Table 2.
Genomic adaptation in FeSO4 selected populations
| Gene | Mutation | Fe2+_1 | Fe2+_2 | Fe2+_3 | Fe2+_4 | Fe2+_5 | Gene description *BreSeq and Uniprot |
|---|---|---|---|---|---|---|---|
| murC→ | P14S (CCC→TCC) | 0.208 | –– | –– | –– | –– | Cell wall formation, UDP-N-acetylmuramate: L-alanine ligase |
| cueR→ | V6L (GTA→CTA) | –– | –– | –– | –– | 0.747 | Copper-responsive regulon transcriptional regulator |
| mrdA← | G69R (GGC→CGC) | –– | –– | 0.348 | –– | –– | Transpeptidase involved in peptidoglycan synthesis (penicillin-binding protein 2) |
| mdfA→ | E250G (GAG→GGG) | –– | –– | –– | 0.197 | –– | Multi-drug efflux system protein |
| yeaG→ | A441V (GCA→GTA) | –– | –– | –– | –– | 1.000 | Protein kinase, endogenous substrate unidentified; autokinase |
| ptsP← | R526C (CGC→TGC) | –– | –– | 0.155 | –– | –– | Component of the PEP-dependent nitrogen-metabolic phosphotransferase system |
| ptsP← | C519*(TGC→TGA) | 1.000 | 1.000 | 0.491 | –– | –– | Component of the PEP-dependent nitrogen-metabolic phosphotransferase system |
| ptsP← | (Δ1 bp) coding (1525/2247 nt) | –– | –– | 0.226 | –– | –– | Component of the PEP-dependent nitrogen-metabolic phosphotransferase system |
| yhfZ←/ ←trpS | intergenic (–223/+67) | –– | –– | 0.121 | –– | –– | Putative DNA-binding transcriptional regulator/tryptophanyl-tRNA synthetase |
| yhfZ←/ ←trpS | intergenic (–242/+48) | –– | –– | 0.135 | –– | –– | Putative DNA-binding transcriptional regulator/tryptophanyl-tRNA synthetase |
| rhsB→ | K1374N (AAG→AAT) | –– | –– | 0.229 | –– | –– | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| yidX→ | L29V (CTG→GTG) | –– | 1.000 | –– | –– | –– | Putative lipoprotein |
| yidX→ | coding (87–88/657 nt) | –– | 1.000 | –– | –– | –– | Putative lipoprotein |
| rrsC→ | noncoding (226/1542 nt) | –– | –– | –– | –– | 1.000 | 16S ribosomal RNA of rrnC operon |
| ilvL→/ →ilvX | intergenic (+46/–41) | –– | –– | –– | –– | 1.000 | Biosynthesis of branched-chain amino acids, |
| ilvG→ | (+C) pseudogene (66/663 nt) | 1.000 | 1.000 | 0.667 | –– | –– | Branched-chain amino acids synthesis |
| rpoB→ | D654Y (GAC→TAC) | –– | –– | –– | 0.377 | –– | RNA polymerase, beta subunit |
| fecA← | A559T (GCT→ACT) | 1.000 | 1.000 | –– | –– | –– | Fe3 + dicitrate siderophore transport system |
| fecA← | G243C (GGC→TGC) | –– | –– | –– | –– | 1.000 | Fe3 + dicitrate siderophore transport system |
| fecA← | D120Y (GAC→TAC) | –– | –– | 0.327 | –– | –– | Fe3 + dicitrate siderophore transport system |
Notes: After 200 days of adaptation, all populations were subjected to whole genome resequencing with sequence alignments and variant calling using breseq 0.30.0. Mutations found in both the controls and iron (II)-adapted populations were removed (reported in Supplementary Table S1). The genes/mutations highlighted in orange represent those that were identified in more than one population. In addition to the gene name, the corresponding protein and nucleotide changes are also reported along with the frequency of mutation (f), represented as a value from 0 (not detected, gray box)––1.000 (hard sweep and dark green) with minor variants colored in lighter shades of green. NCBI SRA database PRJNA532971.