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trends in plant science
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Amino acid transport in plants
Wolf-Nicolas Fischer, Bruno André, Doris Rentsch, Sylvia Krolkiewicz,
Mechthild Tegeder, Kevin Breitkreuz and Wolf B. Frommer
Amino acids are transported between different organs through both xylem and phloem. This
redistribution of nitrogen and carbon requires the activity of amino acid transporters in the
plasma membrane. In addition, amino acids can be taken up directly by the roots. Amino acid
transport has been well characterized in the yeast Saccharomyces cerevisiae, and functional
complementation has served as an excellent tool for identifying and characterizing amino
acid transporters from plants. The transporters from yeast and plants are related and can be
grouped into two large superfamilies. Based on substrate specificity and affinity, as well as
expression patterns in plants, different functions have been assigned to some of the individual transporters. Plant mutants for amino acid transporter genes are now being used to study
the physiological functions of many of the cloned genes.

T

he uptake and transport of inorganic nitrogen is essential
for plant growth. Following the carrier-mediated uptake of
nitrate or ammonium from the soil, or of ammonium

derived from symbiotic dinitrogen fixation, inorganic nitrogen is
assimilated into amino acids in an energy-requiring process1. The
assimilation of ammonium usually occurs in the roots, whereas
nitrate assimilation, depending on the species and environmental
conditions, occurs either in the roots or in the leaves, after transport via the xylem2. From the leaves, excess amino acids can be
exported via the phloem. Thus, amino acids are present in both
xylem and phloem, and can be withdrawn from the vascular system by cells that depend on an external supply, such as apices,
newly developing tissues and reproductive organs. In most plants,
the spectra of amino acids found in the phloem and xylem appear
to be similar, the major components being amides such as glutamine
and asparagine, and acidic amino acids such as glutamate and aspartate. However, the relative concentrations of these amino acids
are very different: the xylem contains low concentrations (e.g. 3–
20 mM in Urtica3); and the phloem contains higher concentrations
(e.g. 60–140 mM in sugar beet4). The phloem, as a living system
with cytoplasmic continuity between cells, mediates transport
intracellularly, whereas the xylem can be considered to be an extracellular compartment. Because of loading of amino acids from the
xylem to the phloem (e.g. in the case of seeds that receive their
organic nitrogen mainly via the phloem), the composition of the
phloem sap can differ along its path5. Such complexity in composition, and the multiplicity of cell types that are involved in longdistance transport during the life cycle, suggests that multiple,
highly regulated transport systems for amino acids exist. There is

now physiological and genetic evidence for the activity of multiple, carrier-mediated transport systems responsible for the uptake
and transfer of amino acids6. A molecular dissection of amino acid
transport and characterization of individual carriers is thus required.
Yeast as a model for amino acid transport

Yeast has been invaluable for cloning and expressing plant genes
encoding amino acid transporters, and could also be a good model
for investigating aspects of their regulation. A given amino acid is
typically transported into yeast cells by several permeases with
different specificities, affinities and regulation7. In addition to
their role in uptake, high-affinity amino acid permeases are also
important for retention of intracellular amino acids, which tend to
leak out of the cell8 (Table 1). With the ongoing functional analysis of additional likely amino acid permeases (found during sequencing of the yeast genome9), a complete picture of individual
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amino acid transport systems in this unicellular eukaryote should
soon be available.
All yeast amino acid permeases that have been characterized

fall into the APC (‘amino acid–polyamine–choline facilitator’)
superfamily10, which may itself be subdivided (Fig. 1a). The
largest family of Gap1 (‘general amino acid permease’)-related
amino acid transporters includes Gap1; ten additional, more specific, permeases; and seven others found by genome sequencing
(Table 1). These proteins are very similar, and are closely related
to amino acid permeases found in bacteria and other fungi. Analysis of the predicted topological features of bacterial proteins of
this family (aroP and pheP) suggests a structure of 12 membranespanning domains separated by hydrophilic regions with the Nand C-termini located in the cytosol11. The second family [gaminobutyric acid (GABA) permease-related] includes two very
similar methionine permeases (Mup1 and Mup3) (Ref. 12) that
are homologous to several other proteins: a Schistosoma mansoni
amino acid transporter; the yeast GABA-, choline- and KAPA/
DAPA permeases13; and paralogues found by genome sequencing.
In addition to the APC superfamily, yeast cells contain seven
highly related proteins that are similar to the ATF (‘amino acid
transporter family’) superfamily in plants9. However, the functional
role of these proteins has yet to be tested. There might also be
additional classes of amino acid transport proteins, which could,
for example, be involved in compartmentalization of amino acids
into the vacuole. It has been suggested that these proteins are
members of a large family (31 members in yeast) of putative H+antiporters9. The large ABC superfamily of transport proteins14
might also include amino acid transport systems – several members

of this family from other organisms have been shown to transport
amino acids15.
Regulation of amino acid transport in yeast occurs mainly by
transcriptional control of amino acid permease genes and by targeting and turnover of the proteins. Transcription of several of the
permease genes, such as GAP1, is subject to nitrogen repression:
transcription is highest on media containing nitrogen sources that
support only limited growth rates (urea or proline), and is downregulated in the presence of preferred nitrogen sources (NH4+, glutamine or asparagine7). Four transcription factors of the GATA
family (Gln3, Nil1/Gat1, Uga43/Dal80 and Gzf3/Nil2/Deh1) play
key functions in this global regulation and seem to be part of a
complex network of auto- and cross-regulation16. Among genes
subject to nitrogen repression, some are induced in the presence of
their own substrates (e.g. UGA4); expression of other amino acid
permease genes (e.g. HIP1) does not appear to be influenced by the

Copyright © 1998 Elsevier Science Ltd. All rights reserved. 1360 - 1385/98/$19.00 PII: S1360-1385(98)01231-X

trends in plant science
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quality of the nitrogen source or the presence of amino acid substrates. Intracellular
traffic of synthesized permeases is also

subject to nitrogen control. For example, it
was recently shown that on urea medium,
newly synthesized Gap1 proteins are transported from the Golgi complex to the
plasma membrane, whereas, on glutamate
medium, they are transported from the Golgi
to the vacuole or lysosome, where they are
degraded17. Another level of regulation of
amino acid permeases is the control of their
stability at the plasma membrane. Upon addition of a preferred nitrogen source, such
as NH4+, to cells growing on a poor nitrogen
medium, Gap1 proteins previously accumulated at the plasma membrane undergo
endocytosis, polyubiquitination and degradation in the vacuole18. Genetic dissection
of this down-regulation showed that it involves a ubiquitin–protein ligase (Npi1/
Rsp5), which is essential for cell viability19.
The cytosolic C-terminal extremity of the
Gap1 permease contains several features,
including a di-leucine motif, that are essential for sensitivity to NH4+-triggered downregulation20.
The lifestyle of yeast is very different
from that of most plants. Saccharomyces
spp. grow as saprophytes under varying substrate conditions, and therefore must adapt

rapidly to a changing nutrient supply. For
plant cells, the situation is usually very different, because cells do not normally experience dramatic changes in the extracellular
composition of amino acids. Thus, the spectrum of amino acid transporter genes from
yeast, though similar to that found in higher
plants, is also likely to have important
differences.

Table 1. Families of yeast amino acid transportersa
Gene

Official nameb

Function of encoded protein

Gap1-related transporter family (APC superfamily)
GAP1
YKR039W
General amino acid permease
CAN1
YEL063C

Arginine permease
HIP1
YGR191W
Histidine permease
PUT4
YOR348C
Proline permease
LYP1
YNL268W
Lysine permease
BAP2
YBR068C
Leucine, valine and isoleucine permease
TAT1
YBR069C
Tyrosine and tryptophan permease
TAT2
YOL020W
Tryptophan permease
GNP1

YDR508C
Glutamine permease
DIP5
YPL265W
Glutamate and aspartate permease
PAP1
YDR046C
Low-affinity branched amino acid permease
APL1
YNL270C
Probable amino acid permease
YCL025C
YCL025C
Probable amino acid permease
YDR160W
YDR160W
Probable amino acid permease
YBR132C
YBR132C
Probable amino acid permease

YPL274W
YPL274W
Probable amino acid permease
YFL055W
YFL055W
Probable amino acid permease
YLL061W
YLL061W
Probable amino acid permease
GABA permease-related family (APC superfamily)
MUP1
YGR055W
Methionine permease I
MUP3
YHL036W
Methionine permease III
UGA4
YDL210W
GABA permease
HNM1/CTR1

YGL077C
Choline permease
BIO5
YNR056C
Permease of keto-aminopelargonic acid and
diaminopelargonic acid
YKL174C
YKL174C
Protein of unknown function
a

These families were formed based on functional analyses and data from the yeast genome project.
Official names are the open reading frame (ORF) designations according to the yeast genome project.
Additional genes that belong to the ATF family include: YNL101W, YKL146W, YJR001W, YER119C,
YEL064C, YIL088C and YBL089W. The official ORF names of all these are simply the non-italicized
gene names; they all encode proteins of unknown function.
b

A myriad of plant amino acid transporter genes

Biochemical approaches for identifying and isolating transport
proteins are problematic and, to circumvent this, a technique has
been devised to exploit Saccharomyces as a model system. Yeast
mutants lacking uptake systems for certain amino acids, and
which therefore cannot grow on media containing such amino
acids as the sole nitrogen source, were chosen as a complementation system. The mutants were transformed with plant cDNA
libraries in order to screen for transporters that would be able to
suppress the growth-deficient phenotype. Using various yeast
amino acid transport mutants, many plant amino acid transporter
genes were identified (>13 genes from Arabidopsis). Based on
sequence similarities, the plant transporters can be classified into
two major superfamilies: the ATFs and the APCs (Table 2).
The ATF superfamily is so far the largest and best-characterized family. Detailed computer analysis indicates that the transporters are built up from ten membrane-spanning domains,
whereas experimental evidence suggests the presence of 11
hydrophobic segments, with the N-terminus exposed to the
cytosol21,22. Several members of this family were shown to function as proton symporters23,24. Based on sequence similarities and
substrate specificity, four families can be distinguished: ProTs,
AAPs; LHT-related proteins and AUX1-related proteins (Fig. 1b).

The two members of the ProT family found in Arabidopsis have a
strong preference for proline25. In contrast, the members of the AAP
family recognize a large spectrum of different amino acids, including amides and ureides26,23,24. The AtAAP1, AtAAP2, AtAAP4 and
AtAAP6 proteins have a preference for neutral and acidic amino
acids, AtAAP6 displaying the highest affinity for most substrates.
AtAAP3 and AtAAP5, in addition to transporting neutral and acidic
amino acids, transport basic amino acids with high efficiency.
Therefore, the AAPs are classified either as neutral and acidic
amino acid transporters or as general amino acid transporters21.
Individual carriers belonging to one subgroup might also differ
with respect to their affinity for some amino acids (e.g. for large
hydrophobic amino acids); the physiological relevance of these differences remains to be demonstrated. New members of the AAP
family from Arabidopsis are being identified by the genome sequencing project (Table 2). The family of LHT-related transporters
was found by homology with known sequences and comprises expressed sequence tags (ESTs) and genomic clones distantly related
to the AAPs. So far only one member of this family (LHT1) has
been functionally characterized, and was shown to transport lysine
and histidine27. A member of the fourth family, the AUX1-related
proteins, was identified as being defective in an auxin-resistant
mutant of Arabidopsis 28. Auxins are structurally very similar to
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Fig. 1. Computer-aided analyses of sequence homology between
amino acid transporters. (a) Analysis of all known yeast amino
acid transporter homologues. The comparison was restricted to the
region in MUP1p from amino acid position 54 to 518; AtCAT1
was used as an outgroup. (b) Analysis of plant ATF (‘amino acid
transporter family’) amino acid transporters. The analysis was
performed with sequences of AtAAP1-7, AtLHT1-3, AtProT1-2
and the putative auxin transporter AtAUX1. The comparison was
restricted to the region in AtAAP1 from amino acid position 38 to
360; AtAUX1 was used as outgroup. The analyses were performed using the Phylogeny Interference Package version 3.5c
(J. Felsenstein, unpublished). Numbers indicate the occurrence of
a given branch in 100 ‘bootstrap’ replicates of the given data set
(i.e. they are a measure of the certainty of a given branch). Groups
of closely related proteins are circled.

tryptophan, and thus AUX1 might have developed from an AAP
amino acid transporter into an auxin transporter. Alternatively,
AUX1 might function as an auxin receptor, as in the case of yeast
hexose transporters, where at least two members of the hexose
transporter family serve as glucose receptors involved in the activation of hexose uptake29.
The plant APCs can be subdivided into two families, the CATs
and proteins most homologous to the yeast GABA permease-related
transporter family. The plant CAT family shares significant homology with the mammalian CATs, and is similarly composed of
14 putative membrane-spanning domains. The CATs are also
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distantly related to the yeast APC transporters, such as GAP1. So
far, from plants, only a single member of this family (AtCAT1)
has been identified, by complementation of a yeast histidine transport mutant30. However, an EST falling into the same family has
been identified and is currently under investigation (Table 2).
Transport studies in yeast support the hypothesis that AtCAT1 is
an H+-coupled transport system with high affinity for basic amino
acids that also recognizes many other amino acids with lower
efficiency30.
A member of the GABA permease-related family of amino
acid transporters, originally described in yeast, has recently been
identified (Table 2). Similar to the yeast transporters, it contains
12 putative membrane-spanning domains (K. Breitkreuz et al.,
unpublished).
As with many other organisms, plants contain a large number
of proteins that belong to the ABC superfamily of transporters14.
In other organisms, these proteins are found in different subcellular compartments and have been shown to transport many different substrates, including amino acids. So far, none of the members
of the plant family has been shown to function in amino acid
transport, and thus any role in cellular import or release of amino
acids must remain speculative.
In summary, both yeast and plants contain multiple sets of amino
acid transport proteins. Even before the genomic sequencing of
Arabidopsis has been completed, the number of putative amino
acid transporter genes from plants already exceeds the total number in yeast. This is not surprising, given that the plant contains so
many different cell types. There are also a large number of general
amino acid transporters, which can transport many different
amino acids. This might be the standard situation in a plant, where
an excess of amino acids is exported into the vascular system.
Seeds require the rapid import, translocation and export of large
amounts of transiently stored amino acids within a short time.
Transient storage occurs mainly in the form of proteins. Thus,
during the life cycle of a plant, organic nitrogen stored in the form
of proteins has to be remobilized, especially from vegetative storage proteins in leaves, for retrieval during leaf senescence, or during germination from storage in cotyledons or endosperm. In all
these situations, an efficient mechanism would be to use general
amino acid transport systems to mobilize as many of the amino
acids released by proteolysis as possible. In contrast, more-specific
systems such as the proline transporters might be required only
under defined conditions such as drought or salt stress, where specific amino acids have to be mobilized preferentially25.
Multiple transporters with overlapping specificity:
redundancy or necessity?

If plants use predominantly general amino acid transporters, why
did they develop so many similar systems? As a first step towards
answering this question, expression of the different carriers was
studied at the RNA level. All characterized members of the plant
ATF and APC superfamily show differential expression patterns25,26,31 (Fig. 2; Table 3). The expression of a given transporter
gene can be very specific or can overlap with other genes (e.g.
AtAAP3 was found only in roots, AtAAP6 only in sink tissues and
StAAP1 mainly in leaves; M. Kwart and W.B. Frommer, unpublished). However, the expression patterns derived from northern
blots yield only limited information: as with the sucrose transporter, the expression of many amino acid transporters might be
restricted to the vascular system, and thus the relative density of
the vascular strands within the harvested material could determine
the signal strength and spuriously indicate a particular tissue
specificity. To address this problem, promoters were isolated for
most AtAAP and AtCAT1 genes (Refs 30 and 31; W-N. Fischer

trends in plant science
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and W.B. Frommer, unpublished). At the
RNA level, AtAAP1 and AtAAP2 seem to
be co-regulated developmentally during
silique maturation, with the induction of
both preceding the accumulation of 2S
albumin mRNAs (Ref. 31). Promoter–
GUS fusion analysis revealed that AtAAP2
is expressed in the vascular strands entering the siliques, thus strongly suggesting a
role in the uptake of amino acids into the
seeds (Fig. 3) and in xylem-to-phloem
transfer. In contrast, AtAAP1 is expressed
in the endosperm and in the embryo proper,
supporting a function in the import of
amino acids into the endosperm and subsequently into the cotyledons of the developing embryo. Expression of AtCAT1
was detected in roots, stems, major veins of
leaves and in flowers30.
How does the molecular analysis fit with
genetic studies?

Table 2. Plant amino acid transporter familiesa
Gene

Function of encoded protein

Database
accession no.

CAT family (APC superfamily)
AtCAT1
High-affinity transport of basic amino acids
AtCAT2
Putative amino acid permease

X77502
AC000103

GABA permease-related family (APC superfamily)
10408T7
Putative amino acid transporter

T22007

ATF superfamily
AtAAP1

L16240

AtAAP2
AtAAP3
AtAAP4
AtAAP5
AtAAP6

Low-affinity transporter of neutral and
acidic amino acids
Low-affinity transporter of neutral and
acidic amino acids
Low-affinity general amino acid transporter
Low-affinity transporter of neutral and
acidic amino acids
Low-affinity general amino acid transporter
High-affinity transporter of neutral and
acidic amino acids
Putative amino acid transporter
Lysine/histidine transporter
Putative amino acid transporter
Putative amino acid transporter
Proline transporter
Proline transporter
Putative auxin transporter
Function unknown
Function unknown
Putative amino acid transporter
Putative amino acid transporter
Putative amino acid transporter
Putative amino acid transporter
Putative amino acid transporter

X71787
X77499
X77500
X77501
X95736

Mutant analysis is a powerful strategy for
AtAAP7
AB005244
studying the function of transporters in
AtLHT1
T13994
vivo. The classical approach for identifying
AtLHT2
AC00103
transport mutants is selection on media
AtLHT3
AC002294
containing toxic concentrations of comAtProT1
X995737
pounds or toxic analogues. Mutants with
AtProT2
X995738
non-redundant and selective transport sysAUX1
X98772
tems exclude the toxic compounds from
AUXR2
T75723
the interior and thus survive. Using this
AUXR3
Z29120
type of approach, at least three classes
NsAAP1
U31932
of amino acid transport systems could be
StAAP1
Y009825
differentiated in the unicellular green alga
StAAP2
Y009826
RcAAP1
Z68759
Chlorella32. The selection of tobacco
RcAAP2
Y11121
protoplasts on high concentrations of valine, and subsequent regeneration of intact
a
These families were formed on the basis of sequence similarity (with data from the Arabidopsis
plants, led to the identification of amino
genome
project) and functional analyses.
acid transport mutants resistant to high
external valine concentrations. Different
types of mutants were identified in Arabidopsis by selection of seedlings on high concentrations of valine or
threonine, or on the proline analogue azetidine-2-carboxylic acid
(Table 4).
The Arabidopsis raz1 mutant, which lacks activity of a highaffinity proline transporter, might carry a mutation in a member
of the ATF superfamily, all of which are able to mediate proline
transport33; a potential candidate is one of the ProT proline transporters. The Arabidopsis rlt1 and raec1 mutants are characterized by reduced uptake of basic amino acids34. Both mutations
were mapped to chromosome 1. Because AtAAP5 transports arginine, lysine and histidine with high affinity, the AtAAP5 gene
might be affected in these mutants26. The AtLHT1 protein does
not transport arginine, and thus cannot be the target; however, another member of the LHT-family, AtLHT3 (which maps to chromosome I), could carry the mutation. In the case of the barley aec1
mutants, defects in orthologues of AtLHT1, AtCAT1 or AtAAP5,
all representing high-affinity basic amino acid transporters, could
explain the lack of basic amino acid uptake into the roots35.
The wheat aec1 mutant is deficient in the uptake of basic, neutral
Fig. 2. Tissue specificity of plant amino acid transporters. The
and acidic amino acids36. A mutation in an AtAAP3 orthologue
diagram is based on results obtained from northern analyses and
could lead to the described phenotype, because so far AtAAP3 is
promoter–reporter gene fusions25,26.
the only amino acid transporter known to be able to mediate transport of acidic, basic and neutral amino acids26. High AtAAP4
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How do the biochemical properties of the carriers fit with
physiological studies?

Expression of plant amino acid transporters in different systems
allows precise characterization of individual properties, such as
substrate specificity. However, under physiological conditions,
the relative composition of the intra- and extracellular fluids will
determine which amino acids are actually transported. Thus, how
relevant are the observed differences in substrate specificity? The
intrinsic biochemical properties of both broad and general AAPs
and the cationic CAT transporters might be overruled by the
actual amino acid composition of the cytosol and extracellular
space. For example, a transporter that has been characterized as a
high-affinity transporter for cationic amino acids, but has a low
affinity for glutamate, might mainly function as a glutamate carrier in vivo, because glutamate concentrations are much higher
than lysine concentrations. The problem is to identify the actual
concentrations encountered by the carriers. For this, imaging techFig. 3. Light microscope image of a silique from Arabidopsis. The
niques with resolution down to the subcellular level are required.
seeds are stained pink/purple with fuchsin-red. Courtesy of Brigitte
Our current understanding is based almost exclusively on data
Hirner and Wolf Frommer.
obtained from whole organs, such as by grinding leaves or analyzing apoplastic wash fluids. These results must be interpreted
with caution, because they are averaged across the whole leaf –
local differences may well be important, as was elegantly demonexpression was found in mature leaves of Arabidopsis26. As strated by imaging of photosynthesis40.
AtAAP4 efficiently transports valine, a mutation in an AtAAP4
At present, there is no efficient technique available for determinorthologue of tobacco might explain the valine resistance of this ing the concentration of different amino acids in the subcellular commutant37,38. In several cases, the chromosomal location of the partments of plant cells under non-invasive conditions. However, in
mutation has been mapped. Comparison of mapping data from vivo NMR might be able to clarify this situation. NMR correlationmutants and amino acid transporter genes will be an excellent way peak imaging can resolve the spatial distribution of various amino
of assigning physiological functions to the individual carriers. acids and sugars in the hypocotyl of castor bean seedlings almost
However, it is also conceivable that other genes involved (e.g. in down to the level of individual cells. Glutamine and/or glutamate
the regulation of amino acid transport) will be identified, as with was detected in the cortex parenchyma and in the vascular bundles.
the yeast shr3 mutant, which is defective in targeting yeast amino Lysine and arginine were mainly present in the vascular bundles,
acid permeases to the plasma membrane39.
whereas valine was observed in the cortex parenchyma, but not
in the vascular bundles41. The finding that
valine shows a different distribution to the
other amino acids is surprising, because the
broad-specificity AAPs are able to transport
Table 3. Organ-specific expression patterns of different plant amino acid
acidic and neutral amino acids, including
a
transporter genes
valine, with comparable efficiency. NMRimaging techniques are also excellent tools
Tissue
for determining both the direction and the
velocity of fluxes in the vascular system42.
Gene
Sink leaf Source leaf Stem Flower Fruit Root
Seedling Refs
Until such tools become available for the
AtAAP1 –
–
–
–
S
–
–
50, 51
analysis of mutants and transgenic plants,
AtAAP2 –
V
V
–
V
V
V
52
we have to rely on the whole-organ experiAtAAP3 –
–
–
–
–
+++++ +++
26
ments. Nevertheless, the tools for such
AtAAP4 –
+++
++++ ++
–
–
–
26
analyses are highly developed. By a combiAtAAP5 –
++++
++++ ++++
++
++
–
26
nation of non-aqueous fractionation with
AtAAP6 +++
–
–
–
–
++++
–
25
apoplastic washing techniques and laser
AtProT1 +++
+++
++++ ++++
–
++++
–
25
stylectomy from aphid stylets, the sucrose
AtProT2 –
++
+
++++
++
++++
–
25
and amino acid compositions for vacuolar,
AtCAT1 –
++
+
++++
++
+++
–
30
cytosolic, apoplastic and phloem sap can be
StAAP1 –
+++
–
–
–
–
–
b
StAAP2 –
–
+++ –
–
–
–
b
studied in the same plant43. For both sugars
AtLHT1 ++++
–
–
P
++++ –
–
27
and amino acids, a large drop in concenRcAAP1 +++
+++
–
–
–
+++
++++
c
tration was observed in the apoplast. It is
RcAAP2 ++
+++
–
–
–
++
++++
c
still a matter of debate whether the wash
fluids represent the actual concentrations
a
Amount of expression is shown by ‘plus’ symbols, from low (one symbol) to high (five symbols).
found at sites of phloem loading, especially
Dashes indicate no detectable expression. Other abbreviations: V, expression in the vascular bundle; S,
because the loading occurs at the surface of
expression in the seed; P, expression in the pollen.
b
only a few cells, as was shown for sucrose
W.B. Frommer and M. Kwart, unpublished.
c
transporters that are localized at the small
See note added in proof.
sieve elements in minor veins44. The concentration drop, and thus the steep gradient
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Table 4. Plant amino acid transport mutants
Mutant

Species

Selected on

Properties

Refs

aup
pup

Chlorella vulgaris
C. vulgaris

L-canavanine
L-azetidine-2-

32
32

aec1a, aec1b

ValR-2 (recessive)

Hordeum
vulgare
Triticum aestivum cv.
Chinese spring
(hexaploid)
Nicotiana
plumbaginifolia
cv. Viviani
Tobacco cv. Xanthi

Impaired in basic amino acid transport.
Impaired in alanine, glycine, proline and serine
transport.
Impaired in basic amino acid transport; unaffected in
transport of neutral and acidic amino acids.
Impaired in basic amino acid transport; Km increased
and Vmax reduced; reduced uptake of several neutral
and acidic amino acids.
Deficient in transport of neutral amino acids.
Slightly affected in the uptake of basic amino acids.

aec1

Potato (H2578)

azcaR

Carrot cv. Lunga di
Amsterdam

rlt1, raec1
(recessive; maps to
chromosome 1)
ValR

Arabidopsis

S-(2-aminoethyl)cysteine

Arabidopsis

Valine

aec1
Val-16 (recessive)

raz1
Arabidopsis
(semidominant; maps
to chromosome 5 at
position approximately
70 cM

carboxylic acid
S-(2-aminoethyl)cysteine
S-(2-aminoethyl)cysteine
Valine
Valine

S-(2-aminoethyl)cysteine
Azetidine-2carboxylic acid

Azetidine-2carboxylic acid

towards the phloem sap, indicates that an active transport step
using proton-coupled transport systems is required for loading
amino acids into the phloem. This finding supports a function for
members of the AAP family in phloem loading. Interestingly, the
relative concentrations of a given amino acid were found to be
very similar in the cytosol of mesophyll cells, in the apoplastic
wash fluids and in the phloem sap. This result is in agreement with
the assumption that low-selectivity transporters such as the AAPs
import those amino acids into the sieve tubes that are produced in
excess and then released by the mesophyll. Such a low selectivity
of the transporters involved might also ensure that none of the various amino acids can accumulate in the apoplast and serve as a
source of nutrients for potential pathogens.
If fluxes can be modified, what is the aim?

Classically, it is assumed that the first enzymatic step in a pathway
is rate limiting and has the highest control coefficient. However,
this does not take into account that in many cases the first (or last)
step in a metabolic pathway is the transport into or out of the cell
or subcellular compartment. Theoretically, transporters are located
at ideal strategic positions for control. The available transporter
genes constitute an ideal set of tools for redirecting and modifing
fluxes of amino acids in transgenic plants. Attractive long-term
goals may therefore be specifically to adapt plants to local environments (e.g. to improve nitrogen efficiency or salt-stress tolerance),
or to alter the allocation and thus the quantity or quality of products.
Potatos are crops used for both food and starch production.
Potatos accumulate a relatively low level of organic nitrogen in

35
36
37

Impaired in neutral and acidic amino acid transport;
low-affinity uptake (Km = 1.5 mM) is unaltered; highaffinity system (Km = 40 mM) is strongly reduced;
slightly affected in transport of basic amino acids.
Uptake deficiency not proven.

38

Resistance to amino acid analogues: may represent
mutations in general amino acid transporters or a
secondary effect due to overproduction of amino acids
(e.g. proline).
Impaired in low-affinity transport of basic amino acids;
high-affinity uptake of lysine is mediated by a general
amino acid transporter.
High valine concentrations; uptake deficiency (not
proven).
Affected in the high-affinity uptake of proline.

54

53

34, 55
56
33

tubers, but the relative contribution of soluble organic nitrogen
(amino acids such as glutamate and aspartate) is approximately
50%. Thus, for food production, an optimized export of amino
acids from leaves or an optimized allocation to tubers could be
achieved by altering amino acid transporter gene expression.
However, potato starch is also used for many non-food purposes.
When potato tubers are used for starch production, the high levels
of free amino acids are a serious ecological problem. Energy-consuming techniques such as evaporation are required to concentrate
the amino acids present in the tuber juice. A solution to this problem would be to reduce the import of amino acids into the tubers.
Besides amino acid transport, plants also use oligopeptides
for rapid mobilization of protein-derived degradation products.
Relevant genes have been cloned using yeast peptide-transport
mutants45,46. Antisense repression of AtPTR2a leads to severe
problems during seed development, underlining the importance of
oligopeptide transport in nitrogen allocation47.
Future prospects

The remaining transporters will now mainly be identified by the
Arabidopsis genome project, with the function of new genes identified by sequence homology tested in yeast mutants and Xenopus
laevis oocytes. Furthermore, comparison of the map positions of
the genes isolated and of the mutations, together with detailed
expression and localization studies, will provide a better understanding of amino acid transport in plants. Systematic searches for
knockout mutants will, however, be necessary to obtain a full understanding of the role of the individual transporter genes48. Another
May 1998, Vol. 3, No. 5

193

trends in plant science
reviews
important field is the analysis of the regulation of amino acid
transport. Important questions waiting to be resolved can be
approached now, such as whether AAPs involved in phloem loading of amino acids might be localized in sieve elements [similar to
what has been described for the sucrose transporter SUT1 (Ref.
44)], or which transporters play a role in the uptake of amino acids
into the endosperm or transfer cells in developing seeds29,49. Yeast
will continue to serve as a model system and perhaps as a tool for
obtaining a better understanding of the regulation of plant amino
acid transport. Knowledge gained from studies with Arabidopsis
might eventually provide sufficient information for engineering
improvements in crop species.
Acknowledgements

We would like to thank John M. Ward for criticism of this
manuscript. This work was supported by grants from Deutsche
Forschungsgemeinschaft to W.B.F. (Aminosäuretransport and
SFB 446).
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Note added in proof
Information on two putative amino acid transporter cDNAs (RcAAP1 and
RcAAP2) from Ricinus communis has recently been published [Bick, J.A. et al.
(1998) Plant Mol. Biol. 36, 377–385].

Wolf-Nicolas Fischer, Doris Rentsch, Sylvia Krolkiewicz, Mechthild
Tegeder, Kevin Breitkreuz and Wolf B. Frommer* are at the
Botanical Institute, Eberhard Karls University, Auf der Morgenstelle
1, D-72076 Tübingen, Germany; Bruno André is at the Université
Libre de Bruxelles, Laboratoire de Physiologie Cellulaire et de
Genetique des Levures, Campus Plaine, CP244, Belgium.
*Author for correspondence (tel +49 7071 29 72605;
fax +49 7071 29 3287; e-mail frommer@uni-tuebingen.de).

Genomes, genes and junk:
the large-scale organization of
plant chromosomes
Thomas Schmidt and J.S. Heslop-Harrison
Plants from wide taxonomic groupings have similar genes and ordering of
genes along the chromosomes. However, the repetitive DNA, much of no
known function and often constituting the majority of the genome, varies
extensively from species to species in absolute amount, sequence and
dispersion pattern. Despite this, it is known that families of repeated DNA
motifs each have a characteristic genomic location within a genus, and that
there are different constraints on the evolution of repetitive DNA and genes.
There are now enough data about different types of repetitive DNA – from
sequencing, Southern analysis and in situ hybridization – to build a model of
the organization of a typical plant genome, and apply it to gene cloning,
evolutionary studies and gene transfer.

L

earning about the physical organization of genes and repetitive
sequences, regarded by some as
‘junk’, and seeing where the sequences lie, is
a critical element for understanding genome
organization and evolution in plants. The

approach enables data to be linked from
Arabidopsis and the handful of smaller
genomes for which sequencing is under way
with other genomes that are too large and too
numerous to sequence at the present time
(Fig. 1).

Copyright © 1998 Elsevier Science Ltd. All rights reserved. 1360 - 1385/98/$19.00 PII: S1360-1385(98)01223-0

Species from wide taxonomic groupings
have similar genes and arrangements of
genes along the chromosomes – they show
conserved synteny. However, knowledge of
synteny – provided by high-density, markersaturated genetic maps and genomic DNA
sequence data – tells us relatively little about
the large-scale physical organization of the
chromosomes and the repetitive DNA elements that make up the bulk of most
genomes. When a chromosome of an organism such as wheat or pine is dissected at the
molecular level, stretches of nucleotide sequence that occur once or only a few times in
the genome represent as little as 5% of the
DNA. Most plant and animal genomes consist largely of repetitive DNA – perhaps 30
sequence motifs, typically one to 10 000
nucleotides long, present many hundreds or
thousands of times in the genome – which
may be located at a few defined chromosomal sites or widely dispersed. However,
this repetitive DNA, with different selective
pressures from those acting on genes and evolutionarily successful multigene modules,
can show extensive differences in sequence
motifs and abundance1–3 even between closely
related species. The repetitive DNA in the
genome is also important for evolutionary,
genetic, taxonomic and applied studies.
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