No abstract

The p53 isoform, Δ133p53β, is critical in promoting cancer. Here we report that Δ133p53β activity is regulated through an aggregation-dependent mechanism. Δ133p53β aggregates were observed in cancer cells and tumour biopsies. The Δ133p53β aggregation depends on association with interacting partners including p63 family members or the CCT chaperone complex. Depletion of the CCT complex promotes accumulation of Δ133p53β aggregates and loss of Δ133p53β dependent cancer cell invasion. In contrast, association with p63 family members recruits Δ133p53β from aggregates increasing its intracellular mobility. Our study reveals novel mechanisms of cancer progression for p53 isoforms which are regulated through sequestration in aggregates and recruitment upon association with specific partners like p63 isoforms or CCT chaperone complex, that critically influence cancer cell features like EMT, migration and invasion.

There has been an increased interest in computational methods for amyloid and (or) aggregate prediction, due to the prevalence of these aggregates in numerous diseases and their recently discovered functional importance. To evaluate these methods, several datasets have been compiled. Typically, aggregation-prone regions of proteins, which form aggregates or amyloids in vivo, are more than 15 residues long and intrinsically disordered. However, the number of such experimentally established amyloid forming and non-forming sequences are limited, not exceeding one hundred entries in existing databases. In this work, we parsed all available NMR-resolved protein structures from the PDB and assembled a new, sevenfold larger, dataset of unfolded sequences, soluble at high concentrations. We proposed to use these sequences as a negative set for evaluating methods for predicting aggregation in vivo. We also present the results of benchmarking cutting edge tools for the prediction of aggregation versus solubility propensity.

The relationship between amino acid sequences of the β‐hairpin structures and amyloidogenic β‐arcade‐forming motifs are of special interest because, similar to amyloid fibrils, most of the β‐hairpin repeat (BHR) structures have the so‐called cross‐β arrangement. Moreover, β‐hairpin is considered as a probable intermediate structure in amyloidogenesis. In this work, a bioinformatics sequence analysis of the known BHR structures is performed in search of amylodogenic motifs able to form β‐arcade fibrils. The analysis shows that the occurrence of the predicted β‐arcade motifs in the BHR regions is very different depending on the BHR structural fold, cellular localization, and phylogeny. One of the most striking observations is the high level of sequence similarity between the BHRs of membranous porins and β‐arcade motifs. This sequence similarity provides additional evidence that the structure of the membranous porins and annular amyloid oligomers may bear a resemblance. Moreover, these results explain how some amyloidogenic sequence can fold in either the ring‐like shape oligomers or elongated amyloid fibrils. It has been also found that potentially lethal amyloidogenic β‐arcade motifs are absent in the elongated BHR structures of intracellular eukaryotic proteins. It allows to hypothesize that, in this case, the selective evolutionary pressure acts against aggregation.

In all cells, DNA topoisomerases dynamically regulate DNA supercoiling allowing essential DNA processes such as transcription and replication to occur. How this complex system emerged in the course of evolution is poorly understood. Intriguingly, a single horizontal gene transfer event led to the successful establishment of bacterial gyrase in Archaea, but its emergent function remains a mystery. To better understand the challenges associated with the establishment of pervasive negative supercoiling activity, we expressed the gyrase of the bacterium Thermotoga maritima in a naïve archaeon Thermococcus kodakarensis which naturally has positively supercoiled DNA. We found that the gyrase was catalytically active in T. kodakarensis leading to strong negative supercoiling of plasmid DNA which was stably maintained over at least eighty generations. An increased sensitivity of gyrase-expressing T. kodakarensis to ciprofloxacin suggested that gyrase also modulated chromosomal topology. Accordingly, global transcriptome analyses revealed large scale gene expression deregulation and identified a subset of genes responding to the negative supercoiling activity of gyrase. Surprisingly, the artificially introduced dominant negative supercoiling activity did not have a measurable effect on T. kodakarensis growth rate. Our data suggest that gyrase can become established in Thermococcales archaea without critically interfering with DNA transaction processes.