ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes

Abstract

The ATP-binding cassette (ABC) transporters are one of the major classes of active transporters. They are widespread in archaea, bacteria, and eukaryota, indicating that they have arisen early in evolution. They are involved in many essential physiological processes, but the majority import or export a wide variety of compounds across cellular membranes. These systems share a common architecture composed of four (exporters) or five (importers) domains. To identify and reconstruct functional ABC transporters encoded by archaeal and bacterial genomes, we have developed a bioinformatic strategy. Cross-reference to the transport classification system is used to predict the type of compound transported. A high quality of annotation is achieved by manual verification of the predictions. However, in order to face the rapid increase in the number of published genomes, we also include analyses of genomes issuing directly from the automated strategy. Querying the database (http://www-abcdb.biotoul.fr) allows to easily retrieve ABC transporter repertories and related data. Additional query tools have been developed for the analysis of the ABC family from both functional and evolutionary perspectives.

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges

“…Accordingly, we also identified putative genes for glycerol and glycerol-3-phosphate transporters (both expressed), and we readily identified gene candidates for a complete TCA cycle and the gluconeogenesis pathway. Additional genes suggested a group of ATP-binding cassette (ABC) transporters that highly likely import monosaccharides according to classification of the ABC transporter database AbcDB (26) and that are expressed based on our proteomics data. Genes for the breakdown of polysaccharides (e.g., for glycogen-debranching enzyme, for glycogen phosphorylase) are also present in both genomes, but their corresponding proteins could not be detected by proteomics.…”

Crossing Isorthology and Microsynteny to Resolve Multigenic Families Functional Annotation

“…The importers require a supplementary protein, a Solute-Binding Protein (SBP), that binds specific substrate(s). The existing classification schemes agree on a set of about 20 to 30 subfamilies that diverged very early in the evolution and that can be distinguished according to sequence conservation [14][15]. Moreover, for some of these families, it is possible to associate a type of substrate, such as for example carbohydrates for subfamily 1 of [15].…”

“…Thus, this experiment will allow to check (i) if our strategy is able to reconstruct manually annotated ABC systems, and (ii) if it is able to detect and isolate paralogous systems within the subfamily. The setup of this experiment was as follows: all the genes involved in the manually curated subfamily 1 of [15] were used as the initial pool. Then the procedure described in the methods section was applied i.e., genomic neighbors extraction, isorthology link inference for graph reconstruction, graph filtering and partitioning, and finally biclustering of isortholog partitions and genomic neighbors.…”

Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network

“…Of these 107 genes, 38, 33, and 39 were differentially expressed for eTMglc1, eTMglc2, and eTMglc3, respectively, representing 13 to 14% of all differentially expressed genes. Genes in these categories were characterized based on their predicted function using the categorization provided by ABCdb (57). This divided the cohort into three groups: solute binding proteins (S), proteins with membrane spanning-domains (M), and proteins with nucleotide binding domains that hydrolyze ATP to ADP (N).…”