Table 3. Deletion of MSMEG_6129 results in induction of antibiotic resistance genes.
Total RNA was prepared from wild type and mc2155: Δ6129 strains followed by high throughput cDNA sequencing. The data is normalized to a million reads as well as for gene length for both strains (Reads per million bases per kilobase of ORF= RPKM) and expressed as a ratio of RPKM values of the wild typestrain and the mutant. The 3 categories of proteins where the ratio of RPKM values of Δ6129 to the wild type strain is >2.5 and are immediately relevant to the observed drug resistance phenotype of mc2155: Δ6129 are shown. The results of RNA seq were verified using qPCR for the pertinent genes from the above three categories highlighted in grey.
| Category | Gene ID | Fold change | Gene description |
|---|---|---|---|
| in Δ6129 | |||
| Drug Resistance & ABC Transporters | MSMEG_5187 | 9 | tetracycline-resistance determinant TetV |
| MSMEG_5102 | 7.5 | ABC transporter ATP-binding protein | |
| MSMEG_3203 | 4.3 | transporter, LysE family | |
| MSMEG_5047 | 3.7 | drug resistance transporter (Bcr/CfIA) | |
| MSMEG_0422 | 3.5 | Transferase. Toxin production & resistance | |
| MSMEG_5659 | 3.1 | ABC transporter, ATP-binding protein | |
| MSMEG_5660 | 3 | ABC transporter ATP-binding protein | |
| MSMEG_6245 | 2.9 | chloramphenicol resistance protein | |
| MSMEG_6595 | 2.6 | ABC transporter complex | |
| Transcription Regulators | MSMEG_1953 | 6.5 | transcription factor WhiB7 |
| MSMEG_0051 | 6 | transcription factor WhiB6 family | |
| MSMEG_1025 | 37 | TetR-family transcriptional regulator | |
| MSMEG_1420 | 3.7 | probable transcriptional regulatory protein | |
| MSMEG_5610 | 3.6 | putative transcriptional regulator family | |
| MSMEG_2305 | 3.4 | TetR-family transcriptional regulator | |
| MSMEG_6441 | 2.9 | transcriptional regulator, TetR family | |
| MSMEG_0473 | 2.8 | transcriptional regulator, LuxR family | |
| MSMEG_1117 | 2.8 | transcriptional regulator | |
| MSMEG_1970 | 2.7 | sigma factor | |
| MSMEG_5872 | 2.7 | DNA-binding response regulator PhoP | |
| MSMEG_0545 | 2.6 | transcriptional regulator, LuxR family | |
| MSMEG_6199 | 2.6 | Transcription factor WhiB2 | |
| MSMEG_2905 | 2.5 | DNA binding transcription factor | |
| Catalases | MSMEG_6213 | −2.5 | Manganese containing catalase |
| MSMEG_6232 | −2.6 | catalase KatA |