transcription factors regulating the progression of monocot and dicot seed development

Prospects & Overviews

Transcription factors regulating theprogression of monocot and dicot seeddevelopment

Pinky Agarwal1), Sanjay Kapoor1) and Akhilesh K. Tyagi1)2)�

Seed development in this paper has been classified into

the three landmark stages of cell division, organ initiation

and maturation, based on morphological changes, and

the available literature. The entire process proceeds at

the behest of an interplay of various specific and general

transcription factors (TFs). Monocots and dicots utilize

overlapping, as well as distinct, TF networks during the

process of seed development. The known TFs in rice

and Arabidopsis have been chronologically categorized

into the three stages. The main regulators of seed devel-

opment contain B3 or HAP3 domains. These interact

with bZIP and AP2 TFs. Other TFs that play an indispen-

sable role during the process contain homeobox-, NAC-,

MYB-, or ARF-domains. This paper is a comprehensive

analysis of the TFs essential for seed development and

their interactions. An understanding of this interplay will

not only help unravel an integrated developmental pro-

cess, but will also pave the way for biotechnological

applications.

Keywords:.dicot; embryogenesis; monocot; seed development;

transcription factor

Introduction

Seed is the progenitor of a new generation and contains storednutrients, which are the source of food not only for the grow-ing seedling but also for human beings and animals. The seedconsists of an embryo, which gives rise to the new plant, a foodstorage section called the endosperm and a protective seedcoat. On the basis of the presence of one or two cotyledons inthe embryo, angiosperms are classified into monocots anddicots, respectively. The development of seed from the timeof fertilization to maturity has been studied in great detail. Notonly have the morphological changes occurring in the seedduring its development been elucidated [1, 2], but the gamut ofgenes regulating this process are also known. A large numberof genes important for seed development have been revealedby studies on the complete transcriptome during this process.The regulation of this process is controlled by an intricatenetwork of transcription factors (TFs), many of which havebeen characterized. These, in conjunction with components ofsignal transduction pathways including plant hormones, con-trol the whole developmental process by forming a regulatoryweb. TFs preside over all the processes occurring during seeddevelopment [3–7]. Most plant TFs have domains for DNAbinding (DBD), oligomerization, transcriptional regulation,and a nuclear localization signal. The TFs have been dividedinto families on the basis of their structural features, mainlythe conserved DBD, and oligomerization domains. TFs areeither expressed constitutively or in response to a particularcondition, which here refers to seed development.

DOI 10.1002/bies.201000107

1) Interdisciplinary Centre for Plant Genomics, Department of PlantMolecular Biology, University of Delhi South Campus, New Delhi, India

2) Present Address: National Institute for Plant Genome Research, NewDelhi, India

*Corresponding author:Akhilesh K. TyagiE-mail: [email protected]

Abbreviations:ABA, abscisic acid; bZIP, basic leucine zipper; CE, coupling element; DBD,domains for DNA binding; HAP, heme associated protein; LEA, lateembryogenesis abundant; PCD, programmed cell death; PcG, polycombgroup; SAM, shoot apical meristem; SSP, seed storage protein; TF,transcription factor.

Bioessays 33: 189–202,� 2011 WILEY Periodicals, Inc. www.bioessays-journal.com 189

Review

essays

We have attempted to include TFs that have been implicated inseed development in monocots as well as in dicots, based ontheir expression and/or functional validation in rice andArabidopsis, respectively. The entire process of seed develop-ment has been classified into three major stages and the TFsassigned to these stages according to their roles. Certain TFfamilies are stage-specific. This can be exemplifiedby homeoboxgenes that are expressed during the early stages of seed develop-ment. Similarly, LEC genes are said to be master regulators. Thetemporal expression patterns of TFs may help in developing anunderstanding of their inter-dependence. It would be interestingto examine if the TFs that are expressed early somehow influ-ence the expression of those functioning later during the proc-ess. In terms of integrated plant biology and potentialbiotechnological applications, once the TFs involved in seeddevelopment and their order of action is completely revealed,researchers can manipulate the process as required, in particu-lar for yield-related components. It would also help in theexpression of desired proteins, like those associated withimproved nutrition, spatially as well as temporally, directedby the promoters of these TFs, in the same way that promotersof seed storage protein genes are currently exploited.

Landmark events during seeddevelopment

Seed development in higher plants involves embryo/endo-sperm development and seed maturation [8]. After fertiliza-tion, the primary endosperm nucleus undergoes uninhibitednuclear divisions to form a syncytial endosperm [9].Embryogenesis involves morphogenesis and maturation.Morphogenesis involves the establishment of the embryo bodyplan, while the cell expansion and accumulation of storagemacromolecules that are related to desiccation, germination,and early seedling growth, occur during maturation [10].Auxins, abscisic acid (ABA), cytokinins, and gibberellins(GAs) are also important for maturation. A group of seedstorage proteins (SSPs), called albumins in dicots and prola-mins in monocots, accumulate during maturation. As the seedprogresses toward maturity, it undergoes dehydration, meta-bolic activities are inhibited and it enters a phase of dormancy.On the basis of available data and observed morphologicalchanges in embryo and endosperm, the entire process of seeddevelopment can be classified into three landmark events inboth rice and Arabidopsis (Box 1) [1, 2, 4, 9–12]. TFs controlvarious stages of seed development (Fig. 1) and they belong tovarious families (Table 1).

TFs involved in the post-fertilization phaseof seed development (Stage 1)

A flurry of transcriptional activity exists at the first celldivisions

Post-fertilization, the zygote undergoes division to form twocells (Box 1). As emphasized by mutant phenotypes andexpression pattern analyses, WOX genes are required for pat-tern formation during early embryogenesis and region-specific

regulatory programs. WOX2 and WOX8/STIMPY-LIKE/STPL,which are expressed in the fertilized zygote, become restrictedto the apical and basal cells, respectively; WOX9/STIMPY/STIP starts to express in the basal cell but later also appearsin the apical cell and WOX5 expression is localized to thequiescent center [13–15]. Thus, in Arabidopsis, WOX genesexpress immediately after fertilization and participate inpolarity establishment (Fig. 1). Maize ZmWOX2A, ZmWOX4,and ZmWOX9A/B/C have also been shown to be important forembryo development [16]. In the two-celled embryo,MINISEED3/MINI3/WRKY10, a transcriptional repressor ofGA activation is present. It has been identified by mutantstudies and is involved in controlling seed size in conjunctionwith an LRR receptor kinase (HAIKU2). Both MINISEED3/MINI3/WRKY10 and HAIKU2 are, in turn, regulated bySHORT HYPOCOTYL UNDER BLUE1/SHB1 [17]. CUP SHAPEDCOTYLEDON3/CUC3, identified by an enhancer trap screen,expresses in the apical half of the eight-celled embryo (Box 1)and controls apical patterning [18]. TF genes controllingbasal embryonic patterning and isolated as mutants,MONOPTEROS/AUXIN RESPONSE FACTOR5 (MP/ARF5) andBODLENOS (BDL/IAA12), express in the apical cell and controlbasal cell specification [19]. TARGET OF MP5/TMO5 and TMO7participate in root initiation [20]. Additionally, TOPLESS/TPL,a transcriptional co-repressor, interacts with BDL, whichtogether then interact with MP/ARF5 and the complex actsas a repressor of auxin responsive genes [21]. Once auxin isproduced in the apical cell of the embryo, BDL is degraded andMP along with SCARFACE/SFC activates and transports PIN-FORMED1/PIN1 (an auxin efflux carrier), resulting in hypo-physis specification [22]. PLETHORA1/PLT1 expresses in thebasal cells of the four-celled embryo. From the octant stageonwards, PIN and PLT control each others expression, andlead to the formation of a quiescent-center (Fig. 2B) [23]. Also,TPL targets the PLT genes [24]. Research is on-going to extendthe aforementioned knowledge from Arabidopsis to monocots,maize and rice [19]. Auxin signaling evolved early duringevolution: though it is absent in unicellular alga, it is alreadypresent in mosses, lycopods, and gymnosperms. HomologousWOX genes and auxin transport genes are involved in gym-nosperm embryogenesis [19, 25, 26]. It would be interesting toexamine the role of WOX genes on the polarity of the zygoteand their influence on the expression of patterning genes andon genes expressing in subsequent stages. Furthermore, anunderstanding of DNA-protein and protein-level interactionsas well asmodifications could help develop a functional modelfor early seed development.

Master regulators take charge

The master regulators of Arabidopsis seed development arethe LEAFY COTYLEDON/LEC genes (Figs. 1, 2A). In leafy coty-ledon mutants, the leaves and cotyledons cannot be distin-guished [27]. Of these genes, seed-specific LEC1 startsexpressing at high levels in the pre-globular to heart-stageembryos (Box 1). LEC1 is a transcriptional activator of genesinvolved in embryo morphogenesis and cellular differen-tiation. LEC1 acts downstream of auxin and sucrose signals[6]. LEC1-LIKE/L1L also begins to express in the early embryo,suspensor, and endosperm, though later than LEC1, implying

P. Agarwal et al. Prospects & Overviews....

190 Bioessays 33: 189–202,� 2011 WILEY Periodicals, Inc.

Review

essays

Box 1ASeed development stages in Arabidopsis

The diagram represents cells in a single plane

Landmark event I – Cell division

The post-fertilization to pro-embryo stage of the embryo(0-2 DAF, days after fertilization) involves rapid cell divisionin both the embryo and endosperm. The endosperm formsa syncytium by the end of this stage. (a) During doublefertilization, one sperm nucleus fuses to the egg cell to formthe zygote (zy). Another sperm nucleus fuses to the centralcell (cc), which divides to form the endosperm. (b) The firstasymmetric division of the zygote results in formation of abi-nucleate embryo. The smaller apical (ac) and largerbasal (bc) cells are the precursors of the embryo and thesuspensor, respectively. The polarity of the zygote is estab-lished either prior to this first zygotic division or immediatelyafter it. Simultaneously, the fertilized central cell nucleusdivides rapidly without cell wall formation to form a coe-nocytic endosperm (endo) and nuclei arrange at the per-iphery surrounding a central vacuole (cv). (c) The seconddivision of the apical cell is vertical while that of the basalcell is horizontal. The endosperm nuclei also continue todivide. The differential expression of TFs in the apical celland basal cell lead to apical and basal patterning, respect-ively. (d) The apical cell divides to form an 8-celled embryocalled an octant. The uppermost cell of the suspensor istermed a hypophysis (hy).

Landmark event II – Initiation of organs

Organ initiation begins during the globular-heart transitionstage of the embryo (3-4 DAF) and the endosperm under-goes cellularization. (e) In the 16-celled globular shapedembryo (emb), the outermost layer of cells is the proto-derm (proto). (f) Cell division in the inner cells of theglobular embryo lead to axis formation and regional differ-entiation. (g) The triangular-shaped, late globular/tran-sition embryo has approximately 200 cells. At the final

round of coenocytic mitosis of the endosperm, cellulari-zation (ce) rapidly begins from the region surrounding theembryo. The outer-most cellularized layer of the endo-sperm is called the aleurone (aleu). Formation of the innerpro-cambium tissue layer and the middle layer of groundmeristem cells, specification of cotyledons, and differen-tiation of root meristem from the hypophyseal cells occurduring this period.

Landmark event III – Maturation

Organ expansion and seed maturation occur from 5-24DAF. The embryo proceeds from the heart stage to themature green stage through the linear and bent cotyledonstages. The endosperm undergoes endoreduplication, fol-lowed by programmed cell death (PCD). (h) The transitionembryo starts forming cotyledons and acquires a heartshape. Simultaneously, endospermcellularization also pro-ceeds. Cell division and expansion lead to an increase inthe size of the cotyledons and axis and (i) the embryoacquires a torpedo shape. The suspensor begins to sen-esce. (j) The embryo acquires a linear-cotyledon shape.Once endosperm cellularization is completed, endoredu-plication occurs. There is nomitosis at this point, as occursin monocots. As the embryo grows and bends, there isdegeneration of the endosperm by PCD. (k) A mature seedis completely occupied by the embryo surrounded by anepidermal layer of endosperm called the aleurone (aleu).Themature embryo consists of the cotyledons (coty), shootapical meristem (SAM), and rootmeristem (rm). The seed issurrounded by a protective seed coat (sc). Large amountsof storage proteins and oils accumulate. By the end of thisphase, the seed is dehydrated, RNA and protein synthesisstops and the embryo enters a dormant phase.

....Prospects & Overviews P. Agarwal et al.

Bioessays 33: 189–202,� 2011 WILEY Periodicals, Inc. 191

Review

essays

Box 1BSeed development stages in rice

The diagram represents structures in a single plane

Landmark event I – Cell division

Rapid cell division occurs in the post-fertilization tomiddle-globular embryo stages (0-2 DAP, days after pol-lination). The endosperm forms a syncytium. (a) On theday of pollination, the filaments (fil) of rice florets elongateso that the anthers (anth) grow above the stigma (stig) anddeposit the pollen. The lemma (L) and palea (P) of theflorets open up. Fertilization occurs on the same day toform a zygote (zy). (b) After pollination, the floret is closed.The anthers and stigma dry up. The embryo undergoesvariably-oriented cell divisions to form a 25-celled earlyglobular embryo (1 DAP). At 2 DAP, a 150-celled middlestage globular embryo (emb) is formed. The fertilizedcentral nucleus also begins dividing. The endosperm(en) nuclei divide faster than the zygote nuclei and migrateto the periphery because of an enlarged central vacuole(cv).

Landmark event II – Initiation of organs

The embryo undergoes pattern formation and region-alization and the endosperm cellularizes (3-4 DAP).(c) At 3 DAP, the embryo is in the late globular stageand organ formation initiates. A cell size gradient isestablished in the embryo along the dorso-ventralaxis, with the ventral cells being smaller. Cell wall for-mation occurs centripetally in the endosperm (en). (d) At4 DAP, a coleoptile (cl), radical primordium (rm), a flatSAM (s), and scutellum are all initiated. The endospermis in a green-colored, liquid state and its size increasesdramatically. Cellularization is followed by a mitoticphase which starts at 4 DAP and continues until 20DAP.

Landmark event III – MaturationOrgan enlargement and maturation of the embryo occurs.The endosperm also undergoes differentiation and matu-ration (5-29 DAP). (e) At 5 DAP, the first leaf primordium(lp) can be seen on the opposite side of the coleoptile. Thescutellum (sc) enlarges. The scutellum is the modifiedcotyledon that helps in nutrient transfer from the endo-sperm. Second and third leaf primordia emerge at 7 and 8DAP, respectively. The SAM becomes dome-shaped andthe epiblast (epi) also enlarges. Organ enlargement con-tinues until 10 DAP when all the organs are developed.The endosperm is in the milky stage. Due to continuingmitosis from the previous stage, various regions differen-tiate in the endosperm; namely transfer cells near theplacenta, the aleurone layer surrounding the endosperm(except in the transfer cell region), and the starchy endo-sperm. At 8-10 DAP, the endosperm endoreduplicatesand becomes polyploid. (f) At 14 DAP, the embryo con-sists of the SAM (s), coleoptile (cl), scutellum (sc), radicle(rm), and epiblast (epi). The epiblast is opposite to thescutellum and is a rudimentary cotyledon. The endospermenters the soft dough stage and hardens to the harddough stage. The storage phase of the endosperminvolves starch synthesis and the accumulation ofstorage proteins – prolamins and globulins. PCD in theendosperm begins at 16 DAP. Therefore, only the aleur-one layer is alive in the mature endosperm. The embryomatures until 20 DAP and is dormant thereafter. (g) Amature rice seed is enclosed in the husk (hu), whichhas been formed by the hardening and drying of thelemma and palea. The embryo is present on the ventralside. Unlike Arabidopsis, the endosperm covers a majorarea of the seed. The tegmen (teg) or seed coat covers theendosperm. The outermost layer of endosperm is calledthe aleurone (aleu).



Review

essays

different roles for these two genes [4]. The transcripts ofanother seed-specific LEC, LEC2, are detected mainly in theearly- and middle-stage siliques that contain early globular toheart stage embryos, and decline in the mature greenstage [27]. Members of rice heme associated protein (HAP3)family, OsHAP3D, F and G, have also been implicated inembryo development on the basis of their expression [28].LEC1 homologs have also been identified in other plants, such

Figure 1. TFs from Arabidopsis and rice expressed during the threelandmark stages of seed development. Representative diagramsshow the progression of seed development in both. The stages ofembryo development for Arabidopsis and number of days after polli-nation (DAP) for rice are noted in purple. Arabidopsis genes thatparticipate in the same network are shown in the same color. Fordetails of the stages of seed development, refer to Box 1.



Review

essays

Table 1. TF families involved in seed development.

TF Family Description Genes involved in seed development

APETALA2 A plant-specific TF family characterized by the presence of

a 70-amino acid AP2 repeat domain, initially found in the

floral homeotic protein APETALA2. This is a DNA-binding

domain. A group of AP2 proteins that bind to the ethyleneresponsive element have been designated as EREBP.

ABA INSENSITIVE 4/ABI4, AINTEGUMENTA/ANT,

AtERF38, DORNROSCHEN (DRN)/ENHANCER OF SHOOT

REGENERATION (ESR1), DRN-LIKE (DRNL)/ESR2,

OsEBP-89, PLETHORA1/PLT1

B3 The plant-specific B3 superfamily of TFs contains aconserved 110-amino acid region called the B3 domain.

The nameoriginated due to this region being the third basic

domain of maize protein VIVIPAROUS1, in which two basic

domains B1 and B2 had earlier been identified. B1 and B2are confined to VP1. The B3 superfamily is divided into

several families; ARF (AUXIN RESPONSE FACTOR), LAV

(LEAFY COTYLEDON2 [LEC2]–ABSCISIC ACID

INSENSITIVE3 [ABI3]–VAL), RAV (RELATED TO ABI3 andVP1), and REM (REPRODUCTIVE MERISTEM). Of these,

members of LAV and ARF are known to be involved in seed

development. Auxin response factors bind to the auxinresponse elements (AuxREs) located in the promoters of

auxin responsive genes and mediate auxin signaling. They

recruit another group of TFs after binding to AuxREs, called

Aux/IAA repressors, which carry forward the auxinresponse. ARFs can act either as repressors or as

activators. They contain a B3 domain for DNA binding, a

central activator or repressor domain, and may contain

domains III and IV at the C-terminal for dimerization.

ABA INSENSITIVE 3/ABI3, ARF1, FUSCA3/FUS3, LEAFYCOTYLEDON2/LEC2, MEGAINTEGUMENTA/AUXIN

RESPONSE FACTOR2 (MNT/ARF2), MONOPTEROS/

AUXIN RESPONSE FACTOR5 (MP/ARF5), OsVP1,

SCARFACE/SFC, VIVIPAROUS1/VP1

bHLH The characteristic domain is approximately 60 amino acids

long with a DNA-binding basic region and a HLH(helix-loop-helix) region. The HLH region has two

amphipathic a-helices that allow dimerization.

ENHANCER OF GLABRA3/EGL3, GLABRA3/GL3,

RETARDED GROWTH OF EMBRYO1/ZHOUPI (RGE1/ZHO), TARGET OF MP5/TMO5, TMO7

bZIP The characteristic 16-amino acid long basic region with a

NLS- and a DNA-binding domain is followed by several

leucine residues, separated by seven other residues, for

homo- and hetero-dimerization.

ABA-RESPONSIVE ELEMENT BINDING FACTOR 4/ABF4,

ABA-RESPONSIVE ELEMENT BINDING PROTEIN 3/

AREB3, ABSCISIC ACID5/ABI5, ASYMMETRIC LEAVES2/

AS2, AtbZIP10, AtbZIP12/EEL (Enhanced Em Level),AtbZIP25, AtbZIP53, AtbZIP67, JAGGED LATERAL

ORGANS/JLO,OPAQUE2/O2, REB (rice endosperm bZIP),

RISBZ1, RISBZ3, RISBZ4, ROM2HAP HAP complex is made up of HAP2, HAP3, and HAP5 and is

a CCAAT box-binding factor/CBF.

LEAFY COTYLEDON1/LEC1, LEC1-LIKE/L1L, OsHAP3D,

OsHAP3E, OsHAP3F, OsHAP3GHomeobox A 180 bp homeobox sequence codes for a 60-amino acid

long homeodomain. These genes are involved in

developmental processes in both plants and animals. Thehomeodomain is a DNA-binding domain that has three

a-helices separated by a loop and a turn and binds to the

ATTA core sequence. The homeodomains in plants can be

classified into six families: Knotted related, HD-Zip,PHD-finger, BELL, ZF-HD, and Wuschel related (WOX)

homeobox families. The first homeoboxgenediscovered in

plants was KNOTTED1 (KN1). KN1-like proteins are 400

residues long and contain three extra residues between thefirst and second helices of the homeodomain and, hence,

belong to the TALE (three-amino acid extension loop)

super-class of homeodomain proteins. This family isdivided into two classes. Both Kn-class I and Kn-class II

proteins contain a motif toward the N-terminal of the

homeodomain that has ELK as the first three residues.

HD-Zip family is divided into four classes: HD-ZIP I, II, III,and IV. HD-Zip (classes I and II) proteins are about 300

residues long and contain an acidic domain, which lies

toward the N-terminal of the homeodomain and a leucine

zipper toward the C-terminal of the domain. Leucine zipperis required for dimerization, which is essential for DNA

binding.

ATH88, ATML1, CORONA/ATHB15, GLABRA2/ATHB-10/

GL2, HAZ1, KNOTTED1/KN1, KNOTTED-LIKE/KNAT6,

Oryza sativa transcription factor 1/OSTF1, OSH1/OSKN1(Rice homeobox gene/KNOTTED1-like), OSH15 (Oryza

sativa homeobox 15), OSKN2, OSKN3/OSH15,

PHABULOSA/PHB, PHAVOLUTA/PHV, QUIESCENT-

CENTER-SPECIFIC HOMEOBOX/QHB, REVOLUTA/REV,RICE BICOID 24/RB24, RICE OUTERMOST CELL-

SPECIFIC GENE1/ROC1, SHOOT MERISTEMLESS/STM,

TRAUCO, WOX2, WOX5, WOX8/STIMPY-LIKE/STPL,

WOX9/STIMPY/STIP, WUSCHEL/WUS, ZmWOX2A,ZmWOX4, ZmWOX9A/B/C



Review

essays

as carrot and pine. It has been postulated that HAP3 genessimilar to LEC1 evolved early in non-seed plants and played arole in desiccation [25, 29]. Further research in monocots andgymnosperms may establish LEC1 as a universal master reg-ulator of seed development.

Other TFs that start expressing during early seeddevelopment

Eight MADS box genes (AGL70/MAF3,AGL53, 93, 67, FLC, FLM,AGL15 and 18) show higher expression in the Arabidopsisembryonic phase [30]. Of these, the Arabidopsis pro-embryoand developing endosperm show the accumulation of a tran-scriptional repressor, AGAMOUS-LIKE15/AGL15, that promotesembryonic development by targeting downstream genes [31]. ATFIIIA-type gene, TRANSPARENT TESTA/TT1, which isexpressed in the early stages, is involved in seed coat coloras the mutant seeds do not contain tannin pigmentation in theseed coat and, hence, are yellow in color [32]. A rice homeoboxgene,RICEOUTERMOSTCELL-SPECIFIC GENE1/ROC1, has beenshown to be required for early protoderm differentiation. Thegene was isolated by PCR as a homolog of Arabidopsis ATML1gene, which is a molecular marker of embryogenic protoderm[33]. The expression of all these genes (Fig. 1) at the initial stagesof seed development suggests that cell fate is also determinedconcurrently with zygotic divisions.

TFs controlling organ initiation (Stage 2):A stage dominated by homeobox genes

After the initial globular stage generated by cell divisions,various organs, which would later form parts of the mature

seed, begin to initiate (Box 1). In Arabidopsis, SHOOTMERISTEMLESS/STM is required for SAM initiation andmaintenance. It was isolated as a shoot-meristem mutant.STM expression is maintained by RNA-binding proteins,PINHEAD/ZWILLE/ZLL and ARGONAUTE1/AGO1. WUSCHEL/WUS establishes shoot stem cell identity through ZLL [34, 35].The rice homolog of WUS, QUIESCENT-CENTER-SPECIFICHOMEOBOX/QHB, isolated by screening an embryonic mRNAlibrary, is first detected at 3 days after pollination (DAP), andspecifies as well as maintains quiescent cells in RAM [36]. STMalso requires CUC1 and CUC2 to form SAM, and STM in turn isrequired for CUC2 function. CUC1 and CUC2 control separation ofadjacent organs in developing embryos, as validated by theirrespective mutants. They regulate cell division during embryo-genesis and are involved in vegetative and embryonic SAMformation. CUC3 is homologous to CUC1 and 2 and definesmeristem and organ boundaries. The CUC genes are upregulatedbyAtBRM, a chromatin remodelingATPase. In the central regionaround SAM, CUC genes are downregulated by STM, miR164(microRNA), and TCP (TEOSINTE BRANCHED1, CYCLOIDEA,PCF1) [18]. CUC1 is also a positive regulator of SAM formationby an STM-independent pathway, which is regulated byASYMMETRIC LEAVES1/AS1 and AS2 [37]. KNOTTED-LIKE/KNAT6 is redundant with STM. KNAT6 expresses at theboundary between SAM and cotyledons, downstream of STMand CUC (Fig. 2B) [38]. NAM and CUC are essential for SAM andcotyledon separation in both monocots and dicots [39].

HD-Zip III (Table 1) genes are the master regulators of thesubsequent development of the apical cell and are antagonisticto the PLT genes [24]. They operate in Arabidopsis probably inan auxin-mediated manner [40]. The genes involved arePHABULOSA/PHB, REVOLUTA/REV, PHAVOLUTA/PHV, andCORONA/ATHB15, which act along with ATH88. These genes

Table 1. (continued )

TF Family Description Genes involved in seed development

MADS box The MADS box consensus consists of a 57 residue region

that forms an a-helix and 2 b-strands.

AGL15, AGL18, AGL53, AGL67, AGL70/MAF3, AGL93,

FLC, FLM, TRANSPARENT TESTA16/TT16MYB The DNA binding domain of MYB TF consists of three

helix-turn-helix structures, each of which has three

regularly spaced tryptophan residues forming a cluster.Depending on the number ofMYB repeats, they are divided

into MYB1R, R2R3-typeMYB, andMYB3Rwith 1, 2, and 3

helices, respectively.

ASYMMETRIC LEAVES1/AS1, AtMYB23, CAPRICE/CPC,

GLABRA1/GL1, MYB5, OSMYB1, OSMYB4, PAP1, PAP2,

TRANSPARENT TESTA2/TT2, TRY, WEREWOLF/WER

NAC The plant-specific NAC family has been named after its

members, NAM (NO APICAL MERISTEM), ATF, and CUC(CUP-SHAPED COTYLEDON). The DNA binding domain

has been called the NAC domain.

CUP SHAPED COTYLEDON1/CUC1, CUC2, CUC3

Zinc finger This family is designated after the finger motif, which bindsto a zinc ion, co-ordinated by cysteine and/or histidine

residues. Various types of zinc finger proteins exist.

Cysteine2/Histidine2 TFs contain 2 cysteine residuesfollowed by 2 histidine residues, to which the zinc ion

binds. The plant-specific WRKY class of TFs has a

WRKYGQK motif at the N-terminal end along with a zinc

finger motif. The Dof (DNA binding with one finger) TFsconsist of a conserved 50 amino acid region that also

contains a C2C2 zinc finger and is associated with a basic

DNA-binding region. The RING (Really Interesting New

Gene) finger proteins have a C3HC4 zinc finger and act asE3-ubiquitin ligases.

AthPEX10/PEROXIN, DESPIERTO, MINISEED3/MINI3/WRKY10,RICE PROLAMIN BOXBINDINGFACTOR/RPBF,

RING FINGER PROTEIN FOR EMBRYOGENESIS/RIE1,

SERRATE, TRANSPARENT TESTA GLABRA2/TTG2,TRANSPARENT TESTA/TT1



Review

essays

interact with DORNROSCHEN (DRN)/ENHANCER OF SHOOTREGENERATION (ESR1) and DRN-LIKE (DRNL)/ESR2, whichalso interact with each other. Further, a brassinosteroid signal-ing member BM1 interacts with DRN, DRNL, and PHV. Thesegenes thereby regulate embryo patterning [18, 41]. Even in rice,

during SAM formation, a trans-acting siRNA pathway regulatesHD-ZIP III expression through miR166 [42]. In Arabidopsis,TRAUCO is also essential for early embryogenesis as demon-strated by mutant analysis and in situ hybridization [43].

As in Arabidopsis, homeobox genes play an important rolein the initial stage of monocot seed development (Fig. 1).KNOTTED1/KN1 in maize is required for SAM maintenance.It defines the boundaries of initiation of various organs [44].In situ hybridization experiments prove that OSH1/OSKN1 andOSKN3/OSH15 are expressed in the globular embryo (Box 1) inthe region of future SAM. OSH1/OSKN1 maintains the indeter-minate state of SAM. OSKN2 and OSKN3 control cell fatedetermination. OSH15 controls SAM formation and mainten-ance [45]. In the early rice embryo, polarity formation andestablishment of the apical-basal axis is controlled by RICEBICOID 24/RB24. It expresses mainly in the early globularembryo and later shows a dorso-ventral pattern [46]. Radialaxis differentiation is indicated by HAZ1, which is expressedmost in the outer layers of the globular embryo at 3 DAP andbecomes more intense in the ventral parts at 4 and 5 DAP, thusmarking the outer layer of cells before the commencement ofmorphological differentiation [47]. Screening of a rice paniclecDNA library led to the identification of Oryza sativa TF 1/OSTF1, which expresses in the embryo at the globular stage, inthe protoderm at 3-6 DAP, in the integument and throughoutthe development of the endosperm [48]. Since HAZ1, ROC1,and OSTF1 are present in the outer layers of the embryo, theirinteractions should be examined. Homologs of some homeo-box genes, as well as NAC genes, have been found to expressduring pine embryogenesis [25]. Thus, in both rice andArabidopsis and maybe also in gymnosperms, homeoboxgenes are involved in the regulation of polarity establishment,embryo patterning and initiation, andmaintenance of SAM. Ascan be seen here, the homeobox genes continue to play anessential role during the stage of organ initiation and controlSAM initiation and maintenance. Along with these, NAC andAP2 TFs are also considerably important at this stage as theywork in co-ordination with homeobox genes (Fig. 1). Keepingin mind the expression patterns and roles of these genes,investigation on the aspects involving interactions betweenNAC and AP2 TF families along with homeobox TFs wouldreveal their role in early seed development.

TFs regulating seed maturation process(Stage 3)

ABA acts through ABA INSENSITIVE genes

Seed maturation involves the role of phytohormone ABA. Earlyduring this stage in Arabidopsis, one of the key players of theABA response, ABI3, starts expressing. This gene was detectedas an ortholog of maize VIVIPAROUS1/VP1. ABI3 is embryo-specific from the early heart-shape to dry-seed stages andreaches a plateau at 16 DAP [3]. For rice OsVP1, expressionstarts at 2-3 DAP and becomes concentrated in the shoot,radicle, and vascular tissues during embryo development. Itis detected in the aleurone layers after 6 DAP. Maize VP1 isdetected in the embryo and aleurone of developing seeds and,during drought stress, additionally in the phloem cells of

LEC1

3SUF3IBA2CEL

ABI5 ABI4EEL

PINHEAD

STMWUS

MP + SCF

KNAT6UFO

CUC1 CUC2

ESR2

AS1, AS2

PIN1 PID1

PLT

ENP

A)

B)

C)

GL1 TT2

TTG2

GL2

MYBL2

GL3 EGL3MYB5

TTG1WER

Figure 2. The regulatory web of TFs in Arabidopsis. Dark green lineswith arrowheads represent activation, light green lines representauto-activation, while dark red lines with T-bars represent repression.A: The major regulators of seed development are the LEAFYCOTYLEDON genes along with ABA-INSENSITIVE genes. B: STMand CUC genes control SAM initiation and organ formation. C:MYB, bHLH, and WRKY proteins interact with each other to controlvarious functions as seed coat and trichome development. Memberswithin a colored box denote interacting protein partners. Refer to thetext for details.



Review

essays

vegetative tissues [49]. VP1/ABI3 is an activator of embryomaturation and a repressor of germination through independ-ent domains. Its B2 domain trans-activates other seed genes,such as OPAQUE2 in maize [50, 51]. The N-terminal domain isessential for the ABA-mediated response, while the B3 domainhas been implicated in controlling the expression of other seed-specific genes by binding to the RY element of their promoters[52]. VP1 acts downstream of both GA and ABA programming[53]. Arabidopsis DESPIERTO regulates ABI3 and expresses lateduring maturation [54]. A similar role has been found in gym-nosperms where the ABI3 homolog of cedar, CnABI3, activatesseed-protein (vicilin and napin) promoters [55]. This indicatesthat the role of ABA as a controller of seed development evolvedprior to the separation of angiosperms and gymnosperms.Another seed-preferential ABA responsive gene, ABI4, func-tions in co-ordinationwith itself,ABI3 andABI5.ABI4 is respon-sible for repression of lipid breakdown in the embryos. ABI5, abasic leucine zipper (bZIP) protein (Table 1), is involved in ABAsignaling in the micropylar endosperm cap [56]. ZmABI4 bindsto coupling element 1 (CE1) and then, along with VP1 and otherfactors, leads to the activation of storage and maturation phasegenes [57]. HvABI5 binds to ABRC to induce expression in thealeurone cells and is dependent on HvVP1 [58]. These three ABIgenes exist both in monocots and dicots and function similarlyand interchangeably. This also indicates a parallel role of ABAduring seed development in both.

bZIP and DOF TFs interact to regulate seed storageprotein genes

One of the first seed-specific bZIP TFs to be identified wasOPAQUE2 (O2) in maize. OPAQUE-2 is endosperm-specific andexpresses from 8 DAP to maturity and specifically trans-acti-vates the 22 kDa zein promoter [59]. O2 is also involved in PCDthrough ABA and ethylene signaling [60]. The expressionpatterns of maize PROLAMIN BOX BINDING FACTOR/PBFand O2 are identical and the two interact with each other.Both are present 2 days before zein expression begins.Endosperm-specific PBF is postulated to be themost abundantand the only Dof protein expressed in the maize endosperm.PBF first appears at 10 DAP, peaks at 15 DAP, and remains atthis level throughout the rest of endosperm development.Maize PBF and wheat WPBF show similar expression patternsin the endosperm. Barley BPBF and WPBF bind to prolaminbox in the promoters of storage protein genes [61, 62]. RiceRPBF interacts with rice seed b-Zipper/RISBZ1, and they quan-titatively control the expression of storage proteins. RPBFbinds specifically to AAAG-like sequences while RISBZ1 bindsto GCN4 motifs. The expression of RPBF is highest at 14 DAP[63]. RISBZ1, detected by screening of a rice seed cDNA library,expresses prior to the expression of seed storage genes[64, 65]. Assessment of the bZIP-Dof interaction may proveuseful as it seems to be unique to the monocot endosperm, themajor edible component, and might have evolved to developthe endosperm as the main storage tissue in monocot seeds.

Another LEAFY COTYLEDON gene controls maturation

Another important seed-preferential gene in Arabidopsis isFUSCA3/FUS3 ( Table 1, Fig. 1), which has a putative

transcriptional activation domain. fus3 is a leafy-cotyledonmutant and like ABI3/VP1, the B3 domain of FUS3 is importantfor the regulation of seed maturation. FUS3 is responsible foracquiring embryo-dependent seed dormancy by arrestingembryo growth, inhibition of precocious germination, estab-lishment of cotyledonary cell identity and synthesis andaccumulation of storage compounds [66]. FUS3 delimits thespatial expression of TTG1 during embryogenesis, which isrequired for the maintenance of testa epidermal differentiation(Fig. 2C) [67]. It is interesting to note thatArabidopsis and barleyFUS3 genes complement each other in the activation of storageprotein gene promoters [68], indicating a functional similarityamongst monocots and dicots. FUS3 works in co-ordinationwith LEC1, LEC2, and ABI3, which is elaborated below.

Certain TFs only control early seed maturation

It has been demonstrated by promoter-GFP-cDNA fusion experi-ments that bZIPs, such as Arabidopsis ABA-RESPONSIVEELEMENT BINDING PROTEIN 3/AREB3, AtbZIP12/EnhancedEm Level/EEL, AtbZIP67, AtbZIP25, ABA-RESPONSIVEELEMENT BINDING FACTOR 4/ABF4 (Fig. 1) are expressedduring embryo maturation [64]. GLABRA2/ATHB-10/GL2 startsbeing expressed in Arabidopsis at the heart-shape embryo stage(Box 1) in the protodermal cells and controls seed coat develop-ment and oil accumulation [69]. RETARDED GROWTH OFEMBRYO1/ZHOUPI (RGE1/ZHO) expresses in the endospermat the heart-shape stage and is involved in embryo growthand morphology. It regulates the breakdown of endospermduring embryo expansion [70, 71].

Few TFs only express during the middle phase of seedmaturation

Arabidopsis SERRATE is required for normal development ofembryos and expresses maximally in the adaxial portion ofcotyledon and torpedo-shaped embryos [72]. As shown by RT-PCR, rice OSMYB1 reaches a maximum level in seeds at 14 DAF(Box 1) and decreases at 21 DAF. Seed-preferential OSMYB4 isat its maximum level at 14 DAF and declines at 35 DAF [73].

TFs regulate processes until the end of seed maturity

Arabidopsis AtERF38 is detected in the outer integument cellsof mature seeds, as shown by promoter-GUS expression, and isresponsible for secondary wall metabolism in cells thatundergo suberization [74]. AtMYB23 regulates epidermal celldevelopment in seeds as well as vegetative tissues, as vali-dated by fusion with the EAR repression domain [75].Identified as a yellow seed mutant, TRANSPARENTTESTA16/TT16 is required for proanthocyanidin accumulationin the endothelium of the seed coat and for specification ofendothelial cells [76]. Mutant analysis and gene expressiondata suggest that MEGAINTEGUMENTA/AUXIN RESPONSEFACTOR2 (MNT/ARF2) represses cell division and organgrowth and, hence, determines seed size [77] and, along withARF1, promotes silique ripening [78]. A T-DNA insertionmutant of PEROXIN/AthPEX10 suggests its participation inperoxisome, oleosome and protein transport vesicle formationduring embryogenesis [79]. Though RING FINGER PROTEIN



Review

essays

FOR EMBRYOGENESIS/RIE1 expresses constitutively, embryo-lethal insertion mutant lines validate its important role in seeddevelopment [80]. Northern blots show that rice RISBZ3 andRISBZ4 are foundmaximally in latematuring seeds at 20DAF [65].The northern blots of OsEBP-89, isolated from cDNAlibraries, highlight its role in ethylene-dependent seed matu-ration in rice [81]. Rice endosperm bZIP protein/REB bindsto the promoters of a-globulin and WAXY genes, as shown bygel-shift analysis [82]. Thus, the TFs which control this phase(Fig. 1) regulate embryo and endosperm maturation, theexpression of SSPs, late embryogenesis abundants (LEAs),cause PCD and induce dormancy. The interplay amongst theseTFs needs to be studied to understand the processes, likePCD and dormancy, which are responsible for shaping seeddevelopment and survival. Additionally, PCD is a process thatoccurs in both monocot and dicot endosperm. However, thedicot endosperm is degraded, whereas the monocot endospermremains to serve as the main storage component by a distinctbut, as yet, unknown mechanism (Box 1). As stated earlier, O2participates in monocot PCD. The TFs responsible for the majordifferences between both would form an interesting study.

The regulatory web of TFs in Arabidopsis

The LEAFY COTYLEDON genes interact to control seeddevelopment

In Arabidopsis, the LEAFY COTYLEDON genes (LEC1, LEC2,and FUS3) along with ABI3, i.e. the AFL genes, are the masterregulators of seed development (Fig. 2A) and prepare thedeveloping seeds for desiccation and dormancy [3]. LEC2,FUS3, and ABI3 contain B3-domains and LEC1 has an HAP3domain (Table 1) [4]. LEC1, LEC2, and FUS3 are required fromearly embryogenesis onwards [5], as indicated by their expres-sion patterns described above. Mutant analysis has shown thatLEC1 upregulates LEC2, FUS3, and ABI3. LEC2 upregulatesLEC1, ABI3, and FUS3; FUS3 upregulates itself and ABI3; whileABI3 upregulates FUS3 and ABI5 [83]. ABI3, LEC1, and FUS3proteins act in distinct regulatory pathways and control differ-ent maturation genes. During the process of seed-filling, thesucrose:hexose ratio increases. ABI3 interacts with bZIPs,ABI5, and EEL, and they bind to ABREs. ABI3, FUS3,bZIP10, and bZIP25 interact and bind with the RY/G-boxand, together, they activate SSP genes [6]. Seed maturationinvolves seed storage protein accumulation, trichome for-mation, vascular system repression, anthocyanin repression,all of which are controlled by LEC1, LEC2, and FUS3; chlor-ophyll degradation that is controlled by ABI3; desiccationtolerance imparted by LEC1 and FUS3; ABA sensitivity medi-ated by LEC1 and FUS3 [5]; oil synthesis controlled by LEC2[84] and seed storage protein accumulation by ABI5. Also,ABI4 and ABI5 interact with LEC1 and FUS3, as shown by yeasttwo-hybrid assays [85] and discussed below. These TFs regulateoverlapping aspects of development and regulate pigmentaccumulation, vivipary suppression, mid- and late-embryogen-esis gene expression, sugar metabolism, sugar sensitivity, etio-lated growth, and suppress leafy traits in cotyledons. ABAinhibits germination and upregulates seed-storage proteinsand desiccation tolerance. FUS3 promotes ABA synthesis; while

LEC2 inhibits GA synthesis, maintaining the balance of thesehormones during seed maturation. LEC1, LEC2, ABI3, auxin,sucrose, and hexose promote embryogenesis; while PICKLE/PKL (a CHD3 chromatin remodeling factor), AIP2, VAL, HSI1,and HSL1 inhibit it. The AFL and VAL genes function throughchromatinmodification [3–6, 27, 83, 84]. LEC1 and L1L also forma complex with ABRE-binding factors and strongly upregulateseed protein genes even in the absence of ABA, implying thepresence of a distinct developmental network [86]. These inter-actions suggest that, in Arabidopsis, certain TFs with B3-,HAP3-, and bZIP-domains regulate various steps in the processof seed development in conjunction with each other. In mono-cots, such a detailed study of the TFs with these domains ismuch awaited. Additionally, the integration of L1L in this path-way needs to be studied in greater detail.

The ABI genes are common to seed developmentin monocots and dicots

There is inter-dependency between ABI3, 4 and 5, which areexpressed throughout seed development (Fig. 2A) [5, 85].These genes inhibit germination and lead to SSP and LEAproduction and impart seed dormancy and desiccation toler-ance [3, 85]. ABA upregulates the auto-regulated ABI5 [3, 58].ABI4 and ABI5, along with additional factors, regulate ABI3.ABI3 and ABI5 cross-regulate one another, as shown by yeasttwo-hybrid assays. Additionally, certain seed-specific regula-tors control these three genes [85, 87, 88] and are important forthe expression of seed proteins in Arabidopsis [89]. In themonocots, maize and barley, ABA and certain seed factorscontrol the auto-regulated TF genes VP1 and ABI5 [49]. VP1also upregulates ABI5 [51]. Apart from ABA, other unknownfactors also regulate ABI4 [56]. VP1, along with a bZIP dimer,binds to ABREs or Sph elements and ABI4 binds to CEs. In thiscombination, these genes lead to the expression of storage andseed maturation genes [49]. The bZIP dimer in Arabidopsis isformed by AtbZIP10 and AtbZIP25 which are regulated bybZIP53 [90]. In French bean, PvALF (an ABI3-like factor) actsas a transcriptional activator of MAT (maturation) genes.ROM2 acts antagonistically to PvALF and represses thesegenes during late embryogenesis, after the onset of desicca-tion. ROM2 can be detected mainly in embryos when itsexpression begins from 14 DAF and reaches a maximum at27 DAF [6]. It is rather interesting to note that ABI3, 4 and 5seem to play comparable roles in both monocots and dicots.

Interactions amongst MYB and bHLH TFs regulate seedcoat development

In Arabidopsis, R2R3 MYB TFs WEREWOLF/WER, GLABRA1/GL1, and TRANSPARENT TESTA2/TT2, along with bHLHproteins GLABRA3/GL3 and ENHANCER OF GLABRA3/EGL3,regulate HD-ZIPIV gene GLABRA2/GL2. WER physically bindsto the promoter of a WRKY TF, TRANSPARENT TESTAGLABRA2/TTG2, and thus regulates GL2. GL3 and EGL3 as acomplex, along with WER, interact with a WD repeat protein,TTG1. Interaction amongst these gene products has beenshown in yeast. This complex regulates TTG2. Mutant analysisshows that TTG2 controls GL2 [91]. Mutants reveal that MYB5and TTG1 regulate GL2. MYB5 upregulates the repressor of this



Review

essays

mechanism, MYBL2 [92] (Fig. 2C). WER upregulates anotherR3MYB TF, CAPRICE/CPC. Additionally, GL3-EGL3 interactswith other MYB proteins; namely GL1, PAP1, PAP2, andTRY. WER and CPC are expressed in the root epidermal layerin the torpedo stage embryo and GL2 expresses in the futureepidermis. GL2 controls elongated cell development of non-hair cells, while CPC controls hair cell development. TTG2 isinvolved in trichome development and tannin and mucilageproduction in the seed coat. TTG1 controls the differentiationof the seed coat. PAP1 and PAP2 regulate anthocyanain pro-duction [91–93]. Though a complex network of genes for seeddevelopment in Arabidopsis has been established, orthologsof these or new candidates involved in monocot-specificaspects of seed development remain to be identified.

TFs controlling SAM organization

During embryogenesis, the molecular organization typical ofthe vegetative SAM forms gradually and is not present in theglobular embryo. The apical portion of the embryo shows theformation of a radial pattern, depicted by AINTEGUMENTA/ANT, which is expressed exclusively in a peripheral ring inthe late globular/early transition stage embryo. STM startsexpressing a little later than ANT in a stripe across the apicalhalf of the transition/early heart stage embryo to divide theapical portion of the embryo into two bilaterally-symmetricalhalves. UNUSUAL FLORAL ORGANS/UFO, an F-box protein,then expresses in the future SAM region at the early heartstage and this requires STM. By the torpedo stage, UFOexpresses in a cup-shaped region within the SAM.CLAVATA1 starts expression at the heart stage in the centerof SAM and does not depend on the presence of STM. STM alsoupregulates CUC1. At the boundaries of cotyledon primordia,PIN-FORMED1/PIN1, MP, and PINOID/PID1 suppress CUC1,CUC2, and STM [94]. CUC1 is also regulated by DRNL/ESR2[95]. PID1 is a protein kinase that enhances polar transport ofauxin [96]. During cotyledon development, PIN1 and PIDregulate each other. PIN1 is also regulated by ENHANCEROF PINOID/ENP [97, 98]. In the octant stage, and also duringsubsequent stages of embryogenesis, PIN controls the expres-sion of PLT, which exerts a feed back control on PIN (Fig. 2b)[99]. Beyond the globular stage, PIN and KNOX are regulatedby JAGGED LATERAL ORGANS/JLO, which expresses at theboundary between the meristem and organ primordia. Theseinteractions control the initiation and development of cotyle-dons [100]. In summary, the TFs start playing regulatory roleseven in the single-celled zygote and control divisions andorgan initiation/formation. They participate in embryogene-sis, morphogenesis, endosperm development, and continue tobe active late into seed maturation.

TF loop is involved in epigenetic regulation of seeddevelopment TFs

Certain genes are expressed preferentially from the maternal orpaternal allele. They undergo chromatin/histone modificationor demethylation in the central maternal cell and thus startexpressing. This expression continues in the endosperm. Thus,all imprinted alleles are expressed specifically in the endo-sperm. In all other plant parts, including the embryo and other

vegetative parts, they remainmethylated and hence inactivated[101]. This has been observed in Arabidopsis as well as maize.Almost 50 imprinted genes have been deduced in Arabidopsis,most of which are TFs or genes which modify chromatin. Someof these are the homeodomain TFs HDG3, HDG9, FWA/HDG6,HDG8; others are ATMYB3R2, MEA, NRPD1b, FIS2, etc. [101,102]. Recently, a loop mechanism has been proposed by whichepigenetic inheritance occurs [103]. The VAL (VP1/ABI3-LIKE)proteins are repressors of seed development. These proteinsbind to the promoters of seed-specific genes, in tissues otherthan seed. They further recruit the PICKLE (PKL) repressor andother polycomb group (PcG) proteins that silence genes. Thisoccurs by histone H3 methylation at lysine 27 (H3K27me3),which is a known repressive epigenetic marker. The methyl-ation also occurs in the master regulators, LEC1 and LEC2. ThePKL and PcG proteins also seem to maintain the repressed stateof chromatin. At the appropriate time, the seed-specific genes,including LEC1, are derepressed. The mechanism for this is yetto be deciphered. Once activated, LEC1, the master regulator ofseed development, further activates other genes responsible forseed development. The expression of seed-specific b-PHASEOLIN (PHAS) of French bean is regulated by chromatinmodification of its promoter by PvALF (an ABI3-like TF) orFUS3. Then, ABA activates the gene. Both PvALF and ABAmodify the chromatin by distinct mechanisms, emphasizingthe presence of different pathways. Thus, the master regulatorsof seed development once activated lead to downstream acti-vation of other seed development genes by chromatin modifi-cation [103]. Genomic imprinting is a relatively oldphenomenon, supposedly observed even in gymnosperms.The homologs of maternal effects genes from Arabidopsis havebeen discovered to express during embryogenesis in pine [25]. Itis expected that epigenetic controls, like genomic imprintingand chromatin modification, will emerge as significant regu-lators of seed development.

Conclusions

Various TFs are triggered soon after fertilization to initiate theprocess of seed formation. The majority of TFs present in thepostfertilization phase contain a homeobox or are auxinregulated. Downstream of auxin, one of the master regulators,LEC1, an HAP3 family member, comes into play. In rice,members of this family express during embryogenesis, indi-cating their importance. Just like Arabidopsis, rice homeoboxfamily members participate in apical-basal cell specification.Apart from this, NAC TFs have been found to be essential forseed development in both monocots and dicots. ABA controlsseed maturation in both, as wonderfully exemplified by B3domain-containing ABI3/VP1, which regulates the expressionof seed-specific genes. The interactions amongst ABI3, 4 and 5are also similar in monocots and dicots. Yet another B3 TF,FUS3, functions similarly during seedmaturation in both. bZIPTFs also play important regulatory roles. The role of brassino-steroids, ethylene, jasmonic acid, and cytokinins in seeddevelopment is slowly being brought to light with the discov-ery of downstream genes, such as ERFs and BIM1. TFs withB3-, HAP3-, bZIP-, and NAC-domains play indispensableroles during the progression from zygote to seed in



Review

essays

Arabidopsis. It would be interesting to discover their orthologsor alternatives in monocots. Another point of significanceis the establishment of temporal/hormonal/environmentaltriggers of seed development. Whether different TFs withsimilar expression profiles form part of the same network ornot needs to be examined. For this, the seed interactome needsto be looked into and mutants studied. Much work has beendone to date on the transcriptome during seed development bymeans of EST and cDNA analysis and microarray experiments.The genes highlighted through these studies need to beexamined to establish their functional roles. Genes down-stream of TFs essential for seed development should also bedetermined by the study of mutants or by modifying the TFsand studying the subsequent effects. An integrated approachis now required to deduce the order of action of these TFs,starting from the first zygotic division up to maturation. Thisshould ultimately provide a mechanism for modifying seed-related traits, such as seed size, weight, and composition, seedviability and vigor, as well as seed dormancy.

AcknowledgmentsThe authors acknowledge the Department of Biotechnology,Government of India for providing funds for research.

References

1. Goldberg RB, de Paiva G, Yadegari R. 1994. Plant embryogenesis:zygote to seed. Science 266: 605–14.

2. Itoh J, Nonomura K, Ikeda K, Yamaki S, et al. 2005. Rice plantdevelopment: from zygote to spikelet. Plant Cell Physiol 46: 23–47.

3. Suzuki M, McCarty DR. 2008. Functional symmetry of the B3 networkcontrolling seed development. Curr Opin Plant Biol 11: 548–53.

4. Holdsworth MJ, Bentsink L, Soppe WJ. 2008. Molecular networksregulating Arabidopsis seed maturation, after-ripening, dormancy andgermination. New Phytol 179: 33–54.

5. Santos-Mendoza M, Dubreucq B, Baud S, Parcy F, et al. 2008.Deciphering gene regulatory networks that control seed developmentand maturation in Arabidopsis. Plant J 54: 608–20.

6. Verdier J, Thompson RD. 2008. Transcriptional regulation of storageprotein synthesis during dicotyledon seed filling. Plant Cell Physiol 49:1263–71.

7. Le BH, Cheng, C, Bui AQ, Wagmaister JA, et al. 2010. Global analysisof gene activity during Arabidopsis seed development and identificationof seed-specific transcription factors. Proc Natl Acad Sci USA 107:8063–70.

8. Gutierrez L, Van Wuytswinkel O, Castelain M, Bellini C. 2007.Combined networks regulating seed maturation. Trends Plant Sci 12:294–300.

9. Becraft PW. 2001. Cell fate specification in the cereal endosperm.Semin Cell Dev Biol 12: 387–94.

10. Park S, Harada JJ. 2008. Arabidopsis embryogenesis. Methods MolBiol 427: 3–16.

11. Vicente-Carbajosa J, Carbonero P. 2005. Seed maturation: develop-ing an intrusive phase to accomplish a quiescent state. Int J Dev Biol 49:645–51.

12. Sabelli PA, Larkins BA. 2009. The development of endosperm ingrasses. Plant Physiol 149: 14–26.

13. Abrash EB,Bergmann DC. 2009. Asymmetric cell divisions: a view fromplant development. Dev Cell 16: 783–96.

14. Wu X, Chory J, Weigel D. 2007. Combinations of WOX activitiesregulate tissue proliferation during Arabidopsis embryonic development.Dev Biol 309: 306–16.

15. Dumas C, Rogowsky P. 2008. Fertilization and early seed formation.C R Biol 331: 715–25.

16. Nardmann J, Zimmermann R, Durantini D, Kranz E, et al. 2007. WOXgene phylogeny in Poaceae: a comparative approach addressing leafand embryo development. Mol Biol Evol 24: 2474–84.

17. Zhou Y, Zhang X, Kang X, Zhao X, et al. 2009. SHORT HYPOCOTYLUNDER BLUE1 associates with MINISEED3 and HAIKU2 promotersin vivo to regulate Arabidopsis seed development. Plant Cell 21:106–17.

18. Chandler J, Nardmann J, Werr W. 2008. Plant development revolvesaround axes. Trends Plant Sci 13: 78–84.

19. De Smet I, Lau S, Mayer U, Jurgens G. 2010. Embryogenesis – thehumble beginnings of plant life. Plant J 61: 959–70.

20. Schlereth A, Moller B, Liu W, Kientz M, et al. 2010. MONOPTEROScontrols embryonic root initiation by regulating a mobile transcriptionfactor. Nature 464: 913–6.

21. Szemenyei H, Hannon M, Long JA. 2008. TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogene-sis. Science 319: 1384–6.

22. Sieburth LE, Muday GK, King EJ, Benton G, et al. 2006. SCARFACEencodes an ARF-GAP that is required for normal auxin efflux and veinpatterning in Arabidopsis. Plant Cell 18: 1396–411.

23. Chapman EJ, Estelle M. 2009. Mechanism of auxin-regulated geneexpression in plants. Annu Rev Genet 43: 265–85.

24. Smith ZR, Long JA. 2010. Control of Arabidopsis apical-basal embryopolarity by antagonistic transcription factors. Nature 464: 423–6.

25. Cairney J, Pullman GS. 2007. The cellular and molecular biology ofconifer embryogenesis. New Phytol 176: 511–36.

26. Palovaara J, Hallberg H, Stasolla C, Hakman I. Comparative expres-sion pattern analysis of WUSCHEL-related homeobox 2 (WOX2) andWOX8/9 in developing seeds and somatic embryos of the gymnospermPicea abies. New Phytol 188: 122–35.

27. Braybrook SA, Harada JJ. 2008. LECs go crazy in embryo develop-ment. Trends Plant Sci 13: 624–30.

28. Thirumurugan T, Ito Y, Kubo T, Serizawa A, et al. 2008. Identification,characterization and interaction of HAP family genes in rice. Mol GenetGenomics 279: 279–89.

29. Xie Z, Li X, Glover BJ, Bai S, et al. 2008. Duplication and functionaldiversification of HAP3 genes leading to the origin of the seed-devel-opmental regulatory gene, LEAFY COTYLEDON1 (LEC1), in non-seedplant genomes. Mol Biol Evol 25: 1581–92.

30. Lehti-Shiu MD, Adamczyk BJ, Fernandez DE. 2005. Expression ofMADS-box genes during the embryonic phase in Arabidopsis. Plant MolBiol 58: 89–107.

31. Hill K, Wang H, Perry SE. 2008. A transcriptional repression motif in theMADS factor AGL15 is involved in recruitment of histone deacetylasecomplex components. Plant J 53: 172–85.

32. Sagasser M, Lu GH, Hahlbrock K, Weisshaar B. 2002. A. thalianaTRANSPARENT TESTA 1 is involved in seed coat development anddefines the WIP subfamily of plant zinc finger proteins. Genes Dev 16:138–49.

33. Ito M, Sentoku N, Nishimura A, Hong SK, et al. 2002. Position depend-ent expression of GL2-type homeobox gene, Roc1: significance forprotoderm differentiation and radial pattern formation in early riceembryogenesis. Plant J 29: 497–507.

34. Tucker MR, Hinze A, Tucker EJ, Takada S, et al. 2008. Vascularsignalling mediated by ZWILLE potentiates WUSCHEL function duringshoot meristem stem cell development in the Arabidopsis embryo.Development 135: 2839–43.

35. Long JA, Barton MK. 1998. The development of apical embryonicpattern in Arabidopsis. Development 125: 3027–35.

36. Kamiya N, Nagasaki H, Morikami A, Sato Y, et al. 2003. Isolation andcharacterization of a rice WUSCHEL-type homeobox gene that isspecifically expressed in the central cells of a quiescent center in theroot apical meristem. Plant J 35: 429–41.

37. Hibara K, Takada S, Tasaka M. 2003.CUC1 gene activates the expres-sion of SAM-related genes to induce adventitious shoot formation.Plant J 36: 687–96.

38. Belles-Boix E, Hamant O, Witiak SM, Morin H, et al. 2006. KNAT6: anArabidopsis homeobox gene involved in meristem activity and organseparation. Plant Cell 18: 1900–7.

39. Zimmermann R, Werr W. 2005. Pattern formation in the monocotembryo as revealed by NAM and CUC3 orthologues from Zeamays L. Plant Mol Biol 58: 669–85.

40. Izhaki A, Bowman JL. 2007. KANADI and class III HD-Zip gene familiesregulate embryo patterning and modulate auxin flow during embryo-genesis in Arabidopsis. Plant Cell 19: 495–508.

41. Chandler JW, Cole M, Flier A, Werr W. 2009. BIM1, a bHLH proteininvolved in brassinosteroid signalling, controls Arabidopsis embryonicpatterning via interaction with DORNROSCHEN and DORNROSCHEN-LIKE. Plant Mol Biol 69: 57–68.



Review

essays

42. Nagasaki H, Itoh J, Hayashi K, Hibara K, et al. 2007. The smallinterfering RNA production pathway is required for shoot meristeminitiation in rice. Proc Natl Acad Sci USA 104: 14867–71.

43. Aquea F, Johnston AJ, Canon P, Grossniklaus U, et al. 2010.TRAUCO, a trithorax-group gene homologue, is required for earlyembryogenesis in Arabidopsis thaliana. J Exp Bot 61: 1215–24.

44. Vollbrecht E, Reiser L, Hake S. 2000. Shoot meristem size is depend-ent on inbred background and presence of the maize homeobox gene,knotted1. Development 127: 3161–72.

45. Itoh J, Sato Y, Nagato Y, Matsuoka M. 2006. Formation, maintenanceand function of the shoot apical meristem in rice. Plant Mol Biol 60: 827–42.

46. Yang ZX, An GY, Zhu ZP. 2001. Rice bicoid-related cDNA sequenceand its expression during early embryogenesis. Cell Res 11: 74–80.

47. Ito Y, Chujo A, Eiguchi M, Kurata N. 2004. Radial axis differentiation ina globular embryo is marked by HAZ1, a PHD-finger homeobox gene ofrice. Gene 331: 9–15.

48. Yang JY, Chung MC, Tu CY, Leu WM. 2002. OSTF1: a HD-GL2 familyhomeobox gene is developmentally regulated during early embryogen-esis in rice. Plant Cell Physiol 43: 628–38.

49. Cao X, Costa LM, Biderre-Petit C, Kbhaya B, et al. 2007. Abscisic acidand stress signals induce Viviparous1 expression in seed and vegetativetissues of maize. Plant Physiol 143: 720–31.

50. Kurup S, Jones HD, Holdsworth MJ. 2000. Interactions of the devel-opmental regulator ABI3 with proteins identified from developingArabidopsis seeds. Plant J 21: 143–55.

51. Marella HH, Quatrano RS. 2007. The B2 domain of VIVIPAROUS1 is bi-functional and regulates nuclear localization and transactivation. Planta225: 863–72.

52. Monke G, Altschmied L, Tewes A, Reidt W, et al. 2004. Seed-specifictranscription factors ABI3 and FUS3: molecular interaction with DNA.Planta 219: 158–66.

53. White JA, Todd J, Newman T, Focks N, et al. 2000. A new set ofArabidopsis expressed sequence tags from developing seeds. Themetabolic pathway from carbohydrates to seed oil. Plant Physiol 124:1582–94.

54. Barrero JM, Millar AA, Griffiths J, Czechowski T, et al. 2010. Geneexpression profiling identifies two regulatory genes controlling dor-mancy and ABA sensitivity in Arabidopsis seeds. Plant J 61: 611–22.

55. Zeng Y,Raimondi N,Kermode AR. 2003. Role of an ABI3 homologue indormancy maintenance of yellow-cedar seeds and in the activation ofstorage protein and Em gene promoters. Plant Mol Biol 51: 39–49.

56. Penfield S, Li Y, Gilday AD, Graham S, et al. 2006. Arabidopsis ABAINSENSITIVE4 regulates lipid mobilization in the embryo and revealsrepression of seed germination by the endosperm. Plant Cell 18: 1887–99.

57. Niu X, Helentjaris T, Bate NJ. 2002. Maize ABI4 binds couplingelement1 in abscisic acid and sugar response genes. Plant Cell 14:2565–75.

58. Casaretto JA, Ho TH. 2005. Transcriptional regulation by abscisic acidin barley (Hordeum vulgare L.) seeds involves autoregulation of thetranscription factor HvABI5. Plant Mol Biol 57: 21–34.

59. Gavazzi F, Lazzari B, Ciceri P, Gianazza E, et al. 2007. Wild-typeopaque2 and defective opaque2 polypeptides form complexes in maizeendosperm cells and bind the opaque2-zein target site. Plant Physiol145: 933–45.

60. Holding DR, Hunter BG, Chung T, Gibbon BC, et al. 2008. Geneticanalysis of opaque2 modifier loci in quality protein maize. Theor ApplGenet 117: 157–70.

61. Dong G, Ni Z, Yao Y, Nie X, et al. 2007. Wheat Dof transcription factorWPBF interacts with TaQM and activates transcription of an alpha-gliadin gene during wheat seed development. Plant Mol Biol 63: 73–84.

62. Vicente-Carbajosa J, Moose SP, Parsons RL, Schmidt RJ. 1997.A maize zinc-finger protein binds the prolamin box in zein gene pro-moters and interacts with the basic leucine zipper transcriptional acti-vator Opaque2. Proc Natl Acad Sci USA 94: 7685–90.

63. Kawakatsu T, Yamamoto MP, Touno SM, Yasuda H, et al. 2009.Compensation and interaction between RISBZ1 and RPBF during grainfilling in rice. Plant J 59: 908–20.

64. Bensmihen S, Giraudat J, Parcy F. 2005. Characterization of threehomologous basic leucine zipper transcription factors (bZIP) of the ABI5family during Arabidopsis thaliana embryo maturation. J Exp Bot 56:597–603.

65. Onodera Y, Suzuki A, Wu CY, Washida H, et al. 2001. A rice functionaltranscriptional activator, RISBZ1, responsible for endosperm-specificexpression of storage protein genes through GCN4 motif. J Biol Chem276: 14139–52.

66. Tiedemann J, Rutten T, Monke G, Vorwieger A, et al. 2008. Dissectionof a complex seed phenotype: novel insights of FUSCA3 regulateddevelopmental processes. Dev Biol 317: 1–12.

67. Tsuchiya Y, Nambara E, Naito S, McCourt P. 2004. The FUS3 tran-scription factor functions through the epidermal regulator TTG1 duringembryogenesis in Arabidopsis. Plant J 37: 73–81.

68. Moreno-Risueno MA, Gonzalez N, Diaz I, Parcy F, et al. 2008.FUSCA3 from barley unveils a common transcriptional regulation ofseed-specific genes between cereals and Arabidopsis. Plant J 53:882–94.

69. Shen B, Sinkevicius KW, Selinger DA, Tarczynski MC. 2006. Thehomeobox gene GLABRA2 affects seed oil content in Arabidopsis.Plant Mol Biol 60: 377–87.

70. Yang S, Johnston N, Talideh E, Mitchell S, et al. 2008. The endo-sperm-specific ZHOUPI gene of Arabidopsis thaliana regulates endo-sperm breakdown and embryonic epidermal development.Development 135: 3501–9.

71. Kondou Y, Nakazawa M, Kawashima M, Ichikawa T, et al. 2008.RETARDED GROWTH OF EMBRYO1, a new basic helix-loop-helixprotein, expresses in endosperm to control embryo growth. PlantPhysiol 147: 1924–35.

72. Prigge MJ, Wagner DR. 2001. The Arabidopsis SERRATE gene enc-odes a zinc-finger protein required for normal shoot development. PlantCell 13: 1263–79.

73. Suzuki A, Suzuki T, Tanabe F, Toki S, et al. 1997. Cloning and expres-sion of five myb-related genes from rice seed. Gene 198: 393–8.

74. Lasserre E, Jobet E, Llauro C,Delseny M. 2008.AtERF38 (At2g35700),an AP2/ERF family transcription factor gene from Arabidopsis thaliana, isexpressed in specific cell types of roots, stems and seeds that undergosuberization. Plant Physiol Biochem 46: 1051–61.

75. Matsui K, Hiratsu K, Koyama T, Tanaka H, et al. 2005. A chimericAtMYB23 repressor induces hairy roots, elongation of leaves and stems,and inhibition of the deposition ofmucilage on seed coats inArabidopsis.Plant Cell Physiol 46: 147–55.

76. Nesi N, Debeaujon I, Jond C, Stewart AJ, et al. 2002. TheTRANSPARENT TESTA16 locus encodes the ARABIDOPSISBSISTER MADS domain protein and is required for proper developmentand pigmentation of the seed coat. Plant Cell 14: 2463–79.

77. Schruff MC, Spielman M, Tiwari S, Adams S, et al. 2006. The AUXINRESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, celldivision, and the size of seeds and other organs.Development 133: 251–61.

78. Ellis CM, Nagpal P, Young JC, Hagen G, et al. 2005. AUXINRESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulatesenescence and floral organ abscission in Arabidopsis thaliana.Development 132: 4563–74.

79. Schumann U, Wanner G, Veenhuis M, Schmid M, et al. 2003.AthPEX10, a nuclear gene essential for peroxisome and storage organ-elle formation during Arabidopsis embryogenesis. Proc Natl Acad SciUSA 100: 9626–31.

80. Xu R, Li QQ. 2003. A RING-H2 zinc-finger protein gene RIE1 is essentialfor seed development in Arabidopsis. Plant Mol Biol 53: 37–50.

81. Yang HJ, Shen H, Chen L, Xing YY, et al. 2002. The OsEBP-89 gene ofrice encodes a putative EREBP transcription factor and is temporallyexpressed in developing endosperm and intercalary meristem. Plant MolBiol 50: 379–91.

82. Cheng S, Wang Z, Hong M. 2002. Rice bZIP protein, REB, interactswith GCN4 motif in promoter of Waxy gene. Sci China C Life Sci 45:352–60.

83. To A, Valon C, Savino G, Guilleminot J, et al. 2006. A network of localand redundant gene regulation governs Arabidopsis seed maturation.Plant Cell 18: 1642–51.

84. Baud S, Mendoza MS, To A, Harscoet E, et al. 2007. WRINKLED1specifies the regulatory action of LEAFY COTYLEDON2 towards fattyacid metabolism during seed maturation in Arabidopsis. Plant J 50: 825–38.

85. Brocard-Gifford IM, Lynch TJ, Finkelstein RR. 2003. Regulatory net-works in seeds integrating developmental, abscisic acid, sugar, and lightsignaling. Plant Physiol 131: 78–92.

86. Yamamoto A, Kagaya Y, Toyoshima R, Kagaya M, et al. 2009.ArabidopsisNF-YB subunits LEC1 and LEC1-LIKE activate transcriptionby interacting with seed-specific ABRE-binding factors. Plant J 58: 843–56.

87. Soderman EM, Brocard IM, Lynch TJ, Finkelstein RR. 2000.Regulation and function of the Arabidopsis ABA-INSENSITIVE4 genein seed and abscisic acid response signaling networks. Plant Physiol124: 1752–65.



Review

essays

88. Finkelstein R, Gampala SS, Lynch TJ, Thomas TL, et al. 2005.Redundant and distinct functions of the ABA response loci ABA-INSENSITIVE(ABI)5 and ABRE-BINDING FACTOR (ABF)3. Plant MolBiol 59: 253–67.

89. Nakashima K, Fujita Y, Katsura K, Maruyama K, et al. 2006.Transcriptional regulation of ABI3- and ABA-responsive genes includingRD29B and RD29A in seeds, germinating embryos, and seedlings ofArabidopsis. Plant Mol Biol 60: 51–68.

90. Alonso R, Onate-Sanchez L, Weltmeier F, Ehlert A, et al. 2009.A pivotal role of the basic leucine zipper transcription factor bZIP53in the regulation of Arabidopsis seed maturation gene expression basedon heterodimerization and protein complex formation. Plant Cell 21:1747–61.

91. Ishida T, Hattori S, Sano R, Inoue K, et al. 2007. ArabidopsisTRANSPARENT TESTA GLABRA2 is directly regulated by R2R3 MYBtranscription factors and is involved in regulation of GLABRA2 tran-scription in epidermal differentiation. Plant Cell 19: 2531–43.

92. Li SF, Milliken ON, Pham H, Seyit R, et al. 2009. The ArabidopsisMYB5transcription factor regulates mucilage synthesis, seed coat develop-ment, and trichome morphogenesis. Plant Cell 21: 72–89.

93. Gonzalez A, Mendenhall J, Huo Y, Lloyd A. 2009. TTG1 complexMYBs, MYB5 and TT2, control outer seed coat differentiation. DevBiol 325: 412–21.

94. Gordon SP, Heisler MG, Reddy GV, Ohno C, et al. 2007. Patternformation during de novo assembly of the Arabidopsis shoot meristem.Development 134: 3539–48.

95. Ikeda Y, Banno H, Niu QW, Howell SH, et al. 2006. The ENHANCEROFSHOOT REGENERATION 2 gene in Arabidopsis regulates CUP-SHAPED COTYLEDON 1 at the transcriptional level and controls coty-ledon development. Plant Cell Physiol 47: 1443–56.

96. Benjamins R, Quint A, Weijers D, Hooykaas P, et al. 2001. The PINOIDprotein kinase regulates organ development in Arabidopsis by enhanc-ing polar auxin transport. Development 128: 4057–67.

97. Treml BS, Winderl S, Radykewicz R, Herz M, et al. 2005. The geneENHANCER OF PINOID controls cotyledon development in theArabidopsis embryo. Development 132: 4063–74.

98. Furutani M,Vernoux T,Traas J,Kato T, et al. 2004. PIN-FORMED1 andPINOID regulate boundary formation and cotyledon development inArabidopsis embryogenesis. Development 131: 5021–30.

99. Long TA, Benfey PN. 2006. Transcription factors and hormones:new insights into plant cell differentiation. Curr Opin Cell Biol 18:710–4.

100. Borghi L, Bureau M, Simon R. 2007. Arabidopsis JAGGED LATERALORGANS is expressed in boundaries and coordinates KNOX and PINactivity. Plant Cell 19: 1795–808.

101. Berger F, Chaudhury A. 2009. Parental memories shape seeds. TrendsPlant Sci 14: 550–6.

102. Gehring M, Bubb KL, Henikoff S. 2009. Extensive demethylation ofrepetitive elements during seed development underlies gene imprinting.Science 324: 1447–51.

103. Zhang H, Ogas J. 2009. An epigenetic perspective on developmentalregulation of seed genes. Mol Plant 2: 610–27.



Review

essays

transcription factors regulating the progression of monocot and dicot seed development

Documents