Discoveries in 2023

This year, scientists at the GMI uncovered a molecular switch regulating autophagy, demonstrated the crucial role of histone variants in shaping the genome landscape, and discovered how plant stem cells fight off viruses. Here are some of the intriguing discoveries that came out of the GMI in 2023.

Bryophytes branch differently … Also at the molecular level

Non-vascular bryophytes live in colonies that cover the ground and resemble tiny forests. In a real forest, plants compete for light in different layers of the canopy. If a plant does not receive enough sunlight, it stops lateral branching and instead grows vertically to reach the sunlight. In a new study, the group of Liam Dolan discovered that the liverwort Marchantia polymorpha, whose plant body is fundamentally different from those of vascular plants, also adapts its architecture in response to shade.

The researchers phenotyped liverworts and found that in full white light, the flat liverwort body, also known as the thallus, branched regularly. Similarly to vascular land plants, the phytochrome signaling pathway guides the shade-avoidance response in the liverwort – however, the genes controlling these responses are evolutionarily distant from those involved in Arabidopsis branching.

With these results, the team speculates that the molecular mechanisms regulating branching might have evolved independently in bryophytes and vascular plants. “Overall, our findings demonstrate that a partly conserved mechanism of phytochrome-regulated miRNA and SPL gene activity controls branching in completely divergent families of land plants with fundamentally different modes of branching,” says Dolan.

Autophagy: The molecular regulation of self-eating

Autophagy, or “self-eating”, is an essential cellular quality control mechanism that clears the cell of protein aggregates and damaged organelles. This mechanism is inactive under normal conditions and only triggered upon persistent cellular stress. In 2023, researchers from the group of Yasin Dagdas at the GMI and at the Max Perutz Labs uncovered a molecular switch that regulates autophagy in plants.

Using a combination of evolutionary biology and mechanistic experimentation, the researchers demonstrated that the competition between two ubiquitin-like molecules, UFM1 and ATG8 creates a molecular switch in the master regulator C53, which then initiates ER-phagy. The research team also showed that this regulatory mechanism is conserved in eukaryotes.

Histone variants shape the Arabidopsis epigenome

DNA can be transcriptionally active or silent, depending on its state of packaging into chromatin. The “packaging proteins”, called histones, exist in many variants. A new study by the laboratory of Frederic Berger now showed that these histone variants are key drivers to determine whether chromatin is in a transcriptionally active state – or not.

Among four core histones, H2A variants appeared to be key factors that define euchromatin, facultative heterochromatin, and constitutive heterochromatin. “In a hierarchy of importance, the H2A variants, and only then the posttranslational modifications, set up in which of these three states chromatin is. The relative enrichment of other histone variants and modifications further defines subdomains of chromatin states”, Berger says. “This is the first time that histone variants have been assessed systematically in eukaryotes. We have no reason to assume that what we found is not valid in other eukaryotes – including in mammals, which have a similar diversification in histone variants as flowering plants.”

Unearthing the hidden trove of long non-coding RNAs in plants

Long non-coding RNAs, an enigmatic class of genes that do not encode proteins, exhibit greater variability and are subject to more silencing mechanisms than previously known, a new study in Arabidopsis shows. Some lncRNAs even resemble transposons and are controlled by transposon silencing mechanisms, as the Nordborg group showed in a new study.

The researchers demonstrated that almost 12,000 lncRNA cover 10% of the Arabidopsis genome. Moreover, plant lncRNAs exhibited considerable variability in their expression patterns: only half of the lncRNAs expressed in one Arabidopsis natural variant were expressed in another. However, the GMI scientists also revealed that the majority of lncRNAs appear to be actively silenced. By looking closer, they could show that this variability in expression might arise from the high variability in silencing mechanisms, including repressive chromatin.

The last stand: Plant stem cells put up a fight against viruses

Plant viruses threaten the health of their hosts, can spread swiftly and globally, and challenge agricultural productivity. When viruses successfully infect plants, the infection often spreads through the entire organism. Well, not entirely: One small group of indomitable cells still holds out, the stem cells within the shoot tip. This small group of cells generates all plant tissues above ground, including the next plant generation, and for reasons still poorly understood, viruses are unable to proliferate in these cells.

Marco Incarbone, now at MPIMP Golm, Gabriele Bradamante and their co-authors in the group of Ortrun Mittelsten Scheid sought to uncover the molecular bases of how stem cells in the shoot apical meristem fight off viruses. They uncovered that in the fight against Turnip mosaic virus, both salicylic acid and RDR1 are necessary to expel the virus from the stem cells. “Based on our experiments also with other viruses we can conclude that RNA interference is always necessary to defend stem cells from infection,” says Incarbone.