Dynamic chromatin accessibility and stomatal cell-fate commitment

Dynamic chromatin accessibility deploys heterotypic cis/trans-acting factors driving stomatal cell-fate commitment

Kim E. D., Dorrity M. W., Fitzgerald B. A., Seo H., Sepuru K. M., Queitsch C., Mitsuda N., Han S.-K., Torii K. U. (2022)

Eun-Deok KimMichael W. DorrityBridget A. FitzgeraldHyemin SeoKrishna Mohan SepuruChristine QueitschNobutaka MitsudaSoon-Ki HanKeiko U. Torii,

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Nature Plants (2022) – https://doi.org/10.1038/s41477-022-01304-w

https://www.nature.com/articles/s41477-022-01304-w#citeas

Abstract

Chromatin architecture and transcription factor (TF) binding underpin cell-fate specification during development, but their mutual regulatory relationships remain unclear.

Here we report an atlas of dynamic chromatin landscapes during stomatal cell-lineage progression, in which sequential cell-state transitions are governed by lineage-specific bHLH TFs. Major reprogramming of chromatin accessibility occurs at the proliferation-to-differentiation transition. We discover novel co-cis regulatory elements (CREs) signifying the early precursor stage, BBR/BPC (GAGA) and bHLH (E-box) motifs, where master-regulatory bHLH TFs, SPEECHLESS and MUTE, consecutively bind to initiate and terminate the proliferative state, respectively. BPC TFs complex with MUTE to repress SPEECHLESS expression through a local deposition of repressive histone marks.

We elucidate the mechanism by which cell-state-specific heterotypic TF complexes facilitate cell-fate commitment by recruiting chromatin modifiers via key co-CREs.

A timely proliferative cell cycle is critical for stomatal-lineage identity

(E) Schematic model. SPCH·SCRM/2 initiate and sustain ACD and MUTE·SCRM/2 trigger SCD (gray arrows) by transcriptionally activating CYCD3;1 and CYCD5;1 (shaded blue arrows), respectively. MUTE directly up-regulates SMR4 transcription (Blue arrow). SMR4 (and SMR8 in part) suppress the activity of CYCD3;1 and possibly CYCD7;1 complexed with CDKs (red line), but not CYCD5;1, to terminate the ACD mode and ensure faithful progression of SCD. Question marks and dotted line indicate the possible roles of SMR8 in termination of ACD and SMR4 with CYCD7;1 in symmetric cell division, respectively.

Deceleration of the cell cycle underpins a switch from proliferative to terminal divisions in plant stomatal lineage

Han S. K., Herrmann A., Yang J., Iwasaki R., Sakamoto T., Desvoyes B., Kimura S., Gutierrez C., Kim E.-D., Keiko U. Torii K. U. (2022)

Soon-Ki Han, Arvid Herrmann, Jiyuan Yang, Rie Iwasaki, Tomoaki Sakamoto, Bénédicte Desvoyes, Seisuke Kimura, Crisanto Gutierrez, Eun-Deok Kim, Keiko U. Torii,

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Developmental Cell 57(5): 569-582.e6 – ISSN 1534-5807 – https://doi.org/10.1016/j.devcel.2022.01.014

https://www.sciencedirect.com/science/article/pii/S1534580722000399

Highlights

• During stomatal differentiation, asymmetric divisions are faster than terminal divisions

• Upon commitment to differentiation, MUTE induces the cell-cycle inhibitor SMR4

• SMR4 decelerates the asymmetric cell division cycle via selective binding to cyclin D

• Regulating duration of the G1 phase is critical for epidermal cell fate specification

Summary

Differentiation of specialized cell types requires precise cell-cycle control. Plant stomata are generated through asymmetric divisions of a stem-cell-like precursor followed by a single symmetric division that creates paired guard cells surrounding a pore. The stomatal-lineage-specific transcription factor MUTE terminates the asymmetric divisions and commits to differentiation. However, the role of cell-cycle machineries in this transition remains unknown. We discover that the symmetric division is slower than the asymmetric division in Arabidopsis. We identify a plant-specific cyclin-dependent kinase inhibitor, SIAMESE-RELATED4 (SMR4), as a MUTE-induced molecular brake that decelerates the cell cycle. SMR4 physically and functionally associates with CYCD3;1 and extends the G1 phase of asymmetric divisions. By contrast, SMR4 fails to interact with CYCD5;1, a MUTE-induced G1 cyclin, and permits the symmetric division. Our work unravels a molecular framework of the proliferation-to-differentiation switch within the stomatal lineage and suggests that a timely proliferative cell cycle is critical for stomatal-lineage identity.

Self-inhibition as a mechanism for ensuring proper stomatal development

Expression patterns of ERL1 during stomatal development.
Expression pattern of ERL1pro::ERL1-YFP. (A–J) Time-lapse live imaging of developing abaxial cotyledon epidermis of the 1-day-old T4 seedling of ERL1pro::ERL1-YFP erl1-2. Time points after image collection are indicated in hours:(A) 0.0 hr; (B) 3.5 hr; (C) 13.0 hr; (D) 16.0 hr; (E) 24.5 hr; (F) 26.0 hr; (G) 36.0 hr; (H) 50.5 hr; (I) 68.0 hr; and (J) 71.0 hr. Arrowheads point to two representative cells. Images for (A–J) are taken at the same magnification. Scale bar, 10 µm. (K–L) High resolution live images of stomatal precursors expressing ERL1-YFP. (K, L) meristemoid mother cells (MMC); (M) meristemoid (M); (N) late meristemoid (late M); (O) late meristemoid to guard mother cell transition (late M~GMC); (P) GMC; (Q) immature guard cells (im GC). Images for (K–L) are taken at the same magnification. Scale bar, 7.5 µm. ERL1-YFP signals are detected at the plasma membrane from early meristemoids (AKL; arrowheads) and accumulate high at the asymmetric division site (e.g. DFM; cyan asterisks). ERL1-YFP signals boost during the late meristemoid-to-GMC transition (GHNO; cyan plus), and diminishes after GMC symmetric division (IJPQ; arrowheads). See accompanying Video 1. Experiments were repeated three times. Total seedlings analyzed; n = 9.

Autocrine regulation of stomatal differentiation potential by EPF1 and ERECTA-LIKE1 ligand-receptor signaling

Qi X., Han S.-K., Dang J. H., Garrick J. M., Ito M., Hofstetter A. K., Torii K. U. (2017)

Xingyun QiSoon-Ki HanJonathan H. DangJacqueline M. GarrickMasaki ItoAlex K. HofstetterKeiko U. Torii,

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In Plant Biology, Developmental Biology – https://doi.org/10.7554/eLife.24102.001

https://elifesciences.org/articles/24102

Absolute co-expression of ERL1 and MUTE confers meristemoid arrests.
Shown are confocal microscopy images of cotyledon abaxial epidermis from 7-day-old seedlings of the following genotypes: (Aer erl1 erl2; (BMUTEpro::ERL1-YFP in er erl1 erl2; (Der erl1 erl2 epf1 epf2; (EMUTEpro::ERL1-YFP in er erl1 erl2 epf1 epf2; (FMUTEpro::ERL1-YFP in er erl1 erl2 mock treated; (GMUTEpro::ERL1-YFP in er erl1 erl2 treated with 5 µM Stomagen peptide; (Her erl1 erl2 tmm; (IMUTEpro::ERL1-YFP in er erl1 erl2 tmm. T1 transgenic seedlings of MUTEpro::ERL1-YFP er erl1 erl2; MUTEpro::ERL1-YFP er erl1 erl2 epf1 epf2; and MUTEpro::ERL1-YFP er erl1 erl2 tmm were used for the analysis. T2 seedlings of MUTEpro::ERL1-YFP er erl1 erl2 were used for the mock or Stomagen treatment. Scale bars, 10 µm (A, B, D, E, H, I), 25 µm (F, G). (C) Quantitative analysis. Stomatal index (SI) of the cotyledon abaxial epidermis from 7-day-old seedlings of respective genotypes. For each genotype, images from six seedlings were analyzed. Welch’s Two Sample T-test was performed for mock vs. Stomagen application (Left). One-way ANOVA followed by Tukey’s HSD test was performed for comparing all other genotypes and classify their phenotypes into three categories (a, b, and c).

Abstract

Development of stomata, valves on the plant epidermis for optimal gas exchange and water control, is fine-tuned by multiple signaling peptides with unique, overlapping, or antagonistic activities. EPIDERMAL PATTERNING FACTOR1 (EPF1) is a founding member of the secreted peptide ligands enforcing stomatal patterning. Yet, its exact role remains unclear. Here, we report that EPF1 and its primary receptor ERECTA-LIKE1 (ERL1) target MUTE, a transcription factor specifying the proliferation-to-differentiation switch within the stomatal cell lineages. In turn, MUTE directly induces ERL1. The absolute co-expression of ERL1 and MUTE, with the co-presence of EPF1, triggers autocrine inhibition of stomatal fate. During normal stomatal development, this autocrine inhibition prevents extra symmetric divisions of stomatal precursors likely owing to excessive MUTE activity. Our study reveals the unexpected role of self-inhibition as a mechanism for ensuring proper stomatal development and suggests an intricate signal buffering mechanism underlying plant tissue patterning.

How cell cycle regulators are transcriptionally regulated and contributing to each step of stomatal lineage progression

Linking cell cycle to stomatal differentiation

by Han S. K., Torii K. U. (2019)

Soon-Ki Han1, Keiko U. Torii123

In Current Opinion in Plant Biology 51: 66-73 – https://doi.org/10.1016/j.pbi.2019.03.010

https://www.sciencedirect.com/science/article/pii/S1369526619300202#fig0005

Highlights

Cell-cycle components and transcription factors coordinate formative- and terminal divisions within stomatal cell lineages.

• MUTE induces cell-cycle genes and their transcriptional repressors, forming a feed-forward loop to ensure only one cell division.

• Timely expression and repression of two D-type cyclins, CYCD5;1 and CYCD7;1, are crucial to form a pair of guard cell.

• Components of the DREAM-like complex implicated in fate transition, activation, and restriction of stomatal terminal division.

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Stomatal differentiation manifests via several rounds of asymmetric cell division and a single symmetric cell division: the former, formative divisions amplify the number of epidermal cells, and the latter is essential for creating a functional guard cell pair. These cell division patterns are coordinated with progressive fate specification and cell-state transitional steps, which rely on the transcriptional regulation by a set of cell type-specific basic helix loop helix (bHLH) transcription factors. It has been proposed that the mechanisms underlying cell-fate decision and cell cycle progression are interconnected in a wide range of developmental processes. This review highlights the recent findings on how cell cycle regulators are transcriptionally regulated and contributing to each step of stomatal lineage progression.

MUTE, Cell-State Switch and the Single Symmetric Division to Create Stomata

Transcriptomic Profiling of MUTE Target Genes Reveals a Framework of Stomatal Cell-State Switch

(A–E) Epidermal phenotypes of 3-day-old seedlings. Mock (A and C), iMUTE (B and D), and iSPCH (E). Mature stomata of mock (C) and iMUTE (D) cotyledon epidermis expressing GC GFP marker E994. Scale bars, 50 μm.

MUTE Directly Orchestrates Cell-State Switch and the Single Symmetric Division to Create Stomata

by Han S. K., Qi X., Sugihara K., Dang J. D., Endo T. A., Miller K. L., Kim E.-D., Miura T., Torii K. U. (2018)

Soon-Ki HanXingyun QiKei Sugihara Jonathan H. Dang Takaho A. Endo Kristen L. Miller Eun-Deok Kim Takashi Miura Keiko U. Torii7

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in Dev. Cell 45(3): 303-315 –

https://www.cell.com/developmental-cell/fulltext/S1534-5807(18)30285-5 

Highlights

  • Comprehensive inventories of gene expression in stomatal differentiation reported

  • MUTE switches stomatal patterning program initiated by its sister bHLH, SPEECHLESS

  • MUTE directly induces cell-cycle genes and their direct transcriptional repressors

  • Incoherent feed-forward loop by MUTE ensures stomata composed of paired guard cells

Summary

Precise cell division control is critical for developmental patterning. For the differentiation of a functional stoma, a cellular valve for efficient gas exchange, the single symmetric division of an immediate precursor is absolutely essential. Yet, the mechanism governing this event remains unclear. Here we report comprehensive inventories of gene expression by the Arabidopsis bHLH protein MUTE, a potent inducer of stomatal differentiation.

MUTE switches the gene expression program initiated by SPEECHLESS. MUTE directly induces a suite of cell-cycle genes, including CYCD5;1, in which introduced expression triggers the symmetric divisions of arrested precursor cells in mute, and their transcriptional repressors, FAMA and FOUR LIPS.

The regulatory network initiated by MUTE represents an incoherent type 1 feed-forward loop. Our mathematical modeling and experimental perturbations support a notion that MUTE orchestrates a transcriptional cascade leading to a tightly restricted pulse of cell-cycle gene expression, thereby ensuring the single cell division to create functional stomata.

The intrinsic and extrinsic factors that control stomatal development

Screen Shot 2017-11-24 at 12.28.17

Stomatal development in Arabidopsis. (A) Cell transitions and key regulatory pathways within the stomatal lineage. In the developing epidermis of photosynthetic tissues, an undifferentiated protodermal cell adopts a meristemoid mother cell (MMC, purple) identity and undergoes an asymmetric cell division (ACD), giving rise to a meristemoid (cyan). This initial step is directed by SPCH-SCRM protein heterodimers, which amplify their own expression while inducing the inhibitory secreted signals EPF2 and TMM. Signal transduction via ER family proteins and MAPKs, in turn, inhibits SPCH-SCRM, preventing neighboring cells from adopting a stomatal identity. The meristemoid reiterates ACDs, renewing itself and amplifying the surrounding stomatal-lineage ground cells (SLGCs, gray). A MUTE-SCRM module drives a meristemoid-to-guard mother cell (GMC, light green) transition, which terminates the stem cell-like state. EPF1 peptides, which signal via ERL1, TMM and the stomatal MAPK cascade, inhibit differentiation. The same pathway enforces the orientation of a secondary ACD of an SLGC, known as asymmetric spacing division. The transition from GMC to guard cell (GC, green) is specified by the FAMA-SCRM module. The MAPK cascade also promotes this step, although the upstream signal is unknown. FAMA and two paralogous MYB proteins, FLP and MYB88, restrict the GMC symmetric division by repressing cell cycle regulators such as CDKB1;1 and CYCA2. (B) The loss or gain of function of key stomatal regulators can alter epidermal cell patterning. Shown are false-colored confocal microscope images of developing Arabidopsis epidermis from wild-type plants (left), spch mutants (middle) and scrm-D mutants (right). In spch mutants [as well as in scrm scrm2 mutants, and in the case of EPF2-overexpression (OX) or constitutively active (CA) MAPK signaling], the epidermis is composed solely of pavement cells. Conversely, in scrm-Dmutants [and in the case of MUTE overexpression (OX) and dominant-negative (DN) MAPK signaling], the epidermis is entirely composed of stomata. Cyan, meristemoids; light green, GMCs; green, GCs. Images are modified from Horst et al. (2015).

Lineage-specific stem cells, signals and asymmetries during stomatal development.

by Han S. K., Torii K. U. (2016)

Soon-Ki HanKeiko U. Torii,

Howard Hughes Medical Institute, University of WashingtonSeattle, WA 98195USADepartment of BiologyUniversity of WashingtonSeattle, WA 98195USA

in Development 143: 1259-1270. [PubMed Abstract]

http://dev.biologists.org/content/143/8/1259

Screen Shot 2017-11-24 at 12.30.41

A model for guard cell maintenance by epigenetic mechanisms. (A) In the mature guard cells (GCs) of wild-type plants, stomatal lineage genes are terminally turned off. In this context, FAMA physically interacts with RBR via its LxCxE motif, which might recruit a PRC2 complex that deposits H3K27me3 marks (red circles) to give rise to a repressive chromatin state. (B) When a GFP FAMA transgene or mutant FAMA lacking the LxCxE motif is introduced, stomatal lineage genes re-initiate their expression in mature GCs. In this case, RBR and the repressive complex are no longer recruited to target loci. As such, the chromatin state remains open, thereby resetting the stomatal differentiation program resulting in a stoma-in-stoma (SIS) phenotype. Confocal image in B was provided courtesy of Dr Eunkyoung Lee (University of British Columbia, Canada).

 

Abstract

Stomata are dispersed pores found in the epidermis of land plants that facilitate gas exchange for photosynthesis while minimizing water loss.

Stomata are formed from progenitor cells, which execute a series of differentiation events and stereotypical cell divisions. The sequential activation of master regulatory basic-helix-loop-helix (bHLH) transcription factors controls the initiation, proliferation and differentiation of stomatal cells.

Cell-cell communication mediated by secreted peptides, receptor kinases, and downstream mitogen-activated kinase cascades enforces proper stomatal patterning, and an intrinsic polarity mechanism ensures asymmetric cell divisions. As we review here, recent studies have provided insights into the intrinsic and extrinsic factors that control stomatal development. These findings have also highlighted striking similarities between plants and animals with regards to their mechanisms of specialized cell differentiation.

Screen Shot 2017-11-24 at 12.32.41

The integration of environmental and hormonal signals during stomatal development. During stomatal development, EPF peptides are perceived by ER family (green) and TMM (dark green) receptor complexes, which also include a receptor mediator BAK1 (gray). The actual architecture of these receptor complexes is unknown. The signal is mediated via a MAPK cascade (orange), involving YDA, MKK4/5 and MPK3/6, that inhibits SPCH-SCRM via direct phosphorylation. Signaling via the plant steroid hormone brassinosteroid (BR) is mediated by the ligand-triggered heterodimerization of BRI1 (light green) and BAK1 (gray), which activates the BSU1 phosphatase that inhibits BIN2, a downstream negative regulator of BR signaling. BIN2 inhibits not only the BR downstream TFs BZR1 and BES1, but also YDA, MKK4/5 and SPCH to modulate stomatal development. Pathogen effector signaling, via AvrPtO and HopAI1 (marine blue), probably interferes with stomatal development by suppressing the activities of BAK1 and MPK3/6, respectively. Light, auxin and CO2 induce or suppress STOMAGEN or EPF2, thereby altering the balance of positive and negative signals instructing stomatal differentiation. For example, elevated CO2 induces the expression of CRSP, a protease that cleaves the EPF2 prepeptide. Light signals perceived by phytochrome (PHY) and cryptochrome (CRY) photoreceptors probably attenuate the stomatal MAPK cascade acting via COP1.

Screen Shot 2017-11-24 at 12.35.10

The intrinsic and extrinsic control of polarity within the stomatal lineage. (A) In wild-type (wt) meristemoids (light cyan), BASL (orange) accumulates in the nucleus. Prior to asymmetric cell division (ACD), a fraction of BASL translocates to the cell cortex at the distal end of the cell. After the ACD, BASL stays in the nucleus of the meristemoid, which eventually expresses MUTE (cyan) and differentiates into a stomata. In the sister SLGC, BASL stays localized at the cell cortex, and this leads to high MAPK activity, loss of stomatal precursor state, and eventual differentiation to a pavement cell. In basl mutants, meristemoids occasionally produce two daughter cells of the same fate; this can be termed a symmetric cell division (SCD). Here, both daughter cells express MUTE (cyan) and hence differentiate into stomata. The confocal microscopy image shows a meristemoid preceding the ACD. BASL-GFP (orange) fusion protein is detected both in the nucleus and at the cell-cortex of the future SLGC. The confocal image was provided courtesy of Dr Juan Dong (Rutgers University, NJ, USA). (B) Extrinsic signals influence BASL dynamics. In wild-type plants, prior to an asymmetric spacing division, BASL protein (orange) switches its polar localization within the SLGC (gray), which re-acquires a meristemoid mother cell (MMC) fate. This ensures that the secondary meristemoid (cyan) forms at least one cell apart from the pre-existing stoma (one-cell spacing rule). In epf1 or tmmmutants, this polarity switch is abrogated, resulting in mis-orientation of the spacing division and, consequently, stomatal clustering.

Autocrine regulation of stomatal differentiation

 

 

 

Autocrine regulation of stomatal differentiation potential by EPF1 and ERECTA-LIKE1 ligand-receptor signaling

Qi X., Han S.-K., Dang J. H., Garrick J. M., Ito M., Hofstetter A. K., Torii K. U. (2017)

  1. Xingyun Qi,
  2. Soon-Ki Han,
  3. Jonathan H Dang,
  4. Jacqueline M Garrick,
  5. Masaki Ito,
  6. Alex K Hofstetter,
  7. Keiko U Torii, 

 

in  eLife 2017;6:e24102 DOI: 10.7554/eLife.24102

https://elifesciences.org/articles/24102

Abstract

 

Development of stomata, valves on the plant epidermis for optimal gas exchange and water control, is fine-tuned by multiple signaling peptides with unique, overlapping, or antagonistic activities.

EPIDERMAL PATTERNING FACTOR1 (EPF1) is a founding member of the secreted peptide ligands enforcing stomatal patterning. Yet, its exact role remains unclear.

Here, we report that EPF1 and its primary receptor ERECTA-LIKE1 (ERL1) target MUTE, a transcription factor specifying the proliferation-to-differentiation switch within the stomatal cell lineages.

In turn, MUTE directly induces ERL1.

The absolute co-expression of ERL1 and MUTE, with the co-presence of EPF1, triggers autocrine inhibition of stomatal fate.

During normal stomatal development, this autocrine inhibition prevents extra symmetric divisions of stomatal precursors likely owing to excessive MUTE activity.

Our study reveals the unexpected role of self-inhibition as a mechanism for ensuring proper stomatal development and suggests an intricate signal buffering mechanism underlying plant tissue patterning.