A Comparative Analysis of ABC Transporters in Complete Microbial Genomes

Abstract

The ABC transporter is a major class of cellular translocation machinery in all bacterial species encoded in the largest set of paralogous genes. The operon structure is frequently found for the genes of three molecular components: the ATP-binding protein, the membrane protein, and the substrate-binding protein. Here, we developed an ''ortholog group table'' by comparison and classification of known and putative ABC transporters in the complete genomes of seven microorganisms. Our procedure was to first search and classify the most conserved ATP-binding protein components by the sequence similarity and then to classify the entire transporter units by examining the similarity of the other components and the conservation of the operon structure. The resulting 25 ortholog groups of ABC transporters were well correlated with known functions. Through the analysis, we could assign substrate specificity to hypothetical transporters, predict additional transporter operons, and identify novel types of putative transporters. The ortholog group table was also used as a reference data set for functional assignment in four additional genomes. In general, the ABC transporter operons were strongly conserved despite the extensive shuffling of gene locations in bacterial evolution. In Synechocystis, however, the tendency of forming operons was clearly diminished. Our result suggests that the ancestral ABC transporter operons may have arisen early in evolution before the speciation of bacteria and archaea.

Identification of Genes Encoding Amino Acid Permeases by Inactivation of Selected ORFs from the Synechocystis Genomic Sequence

“…As pointed out by Tomii and Kanehisa (1998), in the Synechocystis genome there are less cases of conserved operons, but more cases of multiple components of a transporter being fused into a single gene, than in other genomes.…”

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

“…Global comparisons of the ABC protein contents of several genomes have also been made (161,219,356,359,485). In the course of the constitution of ABCISSE, our database of ABC systems, we have analyzed the compositions of more than 250 completely sequenced genomes.…”

A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters

“…Almost all transmembrane transport processes are mediated by integral membrane proteins, sometimes functioning in conjunction with extracytoplasmic receptors or receptor domains as well as with cytoplasmic energy-coupling and regulatory proteins or protein domains (51,112,130,139). Each such complex of these proteins and/or protein domains is referred to as a transport system, transporter, porter, permease system, or permease.…”

“…There are more than 250 entries, each of which usually describes a single family. Some of these families are actually large superfamilies with more than a thousand currently sequenced members (e.g., the voltage-gated ion channel (VIC) family (TC 1.A.1) (88); the major facilitator superfamily (MFS) (TC 2.A.1) (96,125), and the ATP-binding cassette (ABC) superfamily (TC 3.A.1) (130,139)). Others are very small families with only one or a few currently sequenced members.…”