# From the archives: Somatic DNA demethylation, circadian rhythms LNKed to transcriptional machinery, and induction of Kranz anatomy in a submerged amphibious plant

Louis-Valentin Méteignier

► To cite this version:

Louis-Valentin Méteignier. From the archives: Somatic DNA demethylation, circadian rhythms LNKed to transcriptional machinery, and induction of Kranz anatomy in a submerged amphibious plant. The Plant cell, 2023, 35 (4), pp.1161-1162. 10.1093/plcell/koad016 . hal-04160171

HAL Id: hal-04160171

https://hal.inrae.fr/hal-04160171

Submitted on 12 Jul 2023

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# From the archives: Somatic DNA demethylation, circadian rhythms LNKed to transcriptional machinery, and induction of Kranz anatomy in a submerged amphibious plant

Louis-Valentin Méteignier ID <fnref n="1" />,<fnref n="2" />,*

## April 2022: Somatic DNA demethylation

Cytosine DNA methylation controls cell fate and stress responses by silencing transposable elements and regulating gene expression. The level of DNA methylation results from the balance between methyltransferase and demethylase activities. In Arabidopsis, active DNA demethylation is controlled by four DNA glycosylases/lyases: DEMETER (DME), REPRESSOR OF SILENCING1 (ROS1), DME-LIKE2 (DML2), and DML3. Heterozygous *dme/DME* plants produce only 50% of viable seeds without the *dme* mutation due to aborted embryos (Choi et al., 2002), precluding analysis of the role of *DME* in somatic tissues. To bypass this issue, **Ben P. Williams and colleagues** (Williams et al., 2022) created a somatic quadruple homozygous mutant of the entire DME family (called *drdd*). They constructed a *DME* transgene under the control of an embryo-specific promoter and introduced it into a triple mutant of ROS1, DML2, and DML3 (termed *rdd* mutant). They then crossed the transgenic homozygous *rdd/rdd* mutant with heterozygous *dme/DME* plants, and obtained transgenic wild type along with *dme*, *rdd*, *drdd* plants in which *DME* was expressed primarily in the embryo, thus rescuing the seed abortion phenotype of homozygous *dme* and *drdd* plants.

The authors analyzed leaf DNA methylomes and observed 276 differentially methylated regions in *dme*, 2,091 hypermethylated regions in *rdd*, and 2,601 hypermethylated regions in *drdd* compared to wild type, suggesting that the four demethylases function redundantly in leaves.

By transcriptomic analysis, the scientists observed a correlation between gene hypermethylation and reduced transcript accumulation in *drdd*, suggesting that the DRDD pathway safeguards gene expression by “cleaning up” excessive DNA methylation. Among hypermethylated genes in *drdd*, the flowering time regulator *FLOWERING LOCUS C* was the most down-regulated gene, and *drdd* plants flowered earlier than the other genotypes. Importantly, natural Arabidopsis accessions with high DNA methylation at *FLOWERING LOCUS C* tended to flower earlier than low methylation accessions. By bypassing the embryo abortion phenotype of *dme*, the authors were able to explore how somatic DNA demethylation impacts flowering in Arabidopsis.

## April 2018: Circadian rhythms LNKed to transcriptional machinery

Biological systems possess circadian clocks that enable the coordination of cellular functions with diurnal light/dark cycles. In Arabidopsis, the regulatory component of the circadian clock is composed of numerous transcriptional regulators. Among them, the MYB transcription factor REVEILLE8 (RVE8) interacts with NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED (LNK) proteins to regulate the transcription of dusk-expressed genes (Xie et al., 2014). Yuan Ma and co-workers (Ma et al., 2018) showed that the LHY-CCA1-LIKE (LCL) domain in RVE8 was required for the rhythmicity and amplitude of dusk gene expression,

<footnote n="1">1 Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA</footnote>

<footnote n="2">2 PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France</footnote>

<footnote>*Author for correspondence: louis-valentin.meteignier@inrae.fr</footnote>
<figure><img src="image_2.png" /><figcaption>**Figure** Cross-sections of culms of the terrestrial form (left) and submerged form (right) of *E. vivipara*. AC, air cavity, bars 100 µm (left), 50 µm (right). Adapted from Ueno (1998), Figure 1.</figcaption></figure>

although a truncated form of RVE8 without LCL still inter-
acted with dusk gene promoters through its MYB domain.
To understand the DNA-binding-independent role of the
LCL domain, they performed a genome-wide screen for
LCL-interacting proteins and identified LNK proteins.

The authors then discovered that the enrichment of RNA
polymerase II and a histone modification of active chromatin
at dusk genes decreased in *Ink* plants. LNK physically inter-
acted with RNA polymerase II and a histone chaperone sub-
unit, and the association of RNA polymerase II and the
histone chaperone with dusk-expressed genes decreased in
*Ink* plants. The authors also showed that LNK and the histone
chaperone are part of the same protein complex and that the
chaperone is required for RNA polymerase II occupancy at
dusk genes. Finally, the authors demonstrate that nascent
RNA accumulation of dusk genes decreased in *Ink* mutant
plants. This study provides a model for LCL action in RVE8
that is required for the interaction with LNK. In turn, LNK in-
teracts with a histone chaperone complex. The results sup-
ported a role for this interaction in promoting the
progression of RNA polymerase II along dusk-expressed
genes.

April 1998: Induction of Kranz anatomy in a
submerged amphibious plant

Photosynthesis is the major player in atmospheric carbon fix-
ation on earth and is essential for numerous heterotrophic
organisms. C3 photosynthesis occurs in a single cell type:
mesophyll cells. In contrast, C4 photosynthesis occurs in
two distinct cell types: atmospheric CO2 is fixed in mesophyll
cells as C4 acids that are then transferred to Kranz cells
where they are decarboxylated to generate CO2 that will
be re-fixed by ribulose-1,5-bis-phosphate carboxylase/oxyge-
nase (Rubisco). The partitioning of C4 photosynthesis in two
distinct cell types concentrates CO2 at the site of Rubisco ac-
tivity and reduces competition for oxygen, hence favoring
photosynthesis over photorespiration (Langdale, 2011). It is
therefore crucial to understand the genetic regulation of

C3 and C4 photosynthesis to envision the biological engineer-
ing of photosynthesis.

In general, plant species are either C3 or C4, but exceptions
to the rule exist. The amphibious leafless sedge *Eleocharis vivipara* develops C4 anatomy and biochemistry when grown
in terrestrial conditions, in contrast to C3 anatomy and bio-
chemistry when grown in submerged conditions (see Figure).
Twenty-five years ago, Osamu Ueno discovered that treating
submerged *E. vivipara* plants with abscisic acid induced a
shift from C3 to C4 anatomy and biochemistry (Ueno,
1998). The same research group recently discovered that gib-
berellic acid induces a shift from C4 to C3 anatomy, but not
biochemistry, in terrestrial forms of *E. vivipara* (Suizu et al.,
2021). The Ueno group studies suggest that transitions be-
tween C3 and C4 biochemistry are genetically uncoupled
from anatomical transitions.

**References**

Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, Jacobsen SE, Fischer RL (2002) DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell **110**(1): 33–42

Langdale JA (2011) C4 cycles: past, present, and future research on C4 photosynthesis. Plant Cell **23**(11): 3879–3892

Ma Y, Gil S, Grasser KD, Mas P (2018) Targeted recruitment of the basal transcriptional machinery by LNK clock components controls the circadian rhythms of nascent RNAs in Arabidopsis. Plant Cell **30**(4): 907–924

Suizu Y, Takao K, Ueno O (2021) Gibberellic acid induces non-Kranz anatomy with C4-like biochemical traits in the amphibious sedge *Eleocharis vivipara*. Planta **254**(1): 10

Ueno O (1998) Induction of Kranz anatomy and C4-like biochemical characteristics in a submerged amphibious plant by abscisic acid. Plant Cell **10**(4): 571–583

Williams BP, Bechen LL, Pohlmann DA, Gehring M (2022) Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time. Plant Cell **34**(4): 1189–1206

Xie Q, Wang P, Liu X, Yuan L, Wang L, Zhang C, Li Y, Xing H, Zhi L, Yue Z, et al. (2014) LNK1 and LNK2 are transcriptional coactivators in the Arabidopsis circadian oscillator. Plant Cell **26**(7): 2843–2857