Biology subjects

Walhout, A. J. M.

Publications and source records attributed to Walhout, A. J. M..

6 recordsLinked to original sources

bioRxiv2026

Glycolytic Specialization Shapes Neuronal Physiology and Function in vivo

Neurons perform diverse functions that impose distinct energetic demands, but how energy-metabolic pathways are matched to these functions in vivo remains unknown. Here we show that two functionally divergent sister chemosensory neurons in C. elegans, ASEL and ASER, exhibit asymmetric glycolytic flux, with ASER exhibiting high and ASEL having low levels of glycolysis. Metabolic imaging, metabolic network modeling, and electrophysiology measurements reveal that ASERs elevated glycolysis supports a hyperpolarized resting potential, low input resistance, and rapid repolarization that enable a distinct functional role compared to ASEL. Impairing glycolysis collapses these electrophysiological specializations without abolishing neuronal excitability, and selectively disrupts ASERs calcium responses while leaving ASEL largely unaffected. These findings demonstrate that neuron-specific glycolytic programs shape core biophysical properties and are required for functional identity in vivo, establishing metabolism as an active determinant of neuronal physiology.

neuroscience↗

bioRxiv2025

Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq

The transcriptome provides a highly informative molecular phenotype to connect genotype to phenotype and is most frequently measured by RNA-sequencing (RNA-seq). Therefore, an ultimate goal is to perturb every gene and measure changes in the transcriptome. However, this remains challenging, especially in intact organisms due to different experimental and computational challenges. Here, we present Worm Perturb-Seq (WPS), which provides high-resolution RNA-seq profiles for hundreds of replicate perturbations at a time in a living animal. WPS introduces multiple experimental advances that combine strengths of bulk and single cell RNA-seq, and that further provides an analytical framework, EmpirDE, that leverages the unique power of the large WPS datasets. EmpirDE identifies differentially expressed genes (DEGs) by using gene-specific empirical null distributions, rather than control conditions alone, thereby systematically removing technical biases and improving statistical rigor. We applied WPS to 103 Caenhorhabditis elegans nuclear hormone receptors (NHRs) to delineate a Gene Regulatory Network (GRN) and found that this GRN presents a striking pairwise modularity where pairs of NHRs regulate shared target genes. We envision that the experimental and analytical advances of WPS should be useful not only for C. elegans, but will be broadly applicable to other models, including human cells.

genomics↗

bioRxiv2022

Vitamin B12 produced by gut bacteria modulates excitatory neurotransmission

A growing body of evidence indicates that gut microbiota influence brain function and behavior. However, the molecular basis of how gut bacteria modulate host nervous system function is largely unknown. Here we show that vitamin B12-producing bacteria that colonize the intestine can modulate excitatory synaptic transmission and behavior in the host Caenorhabditis elegans. We find that vitamin B12 reduces cholinergic signaling in the nervous system through rewiring of the methionine (Met)/S-Adenosylmethionine (SAM) cycle in the intestine. We identify a conserved metabolic crosstalk between the Met/SAM cycle and the choline oxidation pathway. We show that metabolic rewiring of these pathways by vitamin B12 reduces cholinergic transmission by limiting the availability of free choline required by neurons to synthesize acetylcholine. Our study reveals a gut-brain communication pathway by which enteric bacteria modulate host behavior and may affect mental health.

neuroscience↗

bioRxiv2022

D-2-Hydroxyglutarate dehydrogenase connects the propionate shunt to ketone body metabolism in Caenorhabditis elegans

In humans, mutations in D-2-hydroxyglutarate (D-2HG) dehydrogenase (D2HGDH) result in D-2HG accumulation, delayed development, seizures, and ataxia. While the mechanisms of 2HG-associated diseases have been studied extensively, the endogenous metabolism of D-2HG remains unclear in any organism. Here, we find that, in Caenorhabditis elegans, D-2HG is produced in the propionate shunt, which is transcriptionally activated when flux through the canonical, vitamin B12-dependent propionate breakdown pathway is perturbed. Deletion of the D2HGDH ortholog, dhgd-1, results in embryonic lethality, mitochondrial defects, and the upregulation of ketone body metabolism genes. Viability can be rescued by RNAi of hphd-1, which encodes the enzyme that produces D-2HG, or by supplementing either vitamin B12 or the ketone body 3-hydroxybutyrate (3HB). Altogether, our findings support a model in which C. elegans relies on ketone bodies for energy when vitamin B12 levels are low, and in which a loss of dhgd-1 causes lethality by limiting ketone body production. HIGHLIGHTS- D-2-hydroxyglutarate is produced by HPHD-1 in the propionate shunt pathway - DHGD-1 recycles 2-hydroxyglutarate to sustain flux through the propionate shunt - dhgd-1 loss perturbs ketone body metabolism and causes embryonic lethality - 3-Hydroxybutyrate, vitamin B12 or hphd-1 RNAi rescue dhgd-1 mutant lethality

biochemistry↗

bioRxiv2021

Bacteria modulate tamoxifen-induced death via host fatty acid metabolism

Tamoxifen is a selective estrogen receptor (ER) modulator that is used to treat ER-positive breast cancer, but that at high doses kills both ER-positive and ER-negative breast cancer cells. We recapitulate this off-target effect in Caenorhabditis elegans, which does not have an ER ortholog. We find that different bacteria dramatically modulate tamoxifen toxicity in C. elegans, with a three-order of magnitude difference between animals fed Escherichia coli, Comamonas aquatica, and Bacillus subtilis. Remarkably, host fatty acid (FA) biosynthesis mitigates tamoxifen toxicity, and different bacteria provide the animal with different FAs, resulting in distinct FA profiles. Surprisingly these bacteria modulate tamoxifen toxicity by different death mechanisms, some of which are modulated by FA supplementation and others by antioxidants. Together, this work reveals a complex interplay between microbiota, FA metabolism and tamoxifen toxicity that may provide a blueprint for similar studies in more complex mammals.

systems biology↗

bioRxiv2021

ERK signaling licenses SKN-1A/NRF1 for proteasome production and proteasomal stress resistance

The ubiquitin-proteasome system is vital for cell growth and homeostasis, but for most cancers proteasomal inhibition has not been effective as a therapy. Normal and cancer cells adapt to proteasomal stress through an evolutionarily conserved recovery response, in which the transcription factor NRF1 upregulates proteasome subunit genes. Starting with a C. elegans screen to identify regulators of the recovery response, here we show that this response depends upon phosphorylation of NRF1 on a single residue by the growth factor-activated kinase ERK1/2. Inhibition of this phosphorylation impairs NRF1 nuclear localization and proteasome gene activation, sensitizes C. elegans and cancer cells to proteasomal stress, and synergizes with proteasome inhibition to retard human melanoma growth in vivo in a mouse model. The evolutionarily conserved ERK1/2-NRF1 axis couples proteasome production to growth signaling, and represents a promising new strategy for expanding the range and efficacy of proteasomal inhibition therapy in cancer.

cell biology↗