Systematic identification of novel protein domain families associated with nuclear functions

European Molecular Biology Laboratory, 69114 Heidelberg, Germany.
Genome Research (Impact Factor: 14.63). 02/2002; 12(1):47-56.
Source: PubMed


A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic lineages, but 3 are species specific. For about 500 of the 1200 proteins that contain these new domains, nuclear localization could be inferred, and for 700, additional features could be predicted. For example, we identified a new domain, likely to have a role downstream of the unfolded protein response; a nematode-specific signalling domain; and a widespread domain, likely to be a noncatalytic homolog of ubiquitin-conjugating enzymes.

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Available from: Tobias Doerks, Jun 03, 2014
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    • "The RWD domain of Gcn2 is related to the ubiquitin-conjugating enzymes (UBC) domain, forming the clade of Ubiquitin-conjugating enzyme/RWD-like domain (InterPro IPR016135, [65]), predicted to have a function in protein–protein interaction [66]. RWD domains including the Gcn2 RWD domain, however, lack the catalytic cysteine residue critical for ubiquitin-conjugating activity [66]. The structure of the GCN2 RWD domain has been solved by NMR [63]. "
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    Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 01/2014; · 5.02 Impact Factor
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    • "Most of Ash1 SET proteins have one SET domain that is preceded by an AWS (associated with SET) domain and followed by a cysteine-rich PostSET domain except for the members in II-2 group that lack the AWS domain (Fig. 1). The AWS domain is a subdomain of the PreSET domain that contains several highly conserved Cys residues, which are often found in association with the SET domain, suggesting a role in methylation of lysine residues in histones and other proteins (Doerks et al. 2002). Compared to other classes of SET domain proteins, in which the SET domain is found very near the C terminus of the protein (Springer et al. 2003; Ng et al. 2007), the members in the II-1 group possess a relatively centrally located SET domain (Fig. 1). "
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    ABSTRACT: Plant Ash1 SET proteins are involved in H3K36 methylation, and play a key role in plant reproductive development. Genes encoding Ash1 SET proteins constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. To investigate the evolutionary history and functional differentiation of the Ash1 SET gene family, we made a comprehensive evolutionary analysis of this gene family from eleven major representatives of green plants. A novel deep sister relationship grouping previously resolved II-1 and II-2 orthologous groups was identified. The absence of AWS domain in the group II-2 suggests that the independent losses of AWS domain have occurred during evolution. A diversity of gene structures in plant Ash1 SET gene family have been presented since the divergence of Physcomitrella patens (moss) from the other land plants. A small proportion of codons in SET domain regions were detected to be under positive selection along the branches ancestral to land plant and angiosperms, which may have allowed changes of substrate specificity among different evolutionary groups while maintaining the primary function of SET domains. Our predictive subcellular localization and comparative anatomical meta-expression analyses can assort with the structural divergences of Ash1 SET proteins.
    Genes & genomics 08/2013; 35(4). DOI:10.1007/s13258-013-0056-x · 0.60 Impact Factor
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    • "In this study, a homologue of P. monodon SARIP1 cDNA and gene were successfully identified. The deduced PmSARIP1 protein contained an RWD domain which is functionally proposed as a protein–protein interaction domain (Doerks et al., 2002). A highly conserved YPXXXP motif of the RWD domain (Nameki et al., 2004) is also found in the deduced PmSARIP1 protein. "
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    ABSTRACT: The full-length cDNA and genomic organization of small androgen receptor-interacting protein 1 (SARIP1; also called RWD-containing protein 1, Rwdd1) in the giant tiger shrimp (Penaeus monodon) was isolated and character-ized. PmSARIP1 was 1366 bp in length containing an open reading frame (ORF) of 738 bp corresponding to a polypeptide of 245 amino acids. Its genomic sequence contained 5 exons, 4 introns and untranslated regions (UTRs) spanning 5937 bp in length. Tissue distribution analysis indicated that PmSARIP1 was specifically expressed in gonads (ovaries N testes) but not in other tissues of wild P. monodon adults. The expression level of PmSARIP1 was not differentially expressed during ovarian maturation in intact wild adults (P N 0.05). Eyestalk ablation resulted in up-regulation of PmSARIP1 throughout the ovarian maturation of wild adults where the peak level was observed at stage I (previtellogenic) ovaries (P b 0.05). PmSARIP1 mRNA was clearly localized in ooplasm of previtellogenic oocytes. Serotonin injection (5-HT, 50 μg/g body weight; 18-month-old shrimp) pro-moted the expression level of ovarian PmSARIP1 at 6–72 h post injection (hpi) with the peak level at 12 hpi (P b 0.05). Exogenous progesterone administration (0.1 μg/g BW; 14-month-old shrimp) did not significantly affect the expression level of ovarian PmSARIP1. In contrast, 17β-estradiol treatment (0.01 μg/g BW) resulted in an increase of PmSARIP1 in 14-month-old shrimp at 7 days post injection (dpi). Results from this study suggested that PmSARIP1 should play an important role during ovarian maturation of P. monodon.
    Aquaculture 07/2013; 412-413:151-159. DOI:10.1016/j.aquaculture.2013.07.011 · 1.88 Impact Factor
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