Biology subjects

Ristova, M.

Publications and source records attributed to Ristova, M..

3 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↗

bioRxiv2024

Pin4 Links Post-transcriptional and Transcriptional Responses to Glucose Starvation in Yeast

Adaptation to environmental change is essential in all organisms, with RNA-binding proteins (RBPs) playing critical roles in rapid cellular responses. We analyzed the largely uncharacterized yeast RBP Pin4, and its involvement in adaptation to glucose depletion. UV crosslinking (reCRAC) revealed that in glucose conditions Pin4 binds mRNA 3 UTRs with preference for a specific motif in mRNAs involved in glycolysis, amino acid, and mitochondrial metabolism. Following glucose withdrawal, Pin4-RNA binding was greatly reduced, with residual binding favoring transcripts associated with protein translation. Cells lacking Pin4 were greatly impaired in recovery from nutrient starvation and hypersensitive to oxidative stress, consistent with the mRNA targets. RNAseq and reporter assays indicated that loss of Pin4 correlated with some increases in target mRNA abundance. In wildtype yeast, glucose depletion induces diauxic shift, with massive changes in transcription patterns. Unexpectedly, this response was almost entirely abolished in cells lacking Pin4, its C-terminal prion-like domain, the RNA-recognition motif (RRM) or with an RRM point mutation. Pin4 is implicated in sensing energy depletion, which also occurs during the approach to stationary phase. We postulate that Pin4 helps coordinate post-transcriptional and transcriptional responses to energy stress, via riboregulation.

cell biology↗

bioRxiv2024

reCRAC: A Stringent Method for Precise Mapping of Protein-RNA Interactions in Yeast

Intricate interactions between RNA-binding proteins (RBPs) and RNA play pivotal roles in cellular homeostasis, impacting a spectrum of biological processes vital for survival. UV crosslinking methods to study protein-RNA interactions have been instrumental in elucidating their interactions but can be limited by degradation of target proteins during the process, low signal-to-noise ratios, and non-specific interactions. Addressing these limitations, we describe reCRAC (reverse CRAC), a novel adaptation of the CRAC (crosslinking and analysis of cDNA) technique, optimized for yeast Saccharomyces cerevisiae. Like CRAC, reCRAC applies tandem affinity purification to yield highly enriched protein preparations. However, reCRAC is redesigned to work with unstable proteins. This is achieved by lysing the cells directly into highly denaturing buffer conditions, followed by stringent purification steps. The reCRAC method was successfully applied to the easily degraded yeast protein Pin4, allowing identification of precise binding sites at base-pair resolution with greatly reduced target protein degradation and improved signal-to-noise ratios.

molecular biology↗