TABLE 2.
Single nucleotide polymorphism mutations in genes developed in all treated strains with selected GO terms for biological processes
| Treated strain | Mutation typea | Original codon/base (AA)b | Alternative codon/base (AA)c | SNP location on contigd | Genes | Affected producte | Product location on contigf | GO terms BPg |
|---|---|---|---|---|---|---|---|---|
| ZnO40 | SNP | ACC (T) | CCC (P) | 30009 | mltF | Membrane-bound lytic murein transglycosylase MltF | 30162–28606 | Cell wall macromolecule catabolic process, cell wall organization, peptidoglycan catabolic process |
| SNP | TAG (*) | CAG (Q) | 49777 | rpoS | RNA polymerase sigma factor RpoS | 49951–49775 | Positive regulation of single-species biofilm formation on inanimate substrate, regulation of cell motility, regulation of cellular response to heat and oxidative stress, regulation of response to salt stress | |
| SNP | CTG (L) | CTT (L) | 88393 | topA | Type I DNA topoisomerase | 89784–87187 | Metal ion binding | |
| SNP | GTT (V) | ATT (I) | 50610 | ins1 | IS1 transposase | 50502–51195 | DNA recombination, transposition | |
| SNP | CTG (L) | ATT (I) | 10048 | cpxA | Envelope stress sensor histidine kinase CpxA | 10565–9192 | Cell adhesion involved in biofilm formation, cellular response to cell envelope stress | |
| SNP | AAC (N) | AAT (N) | 429 | Hypothetical protein | 620–1 | |||
| ZnONPs40 | SNP | GTA (V) | GTC (V) | 99400 | tRNA-Leu | tRNA-Leu | 99317–99403 | Protein biosynthesis |
| SNP | TAG (*) | CAG (Q) | 49777 | rpoS | RNA polymerase sigma factor RpoS | 49951–49775 | Positive regulation of single-species biofilm formation on inanimate substrate, regulation of cell motility, regulation of cellular response to heat and oxidative stress, regulation of response to salt stress | |
| SNP | TTA (L) | TCA (S) | 19732 | cdsA | Phosphatidate cytidylyltransferase CdsA | 20417–19560 | Lipid biosynthesis and metabolism, phospholipid biosynthesis and metabolism | |
| SNP | TTC (F) | GTC (V) | 20336 | cdsA | Phosphatidate cytidylyltransferase CdsA | 20417–19560 | Lipid biosynthesis and metabolism, phospholipid biosynthesis and metabolism | |
| Deletion | −5584 bp | vgrG_1–vgrG_2 | T6SS protein VgrG (two copies), T6SS PAAR protein, hypothetical proteins | Cytolysis, bacteriocin, hydrolase | ||||
| ZnO20 + 20 | SNP | GGC (G) | GAC (D) | 115147 | deaD | ATP-dependent RNA helicase DeaD | 113613–115502 | Processes at low temperatures, cold-shock degradosome with Rnase E |
| SNP | GGT (G) | TGT (C) | 63243 | cysJ | NADPH-dependent assimilatory sulfite reductase flavoprotein subunit CysJ | 64878–63079 | FMN binding, sulfite reductase (NADPH) activity, cysteine biosynthesis | |
| SNP | GTG (V) | ATG (M) | 49967 | qorB | NAD(P)H:quinone oxidoreductase QorB | 50507–49647 | Oxidoreductase activity | |
| ZnONPs20 + 20 | SNP | ATT (I) | GTT (V) | 126557 | hns | DNA-binding transcriptional regulator H-NS | Stress response |
a
Detected mutation type where SNP represents single nucleotide polymorphism.
b
Original codon (if present in coding sequence) or base (if intergenic) in C40 with amino acid (AA) change for coding sequences.
c
Alternative codon (if present in coding sequence) or base (if intergenic) in a treated strain with AA change for coding sequences.
d
Location of SNP or product in short-read assembly.
e
Product(s) affected by the mutation.
f
Product(s) location on contig.
g
Biological process in GO terms specified in UniProt database, accessed 2 March 2023.