Table 3.
Analysis of M. leprae pseudogene promoters in silico and in vitro promoter in E. coli analyses.
|
Pseudogene1 Mycobact Ortholog2 |
Distance Upstream of Start Codon |
Intrinsic Peak Height3 |
Protein Bend Peak Height3 |
Promoter Sequence (5'3')4 -35 -10 (+1) |
ML gfp Express5 |
| ML0086c | -77 | 10.4 | 9.5 | AATCAGccagagcaggcgagcaaaCTGAAT--acagtcccgT | + |
| Rv3817 | TATGCGccaggacaagcgagcaagCCGAAT--acggtgccgT | ||||
| ML0211 | -100 | 5.8 | 5.6 | TCACGTcgaattgcaccgtgtcggCCTTAAatct---agctA | + |
| Rv3627 | TCACGTcgaattggcacgcgtcggCCTTCAgatcagagtgcA | ||||
| ML0357c | -86 | 6.5 | 6.5 | GTTGCTggaattc-acactagaacGTGTTA--atcagcaagA | + |
| Rv3504 | GTCGCTggattcagagactagaacGTGTTAcaaccgggaagA | ||||
| ML0531 | -44 | 5.5 | 7.8 | TAGGCTgcccggcagtcgacgtCCTTTAtc-----gatccgT | + |
| Rv1379 | TACGCTgccgagcggtcgacatCCTTTAac-----gatccgT | ||||
| ML0585c | -31 | 8 | 8 | GCCAACacgatgtggggatggaAGAGGTct-----ggtcgtG | + |
| Rv1454c | GCCAAAacgacgcgcggatggaAGACGTcc-----ggccggG | ||||
| ML0684 | -128 | 6.8 | 8.6 | ACGCTGgcgctcatgaccgcgttgcAGCCTA--ccgtatcgC | + |
| Rv3339 | ACGCTGgcgctcatgaccgactcgaAGCCTA--gcgcatggC | ||||
| ML1295c | -89 | 5.6 | 8 | CGGTGAcagtcatactgtcaagaTACCTCatcccgaaccggT | + |
| Rv 2138 | CGGTGAcggtcatgcccagagaaTACCTC-tggagtaccatT | ||||
| ML1674 | -81 | 7.8 | 7.2 | GTGGTTgcccacaacagtcgcTATCCTgag-------ctggC | + |
| MUL1983 | GTGCTTgccggggac-gtcggTATCCTagg-------acggC | ||||
| ML2282c | -92 | 7.5 | 6.2 | TGTGTAgctttcgcgacggattTACAGTcc-----gctcccA | + |
| Rv0566 | TGCGTAgctttcgcgacggattTACAGTcc-----gctcccA | ||||
| ML2521 | -102 | 9 | 9 | ATGACAaagtggtcgatcacatgcCCGATC--accagcaatT | + |
| Rv0310 | ATGCCCgatcggtcgatcagctggCCGATC--aacaacagcT | ||||
| ML0416 | -103 | 7.8 | 9 | GTTAAAaacgtgtttaagagttGAAGAGgg-----ggttaaC | ND |
| MAV4335 | GTTAAGaccttgtttaggagttGAAGATcg-----gtttaaC | ||||
| ML0459 | -89 | 6.8 | 11 | ACCTTCaggtcgccaccgagcgTGAACGct-----ccggatG | ND |
| Rv2616 | ACGGTCaggtcgccgccgagggTCAACGtt-----ccggatG | ||||
| ML1335c | -56 | 6.7 | 10.2 | TACACTtcggtttctaatctgtg-gaATCCAT--ggcagtcA | ND |
| Rv2090 | TAAACCtcggcgtcgaatcggcgagaACCCAT--gtcagccA | ||||
| ML1503c | -105 | 9.8 | 9 | AGTGCCgcgtctacttgctcatcAGTTAGcac----agccaT | ND |
| Rv1160 | AGTGCGgcgtcgacctgctcatcCGTTAAcac----agccaT | ||||
| ML2325c | -110 | 6.2 | 7.1 | GTGCAGtttagggcgatcgTAAGCGcggcgct--------tG | ND |
| Rv3711 | GTTGGAttcagggcgatcgCAAGCTcggcgct--------tG |
1Mycobacterium leprae gene #: http://genolist.pasteur.fr/Leproma/.
2Mycobacterial orthologous gene: Rv = M. tuberculosis H37Rv http://genolist.pasteur.fr/Tuberculist/.; MUL = M. ulcerans http://genolist.pasteur.fr/BuruList/.; and MAV = M. avium http://www.ncbi.nlm.nih.gov/sites/entrez?.
3Bend-it analysis of pseudogenes.
4Alignment of mycobacterial promoters performed using ClustalW: http://www.ebi.ac.uk/Tools/clustalw2/index.html.
5PCR-amplified promoter-like regions of M. leprae genes (Additional File 6) were cloned into pGlow-TOPO-TA promoterless reporter-gfp vector and expressed in E. coli XL1-Blue Supercompetent cells. (+) = positive for GFP expression using fluorescent microscopy.
6ND = not done