Figure 1

Rhizosphere-induced genes in the Rlv3841 transportome. Genes induced (by three-fold or more, P ≤ 0.05) are color coded: black, all rhizospheres; green, pea-specific; red, alfalfa-specific; orange, sugar beet-specific; blue, legume-specific; purple, alfalfa and sugar beet; gold, pea and sugar beet. Genes are scored as elevated in more than one rhizosphere if they are up-regulated by three-fold or more in one and two-fold or more in one or two other rhizospheres (Additional file 8). Identified transported solutes are shown. Uncharacterized ABC uptake systems are classified according to Saier [12]. For uptake ABC transporter family: CUT1, carbohydrate uptake transporter 1; CUT2, carbohydrate uptake transporter 2; HAAT, hydrophobic amino acid transporter; MolT, molybdate transporter; NitT, nitrate/nitrite/cyanate transporter; PAAT, polar amino acid transporter; PepT, peptide/opine/nickel transporter; POPT, polyamine/opine/phosphonate transporter; QAT, quaternary amine transporter. Classification of ABC transporters is as follows: MolT, RL3040; CUT1, RL2418 (MtlE); CUT2, RL4655 (IntA), RL3840 and RL2720; PepT, pRL110281 and pRL110243; PAAT, pRL80060 and pRL80064; POPT, pRL100248; NitT, RL3721. Asterisks indicate a compound metabolized by an enzyme whose expression is elevated (Figure 2) or, in the case of Nod factor, synthesized for export (Figure 3). Abbreviations: ABC, ATP-binding cassette; MATE, multidrug and toxic compounds extrusion; MDR, multi-drug resistance; MFS, multi-facilitator superfamily; MscS, mechanosensitive channel small; RND, resistance-nodulation-cell division; TRAP, tripartite ATP-independent periplasmic. Genes underlined have been mutated and results of their competitiveness in the rhizosphere are shown in Additional file 8.