Behind the paper: The relationship between an oncometabolite and propionate degradation in nematodes

In this ‘behind the paper’ post, Olga Ponomarova discusses how testing many diverse hypothesis brought them to find the relationship between apparently unrelated metabolic pathways.

My name is Olga Ponomarova, I recently established my own lab at the University of New Mexico to explore what I consider the most thrilling questions in metabolic science. Before this, I honed my skills as a postdoc in Dr. Walhout’s lab, and this story is about our latest publication. The project started from an intriguing observation: a metabolic pathway, known as the propionate shunt, tightly synchronized its expression with a seemingly unrelated metabolic gene, dhgd-1. While propionate shunt breaks down short chain fatty acid propionate to acetyl-CoA, dhgd-1 is known to detoxify D-2-hydroxyglutarate (2HG), a metabolite known for its oncogenic properties. What could be linking them together? I was always intrigued by tangled dependencies in metabolic networks, so this was a compelling challenge. 

To be frank, I cannot recall my first experiments. What I do remember is coming to the lab and testing any hypothesis I could think of. Thankfully, working with nematodes Caenorhabditis elegans made it pretty easy to test a bunch. My days were spent pouring agar plates, bleaching and chunking worms (yes, those are genuine C. elegans techniques), and discussing science over Dunkin Donuts’ coffee with my labmates. The latter was the highlight of these times (talking to colleagues, not the coffee – the coffee was terrible).

Image credit

Olga Ponomarova, CC BY 4.0

Our first significant breakthrough emerged as a genetic interaction between dhgd-1 and the shunt pathway. The dhgd-1 mutants had a high embryonic mortality rate, but when we suppressed the expression of one of the shunt pathway genes, hphd-1, virtually every dhgd-1 mutant embryo survived! Functional connection – check. The mechanism of this interaction soon became clear: hphd-1 produces a toxic metabolite D-2-hydroxyglutarate, which dhgd-1 eliminates.

Yet, one more question remained: why was 2HG harmful? We needed another major insight. And it surfaced unexpectedly when Tom Leland, a rotation student working with me on a different project, decided to give worms the metabolite 3-hydroxybutyrate (3HB). On a whim, he included a dhgd-1 mutant in the experiment. While his original idea did not pan out, he found an amazing thing about dhgd-1 mutant. Its embryonic lethality was rescued by 3HB.

Image credit

Olga Ponomarova, CC BY 4.0

From there, everything began to fall into place, albeit gradually. There was no dramatic sprinting through the lab in revelation; instead, we connected and reconnected the dots until the picture became most coherent. 2HG causes embryonic energy deficiency. In hindsight, it seems obvious, but many other promising hypotheses were born, just to be put to rest by cold data. It still surprises me how tough it can be to let go of a favourite hypothesis.

Reflecting on this project, I took away two main lessons. First, to be open to conducting seemingly fruitless, off-the-wall experiments – they might invite serendipitous discoveries. Secondly, to allow your hypotheses to die quickly. It’s tempting to endlessly seek technical reasons for a negative result, but considering other possibilities often leads to faster progress. Now, I view hypotheses like newborn queen bees, allowing them to battle until the strongest is the only one left.

About the author

Olga Ponomarova is an Assistant Professor in the Biochemistry and Molecular Biology Department at the University of New Mexico. @OlgaPonomarova 0000-0001-6331-9949