Table 5 Relevant gene clusters identified on the R4 genome associated with plant-microbe interactions
Module | Components | Associated genes | Function in strain R4 |
|---|---|---|---|
Tricarboxylic acids cycle | Catabolic genes | 15 | Carbon metabolism from plant exudates (mannitol, sorbitol, sucrose, trehalose, mannose, arabinose, maltose, xylose and glucose) |
Entner-Doudoroff pathway | Catabolic genes | 5 | |
Pentose cycle | Catabolic genes | 14 | |
Rizosphere nutrients uptake | ABC tranporters regulated by PTS | 23 | |
Chemotaxis | CheA, CheB, CheR, CheW, CheY and chemoreceptors | 70 | Sensing chemical stimulus and direct motility |
Motility | Flagello: estructural genes and regulatory genes | 85 | Motility |
Root colonization | Type IV pili: estructural genes and two components signal transduction proteins | 24 | Host cell surface association and host growth inhibition by contact |
Haemagglutinin genes | 4 | ||
Alginate: biosinthetic and regulatoy genes | 24 | Biofilms | |
Transporters | MFS genes | 32 | Transporters involved in bacterium - rizosphere interaction |
RND genes | 43 | ||
ABC genes | 162 | ||
Acetoin and 2,3-butanediol synthesis | ilvBN; budC; bdh; acoABCX adh | 10 | Plant growth regulators synthesis and catabolism |
IAA | Two synthetic pathways: from indol-3-acetamide and from indole-3-acetonitrile | 9 | |
Ethylene | acdS | 1 | ACC catabolism |
GABA | gadT, gadD, GABA permease gene | 5 | c-aminobutiric acid synthesis |
Proteases and lipases | Exportable protease (AprA), lipase (LipA) and phopholipase ExoU-like | 8 | biocontrol activity |
Secondary metabolites | Pyoverdine: estructural genes, and regulatory genes | 19 | |
Pyochelin: estructural genes and regulatory genes | 30 | ||
Secretion systems | Type I; Type II; TypeIII and Type VI | 85 | Transport of biocontrol molecules |