K-box gene transcriptions

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

"In fact, the groE genes were greatly induced upon heat shock in the hrcA mutant which was dark-treated prior to the heat shock in order to keep the background initial level of the groE mRNA accumulation as low as possible. These results led us to find a novel regulatory sequence which is involved in a heat and/or light mediated regulation of the groESL1 operon (Kojima and Nakamoto, 2007). This DNA element (GTTCGG-NNAN-CCNNAC) is located upstream of the groE promoters. It is highly conserved among the groESL1 operons from various cyanobacterial genomes. We designated this DNA element to be K-box. Removal of the K-box containing region upstream of the groESL1 promoter abolished heat- and/or light-induced transcription of the operon completely. K-box is also present upstream of dnaK2, one of the three dnaK genes in cyanobacteria (Kojima and Nakamoto, 2007; Sato et al., 2007)."^[1]

K-box samplings

Copying a responsive elements consensus sequence GTTCGG-NNAN-CCNNAC and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GTTCGGNNANCCNNAC (starting with SuccessablesK-box.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, negative direction, looking for GTTCGGNNANCCNNAC, 0.
positive strand, negative direction, looking for GTTCGGNNANCCNNAC, 0.
positive strand, positive direction, looking for GTTCGGNNANCCNNAC, 0.
negative strand, positive direction, looking for GTTCGGNNANCCNNAC, 0.
complement, negative strand, negative direction, looking for CAAGCCNNTNGGNNTG, 0.
complement, positive strand, negative direction, looking for CAAGCCNNTNGGNNTG, 0.
complement, positive strand, positive direction, looking for CAAGCCNNTNGGNNTG, 0.
complement, negative strand, positive direction, looking for CAAGCCNNTNGGNNTG, 0.
inverse complement, negative strand, negative direction, looking for GTNNGGNTNNCCGAAC, 0.
inverse complement, positive strand, negative direction, looking for GTNNGGNTNNCCGAAC, 0.
inverse complement, positive strand, positive direction, looking for GTNNGGNTNNCCGAAC, 0.
inverse complement, negative strand, positive direction, looking for GTNNGGNTNNCCGAAC, 0.
inverse negative strand, negative direction, looking for CANNCCNANNGGCTTG, 0.
inverse positive strand, negative direction, looking for CANNCCNANNGGCTTG, 0.
inverse positive strand, positive direction, looking for CANNCCNANNGGCTTG, 0.
inverse negative strand, positive direction, looking for CANNCCNANNGGCTTG, 0.

K-box1 samplings

Copying a responsive elements consensus sequence GTTCGG and putting the sequence in "⌘F" finds one between ZNF497 and A1BG and one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GTTCGG (starting with SuccessablesK-box1.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, negative direction: 1, GTTCGG at 456.
Positive strand, negative direction: 0.
Negative strand, positive direction: 0.
Positive strand, positive direction: 1, GTTCGG at 340.
inverse complement, negative strand, negative direction: 1, CCGAAC at 3400.
inverse complement, positive strand, negative direction: 0.
inverse complement, negative strand, positive direction: 0.
inverse complement, positive strand, positive direction: 0.

K-box1 (4560-2846) UTRs

Negative strand, negative direction: CCGAAC at 3400.

K-box1 negative direction (2596-1) distal promoters

Negative strand, negative direction: GTTCGG at 456.

K-box1 positive direction (4050-1) distal promoters

Positive strand, positive direction: GTTCGG at 340.

K-box1 random dataset samplings

K-box1r0: 0.
K-box1r1: 2, GTTCGG at 2953, GTTCGG at 1973.
K-box1r2: 0.
K-box1r3: 0.
K-box1r4: 1, GTTCGG at 572.
K-box1r5: 4, GTTCGG at 4482, GTTCGG at 3770, GTTCGG at 3288, GTTCGG at 2589.
K-box1r6: 4, GTTCGG at 2411, GTTCGG at 1949, GTTCGG at 864, GTTCGG at 120.
K-box1r7: 0.
K-box1r8: 0.
K-box1r9: 1, GTTCGG at 503.
K-box1r0ci: 1, CCGAAC at 670.
K-box1r1ci: 1, CCGAAC at 3187.
K-box1r2ci: 3, CCGAAC at 4057, CCGAAC at 2236, CCGAAC at 1530.
K-box1r3ci: 2, CCGAAC at 1397, CCGAAC at 672.
K-box1r4ci: 1, CCGAAC at 3814.
K-box1r5ci: 2, CCGAAC at 3068, CCGAAC at 2890.
K-box1r6ci: 2, CCGAAC at 2719, CCGAAC at 1604.
K-box1r7ci: 1 CCGAAC at 42.
K-box1r8ci: 0.
K-box1r9ci: 1, CCGAAC at 2101.

K-box1r arbitrary (evens) (4560-2846) UTRs

K-box1r2ci: CCGAAC at 4057.
K-box1r4ci: CCGAAC at 3814.

K-box1r alternate (odds) (4560-2846) UTRs

K-box1r1: GTTCGG at 2953.
K-box1r5: GTTCGG at 4482, GTTCGG at 3770, GTTCGG at 3288.
K-box1r1ci: CCGAAC at 3187.
K-box1r5ci: CCGAAC at 3068, CCGAAC at 2890.

K-box1r arbitrary negative direction (evens) (2811-2596) proximal promoters

K-box1r6ci: CCGAAC at 2719.

K-box1r alternate positive direction (evens) (4265-4050) proximal promoters

K-box1r2ci: CCGAAC at 4057.

K-box1r arbitrary negative direction (evens) (2596-1) distal promoters

K-box1r4: GTTCGG at 572.
K-box1r6: GTTCGG at 2411, GTTCGG at 1949, GTTCGG at 864, GTTCGG at 120.
K-box1r0ci: CCGAAC at 670.
K-box1r2ci: CCGAAC at 2236, CCGAAC at 1530.
K-box1r6ci: CCGAAC at 1604.

K-box1r alternate negative direction (odds) (2596-1) distal promoters

K-box1r1: GTTCGG at 1973.
K-box1r5: GTTCGG at 2589.
K-box1r9: GTTCGG at 503.
K-box1r3ci: CCGAAC at 1397, CCGAAC at 672.
K-box1r7ci: CCGAAC at 42.
K-box1r9ci: CCGAAC at 2101.

K-box1r arbitrary positive direction (odds) (4050-1) distal promoters

K-box1r1: GTTCGG at 2953, GTTCGG at 1973.
K-box1r5: GTTCGG at 3770, GTTCGG at 3288, GTTCGG at 2589.
K-box1r9: GTTCGG at 503.
K-box1r1ci: CCGAAC at 3187.
K-box1r3ci: CCGAAC at 1397, CCGAAC at 672.
K-box1r5ci: CCGAAC at 3068, CCGAAC at 2890.
K-box1r7ci: CCGAAC at 42.
K-box1r9ci: CCGAAC at 2101.

K-box1r alternate positive direction (evens) (4050-1) distal promoters

K-box1r4: GTTCGG at 572.
K-box1r6: GTTCGG at 2411, GTTCGG at 1949, GTTCGG at 864, GTTCGG at 120.
K-box1r0ci: CCGAAC at 670.
K-box1r4ci: CCGAAC at 3814.
K-box1r6ci: CCGAAC at 2719, CCGAAC at 1604.

K-box1 analysis and results

"This DNA element (GTTCGG-NNAN-CCNNAC) is located upstream of the groE promoters."^[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	2	10	0.2	0.45 ± 0.25
Randoms	UTR	alternate negative	7	10	0.7	0.45 ± 0.25
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	0.05
Randoms	Proximal	alternate positive	1	10	0.1	0.05
Reals	Distal	negative	1	2	0.5	0.5 ± 0.5 (--1,+-0)
Randoms	Distal	arbitrary negative	9	10	0.9	0.8 ± 0.1
Randoms	Distal	alternate negative	7	10	0.7	0.8 ± 0.1
Reals	Distal	positive	1	2	0.5	0.5 ± 0.5 (-+0,++1)
Randoms	Distal	arbitrary positive	13	10	1.3	1.05 ± 0.25
Randoms	Distal	alternate positive	9	10	0.9	1.05 ± 0.25

Comparison:

The occurrences of real K-box1 UTRs and negative direction distals are greater than the randoms. The positive direction distals are likely random. This suggests that the real K-box1s are likely active or activable.

Acknowledgements

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

References

↑ ^1.0 ^1.1 Masakazu Saito, Satoru Watanabe, Kaori Nimura-Matsune, Hirofumi Yoshikawa, Hitoshi Nakamoto (10 April 2020). "Regulation of the groESL1 transcription by the HrcA repressor and a novel transcription factor Orf7.5 in the cyanobacterium Synechococcus elongatus PCC7942". The Journal of General and Applied Microbiology. 66 (2): 85–92. doi:10.2323/jgam.2020.02.001. Retrieved 17 March 2021.

External links

[Saito-1] 1.0 ^1.1 Masakazu Saito, Satoru Watanabe, Kaori Nimura-Matsune, Hirofumi Yoshikawa, Hitoshi Nakamoto (10 April 2020). "Regulation of the groESL1 transcription by the HrcA repressor and a novel transcription factor Orf7.5 in the cyanobacterium Synechococcus elongatus PCC7942". The Journal of General and Applied Microbiology. 66 (2): 85–92. doi:10.2323/jgam.2020.02.001. Retrieved 17 March 2021.

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transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions