Enabling photoperiodic control of flowering by timely chromatin silencing of the florigen gene

Abstract

Many plants synchronize their flowering times with changing seasons to maximize reproductive success. A key seasonal cue is the change in day length (photoperiod), that induces the production of a systemic flowering signaling molecule called florigen. A major florigen component is FLOWERING LOCUS T (FT) or its orthologs. In the long-day plant Arabidopsis thaliana, FT expression is well known to be activated by the photoperiod pathway output specifically near dusk in long days; however, underappreciated is the importance of FT silencing at other times of the day, in enabling Arabidopsis to respond only to long days in flowering. We have recently reported that a plant-specific chromatin-silencing complex called EMF1c represses FT expression at times other than around dusk in long days to prevent its temporal ectopic expression from “spoiling” the long-day floral induction in Arabidopsis. Here I further discuss in other day-length sensitive plants the potential involvement of a chromatin mechanism similar to the Arabidopsis EMF1c-mediated silencing, in repressing the expression of FT orthologs to enable diverse photoperiodic control of flowering.

Abbreviations

EMF1

EMBRYONIC FLOWER 1

FT

FLOWERING LOCUS T

CO

CONSTANS

NF-Y

nuclear factor Y

H3K27me3

Histone 3 lysine-27 trimethylation

PcG

Polycomb group

PRC1

Polycomb repressive complex 1

PRC2

Polycomb repressive complex 2

H2Aub

Histone 2A monoubiquitination

LHP1

LIKE HETEROCHROMATIN PROTEIN 1

Many plants synchronize their timing of developmental transition from vegetative to reproductive growth (i.e., flowering) with changing seasons to maximize reproductive success. A key seasonal cue is the change in day length (photoperiod) at different times of the year, quite noticeable at higher latitudes.^1,2 Through a photoperiod pathway of floral induction, plants sense such cue to flower at a right season.² According to their flowering responses to photoperiodic changes, plants are classified into long-day, short-day and day-neutral plants. Long-day plants flower when days getting longer than a threshold length or flower rapidly in long days, whereas short-day plants flower when the day becomes shorter; plants that flower regardless of day length changes are day-neutral.¹

The day-length changes are perceived in leaves by photoreceptors such as phytochrome and cryptochrome.^3,4 Upon perception of inductive photoperiods, plants produce a systemic flowering signaling molecule called florigen in leaf phloem tissues, which is subsequently transported through the phloem to shoot apex to induce flowering.^5-7 A key component of the mobile florigen is FT, first discovered in the model flowering plant Arabidopsis thaliana and conserved among flowering plants so far examined.^2,8,9 In the long-day plant Arabidopsis, FT expression is activated by the photoperiod pathway output CONSTANS (CO).¹⁰ In long days, CO mRNA expression is set at a high level during late afternoon by the interplay of several circadian clock-controlled activities of gene regulation.¹⁰ The coincidence of high-level CO mRNAs with light exposure that stabilizes the CO protein, results in CO accumulation in leaf veins in late afternoon (peaking at the end of long day).^3,11 CO forms a complex with nuclear factor Y (NF-Y) proteins to promote FT expression specifically in the phloem near dusk.^12,13 This CO-triggered FT expression near dusk is well known to be essential for floral induction in Arabidopsis by the long-day photoperiods; however, underappreciated is the importance of FT silencing at other times of the day (i.e., prior to late afternoon and after dusk), in enabling Arabidopsis to respond to long days in floral induction.

The silencing of gene expression through covalent chromatin modifications plays a crucial role in eukaryotic gene regulation. Various repressive modifications of the chromatin constituents including DNA and histones such as DNA methylation and Histone 3 lysine-27 trimethylation (H3K27me3) can lead to gene silencing.^14,15 The repressive H3K27me3 is deposited by a Polycomb group (PcG) protein complex.¹⁴ PcG proteins assemble into two main families of complex including Polycomb repressive complex 1 (PRC1) and Polycomb repressive complex 2 (PRC2), to modify chromatin leading to transcriptional repression of gene expression.¹⁴ PRC2, conserved from plants to animals, catalyzes H3K27me3, whereas PRC1 typically acts to maintain this mark, catalyze another repressive modification-Histone 2A monoubiquitination (H2Aub), and/or compact chromatin to repress gene expression.^14,16 PcG complex-mediated chromatin silencing plays a critical role in developmental gene regulation in plants and animals.

The expression control of florigen gene FT involves not only CO-triggered activation, but also chromatin silencing mechanisms. In Arabidopsis, a PRC2 complex catalyzes H3K27me3 at the FT locus, and is required for FT repression;¹⁷ moreover, LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) recognizes and binds to H3K27me3 and mediates FT silencing.¹⁸ In addition, a JmjC domain-containing H3 lysine-4 demethylase known as JMJ14 /PKDM7B localizes at the FT locus to mediate H3K4 demethylation and repress FT expression.^19,20 Recently, we have uncovered that LHP1 and JMJ14 are part of a PcG complex that silences FT expression.²¹

In plants and animals PRC2 subunits are well conserved, but there are no apparent homologs of most animal PRC1 components in plants.^16,22 In quest for a plant PcG complex with PRC1-like activities, we have uncovered that the plant-specific EMBRYONIC FLOWER 1 (EMF1) protein,²³ LHP1, JMJ14 and a homolog of the human PRC1 subunit BMI1¹⁴ are part of a PcG complex termed as EMF1c that plays PRC1-like roles to mediate gene repression in Arabidopsis.²¹ EMF1 is a core subunit and possesses a chromatin compaction activity inhibitory of transcription, a key function of animal PRC1.²⁴ EMF1c is expected to maintain the repressive H3K27me3 mark, erase the active H3K4me3, deposit the repressive H2Aub, and /or compact target gene chromatin, leading to the silencing of various genes in the Arabidopsis genome.²¹

To explore the biological function of EMF1c-PcG in photoperiodic flowering control, we undertook a genetic approach by knocking down the core complex subunit EMF1 in leaf phloem tissues²¹ where FT expression is activated by CO specifically near dusk in long days. This phloem-specific knockdown resulted in largely constitutive FT expression across day and night (from dawn to dusk to dawn again).²¹ Apparently, EMF1c is essential for keeping FT silenced. The EMF1-knockdown plants flowered rapidly and around the same time under long-day and short-day conditions²¹ (note that Arabidopsis typically flowers rapidly in long days, whereas the short-day condition inhibits its flowering); in other words, these plants became day-neutral, and flowered rapidly regardless of day length conditions. Loss of EMF1c function in the leaf phloem tissues converted Arabidopsis from a long-day plant to day-neutral plant. Therefore, in Arabidopsis EMF1c-mediated FT silencing enables the photoperiodic control of flowering (i.e., long-day induction of the floral transition).

We have further determined at what times of the day (in long days) EMF1c acts to silence FT expression by examining the temporal localization pattern of EMF1 at the FT locus. In the morning, EMF1 binds to FT chromatin to silence FT expression.²¹ When the day advances, CO starts to accumulate in late afternoon with a peak at dusk; CO, together with a dimer of NF-YB and NF-YC, forms a trimer (CO-NF-Y) that binds directly to the FT promoter to disrupt EMF1 binding to FT chromatin, as suggested by the ectopic accumulation of CO in the morning resulting in an elimination of EMF1 binding to FT chromatin.²¹ This CO-triggered reduction of EMF1 abundance at the FT locus gives rise to FT expression activation near dusk to induce flowering, conferring a long-day flowering induction in Arabidopsis.²¹ When it reaches night, the CO protein is degraded rapidly by proteasomes, EMF1/EMF1c comes back to FT chromatin again to silence FT expression.²¹ In short, FT repression at times other than around dusk in long days is not by default, but achieved by ‘active’ EMF1c-mediated chromatin silencing. This silencing is relieved only when the CO level reaches a threshold near dusk; thus, it creates a situation where only long days can induce the florigen expression because of the silencing breaker – CO reaching a threshold level only near the end of day time (Fig. 1). FT silencing at other times of the day prevents its temporal ectopic expression from ‘spoiling’ the long-day floral induction in Arabidopsis; in other words, EMF1c-mediated FT silencing enables such photoperiodic response of flowering.

Figure 1.

A working model for the chromatin silencing of FT expression in Arabidopsis by the phloem EMF1c-PcG in long days. EMF1c-PcG silences FT expression at times other than around dusk, and the silencing is relieved only when the CO level reaches a threshold near dusk, as CO functions to disrupt EMF1-PcG binding to FT chromatin.²¹ This disrupted binding is indicated by the dotted line; solid lines with bars denote repression or disruption.

The EMF1c components including EMF1, LHP1, JMJ14 and BMI1s are widely conserved in angiosperms.^21,23,25-27 This raises a possibility that EMF1c-mediated silencing of FT (or FT orthologs) might be conserved in other day-length sensitive plants as well. In the model short-day plant Oryza sativa (rice), the expression of an FT ortholog called Hd3a that plays a key role in rice floral induction,²⁸ is activated around dawn in short days (8-hour light /16-hour night) by concerted action of a rice ortholog of the Arabidopsis CO and a B-type response regulator known as Ehd1 (see illustration in Fig. 2).^1,29,30 It would be interesting to determine whether in rice there is an EMF1c-like PcG complex with subunit composition and function similar to the Arabidopsis EMF1c, which silences Hd3a expression at times other than around dawn to enable short-day induction of rice flowering (Fig. 2). Future study of the role of EMF1c-like complexes in silencing of FT orthologs in various long-day and short-day plants will further our understanding of whether EMF1c-mediated silencing of FT or FT orthologs in leaf veins is a general feature in enabling photoperiodic control of flowering in angiosperms.

Figure 2.

A hypothetic model for chromatin silencing of the rice Hd3a expression by an EMF1c-PcG like complex in short days. In the indicated short days, Hd3a expression is activated around dawn¹ (by a concerted action of Ehd1 and Hd1, a CO ortholog), and at times other than around dawn it might be silenced by an EMF1c-PcG like complex to prevent its temporal ectopic expression from ‘spoiling’ rice floral induction only by short days.

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.