Article

RAP–a putative RNA-binding domain

Computational Molecular Biology Programme, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673.
Trends in Biochemical Sciences (Impact Factor: 11.23). 12/2004; 29(11):567-70. DOI: 10.1016/j.tibs.2004.09.005
Source: PubMed

ABSTRACT

A novel approximately 60-residue domain has been identified in Homo sapiens MGC5297 and various other proteins in eukaryotes. Sequence searches reveal that the domain is particularly abundant in apicomplexans and is predicted to be involved in diverse RNA-binding activities.

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    • "Stage II was accompanied by over-represented gains of various cytoskeletal components, including alveolins, those of the actomyosin complex (e.g., myosins) and glideosome-associated proteins with multiple membrane spans 1 and 3 (GAPM1 and GAPM3), suggesting that the molecular machinery powering gliding motility, which is essential for host cell invasion arose during evolution to apicomplexans (Frenal et al., 2010) (Figure 3, Figure 3—figure supplement 2, and Appendix 4). Gene gains during Stage I were overrepresented by proteins with 'RBD abundant in Apicomplexans' (RAP, Pfam: PF08373) (Lee and Hong, 2004), many of which were conserved as one-to-one orthologs across descending lineages, suggesting development of evolutionarily conserved functions before apicomplexans and chromerids diverged (Figure 3, and Figure 3—figure supplement 3). Chromerid genomes encode many orthologs of apicomplexan cytoskeletal proteins (Appendix 4), including GAPM2, a member of an important protein family for apicomplexan cytoskeletal structure and gliding motility (Bullen et al., 2009), and the IMC sub-compartment protein family (ISP), implicated in establishing apical polarity and coordinating the unique cell cycle of apicomplexans (Poulin et al., 2013) (Figure 2—figure supplement 5E). "
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    ABSTRACT: The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga.
    Full-text · Article · Jul 2015 · eLife Sciences
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    • "Stage II was accompanied by over-represented gains of various cytoskeletal components, including alveolins, those of the actomyosin complex (e.g., myosins) and glideosome-associated proteins with multiple membrane spans 1 and 3 (GAPM1 and GAPM3), suggesting that the molecular machinery powering gliding motility, which is essential for host cell invasion arose during evolution to apicomplexans (Frenal et al., 2010) (Figure 3, Figure 3—figure supplement 2, and Appendix 4). Gene gains during Stage I were overrepresented by proteins with 'RBD abundant in Apicomplexans' (RAP, Pfam: PF08373) (Lee and Hong, 2004), many of which were conserved as one-to-one orthologs across descending lineages, suggesting development of evolutionarily conserved functions before apicomplexans and chromerids diverged (Figure 3, and Figure 3—figure supplement 3). Chromerid genomes encode many orthologs of apicomplexan cytoskeletal proteins (Appendix 4), including GAPM2, a member of an important protein family for apicomplexan cytoskeletal structure and gliding motility (Bullen et al., 2009), and the IMC sub-compartment protein family (ISP), implicated in establishing apical polarity and coordinating the unique cell cycle of apicomplexans (Poulin et al., 2013) (Figure 2—figure supplement 5E). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free- living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga.
    Full-text · Article · Jul 2015 · eLife Sciences
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    • "The RAP Domain of FASTK Plays a Central Role in the Regulation of ND6 mRNA Among the conserved domains of the FASTK family, the RAP domain has been predicted to bind RNA (Lee and Hong, 2004; Figure 5A). This may explain the presence of the FASTK family members in recent studies that identified mRNA-interacting proteins (Baltz et al., 2012; Castello et al., 2012). "
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    ABSTRACT: The mitochondrial genome relies heavily on post-transcriptional events for its proper expression, and misregulation of this process can cause mitochondrial genetic diseases in humans. Here, we report that a novel translational variant of Fas-activated serine/threonine kinase (FASTK) co-localizes with mitochondrial RNA granules and is required for the biogenesis of ND6 mRNA, a mitochondrial-encoded subunit of the NADH dehydrogenase complex (complex I). We show that ablating FASTK expression in cultured cells and mice results specifically in loss of ND6 mRNA and reduced complex I activity in vivo. FASTK binds at multiple sites along the ND6 mRNA and its precursors and cooperates with the mitochondrial degradosome to ensure regulated ND6 mRNA biogenesis. These data provide insights into the mechanism and control of mitochondrial RNA processing within mitochondrial RNA granules. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
    Full-text · Article · Feb 2015 · Cell Reports
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