ProtPhylo: identification of protein–phenotype and protein–protein functional associations via phylogenetic profiling

Abstract

ProtPhylo is a web-based tool to identify proteins that are functionally linked to either a phenotype or a protein of interest based on co-evolution. ProtPhylo infers functional associations by comparing protein phylogenetic profiles (co-occurrence patterns of orthology relationships) for more than 9.7 million non-redundant protein sequences from all three domains of life. Users can query any of 2048 fully sequenced organisms, including 1678 bacteria, 255 eukaryotes and 115 archaea. In addition, they can tailor ProtPhylo to a particular kind of biological question by choosing among four main orthology inference methods based either on pair-wise sequence comparisons (One-way Best Hits and Best Reciprocal Hits) or clustering of orthologous proteins across multiple species (OrthoMCL and eggNOG). Next, ProtPhylo ranks phylogenetic neighbors of query proteins or phenotypic properties using the Hamming distance as a measure of similarity between pairs of phylogenetic profiles. Candidate hits can be easily and flexibly prioritized by complementary clues on subcellular localization, known protein–protein interactions, membrane spanning regions and protein domains. The resulting protein list can be quickly exported into a csv text file for further analyses. ProtPhylo is freely available at http://www.protphylo.org.

MICU1 modulates MCU ion selectivity and tolerance to manganese stress

“…To investigate the direct contribution of MICU1 on MCU function, we employed the yeast S. cerevisiae as a model system, which lacks homologs of all mammalian uniporter components (Bick et al, 2012;Cheng and Perocchi, 2015), as well as endogenous mt-Ca 2+ uptake activity Carafoli and Lehninger, 1971;Kovacs-Bogdan et al, 2014;Yamamoto et al, 2016). Previous results, including ours, have shown that Hs-MCU and Hs-EMRE are sufficient to drive Ca 2+ uptake in vitro into the matrix of isolated mitochondria Kovacs-Bogdan et al, 2014;Yamamoto et al, 2016).…”

“…Our phylogenetic analyses, as well as a previous comparative genomics study (Bick et al, 2012), have highlighted a widespread co-occurrence of MCU and MICU1 across Metazoa, Plants and Protozoa, with the exception of Fungi. The presence of MCU homologs in several Ascomycota and Basidiomycota fungal clades devoid of a detectable MICU1, together with the absence of EF-hands containing proteins co-evolving with fungal MCUs (Cheng and Perocchi, 2015) and the existence of a MCU homolog that is sufficient to drive Ca 2+ uptake in mitochondria of D. discoideum (Kovacs-Bogdan et al, 2014), led to the hypothesis that MCU could exist independently of a Ca 2+ -sensing regulator. However, this hypothesis stems from the assumption that fungal MCU homologs per se are able to mediate mt-Ca 2+ uptake.…”

“…Correlated patterns of presence and absence of two or more proteins of the channel across a large number of genomes (co-occurrence) may indicate strong evolutionary constrains for their functional interdependence (de Juan et al, 2013). Here, we examined the phylogenetic profiles and predicted mitochondrial co-localization of the two founding members of the uniporter, MCU and MICU1 De Stefani et al, 2011;Perocchi et al, 2010), across 247 fullysequenced eukaryotic species from multiple taxonomic levels at different evolutionary distances, in order to maximize the resolution of coupled evolutionary patterns (Fig 1A; see also https://itol.embl.de/tree/774755176425021526503446) (Cheng and Perocchi, 2015).…”

“…However, the respective functional and mechanistic roles of those subunits in regulating uniporter activity have been so far investigated in mammalian systems where the interpretation of results is hampered by differences in the degree of gene silencing and tissue-specific protein composition (Murgia and Rizzuto, 2015;Vecellio Reane et al, 2016), stoichiometry and compensatory remodeling Paillard et al, 2017) of the channel. Instead, the budding yeast S. cerevisiae represents an ideal testbed for dissecting the functional contribution of each exogenous component of the human uniporter, given that it completely lacks any detectable MCU homolog (Bick et al, 2012;Cheng and Perocchi, 2015) and endogenous mt-Ca 2+ transport activity Carafoli and Lehninger, 1971;Kovacs-Bogdan et al, 2014;Yamamoto et al, 2016), while enabling the facile expression and targeting of human mitochondrial proteins.…”

Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome

“…This led to the successful application of phylogenetic profiling to a genome-wide analysis of S. cerevisiae (Marcotte et al, 1999), the discovery of novel Drosophila cilia genes (Avidor-Reiss et al, 2004), a screen for novel small RNA pathway components in C. elegans (Tabach et al, 2013a), and multiple components of a key mitochondrial uniporter (Baughman et al, 2011; De Stefani et al, 2011). In recognition of the method’s utility, web servers for comprehensive phylogenetic profiling continue to be developed (Cheng and Perocchi, 2015) and coevolution metrics have been incorporated in some major interactome databases (von Mering et al, 2005; Szklarczyk et al, 2015). …”