Unlocking Plant Resilience: The H4.V Histone’s Role in Appropriate Response to Salt Stress

The biggest problem with conventional breeding programmes and the cutting-edge genetic engineering is that only a small set of genes are programmed to behave differently and the impact of that is also limited. On the other hand, with identification of a global switch for salt-stress, this study opens a new realm of possibilities

All the crop plants that produce the food we consume grow in specific growth conditions and environment. The challenges posed by climate change and weather patterns immensely affects crop systems and, in turn, food security. To engineer climate resilient crop plants, it is crucial to understand how plants sense environmental changes and respond to environmental conditions.

Globally, researchers have been interested in and focussed on understanding how plants react to higher salt concentration, and undertake targeted tweaks to enable plants to tolerate high salt content in non-arable lands, especially the coastal wastelands.

The discovery

Led by Dr. P.V. Shivaprasad, our study at the National Centre for Biological Sciences (NCBS) uncovered a novel epigenetic module that can act as a single master-switch that triggers and/or prevents plants from reacting to salt stress. The findings were published recently in the journal Nature Plants.

The interesting aspect of the finding is that this switch is not an ordinary gene that controls the response to salt. Rather, it is a fundamental, previously unknown, epigenetic feature unique to rice plants. In all eukaryotes, the code of life — DNA is wrapped in a well-orchestrated protein complex. This fundamental unit of gene packaging is made of five flavours of proteins called histones. Histones are positively charged small proteins that bind to the negatively charged DNA molecules in a cell and package them. Histones H2A, H2B, H3 and H4 occur in an octet configuration, made of two units of each. These octamers wrap around 150 bp of DNA to form nucleosome complex. Nucleosomes dictate where and when genes are expressed.

We identified a variant of histone H4 in rice — H4.V — and this unique protein variant is distinct from the conventional histone H4. H4.V forms nucleosomes in a subtly different configuration compared with the normal nucleosomes. H4.V nucleosomes are significantly compact and less stable compared with the conventional nucleosomes. Their atomic structures reveal a whole lot of detail that are unique to H4.V.

The most interesting aspect of the study was revealed when we genetically removed H4.V from rice using CRISPR/Cas9 molecular scissors. The plants that lacked the H4.V displayed stunted growth. Using high throughput genomics analyses, we identified that the mutant plants lacking H4.V showed exact similar molecular phenotypes like that of salt-stressed plants. This suggested that H4.V plays a crucial role in switching-on and off the salt stress responses.

To further understand how H4.V acts as a switch, we took a deep-dive into the nucleosome arrangement. Using a technique to profile how the histone proteins are modified when H4.V is present or absent, we discovered that there is another histone modification — H4 acetylation — a small chemical entity that is added to the canonical histone H4. This modification is lost in plants that lack the H4.V on salt-responsive genes. In its absence the salt-responsive genes are always kept switched on leading to stunted growth.

Implications of the study

The biggest problem with conventional breeding programmes and the cutting-edge genetic engineering is that only a small set of genes are programmed to behave differently and the impact of that is also limited. On the other hand, with identification of a global switch for salt-stress, this study opens a new realm of possibilities.

Using this histone variant, one can touch upon the possibility of cross-applicability of the switch beyond rice in other crops. With the huge diversity of native rice varieties in India, this discovery paves way for enabling salt tolerance in elite lines enabling cultivation in marshy-wastelands near coasts. This would boost the agricultural produce several folds, potentially. Since all the changes are epigenetic in nature, the effects are reversible and can be tuned.

Featured image credit: Declan Sun/Unsplash