A newly developed method enables research teams to analyze and compare various types of proteins and protein complexes, revealing an undiscovered molecular signature that explains how algal genomes are regulated throughout the cell cycle. This method was detailed in a recent publication titled “pyMS-Vis, an open-source Python application for visualizing and investigating deconvoluted top-down mass spectrometric experiments: A histone proteoform case study,” which appeared in the journal Analytical Chemistry in 2024.
The research was a collaborative effort that included experts such as James Umen, PhD, a member and principal investigator at the Danforth Plant Science Center; Jim Pesavento, PhD, an associate professor at Saint Mary’s College of California (SMC); Mowei Zhou, PhD, a Qiushi scholar from Zhejiang University; and Ljiljana PaÅ¡a-Tolić, PhD, a lead scientist in Visual Proteomics at the Department of Energy Environmental and Molecular Sciences Laboratory in Richland, WA.
The Umen lab is renowned for its extensive research on the multiplication and differentiation of algal cells into distinct sexual types. Pesavento specializes in mass spectrometry, focusing on the precise identification and quantification of biological molecules. His key area of expertise is a vital group of proteins known as histones, which package DNA in all organisms with nucleated cells, including plants, algae, and humans. Histones not only condense DNA into chromatin but are also modified chemically, creating signals that mark gene locations and regulate their expression. These chemical tags contribute an additional layer of information known as the epigenome, associating with the DNA they modify.
A significant challenge in this area of research has been discerning the specific chemical changes on histones, their locations on the protein, and whether these changes are dynamic—being added or removed in response to certain conditions. The vast combinations of possibilities complicate the task, despite the use of advanced mass spectrometry equipment and software. Also, each organism category, such as plants and green algae, appears to have its own unique “histone code,” making it crucial to decode this language for developing improved varieties with desirable traits.
While some commercial software exists for analyzing histone modifications, none have proven capable enough for handling modifications on entire histone proteins. Recognizing this gap, Pesavento aimed to automate the tedious process of identifying histone modifications by creating an open-source software tool called pyMS-Vis to benefit researchers studying algal histones and others in the field.
“This initiative began as a collaborative effort with SMC professor Udayan Das, PhD, as we co-mentored an undergraduate student, Megan Bindra, during the SMC undergraduate Summer Research Program in 2022,” Pesavento explained. “We made notable advancements, and Bindra presented our findings at a professional conference the following year (2023). The combination of NSF funding for my small lab at SMC and the dedication of collaborators from various scientific backgrounds was crucial to the success of this publication.”
To validate this method, Pesavento utilized histone samples that the Umen lab prepared from cells at different stages of their cell division cycle. This allowed them to investigate what happens to histone marks in cells when they are undergoing DNA replication, compared to when they’re growing without replicating DNA or dividing. With pyMS-Vis, they were able to quickly analyze data and uncover a previously unanticipated and significant population of a specific histone subtype that lacked a chemical mark believed to be present on nearly all histones of that subtype.
“With pyMS-Vis, we’ve been able to observe histone dynamics that were previously difficult to detect, paving the way for a deeper understanding of algal gene expression,” Umen stated. “This enhanced understanding is crucial for developing algae as viable crop species capable of consistently expressing advantageous traits, such as higher oil yields or valuable products.”
