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A comprehensive view of molecular chaperone function in the cell was obtained through a systematic global integrative network approach based on physical (protein-protein) and genetic (gene-gene or epistatic) interaction mapping. This allowed us to decipher interactions involving all core chaperones (67) and cochaperones (15) of Saccharomyces cerevisiae. Our analysis revealed the presence of a large chaperone functional supercomplex, which we named the naturally joined (NAJ) chaperone complex, encompassing Hsp40, Hsp70, Hsp90, AAA+, CCT, and small Hsps. We further found that many chaperones interact with proteins that form foci or condensates under stress conditions. Using an in vitro reconstitution approach, we demonstrate condensate formation for the highly conserved AAA+ ATPases Rvb1 and Rvb2, which are part of the R2TP complex that interacts with Hsp90. This expanded view of the chaperone network in the cell clearly demonstrates the distinction between chaperones having broad versus narrow substrate specificities in protein homeostasis.

In phylogenomics, reconciliations aim at explaining the discrepancies between the evolutionary histories of genes and species. Several reconciliation models are available when the evolution of the species of interest is modelled via phylogenetic trees; the most commonly used are the DL model, accounting for duplications and losses in gene evolution and yielding polynomially-solvable problems, and the DTL model, which also accounts for gene transfers and implies NP-hard problems. However, when dealing with non-tree-like evolutionary events such as hybridisations, phylogenetic networks - and not phylogenetic trees - should be used to model species evolution. Reconciliation models involving phylogenetic networks are still at their early days. In this paper, we propose a new reconciliation model in which the evolution of species is modelled by a special kind of phylogenetic networks - the LGT networks. Our model considers duplications, losses and transfers of genes, but restricts transfers to happen through some specific arcs of the network, called secondary arcs. Moreover, we provide a polynomial algorithm to compute the most parsimonious reconciliation between a gene tree and an LGT network under this model. Our method, when combined with quartet decomposition methods to detect putative "highways" of transfers, permits to refine their analyses by allowing to examine the two possible directions of a highway and even consider combinations of highways., (Copyright © 2017 Elsevier Ltd. All rights reserved.)