Table 1.
Genetic characterization for the evolved clones of P. fluorescens SBW25 (A: in the absence, and B: in the presence of the microbial community). The occurrence of non-synonymous single nucleotide polymorphisms (SNPs) is marked in binary format (0: absence, 1: presence) after filtering with a cut-off of 95% frequency. The reference of each gene, in addition to the subcellular localization and the biological processes are provided along with the end-product affected by functional categories.
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P. fluorescens SBW25 clone |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A |
B |
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| 1 | 2 | 3 | 4 | 5 | 6 | 1 | 2 | 3 | 4 | 5 | 6 | gene | product name | subcelullar localization | biological process (GO term) | functional category |
| 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU0988 | putative alginate biosynthesis-like protein | periplasmic | efflux pump membrane protein (multidrug resistance protein A) | drug transport |
| 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU1511 | putative transporter-like membrane protein | cytoplasmic membrane | response to drug | drug binding |
| 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU3233 | putative general secretory pathway protein | unknown | type II secretory pathway, component PulM | transport |
| 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ureC | urease subunit alpha | cytoplasmic | urea metabolic process | resource utilization |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | gltP | glutamate/aspartate:proton symporter | cytoplasmic membrane | Na+/H+-dicarboxylate symporters | transport |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | lepB | signal peptidase I | cytoplasmic membrane | protein secretion | resource utilization |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU0808 | putative transporter-like membrane protein | cytoplasmic membrane | sulfite reductase complex (NADPH) | cellular component |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU1694 | putative ABC transporter ATP-binding protein | cytoplasmic membrane | ABC-type multidrug transport system, ATPase component | resource utilization |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU1829 | hypothetical protein | unknown | PaaI_thioesterase | catalytic activity |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU2096 | putative transporter-like membrane protein | cytoplasmic membrane | arabinose efflux permease | resource utilization |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU2490 | putative chloride transport channel membrane protein | cytoplasmic membrane | chloride channel protein EriC | membrane component |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU2809 | UDP pyrophosphate phosphatase | cytoplasmic membrane | undecaprenyl-diphosphatase activity | unknown |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU2923 | AraC family transcriptional regulator | cytoplasmic | AraC-type DNA-binding domain-containing proteins | regulation biological process |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU2961 | arsenical pump membrane protein | cytoplasmic membrane | response to arsenic-containing substance | response to stimulus |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU4512 | putative transmembrane transport protein | cytoplasmic membrane | purine-cytosine permease and related proteins | catalytic activity |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU4789 | putative glycerophosphoryl diester phosphodiesterase | periplasmic | glycerophosphoryl diester phosphodiesterase | catalytic activity |
| 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | rpoN | RNA polymerase factor sigma-54 | cytoplasmic | sigma factor activity | resource utilization |
| 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU0584 | putative amino acid ABC transporter ATP-binding protein | cytoplasmic membrane | ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing | membrane component |
| 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU1686 | putative RHS repeat-like protein | outer membrane | Rhs family protein | cellular component |
| 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU3083 | putative dioxygenase | cytoplasmic | catechol 2,3-dioxygenase activity | catalytic activity |
| 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU5328 | hypothetical protein | cytoplasmic membrane | putative threonine efflux protein | transport |
| 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU5329 | putative sensory box GGDEF/EAL domain-containing protein | cytoplasmic membrane | signal transduction | regulation biological process |
| 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | potF1 | putrescine ABC transporter substrate-binding periplasmic protein | periplasmic | ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing | membrane component |
| 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | recG | ATP-dependent DNA helicase RecG | cytoplasmic | DNA recombination | DNA recombination |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU0052 | putative dehydrogenase | unknown | choline dehydrogenase and related flavoproteins | catalytic activity |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU0310 | hypothetical protein | cytoplasmic | unknown | unknown |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU0458 | hypothetical protein | cytoplasmic membrane | cyclase activity | catalytic activity |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU1581 | hypothetical protein | outer membrane | surface lipoprotein | transport |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU2489 | hypothetical protein | cytoplasmic | methylisocitrate lyase activity | catalytic activity |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU2753 | putative EAL/GGDEF domain-containing signalling protein | cytoplasmic membrane | cyclase activity | catalytic activity |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU3370 | hypothetical protein | cytoplasmic membrane | oxidoreductase activity | metabolic process |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU3508 | hypothetical protein | cytoplasmic membrane | unknown | unknown |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU3940 | allantoate amidohydrolase | cytoplasmic | acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase and related deacylases | catalytic activity |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU3948 | putative family S43 non-peptidase protein | outer membrane | unknown | unknown |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU4304 | LysR family transcriptional regulator | cytoplasmic | transcriptional regulator | regulation biological process |
| 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | PFLU5618 | hypothetical protein | unknown | predicted phosphatase | resource utilization |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | cyaA | adenylate cyclase | cytoplasmic membrane | adenylate cyclase | resource utilization |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | PFLU0916 | putative methyl-accepting chemotaxis protein | cytoplasmic membrane | methyl-accepting chemotaxis protein | catalytic activity |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | PFLU2428 | hypothetical protein | extracellular | unknown | unknown |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | PFLU2600 | cyn operon positive regulator | cytoplasmic | transcriptional regulator | regulation biological process |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | PFLU2693 | putative haloacid dehalogenase-like hydrolase | unknown | hydrolase activity | catalytic activity |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | PFLU3596 | hypothetical protein | outer membrane | unknown | unknown |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | phnH | carbon-phosphorus lyase complex subunit | cytoplasmic | uncharacterized enzyme of phosphonate metabolism | unknown |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | pobA | 4-hydroxybenzoate 3-monooxygenase | cytoplasmic | benzoate metabolic process | resource utilization |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | PFLU0850 | putative aldehyde dehydrogenase | cytoplasmic | betaine-aldehyde dehydrogenase activity | catalytic activity |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | PFLU3230 | general secretion pathway protein F/S | cytoplasmic membrane | protein secretion by the type II secretion system | resource utilization |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | PFLU3585 | putative FAD-dependent oxidoreductase | cytoplasmic | glycine/d-amino acid oxidases (deamination) | catalytic activity |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | PFLU3747 | putative sigma-54-activated regulatory protein | cytoplasmic | transcriptional activator of acetoin/glycerol metabolism | resource utilization |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | PFLU3920 | 2-oxoacid dehydrogenase subunit E1 | cytoplasmic | cytosolic pyruvate dehydrogenase complex | cellular component |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | PFLU4306 | putative GGDEF/GAF domain sensory box protein | cytoplasmic | cyclase activity | catalytic activity |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | PFLU4516 | LysR family transcriptional regulator | cytoplasmic | transcriptional regulator | regulation biological process |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | ddl | d-alanyl-alanine synthetase A | cytoplasmic | peptidoglycan biosynthetic process | resource utilization |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | PFLU0087 | putative two-component system sensor kinase | cytoplasmic membrane | phosphate ion transport | transport |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | PFLU0478 | putative glycosyl transferase | cytoplasmic | glycosyltransferase | catalytic activity |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | PFLU1394 | putative hydrolase | unknown | beta-lactamase class C and other penicillin-binding proteins | drug binding |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | PFLU3262 | putative amidase | cytoplasmic | glutaminyl-tRNA synthase (glutamine-hydrolysing) activity | catalytic activity |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | PFLU3345 | hypothetical protein | unknown | unknown | unknown |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | PFLU3969 | putative acetyltransferase | unknown | ribosome biogenesis | cellular component |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | PFLU6085 | putative cobalamin biosynthesis-like protein | cytoplasmic | cobalamin biosynthetic process | catalytic activity |
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | prfA | peptide chain release factor 1 | cytoplasmic | translational termination | resource utilization |