title: Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family.
abstract: Reconstructing the transition from a single compartment bacterium to a highly compartmentalized eukaryotic cell is one of the most studied problems of evolutionary cell biology. However, timing and details of the establishment of compartmentalization are unclear and difficult to assess. Here, we propose the use of molecular markers specific to cellular compartments to set up a framework to advance the understanding of this complex intracellular process. Specifically, we use a protein family related to ribosome biogenesis, YRG (YlqF related GTPases), whose evolution is linked to the establishment of cellular compartments, leveraging the current genomic data. We analyzed orthologous proteins of the YRG family in a set of 171 proteomes for a total of 370 proteins. We identified ten YRG protein subfamilies that can be associated to six subcellular compartments (nuclear bodies, nucleolus, nucleus, cytosol, mitochondria, and chloroplast), and which were found in archaeal, bacterial and eukaryotic proteomes. Our analysis reveals organism streamlining related events in specific taxonomic groups such as Fungi. We conclude that the YRG family could be used as a compartmentalization marker, which could help to trace the evolutionary path relating cellular compartments with ribosome biogenesis.
authors.affiliation: Institute of Molecular Biology (IMB), Faculty of Biology, Johannes-Gutenberg University of Mainz, Mainz, Germany.
authors.forename: Pablo
authors.identifier: http://orcid.org/0000-0003-3663-2352
authors.initials: P
authors.lastname: Mier
authors.affiliation: Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, Sevilla, Spain.
authors.forename: Antonio J
authors.initials: AJ
authors.lastname: Pérez-Pulido
authors.affiliation: School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
authors.forename: Emmanuel G
authors.initials: EG
authors.lastname: Reynaud
authors.affiliation: Institute of Molecular Biology (IMB), Faculty of Biology, Johannes-Gutenberg University of Mainz, Mainz, Germany.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade-Navarro
mesh_terms: D000818:Animals; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002451:Cell Compartmentation / Q000235:genetics*; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020558:GTP Phosphohydrolases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D021381:Protein Transport; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism*
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D005656:Fungal Proteins; D020558:GTP Phosphohydrolases