Rice lab gives structure to histone discovery

Yizhi Jane Tao lab, MD Anderson collaborate to uncover cell mechanism with implications for cancer treatment

Researchers have uncovered a subtle mechanism that modifies histone proteins, the spindles around which DNA wraps in every cell, in a way that promotes the formation and spread of tumors.

The new research by Rice University, the University of Texas MD Anderson Cancer Center and other institutions examines succinylation of histones in the nucleus of cells, a process believed to support cancer cells.

Their study in Nature is essentially a tale of two proteins – lysine acetyltransferase (KAT2A, aka Gcn5) and a-KGDH. The first resides in the nucleus of a human cell and awaits the arrival of the second, whereupon they bind and catalyze histone modification.

Yizhi Jane Tao, left, and Yusong Guo. Photo by Jeff Fitlow

There are four histones in each nucleosome (the basic “beads-on-a-string” in DNA). Histones help control protein structure and function by exposing genes for activation. Succinylation is one of 16 known histone modifiers that serve as a kind of switch in the process.

Until recently, scientists knew little about succinylation, said Yizhi Jane Tao, a structural biologist at Rice who co-led the project with Dr. Zhimin Lu at MD Anderson and Dongming Xing, an associate professor at Tsinghua University.

The researchers studied histone modifications catalyzed by KAT2A through two different helper proteins: acetyl-coenzyme A (or CoA) and succinyl-CoA, the latter of which is generated by the a-KGDH complex in the nucleus. Both CoA substrates are part of the tricarboxylic acid cycle that delivers energy to cells.

KAT2A normally binds to acetyl-CoA molecules, serving them up to histones. But the researchers learned through experiments that KAT2A has a higher binding affinity to succinyl-CoA and that KAT2A adds a succinyl group to histone H3 about 20 percent faster than it adds an acetyl group.

When it couples with a-KGDH in the nucleus, KAT2A gains access to a concentrated supply of succinyl-CoA. The work by Tao’s lab was critical to the discovery that KAT2A and succinyl-CoA bind so readily.

Tao’s lab specializes in X-ray crystallography to determine the structures of molecules like proteins. The structures help researchers see how molecules fit together and sometimes identify mutations that can be addressed with drugs or other therapies. Tao and Rice alumna Yusong Guo, co-first author of the paper and now a postdoctoral associate at the Rockefeller University, generated the crystal structures of KAT2A and its complex with succinyl-CoA that allowed the team to identify specific binding sites.

With prior knowledge that succinylation of histones is instrumental in tumor development, the researchers at MD Anderson tested brain tumor cell lines and showed that a-KGDH-coupled KAT2A promotes proliferation. When they blocked a-KGDH from entering the nucleus or disrupted KAT2A’s binding to succinyl-CoA, tumor growth was inhibited.

What follows is a conversation with Tao about the research and her lab’s work. For more details about the study, go to the paper or the news story by MD Anderson.

RN: Is there a simple way to describe what you found?

YJT: It tells us about the mechanism of a histone modification, which is succinylation. Succinylation is relatively new to the field. Histone proteins can be modified in different ways in regulating gene expression activity. This paper identified one of the mechanisms — how succinylation can be accomplished by host enzymes.

The crystal structure of KAT2A with succinyl-CoA bound in a deep cleft, as first modeled by the lab of Rice bioscientist Yizhi Jane Tao. The catalytic domain of KAT2A is rainbow colored with its N-terminus in blue and C-terminus in red. The succinyl-CoA substrate is shown in magenta as a space-filling model. Courtesy of the Yizhi Jane Tao Laboratory

RN: Why is this significant?

YJT: The human genome carries all the genetic information, but of course functions won’t be realized until those genes are properly expressed. Succinylation is one of the modifications that help to regulate gene expression.

RN: What’s succinylation?

YJT: Succinylation is the addition of a succinyl group to this particular histone protein, H3. Through this paper, we have also found that those succinylation modifications are usually associated with gene promoter regions, which are regulatory sequences for gene expression.

RN: When I hear succinylation, I think of sugar.

YJT: Yes, both succinate and succinyl-CoA are intermediates in the tricarboxylic acid cycle that is important for the breakdown of sugars as well as fat and proteins. The enzyme that carries out succinylation, KAT2A, forms a complex with the enzymatic complex (a-KGDH) that produces succinyl-CoA in the tricarboxylic acid cycle. This large enzyme complex that produces succinyl-CoA is usually found in mitochondria. But in this paper, it was shown that this enzyme complex can relocate to the nucleus and interact with KAT2A.

RN: You talk in the paper about competition between succinylation and acetylation.

YJT: KAT2A has more of a conventional role for acetylation, which means the addition of an acetyl group to histone proteins. But now we have found that KAT2A can also perform succinylation as well. It perhaps can perform some additional types of modifications, which has yet to be found out.

RN: It seems like those modifications might be significant if you want to affect cell functions.

YJT: Right. For example, we know that in the nucleus, DNA is wrapped around the histone core and forms the chromatin. So the histone proteins and their modifications play a very important role in regulating gene expression activity.

For instance, if a histone protein is not succinylated, the bound DNA sequence may have a different expression activity compared with the sequence if it is associated with a histone protein that has the succinylation modification.

RN: Could this be used to slow down or speed up a cellular mechanism?

YJT: I think that is hinted at in this paper. Right now, there’s not specific information yet as to how the succinylation pattern can be modified, but at least it was found that succinylation is associated with gene promoters, including those for cell signaling pathways.

RN: How did you get involved with this study?

YJT: Dr. Lu and I are neighbors. We can see each other’s backyards from our houses. I’m a structural biologist, so he talked to me and I thought it was interesting and Yusong then took on the project.

Yusong is very good. In my lab, she succeeded at almost anything she touched. At first we got the structure of KAT2A by itself, and then we got the structure of KAT2A in a complex with succinyl-CoA, so we could see how succinyl-CoA binds to the active site.

RN: Nobody had found the structure before you decided to take a look at it?

YJT: There had been structures of KAT2A in complex with acetyl-CoA, but not KAT2A with succinyl-CoA. Acetylation is the conventional reaction carried out by KAT2A, so there have been complex structures of KAT2A with acetyl-CoA, but succinyl-CoA in complex with KAT2A is new.

RN: And that makes this a Nature-worthy paper.

YJT: Right. It provides convincing evidence that KAT2A can catalyze succinylation. And there are tremendous data from Dr. Lu’s lab that H3 succinylation regulates gene expression and is implicated in tumor formation and development.