The evolution of the ribosome biogenesis pathway from a yeast perspective.
Ribosome biogenesis is fundamental for cellular life, but surprisingly little is known about the underlying pathway. In eukaryotes a comprehensive collection of experimentally verified ribosome biogenesis factors (RBFs) exists only for Saccharomyces cerevisiae. Far less is known for other fungi, animals or plants, and insights are even more limited for archaea. Starting from 255 yeast RBFs, we integrated ortholog searches, domain architecture comparisons and, in part, manual curation to investigate the inventories of RBF candidates in 261 eukaryotes, 26 archaea and 57 bacteria. The resulting phylogenetic profiles reveal the evolutionary ancestry of the yeast pathway. The oldest core comprising 20 RBF lineages dates back to the last universal common ancestor, while the youngest 20 factors are confined to the Saccharomycotina. On this basis, we outline similarities and differences of ribosome biogenesis across contemporary species. Archaea, so far a rather uncharted domain, possess 38 well-supported RBF candidates of which some are known to form functional sub-complexes in yeast. This provides initial evidence that ribosome biogenesis in eukaryotes and archaea follows similar principles. Within eukaryotes, RBF repertoires vary considerably. A comparison of yeast and human reveals that lineage-specific adaptation via RBF exclusion and addition characterizes the evolution of this ancient pathway.
Institute for Cell Biology and Neuroscience, Goethe University, Frankfurt 60438, Germany, Center for Integrative Bioinformatics, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna 1030, Austria, Institute for Molecular Biosciences, Goethe University, Frankfurt 60438, Germany, Faculty of Computer Science, University of Vienna, Vienna 1030, Austria, Cluster of Excellence Macromolecular Complexes, Goethe University, Frankfurt 60438, Germany, Department of Biochemistry I, Universitätsmedizin Göttingen, Göttingen 37073, Germany and Center of Membrane Proteomics, Goethe University, Frankfurt 60438, Germany.
Ingo
I
Ebersberger
Stefan
S
Simm
Matthias S
MS
Leisegang
Peter
P
Schmitzberger
Oliver
O
Mirus
Arndt
A
von Haeseler
Markus T
MT
Bohnsack
Enrico
E
Schleiff
D001105:Archaea / Q000235:genetics; D056890:Eukaryota / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D006801:Humans; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012270:Ribosomes / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*
D029701:Saccharomyces cerevisiae Proteins