About metabolism and cellular function in the rhizosphere, we have avoided
About metabolism and cellular function in the rhizosphere, we have avoided a tedious list of genes and instead distilled key features of bacterial life in the rhizosphere into diagrams for membrane transport (Figure 1), metabolism (Figure 2) and cellular activities (Figure 3) (data in Additional file 8). In PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28914615 order to determine the importance of bacterial genes up-regulated in the rhizosphere, competition assays wereRL2720 RLpRL110281 pRLpRL100248 RL2895 (GstA) RL0082 RL2418 pRL120351 pRL80060 RL3721 pRLpRL120593 RL3862 RL3860 RLMelibiose/ */ Raffinose Lactose RL4655 (IntA) RL4218 (MtlE) RL3040 pRL120499 pRL120500 RL0996 RL4709 RL4564 (AmtB) RL0992 (MatC) RL3424 (DctA) myo-inositol Arabino -galactan* -galactoside * ArabinanMimosine likeGABA-like Uracil/ UridinepRL120226 RLSorbitol/Mannitol*/Dulcitol Molybdate* * Protocatechuate TRAP transporter Tartrate* Shikimate Ammonium * Malonate ABC exporter C4dicarboxylate* LysE family MATE family RND family MDR family MFS transporters Export systems ABC uptake systemsCUTRL3805 pRL100265 RL4229 CUT2 pRL90085 RL4172 POPT PAAT HAAT pRL120170 pRL120079 pRL80026 pRL90101 pRL120243 pRL120609-10 QAT NitT pRLPepTRLMg2+ pRL100188-9 pRL120317 pRL90059 MscS MscS (NodIJ)RL4640 RL2856 (VbsD) RL0680 (RmrA) RL2561 (NdvA) (MsiA) RL1522 RL1908 (SecDF2)RLpRL90091 -1-2-glucan Nod factor* Canavanine Mechanosensi ve ion channels RL4532 (Unclass)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 twofold or more in one or two other PX-478MedChemExpress PX-478 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.Ramachandran et al. Genome Biology 2011, 12:R106 http://genomebiology.com/2011/12/10/RPage 4 ofpRL120517 a RL0502 pRL120559c 1- pyroline-5-carboxylate DHAP RL3322 (Frk) Fructose-1,6 (Pfp) Fructose-6* Fructose ? Raffinose RL3095b -biphosphate phosphate RL2513 Homoserine (ArcB1) Lglutamate-semialdehyde (TpiA) RL4012 Mannitol* RL4118 RL050.