Table 3.
Transcription rates of genes involved in basic metabolisma
| Hfx. alexandrinus DSM 27206 ORFb | Gene name | Log2FC | Annotation | ||
|---|---|---|---|---|---|
| 0.1 mM | 0.25 mM | 0.5 mM | |||
| Carbohydrate metabolim | |||||
| Hfx-2019-SC1-cds280 | - | - | 2.23 | ABC.SS.P simple sugar transport system permease protein | |
| Hfx-2019-SC1-cds281 | - | - | 2.22 | ABC.SS.P simple sugar transport system permease protein | |
| Hfx-2019-SC1-cds378 | gatC | 2.51 | - | - | Galactitol-specific IIC component |
| Hfx-2019-SC2-cds179 | ppsA | 2.13 | - | - | Pyruvate water dikinase |
| Hfx-2019-SC2-cds823 | - | - | 3.49 | COG0701 Predicted permeases | |
| Hfx-2019-SC2-cds834 | fbp | 3.74 | - | - | Fructose-1 6-bisphosphatase I |
| Hfx-2019-SC3-cds294 | gap2 | 2.53 | - | - | Glyceraldehyde-3-phosphate dehydrogenase (NAD(P)) |
| Hfx-2019-SC5-cds125 | galE | 3.83 | - | 3.63 | UDP-glucose 4-epimerase |
| Hfx-2019-SC5-cds135 | ich-Y | - | - | 2.2 | Itaconyl-CoA hydratase |
| Hfx-2019-SC1-cds496 | ugpB | - | - | -2.01 | sn-glycerol 3-phosphate transport system substrate-binding protein |
| Hfx-2019-SC1-cds980 | iolG | -2.32 | - | - | Myo-inositol 2-dehydrogenase / D-chiro-inositol 1-dehydrogenase |
| Hfx-2019-SC2-cds552 | - | -2.27 | - | AAA-type ATPase, core component | |
| Hfx-2019-SC2-cds877 | gnaD | -2.9 | - | - | Gluconate/galactonate dehydratase |
| Hfx-2019-SC3-cds298 | gapA | -2.47 | - | - | Glyceraldehyde 3-phosphate dehydrogenase |
| Hfx-2019-SC3-cds336 | gtsA | -3.46 | - | - | Glucose/mannose transport system substrate-binding protein |
| Hfx-2019-SC3-cds337 | gtsB | -3.83 | - | - | Glucose/mannose transport system permease protein |
| Hfx-2019-SC3-cds338 | gtsC | -3.06 | - | - | Glucose/mannose transport system permease protein |
| Hfx-2019-SC3-cds339 | msmX | -3.78 | - | - | Multiple sugar transport system ATP-binding protein |
| Hfx-2019-SC3-cds350 | araE | - | - | -2.44 | Arabinose:H+ symporter |
| Hfx-2019-SC4-cds36 | iolE | - | - | -6.43 | Sugar phosphate isomerases/epimerases |
| Hfx-2019-SC4-cds78 | msmX | - | -2.34 | - | Multiple sugar transport system ATP-binding protein |
| Hfx-2019-SC4-cds146 | thuA | - | -2.92 | -4.28 | Trehalose utilization protein |
| Hfx-2019-SC4-cds211 | gtsC | - | - | -5.63 | Glucose/mannose transport system permease protein |
| Lipid metabolim | |||||
| Hfx-2019-SC2-cds258 | acs | 2.2 | - | 2.5 | AMP-forming acetyl-CoA synthetase |
| Hfx-2019-SC2-cds631 | acs | 2.39 | - | - | AMP-forming acetyl-CoA synthetase |
| Hfx-2019-SC2-cds779 | caiC | 2.01 | - | - | Fatty-acyl-CoA synthase |
| Hfx-2019-SC5-cds129 | 2.6 | - | - | Enoyl-CoA hydratase | |
| Hfx-2019-SC5-cds130 | paaH | 2.82 | - | 4.02 | 3-hydroxybutyryl-CoA dehydrogenase |
| Hfx-2019-SC5-cds131 | pksG | 3.19 | - | 3.59 | hydroxymethylglutaryl-CoA synthase |
| Hfx-2019-SC5-cds132 | paaJ | 2.28 | - | 3.15 | Acetyl-CoA C-acetyltransferase |
| Hfx-2019-SC5-cds133 | paaK | 3.3 | - | 3.49 | Phenylacetate-CoA ligase |
| Hfx-2019-SC5-cds134 | paaI | 2.86 | - | 3.83 | Acyl-CoA thioesterase |
| Hfx-2019-SC5-cds136 | epi | 2.14 | - | 2.16 | Methylmalonyl-CoA/ethylmalonyl-CoA epimerase |
| Hfx-2019-SC5-cds142 | paaI | 2.75 | - | 2.95 | Acyl-CoA thioesterase |
| Hfx-2019-SC5-cds145 | paaD | 2.9 | - | - | Predicted metal-sulfur cluster biosynthetic enzyme |
| Hfx-2019-SC5-cds146 | paaC | 3.17 | - | 2.45 | Ring-1,2-phenylacetyl-CoA epoxidase subunitPaaC |
| Hfx-2019-SC5-cds147 | paaB | 3.17 | - | 2.44 | Ring-1 2-phenylacetyl-CoA epoxidase subunitPaaB |
| Hfx-2019-SC5-cds148 | paaA | 2.69 | - | - | Ring-1 2-phenylacetyl-CoA epoxidase subunit PaaA |
| Hfx-2019-SC5-cds76 | prpD | - | -4.03 | - | 2-methylcitrate dehydratase |
| Hfx-2019-SC5-cds77 | prpD | - | -3.36 | - | 2-methylcitrate dehydratase |
| Amino acid metabolism | |||||
| Hfx-2019-SC1-cds368 | puuE | 2.81 | - | 2.17 | 4-aminobutyrate aminotransferase |
| Hfx-2019-SC2-cds36 | pdhC | 2.56 | - | - | Pyruvate dehydrogenase E2 component |
| Hfx-2019-SC4-cds252 | hyuA | - | - | 2.19 | N-methylhydantoinases |
| Hfx-2019-SC5-cds98 | hutH | 2.17 | - | - | Histidine ammonia-lyase |
| Hfx-2019-SC5-cds118 | hyuA | - | - | 2.30 | N-methylhydantoinase |
| Hfx-2019-SC5-cds119 | hyuB | 2.18 | - | 2.23 | N-methylhydantoinases |
| Hfx-2019-SC5-cds120 | pepQ | 3.56 | - | 2.11 | Xaa-Pro dipeptidase |
| Hfx-2019-SC5-cds126 | ilvB | 3.59 | - | 4.02 | Acetolactate synthase I/II/III large subunit |
| Hfx-2019-SC5-cds151 | 2.1 | - | - | Amidohydrolase | |
| Hfx-2019-SC1-cds54 | RP-S6e | -2.72 | - | - | RPS6 small subunit ribosomal protein S6e |
| Hfx-2019-SC3-cds359 | livK | - | - | -2.59 | Branched-chain amino acid transport system substrate-binding protein |
| Hfx-2019-SC4-cds106 | ilvA | - | -2.53 | -2.05 | Threonine dehydratase |
| Hfx-2019-SC4-cds221 | - | -2.08 | - | Aspartate aminotranferase family member | |
| Hfx-2019-SC4-cds222 | dat | - | -2.99 | -2.48 | Diaminobutyrate-2-oxoglutarate transaminase |
| Hfx-2019-SC5-cds223 | pydC | - | - | -2.05 | Beta-ureidopropionase/ N-carbamoyl-L-amino-acid hydrolase |
| Hfx-2019-SC6-cds119 | lysK | -2.16 | - | -2.15 | LysW-gamma-L-lysine/LysW-L-ornithine carboxypeptidase |
| Hfx-2019-SC6-cds120 | lysJ | -2.01 | - | - | LysW-gamma-L-lysine/LysW-L-ornithine aminotransferase |
| Nucleotide metabolism | |||||
| Hfx-2019-SC7-cds82 | draG | - | -2.37 | - | ADP-ribosylglycohydrolase |
aRNA-Seq was used to determine the expression levels of the genes in Hfx. alexandrinus DSM 27206, as detailed in the section on Materials and Methods. The data are the average of three replicates. The threshold of differential expression genes was: |log2(FoldChange)|> 1 and qvalue < 0.00. Dashes indicate that there were minimal changes to the transcription, not considered statistically significant. bThe gene name, number, and annotation were generated through the gDNA sequencing of the tested strain, as described in the Materials and Methods section