Doubling the Dictionary of Protein Modification

yingming-cellA cell is full of language. There’s the four-letter code of DNA, the slightly different four-letter dialect of RNA, and the three-letter words that direct the construction of proteins, which are built out of an alphabet of 20 amino acids. In recent years, scientists have slowly revealed another vocabulary superimposed on top of this language, comprised of chemical groups attached to genes and proteins. When groups such as methyl or phosphate are stuck to various places on a protein or gene, they can dramatically change its function, switching it on or off or marking it for transport or destruction. On a disease level, these changes can contribute to cancer, aging, and other conditions, making them an enticing target for drug design.

One area where protein modification is making a big splash is the relatively new field of epigenetics, which looks at how changes to DNA and DNA-related proteins can affect gene expression. The methylation of DNA is known to turn genes off, and a number of modifications to histones – proteins that package and organize DNA – can also have functional consequences. Scientists suspected that they hadn’t found all of the modifications possible on histones, but discovering each new modification and proving its role was considered a painstaking process requiring years of experiments. Finding a new modification, such as Yingming Zhao’s 2010 discovery of lysine succinylation, is an achievement worthy of publication in a high-ranking journal.

So what happened when Zhao’s laboratory discovered sixty-seven new modifications to histones in one paper? The research not only was published in the esteemed journal Cell, but was featured by the journal as one of its top five 2011 highlights.

Zhao, a professor in the Ben May Department of Cancer Research at the University of Chicago Medicine, said he believes the extra accolades reflect the volume of his laboratory’s latest breakthrough, and the paper’s expected influence on how scientists will understand the language of protein modification and epigenetic mechanism.

“If we are going to understand epigenetics and its role in disease we need to identify the full vocabulary of the histone modifications, a major group of epigenetic marks,” Zhao said. ” We thought we had a comprehensive histone vocabulary because of extensive studies by the whole research community in the past 3-4 decades, but in our study, in a single paper, we increased it by 70 percent.”

The laboratory put the pedal to the floor on histone modification discovery by developing new technologies and improving the resolution of pre-existing methods. By using the staple lab method of mass spectometry, which measures the mass and charge of particles, and an algorithm of their own design called PTMap, the researchers could scan the entire histone at once and detect more protein modifications than ever before. Their scan yielded a total of 130 different modification sites — 63 that had previously been observed and reported, and 67 that were new to science.

So large was the yield of new modifications that the current paper wasn’t big enough to fully explore the dynamics and function of all of them. The research team chose to more thoroughly study the novel modification that appeared the most: lysine crotonylation, where a crotonyl group is added to the amino acid lysine. Experiments determined that histone lysine crotonylation is evolutionarily conserved (found in yeast, flies, and humans), is often found in promoter or enhancer regions upstream of genes, suggesting a role in transcriptional control. Furthermore, histone lysine crotonylation was found to be enriched on sex chromosomes, specifically marking testis-specific genes, which implies a role in spermatogenesis.

As for what the other never-before-seen modifications are doing in cells, that will have to wait for future papers, Zhao said.

“This is still a very preliminary study,” Zhao said. “Hopefully, we and the research community will figure out if these modifications have a role in cancer and other diseases. Given the fact that lysine methylation and acetylation pathways are already popular drug targets, I assume these new modifications and the enzymes that regulate these modifications and pathways are highly likely to be drug targets for diseases.”

The contributions of Zhao’s lab to the field of epigenetics go beyond the Cell paper. In addition to the 67 new histone marks described there, recent papers from the group have also reported four other types of new epigenetic codes: histone lysine propionylation, lysine butyrylation, lysine succinylation, and lysine malonylation. Taken together, the laboratory has discovered more histone marks in this handful of papers than the total number of marks uncovered by the entire research community in the past 4 decades, Zhao said.

While many scientists might be content to spend the rest of their career sorting through the bounty of this one paper, Zhao is already thinking about the next frontiers for cellular vocabulary. All of the newly discovered modifications necessarily must have enzymes to add and remove the chemical groups, and the modified proteins likely produce downstream effects through networks that have yet to be described.

“While these were found through histone modification, some of them will be on other proteins as well,” Zhao said. “We are interested to discover new cellular pathways, and protein modification is only one type of new pathway.”

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Tan, M., Luo, H., Lee, S., Jin, F., Yang, J., Montellier, E., Buchou, T., Cheng, Z., Rousseaux, S., Rajagopal, N., Lu, Z., Ye, Z., Zhu, Q., Wysocka, J., Ye, Y., Khochbin, S., Ren, B., & Zhao, Y. (2011). Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification Cell, 146 (6), 1016-1028 DOI: 10.1016/j.cell.2011.08.008

About Rob Mitchum (523 Articles)
Rob Mitchum is communications manager at the Computation Institute, a joint initiative between The University of Chicago and Argonne National Laboratory.
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