TABLE 1.
Function of the P. putida rap genes identified during maize root colonization
| Function and/or role | Gene and/or rap fusion | Locus |
|---|---|---|
| Cell envelope (GDP-mannose 6-dehydrogenase) | algD (rap2-45) | PP1288 |
| Chemotaxis and motility (flagellar assembly protein) | fliO (rap1-8) | PP4356 |
| Transport | ||
| ABC-type sulfate transport system, periplasmic component | rap2-16 | PP4305 |
| Gamma-aminobutyrate (GABA) transporter permease | rap2-21 | PP2543 |
| Sodium/proline symporter | putP (rap2-40) | PP4946 |
| Secretion | ||
| Protein chaperone | secB (rap1-2) | PP5053 |
| Preprotein translocase subunit | yidO (rap2-26) | PP0006 |
| DNA metabolism and defense mechanism | ||
| Type 1 restriction-modification system, M subunit | hsdM (rap1-19) | PP4741 |
| Single-stranded DNA-specific exonuclease | recJ (rap2-28) | PP1477 |
| DNA topoisomerase IV, A subunit | parC (rap2-37) | PP4912 |
| Energy metabolism | ||
| Pyruvate dehydrogenase, decarboxylase component | aceE (rap2-2) | PP0339 |
| Isocitrate lyase putative (glyoxylate bypass) | aceA (rap2-14) | PP4116 |
| 6-Phosphogluconate dehydrogenase | gnd (rap2-15) | PP4043 |
| 2,3-Biphosphoglycerate-independent phosphoglycerate mutase | pgm (rap2-77) | PP5056 |
| Regulatory functions | ||
| SAM-dependent methyltransferase transcriptional regulator | rap1-4 | PP4966 |
| Transcriptional regulator, AsnC family | rap1-12 | PP4424 |
| Transcriptional regulator, AraC family | rap2-44 | PP2070 |
| Sensor histidine kinase | colS (rap2-63) | PP0902 |
| Stress (general stress protein Ctc [ribosomal 5S rRNA E-loop binding protein Ctc/L25/TL5]) | rap1-9 | PP0721 |
| Detoxification (lactoylglutathione lyase [methylglyoxal metabolism]) | gloA (rap2-53) | PP3766 |
| Protein synthesis (glutamyl-tRNA synthetase tRNA-Ala, tRNA-Glu) | gltX (rap2-1) | PP1977 |
| Unknown | ||
| Seed adhesion, antisense | mus-5 (rap2-74) | PP4615 |
| Hypothetical protein | rap2-7 | PP5390 |
| Hypothetical putative lipoprotein of unknown function | rap2-18 | Between PP3854 and PP3855a |
| Conserved hypothetical protein alpha/beta hydrolase fold superfamily, antisense | rap2-19 | PP4634 |
| Amino oxidase, putative | rap2-23 | PP0383 |
| Conserved hypothetical protein (predicted SAM-dependent methyltransferases) | rap2-39 | PP4306 |
| Hypothetical protein | rap2-73 | PP2298 |
a
The junction was at a position between the two indicated proteins. A putative 348-bp open reading frame was detected (4.378.820-4.379.167). See the text for details.