Update on Genomics of Agrobacterium-Mediated Plant Transformation

Agrobacterium in the Genomics Age

Stanton B. Gelvin*
Department of Biological Sciences, Purdue University, West Lafayette, Indiana 479071392
Members of the genus Agrobacterium cause the neoplastic diseases crown gall, hairy root, and cane gall on
numerous plant species. Extensive genetic analyses
conducted in the 1980s identified key bacterial genes
involved in virulence. During the past decade, however, genomic technologies have revealed numerous
additional bacterial genes that more subtly influence
transformation. The results of these genomic analyses
allowed scientists to develop a more integrated view
of how Agrobacterium interacts with host plants. In a
similar manner, genomic technologies have identified
numerous plant genes important for Agrobacteriummediated genetic transformation. Knowledge of these
genes and their roles in transformation has revealed
how Agrobacterium manipulates its hosts to increase
the probability of a successful transformation outcome. In this article, I review our current knowledge of
Agrobacterium-plant interactions and how genomic
and proteomic technologies have increased our understanding of this unique plant-microbe interaction.
Agrobacterium species are phytopathogens that
cause a variety of neoplastic diseases, including crown
gall (Agrobacterium tumefaciens and Agrobacterium vitis), hairy root (Agrobacterium rhizogenes), and cane gall
(Agrobacterium rubi). Virulent strains of Agrobacterium
contain tumor-inducing (Ti) or root-inducing (Ri) plasmids. During infection, enzymes encoded by plasmidlocalized virulence (vir) genes process the T-DNA
region of these plasmids. The resulting single-strand
DNA (T-strand) linked to VirD2 protein exits the
bacterium via a type IV protein secretion system and
enters the plant cell. Within the plant, T-strands likely
form complexes with other secreted virulence effector
proteins, including VirE2, VirE3, VirD5, and VirF, and
supercomplexes with plant proteins as they traverse
the cytoplasm and target the nucleus. Once inside the
nucleus, T-strands integrate randomly into the plant
genome and express T-DNA-encoded transgenes. Two
classes of T-DNA genes mediate the pathology of
Agrobacterium infection. The first group, the oncogenes, either effect phytohormone production (iaa
and ipt; Akiyoshi et al., 1984; Schroder et al., 1984),
sensitize the plant to endogenous hormone levels (rol
and other genes of pRi, gene5 and gene6 of pTi; Shen
et al., 1988; Spanier et al., 1989; Tinland et al., 1990;
* E-mail [email protected].
The author responsible for distribution of materials integral to the
findings presented in this article in accordance with the policy
described in the Instructions for Authors (www.plantphysiol.org) is:
Stanton B. Gelvin ([email protected]).
www.plantphysiol.org/cgi/doi/10.1104/pp.109.139873

Korber et al., 1991), or may be involved in chromatin

remodeling (gene6b; Terakura et al., 2007). Expression
of these genes results in tumorigenic or rhizogenic
growth. A second set of genes directs the synthesis of
various low Mr compounds, opines, that can serve as
energy sources for the inciting bacterial strain and can
perhaps affect virulence (Veluthambi et al., 1989). For
reviews, the reader should see Gelvin (2000, 2003),
Tzfira and Citovsky (2001, 2003), McCullen and Binns
(2006), and Citovsky et al. (2007). In addition, the
reader is directed to an excellent new book on Agrobacterium biology (Tzfira and Citovsky, 2008).
Most plant biologists, however, best know Agrobacterium as an agent of horizontal gene transfer that
plays an essential role in basic scientific research and
in agricultural biotechnology. In the 1980s, scientists
learned to disarm (delete the oncogenes and, usually,
the opine synthase genes) virulent Agrobacterium
strains such that tissues infected by the bacteria could
regenerate into normal plants (Bevan et al., 1983;
Fraley et al., 1983; Herrera-Estrella et al., 1983).
Substituting genes of interest for oncogenes and opine
synthase genes resulted in plants expressing these
novel transgenes and, thus, novel phenotypes. Although transgene substitution for oncogenes within
T-DNA was initially conducted in cis (i.e. novel transgenes were placed within T-DNA of Ti-plasmids;
Caplan et al., 1983; Fraley et al., 1985), the development of binary systems, in which T-DNA and virulence helper plasmids were separated into two
different replicons (de Framond et al., 1983; Hoekema
et al., 1983), greatly increased the utility of Agrobacterium as a vehicle for gene transfer in plant biology
laboratories.
Throughout its development as a gene jockeying
tool, genomic studies on Agrobacterium and its plant
hosts guided scientists in basic science and agricultural biotechnology developments. In this article, I
review some of the key genomic methodologies and
findings that have contributed to our knowledge of
how Agrobacterium works and will contribute in the
future better to utilize Agrobacteriums amazing gene
transfer abilities in the laboratory and in the agricultural biotechnology industry.
GENOMICS OF AGROBACTERIUM
Whole-Genome Mutagenesis

Although not frequently considered genomics, important early studies on A. tumefaciens and A. rhizogenes utilized whole-genome mutagenesis and mass

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phenotypic screening to define Agrobacterium genes

important for transformation (i.e. T-DNA and Vir
protein transfer) and tumorigenesis. Transposon mutagenesis was generally the method of choice because
of the relatively random integration pattern of transposons in the bacterial genome and because the positions of transposon insertions could easily be
determined by restriction endonuclease mapping.
Thus, scientists localized genes involved in opine
catabolism to a specific region of the Ti-plasmid and
identified genes involved in crown gall tumorigenesis
in the T-DNA, in regions of the Ti-plasmid not within
the T-DNA (later to be identified as the virulence
region), and in the bacterial chromosome (chromosomal virulence [chv] genes; Garfinkel and Nester,
1980; Holsters et al., 1980; Ooms et al., 1980; De Greve
et al., 1981). More directed mutagenesis studies identified opine synthase genes and oncogenes in T-DNA
regions of Ti- and Ri-plasmids and specific virulence
genes within the vir gene region (Garfinkel et al., 1981;
Leemans et al., 1981; Ooms et al., 1981; Ream et al.,
1983; Inze et al., 1984; White et al., 1985; Stachel and
Nester, 1986; Stachel and Zambryski, 1986). These
studies involved testing of hundreds or thousands of
individually mutagenized Agrobacterium strains for
virulence, opine catabolism and synthesis, and tumor
morphology and may thus be categorized as early
Agrobacterium genomic studies.
Rong et al. (1990) conducted a second type of genetic
screening, using the promoter-less lacZ-containing
transposon MuDI-1681, to identify plant-inducible
Agrobacterium genes on the chromosome of A. tumefaciens A136 (C58 chromosomal background lacking a
Ti-plasmid). These authors assayed several thousand
randomly mutagenized Agrobacterium strains for induced gene expression on plates containing carrot root
extract and X-gal. Insertion of the transposon into the
picA gene revealed that this gene was .10-fold inducible by the root extract. The picA gene, currently
identified as encoding a polygalacturonase-like protein (Atu3129), was the first identified plant-inducible
Agrobacterium chromosomal gene.
Agrobacterium Whole-Genome Sequencing

Scientists had sequenced large portions of the Agrobacterium genome, including entire Ti-plasmids, by the
late 1990s and the following years (Barker et al., 1983;
Gielen et al., 1984; Slightom et al., 1986; Thompson
et al., 1988; Ward et al., 1988; Rogowsky et al., 1990;
Suzuki et al., 2000; Moriguchi et al., 2001; Oger et al.,
NC_010929; Kalogeroki and Winans, NC_002377).
Generation of a complete nucleotide sequence of the
nopaline-type strain A. tumefaciens C58 (Goodner et al.,
2001; Wood et al., 2001), from which many Agrobacterium strains commonly used for plant genetic engineering are derived [e.g. GV3010::pMP90, C58-Z707,
NT1(pKPSF2), EHA101/105, AGL-0/-1; see Lee and
Gelvin (2008) for characteristics of these strains],
opened the door for more extensive analyses of this
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important phytopathogen. A. tumefaciens C58 contains

four replicons: a circular and a linear chromosome and
two plasmids (pTiC58 and pAtC58). The genome
contains approximately 30 insertion sequence elements
and encodes an unusually large number of transporters (at least 153) and two-component regulatory
systems (at least 25). Recently, Ulker et al. (2008) described the surprising observation that Agrobacterium
can transfer its chromosomal DNA to plants. Interestingly, particular insertion sequence elements and
transporter gene sequences are hot spots for chromosomal DNA transfer. The preferential appearance of
these chromosomal sequences associated with T-DNA
in Arabidopsis (Arabidopsis thaliana) and rice (Oryza
sativa) T-DNA/plant DNA junctions suggests multiple
mechanisms for chromosomal DNA mobilization during T-DNA transfer (Gelvin, 2008).
The complete genome sequence and annotation of A.
tumefaciens C58 is posted on http://depts.washington.
edu/agro/. In addition to this biovar I A. tumefaciens
strain, DNA sequence analysis of the Agrobacterium
radiobacter biovar II strain K84 and the A. vitis biovar III
strain S4 has recently appeared (Slater et al., 2009). A.
radiobacter K84 is an especially important strain because it and its derivatives are widely used as biocontrol agents against tumorigenic Agrobacterium strains
(Kerr and Panagopoulos, 1977; Jones et al., 1988).
Comparative analysis of the sequences of the three
Agrobacterium strains and several other species of the
family Rhizobiaceae indicate a complex genome evolution, including the migration of gene blocks among
replicons within and between species. Sequencing of
other Agrobacterium strains (the biovar III strain A. vitis
F5R19 and the biovar II strain A. rhizogenes A4) is in
progress.
Agrobacterium Transcriptional Profiling

Based upon the A. tumefaciens C58 sequence, scientists have generated microarrays to probe the response
of bacterial genes to environmental and chemical
conditions important for Agrobacterium virulence and
plant defense.
The first such study investigated genes on the
octopine-type Ti-plasmid pTiA6 and the nopaline-type
Ti-plasmid pTiC58. Cho and Winans (2005) incubated
bacteria individually containing these Ti-plasmids
with acetosyringone (AS), a potent inducer of the vir
gene regulon synthesized by wounded plant cells
(Stachel et al., 1985; Stachel and Nester, 1986; Stachel
and Zambryski, 1986). They used RNA extracted from
induced and noninduced cells as probes of microarrays containing all Ti-plasmid genes. As expected,
they observed an increase in all previously identified
vir genes, along with several other Ti-plasmid genes
previously not identified as part of the vir regulon.
Most interestingly, they noted an increase in expression of all Ti-plasmid-encoded genes, suggesting that
AS induction of the vir regulon increases the copy
number of the Ti-plasmid relative to that of the bacPlant Physiol. Vol. 150, 2009

Genomics of Agrobacterium-Mediated Plant Transformation

terial chromosomes. Veluthambi et al. (1988) previously observed a similar increase in Ti-plasmid copy
number in bacteria cocultivated with plant cells. Further investigation by Cho and Winans (2005) demonstrated that the repABC operon, essential for
replication of these Ti-plasmids, was induced by AS.
Induction was under the control of the two-component
VirA/VirG regulatory system also responsible for vir
gene induction. Thus, when Agrobacterium is in the
environment of a wounded plant cell, the Ti-plasmid
overreplicates, perhaps increasing the probability of
T-DNA transfer to the plant.
The plant wound environment in which Agrobacterium effects horizontal gene transfer is acidic (Fierer
and Jackson, 2006), and the bacterium must maintain
pH homeostasis. An acidic environment is also essential for efficient vir gene induction (Stachel et al., 1986),
and two promoters regulate virG, one of which is acid
inducible (Mantis and Winans, 1992; Chang and
Winans, 1996). In addition, two chromosomal genes
important for vir gene induction and transformation,
chvG and chvI, are acid inducible (Charles and Nester,
1993; Li et al., 2002). With these facts in mind, Yuan
et al. (2008a) conducted a microarray-based, wholegenome transcriptional profiling study of all Agrobacterium genes responding to acidic conditions. These
authors identified 152 acid-responsive genes. These
included previously identified acid-induced genes,
genes involved in cell envelope synthesis, genes
involved in exopolysaccharide (succinoglycan) synthesis and metabolism, several newly recognized acidinducible vir genes (virE0, virE1, virH1, and virH2), and
genes encoding a recently described type VI secretion
system (Wu et al., 2008). Acidic conditions repressed a
number of genes, including some involved in motility,
chemotaxis, and cellular metabolism.
Salicylic acid (SA) is a major signaling molecule that
is important for plant defense responses. Although
induction of SA and downstream plant defense genes
by bacterial elicitation is well studied, fewer reports
have investigated the effect of plant-derived SA on
pathogen gene expression. Two groups used microarray analysis to investigate the effect of SA on the
accumulation of Agrobacterium transcripts. Yuan et al.
(2007) showed that SA, at concentrations that do not
influence bacterial growth (28 mM), inhibits vir gene
expression in acidified medium containing AS. At
higher concentrations (.10 mM), SA inhibits bacterial
growth in acidic medium. Transcriptional profiling of
RNA from bacteria incubated for 6 h with AS and 6 mM
SA indicated that expression of Ti-plasmid-localized vir
genes and the repABC genes was repressed. However,
SA induced a number of Agrobacterium genes, including
attKLM, which encodes a quormone degradation system. Because plants deficient in SA production are
hypersusceptible to Agrobacterium transformation,
whereas elicitation with SA decreased virulence (Yuan
et al., 2007; Anand et al., 2008; Veena and S.B. Gelvin,
unpublished data), these data suggest that the plant
signaling molecule SA may inhibit transformation by
Plant Physiol. Vol. 150, 2009

shutting down vir gene expression and consequently

T-DNA transfer. Anand et al. (2008) noted another effect
of SA on Agrobacterium. Bacteria treated with 100 mM SA
did not efficiently attach to plant cells. Thus, bacterial
attachment may be yet another process that is disrupted
by this plant hormone.
To explore further the effects of plant-released signal
molecules on Agrobacterium gene expression, Yuan
et al. (2008b) incubated bacteria with physiological
levels of SA, indole-3-acetic acid (IAA), and g-amino
butyric acid (GABA) that do not inhibit Agrobacterium
growth. Previous data had indicated that each of these
compounds affect Agrobacterium virulence (Chevrot
et al., 2006; Liu and Nester, 2006; Yuan et al., 2007;
Anand et al., 2008). Incubation of Agrobacterium at acid
pH with each of these compounds, followed by microarray analysis, revealed 100 to 200 genes for each
treatment whose expression was modulated. In some
instances, different compounds affected the same genes,
whereas numerous Agrobacterium genes showed differential regulation by one compound only. IAA inhibited
expression of the entire Ti-plasmid-localized vir regulon
but did not have appreciable effects on expression of
chromosomal virulence genes. Thus, the effect of IAA
on vir regulon induction was similar to that of SA.
However, the effects of SA and GABA on Agrobacterium gene expression were generally very different. In
a most interesting exception, SA and GABA both
induced the attKLM operon, which is involved in
destroying the quorum sensing homoserine lactone
that serves as a signaling molecule between Agrobacterium cells. In addition, seven genes were coregulated by IAA, SA, and GABA. Most of these were
transporters, and mutation of some of these resulted in
altered AttM lactonase activity. Taken together, these
data suggest that at later times during Agrobacterium
infection, plant signal molecules shut down vir gene
expression (which is no longer needed once infection
has been established) and may destroy quorum sensing signals.
Agrobacterium Proteomics

Engstrom et al. (1987) conducted the first proteomic

study of Agrobacterium. Using one-dimensional SDSPAGE, they identified 10 to 15 protein bands that
appeared in various Agrobacterium strains following
incubation with the vir gene inducer AS. Several of
these bands corresponded to VirB membrane proteins
comprising the type IV secretion system that transfers
T-DNA and virulence effector proteins to plants. They
also identified VirF and VirE2, two proteins of the vir
regulon. In addition, they detected a number of other
AS-induced proteins encoded by the Ti-plasmid or by
the Agrobacterium chromosome. Similarly, Rong et al.
(1990) detected by one-dimensional SDS-PAGE 10 plantinduced Agrobacterium chromosomal protein bands.
Rosen et al. (2004) made the first attempt at experimentally defining the Agrobacterium proteome. Using
two-dimensional gel electrophoresis, they detected ap1667

Gelvin

proximately 300 proteins from exponentially growing

bacteria. Interestingly, approximately 10% of the proteins were represented by multiple spots on the gel. The
authors suggested that a high level of protein modification of the proteome occurs. Similar studies by this
group (Rosen et al., 2001, 2002) investigated stress (high
temperature, oxidative, and mild acid conditions) and
heat shock-induced proteins of Agrobacterium. This
group also identified proteins induced when the bacteria were incubated with and bound to cut tomato
(Solanum lycopersicum) root segments, simulating plant
infection conditions (Rosen et al., 2003). As controls,
they examined, by two-dimensional gel electrophoresis, proteins from unbound bacteria and bacteria not
incubated with root segments. Incubation of bacteria
with roots induced approximately 30 proteins, regardless of whether the bacteria bound to the root segments
or not. Although incubation with root segments induced ChvE, AttK, and AttM (all proteins involved in
virulence), their experiments detected no induced
Ti-plasmid-encoded virulence proteins. Because, for
example, VirE2 is a major virulence protein induced by
phenolic molecules such as AS (Engstrom et al., 1987;
Lai et al., 2006), the results of this study indicate either
that vir gene induction did not efficiently occur or that it
occurred in only a small percentage of the bacteria.
More recently, Lai et al. (2006) investigated Agrobacterium proteins induced by the phenolic vir regulon
inducer AS. Using two-dimensional gel electrophoresis
coupled with mass spectrometry, they identified 11 ASinduced proteins. Nine of these proteins were wellknown Ti-plasmid-encoded Vir proteins (VirE2, several
VirB proteins, Tzs, VirH1, and VirK), thus verifying
their vir regulon induction conditions. In addition, they
identified two proteins encoded by chromosomal
genes, HspL (a small heat shock protein) and Y4mC
(a protein of unknown function). Reverse transcriptionPCR analysis indicated that transcripts of the genes
encoding these proteins also were AS inducible and
that induction was dependent upon the two-component
sensing system VirA/VirG that mediates induction of
the vir regulon. All vir regulon genes previously identified contain a vir box in their promoter regions (Das
et al., 1986). The y4mC gene promoter similarly contains
a vir box, but, interestingly, the hspL promoter does not.
Thus, hspL activation by AS may be an indirect consequence of expression of Vir proteins. In addition, Wu
et al. (2008) analyzed proteins secreted by Agrobacterium into the medium. They identified 12 proteins,
including VirB1* (a cleaved fragment of VirB1 protein)
and Hcp (hemolysin-coregulated protein). Hcp is secreted by a newly discovered type VI secretion system.

GENOMICS OF PLANT GENES IMPORTANT

FOR AGROBACTERIUM-MEDIATED
GENETIC TRANSFORMATION

Scientists have used a variety of genomic techniques

to investigate plant genes important for Agrobacterium1668

mediated transformation. These include forward genetic screens to identify mutant plants with altered
transformation susceptibility, yeast two-hybrid studies to detect plant proteins that interact with Virulence effector proteins, and transcriptional profiling
to discover plant genes whose expression is altered
following Agrobacterium infection. In addition, reverse genetic analyses have been used to probe the
importance of candidate genes in the transformation
process.
Forward Genetic Screens for Plant Mutants with Altered
Transformation Characteristics

Plant species, and even different cultivars/genotypes of the same species, are notoriously varied in
their transformation susceptibility (DeCleene and
DeLey, 1976; Anderson and Moore, 1979; Conner and
Commisse, 1992; van Wordragen and Dons, 1992; Bliss
et al., 1999; Pena and Seguin, 2001; Somers et al., 2003;
Shrawat and Lorz, 2006). In addition, Agrobacterium
can transform Streptomyces, yeast, and other fungal
species (Bundock et al., 1995, 2002; Piers et al., 1996; de
Groot et al., 1998; Abuodeh et al., 2000; Kelly and
Kado, 2002; Roberts et al., 2003; Schrammeijer et al.,
2003; van Attikum and Hooykaas, 2003; Michielse
et al., 2004), HeLa cells (Kunik et al., 2001), and sea
urchin embryos (Bulgakov et al., 2006). Thus, Agrobacterium is incredibly promiscuous in its ability to
mediate horizontal gene flow among numerous species of different phylogenetic kingdoms. A genetic
basis for susceptibility to Agrobacterium exists in many
crop species (Owens and Cress, 1984; Szegedi and
Kozma, 1984; Smarrelli et al., 1986; Robbs et al., 1991;
Bailey et al., 1994; Mauro et al., 1995), and Nam et al.
(1997) also described a genetic basis for various degrees of susceptibility among approximately 40 Arabidopsis ecotypes.
Large-scale forward genetic screening of approximately 20,000 T-DNA mutagenized Arabidopsis lines
resulted in the first identification of plant genes involved in Agrobacterium-mediated transformation
(Nam et al., 1999; Zhu et al., 2003b). These forward
genetic analyses revealed .120 genes encoding proteins involved in transformation and, because the
screen was not saturating (e.g. no gene was discovered
more than once), the authors suggested that .200
Arabidopsis genes likely influence plant transformation susceptibility (Zhu et al., 2003b). The authors
termed mutants with greatly decreased susceptibility
to transformation rat (for resistant to Agrobacterium
transformation) mutants and the corresponding mutant genes, rat genes. The identified genes represent
most of the proposed transformation events that occur
in the plant (bacterial attachment/biofilm formation,
T-DNA and Virulence protein transfer to the plant,
cytoplasmic trafficking and targeting of the proposed
T-complex to the nucleus, virulence protein removal
from the T-strand, T-DNA integration into the plant
genome, and transgene expression).
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Genomics of Agrobacterium-Mediated Plant Transformation

Examples of plant proteins identified in these initial

genetic screens and mediating transformation include
those involved in cell wall structure and biosynthesis
(Rat1 and Rat4, and arabinogalactan and cellulose
synthase-like [CslA9] proteins, respectively; Zhu et al.,
2003a; Gaspar et al., 2004), cytoskeleton proteins potentially involved in cytoplasmic trafficking of T-complex
components (actins and a kinesin; Zhu et al., 2003b),
importin a and b proteins that may mediate nuclear
targeting of T-complex components (Ballas and
Citovsky, 1997; Bako et al., 2003; Bhattacharjee et al.,
2008), chromatin proteins such as various histones,
histone acetyltransferases, histone deacetylases, and
histone chaperones that may facilitate T-DNA integration into the plant genome (Nam et al., 1999; Mysore
et al., 2000; Yi et al., 2002, 2006; Tian et al., 2003; Zhu
et al., 2003b; Gelvin and Kim, 2007), and histone
proteins that can increase transgene expression (G.
Tenea and S.B. Gelvin, unpublished data). The nature
of these rat genes has stimulated reverse genetic experiments to determine the potential roles of candidate
genes in the transformation process (see below).
Recently, the Gelvin laboratory further identified
several Arabidopsis mutants that are hypersusceptible
to Agrobacterium transformation (hat mutants and,
therefore, hat genes; Fig. 1; N. Sardesai and S.B. Gelvin,
unpublished data). Arabidopsis lines containing
T-DNA activation tags (Weigel et al., 2000) provide a
resource for overexpressed genes that may influence
transformation susceptibility. When roots of these
mutagenized plants were assayed at low bacterial
inoculum conditions (102- to 103-fold lower than that
usually used to screen for rat mutants), we identified
seven independent lines that displayed increased

Figure 1. Activation tagging identifies Arabidopsis mutants that are

hypersusceptible to Agrobacterium transformation (hat mutants). Root
segments of wild-type (ecotype Wassilewskija) and T-DNA activationtagged mutants (Weigel et al., 2000) were inoculated with the tumorigenic strain A. tumefaciens A208 at low inoculum density (106 colony
forming units/mL). After 2 d of cocultivation, the root segments were
transferred to Murashige and Skoog medium lacking phytohormones
and tumors were allowed to develop (Zhu et al., 2003b). The plates
were photographed after 4 weeks. Note the larger and more numerous
tumors formed on root segments of the hat1 mutant line, compared to
the tumors formed on wild-type roots. The hat1 mutant has a T-DNA
activation tag inserted into a cellulose synthase-like gene. Expression of
a neighboring UGT gene is greatly enhanced in the hat1 mutant.
Plant Physiol. Vol. 150, 2009

levels of transformation relative to that of wild-type

control plants. T-DNA/plant DNA junction sequences
from five hat mutants identified several new genes
involved in transformation susceptibility, including a
cellulose synthase-like protein (CslB5), a potassium
transporter family protein (two independent T-DNA
insertion lines), a UDP-glucosyltransferase (UGT), and
a myb transcription factor (MTF).
Overexpression of the UGT cDNA in wild-type
plants confirmed that this gene is a hat gene. Interestingly, metabolic profiling of roots from UGT overexpressing plants indicated alterations in the levels of
key defense compounds, and microarray analyses of
these plants revealed decreased expression of most
genes in the phenypropanoid biosynthetic and SA
signaling pathways (N. Sardesai, A. Perera, R. Doerge,
and S.B. Gelvin, unpublished data). These results
further indicate that plant defense response signaling
pathways are involved in susceptibility to Agrobacteriummediated transformation (see the discussion of transcriptional profiling below).
The hat3 mutant has a T-DNA activation tag inserted
into the 5# untranslated region of an MTF gene. Although
we could not isolate any homozygous hat3 mutants
(suggesting that this MTF is essential for normal plant
growth and development), heterozygous hat3 mutants are approximately 10-fold more susceptible to
Agrobacterium-mediated transformation than are wildtype control plants (Fig. 2A; N. Sardesai and S.B.
Gelvin, unpublished data). Three additional independent
T-DNA insertions in this gene are also hat mutants (Fig.
2B), indicating that this MTF is a negative regulator of
Agrobacterium-mediated transformation. Microarray analysis of RNA isolated from roots of mtf mutant plants
indicated that a WRKY transcription factor gene was
expressed to a lower level in the mutant. A homozygous
T-DNA insertion into this WRKY transcription factor
gene also resulted in a hat phenotype. This WRKY
transcription factor is involved in regulating plant defense responses, once again implicating plant defense
responses as a component of transformation susceptibility.
As an alternative to screening T-DNA insertion mutants for hat and rat phenotypes, Anand et al. (2007b)
used virus-induced gene silencing to investigate Nicotiana benthamiana genes important for Agrobacteriummediated transformation. The authors identified 21
genes whose expression, when lowered, resulted in an
altered crown gall phenotype. Proteins encoded by
these genes include a nodulin-like protein, a-expansin,
VIP1, importin-a, and histones H2A and H3.
Identification of rat and hat mutants emphasizes the
utility of large-scale forward genetic screens to understand the plant contribution to the Agrobacteriummediated transformation process.
Yeast Two-Hybrid Screening for Plant Proteins That
Interact with Virulence Effector Proteins

A. tumefaciens transfers at least five Virulence effector proteins to plants (VirD2 attached to the T-strand,
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Gelvin

Figure 2. An MTF negatively affects transformation susceptibility. A,

Transformation efficiency of the hat3 (MTF) mutant and its wild-type
control (ecotype Columbia-7 [Col-7]) and three independent T-DNA
insertion mutants in the MTF gene (mtf1, -2, and -3) and its wild-type
control (ecotype Columbia-0 [Col-0]). Root segments were inoculated
with the tumorigenic strain A. tumefaciens A208 at low inoculum
density (105 colony forming units/mL). After 2 d of cocultivation, the
root segments were transferred to Murashige and Skoog medium lacking phytohormones and tumors were allowed to develop (Zhu et al.,
2003b). The plates were photographed after 4 weeks. Note the more
numerous tumors formed on root segments of MTF mutant lines compared to the tumors formed on wild-type roots. B, Map of the MTF gene
mutated in the hat3 mutant. Numbers below the bar indicate nucleotides (+1 is the start site of translation). hat3, mtf1, mtf2, and mtf3 indicate the positions of three independent T-DNA insertions into the gene.

VirD5, VirE2, VirE3, and VirF; Otten et al., 1984;

Stahl et al., 1998; Vergunst et al., 2000, 2003, 2005;
Schrammeijer et al., 2003). In addition, A. rhizogenes
transfers GALLS-FL (full-length) and GALLS-CT
(C-terminal) to plant cells (Hodges et al., 2006). Several
laboratories have used yeast two-hybrid systems to
search for plant proteins that interact with these effector proteins or with other proteins that appear on the
bacterial surface. The rationale for these experiments is
that if a plant protein interacts with an Agrobacterium
protein, it is likely that this plant protein is involved in
the transformation process.
VirB2 is the major constituent protein of the Agrobacterium T-pilus (Lai and Kado, 1998). The T-pilus is
an important bacterial structure that may come into
contact with the plant during T-DNA and Vir protein
transfer. Although proteins on the plant cell surface
had previously been implicated in bacterial adhesion
(Neff and Binns, 1985; Gurlitz et al., 1987; Neff et al.,
1987; Wagner and Matthysse, 1992; Swart et al., 1994;
Clauce-Coupel et al., 2008), no previously identified
plant surface protein directly influenced bacterial virulence. Hwang and Gelvin (2004) used the processed
form of VirB2 (Lai and Kado, 1998) as a bait protein to
screen in yeast for Arabidopsis VirB2 interacting pro1670

teins. In addition to a RAB8 GTPase, they identified

three reticulon domain proteins termed BTI1, -2, and -3
(for VirB2 Interacting proteins 1, 2, and 3). Decreasing
expression of the Arabidopsis BTI genes by T-DNA
mutagenesis or RNA interference (RNAi) resulted in
reduced susceptibility to Agrobacterium-mediated transformation, whereas overexpression of BTI1 made the
plant hypersusceptible to transformation. As would be
expected of a protein that interacts with the T-pilus, the
BTI proteins localize to the plant surface. Although
more experiments need to be conducted, the BTI
proteins may serve as receptors for VirB2 protein on
the T-pilus.
In addition to VirB2, the role of VirB5 (a minor Tpilus constituent) needs further exploration. In animal
pathogens that have type IV secretion systems, VirB5
orthologs, such as CagL, may serve as specialized
adhesins that interacts with human integrin b1 and
fibronectin during bacterial/animal cell contact (Backert
et al., 2008). It would be interesting to determine, using
yeast two-hybrid systems, whether Agrobacterium VirB5
interacts with a specific plant surface protein.
VirD2 is the pilot protein that guides the T-strand
through the type IV secretion system into the plant
cell, through the plant cytoplasm, and into the nucleus.
VirD2 may also influence T-DNA integration into the
plant genome (Tinland et al., 1995; Mysore et al., 1998).
It is therefore likely that VirD2 interacts with plant
proteins during this journey, and yeast two-hybrid
analyses have identified a number of these proteins.
The first of these was the nuclear transfer importin a
protein AtKAPa (Ballas and Citovsky, 1997), now
known as IMPa-1 (Bhattacharjee et al., 2008). The
Arabidopsis genome encodes nine importin a proteins, and VirD2 interacts in yeast with all tested
importin a isoforms (Ballas and Citovsky, 1997; Bako
et al., 2003; Bhattacharjee et al., 2008). Additionally,
bimolecular fluorescence complementation studies in
planta indicated that each of these isoforms interacts
with VirD2 and localizes the complex to the nucleus
(Bhattacharjee et al., 2008).
Yeast two-hybrid screening additionally identified
several other plant proteins that interact with VirD2.
These include several cyclophilins (Deng et al., 1998;
Bako et al., 2003), the kinase CAK2Ms (Bako et al.,
2003), and a protein phosphatase PP2C (Tao et al.,
2004). Interaction with these latter two proteins suggested that VirD2 may be a phosphoprotein. Bako et al.
(2003) confirmed this hypothesis, and Tao et al. (2004)
showed that PP2C can regulate nuclear entry of VirD2.
The single-strand DNA binding protein VirE2 is
important for transformation. Agrobacterium strains
mutant for virE2 are highly attenuated in virulence
(Stachel and Nester, 1986). VirE2 plays numerous
important roles within the plant cell (Citovsky et al.,
1992; Ward and Zambryski, 2001) and therefore likely
interacts with numerous plant proteins. Yeast twohybrid analyses have confirmed these interactions.
VirE2 interacts with numerous importin a isoforms;
however, only interaction with IMPa-4 results in nuPlant Physiol. Vol. 150, 2009

Genomics of Agrobacterium-Mediated Plant Transformation

clear localization (Bhattacharjee et al., 2008; Lee et al.,

2008). VirE2 also interacts in yeast with the VirE2
interacting proteins VIP1 and VIP2 (Tzfira et al., 2001;
Anand et al., 2007a). Interaction of VirE2 with these
proteins likely contributes to nuclear targeting and
genomic integration of T-strands (Tzfira et al., 2001;
Citovsky et al., 2004; Li et al., 2005; Loyter et al., 2005;
Anand et al., 2007a; Bhattacharjee et al., 2008; Lacroix
et al., 2008)
VirF is a nonessential virulence protein for infection
of most plant species. However, it is required for
efficient transformation of a few species (Melchers
et al., 1990; Regensburg-Tuink and Hooykaas, 1993).
Schrammeijer et al. (2001) screened for VirF interacting
proteins in yeast and identified a plant Skp1 ortholog.
Skp1 (ASK1) is a component of the SCF ubiquitin
ligase complex that identifies and marks proteins for
degradation via the 26S proteosome. Indeed, experiments in both yeast and in planta indicated the importance of VirF in proteolysis of VirE2, suggesting
that VirF plays a role in stripping VirE2 from T-strands
prior to integration (Tzfira et al., 2004).
VirE3 is a nuclear-localized Agrobacterium effector
protein that may serve as a plant transcription factor
(Schrammeijer et al., 2003; Garcia-Rodriguez et al.,
2006). VirE3 may also substitute for plant-encoded
VIP1 when this latter protein is limiting (Lacroix et al.,
2005). In yeast, VirE3 interacts with several importin a
isoforms, with pCsn5-1 (also known as AJH1), a component of the COP9 signalosome involved in protein
degradation, and with pBrp, a plant transcriptional
activator. An intriguing potential function for VirE3
may be as a molecular bridge to transport plant
transcription factors to the nucleus where they may
activate plant genes involved in tumorigenesis or
transformation (Garcia-Rodriguez et al., 2006).
GALLS-FL and GALLS-CT are two effector proteins
encoded by some A. rhizogenes Ri-plasmids (Hodges
et al., 2006). Although these proteins do not share
sequence homology with A. tumefaciens VirE2, they can
substitute for this essential A. tumefaciens virulence
effector protein (Hodges et al., 2004, 2009). Recent
yeast two-hybrid analysis using GALLS-FL as the bait
identified a specific interacting plant protein (GALLS
interacting protein [GIP]; Y. Wang and S.B. Gelvin,
unpublished data). Bimolecular fluorescence complementation experiments confirmed GALLS-FL and
GALLS-CT interaction with GIP in planta (L.-Y. Lee
and S.B. Gelvin, unpublished data). GIP is encoded by
one of an eight-member multigene family whose
functions are unknown. Research in this authors
laboratory is aimed at defining the role of GIP in
both A. rhizogenes- and A. tumefaciens-mediated plant
transformation.
Host Transcriptional Profiling and
Agrobacterium Infection

Several recent studies have investigated host transcriptional responses to Agrobacterium infection or to
Plant Physiol. Vol. 150, 2009

crown gall tumorigenesis. Veena et al. (2003) used

suppressive subtractive hybridization and DNA macroarrays to investigate the transcriptional response of
tobacco BY-2 cells to infection by several nontumorigenic Agrobacterium strains. The authors used nontumorigenic strains to avoid complications resulting
from phytohormone overproduction by expression of
oncogenes and studied the initial plant response by
limiting sampling to times ,36 h after infection. The
results of these experiments indicated that Agrobacterium exquisitely manipulates expression of the plant
genome to facilitate transformation: plant genes important for transformation, such as those encoding
histone proteins, were induced by the bacterium,
whereas expression of genes involved in host defense
responses was suppressed. Interestingly, Anand et al.
(2007a) later showed that expression of numerous
Arabidopsis histone genes was higher in wild-type
Arabidopsis plants than in vip2 (VirE2 interacting
protein 2) mutant plants. Arabidopsis vip2 mutant
plants are highly recalcitrant to Agrobacterium-mediated
transformation. These authors suggested that VIP2, a
putative transcription factor, may play a role in maintaining high-level expression of histone genes important for transformation.
Ditt et al. (2001) used a disarmed Agrobacterium
strain to infect Ageratum cell cultures. Using cDNA/
amplified fragment length polymorphism analyses of
RNA extracted at relatively long times after infection
(48 h), the authors identified a few genes whose
expression was either repressed or induced by cocultivation with Agrobacterium. Whereas expression of
most of the identified genes was similarly affected by
cocultivation with Escherichia coli, expression of two
genes (encoding a nodulin-like protein and a lectinlike protein kinase) was specifically induced by Agrobacterium infection.
Ditt et al. (2006) also used Arabidopsis Affymetrix
ATH1 microarrays to investigate host gene expression
changes following infection of Arabidopsis suspension cell cultures with a tumorigenic Agrobacterium
strain. Interestingly, the authors were only able to
detect transcriptional changes 48 h after infection. In
contrast to the results of Veena et al. (2003), the study
of Ditt et al. (2006) indicated that Agrobacterium infection induced, rather than repressed, defense gene
expression and that infection repressed expression of
genes encoding proteins involved in cell proliferation.
This latter observation was rather surprising considering that growth of the cell cultures was not slowed
by bacterial infection. The seemingly opposing results
of Ditt et al. (2006) and those of Veena et al. (2003) may
be explained by the different plant culture systems
used (tobacco and Arabidopsis) and the fact that one
group used disarmed strains, whereas the other used
tumorigenic strains that would result in the overproduction of phytohormones by the host and, eventually,
production of tumors. Differential gene expression
occurs in Arabidopsis crown gall tumors (Deeken
et al., 2006). The expression of numerous genes, in1671

Gelvin

cluding those involved in cell wall biosynthesis, Suc

degradation, transport, and glycolysis, is up-regulated
in tumors, whereas expression of genes involved in
photosynthesis, nitrogen metabolism, lipid metabolism, and amino acid synthesis is down-regulated.
Differential gene expression in crown gall tumors
correlated with altered solute profiles, leading the
authors to speculate that metabolism in mature crown
gall tumors occurs mainly anaerobically (Deeken et al.,
2006).
In addition to examining host transcriptional responses following Agrobacterium-mediated transformation or the development of crown gall tumors,
Kim et al. (2007) used Arabidopsis Affymetrix ATH1
microarrays and custom macroarrays to investigate
the transcriptional and methylation status of host
T-DNA integration sites. The results of these assays
indicated that, in the absence of selection, T-DNA
target sites were not preferentially transcribed to a
greater extent than were Arabidopsis genes in general
and that T-DNA integration occurred without regard
to the methylation status of the target DNA.
Reverse Genetic Screening for Genes Required for
Agrobacterium-Mediated Transformation

A large number of studies have employed reverse

genetic strategies to determine the role of candidate
genes in the transformation process. Candidate genes
include those identified by yeast two-hybrid and transcriptional profiling analyses, as well as additional
members of multigene families when one family
member clearly plays a role in virulence. Gene/expression disruption techniques have included T-DNA
insertional mutagenesis and RNAi and antisense inhibition of gene expression. Overexpression of several
plant genes has also resulted in a hat phenotype
(Mysore et al., 2000; Tzfira et al., 2002; Hwang and
Gelvin, 2004; Yi et al., 2006; G. Tenea, J. Spantzel, and
S.B. Gelvin, unpublished data). Some genes confirmed
as rat genes by these studies include those encoding
BTI proteins (Hwang and Gelvin, 2004), various importin a family members (Bhattacharjee et al., 2008),
VIP1 (Tzfira et al., 2001, 2002; Li et al., 2005), VIP2
(Anand et al., 2007a), Ku80 (West et al., 2002; Friesner
and Britt, 2003; Li et al., 2005), DNA ligase IV (Friesner
and Britt, 2003; van Attikum et al., 2003), SGA1 (G.
Tenea and S.B. Gelvin, unpublished data), and various
histones (Mysore et al., 2000; Yi et al., 2006; Anand
et al., 2007b; G. Tenea and S.B. Gelvin, unpublished
data). In addition, mutation of several genes involved
in plant defense responses and signal transduction
results in altered susceptibility to Agrobacteriummediated transformation (Veena, N. Sardesai, and
S.B. Gelvin, unpublished data).
Crane and Gelvin (2007) conducted a large-scale
reverse genetic screen for Arabidopsis rat mutants.
Using 340 independent mutant lines containing RNAi
constructions targeted against 109 chromatin genes,
they identified 24 genes important, to various extents,
1672

for transformation. These genes encoded histone acetyltransferases, histone deacetylases, chromatin remodeling proteins, DNA methyltransferases, global
transcription factors, histone H1, nucleosome assembly factors, SET domain proteins, and antisilencing
group proteins. Some of these genes, such as HDT19,
were previously implicated in the transformation process (Tian et al., 2003). Most interesting were three
genes whose expression is important for T-DNA integration: HDT1, HDT2, and SGA1. HDT1 and HDT2
encode histone deacetylases, whereas SGA encodes a
histone H3 chaperone/chromatin assembly protein
also known as ASF1 in yeast and animals.

CONCLUSIONS AND PROSPECTIVE

In addition to its long-described history as a plant

pathogen (Smith and Townsend, 1907), Agrobacterium
is a natural genetic engineer that scientists have used
for gene transfer experiments for the past 25 years.
Whole-genome saturation mutagenesis studies in the
early 1980s defined many Agrobacterium genes important for transformation, but only during the past
decade have scientists applied modern genomic technologies to unravel the full complement of bacterial
and host proteins important for transformation. In the
near future, advances in molecular biology combined
with novel imaging (e.g. Lee et al., 2008) and genetic
(e.g. House et al., 2004) techniques will give scientists a
considerably more refined view of bacterial and host
proteins involved in transformation. This knowledge
will likely result in improved transformation technologies, both to increase our ability to control Agrobacterium host range and to improve the quality (e.g.
single-copy T-DNA insertions that result in predictable and stable transgene expression) of transformation events.
Numerous important questions need to be answered to understand Agrobacterium-mediated plant
genetic transformation more fully. Many of these
questions beg genome-wide answers: (1) What roles
do plant defense responses, and Agrobacteriums ability
to overcome these responses, play in transformation?
(2) How does the transferred VirD2/T-strand assemble
with other virulence effector proteins and host proteins to traverse the plant cytoplasm and nucleus? (3)
What roles do plant proteins play in T-strand targeting
to plant chromatin and in T-DNA integration into the
genome? Can we manipulate Agrobacterium for gene
targeting (site-directed integration) purposes? (4) How
can we best manipulate both the bacterium and the
host to obtain high-quality transformation events? (5)
How does Agrobacterium manipulate host metabolism
for its advantage? (6) How does Agrobacterium interact
with other organisms in the rhizosphere? (7) To what
extent do the lessons we have learned about transformation using laboratory conditions apply to transformation in nature? (8) Has horizontal gene transfer
effected by Agrobacterium species influenced plant
Plant Physiol. Vol. 150, 2009

Genomics of Agrobacterium-Mediated Plant Transformation

evolution? These and other questions will likely be

answered using genomic, proteomic, and metabolomic approaches.
ACKNOWLEDGMENTS
I thank Drs. Erh-Min Lai and Walt Ream for critical reading of this
manuscript and for helpful suggestions. Research in the authors laboratory is
funded by the National Science Foundation, the Department of Energy
through the Corporation for Plant Biotechnology Research, the Biotechnology
Research and Development Corporation, and Dow Agrosciences.
Received April 11, 2009; accepted May 6, 2009; published May 13, 2009.

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