SMART 5: domains in the context of genomes and networks

EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany.
Nucleic Acids Research (Impact Factor: 8.81). 02/2006; 34(Database issue):D257-60. DOI: 10.1093/nar/gkj079
Source: PubMed

ABSTRACT The Simple Modular Architecture Research Tool (SMART) is an online resource ( used for protein domain identification and the analysis of protein domain architectures. Many new features were implemented to make SMART more accessible to scientists from different fields. The new 'Genomic' mode in SMART makes it easy to analyze domain architectures in completely sequenced genomes. Domain annotation has been updated with a detailed taxonomic breakdown and a prediction of the catalytic activity for 50 SMART domains is now available, based on the presence of essential amino acids. Furthermore, intrinsically disordered protein regions can be identified and displayed. The network context is now displayed in the results page for more than 350 000 proteins, enabling easy analyses of domain interactions.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Recent advances in studies of the Schistosoma japonicum genome have opened new avenues for the elucidation of parasite biology and the identification of novel targets for vaccines, drug development and early diagnostic tools. In this study, we surveyed the S. japonicum genome database for genes encoding nucleases. A total of 130 nucleases of 3 classes were found. Transcriptional analysis of these genes using a genomic DNA microarray revealed that the majority of the nucleases were differentially expressed in parasites of different developmental stages or different genders, whereas no obvious transcriptional variation was detected in parasites from different hosts. Further analysis of the putative DNases of S. japonicum revealed a novel DNase II homologue (Sjda) that contained a highly conserved catalytic domain. A recombinant Sjda-GST protein efficiently hydrolysed genomic DNA in the absence of divalent iron. Western-blot and immunofluorescence assays showed that Sjda was mainly expressed on the teguments of female adult parasites and induced early humoral immune responses in infected mice. A novel DNase II homologue, Sjda, was identified in S. japonicum. Sjda was mainly distributed on the teguments of adult female parasites and possessed a typical divalent iron-independent DNA catalytic activity. This protein may play an important role in the host-parasite interaction.
    BMC Genomics 02/2015; 16(1):126. DOI:10.1186/s12864-015-1319-5 · 4.04 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Pathogenic Leptospira is the etiological agent of leptospirosis, a life-threatening disease of human and veterinary concern. The search for novel antigens that could mediate host-pathogen interactions is been pursued. Due to their location, these antigens have the potential to elicit numerous activities, including immune response and adhesion. This study focuses on a hypothetical protein of Leptospira, encoded by the gene LIC11089 and of its three derived fragments: N-terminus, intermediate and C-terminus regions. The gene coding for the full-length protein and fragments were cloned and expressed in Escherichia coli BL21-SI strain by using the expression vector pAE. The recombinant protein and fragments tagged with hexahistidine at N-terminal were purified by metal-charged chromatography. The leptospiral full-length protein, named Lsa32 (Leptospiral surface adhesin, 32 kDa), adheres to laminin, being the C-terminus region responsible for this interaction. Lsa32 binds to plasminogen (PLG), in a dose-dependent fashion, generating plasmin (PLA) when activator is provided. Moreover, antibodies present in leptospirosis serum samples were able to recognize Lsa32. The Lsa32 is most likely a new surface protein of Leptospira as revealed by proteinase K susceptibility. All together, our data suggest that this multifaceted protein is expressed during infection and may play a role in host - L. interrogans interactions.
    Microbiology 01/2015; 161(Pt_4). DOI:10.1099/mic.0.000041 · 2.84 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Toll-like receptor 2 (TLR2) plays an important role in innate immune responses. Here we describe the isolation and characterization of the full-length cDNA sequence of toll-like receptor 2 in large yellow croaker Larimichthys crocea (LcTLR2). The LcTLR2 cDNA contains a 5'-terminal untranslated region (5'-UTR) of 135bp, an open reading frame (ORF) of 2478bp encoding a polypeptide of 825 amino acid residues and a 3'-UTR of 50bp. Subcellular localization analysis suggested that the LcTLR2-pEGFP was mainly expressed in cytoplasm. Quantitative real-time reverse transcription PCR (qRT-PCR) analysis revealed a broad expression of LcTLR2 in most examined tissues, with the most predominant expression in blood, followed by spleen, and the weakest expression in stomach. The expression levels of LcTLR2 after injection with Vibrio parahemolyticus, Lipopolysaccharides (LPS) and poly inosinic: cytidylic (polyI:C) were investigated in spleen, head-kidney and liver. Our results showed that LcTLR2 transcripts increased significantly after all the three immune challenges (p < 0.05). However, compared with polyI:C and LPS, higher expression levels of LcTLR2 were induced in all examined tissues after V. parahemolyticus stimulation. In addition, the expression levels of LcTLR2 after flagellin, polyI:C, peptidoglycan (PGN) and LPS challenge in LCK were investigated, our findings showed that high LcTLR2 transcripts were induced after flagellin and PGN stimulation, suggesting that LcTLR2 might play a vital role in fish defense against bacterial infection. Furthermore, compared with LPS, flaglline and peptidoglycan might play an important role in LcTLR2 induction in large yellow croaker. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Fish &amp Shellfish Immunology 02/2015; 44(1). DOI:10.1016/j.fsi.2015.01.037 · 3.03 Impact Factor