Response Doctoral Program

Have you ever marveled at how a tiny seed grows into a towering tree? Seeds are at the foundation of all life, and their quality and yield are inevitably influenced by environmental conditions. Therefore, it is vital to enhance our understanding of how seeds form, such that sufficient yields can be ensured even during adverse conditions.

Seed formation is a complex process that involves the development of seeds from fertilized ovules, ultimately enabling the propagation of plant species. This process is closely tied to germline initiation, which is the initial phase of reproduction where germ cells are established. These germ cells later differentiate into gametes necessary for fertilization. Germline initiation sets the stage for seed formation by ensuring that the genetic material is prepared and ready for the creation of viable seeds. This process encompasses epigenetic changes, regulating gene expression without altering the underlying DNA to ensure proper germ cell development. Linker histones are special proteins that package DNA, and contribute to the process of epigenetic changes during germline initiation in the process of plant reproduction.

Linker Histones and Germline Initiation

Inside a plant cell’s nucleus, DNA is wrapped around histone proteins called nucleosomes, forming a structure that looks like beads on a string, known as chromatin. Chromatin facilitates these long strings to be contained within the small nucleus by packaging long DNA molecules into more compact, denser structures. Linker histones, also called H1, are proteins that bind the DNA between these nucleosomes, helping structure the chromatin and regulate genes.

Female germline initiation involves the development of the spore mother cell, which undergoes meiosis to produce megaspores, ultimately giving rise to female gametophytes and egg cells necessary for fertilization. Research indicates that during germline initiation, linker histones show a transient disappearance in the spore mother cell for a short period, triggering major epigenetic changes.Danli Fei, is a PhD researcher who aims to uncover why linker histones disappear, and its implications for plant reproduction and thereafter, seed yield, in particular for the model plant, Arabidopsis.  She is at the Department of Plant and Microbial Biology at the University of Zürich, and she is also a RESPONSE fellow in the PhD program Science and Policy.

How Linker Histone Degradation Triggers Reproductive Cell Formation

Proteins in cells are often regulated by a process called ubiquitination, which tags them for a large protein complex called proteasome found in cells to degrade and recycle damaged or unused proteins. Danli hypothesized that ubiquitination controls the loss of linker histones during germline initiation. Through various molecular and genetic experiments, Danli confirmed that ubiquitination is indeed involved in degrading linker histones. The enzyme responsible for linker histones was identified, and through her research, she pinpointed the specific amino acids of linker histones that get tagged as well. Crucially, Danli’s research has identified that if linker histone degradation is blocked during female germline initiation, plants cannot produce functional gametes, and thereafter, become sterile.

Wide-Reaching Implications for Advancements in Scientific and Practical Domains

Danli’s research has revealed the pivotal role of linker histones in determining the ability of a plant to reproduce. She advises future studies to investigate the role of linker histone ubiquitination in other developmental processes and its specificity. This knowledge has far-reaching implications across various fields, including agriculture and conservation biology, among others. Understanding the role of linker histone ubiquitination and its impact on seed fertility can revolutionize crop development. By leveraging this insight, we can create crop varieties with higher yields and improved fertility through selective breeding techniques. Additionally, it paves the way for producing nutrient-rich crops, addressing malnutrition, and enhancing public health. This knowledge can also help develop plant varieties that are more resilient to environmental stresses such as drought, salinity, and pathogens, ensuring robust reproductive processes even under adverse conditions. In conservation biology, applying this understanding can aid in the successful reproduction and seed formation of endangered plant species, as well as ensure the successful reintroduction of plant species in habitat restoration projects.

Interdisciplinary and Collaborative Research

These findings are a result of combining methods in molecular biology (cloning, genotyping, DNA and RNA work, gene expression analyses), cell biology (tissue fixation and staining, immunolabeling) and microscopy imaging (light microscopy, fluorescence confocal microscopy) to describe chromatin organization at a microscopic and quantitative scale. Moreover, Danli pursued this research by collaborating with a software company, which exposed challenges in adapting image analysis tools for specific scientific needs, underscoring the intricacies of developing algorithms capable of processing complex biological data. This means that high-resolution microscopic images collected using a confocal laser scanning microscope were processed, such as partially or fully projected and three-dimensionally rendered using Imaris software, which revealed challenges given the complexity of the biological data. These insights from her collaborations emphasize the nuanced interactions between fundamental biology and technological innovation, thereby opening new avenues for exploration.

Stakeholder Engagement

As part of her RESPONSE fellowship, Danli organized a stakeholder engagement workshop in Schlieren, Switzerland, in 2022 titled, “How Imaris can help with Plant Science”, which was attended by the engineering team of Bitplane in Switzerland, application specialists, and the sales and marketing team of Bitplane in Switzerland and USA. Imaris is the world’s leading Interactive Microscopy Image Analysis software. During this workshop, Danli presented and discussed publications showcasing how Imaris is used in plant science, as well as communicating about survey and analysis of all plant science publications that had made use of Imaris in the previous 5 years. The aims of the workshop were successfully accomplished, which included highlighting the successful functions of Imaris functions, identifying missing or inappropriate Imaris functions for future improvement and development, and showcasing material for motivating a broader use among plant scientists.

This article is co-authored by Danli Fei and Mary Ann George (University of Zurich, RESPONSE Program office assistant).