TABLE 1.
Plasmid and strain list
| Plasmid or strain | Description | Source, reference, and/or strain | Plasmid map | Sequence |
|---|---|---|---|---|
| Plasmids | ||||
| pRADgro | Shuttle vector for E. coli and D. radiodurans using groESL promoter; Chlr (D. radiodurans) Ampr (E. coli) | 57 | Fig. S2A | Fig. S3A |
| pRADgro-GFP | Shuttle vector for E. coli and D. radiodurans with codon-optimized GFP and groESL promoter; Chlr Ampr | This study | ||
| pThRS-GFP | pRADgro with theophylline riboswitch upstream of GFP (pRADgro-ThRS-GFP); Chlr Ampr | This study; 79 | Fig. 3A | Fig. S3B |
| pDR-GFP | pRADgro reporter plasmid with candidate 5′-UTR sequences named by gene number (Table S1) inserted upstream of GFP (pRADgro–5′UTR–GFP); Chlr Ampr | This study; GenScript | Fig. S2B | Fig. S3C |
| pDR1913-GFP (UTR_gyrA) | pRADgro reporter plasmid with DR1913 5′ UTR (DNA gyrase subunit A gene, UTR_gyrA) upstream of GFP; Chlr Ampr | This study; GenScript | ||
| pDR1857-GFP (UTR_ohrP) | pRADgro reporter plasmid with DR1857 5′ UTR (gene encoding organic hydroperoxide resistance protein; UTR_ohrP) upstream of GFP; Chlr Ampr | This study; GenScript | ||
| pGyrUTRgyrA | pRADgro expression plasmid with DNA gyrase subunit A gene (DR1913) FLAG tagged and expressed with native gyrA 5′ UTR (pRADgro-1913UTR-gyrase A-FLAG); Chlr Ampr | This study | Fig. S2C | Fig. S3D |
| pGroUTRgyrA | pRADgro expression plasmid with DNA gyrase subunit A gene (DR1913) FLAG tagged and expressed with groESL 5′ UTR (pRADgro-GroESLUTR-gyrase A-FLAG); Chlr Ampr | This study | Fig. S3E | Fig. S3E |
| Strains | ||||
| D. radiodurans R1 | Wild-type D. radiodurans | ATCC 13939 | ||
| ΔkatA mutant | R1 strain with genomic deletion of catalase, katA (DR1998); Kanr | 67; KKW7003 | ||
| ΔUTR_gyrA mutant | R1 strain with genomic deletion of the DNA gyrase subunit A gene (DR1913) 5′ UTR | This study | Fig. 5A | |
| UTRScramgyrA mutant | R1 strain with the DNA gyrase subunit A gene RDRM 5′ UTR genomically scrambled by compensatory mutations | This study | Fig. 5A | |
| ΔUTR_gyrA-pGyrUTR mutant | ΔUTR_gyrA strain expressing pGyrUTRgyrA plasmid; Chlr Ampr | This study | ||
| ΔUTR_gyrA-pGroUTR mutant | ΔUTR_gyrA strain expressing pRADgro-GroELSUTR-gyrase A-FLAG plasmid; Chlr Ampr | This study | ||
| ΔirrE mutant | ΔirrEΩkan (R1 strain with knockout of irrE); Kanr | 22; GY14127 | ||
| ΔirrE-pDR1913-GFP mutant | ΔirrEΩkan (R1 strain with knockout of irrE) expressing pDR1913GFP; Chlr Ampr Kanr | This study |