The evolution of the eukaryotic endomembrane system
and the transport pathways of their vesicular intermediates
are poorly understood. A common set of organelles
and pathways seems to be present in all free-living
eukaryotes, but different branches of the tree of life have
a variety of diverse, specialized organelles. Rab/Ypt
proteins are small guanosine triphosphatases with
tissue-specific and organelle-specific localization that
emerged as markers for organelle diversity. Here, I characterize
the Rab/Ypt family in the kingdom Fungi, a sister
kingdom of Animals. I identify and annotate these proteins
in 26 genomes representing near one billion years of
evolution, multiple lifestyles and cellular types. Surprisingly,
the minimal set of Rab/Ypt present in fungi is
(application/pdf) - 10-jun-2010
Levy, E.D.; Pereira-Leal, J.B.; Chothia, C.; Teichmann, S.A.
Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and...
(application/pdf) - 10-feb-2010
Rasteiro, R.; Pereira Leal, J.B.
BACKGROUND: Rab proteins are regulators of vesicular trafficking, requiring a lipid modification for proper function, prenylation of C-terminal cysteines. This is catalysed by a complex of a catalytic heterodimer (Rab Geranylgeranyl Transferase - RabGGTase) and an accessory protein (Rab Escort Protein. REP). Components of this complex display domain insertions relative to paralogous proteins. The function of these inserted domains is unclear. RESULTS: We profiled the domain architecture of the components of the Rab prenylation complex in evolution. We identified the orthologues of the components of the Rab prenylation machinery in 43 organisms, representing the crown eukaryotic groups. We characterize in...
(application/pdf) - 10-feb-2010
Pereira Leal, J.B.; Levy, E.D.; Kamp, C.; Teichmann, S.A.
BACKGROUND: Cellular functions are accomplished by the concerted actions of functional modules. The mechanisms driving the emergence and evolution of these modules are still unclear. Here we investigate the evolutionary origins of protein complexes, modules in physical protein-protein interaction networks. RESULTS: We studied protein complexes in Saccharomyces cerevisiae, complexes of known three-dimensional structure in the Protein Data Bank and clusters of pairwise protein interactions in the networks of several organisms. We found that duplication of homomeric interactions, a large class of protein interactions, frequently results in the formation of complexes of paralogous proteins. This route is a common mechanism for...
(application/pdf) - 22-abr-2010