TABLE 3.
Annotation and functional classification of common targets for the three Rsm proteins in P. putida KT2440.
| Locus | Gene | Annotation | Notes |
|---|---|---|---|
| Metabolism | |||
| PP_0053 | sulfide:quinone oxidoreductase | Sulfur metabolism | |
| PP_0158 | gcdH | Glutaryl-CoA dehydrogenase | Operon (PP_0159: family III CoA-transferase) |
| PP_0292 | hisA | Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide isomerase | Operon hisBHAF; histidine synthesis |
| PP_0626 | ndh | NADH dehydrogenase | |
| PP_0711 | ycaC-I | Putative hydrolase | Isochorismatase family |
| PP_1032 | guaA | Glutamine-hydrolyzing GMP synthase | Purine metabolism |
| PP_1073 | glpD | Aerobic glycerol-3-phosphate dehydrogenase | |
| PP_2080 | gdhB | NAD-specific glutamate dehydrogenase | |
| PP_2217 | Enoyl-CoA hydratase | ||
| PP_2437 | Acyl-CoA dehydrogenase | ||
| PP_2640 | GNAT family acetyltransferase | ||
| PP_2681 | pqqD-II | Pyrroloquinoline quinone biosynthesis chaperone | |
| PP_4571 | cysK | Cysteine synthase K | Cysteine biosynthesis |
| PP_5003 | phaA | poly (3-hydroxyalkanoate) polymerase | Synthesis of carbon/energy reserve polymers |
| PP_5079 | aroK | Shikimate kinase | Biosynthesis of aromatic amino acids |
| PP_5199 | ubiH | 2-Octaprenyl-6-methoxyphenyl hydroxylase | Ubiquinone biosynthesis |
| Protein synthesis, degradation and modification | |||
| PP_1434 | era | GTPase Era | Maturation of 16S rRNA and assembly of the 30S ribosomal subunit |
| PP_1443 | lon-I | DNA-binding ATP-dependent protease | Might indirectly regulate the levels and activity of sRNAs through stability of hfq |
| PP_3620 | ycaO | Ribosomal protein S12 methylthiotransferase accessory factor | Post-translational peptide modification |
| PP_4559 | def-II | Peptide deformylase | Processing of nascent peptides |
| PP_5364 | clsA | Cardiolipin synthase | |
| Transport and secretion | |||
| PP_0907 | RND family multidrug transporter | Antimicrobial resistance | |
| PP_1015 | gtsA | Mannose/glucose ABC transporter substrate-binding protein | |
| PP_2195 | Periplasmic putrescine-binding protein | ||
| PP_3089 | hcp1 | Type VI secretion system effector protein | Part of the K1-T6SS |
| PP_3099 | tssC1 | Type VI secretion system | Part of the K1-T6SS |
| PP_3108 | tke2 | Type VI secretion system effector protein | Part of the K1-T6SS |
| PP_4542 | ABC transporter ATP-binding protein/permease | ||
| Stress response | |||
| PP_1210 | dps | DNA-binding stress protein | |
| PP_3156 | Universal stress protein family | ||
| PP_3234 | HSP20 family heat shock protein | Putative chaperone | |
| PP_3312 | HSP20 family heat shock protein | Putative chaperone | |
| PP_4541 | ppiA | Peptidyl-prolyl cis-trans isomerase A | Protein folding; stress response and biofilm in different bacteria |
| Signal transduction and regulation | |||
| PP_0173 | Transcriptional factor-like protein | Winged helix DNA binding domain | |
| PP_0546 | Sigma-54 dependent transcriptional regulator | Putative acetoin metabolism regulator | |
| PP_0563 | Two-component system respose regulator - GGDEF domain | c-di-GMP turnover | |
| PP_1492 | wspE | Two-component system sensor histidine kinase/response regulator (CheA/WspE) | Part of the wsp cluster (biofilm formation) |
| PP_3761 | cfcA | Two-component system sensor histidine kinase/response regulator | CfcR phosphorylation and activation |
| PP_3765 | turB | H-NS family protein (MvaT homolog) | Repressor of gene expression |
| PP_3832 | rsmE | Post-transcriptional regulatory protein RsmE | |
| PP_4099 | uvrY | Two-componenent system response regulator | Operon with uvrC (nucleotide excision repair) |
| Non-coding RNAs | |||
| PP_mr05 | rsmY | Non-coding RNA | |
| PP_mr44 | Non-coding RNA | ||
| PP_mr52 | Non-coding RNA | ||
| DNA recombination and transposition | |||
| PP_1813 | comEA-like protein | DNA binding and recombination domain | |
| PP_1865 | Transposase ISPpu8 + intergenic region | ||
| PP_2114 | Transposase ISPpu8 + intergenic region | ||
| intergenic | Putative ISPpu8 insertion site | Long palindromic region downstream PP_3547 | |
| PP_4318 | Transposase ISPpu8 + intergenic region | ||
| Cell envelope and appendages (LPS, EPS, pili) | |||
| PP_0063 | (lpxL) | Lipid a biosynthesis lauroyl acyltransferase | LPS synthesis |
| PP_2926 | udg | UDP-glucose 6-dehydrogenase | may be involved in LPS synthesis |
| PP_3139 | Group 1 family glycosyl transferase | Part of the pea operon - EPS synthesis | |
| PP_4795 | Lipoprotein | LptE family - LPS assembly | |
| PP_4920 | Lipoprotein | PdaC superfamily (polysaccharide deacetylase) | |
| PP_5083 | pilM | Type IV pili biogenesis protein PilM | Operon 5083-5079 (type IV pili + aroK) |
| Hypothetical/unknown function | |||
| PP_5720 | Pseudogene | ||
| PP_0085 | Hypothetical protein | YqjD/ElaB family (stress response?) | |
| PP_1499 | Hypothetical protein | ||
| PP_1887 | Hypothetical protein - YD repeat domain | Repeats may bind carbohydrates | |
| PP_2219 | Hypothetical protein | ||
| PP_2345 | Hypothetical protein | ||
| PP_2396 | Hypothetical protein | Periplasmic protein | |
| PP_3007 | Hypothetical protein | ||
| PP_3010 | Hypothetical protein | Putative lipoprotein | |
| PP_3130 | Hypothetical protein | Glycoside hydrolase family (EPS turnover?) | |
| PP_3580 | Hypothetical protein | ||
| PP_3662 | Hypothetical protein | Nucleotide 5′-monophosphate nucleosidase YgdH-like superfamily | |
| PP_3901 | Hypothetical protein | Predicted phage protein | |
| PP_3909 | Hypothetical protein | ||
| PP_3963 | Hypothetical protein | Stress-induced protein (KGG repeat) domain | |
| PP_4793 | Hypothetical protein | ||
| PP_5099 | Hypothetical protein | ||
| PP_5209 | Hypothetical protein | FliL-like protein | |
| PP_5232 | Hypothetical protein | ||
| PP_5395 | Hypothetical protein | Branched-chain polyamine synthase domain | |