Table 2.
List of upregulated proteins in SRS-25 and SRS-46 strains, following exposure to uranium. Fold change represents the expression with U amendment normalized to expression without U, respectively.
| Function | Protein | Gene | Fold Change | Strain |
|---|---|---|---|---|
| Protein synthesis, translation and transport | Aspartate-tRNA(Asp/Asn) ligase | aspS | 2.3 | SRS-25 |
| Alanine-tRNA ligase | alaS | 4.5 | SRS-25 | |
| Elongation factor G1 | fusA1 | 2.4 | SRS-25 | |
| Proline-tRNA ligase | proS | 5.6 | SRS-25 | |
| Arginine-tRNA ligase | argS | 3.8 | SRS-25 | |
| Glutamate-tRNA ligase | gltX | 2 | SRS-25 | |
| Methionine-tRNA ligase | metG | 9.6 | SRS-25 | |
| Translation initiation factor IF-2 | infB | 2.3 | SRS-25 | |
| Elongation factor G2 | fusA2 | 2.1 | SRS-25 | |
| Protein translocase subunit SecA | secA | 4.7 | SRS-25 | |
| Threonine-tRNA ligase | thrS | 5.2 | SRS-25 | |
| 50S ribosomal protein L20 | rplT | 1.9 | SRS-25 | |
| 50S ribosomal protein L10 | rplJ | 1.7 | SRS-25 | |
| 30S ribosomal protein S13 | rpsM | 3.2 | SRS-25 | |
| 30S ribosomal protein S7 | rpsG | 1.9 | SRS-46 | |
| 30S ribosomal protein S5 | rpsE | 1.8 | SRS-46 | |
| 50S ribosomal protein L5 | rplE | 1.8 | SRS-46 | |
| Ribosome-recycling factor | frr | 2.7 | SRS-46 | |
| 50S ribosomal protein L25 | rplY | 1.8 | SRS-46 | |
| NADH-quinone oxidoreductase subunit C | nuoC | 2 | SRS-46 | |
| Sec-independent protein translocase protein tatB | tatB | 3.8 | SRS-46 | |
| Peptide deformylase 1 | def1 | 4.7 | SRS-46 | |
| Ribosomal RNA small subunit methyltransferase A | rsmA | 3.8 | SRS-46 | |
| Ribosomal RNA large subunit methyltransferase E | rlmE | 3.8 | SRS-46 | |
| Electron transport coupled proton transport | NADH-quinone oxidoreductase subunit B | nuoB | 2.5 | SRS-25 |
| Ribosome biogenesis | GTPase Der | der | 2.5 | SRS-25 |
| 30S ribosomal protein S13 | rpsM | 3.2 | SRS-25 | |
| Endoribonuclease YbeY | ybeY | 2.5 | SRS-46 | |
| Amino acid biosynthesis | Dihydroxy-acid dehydratase 1 | ilvD1 | 2.3 | SRS-25 |
| Argininosuccinate lyase | argH | 1.8 | SRS-46 | |
| Imidazole glycerol phosphate synthase subunit HisF | hisF | 1.7 | SRS-46 | |
| 3-isopropylmalate dehydratase small subunit | leuD | 1.8 | SRS-46 | |
| Homoserine O-succinyltransferase | metXS | 1.7 | SRS-46 | |
| Imidazole glycerol phosphate synthase subunit HisH | hisH | 2.5 | SRS-46 | |
| Transcription | DNA-directed RNA polymerase subunit beta | rpoB | 3.8 | SRS-25 |
| DNA-directed RNA polymerase subunit beta | rpoC | 2.9 | SRS-25 | |
| Bifunctional protein glk | glk | 3.1 | SRS-25 | |
| DNA Replication, recombination and repair | Chaperone protein DnaK | dnaK | 1.9 | SRS-25 |
| DNA ligase | ligA | 17 | SRS-25 | |
| DNA ligase | ligA | 2.5 | SRS-46 | |
| lexA repressor | lexA | 4.2 | SRS-46 | |
| Holiday junction ATP-dependent DNA helicase RuvA | ruvA | 7 | SRS-46 | |
| Stress response | Chaperone protein HtpG | htpG | 2.6 | SRS-25 |
| Chaperone protein HscA homolog | hscA | 3.5 | SRS-25 | |
| Polyribonucleotide nucleotidyltransferase | pnp | 2.9 | SRS-25 | |
| N-succinylglutamate 5-semialdehyde dehydrogenase | astD | 2.4 | SRS-25 | |
| Lon protease | lon | 3.2 | SRS-46 | |
| Protease HtpC homolog | htpX | 3.1 | SRS-46 | |
| Protein GrpE | grpE | 3 | SRS-46 | |
| Co-chaperone protein HscB homolog | hscB | 3.2 | SRS-46 | |
| 60 kDa chaperonin 2 | groL2 | 1.7 | SRS-46 | |
| Chaperone protein DnaJ | dnaJ | 1.7 | SRS-46 | |
| Heat-inducible transcription repressor HrcA | hrcA | 1.9 | SRS-46 | |
| Nucleotide biosynthesis | CTP synthase | pyrG | 2.8 | SRS-25 |
| Thymidylate kinase | tmk | 11 | SRS-46 | |
| Isoprene and thiamine biosynthesis | 1-deoxy-D-xylulose-5-phosphate synthase | dxs | 5.4 | SRS-25 |
| 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ispF | 2.1 | SRS-25 | |
| CO2 fixation | Phosphoenolpyruvate carboxylase | ppc | 3.6 | SRS-25 |
| Phosphoenolpyruvate carboxylase | ppc | 1.9 | SRS-46 | |
| Outer membrane assembly protein, lipopolysaccharide transport | LPS-assembly protein LptD | lptD | 5.8 | SRS-25 |
| Oxidative stress response and protein repair | Peptide methionine sulfoxide reductase MsrB | msrB | 1.9 | SRS-25 |
| Metabolism | Acetyl-coenzyme A synthetase | acsA | 3.6 | SRS-25 |
| Enolase | eno | 1.7 | SRS-46 | |
| N-succinylarginine dihydrolase | astB | 3.2 | SRS-46 | |
| Thymidine phosphorylase | deoA | 2.5 | SRS-46 | |
| Phophoglucosamine mutase | glmM | 1.7 | SRS-46 | |
| Anhydro-N-acetylmuramic acid kinase | anmk | 2.5 | SRS-46 | |
| dCTP deaminase | dcd | 1.7 | SRS-46 | |
| Nucleotide biosynthesis | Thymidylate kinase | tmk | 11 | SRS-46 |
| Oxidoreductase activity and antibiotic response | Thiol:disulfide interchange protein DsbA | dsbA | 2.2 | SRS-46 |
| Ion channnel, ion transport | Large-conductance mechanosensitive channel | mscL | 2.5 | SRS-46 |
| Aerobic respiration, ATP synthesis | NADH-quinone oxidoreductase subunit 1 | nuol | 3.8 | SRS-46 |
| ATP synthase subunit delta | atpH | 1.9 | SRS-46 | |
| Kinase, transferase | Cytidylate kinase | cmk | 1.7 | SRS-46 |
| Lipid biosynthesis | 3-hydroxy-[acyl-carrier-protein] | fabZ | 1.9 | SRS-46 |
| Lipid-A-disaccharide synthase | lpxB | 1.9 | SRS-46 | |
| Pyridoxine biosynthesis | 4-hydroxythreonine-4-phosphate dehydrogenase | pdxA | 2.5 | SRS-46 |
| Queuosine biosynthesis | 7-carboxy-7-deazaguanine synthase | queE | 2.5 | SRS-46 |
| Ubiquinone biosynthesis | 2-nonaprenyl-3-methyl-6-methoxy-1,4 benzoquinol hydroxylase | coq7 | 1.7 | SRS-46 |
| Glycosyl transferase | Uracil phosphoribosyltransferase | upp | 2.1 | SRS-46 |
| Poorly characterized | UPF0234 protein Bmul_0741/BMUL1_02519 | Bmul_0741 | 1.9 | SRS-46 |
| UPF0307 protein Bcep18194_A4194 | Bcep18194_A4194 | 6.4 | SRS-46 | |
| Probable transcriptional regulatory protein Bphyt_1301 | Bphyt_1301 | 2.1 | SRS-46 | |
| UPF0234 protein Bphy_0527 | Bphy_0527 | 1.7 | SRS-46 | |
| Probable transcriptional regulatory protein Bamb_2332 | Bamb_2332 | 2.3 | SRS-46 | |
| UPF0301 protein Bamb_0737 | Bamb_0737 | 5.1 | SRS-46 |