Understanding Algal Gene Expression Through Histone Dynamics

A previously unknown molecular signature of the regulation of algal genomes during the cell cycle was discovered thanks to a novel technique that research teams can employ to test and compare various protein forms and protein complexes. The study was published in the Analytical Chemistry journal.

The research team consisted of James Umen, PhD, member and Principal Investigator, Danforth Plant Science Center, James (Jim) Pesavento, PhD, Associate Professor at Saint Mary’s College of California (SMC), Mowei Zhou, PhD, Qiushi scholar for experiments, Zhejiang University and Ljiljana Paša-Tolić, PhD, Lead Scientist for Visual Proteomics, Department of Energy Environmental and Molecular Sciences Laboratory in Richland, WA.

The Umen lab has a long history of studying the growth and differentiation of algal cells into sexually differentiated kinds. Pesavento is adept at quantifying the amount of biological molecules and identifying them with a high degree of precision using mass spectrometry.

He is particularly knowledgeable about a crucial class of proteins known as histones, which are involved in the packaging of DNA in all living things with nucleated cells, including humans, plants, and algae.

In addition to being necessary for encapsulating DNA in a tight structure known as chromatin, histones are also embellished with chemical alterations that act as markers or indicators indicating the positions of genes and whether or not they should be expressed because these markers give the DNA they associate with an extra layer of information, they are sometimes referred to as an epigenome.

Determining which histones have which chemical modifications, where those changes occur on the histone protein, and if they are dynamic (added and deleted under specific conditions) has proven to be a significant issue in this research.

Even with the most sophisticated mass spectrometry equipment and software, this process is very challenging due to combinatorial possibilities. Furthermore, it appears that every group of animals, including green algae and plants, has a unique variation of histone code language. Understanding this language is crucial for creating better kinds with advantageous features.

Commercial software is available to assist with this process; however, no software has been sufficiently reliable to address histone alterations on entire histone proteins. To assist algal histones and other histone researchers, Pesavento decided to develop an open-source application called pyMS-Vis after realizing that the tedious and time-consuming processes required to discover histone modifications may be largely automated.

This work started as a collaboration with SMC professor Udayan Das, PhD, as we co-mentored an undergraduate computer science student Megan Bindra during the SMC Undergraduate Summer Research Program in 2022. We were able to make significant progress, and Bindra presented this work at a professional conference the following year (2023). The combination of NSF funding support for my small lab at SMC and invested collaborators across diverse scientific disciplines, were essential to this work's publication.”

James Umen, PhD, Member and Principal Investigator, Donald Danforth Plant Science Center

Using a set of histone samples that the Umen lab had prepared from cells at various stages of their cell division cycle, he tested this approach to find out what happens to histone marks in cells during DNA replication versus growth without DNA replication or division.

A new and surprisingly huge population of a certain histone sub-type that was missing a mark that had long been thought to be present on almost every histone of this sub-type was found thanks to the quick data analysis made available by pyMS-Vis.

pyMS-Vis has allowed us to see histone dynamics that we could not easily see before and opened the door to a more complete understanding of the language of algal gene expression. This deeper understanding will be a critical part of developing algae as productive crop species that stably express beneficial traits such as increased yields of oil or high-value products.”

James Umen, PhD, Member and Principal Investigator, Donald Danforth Plant Science Center