to organelles called plastids and whose abundance is strictly controlled at the

4

transcriptional level by the iron status of the cells (Connolly and Guerinot 2002; Briat 2008; Nilsen and
Orcutt 1996; Suzuki et al. 2006; Gross et al. 2003). The difference between plant ferritin genes and
animal ferretin is that plants do not contain Iron Regulatory Elements (found in animal ferritin genes), but
instead have Iron-Dependent Regulatory Sequences (IDRS), responsible for the repression of
transcription under low iron supply (Gross et al. 2003).
In most plants (excluding grasses), iron deficiency is associated with morphological changes such
as the inhibition of root elongation, increase in the diameter of apical root zones, and abundant root hair
fonnation. This occurs due to the fonnation of transfer cells that are part of the mechanism to enhance
iron uptake and the site of iron deficiency induced root responses in Strategy I plants (Marschner 1995).
Iron Uptake Mechanisms of Plants
Strategy I plants exude protons into the rhizophere as well as reductants/chelators such as
electrons (e·), organic acids, and phenolics, lowering the pH of the soil solution and increasing the
solubility ofFe3+. The release of protons is mediated via a P-type ATPase located in the plasma
membrane. Ferric iron is reduced to Fe2+ at the surface of the plasma membrane of root epidennal cells
by ferric chelate reductase (Alam et al. 2005; Brown 1978; Kim and Guerinot 2007; Brown and Jolley
1989; Ma 2005; Curie and Briat 2003; Guerinot and Yi 1994; Hiradate et al. 2007). Fe2+ is transported
into the root by IRTI (iron regulated transporter 1) protein, a member of the ZIP metal transporter family
(zinc and iron regulated transporter family), an inducible Fe2+ transporter that contributes to metal
homeostasis (Colangelo and Guerinot 2006; Connolly and Guerinot 2002; Kim and Guerinot 2007; Ma
2005; Hiradate et al. 2007; Kraemer et al. 2006). Strategy I plants also show enhanced development of
lateral roots and differentiation of specialized transfer cells. These changes increase the surface area for
reduction and transport of iron (Guerinot and Yi 1994). The iron deficiency induced root response in
Strategy I is located in the apical root zones of the plants (Marschner et al. 1987). Figure 1 shows the
path of iron acquisition in Strategy I plants.

5

Fe(II)

Cytoplasm
H

/ 1\
Cell Membrane

Soil Environment

H

'·
.
l

-:::----1

Fe(III)

Fe(II)

Soluble

Insoluble

Figure 1: Strategy I uptake. This represents the proton release from a Strategy I plants where the
insoluble iron is reduced to a soluble form and then adsorbed through the cell membrane of the root via
IRTl. (Adapted from Ma 2005)
Graminaceous species, such as com, wheat, oats, and rice, use the chelation-based Strategy II,
which retrieves adequate amounts of iron from soils containing scant amounts of iron (Kim and Guerinot
2007; Ma 2005; Curie and Briat 2003). In response to iron deficiency, the grasses secrete Fe3+ chelators
called phytosiderophores, which are small molecular weight compounds that retrieve insoluble iron and
make it available to the plant (Alam et al. 2005; Connolly and Guerinot 2002; Kim and Guerinot 2007;
Brown and Jolley 1989; Curie and Briat 2003; Takagi 1993). The complex is then absorbed into the plant
via a species specific transporter. Figure 2 illustrates the Strategy II uptake mechanism.

6

Cytoplasm

plant specific
phytosiderophore

8
~hytosiclerophore)

Cell Membrane

Soil Environment

@

plant specific
phytosiclerophore

Fe(III)

complex

Figure 2: Strategy II uptake. This represents the chelation based strategy of grasses where each species
puts out its own phytosiderophore which complexes with Fe3+ and then is transported back into the plant
via a phytosiderophore-iron transporter. (Adapted from Ma 2005)

Phytosiderophores
Phytosiderophores were first observed in rice by Takagi in 1976 (Takagi 1976; Bughio et al
2002). The chelation strategy is more efficient than the reduction strategy and allows grasses to survive
under more drastic iron deficiency conditions (Marschner et all 986).
Charlson and Shoemaker (2006) stated that because dicots, gymnosperms, and monocots (both
grass and non-grass species) show Strategy I physiology, and Strategy II is unique to grasses, it can be
postulated that during evolution either grasses gained Strategy II or all other plant species lost Strategy II.
They also saw conservation of the Strategy I genes among dicots, grasses, and a gymnosperm suggesting
that Strategy I may have been established in gymnosperms upon the appearance of flowering plants
(Charlson and Shoemaker 2006).
Grasses can grow via Strategy II because it is less pH dependent than Strategy I (Guerinot and Yi
1994). Phytosiderophores bind tightly to the sparingly soluble iron in the soil, and are then reabsorbed
into the roots, taking their chelated iron with them (Surridge 2001 ). The phytosiderophore system of iron
uptake resembles the siderophore system attributed to microorganisms. The affinity phytosiderophores

7

for Fe3+ is two to three orders of magnitude higher than for synthetic iron chelates such as FeEDDHA
while microbial sideophores such as ferrioxamine B have a higher affinity for iron.. One reason is that a
natural chelator is more stable than a synthetic chelator (Alam et al. 2005; Bocanegra et al. 2004;
Marschner et al 1987; Guerinot and Yi 1994; Marschner 1995). This strategy is clearly less sensitive to
pH than the reduction strategy, but there is a cost to synthesizing and releasing phytosiderophores because
they may or may not be recovered after release into the rhizosphere. However, there is a strong positive
correlation between the amounts of phytosiderophores released from graminaceous plants and the
resistance of those plants to iron deficiency (Guerinot 2001; Guerinot 2007; Takahashi et al. 2001).
The process of iron acquisition by Strategy II plants can be characterized by the biosynthesis of
phytosiderophores inside the roots, secretion of phytosiderophores into the rhizosphere, solubilization of
insoluble iron in soils by chelation of phytosiderophores, and the uptake of phytosiderophore-Fe3+
complexes by the roots (Ma 2005; Murata et al. 2006; Hiradate et al. 2007; Ma and Nomoto 1996). The
regulation of iron uptake in roots of iron deficient graminaceous species is induced at two levels increase in rates of release and uptake of the iron-phytosiderophores (Marschner et al. 1987).
Thermodynamic and kinetic considerations are equally important in the understanding of strategy II iron
acquisition based on subjects such as ligand affinity and the stability of complexes (Kraemer et al. 2006).
The iron-efficiency of Strategy II genotypes is essentially a function of the capacity of plant roots to
produce and release phytosiderophores in response of iron deficiency stress and how the
phytosiderophores are taken up. The phytosiderophores released by the roots in response to iron
deficiency form a complex with Fe3+ and contribute to increased uptake ofFe3+ in the chelated form. The
capacity to produce and release the phytosiderophores is genetically determined. Those plants that show
tolerance to iron chlorosis on calcareous soils have been found to be more efficient in release of
phytosiderophores (Sharma 2006).
Mugineic Acid

Mugineic acid was first identified as a phytosiderophore in barley and its analogues have since
been isolated and identified from various graminaceous species. All form water soluble 1: 1 complexes

8

with Fe3+ (Namba et al. 2007). Mugineic acid and its derivatives (i.e. other phytosiderophores) are
hexadentate ligands with aminocarboxylate and hydroxycarboxylate functional groups. The ligands are
synthesized by hydroxylation of nicotianamine from methionine (Kraemer et al. 2006). Iron deficiency
stress causes the amount of MAs secreted to increase dramatically and the amount of MAs secreted from
the roots of graminaceous plants determines the amount of tolerance to deficiency stress a plant has. For
example, rice secretes small amounts of MAs and is susceptible to iron deficiency, whereas barley
secretes relatively high levels of MAs and can tolerate iron deficiency (Hansen et al. 1996; Higuchi et al.
2001; Ishimaru et al. 2006; Guerinot 2007; Kim and Guerinot 2007). Wheat is also known to secrete
larger amounts of phytosiderophores than maize (Reichard et al. 2005).
MAs are synthesized from methionine and Met synthesis is associated with the Met cycle (Astolfi

et al. 2003; Connolly and Guerinot 2002; Ma 2005). The Met cycle is highly active in roots, allowing for
the increased demand of Met required for the synthesis ofMAs (Kobayashi et al. 2005). The family of
mugineic acids includes MA, 2'-deoxymugineic acid (DMA), 3-epihydroxymugineic acid (epi-HMA),
and 3-epihydroxy 2'-deoxymugineic acid (epi-HDMA) (Kim and Guerinot 2007; Curie and Briat 2003;
Ma and Nomoto 1993; Kawai et al. 1993). In oats, avenic acid A is biosynthesized from 2'deoxymugineic acid by cleavage of the azetidine ring (Ma 2005; Ma and Nomoto 1993). 3-hydroxy-2'deoxymugineic acid (HDMA) from L. perenne, and 2 '-hydroxyavenic acid A (HAVA) from P. pratensis
were the most recent phytosiderophores identified (Ueno et al. 2007). DMA has been shown to be
secreted from two cultivars of F. rubra (Rubina and Bamica) as well (Ma et al. 2003). Each grass
produces its own set of MA and production and secretion of MAs are increased in response to iron
deficiency (Kim and Guerinot 2007; Curie and Briat 2003; Ma and Nomoto 1993; Kawai et al. 1993).
The initial step in the production of MAs is the condensation of three molecules of S..adenosyl
methionine (SAM) to produce one molecule of nicotianamine (NA) (Curie and Briat 2003; Negishi et al.
2002; Roje 2006). SAM is the substrate of a variety of other reactions in plants that lead to the
biosyntehsis of ethylene, polyamines, nicotianamine, phytosiderophores, and biotin. SAM is the methyl
group donor in a wide variety of enzyme catalyzed reactions in plants. 0-, N-, and C-methyltransferases

9

are the three major families of methyltransferases based on the chemical nature of the substrate. Some
methyltransferases exhibit strict specificity for a single substrate; many others accept a broad range of
substrates (Roje 2006).
The general biosynthetic pathway of mugineic acid phytosiderophores begins with L-methionine
as stated above. S-adenosyl methionine synthase converts L-methionine to S-adenosyl methionine.
Nicotianamine synthase then converts the molecule to nicotianamine. Nicotianamine is converted to
3 'oxo intermediate by nicotianamine aminotransferase. Deoxymugineic acid synthase converts the
intermediate to 2'-deoxymugineic acid (OMA). From here, dioxygenases change OMA into other
phytosiderophores such as 3'-epihydroxy mugineic acid and 3'-epihydroxy-2-deoxymugineic acid
(Callahan et al. 2006; Sharma 2006; Suzuki et al. 2006; Bashir et al. 2006). Deoxymugineic acid
synthase (OMAS) is responsible for the synthesis of OMA by reduction of a 3"-keto intermediate. DMAS
was identified as a putative member of the aldo-keto reductase superfamily, upregulated under iron
deficient conditions as was studied in barley and rice (Bashir et al.2006; Briat 2008). The synthesis of
mugineic acids (MA) from methionine also induces the synthesis of ethylene in iron deficient plants.
Ethylene is a by-product in the MA synthesis pathway (Nilsen and Orcutt 1996).
Grasses are the only species that have the ability to convert nicotianamine (NA) to MA by way of
the enzyme nicotianamine aminotransferase (NAAT). NAAT activity is dramatically induced by iron
deficiency and suppressed by iron resupply (Briat 2008). Other genes involved in the biosynthesis of
phytosiderophores includes APRT (adeninephosphoribosyl transferase ), SAMS (S-adenosy }methionine
synthetase), NAS (NA synthase), NAA T (NA aminotrasferase), and iron deficiency specific clones IDS2
and IDS3 (Murata et al. 2006). Methionine recycling for the production of MAs occurs with the help of
the Yang cycle (Negishi et al. 2002). Iron deficiency tolerances depends on an increase in the activity of
both NAS and NAAT, which are also crucial for the enhanced secretion of MAs (Higushi et al. 200 I).
Higuchi et al (2001) showed that the concentration of NA in rice leaves is rather high and that
rice NAS synthase was induced under iron deficiency not only in roots but also in the leaves. Their
results suggest that rice NAS may have roles other than just the biosynthesis of MAs, such as transport

10

within the plant itself (Higuchi et al. 2001; Takahashi et al. 2001). Nicotianamine also appears to be
required for plant fertility. Flowers in iron deficient plants are abnormally shaped and pollen count is
usually lower. NA may function in long distance transport of iron to the reproductive organs and in other
cases as a scavenger of Fe2+ in order to prevent oxidative stress to the plant cells (Briat 2008; Callahan et

al. 2006).
Nicotianamine synthase is a key enzyme in MA biosynthesis, catalyzing three molecules of SAM
into one molecule of nicotianamine. NAS activity in graminaceous plants is well correlated with
tolerance to iron deficiency (Mizuno et al. 2003). NA has been shown to chelate Fe2+, in particular at a
higher pH, which may allow it to serve as an intracellular Fe2+ scavenger thereby protecting the cell from
Fe2+-mediated oxidative damage (Schaaf et al. 2004).
More specifically, the synthesis of nicotianamine from three molecules of SAM includes two
carboxypropyl group transfers and one azetidine ring formation, with three molecules of 5 ' rnethylthioadenosine (5'-MTA) released. All three reactions are catalyzed by the enzyme nicotianamine
synthase. In non-graminaceous plants, nicotianamine is thought to bind metal ions and to participate in
their trafficking inside the plant. In graminaceous plants, nicotianamine is also the precursor of
phytosiderophores, which are essential in acquiring iron from soil (Roje 2006; Romhelf and Schaaf 2004;
Bashir et al. 2006; Higuchi et al. 1999). Nicotianamine synthase (NAS) catalyzes the bonding of three Sadenosyl Met molecules to form nicotianarnine (NA), which is then converted to deoxymugineic acid by
an amino group transfer catalyzed by nicotianamine aminotransferase (NAA

n and subsequent reduction

at the 3 '-carbon of the keto acid (Bashir et al. 2006; Takahashi et al. 1999).
Phytosiderophore Secretion

Phytosiderophore secretion is known to follow a diurnal rhythm, being biosynthesized during the
day and accumulating within the roots until secretion the following morning (Connolly and Guerinot
2002; Ma 2005; Ueno et al. 2007; Reichman and Parker 2007). The trigger for phytosiderophore release
may be a response to some historical rather than current light conditions (Reichman and Parker 2007).
The amount ofbiosynthesis is dependent on the extent ofiron deficiency (Ma and Nomoto 1996).

11

Generally, plants start to secrete phytosiderophores every morning from the third hour after the sunrise or
the onset of the light period. The secretion continues for 3 hours. The timing of secretion is controlled by
the temperature around the root environment; when the temperature is high, the secretion occurs early,
while secretion is delayed when the temperature becomes low (Ma 2005; Ma and Nomoto 1996; Reichard
et al. 2005).
The diurnal rhythm of phytosiderophore secretion would be advantageous for iron acquisition
because more concentrated phytosiderophores could be released into the rhizosphere and microorganisms
that degrade phytosiderophores could not follow the elongation of root tips, thereby phytosiderophores
could persist longer and acquire more iron (Hiradate et al. 2007). The diurnal release of
phytosiderophores creates a strong nonsteady state with respect to the solution saturation state and surface
chemistry of the different iron oxides. These conditions then trigger fast iron oxide dissolution reactions
if other ligands, such as oxalate, citrate, or malate, are also present thereby releasing the iron to complex
with phytosiderophores (Kraemer et al. 2006). The apical root zones are the sites of phytosiderophore
release (Marschner et al. 1987). Under iron deficiency, plants can increase phytosiderophore release by
about 20 times. At the same time, the uptake rate increases by only about 5 times. This finding suggests
that the mechanisms for release and uptake of phytosiderophores are under separate genetic control
(Dakora and Phillips 2002).
In addition to phytosiderophores, Strategy II plants release other organic ligands as well. This
process could be a relic of any Strategy I mechanisms that may have remained with the plants during
evolution (Reichard et al. 2005). Following secretion, phytosiderophores solubilize soil iron by chelation,
forming a complex with iron at a ratio of 1: 1 (Ma 2005). Iron solubilization depends on chelation ability
and affinity (Ma and Nomoto 1996). Phytosiderophores can scavenge iron from a range of iron bearing
minerals and soluble iron species, which are the ultimate sources of iron in soils (Kraemer et al. 2006).
There is a change in the shape of the vesicles in root cells ofiron deficient plats that corresponds
to the diurnal secretion ofphytosiderophores. The vesicles stay swollen until the onset of
phytosiderophore secretion, and become shrunken by the end of secretion. These particular vesicles are

12

the sites of phytosiderophore synthesis and accumulate in the epidermal cells at the cell periphery facing
the rhizosphere just before sunrise (Negishi et al. 2002; Higuchi et al. 1999). These vesicles were found
to be covered with ribosomes and are thought to originate from the rough ER {Takahashi et al. 1999).
There is also an increase in the root hairs under iron deficiency conditions that could results in increased
root surface area and increased contact with soil iron. The conclusion was that this response is probably
advantageous to rapidly increase phytosiderophore release, since it was evident that the release and
biosynthesis of phytosiderophores are mainly localized in the apical root zone (Zhang et al. 2003).

Yellow Stripe 1
Fe3+-MA complexes are transported into the plant via specific plasma membrane transporters
located in the root (Connolly and Guerinot 2002; Kim and Guerinot 2007). Maize is the model grass
organism that has been used to characterize the Fe3+-MA transport system (Briat 2008). The yellow stripe
I (ysl) maize mutant showed a defect in uptake of iron-phytosiderophore complexes, resulting in iron

deficiency and plants developing interveinal chlorosis (yellow-stripe) (Kim and Guerinot 2007). Yellow
stripe I was first identified in 1929 by George W. Beadle, through its distinctive phenotype in which iron

deficiency leads to incomplete pigmentation of leaves showing up as alternating yellow and green stripes
running the length (Surridge 2001 ).
Curie et al (2001) found that YSl cDNA has the ability to allow growth of iron-deficient yeast
mutants on Fe-DMA in the presence ofBPDS, an iron-chelator, strongly suggesting that YSl is a
transporter of phytosiderophore-bound Fe3+ (Curie et al. 2001). YSJ encodes an iron phytosiderophore
transporter, an integral membrane protein with 12 putative transmembrane domains that belongs to the
oligopeptide transporter ( OPT) superfamily (Kim and Guerinot 2007; Surridge 2001; Briat 2008; Curie
and Briat 2003). The OPT family transports tri-, tetra-, penta-, and hexapeptides. It has also been noted
that since phytosiderophores and peptides are amino acid derivatives, and since all functionally
characterized members of the family function with inwardly directed polarity, all members of the OPT

family may function in the uptake of amino acid containing compounds and their derivatives (i.e.

13

phytosiderophores) (Yen et al. 2001 ). The gene also has an E rich N-terminal region containing a specific
motif (REG LE) known for its interaction with Fe3+ (Briat 2008).
In barley, the HvYSJ gene was cloned and the protein it encodes was shown to have the same
characteristics as Zm YSI, although it seemed to have a metal specificity restricted to Fe3+. In addition,
in situ hybridization analysis of iron deficient barley roots revealed that the HvYSl mRNA was localized

in epidermal root cells, as well as the protein as shown by immunohistological staining with an antiHvYSl polyclonal antibody (Briat 2008). HvYSI also belongs to the oligopeptide transporter (OPT)
family, which transports oligopeptides in sever&l organisms, including bacteria, archaea, fungi, and plants.
Hv YS 1 is the closest homo log to Zm YS 1 with 72. 7% identity and 95 .0% similarity (Murata et al. 2006).
The YS 1 transporter from maize also showed a broad specificity as it can transport various
phytosiderophore-bound metals such as zinc, copper, and nickel, and nicotianamine complexed with
nickel, ferrous (Fe2+) and ferric (Fe3 +) iron (Hiradate et al. 2007; Ma 2005; Murata et al. 2006). In spite of
low sequence similarity, Murata (2006) found that the N-terminal domains of both Hv YS I and Zm YS I
share the basic feature of being rich in glutamic and aspartic acid residues. Both proteins also have in this
region an EXXE sequence, which is a F e3+ binding motif in a signal transduction system that responds to
extracellular iron (Murata et al. 2006).
Rice, however, has the ability to transport ferric iron by the phytosiderophore-mediated Fe3+
mechanism, but also possesses an Fe2+ uptake system with the use of a root specific IRTl-like F e2+
transporter (Bughio et al. 2002). This system is unique because rice has adapted for growth under
submerged conditions, where Fe2+ is more abundant than Fe3+. Therefore, it is conceivable that Fe2+ is
taken up by rice in a similar fashion to non-graminaceous plants. This strategy might have evolved
specifically in rice plants because of the need to survive under submerged conditions, and growing well
under Fe2+-rich conditions, which are encountered in paddy fields (lshimaru et al. 2006; Kim and
Guerinot 2007).
To address whether YS 1 might be involved in uptake of metal micronutrients other than iron,
Roberts et al analyzed YS 1 gene and protein accumulation under conditions of metal deficiency. They

14

grew plants in modified Hoagland solution lacking iron, zinc, and copper. They found that Ysl
expression failed to increase under conditions of copper or zinc limitation and that this may be taken as
suggesting that YS 1 is not involved in the primary acquisition of these metals. It was also stated that
although YSI does not transport zinc phytosiderophore complexes, another yellow-stripe-like transporter
could be involved instead (Roberts et al. 2004).
Schaaf et al also observed in three different systems that Zm YSI-mediated Fe3+-DMA transport
depends on the availability of protons. They concluded that ZmYSl represents an W-Fe3+phytosiderophore cotransporter. Their investigation also uncovered another factor that contributes to
more efficient iron acquisition in grasses: coupling the transport ofiron-phytosiderophores, which are
negatively charged at neutral pH, to protons allows efficient root uptake even at high soil pH, because
transport of the proton-coupled substrate can be driven as long as the overall difference of the
electrochemical potential remains negative (Schaaf et al. 2004 ). Other metals thought to be transported
by ZmYSl include Cd and Mn (Hill et al. 2002).
Growth complementation and oocyte transport studies clearly showed that Zm YSI also transports
phytosiderophore-chelated Zn2+. Zm YS 1 also transported phytosiderophore-chelated nickel and copper at
a similar rate to iron and zinc (Schaaf et al. 2004). Barley was also investigated by Suzuki et al (2006) in
the phytosiderophore uptake of zinc. However, the assays used were indirect methods to measure the
amount of phytosiderophores and cannot distinguish mugineic acids from other metal chelating
substances. This could be one reason why there is conflicting data as to whether or not phytosiderophore
secretion increases under conditions of low zinc supply (Suzuki et al. 2006).
The sequence homology ofHvYSl and ZmYSl in the N-tenninal outer membrane regions and
the loops between the sixth and seventh transmembrane helices are significantly lower than the outer
regions. They also showed that residues 314-385 in Hv YS 1 are responsible for the higher selectivity of
Fe3+-DMA over Fe2+-NA. The suggestion by the authors was that the variable regions in the middle outer
membrane loops are essential and sufficient to define the transport specificity, whereas the N-tenninal
regions have no influence on the substrate specificity (Harada et al. 2007).

15

The variety of paralogs found within each family of transporters could be explained by at least
three reasons: 1) affinity to a specific minerall; 2) placement in organs or tissues; 3) placement in
subcellular compartments, such as vacuoles or plastids. Di:fferent iron carrier molecules may also explain
the diversity of iron transporter families in plants. The YSl protein, for example, transporters Fe3+
phytosiderophores, and possibly Fe2+-NA, structurally similar to phytosiderophores. Yellow stripe like
proteins are believed to mediate the uptake of metals that are complexed with nicotianamine and assist in
the long distance transport of metals within the plant. Other metals than iron may rely on yellow stripe
like proteins for transport into or within the plant itself (Chang et al. 1999; Colangelo and Guerinot 2006;
Gross et al. 2003).
One mechanism that is not understood is how plants sense iron and begin the processes of
retrieving iron from the soil. Once these components are identified, the iron deficiency response will be
better understood at the molecular level (Kim and Guerinot 2007).
The purpose of this project was to identify and characterize the iron phytosiderophore transporter
in Avena sativa. This species was selected because it produces a known phytosiderophore, avenic acid.
Upon isolation, the transporter was compared to Hv YS 1 and Zm YS 1 to determine similarity between the
sequences. The results from this project will enhance the understanding of iron-phytosiderophore
mediated transport among graminaceous species as this information is currently limited.

16

Experimental Procedure:

PiantGmwth:
Seedlings were grown in Hoagland's medium for approximately 10 days. Plants were then
transferred to distilled water (Figure 3) and grown until the appearance of yellowing on the leaves. Roots
(Figure 4) were harvested and flash frozen in liquid nitrogen. Harvested roots were stored at -80°C.

Figure 3: Oats grown hydroponically under iron deficient conditions.

Figure 4: Oat roots in iron deficient hydroponic solution.
RNA Isolation and c/gfilJJ!J2_:

RNA was isolated from ground, frozen oat root tissue using the PureLink™ Plant RNA Reagent
from Invitrogen. The reagent was added to ground, frozen plant tissue in order to lyse the cells. The

17

lysate was clarified by centrifugation. Addition of NaCl and chloroform separates the phases and RNA is
then precipitated with isopropyl alcohol. RNA samples were then cleaned by DNase and RNeasy
treatments.
Amplification Grade Dexoyribonuclease I from Sigma was used to digest double and single
stranded DNA. However, to be completely sure that the samples were free of contaminating DNA, the
RNeasy protocol from Quiagen was used as well. This kit utilizes a silica membrane that also removes
DNA from RNA samples; it will also remove the DNase that was used prior to the procedure. The
integrity of the RNA sample was verified by gel electrophoresis.
First Strand Synthesis and Amplification o{Specificity Region:
RNA was used in the Transcriptor First Strand cDNA Synthesis Kit by Roche to obtain cDNA.
A 20ul amplification using TITANIUM™ Taq PCR Kit from Clontech and the following primers was
performed:
Specificity region left: 5' -TTCGGTYTGAAGGCCTGGAAGCAGAC- 3'
Specificity region right: 5' -CCATGTTGATGTCGGTGARCCC- 3'
Gel verification provided visualization of the proper size fragment.
Ligation into Vector and Cloning ofSpecificity Region·
The TOPO TA Cloning® Kit for Sequencing by Invitrogen was used for sequencing preparations.
The PCR product was ligated to the TOPO® Vector and allowed to incubate for 5 minutes at room
temperature. One Shot® TOPl0 competent E.coli cells were used for chemical transformation. The
cloning reaction was added to cells that were transformed following protocol and then plated onto LB
plates containing 50ug/ml of ampicillin. Cells were grown overnight and white colonies were re-streaked
onto the same type of LB plates and allowed to grow overnight. PCR verification of insert using the same
protocol for the amplification of the specificity region. Colonies that showed insert were allowed to grow
overnight in LB broth containing ampicilllin.
Plasmid Isolation and Sequencing:

18

The QIAprep Spin kit from Qiagen was used to lyse bacterial cells, retrieve DNA, and prepared it
for sequencing.
Sequencing was performed by GENEWIZ, Inc., located in South Plainfield, NJ.
5' and 3' RACE

The specificity region was located approximately in the middle of the gene; therefore to obtain
the ends of the gene, 5' and 3' Rapid Amplification of cDNA Ends (RACE) was employed with the use
of the GeneRacer™ Kit from Invitrogen.
RACE amplifies full length 5' and 3' ends of cDNA using primers that were designed based on
the sequence from HvYSl. Total RNA is dephosphorylated, decapped, ligated to an RNA Oligo which
provides a known priming site, reverse transcribed with Superscript™ III RT and amplified using the
following primers:
Nested Primer: 5' - CGACACTGACATGGACTGAAGGAGTA - 3'
GSP2' Primer: 5' -CTGTACGCGATCCAAGCGGGGAGAT- 3'
It should be noted that between each step is an ethanol precipitation of the RNA. This step removes
excess salts from the sample that could be problematic in later reactions.
PCR Products were then cloned using the TOPO TA cloning kit mentioned above. The
sequences were sent to GENEWIZ for sequencing.
3' RACE was performed by cDNA amplification using the RT template obtained from the reverse
transcribing step of the protocol. Amplification was done using the GeneRacer™ 3' Primer and 3' RACE
Forward Primer:
GeneRacer 3' Primer: 5' - GCTGTCAACGATACGCTACGTAACG - 3'
3' RACE Primer: 5' - CGTGCTGAGCGTCGTTGCAGTGGT - 3'
PCR products were cloned into cells using the TOPO TA Cloning Kit from Invitrogen, protocol
listed above, and positive clones were sent to GENEWIZ for sequencing.
Agrostis stolonifera specificity region:

19

To check the diversity in the specificity region, Agrostis stolonifera (creeping bentgrass) was
used for a large scale RNA isolation followed by first strand synthesis and amplification using the
specificity primers listed above. No further analysis was perfonned on this species.
Primer Design

All primers not provided in kits were designed by analyzing HvYSl and its homologs. In
addition to HvYSl, ESTs from putative phytosiderophores from other grasses were also used in primer
design. Table I lists all primers used in the sequencing of the putative iron-phytosiderophore transporter
from A. sativa.

Table 1: Primers. Primers used to amplify the sequence of the iron-phytosiderophore transporter in A.
sativa.
Primer Name
Sequence
Amplification Area
Specificity Left

5' -TTCGGTYTGAAGGCCTGGAAGCAGAC - 3'

Specificity region

Specificity Right

5' -CCATGTTGATGTCGGTGARCCC-3'

Specificity region

GeneRacer 3'

5' - GCTGTCAACGATACGCTACGTAACG-3'

3'end

Avena Sativa 3' End

5' -CGTGCTGAGCGTCGTTGCAGTGGT- 3'

3'end

GeneRacer 5'

5' - CGACACTGACATGGACTGAAGGAGTA- 3'

5'end

5' - CTGTACGCGATCCAAGCGGGGAGAT- 3'

5'end

Primer

Nested Primer
GSP2'

Notes:

All PCR products were purified using the QIAquick Gel Extraction Kit.

20

Res_u/ts;_
Harada et al (2007) has shown that there is an area in HvYSl that confers higher specificity for iron over
the non-iron specific phytosiderophore transporter Zm YSl. This prompted the questioning of a specificity region
within the Avena sativa iron-phytosiderophore transporter. The DNA sequence that was first isolated from Avena
sativa was the putative specificity region utilizing the Specificity Primers listed in Table 1. A 533 base pair

sequence was retrieved. The pink colored region in Figure 10 represents the specificity region of the gene.
Nucleotide BLAST analysis yielded the best match as "Hordeum vulgare HvYSl mRNA for iron-phytosiderophore
transporter, complete eds", accession number AB214183. There was an 83% identity between the sequences.
Residues 793-1324 in Figure 11 represent this same region within the full gene BLAST analysis.
When translated, the product is 177 amino acids in length. The gold area in Figure 12 represents the
specificity region within the amino acid sequence. A protein BLAST reinforced the results of the nucleotide
BLAST; residues 265-441 of Figure 13 are the specificity area, reinforced by the pink area to further show the
diversity. A ClustalW2 analysis, Figure 14, further highlights the diversity in the specificity region, shown by the
area in green. In this type of analysis, the"*" represents an identical amino acid between the two sequences,":"
represents a conserved amino acid substitution, and"." represents a semi-conserved substitution. If none of those
three symbols is shown beneath the alignment, then the substitution shows no conservation between sequences.
Residues 265-441 of the ClustalW2 output represent the sequenced specificity region found in A. sativa.
The putative specificity region also contained a conserved domain, the Oligopeptide Transporter (OPT)
domain. This is expected because the gene is a membrane transporter found in the roots of A. sativa. This result is
published on GenBank under EU619717 and ACC77193
The specificity region of Agrostis stolonifera was also identified using the same primers that were involved
in the identification of the specificity region in A. sativa. Figure 5 shows the nucleotide sequence result from
Gene Wiz. The nucleotide BLAST in Figure 6 shows that the best match was the published specificity region of A.
sativa while Figure 7 shows the next best match as HvYSl. The protein sequence is 171 amino acids in length and

the highlighted area in Figure 8 shows A. stolonifera diversity area.

21

GGCCTGGAAGCAGAC ATTCTTCTTIGACTTTAGCATGACATATGTCGGTGCCGGGATGATITGCCC
GCATATAGTAAATATCTCCACCCTCCTTGGCGCAATTCTITCATACGGATTATTGTGGCCACTCATCAG
TAAGAACAAGGGGGATTGGTACCCTGCAAATGTACCAGAAAGCAGCATGAAAAGTTIGTACGGTTAC
AAGGCCTTCATATGTATCGCTCTGATCATGGGGGATGGACTCTACCACTTCACAAAAATTATTAGCAT
CACTTTIAAGGGCATGTATCGACAGTTIAGCCGTAAGCGCGTTGACAATCGAGTGAAAAATGTGGAC
AATACGGTCTCACTTGAGGATCTGCAGCGCGATGAGATCTTCGGAAAGGGCCATATCCCAGCTTGGAT
GGCTTACACTGGGTATGCCGTGTTAAGCGTCGTTGCGGTGGTTACCACGCCAATAATGTTIAGACAGG
TGAAATGGTACTACGTAGTTATAGCCTATATGGTCGCCCCCGTTCTTGGATTCGCCAATTCCTATGGG
ACAGGGCTCACCGACATCAACATGG
Figure S. Specificity Region of Agrostis stolonifera. The specificity region of A. stolonifera was sequences using
primers Specificity Left and Specificity Right. Primers are shown in red.
Avena sativa putative iron-phytosiderophore transporter mRNA, partial eds
Lengths=755
Score= 669 bits (362), Expect= 0.0, Identities= 471/523 (90%), Gaps= 10/523 (1%)
Strand=Plus/Plus
Agros

1

ATTCTTCTTTGACTTTAGCATGACATATGTCGGTGCCGGGATGATTTGCCCGCATATAGT

60

I II I I I I I I I I I II I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I

Avena

238

ATTCTTCTTTGACTTTAGCCTGACATATGTCGGTGCCGGGATGATTTGCCCACATATAGT

297

Agros

61

AAATATCTCCACCCTCCTTGGCGCAATTCTTTCATACGG-ATTATTGTGGCCACTCATCA

119

111111

11111111

11111

11111

11111

11

11

11

11111111111111111

Avena

298

AAATATATCCACCCTTCTTGGTGCAATCCTTTCTTATGGGAT-ATTGTGGCCACTCATCA

356

Agros

120

GTAAGAACAAGGGGGATTGGTACCCTGCAAATGTACCA-GAAAGCAGCATGAAAAGTTTG

178

11111111 I 1111

1111111111I111111111

I I 111111111111111111

11

Avena

357

GTAAGAACAAGGGTGATTGGTACCCTGCAAATGT-CAAAGAAAGCAGCATGAAAAGTCTG

415

Agros

179

TACGGTTACAAGGCCTTCATATGTATCGCTCTGATCATGGGGGATGGACTCTACCACTTC

238

11

I I I I I I I I I I I I I 11111111111111111111111111111111111111111111

Avena

416

TATGGTTACAAGGCCTTCATATGTATCGCTCTGATCATGGGGGATGGACTCTACCACTTC

475

Agros

239

ACAAAAATTATTAGCATCACTTTTAAGGGCATGTATCGACAGTTTAGC-CGTAAGCGCGT

297

Avena

476

ACCAAAATTATTACCATCACTTTCAAGGGCATGTATCGACAGTTTA-CTCGTAAACGTGC

534

Agros

298

TGACAATCGAGTGAAAAATGTGGACAATACGGTCTCACTTGAGGATCTGCAGCGCGATGA

357

11

1111111111

111111

1111

111111111

I I I I I l 1111111111111111

111111111111111 I I I I I I I I I 11

I 11111

11

I

111111111111111 I I I I

Avena

535

TGACAACCGAGAGAAAAATGTGGACAATACGGTCTCGCTCGAGGATCTGCAGCGCGACGA

594

Agros

358

GATCTTCG-GAAAGGGCCATATCCCAGCTTGGATGGCTTACACTGGGTATGCCGTGTTAA

416

I IIIII

I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I II I I I I I I l I I I

Avena

595

GGTCTTCAAGAA-GGGCCATATCCCCGCTTGGATGGCGTACAGTGGGTACGCCGTGTTGA

653

Agros

417

GCGTCGTTGCGGTGGTTACCACGCCAATAATGTTTAGACAGGTGAAATGGTACTACGTAG

476

I I I I I I I I I I I l I I I I I I I I I I I II I I I I I I

IIII IIIIIIIIIIIIII II I

Avena

654

GCGTCGTTGCAGTGGTGACCACGCCTATAATGTTCCGACAAGTGAAATGGTACTATGTTG

Agros

477

TTATAGCCTATATGGTCGCCCCCGTT-CTTGGATTCGCCAATT
I I I I I 1 I II I I I

Avena

714

713

518

I I I I I I I I I I I I I I I I I I I I II I I I

TTATAGCCTATGTCATCGCCCC-GATGCTTGGATTCGCCAATT

755

Figure 6. Nucleotide BLAST of A. stolonifera specificity region. Nucleotide BLAST results against A. sativa
specificity region.

22

Hordeum vulgare HvYSl mRNA for iron-phytosiderophore transporter, complete eds
Length=2430
Score= 508 bits (275), Expect
(2%)
Strand=Plus/Plus
Agros

1

8e-141, Identities= 453/539 (84%), Gaps= 12/539

ATTCTTCTTTGACTTTAGCATGACATATGTCGGTGCCGGGATGATTTGCCCGCATATAGT

60

I I I I I I I I I II I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I l I I I I I I I I
HvYSl

966

ATTCTACTTTGACTTTAGCATGACATACGTTGGTGCCGGGATGATTTGTCCACATATAGT

1025

Agros

61

AAATATCTCCACCCTCCTTGGCGCAATTCTTTCATACGGATTATTGTGGCCACTCATCAG

120

111111 11 I I I l 1111111 111111 I 1111

111 11 1111111111111111

HvYSl

1026

AAATATATCTACCCTCCTTGGTGCAATTATCTCATGGGGAATAATGTGGCCACTCATCAG

1085

Agros

121

TAAGAACAAGGGGGATTGGTACCCTGCAAATGTACCAGAAAGCAGCATGAAAAGTTTGTA

180

II I 11 11 11 I I I I I I 11 I I I I I I I I I I I I I 11 I 111 I I I I I I I I I I I I I I 11 I I I I I I
HvYSl

1086

TAAAAACAAGGGGGATTGGTACCCTGCAAAAGTACCAGAAAGCAGCATGAAAAGTTTGTA

1145

Agros

181

CGGTTACAAGGCCTTCATATGTATCGCTCTGATCATGGGGGATGG-ACTCTACCACTTCA

239

111111111111111111111 II

11111 11111111111111

I I 1111111111

HvYSl

1146

CGGTTACAAGGCCTTCATATGCATAGCTCTCATCATGGGGGATGGCA-TGTACCACTTCA

1204

Agros

240

CAAAAATTATTAGCATCACTTTTAAGGGCATGTATCGACAGTTTAGCCGTAAGC-GCGTT

298

HvYSl

1205

TAAAAATTGTTGGCATCACTGCTATGAGCATGTATCGGCAATTTAGCCACAAGCAG-GTT

1263

Agros

299

GACAATCGA-GTGAAAAATGTGGACAATACGGTCTCACTTGAGGA-TCTGCAGCGCGATG

356

1111111 II 11111111

IIII I I I

II

I 1111111111 II 1111111

1111 I Ill

I I I I II I I I I I I I I I I I I I 11 I I 111 I I I I I I 11 I I

HvYSl

1264

AACAA-CAAAGCAAAAAATGCGGACGACACTGTCTCGCTTGAGGAGT-TACACCGCCAGG

1321

Agros

357

AGATCTTCG-GAAAGGGCCATATCCCAGCTTGGATGGCTTACACTGGGTATGCCGTGTTA

415

1111111

II

Ill Ill 11111

1111111111

Ill 1111 111111 1111

HvYSl

1322

AGATCTTTAAGAGAGG-CCACATCCCCTCTTGGATGGCATACGCTGGTTATGCCTTGTTT

1380

Agros

416

AGCGT-CGTTGCGGTGGTTACCACGCCAATAATGTTTAGACAGGTGAAATGGTACTACGT

474

11111 I 1111 11111111 I

Ill 1111111 I Ill 11111 11111111 II

HvYSl

1381

AGCGTTC-TTGCAGTGGTTACAATACCAGTAATGTTCAAACAAGTGAAGTGGTACTATGT

Agros

475

AGTTATAGCCTATATGGTCGCCCCCGTTCTTGGATTCGCCAATTCCTATGGGACAGGGC

111111111111
HvYSl

1440

I II 111111

1439
533

I 11111111 11111111 II 1111111111

TGTTATAGCCTATGTCGTTGCCCCCATGCTTGGATTTGCCAATTCATACGGGACAGGGC

1498

Figure 7. Nucleotide BLAST of A. stolonifera specificity region. Nucleotjde BLAST results of A. stolonifera

specificity region against HvYSI.
MTYVGAGMICPHIVNISTLLGAILSYGLL WPLISKNKGDWYPANVPESSMKSL YGYKAFICIALIMGDGLY
HFTKilSIT
AVVTTPI
MFRQVKWYYVVIAYMVAPVLGFANSYGTG
Figure 8: Amino Acid sequence of A. stolonifera specificity region. The highlighted area shows the diversity
region of A. stolonifera specificity region. The sequence is 171 amino acids in length.

23

Another Clustal2W analysis was run on the specificity regions obtained from both A. sativa and A.
sto/onifera against the published protein sequences of Hv YS 1 and Zm YS 1. Figure 9 shows the results of this
analysis with the area of diversity once again highlighted. There is also a point in Zm YS 1 where it has a glycine
and no other sequences contain that particular amino acid, this is highlighted in green. It is a small amino acid, so it
may not change the 3-D structure of the protein very much. The sizes of the amino acids may play an important

role in the specificity of the transporter since the structure is altered. A future analysis on the protein crystal
structure would aid in determining why ZmYSl takes up additional metal-phytosiderophore chelates whereas
HvYSl only accepts iron-phytosiderophore chelates. A similar analysis would benefit A. sativa in determining the
iron specificity of the transporter.
Agrostis
Avena
HvYSl
ZmYSl

-----------------------------------MTYVGAGMICPHIVNISTLLGAILS
-----------------------------FFFDFSLTYIGAGMICPHIVNISTLLGAILS
SFFQWFYTGGDACGFVQFPTFGLKAWKQTFYFDFSMTYVGAGMICPHIVNISTLLGAIIS
SFFQWFYTGGEVCGFVQFPTFGLKAWKQTFFFDFSLTYVGAGMICSHLVNISTLLGAILS

25
296
297
300

:**:******.*:**********:*

Agrostis
Avena
HvYSl
ZmYSl

YGLLWPLISKNKGDWYPANVPESSMKSLYGYKAFICIALIMGDGLYH
YGILWPLISKNKGDWYPADVKESSMKSLYGYKAFICIALIMGDGLYH
WGIMWPLISKNKGDWYPAKVPESSMKSLYGYKAFICIALIMGDGMYH
WGILWPLISKQKGEWYPANIPESSMKSLYGYKAFLCIALIMGDGTYH

85
356
357
360

:*::******:**:****.: *************:********* **

Agrostis
Avena
HvYSl
ZmYSl

AVVTTPIMF
AVVTTPIMF
AVVTIPVMF
SAVIIPHMF
• *

Agrostis
Avena
HvYSl
ZmYSl

144
415
416
420

* **

RQVKWYYVVIAYMVAPVLGFANSYGTG--------------------------------RQVKWYYVVIAYVVAPMLGFANSYGTG--------------------------------KQVKWYYVVIAYVVAPMLGFANSYGTGLTDINMGYNYGKIALFVFAGWAGKENGVIAGLV
RQVKWYYVIVAYVLAPLLGFANSYGTGLTDINMAYNYGKIALFIFAAWAGRDNGVIAGLA

171
442
476
480

:*******::**::**:**********

Figure 9: Clustal Alignment of specificity regions and known transporters. Clustal2W analysis of
specificity regions of putative iron-phytosiderophore transporter in A. sativa, A. stolonifera, and published

phytosiderophore transporters HvYS 1 and ZmYS 1. Diversity region highlighted in gold.
The GeneRacer kit from Invitrogen was used to obtain the 5' and 3' ends of the gene using primers
designed to flank the specificity region that was obtained first. Using primers Avena 3' Primer and GeneRacer 3'
Primer listed in Table 1, the 3' end of the gene was isolated. An 808bp nucleotide sequence that corresponds to the
blue highlighted region in Figure 10 was sequenced. The best match was also "Hordeum vulgare HvYSl mRNA

24

for iron~phytosiderophore transporter, complete eds", accession number AB214183. An 86% identity between the
sequences was listed on the BLAST results. Nucleotides 1231-2024 in Figure 11 represent the 3' end of the
putative iron-phytosiderophore transporter in A. sativa.
The protein is a stretch of 268 amino acids shown in Figure 11 as a non-highlighted region towards the end
of the gene. The area in purple represents an overlap between the specificity region and the 3' end of the gene. The
protein BLAST also resulted in HvYSl as the best match with 88% identity between the sequences. Residues 409675 in Figure 12 represent the 3' end of the gene. Results of the protein BLAST were the conserved domains
COG1297 superfamily and the OPT binding domain. The OPT domain was also a result in the bioinformatics of
the specificity region. The COG1297 superfamily is listed as a predicted membrane protein with an unknown
function. This fact that the sequence is falling into this category is not surprising because the ironphytosiderophore transporter is located in the membrane of root cells of graminaceous species.
The Clustal2W analysis shows conservation between the putative iron-phytosiderophore transporter in
Avena and HvYSl as well as ZmYSl. This can be seen in Figure 14, residues 360-678.
As stated previously, there was an overlap between the sequences of the specificity region and 3' end of the
Avena gene. This overlap was approximately 100 bases and is shown in gold in Figure 10 and in purple in Figure
12 where the combined pieces gave a protein sequence that was 412 amino acids in length. The combined
sequences are 1,240 bases in length, approximately two-thirds of the gene.
The final portion that needed to be identified was the 5' end of the gene. The first set of sequences
produced a domain that was a methyltransferase and members of this family are SAM dependent
methyltransferases. This is not surprising because SAM is in the pathway that produces phytosiderophores.
Another domain was the dimerisation domain that is found at the N-terminus of a variety of plant 0methyltransferases. Although this is not the 5' end of the gene, it is something that would be found in the
biosynthetic pathway of phytosiderophores.
To isolate the 5' end of the gene, the 5' RACE Nested Primer and the GSP2' primer were used. A
nucleotide sequence approximately 800bp in length was obtained. Figure 10 shows this area in maroon and the
start codon is highlighted in turquoise. BLAST analysis came back with "Hordeum vulgare HvYSl mRNA for

25

iron-phytosiderophore transporter, complete eds", accession number AB214183 as the best match again. The
identity here was at 88%. Figure 11 shows the 5' area as nucleotides 1-800.
The protein sequence is 268 amino acids in length and the protein BLAST again revealed the presence of
COG1297 and OPT domains. The pink area in Figure 12 represents the amino acids of the 5' end of the gene as
well as the residues 1-263 of Figure 13, with the overlap against the specificity region in green. An 89% identity
with HvYSl resulted from the protein BLAST. The Clustal2W analysis in Figure 14 shows the 5' end of the A.

sativa gene as residues 1-286. There is also conservation in this area between the putative iron phytosiderophore
transporter and Hv YS 1 and Zm YS 1.

26

'\IGGACGTCCTGGGCCCTGACCGCACGCGGATCGCGCCGGAGATCGAGAAGCACGTGGCCGCGGAGG
GCGACAGGGAGTCTGACCCGGCGCTGGCCGCGGAGCGGGAGCTAGAGCCCCTGGGGCGGTGGCAGG
ACGAGCTGACCGTGCGGGGCATGGTGGCGGCGCTGCTCATCGGGTTCATCTACACCGTCATCGTCATG
AAGATCGCGCTCACCACCGGGCTGGTGCCCACCCTCAACGTCTCCGCCGCGCTGCTCTCCTTCCTCGC
GCTCCGCGGCTGGACGCGCTTGCTGGACCGCTTCGGCATCGTGTCCCGTCCCTTCACGCGGCAGGAGA
ACACCATCGTCCAGACCTGCGGCGTCGCCTGCTACACCATCGCGTTCGCCGGTGGCTTCGGGTCAACC
TTGCTGGGTCTAAACAAGAACACGTACGAGCTGGCCGGCGACTCGCCGGGCAACGGGCCGGGGAGCT
ACAAGGAGCCAGGGATTGGCTGGATGACGGCATTCCTCTTTTCTTGCAGCTTCGGGGGGCTCCTCACC
TTGATTCCCCTTAGACAGGTATTGGTCGTGGACTATAAATTAGTGTACCCAAGTGGGACGGCAACTGC
TGTTCTTATA,~~CGGATTTCATACCGCTCAAGGAGACAAGAACTCCAGGAAGCAAATCCGTGGGTTCT
TGAAGTACTTCGGGGGTAGCTTTTTATGGAGCTTCTTCCAGTGGTTCTACACCGGCGGCGACGTTTGT
GGGTTCATTCAGTTCCCTACTTTTGGTCTCAAGGCCTGGAAGCAGAC

,\ (_ ( \ ( ( ' ( ( \ \

\ \ I ( I ! ! ( (_ ( \ ( \ \ (

I { l \

\

\

I I '( ' I \ (

\( ('I \('I f \ I \(

GCTATAACTATGG
CAAGATAGGGCTCTTCGTCTTCGCGGGTTGGGCTGGCAGGGACAATGGTGTCGTTGCAGGTCTGGTTG
TTGGTACATGTGTGAAGCAGCTGGTGCTGATATCTGCAGATTTGATGCAAGACTTCAAGACGAGTTAT
CTCACTAAGACATCACCAAGATCCATGATGGTGGCACAGGCAATTGGGACAGCCATGGGCTGCGTTG
TCTCTCCCCTTACGTTCATGCTCTTCTACAGGGCATTTGATATTGGCAATCCAGATGGTACCTGGAAGG
CACCGTATGCACTGATATACCGTAATATGGCAATACTCGGTGTGGAGGGCTTCTCAGTACTGCCCAAG
TATTGCCTGGCACTCTCTGGTGGATTTTTCGCGTTTGCAGCAATCCTCAGCATAGCAAGAGATTTCATG
CCGCATAGGTATAGGCAGTATGTGCCCCTGCCAATGGCGATGGCGGTTCCATTCCTTGTCGGCGGGAG
CTTTGCGATTGATATGTGTGTCGGGAGTTTGGTGGTTTTTATCTGGAACAAGATAAACAAGAAGGAGG
CCGGCTTCATGGTCCCTGCAGTTGCATCCGGTTTGATATGTGGGGATGGGATATGGACATTCCCTTCG
TCCATACTTGCTCTTGCCAAGATTACACCACCAATTTGCATGAAGTTTACACCTGCACCCTAG
Figure 10. Full gene analysis, Nucleotide sequence. The full gene analysis of A. sativa putative ironphytosiderophore transporter. Turquoise = start codon; maroon = 5' end; green = overlap between 5' end and
specificity region; pink= specificity region; gold= overlap between specificity region and 3' end; blue = 3' end of
gene; red = stop codon.

27

Hordeum vulgare HvYSl mRNA for iron-phytosiderophore transporter, complete eds
Length=2430
Score= 2165 bits (1172), Expect
(2%)
Strand=Plus/Plus
Avena

1

HvYSl
Avena

0.0, Identities

1763/2048 (86%), Gaps

42/2048

169

ATGGACGTCCTGGGCCCTGACCGCACGCGGATCGCGCCGGAGATCGAGAAGCACGTGGCC
f I I I I I I I I I I I I I I I I II I I I I I I I I I I I I I I I I I I I I I I I I I I I I I II I
ATGGACATCGTCGCCCCGGACCGCACGCGGATCGCGCCGGAGATCGACAGGGACGAGGCC

228

61

GC-GGAGGGCGACAGGGAGTCTGACCCGGCGCT-G-G-C--CGCG-GAGCGGGAGCTAGA

113

I 111111111111111111 11111111111

I I I

1111 Ill II

60

1111 II

HvYSl

229

-CTGGAGGGCGACAGGGAGTCGGACCCGGCGCTGGCGTCGACGCGCGAGTGGCAGCTGGA

287

Avena

114

GCCCCTGGGGCGGTGGCAGGACGAGCTGACCGTGCGGGGCATGGTGGCGGCGCTGCTCAT

173

I

I II

11111111111111111111 111111111

1111111111111111111

HvYSl

288

GGACATGCCACGGTGGCAGGACGAGCTGACGGTGCGGGGCCTGGTGGCGGCGCTGCTCAT

347

Avena

174

CGGGTTCATCTACACCGTCATCGTCATGAAGATCGCGCTCACCACCGGGCTGGTGCCCAC

233

1111111111111111111111111111111 f 1111111111111

11111111111111

HvYSl

348

CGGGTTCATCTACACCGTCATCGTCATGAAGATCGCGCTCACCACGGGGCTGGTGCCCAC

407

Avena

234

CCTCAACGTCTCCGCCGCGCTGCTCTCCTTCCTCGCGCTCCGCGGCTGGACGCGCTTGCT

293

II

l l l l l l l l l l l l l l l l l l l l l l l l l l l l l 11111111111

111111111 1111

HvYSl

408

GCTGAACGTCTCCGCCGCGCTGCTCTCCTTCCTGGCGCTCCGCGGGTGGACGCGCCTGCT

467

Avena

294

GGACCGCTTCGGCATCGTGTCCCGTCCCTTCACGCGGCAGGAGAACACCATCGTCCAGAC

353

111 111111111 1111111111 11111111111111111111111111111111111
HvYSl

468

GGAGCGCTTCGGCGTCGTGTCCCGCCCCTTCACGCGGCAGGAGAACACCATCGTCCAGAC

527

Avena

354

CTGCGGCGTCGCCTGCTACACCATCGCGTTCGCCGGTGGCTTCGGGTCAACCTTGCTGGG

413

111111111 II

11111111111111111 11111111 11111111111111111111

HvYSl

528

CTGCGGCGTGGCATGCTACACCATCGCGTTTGCCGGTGGGTTCGGGTCAACCTTGCTGGG

587

Avena

414

TCTAAACAAGAACACGTACGAGCTGGCCGGCGACTCGCCGGGCAACGGGCCGGGGAGCTA

473

II

11111111 11111111111111111 1111111111111111 Ill

II

till

HvYSl

588

CCTGAACAAGAAGACGTACGAGCTGGCCGGTGACTCGCCGGGCAACGTGCCCGGAAGCTG

647

Avena

474

CAAGGAGCCAGGGATTGGCTGGATGACGGCATTCCTCTTTTCTTGCAGCTTCGGGGGGCT

533

11111111111111 1111111111111

111111

I

1111111111111111

II

HvYSl

648

GAAGGAGCCAGGGATAGGCTGGATGACGGGGTTCCTCCTCGCTTGCAGCTTCGGGGGCCT

707

Avena

534

CCTCACCTTGATTCCCCTTAGACAGGTATTGGTCGTGGACTATAAATTAGTGTACCCAAG

593

111111 1111111 It 11

111111111 1111111 11111

t 1111111

11111111

HvYSl

708

CCTCACTTTGATTCCCCTGAGACAGGTACTGGTCGTCGACTACAAATTAGTTTACCCAAG

767

Avena

594

TGGGACGGCAACTGCTGTTCTTATAAACGGATTTCATACCGCTCAAGGAGACAAGAACTC

653

I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I II I I I I I I I I I I I I II I I I I I I
HvYSl

768

TGGGACTGCAACTGCTATTCTTATAAACGGGTTCCATACCGATCAAGGGGACAAGAATTC

827

Avena

654

CAGGAAGCAAATCCGTGGGTTCTTGAAGTACTTCGGGGGTAGCTTTTTATGGAGCTTCTT

713

II
HvYSl

828

11111111111111 Ill

1111

11111 111111111111 I 11111 11111

AAGAAAGCAAATCCGTGGATTCCTGAAATACTTTGGGGGTAGCTTTCTGTGGAGTTTCTT

887

28

Avena

714

HvYSl

888

Avena

774

HvYSl

948

Avena

834

HvYSl

1008

Avena

892

HvYSl

1065

Avena

950

HvYSl

1124

Avena

1010

HvYSl

1184

Avena

1068

HvYSl

1242

Avena

1127

HvYSl

1301

Avena

1186

HvYSl

1360

Avena

1244

HvYSl

1418

Avena

1304

HvYSl

1478

Avena

1364

HvYSl

1538

Avena

1424

HvYSl

1598

Avena

1483

HvYSl

1657

CCAGTGGTTCTACACCGGCGGCGACGTTTGTGGGTTCATTCAGTTCCCTACTTTTGGTCT
111 11111111111 11 11111 I 111111 11
1111111111 11111 111 I
CCAATGGTTCTACACTGGAGGCGATGCTTGTGGATTTGTTCAGTTCCCAACTTTCGGTTT

773

CAAGGCCTGGAAGCAGACGTTCTTCTTTGACTTTAGCCTGACATACATCGGTGCCGGGAT
I I I I I I I l I I l I I I I I I 111 I 1111111111111 11111111 I 11111111111
GAAGGCCTGGAAGCAGACATTCTACTTTGACTTTAGCATGACATACGTTGGTGCCGGGAT

833

GATCTGCCCACATATAGTAAATATCTCCACCCTC-TTGGGTGCAATTCTTTCTTATGGGI I I I I I 11 I I I I I I I I 11 I I I I I I I I I I I I I I I I II I I I I I I I I I I I I I
GATTTGTCCACATATAGTAAATATATCTACCCTCCTTGG-TGCAATTATCTC--ATGGGG

891

A-TATTGTGGCCACTCATCAGTAAGAACAAGGGTGACTGGTACCCTGCAGATGT-CAAAG
I I I I I I II I I II I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I
AATAATGTGGCCACTCATCAGTAAAAACAAGGGGGATTGGTACCCTGCAAAAGTACCA-G

949

947

1007

1064

1123

AAAGCAGCATGAAAAGTTTGTACGGTTACAAGGCCTTCATATGCATCGCTCTGATCATGG
1111111111111111111111111111111111111111111111 11111 1111111
AAAGCAGCATGAAAAGTTTGTACGGTTACAAGGCCTTCATATGCATAGCTCTCATCATGG

1009

GGGATGG-ACTCTACCACTTCACCAAAATTATTACCATCACTTGCAAGG-GCATGTATCG
I I I I I I I I I 111 I I I I I I I
IIIIII II
I I I I I I I I I I I I I I I I I II I I
GGGATGGCA-TGTACCACTTCATAAAAATTGTTGGCATCACT-GCTATGAGCATGTATCG

1067

ACAGTTCAGCCGTAAACATGCTGACAACCGAG-AGAAAAATGTGGACAATACAGTCTCAC
II I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I
GCAATTTAGCCACAAGCAGGTTAACAACAAAGCA-AAAAATGCGGACGACACTGTCTCGC

1126

1183

1241

1300

TCGAGGATTTGCAGCGCGACGAGGTCTTCAAGAGGGGCCATC-TCCCCGCTTGGATCGCG
I 11111 II II Ill I Ill 1111 11111 11111 I 11111 1111111 II
TTGAGGAGTTACACCGCCAGGAGATCTTTAAGAGAGGCCA-CATCCCCTCTTGGATGGCA

1185

TACAG-TGGGTATGCCGTGCTGAGCGT-CGTTGCAGTGGTTACCACGCCAATAATGTTCC
Ill I Ill 111111 II I 11111 I l l l l l l l l l l l l l I Ill 11111111
TAC-GCTGGTTATGCCTTGTTTAGCGTTC-TTGCAGTGGTTACAATACCAGTAATGTTCA

1243

GACAAGTGAAATGGTACTACGTAGTTATAGCCTATGTCGTCGCCCCCATGCTTGGATTCG
111111111 11111111 II l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l I
AACAAGTGAAGTGGTACTATGTTGTTATAGCCTATGTCGTTGCCCCCATGCTTGGATTTG

1303

1359

1417

1477

CCAATTCCTACGGGACGGGGCTCACCGACATCAACATGGGCTATAACTATGGCAAGATAG
1111111 11111111 11111 l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l l I
CCAATTCATACGGGACAGGGCTTACCGACATCAACATGGGCTATAACTATGGCAAGATCG

1363

GGCTCTTCGTCTTCGCGGGTTGGGCTGGCAGGGACAATGGTGTCGTTGCAGGTCTGGTTG
11111 11111 11111 11111 11 I
II l l l l l l l l l 1111 II II 1111
CTCTCTTTGTCTTTGCGGGATGGGCCGGTAAAGAGAATGGTGTCATTGCCGGCCTTGTTG

1423

TTGGTACATGTG-TGAAGCAGCTGGTGCTGATATCTGCAGATTTGATGCAAGACTTCAAG
I I I I I I I I I I I I I I I I I I I I I I II I I I I I I I I I I I I I I I I I I II I I I I I I
CTGGCACCT-TGGTTAAGCAGTTGGTGCTTATCTCTGCCGATTTGATGCAAGACTTCAAG

1482

ACGAGTTATCTCACT-AAGACATCACCAAGATCCATGATGGTGGCACAGGCAATTGGGAC
11111111 111111 II 1111111111 1111111111 I 11111 I
1111 ti
ACGAGTTACCTCACTCAA-ACATCACCAAAATCCATGATGATTGCACAAGTTGTTGGAAC

1537

1597

1656
1541
1715

29

Avena

1542

HvYSl

1716

Avena

1602

HvYSl

1776

Avena

1662

HvYSl

1836

Avena

1720

HvYSl

1894

Avena

1779

HvYSl

1953

Avena

1839

HvYSl

2013

Avena

1898

HvYSl

2072

Avena

1958

HvYSl

2132

Avena

2018

AGCCATGGGCTGCGTTGTCTCTCCCCTTACGTTCATGCTCTTCTACAGGGCATTTGATAT
111111111 111 1111111 11111 1111111111111111111 111111111111
AGCCATGGGTTGCATTGTCTCCCCCCTCACGTTCATGCTCTTCTACAAGGCATTTGATAT

1601

TGGCAATCCAGATGGTACCTGGAAGGCACCGTATGCACTGATATACCGTAATATGGCAAT
111 11 11111111111 11111111111 11111111 11 I 11111 I I 111111111
TGGTAACCCAGATGGTACTTGGAAGGCACCTTATGCACTCATATACCGCAATATGGCAAT

1661

ACTCGGTGTGGAGGGCTTCTCAGTACTGCCCAAGTATTGCCT-G-GCACTCTCTGGTGGA
111 11111111111111111 11
1111 111111111 I I I I I 11 111111
ACTTGGTGTGGAGGGCTTCTCGGTGTTGCCGAAGTATTGCATCGTG-A-TATCCGGTGGA

1719

TTTTTCGCGTTTGCAGCAATCCTCAGCATAGCAAGAGATTTCATGCCGCATAGGTATAG11111111 I 1111 11 11
I 11 111 11111111 1111111 11 I 1111 I
TTTTTCGCCTTTGCGGCGATTTTAAGTATAACAAGAGATGTCATGCCCCACAAGTAT-GC

1778

GCAGTATGTGCCCCTGCCAATGGCGATGGCGGTTCCATTCCTTGTCGGCGGGAGCTTTGC
I IIIIIIIIIIIIIIIIIIIIII 11111 11111111111111 II 11111111111
GAAGTATGTGCCCCTGCCAATGGCAATGGCAGTTCCATTCCTTGTAGGTGGGAGCTTTGC

1838

GATTGATATGTGTGTCGGGAGTTTGGTGGTTTTTATC-TGGAACAAGATAAACAAGAAGG
11111111111
11111111111 I 111111
I 1111 11111111111111111
TATTGATATGTGCCTCGGGAGTTTGATAGTTTTTG-CATGGACCAAGATAAACAAGAAGG

1897

AGGCCGGCTTCATGGTCCCTGCAGTTGCATCCGGTTTGATATGTGGGGATGGGATATGGA
I I I I I I I I I 11 111 I I I I I I I I I I 11 I I I I I I I I I I I I I I I I I I I I I I I I I I I I I
AGGCTGGCTTCATGGTGCCTGCGGTTGCATCCGCTTTGATATGTGGGGATGGCATATGGA

1957

CATTCCCTTCGTCCATACTTGCTCTTGCCAAGATTACACCACCAATTTGCATGAAGTTTA
I 111111 I 11111 1111 I 11111111111111 1111111111111111111111
CGTTCCCTGCTTCCATTCTTGCTCTTGCCAAGATTAAACCACCAATTTGCATGAAGTTT-

2017

1775

1835

1893

1952

2012

2071

2131

2190

C-ACCTGC 2024
I 111111
HvYSl 2191 CTACCTGC 2198
Figure 11: Full gene nucleotide BLAST of Avena iron phytosideropbore putative transporter. Full nucleotide
BLAST of A. sativa putative iron phytosiderophore transporter. 1-800 represents the 5' end, 793-1324 represents
the specificity region, 1231-2024 represents the 3' end of the gene.

'vlDVLGPDRTRIAPf:.IEKHVAALGDRcSDPALAAI,RI'.Lf-:Pl GRWQDf,LTVRGMVAAl l lGFiYTVI VMK!Al
r Hr! VPTI '\JV'-AALl ~FLAl RGWTRl I DRFGIYSRPF l'ROFNTIYOTCGVACY r (AJ'.. AGGF'(;~l Ll (d NK '1 r
1 ELAGDSPG~GPGSYKEPGIGWYI I AH FSCSFGGL l 1 Li Pl RQVI YVDYKL YYPSG l'A I A YLlNGFHTAQCi
Dh.'\i~RKOIRGFl KYFGGSrtw-::HQWFYTGGDVCGFIOF'PTFCil KA WK Q"I FF I >I \I 'ill \(,\11( l'I 1 1\ \ I
'y(,

\ )'\RI

! ','-!·

;,~',1'<,

)',\'if>\ )\i,.

,,'\H,'-.i ,,.,,, \ill

\l''\h."il I \11

1

l~-1 "If( [

11\I\K_(l1

r-. '\\ )

LTDINMGYNYGK.IGLFVF AGWAGRDNGVV AGL VVGTCVKQLVLISADLMQDFK
TSYLTKTSPRSMMVAQAIGTAMGCVVSPLTFMLFYRAFDIGNPDGTWKAPY ALIYRNMAILGVEGFSVLP
KYCLALSGGFF AF AAILSIARDFMPHRYRQYVPLPMAMAVPFLVGGSF AIDMCVGSLVVFIWNK.INKKEA
GFMVPAVASGLICGDGIWTFPSSILALAK.ITPPICMKFTPAP
Figure 12: Full gene protein analysis of putative Avena iron phytosiderophore transporter.

30

iron-phytosiderophore transporter [Hordeum vulgare subsp. vulgare]
Length=678
Score= 1230 bits (3182), Expect= 0.0, Method: Compositional matrix adjust.
Identities= 583/677 (86%), Positives= 633/677 (93%), Gaps= 2/677 (0%)
Avena

1

HvYSl

1

Avena

59

HvYSl

61

Avena

119

HvYSl

121

Avena

179

HvYSl

181

Avena

239

HvYSl

241

Avena

299

HvYSl

301

Avena

359

HvYsl

361

Avena

419

HvYSl

421

Avena

479

HvYSl

481

Avena

539

HvYSl

541

Avena

599

HvYSl

601

Avena

659

HvYSl

661

MDVLGPDRTRIAPEIEKHVAAEGDRESDPALAAERE--LEPLGRWQDELTVRGMVAALLI
MD++ PDRTRIAPEI++ A EGDRESDPALA+ RE LE+ RWQDELTVRG+VAALLI
MDIVAPDRTRIAPEIDRDEALEGDRESDPALASTREWQLEDMPRWQDELTVRGLVAALLI

58

GFIYTVIVMKIALTTGLVPTLNVSAALLSFLALRGWTRLLDRFGIVSRPFTRQENTIVQT
GFIYTVIVMKIALTTGLVPTLNVSAALLSFLALRGWTRLL+RFG+VSRPFTRQENTIVQT
GFIYTVIVMKIALTTGLVPTLNVSAALLSFLALRGWTRLLERFGVVSRPFTRQENTIVQT

118

CGVACYTIAFAGGFGSTLLGLNKNTYELAGDSPGNGPGSYKEPGIGWMTAFLFSCSFGGL
CGVACYTIAFAGGFGSTLLGLNK TYELAGDSPGN PGS+KEPGIGWMT FL +CSFGGL
CGVACYTIAFAGGFGSTLLGLNKKTYELAGDSPGNVPGSWKEPGIGWMTGFLLACSFGGL

178

LTLIPLRQVLVVDYKLVYPSGTATAVLINGFHTAQGDKNSRKQIRGFLKYFGGSFLWSFF
LTLIPLRQVLVVDYKLVYPSGTATA+LINGFHT QGDKNSRKQIRGFLKYFGGSFLWSFF
LTLIPLRQVLVVDYKLVYPSGTATAILINGFHTDQGDKNSRKQIRGFLKYFGGSFLWSFF

238

QWFYTGGDVCGFIQFPTFGLKAWKQTFFFDFSLTYIGAGMICPHIVNISTLLGAILSYGI
QWFYTGGD CGF+QFPTFGLKAWKQTF+FDFS+TY+GAGMICPHIVNISTLLGAI+S+GI
QWFYTGGDACGFVQFPTFGLKAWKQTFYFDFSMTYVGAGMICPHIVNISTLLGAIISWGI

298

LWPLISKNKGDWYPADVKESSMKSLYGYKAFICIALIMGDGLYHFTKIITITCKGMYRQF
+WPLISKNKGDWYPA V ESSMKSLYGYKAFICIALIMGDG+YH
MWPLISKNKGDWYPAKVPESSMKSLYGYKAFICIALIMGDGMYHFIKIVGITAMSMYRQF

358

60

120

180

240

300

360

SRKHADNREKNVDNTVSLEDLQRDEVFKRGHLPAWIAYSGYAVLSVVAVVTTPIMFRQVK 418
AVVT P+MF+QVK '
SHKQVNNKAKNADDTVSLEELHRQEIFKRGHIPSWMAYAGYALFSVLAVVTIPVMFKQVK 420
WYYVVIAYVVAPMLGFANSYGTGLTDINMGYNYGKIGLFVFAGWAGRDNGVVAGLVVGTC
WYYVVIAYVVAPMLGFANSYGTGLTDINMGYNYGKI LFVFAGWAG++NGV+AGLV GT
WYYVVIAYVVAPMLGFANSYGTGLTDINMGYNYGKIALFVFAGWAGKENGVIAGLVAGTL

478

VKQLVLISADLMQDFKTSYLTKTSPRSMMVAQAIGTAMGCVVSPLTFMLFYRAFDIGNPD
VKQLVLISADLMQDFKTSYLT+TSP+SMM+AQ +GTAMGC+VSPLTFMLFY+AFDIGNPD
VKQLVLISADLMQDFKTSYLTQTSPKSMMIAQVVGTAMGCIVSPLTFMLFYKAFDIGNPD

538

GTWKAPYALIYRNMAILGVEGFSVLPKYCLALSGGFFAFAAILSIARDFMPHRYRQYVPL
GTWKAPYALIYRNMAILGVEGFSVLPKYC+ +SGGFFAFAAILSI RD MPH+Y +YVPL
GTWKAPYALIYRNMAILGVEGFSVLPKYCIVISGGFFAFAAILSITRDVMPHKYAKYVPL

598

PMAMAVPFLVGGSFAIDMCVGSLVVFIWNKINKKEAGFMVPAVASGLICGDGIWTFPSSI
PMAMAVPFLVGGSFAIDMC+GSL+VF W KINKKEAGFMVPAVAS LICGDGIWTFP+SI
PMAMAVPFLVGGSFAIDMCLGSLIVFAWTKINKKEAGFMVPAVASALICGDGIWTFPASI

658

LALAKITPPICMKFTPA
LALAKI PPICMKF PA
LALAKIKPPICMKFLPA

480

540

600

660

675
677

Figure 13: Full Gene Protein BLAST of putative Avena transporter. Protein BLAST of A. sativa putative iron-

phytosiderophore transporter against best match HvYSl. Specificity area shown in pink.

31

Avena
HvYSl
ZmYSl

MDVLGPDRTRIAP---EIEKHVAAEGDRESDPALAAER--ELEPLGRWQDELTVRGMVAA 55
MDIVAPDRTRIAP---EIDRDEALEGDRESDPALASTREWQLEDMPRWQDELTVRGLVAA 57
MDLARRGGAAGADDEGEIERHEPAPEDMESDPAAAREKELELERVQSWREQVTLRGWAA 60
* ***** *
**:
*
**:
·**
*:: :*:**:***

Avena
HvYSl
ZmYSl

LLIGFIYTVIVMKIALTTGLVPTLNVSAALLSFLALRGWTRLLDRFGIVSRPFTRQENTI 115
LLIGFIYTVIVMKIALTTGLVPTLNVSAALLSFLALRGWTRLLERFGWSRPFTRQENTI 117
LLIGFMYSVIVMKIALTTGLVPTLNVSAALMAFLALRGWTRVLERLGVAHRPFTRQENCV 120
*****:*:**********************::*********:*:*:*:. ********

Avena
HvYSl
ZmYSl

VQTCGVACYTIAFAGGFGSTLLGLNKNTYELAGDSPGNGPGSYKEPGIGWMTAFLFSCSF 175
VQTCGVACYTIAFAGGFGSTLLGLNKKTYELAGDSPGNVPGSWKEPGIGWMTGFLLACSF 177
IETCAVACYTIAFGGGFGSTLLGLDKKTYELAGASPANVPGSYKDPGFGWMAGFVAAISF 180
::**.********.**********:*:****** **.* ***:*:**:***:.*: : **

Avena
HvYSl
ZmYSl

GGLLTLIPLRQVLWDYKLVYPSGTATAVLINGFHTAQGDKNSRKQIRGFLKYFGGSFLW 235
GGLLTLIPLRQVLWDYKLVYPSGTATAILINGFHTDQGDKNSRKQIRGFLKYFGGSFLW 237
AGLLSLIPLRKVLVIDYKLTYPSGTATAVLINGFHTKQGDKNARMQVRGFLKYFGLSFVW 240
***:*****:***:****.********:******* *****:* *:******** **:*

Avena
HvYSl
ZmYSl

SFFQWFYTGGDVCGFIQFPTFGLKAWKQTFFFDFSLTYIGAGMICPHIVNISTLLGAILS 295
SFFQWFYTGGDACGFVQFPTFGLKAWKQTFYFDFSMTYVGAGMICPHIVNISTLLGAIIS 297
SFFQWFYTGGEVCGFVQFPTFGLKAWKQTFFFDFSLTYVGAGMICSHLVNISTLLGAILS 300
**********:.***:**************:****:**:******.*:**********:*

Avena
HvYSl
ZmYSl

YGILWPLISKNKGDWYPADVKESSMKSLYGYKAFICIALIMGDGLY
WGIMWPLISKNKGDWYPAKVPESSMKSLYGYKAFICIALIMGDGMY '
WGILWPLISKQKGEWYPANIPESSMKSLYGYKAFLCIALIMGDGTY _ _ __
:**:******:**:****.: *************:********* *** *· ·*
r

Avena
HvYSl
ZmYSl

,I

,

r•·

;.,:

::*:*:

*:

*

*:

:*::*:*:*:*

* :*:* **:***

:*:

*

)

'•,•:1

'
,;

'

I~

355
357
360

PIMF 414
PVMF 416
PHMF 420
* **

Avena
HvYSl
ZmYSl

RQVKWYYWIAYWAPMLGFANSYGTGLTDINMGYNYGKIGLFVFAGWAGRDNGWAGLV 474
KQVKWYYWIAYWAPMLGFANSYGTGLTDINMGYNYGKIALFVFAGWAGKENGVIAGLV 476
RQVKWYYVIVAYVLAPLLGFANSYGTGLTDINMAYNYGKIALFIFAAWAGRDNGVIAGLA 480
:*******::***:**:****************.******.**:**.***::***:***

Avena
HvYSl
ZmYSl

VGTCVKQLVLISADLMQDFKTSYLTKTSPRSMMVAQAIGTAMGCWSPLTFMLFYRAFDI 534
AGTLVKQLVLISADLMQDFKTSYLTQTSPKSMMIAQWGTAMGCIVSPLTFMLFYKAFDI 536
GGTLVKQLVMASADLMHDFKTGHLTMTSPRSLLVAQFIGTAMGCWAPLTFLLFYNAFDI 540
** *****: *****:****.:** ***:*:::** :******:*:****:***.****

Avena
HvYSl
ZmYSl

GNPDGTWKAPYALIYRNMAILGVEGFSVLPKYCLALSGGFFAFAAILSIARDFMPHRYRQ 594
GNPDGTWKAPYALIYRNMAILGVEGFSVLPKYCIVISGGFFAFAAILSITRDVMPHKYAK 596
GNPTGYWKAPYGLIYRNMAILGVEGFSVLPRHCLALSAGFFAFAFVFSVARDVLPRKYAR 600
*** * *****.******************::*:.:*.****** ::*::**.:*::*

Avena
HvYSl
ZmYSl

YVPLPMAMAVPFLVGGSFAIDMCVGSLWFIWNKINKKEAGFMVPAVASGLICGDGIWTF 654
YVPLPMAMAVPFLVGGSFAIDMCLGSLIVFAWTKINKKEAGFMVPAVASALICGDGIWTF 656
FVPLPMAMAVPFLVGGSFAIDMCVGSLAVFVWEKVNRKEAVFMVPAVASGLICGDGIWTF 660
:**********************:*** ** * *:*:*** ********.**********

32

Avena
HvYSl
ZmYSl

PSSILALAKITPPICMKFTPAP 676
PASILALAKIKPPICMKFLPAA 678
PSSILALAKIKPPICMKFTPGS 682
*:********.******* *

Figure 14. Clustal analysis between known transporter and putative Avena tranporter. Full gene Clustal2W
analysis of Avena putative iron-phytosiderophore transporter against published transporters HvYSl and ZmYSl .

33

Discussion:
The isolated gene from A. sativa is 2,031 nucleotides in length and the protein is 676 amino acids
in length. Based on nucleotide BLAST results, the iron-phytosiderophore transporter from A. sativa
showed 86% and 77% identity to HvYSl and Zm YSl, respectively. A protein BLAST of the sequence
from Avena sativa and the two confirmed transporters showed an OPT domain, providing more evidence
of similarity. The closer similarity to Hv YS 1 is also suggestive of the iron specificity of the transporters
and the broad specificity of Zm YSl, which has been tested in various experiments (Meda et al. 2007;
Roberts et al. 2004; Chauhan 2006; Yen et al. 2001; Schaaf et al. 2004; von Wiren et al. 1996). This
diversity can be seen in the nucleotide and amino acid sequences in the area called the "specificity
region"; further verification of this diversity can be seen when comparing the sequences to A. stolonifera,
which exhibits non-similarity in the same region. The difference in the substrate specificity between
HvYSl and Zm YSl may result from the stereostructure of the transport protein. HvYSl has 11 putative
transmembrane spanning domains while Zm YS 1 has 12 putative transmembrane spanning domains
(Murata et al. 2006).
The discovery of the iron-phytosiderophore transporter in a major grain crop, oats, opens the door
for further analysis and engineering into enhancement of iron uptake by non-graminaceous transformants.
Increasing the iron concentration of plant foods will require an increase in total iron input to the plant that
can potentially be achieved through genetic manipulation of the plant itself. Different processes that can
be targeted for genetic transformation include root iron acquisition, transport through the vascular tissues,
and storage in edible tissues (Vasconcelos and Grusak 2006).
Understanding this iron phytosiderophore transporter system may allow the development of a
system to deliver effector molecules with specificity to Avena or a transformed target species using
phytosiderophore conjugates and the transporter as a portal through which to deliver the effector. This
approach has not been investigated elsewhere, but is currently underway in the Davis laboratory. Other
areas that are being considered are the biofortification of major seed and crop plants, phytoremediation
strategies, and re-greening of non-graminaceous plants.

34

WHO recommends enriching plants with iron - a concept termed "Iron Biofortification." Plant
grains are one of the major sources for iron in the human diet, especially in poor countries where anemia
is prevailing. However, the current mechanisms controlling iron homeostasis in plants are not completely
understood. Once these processes are clearer, there will be a starting point for better manipulation of crop
species (Briat 2008; Gross et al. 2003; World Health Organization; Xiong and Ishitani 2006).
Biofortification is a process whereby the plant uses its own mechanisms to fortify or enhance the density
or bioavailability of nutrients (like iron) in its edible tissues. The development of iron biofortified plants
involves four main strategies: (1) cultivar evaluation, (2) plant breeding and marker assisted selection, (3)
alteration of pathways of iron metabolism, and (4) modification of iron bioavailability (Vasconcelos and
Grusak 2006). This process is not a new idea because fortified products such as infant formula and iron
enriched flours are already available. However, by fortifying certain plant species before harvest, there is
I

a higher probability of getting iron fortified products to where they are needed most (Guerinot 2001 ).
There is the possibility that phytosiderophores released by graminaceous species can mobilize
iron from sparingly soluble soil sources; the Fe3+ thus released can be taken up by dicots after reduction.
Results from studies might explain the beneficial effects of intercropping dicots with grasses in order to
supply Strategy I plants with iron from the rhizosphere. Cesco et al showed that the amount of 59Fe taken
up by iron deficient citrus plants increased when iron deficient barley plants were present in the uptake
solution, particularly in the case of the susceptible rootstock. Enhanced 59Fe uptake by citrus rootstocks
was also observed in a separate experiment, where the authors collected exudates from the iron deficient
barley plants during the period of high phytosiderophore release (morning) were added to the solution
(Cesco et al. 2006).
Re-greening of fruit trees observed in calcareous soils when grass is grown along the rows of
trees has been attributed to the capability of graminaceous plant species to increase the availability of iron
by releasing phytosiderophores into the soil, thus favoring the uptake ofthis micronutrient by the fruit
trees. The results indicated that fruit trees growing on calcareous soils can benefit, in terms of iron
nutrition, from intercropping with perennial grasses that increase iron availability for root uptake. This

35

conclusion is further supported by pot experiments: leaf re-greening and increase in iron concentration
were observed when susceptible citrus rootstocks planted in a calcareous soil were co-cultivated with F.

rubra or P. pratensi~; furthermore the levels of iron in the soil solution were increased in the mixed
cultivation (Cesco et al. 2006). The re-greening effect was also shown by Ma et al using Festuca rubra
(Ma et al 2003).
The all around benefits of using Strategy II plants in the above mentioned processes should not be
ignored as the results from biofortification improve human nutrition and the mobiliz.ation of iron by
phytosiderophore relsease alleviates the excess amounts of fertiliz.er used on Strategy I plants that are
cultivated. The isolation of another transporter adds to the infonnation pool regarding iron uptake in
plants.

r

36

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