September 22nd, 2024
Recent Publications Harnessing the Power of Translatomics
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers, El-Hachem N. et al. find that valine aminoacyl-tRNA synthetase re-sensitized RES melanoma cells to BRAF inhibition (vemurafenib) in a dose-dependent manner, Romero Romero ML et al. hypothesize that stop codon readthrough may provide an evolutionary advantage by increasing protein heterogeneity, allowing cells to adapt swiftly to environmental changes, while Nadimpalli HP et al. discovered significant diurnal oscillations in the regulation of key IRE-containing transcripts in the liver.
Valine aminoacyl-tRNA synthetase promotes therapy resistance in melanoma
Nature Cell Biology, 2024
El-Hachem N, Leclercq M, Susaeta Ruiz M, Vanleyssem R, Shostak K, Körner PR, Capron C, Martin-Morales L, Roncarati P, Lavergne A, Blomme A, Turchetto S, Goffin E, Thandapani P, Tarassov I, Nguyen L, Pirotte B, Chariot A, Marine JC, Herfs M, Rapino F, Agami R and Close P
Patients with BRAFV600E melanoma experience continuous MAPK signalling activation and can benefit from MAPK-targeted therapy. However, up to 70% relapse due to acquired resistance, partially explained by the upregulation of valine aminoacyl-tRNA synthetase (VARS). This study uses tRNA sequencing, polysome and ribosome profiling, and quantitative proteomics to elucidate VARS mechanisms in therapy resistance.
First, polysome profiling showed no significant change in global mRNA translation in naive (SENSITIVE) versus MAPK-therapy-resistant (RESISTANT) patient melanoma cultures. Next, the proteome dynamics was assessed by quantitative proteomic analyses. It turned out that only valine, alanine and tyrosine were specifically enriched in proteins upregulated but not in downregulated ones in RESISTANT cultures. Codon content analysis identified enrichment of specific codons in RESISTANT cultures (including valine codons GTG, GTA,and GTT). This led to tRNA-seq, which revealed upregulated tRNA-Val-CAC in RES cells.
Another piece of a puzzle came from the finding that VARS protein expression was upregulated in RES melanoma cultures, as compared with its SENSISTIVE counterpart. VARS depletion re-sensitized RESISTANT melanoma cells to BRAF inhibition (vemurafenib) in a dose-dependent manner while it did not not significantly affect melanoma cells survival in untreated conditions. With the help of ribosome profiling, the authors demonstrated that VARS depletion did not significantly impact global mRNA translation, however, it led to a significant and specific reduction of ribosome occupancy at valine-enriched transcripts compared with those impoverished in valine codons. Those findings were also validated by a polysome-seq experiment.
Overall, the data demonstrate that VARS may represent an attractive therapeutic target for the treatment of therapy-resistant melanoma.
Environment modulates protein heterogeneity through transcriptional and translational stop codon readthrough
Nature Communications, 2024
Romero Romero ML, Poehls J, Kirilenko A, Richter D, Jumel T, Shevchenko A, Toth-Petroczy A.
Stop codon readthrough (SCR) diversifies the proteome from a single gene by introducing C-terminally extended proteoforms. The authors hypothesised that SCR is more frequent than previously believed and may provide an evolutionary advantage by increasing protein heterogeneity, allowing cells to adapt swiftly to environmental changes. They systematically analysed SCR events for all stop codons across various genetic contexts and conditions using E. coli. A library of mScarlet reporters with premature stop codons enabled high-throughput quantification of SCR via fluorescent microscopy.
Findings show that stress conditions, like suboptimal temperatures and nutrient scarcity, significantly increase SCR events. Within all temperatures, TAA is least likely to be read-through while TGA is the most likely, in agreement with previous observations. In some reporters, TGA failed to terminate protein synthesis up to 80% of the time under stress at a given nucleotide context. RNA-seq and mass spectrometry of selected reporters revealed that SCR is due to both ribosomal readthrough and RNA polymerase errors, with the latter contributing non-randomly, primarily at premature and in-frame stop codons. An analysis of the E. coli mass spectrometry dataset againts a customised database that included putative readthrough candidates identified 16 peptides supporting the SCR event.
Diurnal control of iron responsive element containing mRNAs through iron regulatory proteins IRP1 and IRP2 is mediated by feeding rhythms
Genome Biology, 2024
Nadimpalli HP, Katsioudi G, Arpa ES, Chikhaoui L, Arpat AB, Liechti A, Palais G, Tessmer C, Hofmann I, Galy B, Gatfield D.
Cellular iron homeostasis is regulated by iron regulatory proteins (IRP1 and IRP2), which sense iron levels, modulating mRNA translation or stability via interaction with iron regulatory elements (IREs). Although IRP2 is considered the primary regulator in the liver, previous data indicating diurnal rhythms in certain IRE-containing mRNAs suggest a more complex temporal control mechanism. This study aims to understand the daily regulatory dynamics of IRE-bearing mRNAs, the specific roles of IRPs, and the systemic and cellular rhythmicity cues in the mouse liver.
The authors discovered significant diurnal oscillations in the regulation of key IRE-containing transcripts in the liver, aligning with peak IRP activity at the start of the dark phase. IRP2 protein levels also show diurnal variations, peaking at the light-dark transition. Ribosome profiling in IRP2-deficient mice indicates that target mRNA repression at this timepoint still occurs. Additionally, they found that rhythmic feeding can maintain diurnal regulation of IRE-containing mRNAs even without a functional circadian clock.
The data suggest a temporally controlled redundancy in IRP activities: IRP2 regulates IRE-containing transcripts during the light phase, with potential redundancy involving IRP1 at the onset of the dark phase. Additionally, the authors emphasise the role of feeding-associated signals in driving rhythmicity. This research underscores the dynamic and complex regulatory nature of a metabolic pathway previously considered well-understood.