title: A domain dictionary of trimeric autotransporter adhesins.
abstract: Trimeric autotransporter adhesins (TAAs) are modular, highly repetitive outer membrane proteins that mediate adhesion to external surfaces in many Gram-negative bacteria. In recent years, several TAAs have been investigated in considerable detail, also at the structural level. However, in their vast majority, putative TAAs in prokaryotic genomes remain poorly annotated, due to their sequence diversity and changeable domain architecture. In order to achieve an automated annotation of these proteins that is both detailed and accurate we have taken a domain dictionary approach, in which we identify recurrent domains by sequence comparisons, produce bioinformatic descriptors for each domain type, and connect these to structural information where available. We implemented this approach in a web-based platform, daTAA, in 2008 and demonstrated its applicability by reconstructing the complete fiber structure of a TAA conserved in enterobacteria. Here we review current knowledge on the domain structure of TAAs.
authors.affiliation: Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Spemannstr. 35, 72076 Tuebingen, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Bassler
authors.affiliation: Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Spemannstr. 35, 72076 Tuebingen, Germany.
authors.forename: Birte
authors.initials: B
authors.lastname: Hernandez Alvarez
authors.affiliation: Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Spemannstr. 35, 72076 Tuebingen, Germany.
authors.forename: Marcus D
authors.initials: MD
authors.lastname: Hartmann
authors.affiliation: Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Spemannstr. 35, 72076 Tuebingen, Germany. Electronic address: andrei.lupas@tuebingen.mpg.de.
authors.forename: Andrei N
authors.initials: AN
authors.lastname: Lupas
mesh_terms: D018829:Adhesins, Bacterial / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D006090:Gram-Negative Bacteria / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D011487:Protein Conformation; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary
chemical_list: D018829:Adhesins, Bacterial
keywords: Domain dictionary approach; Domain structure; Gram-negative bacteria; Trimeric autotransporter adhesins