Table 2 Description of mutations that directly correlate (p value <0.01) with a growth regime, a phenotype, or a biological replicate
From: Rapid microevolution of biofilm cells in response to antibiotics
Label | Mutation | Annotation | Gene/s | Gene product/s | ||
|---|---|---|---|---|---|---|
SNPs | Non-synonymous | 2.1 | A → G | K5E (AAA → GAA) | rplX | 50S ribosomal protein L24 |
2.2 | A → T | K6N (AAA → AAT) | rplX | 50S ribosomal protein L24 | ||
4 | G → A | Intergenic (−98/−30) | ABUW_0747/ABUW_0748 | Putative transcriptional regulator Cro/CI family/HP | ||
5.1 | A → C | E2690A (GAG → GCG) | ABUW_0885 | Biofilm-associated protein | ||
6 | C → T | P233L (CCG → CTG) | ABUW_0944 | Oxidoreductase α (molybdoprotein)-subunit | ||
10 | C → T | A20V (GCA → GTA) | ABUW_1489 | CsuB, putative secreted protein related to type I pili | ||
13.1 | C → A | G318V (GGC → GTC) | adeS | AdeS kinase | ||
13.2 | C → T | G318D (GGC → GAC) | adeS | AdeS kinase | ||
13.3 | C → A | D167Y (GAT → TAT) | adeS | AdeS kinase | ||
14 | G → A | R41H (CGT → CAT) | ABUW_2055 | Fimbrial protein | ||
17 | T → A | L102I (TTA → ATA) | ABUW_2540 | Transposase | ||
27 | C → T | Intergenic (+446/−139) | ABUW_4067/ABUW_4068 | HP/HP | ||
30 | G → A | Intergenic (+110/−135) | ABUW_1900/ABUW_1901 | Oxidoreductase FAD, FMN binding/HP | ||
Synonymous | 5.2 | A → G | A2635A (GCA → GCG) | ABUW_0885 | Biofilm-associated protein | |
5.3 | T → C | G1510G (GGT → GGC) | ABUW_0885 | Biofilm-associated protein | ||
5.4 | A → G | L2636L (TTA → TTG) | ABUW_0885 | Biofilm-associated protein | ||
5.5 | A → T | V2367V (GTA → GTT) | ABUW_0885 | Biofilm-associated protein | ||
5.6 | T → A | T1913T (ACT → ACA) | ABUW_0885 | Biofilm-associated protein | ||
InDels | Insertions | 1 | (CTTTGGATT)10 → 11 | Intergenic (+257/−590) | tyrS/ABUW_0015 | Tyrosyl-tRNA synthetase/16S rRNA gene |
8 | +C | Intergenic (−206/−47) | ABUW_1059/ABUW_1060 | HP/HP | ||
25.1 | (T)5 → 6 | Coding (737/1212 nt) | ABUW_3824 | Family 1 glycosyl transferase | ||
Deletions | 3.1 | (A)5 → 4 | Coding (236/1239 nt) | ABUW_0633 | Putative methyltransferase | |
15 | (A)7 → 6 | Coding (198/888 nt) | ABUW_2169 | Putative membrane protein | ||
18 | Δ1 bp | Coding (85/708 nt) | vfr | Virulence factor regulator, cAMP receptor-like protein | ||
19 | Δ1 bp | Intergenic (−132/+517) | ABUW_3017/ggt | Integrase/gamma-glutamyltransferase | ||
21.1 | (CGGTGCAGT)19 → 7 | Coding (313–420/1368 nt) | filE | Pilus assembly protein | ||
21.2 | Δ135 bp | Coding (421–555/1368 nt) | filE | Pilus assembly protein | ||
22 | Δ141 bp | Partial loss of the gene | [ABUW_3448] | Glycosyl transferase, group 1 | ||
ISAba1 | Insertions | 3.2 | ISAba1 (–) + 9 bp | Coding (356–364/1239 nt) | ABUW_0633 | Putative methyltransferase |
11 | ISAba13 (–) + 9 bp | Coding (327–335/654 nt) | ABUW_1731 | Transcriptional regulator, TetR family | ||
20 | ISAba1 (+) + 9 bp | Coding (169–177/477 nt) | smpB | SsrA-binding protein | ||
26.1 | ISAba1 (+) + 9 bp | Coding (229–237/1254 nt) | ABUW_3825 | HP | ||
ISAba13 | Insertions | 16 | ISAba13 (–) + 9 bp | Coding (170–178/1470 nt) | ABUW_2208 | Adenylate guanylate cyclase |
23.1 | ISAba13 (+) + 9 bp | Coding (70–78/327 nt) | ABUW_3609 | DNA-binding protein HNS | ||
23.2 | ISAba13 (–) + 9 bp | Coding (70–78/327 nt) | ABUW_3609 | DNA-binding protein HNS | ||
23.3 | ISAba13 (+) + 9 bp | Intergenic (−27/+160) | ABUW_3609/ABUW_3610 | DNA-binding protein HNS/thioesterase superfamily protein | ||
25.2 | ISAba13 (–) + 9 bp | Coding (779–787/1212 nt) | ABUW_3824 | Family 1 glycosyl transferase | ||
26.2 | ISAba13 (+) + 9 bp | Coding (1008–1016/1254 nt) | ABUW_3825 | HP | ||
26.3 | ISAba13 (+) + 9 bp | Coding (1224–1232/1254 nt) | ABUW_3825 | HP | ||
Deletions | 7 | Δ9965 bp | ISAba13-mediated | [ABUW_1758]–ABUW_1764 | Putative acetyl esterase/lipase; extracellular serine protease; sulfate permease; HP; gdhB2 quinoprotein glucose dehydrogenase-B; UspA domain protein; GGDEF family protein | |
9 | Δ8706 bp | ISAba13-mediated | ABUW_1759–ABUW_1764 | Extracellular serine protease; sulfate permease; HP; gdhB2 quinoprotein glucose dehydrogenase-B; UspA domain protein; GGDEF family protein | ||
12 | Δ871 bp | ISAba13-mediated | [ABUW_1764] | GGDEF family protein | ||
24 | Δ34,453 bp | ISAba13-mediated | ABUW_3804–[ABUW_3830] | HP; HP; FE/S-dependent 2-methylisocitrate dehydratase; 2-methylcitrate synthase; methylisocitrate lyase; GntR family transcriptional regulator; aromatic amino acid aminotransferase; d-lactate dehydrogenase; K-capsule biosynthesis genes | ||
ISAba125 | 3.3 | ISAba125 (+) + 3 bp | Coding (696–698/1239 nt) | ABUW_0633 | Putative methyltransferase | |
26.4 | ISAba125 (+) + 3 bp | Coding (695–697/1254 nt) | ABUW_3825 | HP | ||
28 | Δ1985 bp | Between ISAba125 | ABUW_4087–ABUW_4089 | HP; transposase | ||
Loss of plasmid | 29 | Δ83,610 bp | Loss of plasmid 1 | [repAci6]–ABUW_4123 | Loss of plasmid 1 |
