M35 box gene transcriptions

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Associate Editor(s)-in-Chief: Henry A. Hoff

File:Escherichia coli - MUSE.jpg
Escherichia coli - Sculpture is in vitro. Credit: Luke Jerram.{{free media}}

"The trp promoter does not have a consensus Pribnow box sequence (T-T-A-A-C-T) but it does have a consensus -35 sequence (T-T-G-A-C-A)."[1]

The "degenerate -35 sequence, and the location of the Fis binding site, which forces a suboptimal 16 bp spacing between the -35 and -10 elements, allow only σs but not σ70 to function at proP (P2).[2]

Consensus sequences

"Two domains upstream of the start site of transcription have been identified for which a consensus sequence has been formulated (1-5). [One of these domains is] the -35 sequence (5'-T-T-G-A-C-A-3')".[1]

A1BG sampling

For the Basic programs (starting with SuccessablesM35.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesM35--.bas, looking for 3'-TTGACA-5', 2, 2, TTGACA at 4399, TTGACA at 477.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesM35-+.bas, looking for 3'-TTGACA-5', 0,
  3. positive strand in the negative direction is SuccessablesM35+-.bas, looking for 3'-TTGACA-5', 0,
  4. positive strand in the positive direction is SuccessablesM35++.bas, looking for 3'-TTGACA-5', 0,
  5. complement, negative strand, negative direction is SuccessablesM35c--.bas, looking for 3'-AACTGT-5', 0,
  6. complement, negative strand, positive direction is SuccessablesM35c-+.bas, looking for 3'-AACTGT-5', 0,
  7. complement, positive strand, negative direction is SuccessablesM35c+-.bas, looking for 3'-AACTGT-5', 2, 3'-AACTGT-5', 477, 3'-AACTGT-5', 4399,
  8. complement, positive strand, positive direction is SuccessablesM35c++.bas, looking for 3'-AACTGT-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesM35ci--.bas, looking for 3'-TGTCAA-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesM35ci-+.bas, looking for 3'-TGTCAA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesM35ci+-.bas, looking for 3'-TGTCAA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesM35ci++.bas, looking for 3'-TGTCAA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesM35i--.bas, looking for 3'-ACAGTT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesM35i-+.bas, looking for 3'-ACAGTT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesM35i+-.bas, looking for 3'-ACAGTT-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesM35i++.bas, looking for 3'-ACAGTT-5', 0.

M35 UTRs

  1. Negative, negative: TTGACA at 4399.

M35 negative direction distal promoters

  1. Negative, negative: TTGACA at 477.

M35 random dataset samplings

  1. M35r0: 2, TTGACA at 3699, TTGACA at 3168.
  2. M35r1: 1, TTGACA at 3785.
  3. M35r2: 0.
  4. M35r3: 0.
  5. M35r4: 1, TTGACA at 1412.
  6. M35r5: 0.
  7. M35r6: 1, TTGACA at 3332.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

M35r arbitrary (evens) (4560-2846) UTRs

  1. M35r0: 2, TTGACA at 3699, TTGACA at 3168.
  2. M35r6: TTGACA at 3332.

M35r alternate (odds) (4560-2846) UTRs

  1. M35r1: TTGACA at 3785.

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

M35r arbitrary negative direction (evens) (2596-1) distal promoters

  1. M35r4: TTGACA at 1412.

RDr alternate negative direction (odds) (2596-1) distal promoters

RDr arbitrary positive direction (odds) (4050-1) distal promoters

  1. M35r1: TTGACA at 3785.

M35r alternate positive direction (evens) (4050-1) distal promoters

  1. M35r0: TTGACA at 3699, TTGACA at 3168.
  2. M35r4: TTGACA at 1412.
  3. M35r6: TTGACA at 3332.

M35 analysis and results

"Two domains upstream of the start site of transcription have been identified for which a consensus sequence has been formulated (1-5). [One of these domains is] the -35 sequence (5'-T-T-G-A-C-A-3')".[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikiversity.

Initial content for this page in some instances incorporates text from the United States National Library of Medicine.

See also

References

  1. 1.0 1.1 1.2 Herman A. de Boer, Lisa J. Comstock, and Mark Vasser (January 1983). "The tac promoter: A functional hybrid derived from the trp and lac promoters" (PDF). Proceedings of the National Academy of Sciences USA. 80 (1): 21–5. Retrieved 2017-02-19.
  2. Athanasios Typas, Stefano Stella, Reid C. Johnson and Regine Hengge (9 January 2007). "The -35 sequence location and the Fis–sigma factor interface determine σs selectivity of the proP (P2) promoter in Escherichia coli". Molecular Microbiology. 63 (3): 780–796. doi:10.1111/j.1365-2958.2006.05560.x. Retrieved 10 November 2018.

External links

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