Beyond the Divide: Boundaries for Patterning and Stem Cell Regulation in Plants

Abstract

The initiation of plant lateral organs from the shoot apical meristem (SAM) is closely associated with the formation of specialized domains of restricted growth known as the boundaries. These zones are required in separating the meristem from the growing primordia or adjacent organs but play a much broader role in regulating stem cell activity and shoot patterning. Studies have revealed a network of genes and hormone pathways that establish and maintain boundaries between the SAM and leaves. Recruitment of these pathways is shown to underlie a variety of processes during the reproductive phase including axillary meristems production, flower patterning, fruit development, and organ abscission. This review summarizes the role of conserved gene modules in patterning boundaries throughout the life cycle.

Keywords: abscission; dehiscence; flower patterning; fruit patterning; inflorescence architecture; lateral organ boundary; meristem; organ separation.

FIGURE 1

Homologous boundary gene networks controlling biogenesis of shoot apical meristem (SAM), axillary meristems (AMs), and floral meristems (FMs). (A) SAM initiation (gray). Early heart stage is shown. CUC genes are activated in a narrow band of auxin-depleted cells located between the presumptive cotyledons at globular stage. Activation of CUCs in this domain is partly dependent on chromatin remodeling ATPases and various other factors not depicted. Once activated, CUC1 and CUC2 are redundantly required for STM expression to form the presumptive SAM. STM in turn, directly maintains expression of CUC1 and indirectly promotes CUC2 and CUC3 in establishing a feedback loop that ultimately restricts CUC expression to the axils of cotyledons. Reciprocally, STM expression is restricted to the SAM and slightly detected in boundaries. LBD family member JLO promotes PIN1 expression required for formation of auxin maxima and represses STM and KNOX members to allow cotyledon outgrowth. Green arrows, direction of auxin flow. Green, auxin maxima at the cotyledon primordia. (B) SAM maintenance and AM formation (yellow). STM represses BOP1/2 to maintain indeterminacy in the SAM. Conversely, BOP1/2 restrict KNOX expression in the proximal region of leaves to control patterning. Formation of an AM requires depletion of auxin from the leaf axil followed by a burst of CK. CUC1-3 are redundantly required for AM initiation functioning downstream of LFY and RAX1 to promote LAS. LOF1/2 contribute to RAX1 promotion. CUC1, LAS, and ROX activities are required for sustained expression of STM and establishment of the AM. Green arrows, direction of auxin flow. (C) IM activity. PNY and PNF restrict BOP1/2-ATH1-KNAT6 expression to boundary domains flanking the IM essential for meristem maintenance and flowering. FMs (pink). FMs are AMs with determinate fate that form in the axil of leaves whose development are repressed (cryptic bract). Auxin responsive transcription factor MP directly activates ANT and LFY to initiate FM formation. LFY directly promotes the expression of RAX1 and AP1 and CAL whose products confer floral fate. BOPs facilitate establishment of FMs via promotion of LFY expression, activation of AP1, and repression of IM identity genes. UFO is a LFY co-activator also required for formation of boundaries in the flower. Later, CUC factors are required to separate floral organs and maintain boundaries between whorls in association with numerous stage-specific factors including PTL, RBE, and SUP required for localized repression of growth. Inflorescence architecture. BP and PNY are expressed in the stem cortex where they collectively promote internode elongation, stem differentiation, phyllotaxy, and pedicel angle by restricting boundary genes BOP1/2 and downstream effectors ATH1 and KNAT6 to the pedicel axil (blue). Misexpression of these genes in the BP-PNY domain restricts growth, disrupts vascular patterning, and causes ectopic lignification. CUC2 expression is restricted by miR164 to the pedicel axil to maintain internode patterning. FM, floral meristem; IM, inflorescence meristem. P, primordia; stages as indicated. Red lettering, SAM-leaf boundary genes. Red arrows, direct regulation. Dashed line, putative interaction.

FIGURE 2

Summary of hormone profiles and genetic interactions that maintain the leaf-SAM boundary. (A) The shoot apex contains: the meristem, the initium, boundaries, and organ primordia. The predicted distribution of key hormones are summarized (see text for details). Meristem, high CK/IAA ratio and low GA/BR ratio promotes indeterminate growth. Primordia, high IAA activates BR and represses CK biosynthesis and GA increases to promote determinate growth. Boundary, depletion for growth-promoting hormones IAA, GA, BR, and CK inhibits cell division allowing separation of meristem-organ compartments. I, Initium; CK, cytokinin; BR, brassinosteroid; GA, gibberellin; and IAA, auxin. (B) Summary of gene networks at the meristem-boundary interface. Meristem, STM maintains indeterminate growth by promoting CK and repressing GA/BR accumulation (black gradient indicates hormone abundance). Auxin, shown in green, marks the site of primordia initiation and distal blade of emerging leaf. (1) KNOX proteins initialize the boundary through promotion of BR catabolic genes (BAS1) and boundary transcription genes including CUC and BOP2 (blue arrows). CUC factors confer boundary identity required for activation of other classes of boundary regulators including BOP, KNAT-BELL, LOF1, ALOG, and LBD members that collectively restrict growth, modulate meristematic activity, and pattern the boundary. PIN1 auxin efflux carriers (green circles) are orientated facing outward such that auxin is drained away from the boundary. Green arrows indicate direction of auxin flow. (2) Boundary genes contribute to meristem maintenance (see text). (3) STM-BELL meristem factors preserve meristem integrity by restricting BOP1/2 and KNAT6 to boundaries. BR-activated transcription factor BZR1 represses CUC/LOF1 in the meristem domain. (C) Summary of interactions at the leaf-boundary interface. (1) Polar auxin transport establishes auxin maxima in the peripheral zone where leaf initiation takes place. Auxin response factor MP initiates primordium formation by repressing KNOX genes, activating ANT members and leaf identity genes including AS1 and stimulating synthesis of BR where BZR1 binds to the ANT promoter as a positive regulator. Boundary genes BOP1/2 and JLO expressed in the organ initial contribute to organ polarity and stable repression of KNOX genes. (2) Primordium outgrowth coincides with synthesis of auxin and repolarization of PIN transports toward the leaf base, which becomes a low IAA/BR domain. BOPs and JLO now restricted to the boundary reinforce this pattern in hormones via regulation of LOB and PIN1, respectively. CIN-TCPs and BZR1 in leaves maintain repression of CUC/LOF1. JAG in the distal blade represses BOPs. BOPs expressed in the proximal petiole domain of leaves maintain organ polarity and repress KNOX and JAG genes required for simple leaf shape indirectly in part via activation of AS2. YAB contributes to the repression of KNOX and CUC in the abaxial domain.

FIGURE 3

Homologous networks for ovule initiation by the carpel marginal meristem (CMM) and patterning of leaf margin. Two fused carpels in the center of the flower form a tubular structure that constitutes the gynoecium (stages 8 and 9). The inner fused surfaces of the carpels (equivalent to an adaxial leaf surface) form a ridge of meristematic tissue called the CMM that gives rise to ovules and septum. Ovules are initiated in a process that resembles creation of serrations on the leaf margin where CUC2 is required for leaf serration and CUC3 promotes serration growth (see text). (1) CUC1/2 in the placenta together with CK promote the formation of an auxin maximum. (2) Auxin positive feedback reinforces flow of auxin to the primordia tip. (3) Auxin negative feedback restricts CUC1/2 expression to the base of the ovule. (4) Once auxin reaches threshold levels, it switches on ANT which promotes outgrowth of the shoot and MADS box genes SHP1/2 and STK which confer ovule identity. CUC2/3 expression overlaps between ovule primordia and is required for ovule separation (not shown). Adapted from (Cucinotta et al., 2014). Red lettering, SAM-leaf boundary genes.

FIGURE 4

Schematic of an Arabidopsis fruit and summary of networks for fruit patterning compared to the SAM-leaf boundary. (A) The Arabidopsis fruit derived from two fused carpel valves that represent modified leaves. Valve margins are a lateral organ boundary specialized for dehiscence that joins the carpels to a meristematic tissue called the replum. The internal surface of the replum or CMM provides septum and placenta that gives rise to ovules that develop into seeds at fertilization. Differentiation of the valve margins requires GA, CK, and depletion of auxin (see text). When the fruit is mature, the valve margin differentiates to form the dehiscence zone (DZ) comprising two layers: a separation layer (SL) where the fruit will open and a lignified layer (LL) continuous with the lining of the fruit that provides tension required in spring-like opening of the fruit for seed dispersal. (B) Similar to their role in leaves, JAG and YAB factors together with AS1–AS2 are required in restricting expression of meristematic genes BP and PNY to the central replum domain and in restricting valve margin identity genes to the boundary junction. FUL is a stage-specific factor that confers valve identity and functions similarly to AS1–AS2 and JAB/YAB to correctly position the replum and valve margin identity domains. Red lettering, SAM-leaf boundary genes: CUC1/2 activate STM required in formation of the CMM and BOP1/2 and KNAT2/6 expressed in the valve margin of fruit are predicted to antagonize BP-PNY activity in the replum. Dashed arrows, hypothetical interactions.

FIGURE 5

Summary of pathways that control the development of abscission zones (AZs). Placement of AZs (in red) are shown for (A) Arabidopsis flower, (B) tomato pedicel, and (C) Arabidopsis seed and dehiscence zone. (D) The current accepted model for abscission defines four key stages: differentiation of AZ cells (pink), AZ cells acquire competence to respond to hormone inductive signals (red), activation of abscission and detachment (red), and differentiation of a protective layer over the scar (blue). Red lettering, SAM-leaf boundary genes. Dashed lines, hypothetical pathway. IAA, auxin; BR, brassinosteroid; GA, gibberellin; ET, ethylene; CK, cytokinin; JA, jasmonic acid. Adapted from (Leibfried et al., 2005; Niederhuth et al., 2013).