Phylogeny and evolution of Rab7 and Rab9 proteins

Mackiewicz, Paweł; Wyroba, Elżbieta

doi:10.1186/1471-2148-9-101

Cited by 29 publications

(38 citation statements)

References 140 publications

(143 reference statements)

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“…The similarity of these Rab proteins at the sequence level alone is not a sufficient criterion for an annotation as isoforms and indeed they have been found to cluster separately in a phylogenetic analysis of Rab 7 and Rab 9 [32]. The conservation of MIFs, in particular around the switch regions, provides an additional criterion for the functional annotation of Rab proteins as ‘isoforms’ or ‘subfamilies’.…”

Section: Resultsmentioning

confidence: 99%

The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity

et al. 2012

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BackgroundRab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying molecular recognition motifs, binding partner preferences and selectivities are not well understood.Methodology/Principal FindingsComparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic molecular interaction fields of 62 human Rab proteins revealed a wide range of binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics.Conclusions/SignificanceWe have analysed conservation of sequence and of molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their binding partner selectivity.

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Section: Resultsmentioning

confidence: 99%

The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity

et al. 2012

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“…This would reflect a complex role of Rab7, a highly conserved molecule in phylogeny (81). In plants and early animals, engulfment and subsequent degradation of microbes by Rab7-dependent xenophagy would be an important component of immunity.…”

Section: Discussionmentioning

confidence: 99%

B Cell Rab7 Mediates Induction of Activation-Induced Cytidine Deaminase Expression and Class-Switching in T-Dependent and T-Independent Antibody Responses

Pone

Lam

Lou

et al. 2015

The Journal of Immunology

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Class switch DNA recombination (CSR) is central to the maturation of the antibody response, as it diversifies antibody effector functions. Like somatic hypermutation, CSR requires AID, whose expression is restricted to B cells, as induced by CD40 engagement or dual TLR-BCR engagement (primary CSR-inducing stimuli). By constructing conditional knockout Igh+/Cγ1-creRab7fl/fl mice, we identified a B cell-intrinsic role for Rab7, a small GTPase involved in intracellular membrane functions, in mediating AID induction and CSR. Igh+/Cγ1-creRab7fl/fl mice displayed normal B and T cell development, and were deficient in Rab7 only in B cells undergoing IghCγ1-cre Iγ1-Sγ1-Cγ1-cre transcription, as induced – like Igh germline Iγ1-Sγ1-Cγ1 and Iε-Sε-Cε transcription – by IL-4 in conjunction with a primary CSR-inducing stimulus. These mice could not mount T-independent or T-dependent class-switched IgG1 or IgE responses, while maintaining normal IgM levels. Igh+/Cγ1-creRab7fl/fl B cells showed, in vivo and in vitro, normal proliferation and survival, normal Blimp-1 expression and plasma cell differentiation, as well as intact activation of the non-canonical NF-κB, p38 kinase and ERK1/2 kinase pathways. They, however, were defective in AID expression and CSR in vivo and in vitro, as induced by CD40 engagement or dual TLR1/2-, TLR4-, TLR7- or TLR9-BCR engagement. In Igh+/Cγ1-creRab7fl/fl B cells, CSR was rescued by enforced AID expression. These findings, together with our demonstration that Rab7 mediated canonical NF-κB activation, as critical to AID induction, outline a novel role of Rab7 in signaling pathways that lead to AID expression and CSR, likely by promoting assembly of signaling complexes along intracellular membranes.

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“…(1) The emergence of new paralogs by gene duplication, such as the RAB9 GTPase (participating in transport from late endosomes to the TGN) that evolved in the Holozoa clade (Metazoa and their closest protist relatives) from a duplicated RAB7 gene (Mackiewicz and Wyroba 2009); this is probably the most prevalent type of evolutionary novelties associated with the ES.…”

Section: The Es Of Extant Eukaryotes Derives From a Surprisingly Compmentioning

confidence: 99%

Patterns and processes in the evolution of the eukaryotic endomembrane system

Eliáš

2010

Molecular Membrane Biology

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The eukaryotic endomembrane system (ES) is served by hundreds of dedicated proteins. Experimental characterization of the ES-associated molecular machinery in several model eukaryotes complemented by a recent progress in phylogenomics and comparative genomics have revealed a conserved complex core of the machinery that appears to have been established before the last eukaryotic common ancestor (LECA). At the same time, modern eukaryotes exhibit a huge variation in the ES resulting from a multitude of evolutionary processes operating along the ever-branching paths from the LECA to its descendants. The most important source of evolutionary novelty in the ES functioning has undoubtedly been gene duplication followed by divergence of the gene copies, responsible not only for the pre-LECA establishment of many multi-paralog families of proteins in the very core of the ES-associated machinery, but also for post-LECA lineage-specific elaborations via family expansions and the origin of novel components. Extreme sequence divergence has obscured actual homologous relationships between potentially many components of the machinery, even between orthologous proteins, as illustrated by the yeast Vps51 subunit of the vesicle tethering complex GARP hypothesized here to be a highly modified ortholog of a conserved eukaryotic family typified by the zebrafish Fat-free (Ffr) protein. A dynamic evolution of many ES-associated proteins, especially those centred around RAB and ARF GTPases, seems to take place at the level of their domain architectures. Finally, reductive evolution and recurrent gene loss are emerging as pervasive factors shaping the ES in all phylogenetic lineages.Key to a full understanding of evolution of the ES, like of any other aspect of the eukaryotic cell, is a robust phylogenetic scheme bringing an order into the vast

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Phylogeny and evolution of Rab7 and Rab9 proteins

Cited by 29 publications

References 140 publications

The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity

The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity

B Cell Rab7 Mediates Induction of Activation-Induced Cytidine Deaminase Expression and Class-Switching in T-Dependent and T-Independent Antibody Responses

Patterns and processes in the evolution of the eukaryotic endomembrane system

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