Molecular machines and evolutionary riddles: The savvides group Elucidates both

9 July 2019
A research team from Savvas Savvides’ lab in the VIB-UGent Center for Inflammation Research, led by Kenneth Verstraete, has unraveled the three-dimensional structure and molecular mechanism of ATP citrate lyase (ACLY). This is a central metabolic enzyme needed to produce acetyl-CoA which fuels essential biochemical processes in cells, such as the production of fatty acids and cholesterol. Their findings could help with targeting ACLY in cancer and metabolic diseases such as atherosclerosis. The structure of ACLY also unmasked a crucial evolutionary relationship that radically changes our understanding of the origins of cellular respiration.

Where did the idea for this research come from?
Kenneth: “I joined the lab in 2004 as a master thesis student to work on the ACLY project aiming to optimize
the production and purification of human ACLY for structural studies by X-ray crystallography. However,
the size and modular nature of ACLY made structural studies challenging, and admittedly a bit to my disappointment, at the end of my master thesis, the elucidation of the ACLY structure was not in sight. I was so much triggered by the field of structural biology that I started a PhD project with Savvas. After that, during my FWO-funded postdoctoral research, I remained fascinated by the still enigmatic structure of ACLY
and the intriguing evolutionary link with other central metabolic enzymes. Near the end of 2016 and building
on the experience I had gained in structural biology, I took the initiative to revisit the ACLY project. Important
factors that then contributed to an increased feasibility were the availability of affordable custom gene
synthesis and the introduction of highthroughput screening.”

As a child, could you have imagined doing something like this?
Kenneth: “My fascination with research in the biological sciences was ignited in high school when I was first
exposed to the central dogma of molecular biology. I still vividly remember my amazement about the
intricate organization of life at the molecular level.”

At which moment did you realize that this work was going to be so significant?
Kenneth: “Since ACLY is an enzyme of central carbon metabolism found in all domains of life, we anticipated
that elucidating the structure and mechanism for ACLY would be highly significant. moreover, in recent years,
human ACLY gained much interested as a therapeutic target in metabolic diseases and cancer. Finally, our
structure-driven hypothesis that the oxidative Krebs for cellular respiration emerged from the reverse Krebs cycle added a most fascinating insight about the evolution of metabolism on earth.” 

How did the collaboration with others (both within and outside of VIB) improve the scientific research?
Savvas: “This work is the result of great collaborative efforts in the spirit of integrative structural biology and
has relied on state-of-the-art approaches and access to European synchrotron radiation facilities. Our research benefitted from fruitful collaborations with teams from the EMBL (Hamburg, Germany) and ISB-CNRS (Grenoble, France) that allowed us to obtain valuable insights about the structural plasticity of ACLY that could not be attained by crystallographic studies alone.”

But also the result of great team work within your lab?  
Kenneth: “Indeed! Ann Dansercoer and Koen Verschueren were key to the success of this story. Ann performed recombinant production of ACLY enzymes, and Koen and I conducted crystallographic studies. The study is really the result of a close and intense collaboration. I will always look back with a happy
feeling to the period between February and December 2017, when Koen and I travelled about a dozen of
times to different European synchrotrons located in Switzerland, France and Germany. Most importantly,
in that period, we were able to determine different high-resolution structures of ACLY in quick succession,
with the structure of human ACLY in December 2017 providing the icing on the cake.”

In a hypothetical world where funding and time are not an issue, how would you like to follow up this work?
Kenneth: “I have applied for an ERC 2018 starting grant with a research proposal on ACLY and I’m currently
on the reserve list. We aim to unravel the regulatory protein interaction network of ACLY by biophysical and
structural studies. Moreover, our recent results form a molecular framework to develop or optimize ACLY
inhibitors in cancer and metabolic disorders. In the future I very much hope we can contribute in this field.
In this regard, I’m very keen to develop collaborations with academic groups or pharmaceutical companies that have running programs on ACLY inhibitors.”

What was the most pleasant aspect of the entire process from study design to publication?
Kenneth: “Solving the structure of the first ACLY enzyme, from the green sulphur bacterium, Chlorobium
limicola, in February 2017 was an important boost for the project. It demonstrated that structural studies on
ACLY were indeed possible.”

What is the main lesson you learned during the years you dedicated yourself to this research?
Kenneth: “I think my 15-year long journey in this project taught me to not give up easily. In addition, I think it is important to always be critical about, and if necessary  rethink, your research strategy.”

Publication
Verschueren, Verstraete et al., Nature 2019

Kenneth-Verstraete_275.jpg
Koen Verschueren, Ann Dansercoer, Savvas Savvides, Kenneth Verstraete