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Table 3 Analysis of M. leprae pseudogene promoters in silico and in vitro promoter in E. coli analyses.

From: Implications of high level pseudogene transcription in Mycobacterium leprae

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

AATCAG ccagagcaggcgagcaaaCTGAAT-- acagtcccgT

+

Rv3817

   

TATGCG ccaggacaagcgagcaagCCGAAT-- acggtgccgT

 

ML0211

-100

5.8

5.6

TCACGT cgaattgcaccgtgtcggCCTTAA atct---agctA

+

Rv3627

   

TCACGT cgaattggcacgcgtcggCCTTCA gatcagagtgcA

 

ML0357c

-86

6.5

6.5

GTTGCT ggaattc-acactagaacGTGTTA--atcagcaagA

+

Rv3504

   

GTCGCT ggattcagagactagaacGTGTTA caaccgggaagA

 

ML0531

-44

5.5

7.8

TAGGCT gcccggcagtcgacgtCCTTTA tc-----gatccgT

+

Rv1379

   

TACGCT gccgagcggtcgacatCCTTTA ac-----gatccgT

 

ML0585c

-31

8

8

GCCAAC acgatgtggggatggaAGAGGTct-----ggtcgtG

+

Rv1454c

   

GCCAAA acgacgcgcggatggaAGACGT cc-----ggccggG

 

ML0684

-128

6.8

8.6

ACGCTG gcgctcatgaccgcgttgcAGCCTA-- ccgtatcgC

+

Rv3339

   

ACGCTG gcgctcatgaccgactcgaAGCCTA-- gcgcatggC

 

ML1295c

-89

5.6

8

CGGTGA cagtcatactgtcaagaTACCTC atcccgaaccggT

+

Rv 2138

   

CGGTGA cggtcatgcccagagaaTACCTC-tggagtaccatT

 

ML1674

-81

7.8

7.2

GTGGTT gcccacaacagtcgcTATCCT gag-------ctggC

+

MUL1983

   

GTGCTT gccggggac-gtcggTATCCT agg-------acggC

 

ML2282c

-92

7.5

6.2

TGTGTAgctttcgcgacggattTACAGT cc-----gctcccA

+

Rv0566

   

TGCGTA gctttcgcgacggattTACAGT cc-----gctcccA

 

ML2521

-102

9

9

ATGACA aagtggtcgatcacatgcCCGATC-- accagcaatT

+

Rv0310

   

ATGCCC gatcggtcgatcagctggCCGATC-- aacaacagcT

 

ML0416

-103

7.8

9

GTTAAA aacgtgtttaagagttGAAGAG gg-----ggttaaC

ND

MAV4335

   

GTTAAG accttgtttaggagttGAAGAT cg-----gtttaaC

 

ML0459

-89

6.8

11

ACCTTC aggtcgccaccgagcgTGAACG ct-----ccggatG

ND

Rv2616

   

ACGGTC aggtcgccgccgagggTCAACG tt-----ccggatG

 

ML1335c

-56

6.7

10.2

TACACT tcggtttctaatctgtg-gaATCCAT-- ggcagtcA

ND

Rv2090

   

TAAACC tcggcgtcgaatcggcgagaACCCAT-- gtcagccA

 

ML1503c

-105

9.8

9

AGTGCC gcgtctacttgctcatcAGTTAG cac----agccaT

ND

Rv1160

   

AGTGCG gcgtcgacctgctcatcCGTTAA cac----agccaT

 

ML2325c

-110

6.2

7.1

GTGCAG tttagggcgatcgTAAGCG cggcgct--------tG

ND

Rv3711

   

GTTGGA ttcagggcgatcgCAAGCT cggcgct--------tG

 
  1. 1Mycobacterium leprae gene #: http://genolist.pasteur.fr/Leproma/.
  2. 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?.
  3. 3Bend-it analysis of pseudogenes.
  4. 4Alignment of mycobacterial promoters performed using ClustalW: http://www.ebi.ac.uk/Tools/clustalw2/index.html.
  5. 5PCR-amplified promoter-like regions of M. leprae genes (Additional File 6) were cloned into p Glow-TOPO-TA promoterless reporter-gfp vector and expressed in E. coli XL1-Blue Supercompetent cells. (+) = positive for GFP expression using fluorescent microscopy.
  6. 6ND = not done
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BMC Genomics

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