Table 1.
List of predicted genes involved in bacterial endophytic behavior [38] in Serratia sp. LCN16 genome. Burkholderia phytofirmans PsJN (CP001052-54) was used as reference genome for orthologous search in Serratia sp. LCN16, Serratia proteamaculans 568 (Spro568, NC_009832) and S. liquefaciens ATCC 27592 (CP006252). The description presented is based on KEGG annotation [69]
| Gene Function | Description | Gene Identification | Orthologous genes | ||||
|---|---|---|---|---|---|---|---|
| Number | Copies | Name | PsJN | Spro568 | ATCC 27592 | ||
| Transporter | Arabinose operon regulatory | LCN16_02277 | 1 | araC | Bphyt_0033 | Spro_1385 | M495_06380 |
| Lysine exporter protein | LCN16_04024 | 1 | Bphyt_0034 | - | M495_06375 | ||
| High-affinity branched-chain amino acid transport | LCN16_00248 | 1 | livF | Bphyt_3906 | Spro_0232 | M495_01020 | |
| High-affinity branched-chain amino acid transport | LCN16_00245 | 1 | livH | Bphyt_3908 | Spro_3202 | M495_01005 | |
| NAD(P) transhydrogenase subunit beta | LCN16_02610 | 1 | pntB | Bphyt_4261 | Spro_2584 | M495_12845 | |
| ABC transporter related | LCN16_02535 | 1 | malk_1 | Bphyt_4584 | Spro_4470 | M495_22510 | |
| Metabolite:H+ symporter (MHS) family | LCN16_03836 | 1 | citA | Bphyt_5520 | Spro_3179 | M495_10135 | |
| Extracellular solute-binding protein | LCN16_01236 | 1 | modA | Bphyt_5521 | Spro_3180 | - | |
| Gluconate 2-dehydrogenase | LCN16_02150 | 1 | Bphyt_4638 | Spro_2138 | M495_10390 | ||
| Gluconate 2-dehydrogenase | LCN16_02151 | 1 | Bphyt_4639 | Spro_2137 | M495_10385 | ||
| Gluconate 2-dehydrogenase | LCN16_02152 | 1 | Bphyt_4640 | Spro_2136 | M495_10380 | ||
| Secretion and delivery system | TypeVI secretion protein | - | 0 | - | Bphyt_4913 | Spro_3003 | - |
| TypeVI secretion protein | - | 0 | - | Bphyt_4914 | Spro_3004 | - | |
| TypeVI secretion protein | - | 0 | - | Bphyt_4919 | Spro_3013 | M495_03685 | |
| RND family efflux transporter MFP subunit | LCN16_01039 | 1 | acrA | Bphyt_6992 | Spro_1127 | M495_04880 | |
| Plant polymer degradation/modification | Alpha/beta hydrolase family protein | LCN16_01434 | 1 | Bphyt_6134 | Spro_0990 | M495_12205 | |
| Alpha/alpha-trehalase | - | 0 | Bphyt_5350 | - | - | ||
| Cupin | LCN16_02559 | 2 | Bphyt_2288 | - | - | ||
| Peptidase M48 Ste24p | LCN16_04051 | 1 | loiP | Bphyt_3335 | Spro_3955 | M495_20655 | |
| Transcriptional regulator | HTH-type transcriptional regulator LrpC | LCN16_01418 | 1 | lrpC | Bphyt_0434 | Spro_1462 | M495_06820 |
| Regulator protein FrmR | LCN16_01244 | 1 | frmR | Bphyt_0109 | - | - | |
| AraC family transcriptional regulator | LCN16_02277 | 1 | araC | Bphyt_2287 | Spro_2540 | M495_12625 | |
| Transcriptional regulatory protein | LCN16_03523 | 1 | ompR | Bphyt_4604 | Spro_4621 | M495_23305 | |
| Transcriptional regulatory, DeoR family | LCN16_01600 | 1 | deoR | Bphyt_4951 | Spro_2259 | M495_11240 | |
| Transcriptional regulatory, LysR family | LCN16_02297 | 1 | ampR | Bphyt_5523 | Spro_3181 | M495_17720 | |
| LrgB family operon | - | 0 | Bphyt_5345 | Spro_1569 | M495_07365 | ||
| Flavoprotein WrbA | LCN16_01736 | 1 | wrbA | Bphyt_6351 | Spro_1813 | M495_08400 | |
| Detoxification | Glutathione S-transferase | LCN16_01390 | 7 | gst | Bphyt_1366 | Spro_3320 | M495_17060 |
| Short-chain dehydrogenase | LCN16_02779 | 1 | Bphyt_1098 | Spro_1971 | M495_09250 | ||
| S-(hydroxymethyl)-gluthathione dehydrogenase | LCN16_01515 | 1 | frmA | Bphyt_5114 | Spro_1557 | M495_07305 | |
| 2-hydropantoate 2-reductase | LCN16_00995 | 1 | panE | Bphyt_5159 | Spro_3174 | - | |
| Redox potential maintenance | Acetoacetyl-coa reductase | LCN16_01349 | 1 | phbB | Bphyt_5655 | Spro_3465 | M495_17855 |
| Acetaldehyde dehydrogenase | LCN16_02742 | 1 | adhE | Bphyt_1467 | Spro_3026 | M495_05210 | |
| Carbonate dehydratase | LCN16_00514 | 1 | cynT | Bphyt_2146 | Spro_1534 | M495_07235 | |
| Aldehyde dehydrogenase | LCN16_02563 | 3 | gabD | Bphyt_4023 | Spro_4305 | M495_21680 | |
| Malate/L-lactate dehydrogenase | LCN16_02031 | 1 | ybiC | Bphyt_5456 | Spro_2010 | M495_09840 | |
| 3-hydroxyisobutyrate dehydrogenase | LCN16_01348 | 1 | garR | Bphyt_5931 | Spro_1492 | M495_07025 | |
| Others | Amino-acid metabolite efflux pump | LCN16_01419 | 1 | eamA | Bphyt_0435 | Spro_1463 | M495_06825 |
| 2-isopropylmalate synthase | LCN16_00673 | 2 | leuA | Bphyt_0573 | Spro_1875 | M495_00910 | |
| Diaminopimelate decarboxylase | LCN16_03946 | 1 | lysA | Bphyt_7089 | Spro_3836 | M495_20025 | |