Biology subjects

Chabes, A.

Publications and source records attributed to Chabes, A..

6 recordsLinked to original sources

bioRxiv2025

Metabolic tuning enables immediate adaptation to energy stress in yeast

In Saccharomyces cerevisiae, glucose depletion induces metabolic reprogramming through widespread transcriptional and translational reorganization. We report that initial, very rapid translational silencing is driven by a specialized metabolic mechanism. Following glucose withdrawal, intracellular NTP levels drop drastically over 30 sec, before stabilizing at a regulated, post-stress set-point. Programmed translational control results from the differential NTP affinities of key enzymes; ATP falls below the (high) binding constants for DEAD-box helicase initiation factors, including eIF4A, driving mRNA release and blocking 80S assembly. Contrastingly, GTP levels always greatly exceed the (low) binding constants for elongation factors, allowing ribosome run-off and orderly translation shutdown. Translation initiation is immediately lost on all pre-existing mRNAs, before being preferentially re-established on newly synthesized, upregulated stress-response transcripts. We conclude that enzymatic constants are tuned for metabolic remodeling. This response counters energy depletion, rather than being glucose-specific, allowing hierarchical inhibition of energy-consuming processes on very rapid timescales.

molecular biology↗

bioRxiv2025

Uridine cytidine kinases dictate the therapeutic response of molnupiravir via its bioactivation

Molnupiravir is a nucleoside analogue antiviral drug with activities against a broad spectrum of RNA viruses, including its clinical indication SARS-CoV-2. Whilst its antiviral mechanism-of-action is well defined, host pharmacogenetic factors that regulate its therapeutic responses - efficacy as well as selectivity - have not been mechanistically deciphered and characterized. Here we identified that uridine cytidine kinase (UCK), the first and rate-limiting kinase of the pyrimidine salvage pathway, could effectively phosphorylate N4-hydroxycytidine (NHC), the active compound of molnupiravir, and thereby dictate its anti-SARS-CoV-2 efficacy, as well as its selectivity index. Using target engagement and enzyme kinetic assays, we demonstrate that recombinant UCK isoform 1 (UCK1) and 2 (UCK2) effectively bind and phosphorylate NHC, with UCK2 displaying 9-fold higher catalytic efficiency. Accordingly, in SARS-CoV-2-infected cells, downregulation of UCK2 via siRNA hampered the intracellular accumulation of the triphosphate antiviral metabolite of NHC, resulting in 10-fold reduction of antiviral efficacy. Furthermore, we could recapitulate this using a pan-UCK small molecule inhibitor. Critically, both UCK downregulation and inhibition significantly reduced the selectivity index of molnupiravir/NHC. Altogether, this work underscores the pivotal roles of UCK enzymes in upholding molnupiravir efficacy and therapeutic window, and furthermore, highlights their potential as pharmacologically tractable targets for tailoring the therapeutic response to this antiviral agent.

microbiology↗

bioRxiv2025

The modifiers that cause changes in gene essentiality

The phenotype of a mutation often differs across genetically distinct individuals. In the most extreme case, a gene can be essential for viability in one genetic background, but dispensable in another. Although genetic context-dependency of mutant phenotypes is frequently observed, the underlying causes often remain elusive. Here, we investigated the genetic changes responsible for differences in gene essentiality across 18 genetically diverse natural yeast strains. First, we identified 39 genes that were essential in the laboratory reference strain but not required for viability in at least one other genetic background, suggesting that the natural strain contained suppressor variants that could bypass the need for the essential gene. We then mapped and validated the causal bypass suppressor variants using bulk segregant analysis and allele replacements. Bypass suppression was generally driven by a single modifier gene that tended to differ between genetic backgrounds. The suppressors often indirectly counteracted the effect of deleting the essential gene, for instance by changing the transcriptome of a cell. Context-dependent essential genes and their bypass suppressors were frequently co-mutated across 1,011 yeast isolates and identified naturally occurring evolutionary trajectories. Overall, our results highlight the relatively high frequency of bypass suppression in natural populations, as well as the underlying variants and mechanisms. A thorough understanding of the causes of genetic background effects is crucial for the interpretation of genotype-to-phenotype relationships, including those associated with human disease.

genomics↗

bioRxiv2020

Proofreading deficiency in mitochondrial DNA polymerase does not affect total dNTP pools in mouse embryos

Mitochondrial DNA (mtDNA) mutator mice express proofreading-deficient mtDNA polymerase gamma (PolgD257A) and age prematurely1,2, whereas mice with other mitochondrial defects do not show global signs of early aging. The reason for this discrepancy is not completely understood. Hamalainen et al. recently reported that both induced pluripotent stem cells (iPSCs) and primary mutator embryonic fibroblasts harboring PolgD257A demonstrate increased mtDNA replication frequency leading to depletion of the total cellular dNTP pool3. The authors proposed that the decreased availability of cellular dNTPs for nuclear genome replication leads to compromised nuclear genome maintenance and premature aging. Here we report that total cellular dNTP pools are normal in mtDNA mutator mouse embryos (genotype: PolgD257A/D257A), which shows that a living organism exclusively expressing PolgD257A has normal total dNTP pools despite ubiquitous rapid cell division.

cell biology↗

bioRxiv2020

SAMHD1 limits the efficacy of forodesine in leukaemia by protecting cells against cytotoxicity of dGTP

The anti-leukaemia agent forodesine causes cytotoxic overload of intracellular deoxyguanosine triphosphate (dGTP) but is efficacious only in a subset of patients. We report that SAMHD1, a phosphohydrolase degrading deoxyribonucleoside triphosphates (dNTPs), protected cells against the effects of dNTP imbalances. SAMHD1-deficient cells induced intrinsic apoptosis upon provision of deoxyribonucleosides, particularly deoxyguanosine (dG). Moreover, dG and forodesine acted synergistically to kill cells lacking SAMHD1. Using mass cytometry, we found that these compounds killed SAMHD1-deficient malignant cells from patients with chronic lymphocytic leukaemia (CLL). Normal cells and CLL cells from patients without SAMHD1 mutation were unaffected. We therefore propose to use forodesine as a precision medicine for leukaemia, stratifying patients by SAMHD1 genotype or expression. O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/951517v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@69c367org.highwire.dtl.DTLVardef@19be007org.highwire.dtl.DTLVardef@91156corg.highwire.dtl.DTLVardef@1158ec6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 5.C_FLOATNO Graphical Abstract C_FIG Highlights O_LISAMHD1-deficient cells die upon exposure to deoxyribonucleosides (dNs) C_LIO_LIDeoxyguanosine (dG) is the most toxic dN, inducing apoptosis in cells lacking SAMHD1 C_LIO_LISAMHD1-mutated leukaemic cells can be killed by dG and the PNP-inhibitor forodesine C_LI In BriefSAMHD1 degrades deoxyribonucleoside triphosphates (dNTPs), the building blocks of DNA. Davenne et al. found that SAMHD1 protects cells against dNTP imbalances. Exposure of SAMHD1-deficient cells to deoxyguanosine (dG) results in increased intracellular dGTP levels and subsequent apoptosis. This can be exploited to selectively kill cancer cells that acquired SAMHD1 mutations.

cancer biology↗

bioRxiv2019

Age-dependent loss of mitochondrial DNA integrity in mammalian muscle

Ribonucleotides (rNMPs) incorporated in the nuclear genome are a well-established threat to genome stability and can result in DNA strand breaks when not removed in a timely manner. However, the presence of a certain level of rNMPs is tolerated in mitochondrial DNA (mtDNA), although aberrant mtDNA rNMP content has been identified in disease models. We investigated the effect of incorporated rNMPs on mtDNA stability over the mouse lifespan and found that the mtDNA rNMP content increased during early life. The rNMP content of mtDNA varied greatly across different tissues and was defined by the rNTP/dNTP ratio of the tissue. Accordingly, mtDNA rNMPs were nearly absent in SAMHD1-/- mice that have increased dNTP pools. The near absence of rNMPs did not, however, appreciably affect mtDNA copy number or the levels of mtDNA molecules with deletions or strand breaks in aged animals near the end of their lifespan. The physiological rNMP load therefore does not contribute to the progressive loss of mtDNA quality that occurs as mice age.

molecular biology↗