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پاییز  95  برشما عزیزان  تبریک و تهنیت باد



Auxin-responsive gene expression: genes, promoters and regulatory
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Auxin-responsive gene expression: genes, promoters and regulatory

factors

 

 

 

 

 

 

 

 

Abstract

A molecular approach to investigate auxin signaling in plants has led to the identification of several classes of early/primary auxin response genes. Within the promoters of these genes, 

cis  elements that confer auxin responsiveness referred to as auxin-response elements or AuxREs) have been defined, and a family of  trans-acting transcription factors (auxin-response factors or ARFs) that bind with specificity to AuxREs has been characterized. A family of auxin regulated proteins referred to as Aux/IAA proteins also play a key role in regulating these auxinresponse genes. Auxin may regulate transcription on early response genes by influencing the types of interactions between ARFs and Aux/IAAs.

 

             

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Introduction

 

Auxins play a critical role in most major growth

responses throughout the development of a plant. Auxins

are thought to regulate or influence diverse responses

on a whole-plant level, such as tropisms, apical

dominance and root initiation, and responses on a

cellular level, such as cell extension, division and differentiation.

Over the past 20 years, it has been clearly

demonstrated that auxins can also exert rapid and specific

effects on genes at the molecular level. Numerous

sequences that are up-regulated or down-regulated by

auxin have been described (for reviews, see Abel

and Theologis, 1996; Sitbon and Perrot-Rechenmann,

1997; Guilfoyle, 1999). Research efforts in a number

of labs are currently focused on characterizing

the mechanisms involved in the regulation of genes

by auxin. The genes that have been most extensively

studied are those that are specifically induced by active

auxins within minutes of exposure to the hormone,

and are induced by auxin in the absence of protein

synthesis. These genes are referred to as early, or primary

auxin response genes, and fall into three major

classes (

Aux/IAAs, SAURs and GH3

s). In this review,

we will briefly discuss the early/primary auxin response

gene families, the TGTCTC-containing auxin

response promoter elements and the auxin response

factor (ARF) family of transcription factors. A number

of reviews that cover these areas in more detail

have been published (Guilfoyle, 1999; Guilfoyle

et al.

,

1998a, b). This review will expand on these areas and

focus on information that has recently emerged (for

example, information derived from the publication of

the genome sequence of

Arabidopsis

) or has recently

been published. We also present a working model for

the regulation of auxin response genes, based on the

current available information.

Auxin-responsive genes

 

 

genes have been identified in several laboratories

 

 

differential hybridization with probes from untreated

and auxin-treated hypocotyls or epicotyls (Walker and

Key, 1982; Hagen et al., 1984; Theologis et al., 1985).

The original Aux/IAA genes to be described (soybean

 

GmAux22

, GmAux28, GH1 and pea PS-IAA4/5 and

PS-IAA6

) were expressed to moderate levels in elongating

regions of etiolated hypocotyls or epicotyls.

When these elongating regions are excised and incubated

in auxin-freemedium, the Aux/IAA mRNAs are

rapidly depleted, and can be rapidly induced by addition

of auxin to the medium. Aux/IAA mRNAs are

specifically induced by active auxins; protein synthesis

inhibitors, such as cycloheximide, also induce the

accumulation of Aux/IAA transcripts (for review, see

Guilfoyle, 1999).

Aux/IAA

genes are present as multigene families

in soybean (Ainley et al., 1988), pea (Oeller et al.,

1993), mung bean (Yamamoto et al., 1992), tobacco

(Dargeviciute et al., 1998) and tomato (Nebenfuhr et

al

(see article by Liscum and Reed, 2002). Most of the

Arabidopsis

genes are induced by auxin and show a

range of induction kinetics (Abel et al., 1995); however,

IAA 28

is not responsive to exogenous auxin

(Rogg et al., 2001). Aux/IAA genes are also found

in monocots and gymnosperms (GenBank EST database),

but are not found in organisms other than

plants.

Aux/IAA proteins generally range in size from

20 to 35 kDa. They are short-lived and localize to

the nucleus (Abel et al., 1994; Abel and Theologis,

1995). Four conserved motifs are found in most

Aux/IAA proteins, and these are referred to as domains

I, II, III and IV (Figure 1; Ainley et al., 1988;

Abel et al., 1995). Domain II plays a role in destabilizing

Aux/IAA proteins, and may be a target for

ubiquitination (Worley et al., 2000; Colon-Carmona

et al.

, 2000; Ouellet et al., 2001). Domain III is

part of a motif that is predicted to resemble the amphipathic

βαα

-fold found in the β-ribbon multimerization

and DNA-binding domains of Arc and MetJ

repressor proteins (Abel et al., 1994). The predicted

βαα

motif has been shown to play a role in dimerization/

multimerization of Aux/IAA proteins and in

heterodimerization between Aux/IAA and ARF proteins

(Kim et al., 1997;Ulmasov et al., 1997b; Morgan

et al.

, 1999; Ouellet et al., 2001); however, a role

for this motif in DNA binding has not been demonstrated.

The function of domains I and IV in Aux/IAA

proteins is not clear, but recent experiments suggest

that domain I may play a role in homodimerization of

Aux/IAA proteins (Ouellet et al., 2001).

A number of mutations in Aux/IAA genes have

been identified that provide insight into the role played

by these proteins in auxin responses. Some of these

mutants display light-grown phenotypes when grown

in the dark, suggesting that they bypass a requirement

for phytochrome in selected aspects of photomorphogenesis.

In this regard, recent studies have shown that

phytochrome A interacts with and phosphorylates the

amino-terminal half (encompassing domains I and II)

of selected Aux/IAA proteins in vitro (Colon-Carmona

et al.

, 2000). The Aux/IAA mutants are discussed in

more detail in the article by Liscum and Reed in this

issue.

SAUR genes

 

 

A group of small, auxin-induced RNAs, referred to as

SAURs, was identified in a differential hybridization

screen of clones from auxin-treated soybean elongating

hypocotyl sections (McClure and Guilfoyle,

1987). These RNAs are induced within 2-5 min of

exposure to exogenous auxin. SAURs are moderately

abundant in the zone of cell elongation in soybean

hypocotyls, and most strongly expressed in epidermal

and cortical cells; induction by auxin results in

an elevation of transcripts within the same cell types

(Gee et al., 1991). Auxin induction of soybean SAURs

is transcriptionally regulated (McClure et al., 1989)

and specific for active auxins (McClure and Guilfoyle,

1987). Treatment with the protein synthesis inhibitor

cycloheximide (CHX) does not inhibit or enhance

auxin-induced transcriptional activation of soybean

SAURs, but does result in an increase in the abundance

of SAUR transcripts (McClure and Guilfoyle, 1987).

This induction by CHX was shown, however, not to

 

be at the level of transcription, and must result from

the stabilization of SAUR transcripts (Franco et al.,

1990).

Sequence analysis of three soybean SAUR cDNAs

and genes revealed that the genes contain no introns

(McClure et al., 1989). The deduced open reading

frames (ORF) encode proteins of 9-10 kDa. Five soybean

SAUR

genes are clustered in a single 7 kb locus

of the nuclear genome, and each gene is oriented in

an opposing orientation. The 5 ORFs show a high

degree of homology, particularly in the C-terminal

portion of the protein. Database searches indicate that

the predicted structures of SAUR proteins are not

highly homologous to any other published amino acid

sequences.

Auxin-inducible SAURs have also been described

from mung bean (Yamamoto et al., 1992), pea (Guilfoyle

et al.

, 1993), Arabidopsis (Gil et al., 1994),

radish (Anai et al., 1998) and Zea mays (Yang and

Poovaiah, 2000). In addition to auxin, some of these

SAUR mRNAs are induced by CHX (Gil et al., 1994).

In contrast to the soybean SAURs, the Arabidopsis

 

SAUR-AC1 appears to be transcriptionally induced by

CHX (Gil et al., 1994); SAUR-AC1 is also induced

by the plant hormone cytokinin (Timpte et al., 1995).

There are over 70 SAUR genes in Arabidopsis (Table

1). With one exception (AtSAUR11), all genes appear

to lack introns (GenBank annotations for AtSAUR26,

-33, -39

suspect that these annotations are incorrect and that

these genes consist of single exons, because the annotated

3' exons are unrelated to conserved SAUR

 

sequences). Many of the SAUR genes in Arabidopsis

 

are found in clusters, like those originally identified in

soybean. Clusters of eight, five, six and seven, and five

SAUR

genes are found on chromosomes 1, 3, 4 and

5, respectively (Figure 2). It is not known how many

genes in this large gene family are expressed and are

auxin-inducible.

As mentioned above, at least some SAUR genes

are transcriptionally regulated by active auxins. There

is evidence, however, that SAURs are also regulated

post-transcriptionally. SAURs encode unstable mRNAs

(McClure and Guilfoyle, 1989; Franco et al.,

1990), and their high turnover rate may be due, in part,

to a conserved element (DST) in the 3-untranslated

region of the mRNA (McClure et al., 1989; Newman

 

et al.

, 1993) and/or elements within the ORF (Li

et al.

, 1994). SAUR proteins may also be regulated

posttranslationally. Based on studies using anti-SAUR

antibodies, there is evidence that SAUR protein abun-

 

Figure 2.

Chromosome positions of SAUR genes in Arabidopsis.

SAUR

genes are indicated in boxes along with the BAC clone on

which they are found. Gray boxes above chromosomes 1 and 4

indicate that the chromosome position has not been determined.

See Table 1 for SAUR gene nomenclature and GenBank Gen Info

Identifier Number (Gene ID).

dance is low (Guilfoyle, 1999), suggesting that SAUR

protein half-life may be very short.

The function of SAUR proteins is still unknown;

however, they may play some role in an auxin signal

transduction pathway that involves calcium and

calmodulin. This possible role is suggested from recent

experiments that demonstrate in vitro binding

of calmodulin to an amino terminal domain in several

SAUR proteins (i.e., maize ZmSAUR1, soybean

SAUR 10A5 and Arabidopsis SAUR-AC1; Yang and

Poovaiah, 2000). While the amino terminus is not

highly conserved in amino acid sequence among the

SAUR proteins, a putative basic α-amphipathic helix

domain found in the amino terminus may provide a

calmodulin-binding site in these proteins.

GH3 genes

 

 

The GH3 mRNA is one of several sequences that

was recovered in a differential hybridization screen of

auxin-induced cDNA sequences derived from auxintreated,

etiolated soybean seedlings

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Auxin-responsive promoters, promoter elements

and interacting factors 

The promoters of several auxin-responsive genes (soybean

GH3

 

, soybean SAUR15A and pea PS-IAA4/5

)

have been analyzed in some detail, using a variety

of methods (e.g. deletion analysis, linker-scanning,

site directed mutagenesis, gain of function analysis;

reviewed by Guilfoyle, 1999). The smallest element

to be identified as auxin-responsive is a six-base pair

sequence, TGTCTC (Ulmasov

et al.

, 1997a, b). This

element has been shown to function in both composite

and simple auxin-response elements (AuxREs; Figure

3). In composite AuxREs, such as those found

in the GH3 promoter fragments D1 and D4, the

TGTCTC element is only functional if combined with

a coupling or constitutive element (Figure 3; reviewed

by Guilfoyle

et al.

, 1998a; Guilfoyle, 1999). Simple

AuxREs, derived from the alteration of naturally

occurring AuxREs, may function in the absence of

a coupling element if the TGTCTC elements occur

as direct or palindromic repeats that are appropriately

spaced (Figure 3; P3 (4X)-palindromic repeats

spaced by 3 bp; ER7-everted repeats spaced by 7 bp;

DR5-direct repeats spaced by 5 bp; DR5R-direct repeats

in the inverse orientation; reviewed by Guilfoyle

et al.

 

, 1998a; Guilfoyle, 1999). These simple, synthetic

AuxREs are 5-10 times more auxin-responsive

than natural AuxREs (Guilfoyle, 1999).

Natural AuxRE promoter-reporter constructs have

been used to study organ and tissue expression patterns

of auxin-responsive genes (Guilfoyle, 1999). These

constructs have been valuable tools to follow gene

expression events during growth responses associated

with changes in auxin gradients or sensitivities, such

as gravitropismand phototropism(Li

et al.

, 1999), and

in studies of signal transduction pathways in plants

(Kovtun

et al., 1998; Kovtun et al.

, 2000). Synthetic

AuxRE-reporter genes have been shown to respond to

auxin in a wide variety of organs, tissues and cell types

(Ulmasov

et al., 1997b; Oono et al.

, 1998). These

synthetic AuxREs, when fused to minimal promoterreporter

genes, have been used to monitor cell and/or

tissue responses to endogenous auxin in wild type

and mutant plants carrying the reporter gene (Sabatini

et al.

 

, 1999; Mockaitis and Howell, 2000; Zhao et al.

,

2001). In addition, these constructs have provided the

basis to develop genetic screens for auxin response

mutants (Oono

et al., 1998; Murfett et al.

, 2001).

To identify proteins that bind to the TGTCTC element,

Ulmasov

et al.

(1997) used the synthetic AuxRE

P3 (4X) (see Figure 3) as a bait in a yeast one-hybrid

screen of an

Arabidopsis

cDNA expression library.

A novel transcription factor, referred to as auxinresponse

actor 1 or ARF1, was identified and shown to

bind with specificity to TGTCTC AuxREs.

Arabidopsis

 

has 23

ARF

-related genes (Table 3). One of these

genes (ARF23)

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