The genetic code contains only four letters. Different combinations of those letters code for an “alphabet” of 20 amino acids, which are used to construct proteins. From these small collections of building blocks, an incredibly diverse array of proteins can be constructed. But nature always craves more options, and scientists are still learning the ways it has developed to expand its biological vocabulary. With epigenetics, nature can tweak the genetic code without changing the basic four nucleotides. With protein modification, stable constructions can become dynamic machines, changing shape and switching on and off.
The laboratory of Yingming Zhao, associate professor in the Ben May Department of Cancer Research, tracks down previously undiscovered ways nature has found to customize its proteins. Usually, proteins are modified via chemistry, with molecules such as methyl groups (methylation) or phosphate groups (phosphorylation) added to the side chains of amino acids. Attaching these groups can dramatically change the shape and function of a protein, increasing its activity, decreasing it, or sending it to the cellular trash dump. On a larger scale, errors in these modifications can have dramatic consequences; for example, excessive phosphorylation has been targeted as a cause of many cancers, and modification may play a role in aging.
“Think of comparing someone who’s really young, say 1 month old, to someone who is 90 years old,” Zhao said. “Their cells and tissues function so differently. In my personal view, a major pathway that causes those differences is protein modification.”
In the last three years, Zhao’s team has added two new modifications, lysine propionylation and lysine butyrylation, to the menu of protein modifications. But this week, his lab publishes findings in Nature Chemical Biology on a third modification that may be even more biologically important: lysine succinylation. The addition of a succinyl group to the amino acid lysine is a big change in chemical terms, changing the electrical charge of lysine from positive to negative.
“If you take away the positive charge by acetylation, it becomes more hydrophobic, so in terms of its property it is dramatically changed,” Zhao said. “When you put succinylation, it goes from positive charge to negative charge, it’s a two-charge change. The chemical importance of the change with lysine succinylation is more than lysine acetylation and methylation, two protein modifications with critical cellular functions.”
The discovery of lysine succinylation started with a mysterious, very tiny shift in weight in the protein isocitrate dehydrogenase, a member of the citric acid cycle you may have memorized in high school. By the size of the shift (100 Daltons, or one hundred octillionth of a gram) the likely candidate was succinyl, and a series of experiments conducted by a research team led by Zhihon Zhang and Minjia Tan confirmed the hypothesis. By developing an antibody for succinylated lysine, the researchers then confirmed that this modification was common in nature – appearing in everything from e. coli bacteria to cancer cell lines from humans. That persistence is part of the argument that lysine succinylation is an important function, Zhao said.
“It’s evolutionarily conserved and present in all types of cells we examined, from bacteria to mammalian cells,” Zhao said. “It is also very abundant: it’s not only present in a few proteins. Finally, it is a very dynamic protein modification that responds to diverse cellular environments.”
“We know lysine acetylation and methylation are critical to cellular function and diseases,” Zhao continued. “Therefore, it’s reasonable to argue lysine succinylation will be also important for cellular function and diseases.”
Now that lysine succinylation has been dragged into the spotlight, scientists can begin the important business of figuring out exactly what it does and the diseases where it may play a role. It can be a long road from the discovery of a protein modification to its application in medicine; Zhao points out that protein phosphorylation was discovered 50 years ago (and linked to cancer by Janet Rowley in 1973), yet therapies that target the modification, such as the cancer drug Gleevec, hit the market only in the past decade. But with the new scientific tools available today, the impact of lysine succinylation may be felt more immediately.
“This is just a first step. It’s not going to take 50 years, because things have changed, but it’s a first step,” Zhao said. “There are all kinds of possibilities. It will require the community to figure out the details.”