M35 box gene transcriptions

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

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 σ^s 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:

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.
negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesM35-+.bas, looking for 3'-TTGACA-5', 0,
positive strand in the negative direction is SuccessablesM35+-.bas, looking for 3'-TTGACA-5', 0,
positive strand in the positive direction is SuccessablesM35++.bas, looking for 3'-TTGACA-5', 0,
complement, negative strand, negative direction is SuccessablesM35c--.bas, looking for 3'-AACTGT-5', 0,
complement, negative strand, positive direction is SuccessablesM35c-+.bas, looking for 3'-AACTGT-5', 0,
complement, positive strand, negative direction is SuccessablesM35c+-.bas, looking for 3'-AACTGT-5', 2, 3'-AACTGT-5', 477, 3'-AACTGT-5', 4399,
complement, positive strand, positive direction is SuccessablesM35c++.bas, looking for 3'-AACTGT-5', 0,
inverse complement, negative strand, negative direction is SuccessablesM35ci--.bas, looking for 3'-TGTCAA-5', 0,
inverse complement, negative strand, positive direction is SuccessablesM35ci-+.bas, looking for 3'-TGTCAA-5', 0,
inverse complement, positive strand, negative direction is SuccessablesM35ci+-.bas, looking for 3'-TGTCAA-5', 0,
inverse complement, positive strand, positive direction is SuccessablesM35ci++.bas, looking for 3'-TGTCAA-5', 0,
inverse, negative strand, negative direction, is SuccessablesM35i--.bas, looking for 3'-ACAGTT-5', 0,
inverse, negative strand, positive direction, is SuccessablesM35i-+.bas, looking for 3'-ACAGTT-5', 0,
inverse, positive strand, negative direction, is SuccessablesM35i+-.bas, looking for 3'-ACAGTT-5', 0,
inverse, positive strand, positive direction, is SuccessablesM35i++.bas, looking for 3'-ACAGTT-5', 0.

M35 UTRs

Negative, negative: TTGACA at 4399.

M35 negative direction distal promoters

Negative, negative: TTGACA at 477.

M35 random dataset samplings

M35r0: 2, TTGACA at 3699, TTGACA at 3168.
M35r1: 1, TTGACA at 3785.
M35r2: 0.
M35r3: 0.
M35r4: 1, TTGACA at 1412.
M35r5: 0.
M35r6: 1, TTGACA at 3332.
M35r7: 1, TTGACA at 3816.
M35r8: 1, TTGACA at 1179.
M35r9: 0.
M35r0ci: 2, TGTCAA at 3593, TGTCAA at 1157.
M35r1ci: 1, TGTCAA at 3514.
M35r2ci: 1, TGTCAA at 2691.
M35r3ci: 2, TGTCAA at 3612, TGTCAA at 102.
M35r4ci: 0.
M35r5ci: 0.
M35r6ci: 0.
M35r7ci: 1, TGTCAA at 1534.
M35r8ci: 1, TGTCAA at 591.
M35r9ci: 2, TGTCAA at 3574, TGTCAA at 1821.

M35r arbitrary (evens) (4560-2846) UTRs

M35r0: TTGACA at 3699, TTGACA at 3168.
M35r6: TTGACA at 3332.
M35r0ci: TGTCAA at 3593.

M35r alternate (odds) (4560-2846) UTRs

M35r1: TTGACA at 3785.
M35r7: TTGACA at 3816.
M35r1ci: TGTCAA at 3514.
M35r3ci: TGTCAA at 3612.
M35r9ci: TGTCAA at 3574.

M35r arbitrary negative direction (evens) (2811-2596) proximal promoters

M35r2ci: TGTCAA at 2691.

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

M35r4: TTGACA at 1412.
M35r0ci: TGTCAA at 1157.
M35r8ci: TGTCAA at 591.

M35r alternate negative direction (odds) (2596-1) distal promoters

M35r8: TTGACA at 1179.
M35r3ci: TGTCAA at 102.
M35r7ci: TGTCAA at 1534.
M35r9ci: TGTCAA at 1821.

M35r arbitrary positive direction (odds) (4050-1) distal promoters

M35r1: TTGACA at 3785.
M35r7: TTGACA at 3816.
M35r1ci: TGTCAA at 3514.
M35r3ci: TGTCAA at 102.
M35r7ci: TGTCAA at 1534.
M35r9ci: TGTCAA at 3574, TGTCAA at 1821.

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

M35r0: TTGACA at 3699, TTGACA at 3168.
M35r4: TTGACA at 1412.
M35r6: TTGACA at 3332.
M35r0ci: TGTCAA at 3593, TGTCAA at 1157.
M35r2ci: TGTCAA at 2691.
M35r8ci: TGTCAA at 591.

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	1	2	0.5	0.5 ± 0.5 (--1,+-0)
Randoms	UTR	arbitrary negative	4	10	0.4	0.45
Randoms	UTR	alternate negative	5	10	0.5	0.45
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	1	10	0.1	0.05
Randoms	Proximal	alternate negative	0	10	0	0.05
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	1	2	0.5	0.5 ± 0.5 (--1,+-0)
Randoms	Distal	arbitrary negative	3	10	0.3	0.35
Randoms	Distal	alternate negative	4	10	0.4	0.35
Reals	Distal	positive	0	2	0	0
Randoms	Distal	arbitrary positive	7	10	0.7	0.75
Randoms	Distal	alternate positive	8	10	0.8	0.75

Comparison:

The occurrences of real M35s are greater than the randoms. This suggests that the real M35s 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.

References

↑ ^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.
↑ Athanasios Typas, Stefano Stella, Reid C. Johnson and Regine Hengge (9 January 2007). "The -35 sequence location and the Fis–sigma factor interface determine σ^s 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

Template:Sisterlinks

[Boer-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.

[Typas-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 σ^s 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.

[1]

[2]

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