16
Stage-Specific Regulation of Solanum lycopersicum Leaf Maturation by Class 1 KNOTTED1-LIKE HOMEOBOX Proteins C W Eilon Shani, a Yogev Burko, a Lilach Ben-Yaakov, a Yael Berger, a Ziva Amsellem, b Alexander Goldshmidt, b Eran Sharon, c and Naomi Ori a,1 a Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, Rehovot 76100, Israel b Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel c Racah Institute of Physics, Hebrew University, Jerusalem, 91904, Israel Class 1 KNOTTED1-LIKE HOMEOBOX (KNOXI) genes encode transcription factors that are expressed in the shoot apical meristem (SAM) and are essential for SAM maintenance. In some species with compound leaves, including tomato (Solanum lycopersicum), KNOXI genes are also expressed during leaf development and affect leaf morphology. To dissect the role of KNOXI proteins in leaf patterning, we expressed in tomato leaves a fusion of the tomato KNOXI gene Tkn2 with a sequence encoding a repressor domain, expected to repress common targets of tomato KNOXI proteins. This resulted in the formation of small, narrow, and simple leaves due to accelerated differentiation. Overexpression of the wild-type form of Tkn1 or Tkn2 in young leaves also resulted in narrow and simple leaves, but in this case, leaf development was blocked at the initiation stage. Expression of Tkn1 or Tkn2 during a series of spatial and temporal windows in leaf development identified leaf initiation and primary morphogenesis as specific developmental contexts at which the tomato leaf is responsive to KNOXI activity. Arabidopsis thaliana leaves responded to overexpression of Arabidopsis or tomato KNOXI genes during the morphogenetic stage but were largely insensitive to their overexpression during leaf initiation. These results imply that KNOXI proteins act at specific stages within the compound-leaf development program to delay maturation and enable leaflet formation, rather than set the compound leaf route. INTRODUCTION Leaves are lateral organs that are produced from the flanks of the shoot apical meristem (SAM). Leaf development can be divided into three continuous and overlapping phases: initiation, primary morphogenesis (PM), and secondary morphogenesis (SM) or histogenesis (Poethig, 1997; Dengler and Tsukaya, 2001; Holtan and Hake, 2003; Barkoulas et al., 2007; Efroni et al., 2008). During leaf initiation, the leaf emerges from the flanks of the SAM. At PM, the leaf expands laterally and elaborates by the initiation of secondary structures from specific meristematic regions at the leaf margin, termed marginal blastozones (Hagemann and Gleissberg, 1996). SM is characterized by extensive cell expan- sion and histogenesis. The progress of leaf maturation is followed by plastochrons (P), such that P1 is the youngest leaf primordium; it becomes P2 as the next primordium emerges, and so on. Plant leaves can be either simple, with a single continuous lamina, or compound, where lamina units termed leaflets are connected via petiolules to a central rachis. Leaflets are initiated from the marginal blastozone at the PM stage and go through similar developmental stages as leaves (Ori et al., 2007; Barkoulas et al., 2008; Berger et al., 2009). Thus, different regions in the leaf can be at different developmental stages at the same time. Class I Knotted1-like homeobox (KNOXI) genes encode a family of transcription factors that are expressed in the SAM and have conserved functions in maintaining its activity (Hake et al., 2004; Hay and Tsiantis, 2009). In plants with simple leaves, such as Arabidopsis thaliana and maize (Zea mays), expression of KNOXI genes is excluded from leaves throughout their develop- ment (Lincoln et al., 1994; Long et al., 1996; Reiser et al., 2000; Semiarti et al., 2001; Hake et al., 2004). In tomato (Solanum lycopersicum), a plant with compound leaves, the KNOXI genes Tomato KNOTTED1 (Tkn1) and Tkn2 (also called LeT6) are expressed in young leaf primordia, slightly after their initiation, in addition to their expression in the SAM. A dramatic increase in leaf complexity results from KNOXI overexpression in leaves of the dominant tomato mutants Mouse Ears and Curl, as well as in a subset of transgenic plants overexpressing KNOXI genes (Hareven et al., 1996; Chen et al., 1997; Parnis et al., 1997; Janssen et al., 1998). In agreement, in Cardamine hirsuta, an Arabidopsis relative with dissected leaves, KNOXI genes are expressed in developing leaves, and their downregulation leads to the formation of simple leaves, suggesting that KNOXI genes are required for leaf elaboration in this species (Hay and Tsiantis, 2006). Similarly, 1 Address correspondence to [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.plantcell.org) is: Naomi Ori (ori@ agri.huji.ac.il). C Some figures in this article are displayed in color online but in black and white in the print edition. W Online version contains Web-only data. www.plantcell.org/cgi/doi/10.1105/tpc.109.068148 The Plant Cell, Vol. 21: 3078–3092, October 2009, www.plantcell.org ã 2009 American Society of Plant Biologists

Stage-Specific Regulation of Solanum …Arabidopsis promoters (Efroni et al., 2008; Shalit et al., 2009). Tkn1 and Tkn2 affected leaf development similarly during the tested developmental

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Page 1: Stage-Specific Regulation of Solanum …Arabidopsis promoters (Efroni et al., 2008; Shalit et al., 2009). Tkn1 and Tkn2 affected leaf development similarly during the tested developmental

Stage-Specific Regulation of Solanum lycopersicumLeaf Maturation by Class 1 KNOTTED1-LIKEHOMEOBOX Proteins C W

Eilon Shani,a Yogev Burko,a Lilach Ben-Yaakov,a Yael Berger,a Ziva Amsellem,b Alexander Goldshmidt,b

Eran Sharon,c and Naomi Oria,1

a Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Otto Warburg Minerva Center for Agricultural

Biotechnology, Hebrew University, Rehovot 76100, Israelb Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israelc Racah Institute of Physics, Hebrew University, Jerusalem, 91904, Israel

Class 1 KNOTTED1-LIKE HOMEOBOX (KNOXI) genes encode transcription factors that are expressed in the shoot apical

meristem (SAM) and are essential for SAM maintenance. In some species with compound leaves, including tomato

(Solanum lycopersicum), KNOXI genes are also expressed during leaf development and affect leaf morphology. To dissect

the role of KNOXI proteins in leaf patterning, we expressed in tomato leaves a fusion of the tomato KNOXI gene Tkn2 with a

sequence encoding a repressor domain, expected to repress common targets of tomato KNOXI proteins. This resulted in

the formation of small, narrow, and simple leaves due to accelerated differentiation. Overexpression of the wild-type form of

Tkn1 or Tkn2 in young leaves also resulted in narrow and simple leaves, but in this case, leaf development was blocked at

the initiation stage. Expression of Tkn1 or Tkn2 during a series of spatial and temporal windows in leaf development

identified leaf initiation and primary morphogenesis as specific developmental contexts at which the tomato leaf is

responsive to KNOXI activity. Arabidopsis thaliana leaves responded to overexpression of Arabidopsis or tomato KNOXI

genes during the morphogenetic stage but were largely insensitive to their overexpression during leaf initiation. These

results imply that KNOXI proteins act at specific stages within the compound-leaf development program to delay

maturation and enable leaflet formation, rather than set the compound leaf route.

INTRODUCTION

Leaves are lateral organs that are produced from the flanks of the

shoot apical meristem (SAM). Leaf development can be divided

into three continuous and overlapping phases: initiation, primary

morphogenesis (PM), and secondary morphogenesis (SM) or

histogenesis (Poethig, 1997; Dengler and Tsukaya, 2001; Holtan

andHake, 2003; Barkoulas et al., 2007; Efroni et al., 2008). During

leaf initiation, the leaf emerges from the flanks of the SAM. At PM,

the leaf expands laterally and elaborates by the initiation of

secondary structures from specific meristematic regions at the

leaf margin, termed marginal blastozones (Hagemann and

Gleissberg, 1996). SM is characterized by extensive cell expan-

sion and histogenesis. Theprogress of leafmaturation is followed

byplastochrons (P), such that P1 is the youngest leaf primordium;

it becomes P2 as the next primordium emerges, and so on. Plant

leaves can be either simple, with a single continuous lamina, or

compound, where lamina units termed leaflets are connected via

petiolules to a central rachis. Leaflets are initiated from the

marginal blastozone at the PM stage and go through similar

developmental stages as leaves (Ori et al., 2007; Barkoulas et al.,

2008;Berger et al., 2009). Thus, different regions in the leaf canbe

at different developmental stages at the same time.

Class I Knotted1-like homeobox (KNOXI) genes encode a

family of transcription factors that are expressed in the SAM and

have conserved functions in maintaining its activity (Hake et al.,

2004; Hay and Tsiantis, 2009). In plants with simple leaves, such

as Arabidopsis thaliana and maize (Zea mays), expression of

KNOXI genes is excluded from leaves throughout their develop-

ment (Lincoln et al., 1994; Long et al., 1996; Reiser et al., 2000;

Semiarti et al., 2001; Hake et al., 2004). In tomato (Solanum

lycopersicum), a plant with compound leaves, the KNOXI genes

Tomato KNOTTED1 (Tkn1) and Tkn2 (also called LeT6) are

expressed in young leaf primordia, slightly after their initiation,

in addition to their expression in the SAM. A dramatic increase in

leaf complexity results from KNOXI overexpression in leaves of

the dominant tomato mutantsMouse Ears and Curl, as well as in

a subset of transgenic plants overexpressing KNOXI genes

(Hareven et al., 1996; Chen et al., 1997; Parnis et al., 1997; Janssen

et al., 1998). In agreement, in Cardamine hirsuta, an Arabidopsis

relative with dissected leaves, KNOXI genes are expressed in

developing leaves, and their downregulation leads to the formation

of simple leaves, suggesting thatKNOXI genes are required for leaf

elaboration in this species (Hay and Tsiantis, 2006). Similarly,

1 Address correspondence to [email protected] author responsible for distribution of materials integral to thefindings presented in this article in accordance with the policy describedin the Instructions for Authors (www.plantcell.org) is: Naomi Ori ([email protected]).CSome figures in this article are displayed in color online but in blackand white in the print edition.WOnline version contains Web-only data.www.plantcell.org/cgi/doi/10.1105/tpc.109.068148

The Plant Cell, Vol. 21: 3078–3092, October 2009, www.plantcell.org ã 2009 American Society of Plant Biologists

Page 2: Stage-Specific Regulation of Solanum …Arabidopsis promoters (Efroni et al., 2008; Shalit et al., 2009). Tkn1 and Tkn2 affected leaf development similarly during the tested developmental

additional species with compound leaves also express KNOXI

genes in leaf primordia (Bharathan et al., 2002). These observa-

tions suggest that KNOXI proteins are involved in compound leaf

patterning in some species but not others (Champagne et al.,

2007). In Arabidopsis, ubiquitous overexpression of KNOXI

genes led to leaf lobbing (Matsuoka et al., 1993; Sinha et al.,

1993; Lincoln et al., 1994; Chuck et al., 1996; Reiser et al., 2000;

Pautot et al., 2001; Gallois et al., 2002; Dean et al., 2004). Tomato

has been extensively used to study compound leaf development

due to the sensitivity of its leaf shape to genetic changes and the

large collection of mutants with altered leaf shape. This research

has led to important insights on the developmental differences

between simple and compound leaves (Hareven et al., 1996;

Chen et al., 1997; Parnis et al., 1997; Janssen et al., 1998; Brand

et al., 2007; Ori et al., 2007; Kimura et al., 2008; Berger et al.,

2009). However, the lack of KNOXI loss-of-function mutants in

tomato, as well as the inconsistent and sometimes opposite

phenotypes caused by KNOXI overexpression, hindered the

understanding of how KNOXI proteins affect leaf shape in this

and other species.

Here, we addressed the role of KNOXI proteins in leaf pat-

terning by comparing the effects of overexpressing TKN proteins

and their fusion with a repressor domain. These experiments

revealed that KNOXI proteins affect leaf patterning in tomato by

delaying the progression of leaf maturation. KNOXI overexpres-

sion in specific domains in developing leaves implied that the

developmental window during which the leaf is responsive to

KNOXI activity is partially parallel between Arabidopsis and

tomato, suggesting that KNOXI proteins act within these frame-

works to affect leaf shape. Comparison of the effects of different

KNOXI genes revealed that their redundancy is limited to specific

developmental contexts.

RESULTS

Manipulation of KNOXI Activity in Developing Tomato

Leaves Distorts Leaf Shape and Size

To assess whether KNOXI function is required for compound leaf

development in tomato and address the mechanism of this

activity, we compared the effects of impaired KNOXI function

and its overexpression on leaf development. Attempts to identify

loss-of-function mutations through forward-genetic screens or

to downregulate KNOXI expression by synthetic microRNAs

(Alvarez et al., 2006; Schwab et al., 2006) were unsuccessful.

This could have resulted from redundant activities of homolo-

gous or nonhomologous proteins. We thus addressed the ques-

tion of KNOXI function in tomato leaf development using chimeric

repressor silencing technology (CRES-T) (Hiratsu et al., 2003). A

fusion of Tkn2 with the 12–amino acid long EAR repressor motif

of the Arabidopsis SUPERMAN gene (Ohta et al., 2001; Hiratsu

et al., 2002), termed SRDX, was expressed in tomato leaves. We

reasoned that this fusion protein would specifically repress the

transcription of common targets of tomato KNOXI proteins, in-

cluding TKN1-4, aswell as targets that are commonly regulatedby

potential nonhomologous redundant factors. In developmental

contexts in which KNOXI proteins act primarily as activators, this

will lead to the repression of downstream events (Markel et al.,

2002). To distinguish between the functions of KNOXI proteins in

SAMmaintenance and compound leaf development, expression

of Tkn2-SRDX was transactivated by the FIL promoter, which is

expressed throughout developing tomato leaves but not in the

SAM (Figures 1B and 1G) (Lifschitz et al., 2006). FILpro>>Tkn2-

SRDX tomato plants showed a pronounced alteration in leaf

structure (cf. Figures 1C and 1H to Figures 1A and 1F). The first

two leaves produced by these plants were simple and remark-

ably small. Later emerging leaves were small, narrow, and simple.

To further understand KNOXI function in compound leaf de-

velopment, we transactivated each of the tomato KNOXI genes

Tkn1 and Tkn2 specifically in developing leaves by the FIL

promoter. In contrast with the super-compound leaves of tomato

mutants with increased Tkn2 expression and a subset of trans-

genic plants ubiquitously overexpressing KNOXI genes (Hareven

et al., 1996; Chen et al., 1997; Parnis et al., 1997; Janssen et al.,

1998), FILpro>>Tkn1 and FILpro>>Tkn2 plants produced narrow

and simple leaves (Figures 1D, 1E, 1I, and 1J).

KNOXI Proteins Regulate Leaf Complexity by Timing

Leaf Maturation

Surprisingly, leaves of both FILpro>>Tkn1/2 and FILpro>>Tkn2-

SRDX were small, narrow, and simple (Figures 1D, 1E, 1I, and

1J). This prompted us to examine early leaf development in these

genotypes to understand the developmental basis for the pro-

duction of these final leaf shapes. FILpro>>Tkn2 leaves retained

morphological characteristics of very young leaf primordia at the

initiation stage for a prolonged period during their early devel-

opment (Figures 2A to 2D). Thus, at the P5 stage, these leaves

resembled elongated P2 wild-type primordia, with no lamina

expansion, and reduced and delayed trichome development. In

FILpro>>Tkn2 leaves of the plastochron equivalent of late-SM-

phase wild-type leaves, numerous initiation events of ectopic

meristems and leaflet primordia were observed at the leaf margin

(Figures 2H and 2I).

In striking contrast, FILpro>>Tkn2-SRDX leaf primordia showed

precocious leaf maturation, as revealed by the early expansion of

the leaf lamina, its precocious straightening, and the development

of trichomes on the entire surface of the leaf primordia from the P2

stage on (Figures 2E and 2F). Thus, the failure to develop leaflets

resulted from apparently opposite mechanisms in FILpro>>Tkn2

and FILpro>>Tkn2-SRDX: FILpro>>Tkn2 leaves failed to exit the

initiation stage, a transition that normally precedes leaflet initiation,

while in FILpro>>Tkn2-SRDX plants, leaf differentiation was ac-

celerated such that the PM stage was shortened, and leaves

progressed directly to the SM stage without leaflet initiation. In

tobacco (Nicotiana tabacum) and Arabidopsis, KNOXI proteins

have been shown to act as repressors of some of their targets,

such as the gibberellic acid biosynthesis geneGA20ox (Sakamoto

et al., 2001; Hay et al., 2002). Thus, some of the FILpro>>Tkn2-

SRDX phenotypes could represent overexpression phenotypes.

However, the complementary phenotypes of FILpro>>Tkn2-

SRDXandFILpro>>Tkn2 suggest that themajority of the observed

phenotypes resulted from downregulation of genes that are

normally activated by TKN2 (Matsui et al., 2008; Ikeda and

Ohme-Takagi, 2009). In agreement, while transactivation of

Regulation of Leaf Maturation by KNOX 3079

Page 3: Stage-Specific Regulation of Solanum …Arabidopsis promoters (Efroni et al., 2008; Shalit et al., 2009). Tkn1 and Tkn2 affected leaf development similarly during the tested developmental

Tkn2-SRDX later in leaf development by theBLS promoter did not

affect leaf shape (see below), it almost entirely suppressed the

phenotypes caused by expression of either Tkn2 or Tkn1 through

the same promoter (see Supplemental Figure 1 online). This result

confirms that TKN2-SRDX represses the activity of both TKN1and

TKN2 and likely also that of additional redundant factors. This

emphasizes redundancy in the tomatoKNOXI family, demonstrat-

ing CRES-T as a powerful tool to address redundancy in tran-

scription factor activity. The opposing activity of TKN2-SRDX and

TKN2 was further confirmed by analysis of gene expression.

Apices of 13-d-old wild-type, FILpro>>Tkn2, and FILpro>>Tkn2-

SRDX seedlings, which contained the SAM and the five youngest

leaf primordia, differed dramatically in their transcriptome (see

Supplemental Figure 2 online), providing molecular support to the

developmental phenotype. Specifically, in contrast with Tkn2,

whose expressionwas upregulated relative to thewild type in both

FILpro>>Tkn2 and FILpro>>Tkn2-SRDX apices (Figure 2G), S.

lycopersicumGA2ox4wasupregulated ninefold relative to thewild

type in FILpro>>Tkn2 but not in FILpro>>Tkn2-SRDX apices (see

Supplemental Figure 2C online). In agreement, GA2ox4 expres-

sion was shown to be elevated 23-fold in FILpro>>Tkn2 apices

relative to the wild type by quantitative real-time PCR verification

(see Supplemental Figure 2D online). A GA2ox gene was recently

shown tobeadirect target of KNOXI proteins inmaize (Bolduc and

Hake, 2009). While the wild-type apices used for the expression

profiling contained leaf primordia of various developmental

stages, primordia of FILpro>>Tkn2 apices were all at the initiation

stage, and FILpro>>Tkn2-SRDX primordia have differentiated

(Figures 2A, 2C, and 2E). Therefore, some of the differences in

gene expression among these genotypes are likely secondary to

these developmental differences.

Cumulatively, these observations imply that KNOXI proteins

promote compound leaf development by prolonging specific

stages of leaf development. Proper timing and balancing of

KNOXI activity during leaf development is therefore critical for

proper elaboration of the compound tomato leaves.

Differential Spatial and Temporal Competence of the

Developing Tomato Leaf to React to KNOXI Activity

The leaf phenotypes caused by Tkn2 overexpression or impaired

KNOXI activity throughout early leaf development suggested

that KNOXI activity is interpreted in a spatial- and temporal-

dependent manner during leaf development. To test this and

learn which stages in leaf development and which spatial do-

mains of the leaf primordium are sensitive to KNOXI activity, we

expressed Tkn2 and Tkn1 during a series of specific spatial and/

or temporal windows within the developing tomato leaf using

Arabidopsis promoters (Efroni et al., 2008; Shalit et al., 2009).

Tkn1 and Tkn2 affected leaf development similarly during the

tested developmental circumstances. The GH3.3 promoter di-

rected expression at the distal part of young leaf primordia

starting from the early P1 stage. In slightly older primordia, it

showed additional, lower-level expression in more proximal

domains, mainly in the vasculature (Figures 3B, 3F, 3H, and

4G; see Supplemental Figures 3A and 3B online). Expressing

Tkn1 or Tkn2 under the control of the GH3.3 promoter did not

lead to a visible alteration in final leaf shape (Figures 4A and 4D) in

contrast with the profound inhibition caused by their expression

throughout the young leaf primordia using the FIL promoter

(Figures 1, 2, 3A, 3E, and 3H). The distal part of the leaf, in which

the GH3.3 promoter is expressed, is the first to emerge and the

Figure 1. Alteration of KNOXI Activity in Developing Tomato Leaves Impairs Leaf Development.

(A) and (C) to (E) Four-week-old tomato plants.

(F) and (H) to (J) Mature fifth leaves.

(B) Expression pattern of the monomeric red fluorescent protein (mRFP) reporter (in red) driven by the FIL promoter.

(G) Schematic illustration of the expression pattern directed by the FIL promoter (in red) in the SAM and three youngest leaf primordia.

The genotypes are indicated above each column. FILpro>>Tkn2-SRDX, FILpro>>Tkn1, and FILpro>>Tkn2 overexpress Tkn1, Tkn2, and Tkn2-SRDX,

respectively, under the control of the FIL promoter. P1-P3, initiating leaf primordia, such that P1 is the youngest primordium. Bars = 1 cm (A), (C) to (F),

and (H) to (J) and 0.5 mm in (B).

3080 The Plant Cell

Page 4: Stage-Specific Regulation of Solanum …Arabidopsis promoters (Efroni et al., 2008; Shalit et al., 2009). Tkn1 and Tkn2 affected leaf development similarly during the tested developmental

first to differentiate. Similarly, expressing Tkn1 or Tkn2 under the

control of the 650 promoter, which directs expression starting

from the P4 stage in a gradient that increases toward the distal

end of the leaf, and in the leaf vasculature (Figures 3D, 3H, and 4I;

see Supplemental Figure 3D online) (Shalit et al., 2009) had no

obvious effect on leaf structure (Figures 4C and 4F). By contrast,

expressing these genes using the BLS promoter caused a

substantial increase in the degree of leaflet reiteration and an

elaboration of the marginal lobes (Figures 4B and 4E). The BLS

promoter drives expression starting at the P4 stage, in both

abaxial and adaxial domains. It is expressed in leaflets shortly

after their initiation and is nearly absent from both proximal and

distal domains; it thus roughly represents domains that are in the

PM stage (Figures 3C, 3H, and 4H; see Supplemental Figure 3C

online) (Shalit et al., 2009). Primary leaflets were formed relatively

normally in BLSpro>>Tkn1/2 plants, as expected from the BLS

expression domain, but increased number of higher-order leaf-

lets were produced (see Supplemental Figure 4 online). The

differential response of leaf primordia to KNOXI overexpression

by the different promoters could result from either the distinct

expression domains or from differences in expression levels. To

distinguish between these possibilities, we compared the ex-

pression levels driven by these promoters in six locations

representing different spatial and temporal developmental do-

mains (Figures 3G and 3H). Expression from theGH3.3 promoter

was weaker than that from FIL in all locations (Figure 3H; see

Figure 2. TKN2 Inhibits Leaf Maturation.

(A), (C), and (E) Scanning electron micrographs of shoot apices and initiating leaf primordia.

(B), (D), and (F) Successive stages of early leaf development, at stages P2 to P5, as indicated at the top of each column. The genotypes of each row are

indicated at the left. P1 to P5 are as in Figure 1G.

(G) Comparison of the Tkn2 mRNA levels in 13-d-old apices by quantitative RT-PCR. Standard errors (n = 3) are indicated for each genotype.

(H) Scanning electron micrographs of a FILpro>>Tkn2 leaf at a later developmental stage, showing curved growth and an ectopic meristem (arrow,

enlarged in the inset) that was formed at the distal end of the leaf and produced leaf and flower primordia.

(I) A scanning electron micrograph showing multiple events of lateral initiation at the leaf margin.

Bars = 200 mm in (A), (C), (E), (H), the inset, and (I) and 1 mm in (B), (D), and (F).

[See online article for color version of this figure.]

Regulation of Leaf Maturation by KNOX 3081

Page 5: Stage-Specific Regulation of Solanum …Arabidopsis promoters (Efroni et al., 2008; Shalit et al., 2009). Tkn1 and Tkn2 affected leaf development similarly during the tested developmental

Supplemental Figure 5A online). The differential effect of Tkn2

overexpression driven by these promoters could thus stem from

either the expression domain or from the expression level.

However, the expression from GH3.3 in P3 primordia and in

distal domains of P5 primordia was stronger than that of BLS

(Figures 3B, 3C, 3F, and 3H), and expression of BLS in initiating

leaflets and of 650 in distal and abaxial domains were compa-

rable to that of FIL (Figures 3H). The differential responses of

leaves to KNOXI expression driven by these promoters thus

likely stem from the distinct location and timing of expression

rather than from the expression level. In agreement, the differ-

ences in phenotypic severity between BLSpro>>Tkn2 and

650pro>>Tkn2 leaves correlated with the expression domains

directed by these promoters (Figures 3C, 3D, 4E, 4F, 4H, and 4I)

rather than with the relative expression levels of the Tkn2mRNA

(see Supplemental Figure 5B online). These results indicate that

a spatial and temporal gradient of morphogenetic potential

exists within the developing tomato leaf and that only very

specific regions and developmental stages are competent to

react to KNOXI activity. Thus, KNOXI overexpression during the

initiation stage inhibits the progress to the PM stage, while in

regions at the PM stage, KNOXI proteins appear to maintain the

morphogenetic potential. By contrast, regions at the SM stage

are insensitive to KNOXI activity. An alternative interpretation is

Figure 3. Characterization of the Expression Directed by a Series of Leaf-Specific Promoters.

(A) to (D) Confocal microscope images of P5 primordia of the indicated genotypes.

(E) to (F) Confocal microscope images of the SAM and three youngest leaf primordia of the indicated genotypes.

(G) Location of six sites at which the fluorescence signal was quantified and compared among the four leaf-specific promoters, in P3 or P5 primordia.

(H)Relative fluorescence intensity from RFP, expressed by the indicated promoters at six spatial domains of P3 or P5 primordia, as shown in (G). LMFIL,

local mean fluorescence intensity level (see Methods). Standard error (n = 3) is indicated for each combination of genotype and location.

The mRFP fluorescence is shown in green or yellow. Bars = 200 mm.

3082 The Plant Cell

Page 6: Stage-Specific Regulation of Solanum …Arabidopsis promoters (Efroni et al., 2008; Shalit et al., 2009). Tkn1 and Tkn2 affected leaf development similarly during the tested developmental

that proximal and adaxial leaf domains show increased KNOXI

responsiveness. These results explain the variability of the KNOXI

constitutive overexpression phenotypes by demonstrating that

they act differentially during distinct developmental windows.

To examine when KNOXI function is required during normal

leaf development, we expressed Tkn2-SRDX using a subset of

the stage-specific promoters. No obvious alteration of leaf shape

relative to the wild type was observed in plants that expressed

Tkn2-SRDX via either the GH3.3, BLS, or 650 promoters. This

implies that KNOXI proteins are normally active only in very

young regions of the developing tomato leaf.

A Similar Developmental Window of KNOXI Sensitivity in

Simple and Compound Leaves

Strong constitutive overexpression of KNOXI in Arabidopsis

simple leaves leads to leaf lobing and rumpling (Figure 5A,

compare with 5G) (Sinha et al., 1993; Lincoln et al., 1994; Chuck

et al., 1996; Hake et al., 2004). Is the spatial and temporal window

of KNOXI responsiveness similar between simple and com-

pound leaves? To address this question, we overexpressed in

Arabidopsis each of the four Arabidopsis KNOXI genes, BREVI-

PEDICELLUS (BP), KNOTTED-like from Arabidopsis thaliana 2

(KNAT2), KNAT6, and SHOOT MERISTEMLESS (STM), using

each of five representative promoters, which drive expression

transiently at successive stages of leaf development (Efroni

et al., 2008) (Figures 5B to 5F). The effect of transient expression

of the Arabidopsis KNOXI genes at early stages of leaf develop-

ment resulted in mild or no change in leaf shape, depending on

the specific combination of the gene being expressed and the

expression window (Figures 5B and 5C). By contrast, expressing

these genes by theBLS promoter, which drives expression at the

P5-P7 stages of leaf development, approximating the PM stage

(Efroni et al., 2008), altered leaf development (cf. Figures 5D and

5H). Overexpression of STM and BP using the BLS promoter

caused mainly rumpling, whereas KNAT2 and KNAT6 over-

expression with this promoter resulted in the formation of three

lobes (Figure 5D; see Supplemental Figure 6 online). No altera-

tion in leaf shape resulted from KNOXI expression at late stages

of leaf development (Figures 5E and 5F). Roughly, the sensitivity

Figure 4. Developmental Context–Specific Response to Tkn1 and Tkn2 Overexpression.

Tkn1 or Tkn2 overexpression was directed by a series of leaf-specific promoters. Promoters are indicated at the top of each column and the expressed

genes at the left of each row. P1 to P5 are as in Figure 1. Asterisk indicates the SAM. Bars = 5 cm.

(A) to (F) Fifth mature leaves.

(G) to (I) Schematic illustration of the expression domains of the different Arabidopsis promoters.

[See online article for color version of this figure.]

Regulation of Leaf Maturation by KNOX 3083

Page 7: Stage-Specific Regulation of Solanum …Arabidopsis promoters (Efroni et al., 2008; Shalit et al., 2009). Tkn1 and Tkn2 affected leaf development similarly during the tested developmental

to KNOXI overexpression shows a peak at the PM stage, and the

sensitivity decreases with the temporal distance from this peak.

These results suggest that all Arabidopsis KNOXI genes can only

affect the simple leaf structure during a short developmental

window in leaf patterning. However, the specific effect on leaf

development and the exact time window of KNOXI responsive-

ness differed among the four Arabidopsis KNOXI genes. To

confirm that these differences stemmed from differential activity

rather than from the genomic context of the insertion site in the

specific responder line, we crossed the BLS driver line to six to

eight independent responder lines for each of the KNOXI genes.

While the different responder lines of each KNOXI gene pro-

duced a range of phenotypic severities, the phenotypes were

similar among independent lines of each KNOXI, and the

Figure 5. Stage-Specific KNOXI Responsiveness of Developing Arabidopsis Leaves.

Arabidopsis plants expressing the four different Arabidopsis KNOXI genes at different stages of leaf development. The promoters and their respective

expression domains, as deduced from the literature (Efroni et al., 2008), drawn on schemes of transverse sections, are indicated at the top of each

column. The expressed genes are indicated at the left of each row. Bars = 1 cm.

(A) Whole plants.

(B), (C), (E), and (F) Fifth leaves.

(D) Second to seventh rosette leaves of the indicated genotypes. White arrows point to lobes in BLSpro>>KNAT2 and BLSpro>>KNAT6 leaves.

(G) Whole plant of wild-type Landsberg erecta.

(H) A leaf series of wild-type Landsberg erecta.

(I) An illustration indicating the location of the SAM (M) and the different leaf primordia (P1 to P7) on a scheme of a transverse section as those shown in

(A) to (F).

[See online article for color version of this figure.]

3084 The Plant Cell

Page 8: Stage-Specific Regulation of Solanum …Arabidopsis promoters (Efroni et al., 2008; Shalit et al., 2009). Tkn1 and Tkn2 affected leaf development similarly during the tested developmental

phenotype shown in Figure 5D is representative of the relatively

severe phenotype of each responder.

Comparing the results of transient KNOXI overexpression

between tomato and Arabidopsis suggests that leaves of both

species react to KNOXI activity during a comparable develop-

mental window during the PM stage. However, tomato leaves

show an additional window of KNOXI responsiveness during leaf

initiation. Whereas KNOXI overexpression apparently causes an

extension of the initiation stage in tomato plants, initiating

Arabidopsis leaves are comparatively insensitive to KNOXI mis-

expression.

Context-Specific Similarities and Differences in

KNOXI Function

To testwhether tomato andArabidopsis KNOXIgenes differ in their

effect on leaf development in addition to having differences in

expression, we expressed the tomato Tkn1 and Tkn2 genes in

Arabidopsis leavesusing theBLSpromoter.StrongBLSpro>>Tkn2

lines were highly rumpled and lobed (Figures 6E and 6F compared

with Figures 6A and 6B), and higher-order lobeswere initiated from

the margins of the leaf lobes, which partially resembled initiating

leaflets (Figures 6G to 6I). Such a phenomenon of ectopic initiation

eventswasnot observedwithanyof theArabidopsisKNOXIgenes,

implying functional differences between tomato and Arabidopsis

KNOXI proteins. Interestingly, BLSpro>>Tkn1 leaves had a very

mild phenotype with rounded shape but minor lobing (Figures 6C

and 6D), suggesting that while tomato leaves respond similarly to

Tkn1 and Tkn2 overexpression, Arabidopsis leaves display differ-

ential sensitivity to these tomato genes. Comparison of six to eight

independent responder lines each for Tkn1, Tkn2, and the four

Arabidopsis KNOXI genes confirmed that the distinct responses

were due to differential activity rather than an effect of the specific

responder line (data not shown). Tkn1 and Tkn2 expression only at

Figure 6. Overexpression of the Tomato KNOXI Gene Tkn2 but Not Tkn1 Severely Distorts Leaf Development in Arabidopsis.

Genotypes are indicated on the bottom left corner. Bars = 1 cm in (A) to (F) and 500 mm in (G) to (I).

(A), (C), and (E) Whole plants.

(B), (D), and (F) First to eighth rosette leaves of the indicated genotypes.

(G) to (I) Scanning electron micrographs of the initiation events (white arrows) from the leaf lobes of BLS>>Tkn2 leaves. The black rectangle in (G)

indicates the region magnified in (H).

(H) Magnification of part of the leaf shown in (G).

[See online article for color version of this figure.]

Regulation of Leaf Maturation by KNOX 3085

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late stages of Arabidopsis leaf development using the 7470

promoter (Figure 5E) did not show any aberrant leaf shape

phenotypes (see Supplemental Figure 7 online). Cumulatively,

misexpression of the different Arabidopsis and tomato KNOXI

genes through stage-specific promoters in both species argues

against differences in KNOXI activity as the basis for the

distinction between simple and compound leaves. Rather,

KNOXI proteins are used within the compound leaf develop-

ment program to delay differentiation and enable leaflet forma-

tion, rather than set the compound leaf route.

A comparison of the stage-specific effects of tomato and

Arabidopsis KNOXI genes on leaf shape suggests that these

proteins have evolved overlapping but partially distinct activities

at different developmental circumstances. To expand this com-

parison to additional developmental contexts, we tested the

ability of each Arabidopsis KNOXI gene to substitute for BP by

expressing them using the BP promoter in the bp-1 mutant

background. The responder lines that were used for these

experiments all showed a relatively strong phenotype when

crossed to the BLS driver line. bp-1 mutants have impaired

inflorescence stem elongation, short internodes, and downward-

pointing siliques (Douglas et al., 2002; Venglat et al., 2002)

(cf. Figure 7F to 7G). BPpro>>BP, BPpro>>STM, and BPpro>>

KNAT6 partially rescued the bp-1mutant phenotype (Figures 7B

to 7D). This was manifested by taller plant stature, longer

internodes, and partially recovered pedicel-stem angles rela-

tive to bp-1 plants. Interestingly, BPpro>>KNAT2 bp-1 plants

were indistinguishable from bp-1 mutants (Figure 7E). Quanti-

fication of the degree of rescue by measuring the angle be-

tween the first four pedicels and the main inflorescence

stem confirmed these results (Figure 7A). The genotype of

BPpro>>KNAT2 bp-1 plants was confirmed by PCR and by

crossing BPpro>>KNAT2 to the BLSpro driver line, which

resulted in the expected phenotype of lobed leaves (Figure

5D). Similarly, the different KNOXI responder lines that were used

in this evaluation produced the expected phenotype when

crossed to the BLSpro driver line. Thus, while the KNAT2 and

KNAT6 proteins display very similar effects on leaf shape, they

have acquired different functions in the context of inflorescence

development.

DISCUSSION

Developmental Stage–Specific KNOXI Responsiveness

Previously, ubiquitous KNOXI overexpression in tomato was

found to result in variable and even opposite leaf phenotypes

(Hareven et al., 1996; Chen et al., 1997; Parnis et al., 1997;

Janssen et al., 1998). Here, Tknmisexpression in a series of leaf-

specific developmental windows enabled us to dissect these

phenotypes into several context-specific effects. Tkn overex-

pression affected leaf shape only when expressed during the

early initiation or PM stages of leaf development. However, the

effect of Tknoverexpressionwas different between those stages.

Overexpression during leaf initiation prevented further progress

of leaf development, apparently by extending the initiation phase,

while during PM it caused an expansion of the morphogenetic

Figure 7. STM and KNAT6 but Not KNAT2 Can Substitute for BP Function in Arabidopsis.

The four different Arabidopsis KNOXI genes were expressed by the BP promoter in the bp-1 mutant background.

(A) A quantitative representation of the complementation level, presented as the angle between the pedicels and the main stem. Relatively high angles

similar to the wild type represent relatively strong complementation, while low angles similar to those in bp represent little or no complementation.

Standard deviation is shown for each genotype (n = 20 for bp-1, the wild type, BPpro>>BP, BPpro>>STM, and BPpro>>KNAT2; n = 8 for

BPpro>>KNAT6).

(B) to (G) Inflorescences of the indicated genotypes. Wild type, Landsberg erecta. Bars = 1 cm.

[See online article for color version of this figure.]

3086 The Plant Cell

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activity, resulting in a dramatically increased number of leaflet

reiteration orders (Figure 4). Thus, TKN activity is interpreted in a

spatial- and temporal-specific manner. That repression of po-

tential TKN targets affects leaf development only during early

stages of leaf development suggests that TKN is normally active

only transiently during leaf development and further empha-

sizes the context-specific interpretation of KNOXI action. How-

ever, the lack of aberrant phenotype in BLSpro>>Tkn2-SRDX

is surprising, as this promoter acts in tissues approximately at

the PM stage (Figure 3C). This observation suggests that the

BLS promoter drives expression slightly later than the develop-

mental timing at which KNOXI genes act to extend PM, which is

in agreement with its expression slightly following leaflet initia-

tion (Figure 3C).

How Do KNOXI Proteins Affect Leaf Shape?

While KNOXI proteins were shown to play major roles in the

development of compound leaves (Bharathan et al., 2002; Hay

and Tsiantis, 2006; Champagne et al., 2007; Jasinski et al., 2007),

their exact role in compound leaf development is still unclear.

For example, KNOXI activity in leaves could underlie the devel-

opmental choice between simple and compound leaves, be

required for leaflet initiation, or maintain the morphogenetic

competence at the leaf margin by prolonging the indeterminate

developmental phase. Comparing the outcome of overexpress-

ing Tkn1/2 and repressing TKN2 activity at specific stages of

tomato leaf development suggests that TKNs inhibit the progress

of leaf maturation (Figure 8). Thus, when overexpressed at

Figure 8. A Proposed Model for KNOXI Function in Tomato Compound Leaf Development.

The panels present the proposed developmental interpretation of the different genotypes. Left: Schematics describing the progress of leaf

development. The color codes of the different stages are indicated in the wild type. I, initiation. Right: Scanning electron micrographs of shoot apices of

the different genotypes, color coded for the different stages of leaf development. TKN2 is proposed to inhibit the transition between stages during leaf

development. In the wild type, TKN2 acts to extend PM. Repression of TKN2-like function in developing leaves of FILpro>>Tkn2-SRDX plants leads to a

prompt progression to the SM phase. By contrast, overexpressing wild-type Tkn2 throughout leaf development in FILpro>>Tkn2 plants results in an

extended initiation stage and in the failure to progress to PM. Tkn2 expression specifically at the PM stage of developing leaflets in BLSpro>>Tkn2

extends leaflet PM, resulting in higher-order reiteration of leaflet formation. White arrows point to primary leaflets, which are situated in the position

shown in red on the diagram to the left of the micrographs. Numbers 1 to 4 indicate leaflet reiteration levels.

[See online article for color version of this figure.]

Regulation of Leaf Maturation by KNOX 3087

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initiation, TKNs delay the onset of PM and thus prevent leaf

elaboration, while expression in leaflets at PMextends this stage,

resulting in additional levels of reiteration (Figure 8). The rapid

transition from the initiation to the SM phase caused by the

repression of TKN activity is compatible with this model. This,

together with the profound effect of KNOXI overexpression

during leaf initiation, and the narrow window of sensitivity to

TKN2-SRDX, suggests that during normal leaf development,

KNOXI proteins act specifically at the PM stage. The similar

developmental window at which tomato and Arabidopsis

leaves respond to KNOXI activity further supports the model

that KNOXI proteins affect leaf development by inhibiting dif-

ferentiation. The observation that overexpression of KNOXI

genes during leaf initiation in Arabidopsis has very minor

consequences for leaf development in contrast with the dra-

matic effect in tomato may imply that part of the difference

between simple and compound leaves stems from differences

at the initiation stage. This and the observation that in Arabi-

dopsis secondary initiation events caused by Tkn2 overexpres-

sion occur after the lamina has started to expand, leading to

reiteration of lobes rather than leaflets, further support the

conclusion that KNOXI genes are used for leaf elaboration

within the simple or compound developmental programs,

rather than for distinguishing between these developmental

programs.

LANCEOLATE (LA) activity was shown to promote the transi-

tion from the PM to the SM stage of leaf development in tomato.

Elevation of LA activity at early stages of leaf development in the

dominant Lamutant caused precocious leaf differentiation and a

failure to properly initiate leaflets from the leaf margin (Ori et al.,

2007). This phenotype is similar to that of FILpro>>Tkn2-SRDX.

Interestingly, the La mutant phenotype is epistatic to the super-

compound leaf phenotype caused by KNOXI overexpression

(Hareven et al., 1996; Kessler et al., 2001; Ori et al., 2007). This

genetic interaction seems to stem from a developmental rather

than molecular mechanism, as LA downregulation and KNOXI

upregulation display an additive genetic interaction (Ori et al.,

2007). Thus, KNOXI proteins and LA appear to act antagonisti-

cally to define the morphogenetic window in the developing

tomato leaf. This window requires both KNOXI activity and

downregulation of LA activity. The boundary NAC domain gene

GOBLET (GOB) has been recently implicated in the elaboration

of compound leaves (Blein et al., 2008; Berger et al., 2009).

However, overexpressing or downregulating GOB using the FIL

promoter affects mainly the interval between secondary leaflets

and leaflet margin elaboration and has a minor effect on the

initiation stage. This suggests that while balancing the activities

of KNOXI and LA proteins defines the length of the PM stage,

GOB affects the location and timing of leaflet initiation within

the PM.

HowdoKNOXI proteinsmaintain themorphogenetic activity of

the leaf margin? One way by which these proteins regulate the

morphogenetic activity of the SAM is by modulating hormone

levels (Shani et al., 2006). KNOXI genes have been shown to

negatively regulate gibberellic acid levels (Sakamoto et al., 2001;

Hay et al., 2002; Chen et al., 2004; Jasinski et al., 2005) and

positively regulate cytokinin biosynthesis (Jasinski et al., 2005;

Yanai et al., 2005).

Similarities and Differences in KNOXI Function

Our results imply that functional redundancy among KNOXI

proteins is not directly correlated to their sequence homology.

Furthermore, the functional relationships among the Arabi-

dopsisKNOXI proteins appear to be context specific, such that

each specific activity is shared by different subsets of family

members. The different functions might relate to differ-

ential interactors and/or targets (Krizek and Fletcher, 2005;

Sablowski, 2007). The very different effect of the tomato genes

Tkn1 and Tkn2 in Arabidopsis leaves despite their very similar

effects in tomato is intriguing in this respect. The complex

functional relationship among KNOXI proteins, as revealed by

this and previous studies exemplifies how plants use gene

families flexibly for both backup of essential functions and

acquirement of novel activities and processes, as has been

also shown for other families of developmentally related tran-

scription factors (Emery et al., 2003; Ditta et al., 2004; Hibara

et al., 2006).

The context-specific activity of KNOXI proteins is further

emphasized by the observation that ubiquitous STM expression

failed to rescue the bp-1 phenotype (Scofield et al., 2007), in

contrast with its expression driven by the BP promoter (this

study). Furthermore, while in the Landsberg erecta background

the bp-1 phenotype is suppressed by expression ofKNAT6 in the

BP expression domain (this study), in the Columbia background,

BP was reported to negatively regulate KNAT2 and KNAT6

(Ragni et al., 2008). Genetic background was shown to dramat-

ically affect the phenotypes of KNOXI loss-of-function mutants

and KNOXI overexpressing lines (Felix et al., 1996; Mele et al.,

2003; E. Shani and N. Ori, unpublished data). Further character-

ization of the effect of genetic background on KNOXI function

might contribute to the understanding of the context-dependent

function of KNOXI proteins.

In conclusion, these results imply that highly controlled but

flexible tuning of the spatial and temporal progress of organ

maturation is one of themechanisms used by plants to produce a

highly diverse array of organ shapes.

METHODS

Plant Material

Tomato (Solanum lycopersicum cv M82) plants were grown in green-

house conditions under temperatures ranging between 18 and 258C.

Tomato plants were in an sp background. All described transgenic

genotypes were produced by the LhG4 transactivation system (Moore

et al., 1998). This system comprises driver lines that express the

synthetic transcription factor LhG4 under the control of a specific

promoter (PRO:LhG4). In a responder line, a gene of interest is ex-

pressed under the control of several copies of the Escherichia coli

Operator (OP), which is recognized by LhG4 (OP:GENE). A cross

between a driver and a responder line results in the expression of the

gene of interest under the control of the specific promoter. The tomato

driver and responder lines FILpro:LhG4, 650pro:LhG4, and OP:mRFP

have been described (Efroni et al., 2008; Shalit et al., 2009).Arabidopsis

thaliana plants were grown under long-day fluorescent light (16 h light,

218C). The described Arabidopsis plants are all in the Landsberg erecta

background. The Arabidopsis driver lines KAN1pro:LhG4, GH3.3pro:

LhG4, BLSpro:LhG4, 7470pro:LhG4, 650pro:LhG4, and ANTpro:LhG4

3088 The Plant Cell

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have been described (Schoof et al., 2000; Efroni et al., 2008). BPpro:

LhG4 was a gift from Yutaka Sato (Nagoya University). The Arabidopsis

lines OP:STM, OP:BP, OP:KNAT2, OP:KNAT6, OP:Tkn1, and OP:Tkn2

and the tomato lines OP:Tkn1, OP:Tkn2, OP:Tkn2-SRDX, GH3pro:

LhG4, and BLSpro:LhG4 were generated during this research as

described below.

Plasmids and cDNA Clones and Plant Transformation

To generate OP:Tkn2-SRDX, assembly PCR was used to introduce the

36-nucleotide-long SRDX motif: CTCGATCTGGATCTAGAACTCCGTTT-

GGGTTTCGCT + TAA stop codon (Hiratsu et al., 2003) in the C terminus

of the TKN2 protein. Tkn2-SRDX, Tkn1, Tkn2, STM, BP, KNAT2, and

KNAT6 were cloned downstream to an OP array (Moore et al., 1998) and

transferred into the binary pMLBART or pART27 vectors (Eshed et al.,

2001). The GH3.3 and BLS promoters were cloned upstream of LhG4

(Moore et al., 1998) and subsequently cloned into the pART27 binary

vector. Primers used to clone the different cDNAs and promoters are

described in Supplemental Table 1 online. Cotyledon transformation in

tomato was performed according to McCormick (1991). Arabidopsis

transgenic lines were generated by the floral dip method (Clough and

Bent, 1998), and BASTA- or kanamycin-resistant transformants were

selected in soil by spraying. Between 8 and 10 independent lines of each

construct were examined, and further analysis was performed with one

strong and one weak line.

Plant Genetics

Detailed phenotypic analyses were performed with selected OP:GENE

responder lines that were crossed to promoter:LhG4 driver lines. Six to

eight independent responder lines of each KNOXI gene were crossed to

the BLS driver line, and a representative line is presented in Figure 5. To

generate BPpro>>KNOXI bp-1, plants homozygous for BPpro:LhG4

were crossed to plants homozygous for the bp-1 mutation. Similarly,

relatively strong lines of OP:STM, OP:BP, OP:KNAT2, and OP:KNAT6,

selected by the phenotype of the corresponding BLSpro>>KNOXI line,

were each crossed to bp-1. F2 BPpro:LhG4 bp-1 plants, selected by

resistance to BASTA and the bp-1 phenotype, were crossed to each

of the four similarly selectedOP:KNOX1 bp-1plants. All F1 plants showed

the bp-1 phenotype except those possessing both the BPpro:LhG4 and

the OP:KNOXI transgenes, which showed a suppressed phenotype.

Genomic DNA was extracted and analyzed by PCR to verify BPpro>>

KNAT2 bp-1 plants.

Phenotype Quantification

The WinFOLIA image analysis software was used to measure leaf area

and leaf perimeter. The angles between the first four pedicels and the

main stem in Arabidopsis were measured in five individuals using the NIH

ImageJ software program.

RNA Analysis

Thirteen-day-old seedlings were harvested at comparable developmen-

tal stages. Total RNA was isolated using the Qiagen’s RNeasy Mini and

Micro kits, and cDNA was prepared from 1 mg total RNA with a poly(A)

primer using the ABgene Verso RT-PCR kit (AB-1453/B). Quantitative

real-time RT-PCR analysis was performed using the TaKaRa SYBR

Premix Ex Taq II (RR081Q) kit. Reactions were performed using a Corbett

Research Rotor-Gene 6000 cycler. For each gene tested, at least one of

the primers used spanned an exon-exon border to avoid amplification of

genomic DNA. A standard curve was obtained for each gene using

dilutions of a cDNA sample. Quantification of each gene was performed

using the Corbett Research Rotor-Gene software. At least four indepen-

dent technical repeats were performed for each cDNA sample, and at

least three biological repeats were used for each genotype. Relative

expression of each sample was calculated by dividing the expression

level by that of tubulin (in arbitrary units). Gene/tubulin ratios were then

averaged and presented as a ratio of a control treatment, the value of

which was set to 1. Primer sequences are detailed in Supplemental

Table 1 online.

Microarray Analysis

Microarray expression analysis was performed with total RNA from 13-d-

old apices that contained the SAM and the five youngest leaf primordia.

Labeled RNAwas hybridized to an Affymetrix GeneChip TomatoGenome

Array (900738) containing >10,000 probe sets. Two biological repeats

were analyzed for each genotype. Robust multichip average analysis

(Irizarry et al., 2003) was used to simultaneously normalize data from all

groups, and Partek software was used for statistical analysis. One-way

analysis of variance was applied to compare the three genotypes: wild-

type, FILpro>>Tkn2-SRDX, and FILpro>>Tkn2. Contrasts were calcu-

lated between each pair of genotypes. False discovery rate was used to

identify differentially expressed genes. Genes with step-up (P value <

0.05) that met at least one of the following criteria were used for cluster

analysis: filter 1, genes with fold change higher than two between the wild

type and FILpro>>Tkn2; filter 2, genes with fold change higher than two

between the wild type and FILpro>>Tkn2-SRDX; filter 3, genes with fold

change higher than two between FILpro>>Tkn2 and FILpro>>Tkn2-

SRDX. The filtered set of 1221 genes was clustered by the SPC algorithm

into eight unique clusters, and the samples were sorted by the SPIN

algorithm for clearer visualization of the clusters (Blatt et al., 1996; Kela

et al., 2009).

Imaging and Microscopy

Dissected apices and primordia were immediately placed into drops of

buffer (75 mM n-propylgallate, 60% glycerol) on glass microscope slides

and covered with cover slips. The pattern of mRFP expression was

detected by a confocal laser scanning microscope (CLSM model

LSM510; Zeiss) with the argon laser set at 488 nm for excitation, a

long-pass 560-nm filter for chlorophyll emission, and HeNe laser set at

543 nm for excitation, band-pass 560- to 615-nm filter for mRFP emis-

sion. Optical sections from successive focal planes of each primordia

tract region were collected and projected as a reconstructed three-

dimensional image using the LSM image browser (version 3.5.0.376).

Image collection and parameter settings were identical for each of the

different tract regions analyzed. Fluorescence was quantified using the

Image J software by the local mean fluorescence intensity level ap-

proach (Heifetz and Wolfner, 2004). Briefly, fluorescence intensity was

quantified in four different locations of identical areas within each leaf

region and averaged. The background fluorescence intensity was

subtracted. Three biological repeats were tested for each combination

of genotype and location. Stereoscope images were captured by an

Olympus SZX12 zoom stereo microscope using a dsRED florescence

filter set for mRFP. Tissue sectioning was performed as described

(Goldshmidt et al., 2008) and imaged with a Nikon Eclipse E800

microscope using a 4’,6-diamidino-2-phenylindole filter set for flores-

cent brighter and dsRED filter set for mRFP. Scanning electron micros-

copy was performed using a JEOL 5410 LV microscope as described

(Brand et al., 2007).

Accession Numbers

Sequence data from this article can be found in the Arabidopsis Genome

Initiative or GenBank/EMBL databases under the following accession

Regulation of Leaf Maturation by KNOX 3089

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numbers: KAN1, At5g16560; GH3.3, At2g23170; BLS, At3g49950; 7470,

At2g17470; 650, At1g13650; ANT, AT4G37750; BP, AT4G08150; STM,

AT1G62360; KNAT2, AT1G70510; KNAT6, AT1G23380; Tkn1, U32247;

and Tkn2, U76407.

Supplemental Data

The following materials are available in the online version of this article.

Supplemental Figure 1. Tkn2-SRDX Coexpression Represses the

Phenotypes of Both BLSpro>>Tkn1 and BLSpro>>Tkn2.

Supplemental Figure 2. FILpro>>Tkn2 and FILpro>>Tkn2-SRDX

Seedlings Show Opposing Molecular Phenotypes.

Supplemental Figure 3. Characterization of the Expression Directed

by Three Leaf-Specific Promoters.

Supplemental Figure 4. Relative Expression Levels of Tkn2 mRNA in

Seedlings Overexpressing Tkn2 by the Indicated Promoters.

Supplemental Figure 5. Tkn2 Expression in Tomato Leaflets Delays

Differentiation and Enables the Formation of Several Higher-Order

Leaflets.

Supplemental Figure 6. Diverse Levels of Leaf Lobing Caused by

Expression of Different KNOXI Family Members.

Supplemental Figure 7. Tkn1 and Tkn2 Expression in Arabidopsis at

Late Stages of Development Does Not Alter Leaf Shape.

Supplemental Table 1. Primers Used in This Study.

Supplemental Table 2. Differentially Expressed Genes of Cluster 1.

ACKNOWLEDGMENTS

We thank Yuval Eshed and Yutaka Sato for providing genetic material,

Osnat Yanai, Roni Shalev, Ido Shwartz, and Hagay Kohay for help with

cloning and plant transformation, members of the Ori lab for technical

help and stimulating discussions, Itai Kela for help with the microarray

analysis, Einat Zelinger for help with the confocal microscopy analysis,

and David Weiss, John Alvarez, Yuval Eshed, Smadar Harpaz-Saad,

and Sharona Shleizer for critical reading of the manuscript. This work

was supported by grants from U.S.–Israel Binational Agricultural Re-

search and Development Fund (IS 3453-03 and IS 04140-08C), Israel

Science Foundation (689/05), and the Israeli Ministry of Agriculture (837-

0010-06) to N.O. and from the Israel Science Foundation Bikura Pro-

gram (1437/04) to E.S and N.O.

Received April 22, 2009; revised September 6, 2009; accepted Septem-

ber 17, 2009; published October 9, 2009.

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DOI 10.1105/tpc.109.068148; originally published online October 9, 2009; 2009;21;3078-3092Plant Cell

Eran Sharon and Naomi OriEilon Shani, Yogev Burko, Lilach Ben-Yaakov, Yael Berger, Ziva Amsellem, Alexander Goldshmidt,

KNOTTED1-LIKE HOMEOBOX Proteins Leaf Maturation by Class 1Solanum lycopersicumStage-Specific Regulation of

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Supplemental Data /content/suppl/2009/10/09/tpc.109.068148.DC1.html

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