title 'LexA version = 3.23 of lexa.inst 2022 Aug 01'; (* 2022 Aug 01, 3.23: clean up 2022 Aug 01, 3.22: document delila 2022 Aug 01, 3.21: add bibliography at end!!! 2022 Aug 01, 3.20: Switch to version 3: NC_000913.3 I used sebo.p and seboxfr 2022 Jul 31, 3.19: make instructions uniform for upgrade 2020 Sep 11, 3.18: FernandezDeHenestrosa.Woodgate2000 2011 Jun 03, 3.17: no version number on pieces from dbbk 2011 Jun 02, 3.16: To track GenBank, rename: E.coli-str.-K12-substr.-MG1655 to E.coli-str.-K-12-substr.-MG1655 and add version number to piece. 2008 Oct 20, 3.15: yebG 2008 Oct 17, 3.14: official version 2008 Oct 16, 3.13: switch to E.coli-str.-K12-substr.-MG1655 2008 Apr 24, 3.12: dinD 2008 Apr 24, 3.11: ydjM 2008 Apr 23, 3.10: checking 2008 Apr 19, 3.09: a bunch more ... 2008 Apr 19, 3.08: finish recN 2008 Apr 19, 3.07: umuD cleanup. 2008 Apr 19, 3.06: umuD 2008 Apr 18, 3.05: uvrD 2008 Apr 17, 3.04: uvrD is next 2008 Apr 17, 3.03: uvrA done, uvrB, sulA=sfiA 2008 Apr 17, 3.02: uvrA started 2008 Apr 17, 3.01: lexA and recA done 2008 Apr 16, 3.00: rebuild entirely for E. coli genome. 2006 Feb 20, 1.00: add direction to instructions originally: module lexa version = 1.21 of sitein 1991 Feb 5 *) (* This file contains Delila instructions for grabbing the binding sites of the LexA protein of E. coli. The file is stored at: https://alum.mit.edu/www/toms/lexa.inst Information about how to use Delila is at: https://alum.mit.edu/www/toms References at the end are in Bibtex format for use with LaTeX. https://alum.mit.edu/www/toms/latex.html Thomas D. Schneider, Ph.D. *) set out-of-range reduce-range; organism E.coli-str.-K-12-substr.-MG1655; chromosome E.coli-str.-K-12-substr.-MG1655; piece NC_000913.3; (* complete genome *) (****************************************************************) (****************************************************************) (* Proven LexA binding sites - DNase I or mutation **************) (****************************************************************) (****************************************************************) (* lexA \cite{Little.Yanisch-Perron1981} figure 3B DNase I; \cite{Brent.Ptashne1981} Figure 1 DNase I *) (* original name: ecolexa *) name "lexA-1"; get from 4257077 -200 to same +200 direction +; name "lexA-1"; get from 4257078 +200 to same -200 direction -; name "lexA-2"; get from 4257098 -200 to same +200 direction +; name "lexA-2"; get from 4257099 +200 to same -200 direction -; (* lexA \cite{Little.Yanisch-Perron1981} figure 3A DNase I; \cite{Brent.Ptashne1981} Figure 1 DNase I *) (* original name: ecoreca *) name "recA"; get from 2823838 -200 to same +200 direction +; name "recA"; get from 2823839 +200 to same -200 direction -; (* uvrA \cite{Sancar.Mount1982} figure 1 DNase I ssb is in the opposite direction. *) (* original name: ecouvra DNase I *) name "uvrA"; get from 4273964 -200 to same +200 direction +; name "uvrA"; get from 4273965 +200 to same -200 direction -; (* uvrB \cite{Sancar.Rupp1982} figure 2 DNase I *) (* original name: ecouvrb *) name "uvrB"; get from 813441 -200 to same +200 direction +; name "uvrB"; get from 813442 +200 to same -200 direction -; (* ompA *) (* This site is right in front of sulA. ompA is downstream of sulA (1020142). So sulA is now listed by everyone but not ompA (1019276). There is no lexA site >10 bits between the end of sulA and the start of ompA. There is only a bad (black letter) 3 bit lexA site between them. So this was misnamed when I first did it! *) (* original name: ecoompaii *) {NAME "ompA"; GET FROM 1019276 -200 to same +200 direction +;} {NAME "ompA"; GET FROM 1019277 +200 to same -200 direction -;} (* I capitalized the instructions so they will never be recognized. *) (* sulA Cole1983 Figure 4b \cite{Mizusawa.Gottesman1983} consensus match on known promoter. This was originally called ecoompaii, see above. Original name: sulA Berg1988e. So there was a duplication in my previous list!! tactgtacatccatacagta were identical. Also sulA = sfiA (synonym) *) name "sulA"; get from 1020951 -200 to same +200 direction +; name "sulA"; get from 1020952 +200 to same -200 direction -; (* uvrD \cite{Easton.Kushner1983} figure 5 DNase I *) (* original name: uvrD Berg1988e *) name "uvrD"; get from 3997916 -200 to same +200 direction +; name "uvrD"; get from 3997917 +200 to same -200 direction -; (* umuD \cite{Kitagawa.Kato1985} figure 6 DNase I *) (* original name: umuDC Berg1988e *) name "umuD"; get from 1230737 -200 to same +200 direction +; name "umuD"; get from 1230738 +200 to same -200 direction -; (* recN \cite{Rostas.Lloyd1987} figure 2 DNase I but data not shown for recN-1 and recN-2 (see page 5048) and EMSA figure 3. Though Rostas.Lloyd1987 don't seem to notice, there are three discrete bands in the EMSA. So there clearly are three sites. No other data are available for recN-3, it is mentioned in \cite{FernandezDeHenestrosa.Woodgate2000}. RecN-3 is listed in the database of \cite{Robison.Church1998} http://arep.med.harvard.edu/dpinteract/ but the references do not work anymore. --- \cite{Lewis.Mount1994} (page 510) point to \cite{Schnarr.Granger-Schnarr1991} who say it is recN-3 is cooperatively bound (page 427). They say "M Kazmaier, MGS and MS in preparation", however PubMed search for "Kazmaier Schnarr" on 2008 Apr 23 gave no additional papers! *) (* original name: recN-1 Berg1988e *) (* original name: recN-2 Berg1988e *) name "recN-1"; get from 2751736 -200 to same +200 direction +; name "recN-1"; get from 2751737 +200 to same -200 direction -; name "recN-2"; get from 2751758 -200 to same +200 direction +; name "recN-2"; get from 2751759 +200 to same -200 direction -; name "recN-3"; get from 2751776 -200 to same +200 direction +; name "recN-3"; get from 2751777 +200 to same -200 direction -; (* ruv \cite{Shinagawa.Nakata1988} figure 7 DNase I, figure 2 sequence *) name "ruv"; get from 1946035 -200 to same +200 direction +; name "ruv"; get from 1946036 +200 to same -200 direction -; (* sbmC \cite{Baquero.Moreno1995} mutation. See also \cite{Courcelle.Hanawalt2001} Table 1 *) name "sbmC"; get from 2081286 -200 to same +200 direction +; name "sbmC"; get from 2081287 +200 to same -200 direction -; (* polB \cite{Lewis.Mount1994} Figure 1a EMSA, Table 2 polB = dinA *) name "polB=dinA"; get from 65843 -200 to same +200 direction +; name "polB=dinA"; get from 65844 +200 to same -200 direction -; (* ftsK \cite{Lewis.Mount1994} Figure 1b EMSA, Table 2 ftsK = dinH. See \cite{Lewis.Mount1994} - dinH is downstream of lrp and that gene is now called ftsK. *) name "ftsK=dinH"; get from 933137 -200 to same +200 direction +; name "ftsK=dinH"; get from 933138 +200 to same -200 direction -; (* dinI \cite{Lewis.Mount1994} Figure 3 EMSA, Figure 4 EMSA, Table 2 dinI is downstream of pyrC, see \cite{Yasuda.Ohmori1996} *) name "dinI"; get from 1121516 -200 to same +200 direction +; name "dinI"; get from 1121517 +200 to same -200 direction -; (* sosC \cite{Lewis.Mount1994} Figure 7a EMSA, Figure 9 *) name "sosC=hsdS"; get from 4579925 -200 to same +200 direction +; name "sosC=hsdS"; get from 4579926 +200 to same -200 direction -; (* sosD \cite{Lewis.Mount1994} Figure 7b EMSA, Figure 9 *) name "sosD"; get from 1823491 -200 to same +200 direction +; name "sosD"; get from 1823492 +200 to same -200 direction -; (* dinG \cite{Lewis.Mount1994} Table 2; \cite{Lewis.Mount1992b} Table 1 mutations; Figure 1 EMSA. *) name "dinG"; get from 833045 -200 to same +200 direction +; name "dinG"; get from 833046 +200 to same -200 direction -; (* ydjM \cite{Fernandez_De_Henestrosa.Woodgate2000} EMSA: Figure 4, DNase I: Figure 5. *) name "ydjM-1"; get from 1810186 -200 to same +200 direction +; name "ydjM-1"; get from 1810187 +200 to same -200 direction -; name "ydjM-2"; get from 1810168 -200 to same +200 direction +; name "ydjM-2"; get from 1810169 +200 to same -200 direction -; (* @ NC_000913 1808192.0 +1 "lexA" "10.8 bits @ 1808192" 10.837679 -2.701801 0.003448 @ NC_000913 1808210.0 +1 "lexA" "17.8 bits @ 1808210" 17.841963 -0.876828 0.190290 @ NC_000913 1808418.0 +1 "lexA" " 8.7 bits @ 1808418" 8.674640 -3.265383 0.000547 *) (************************************************************************) (************************************************************************) (* Genes known to be under LexA control with moderate experimental data *) (************************************************************************) (************************************************************************) (* dinD \cite{Yasuda.Ohmori1996} \cite{Ohmori.Nagai1995} pcsA = dinD. Listed in the database of \cite{Robison.Church1998} and listed in Table 1 of \cite{Fernandez_De_Henestrosa.Woodgate2000} without a reference! Lewis.Mount1994 Figure 9 and Figure 10. This is supposed to be a real site, but there is no direct evidence! However the indirect evidence is quite strong. Ohmori.Nagai1995 (page 160) measured control with fused lacZ, 3816132 is the location of the AluI site. The region 3815508 to 3816137 covers AluI region that was induced. There really is only one strong site in the region, about 24 bits. There is also a weaker 6 bit site upstream. *) name "dinD"; get from 3817706 -200 to same +200 direction +; name "dinD"; get from 3817707 +200 to same -200 direction -; (* yebG \cite{Lomba.de_Almeida1997} (59 bp sequence) \cite{Kuhner.Gaub2004} (AFM data on sequence that is too short). *) name "yebG"; get from 1930774 -200 to same +200 direction +; name "yebG"; get from 1930775 +200 to same -200 direction -; (**********************************************************************) (**********************************************************************) (* Genes known to be under LexA control but no experimental data ******) (**********************************************************************) (**********************************************************************) (* uvrC nocite{Stark.Moses1989} Figure 2, Figure3 EMSA. nocite{Sharma.Moses1986} sequence data. No LexA model fell into the right places. The data are unclear. DO NOT USE. NAME "uvrC"; GET FROM 1994100 -200 to same +200 direction +; NAME "uvrC"; GET FROM 1994100 +200 to same -200 direction -; I capitalized the instructions so they will never be recognized. *) (***********************************************************************) (***********************************************************************) (* Sites dropped because they are not on the E. coli Chromosome ********) (***********************************************************************) (***********************************************************************) (* mucAB - Plasmid J Bacteriol. 1990 Nov;172(11):6223-31. LexA-independent expression of a mutant mucAB operon. McNally KP, Freitag NE, Walker GC. "pKM101 is a naturally occurring plasmid that carries mucAB, an analog of the umuDC operon, ..." *) (* original name: mucAB Berg1988e *) (* DROP: Plasmid *) (* original name: cle1-1 Berg1988e *) (* DROP: Plasmid *) (* original name: cle1-2 Berg1988e *) (* DROP: Plasmid *) (* original name: Col1b Berg1988e *) (* DROP: Plasmid *) (* original name: ColA-1 Berg1988e *) (* DROP: Plasmid *) (* original name: ColA-2 Berg1988e *) (* DROP: Plasmid *) (* original name: ColE2 Berg1988e *) (* DROP: Plasmid *) (* original name: clodf13pro *) (* DROP: Plasmid *) (****************************************************************) (****************************************************************) (* other sites *) (* \cite{Lewis.Mount1994} Table 2 (no sites) Mutat Res. 1989 Nov;218(3):207-10. The LexA protein does not bind specifically to the two SOS box-like sequences immediately 5' to the phr gene. Payne NS, Sancar A. NAME "phr"; GET FROM 740149 -200 to same +200 direction +; *) (* I capitalized the instruction so it will never be recognized. *) (* no sites found by model lexA 1.00 within 500 bp of start name "recQ"; GET FROM 740149 -200 to same +200 direction +; See: Lewis.Mount1994 page 510: "the non-canonical site near recQ ... has not been shown to bind LexA" *) (* I capitalized the instruction so it will never be recognized. *) (* % title 'LexA version = 3.20 of lexa.inst 2022 Aug 01'; @article{aaaaa, author = "A. A. Aaaaa", title = "{version = 56.98 of all.bib 2022 Jul 30}", journal = "Tom Schneider's all.bib BibTeX reference Database", comment = "MISSING object \rule{0.5em}{1ex}", anothercomment = "the year is set to 1900 to provide a lower endpoint for the year program", year = "1900"} -- @article{Baquero.Moreno1995, author = "M. R. Baquero and M. Bouzon and J. Varea and F. Moreno", title = "{\emph{sbmC}, a stationary-phase induced SOS \emph{Escherichia coli} gene, whose product protects cells from the DNA replication inhibitor microcin B17}", journal = "Mol. Microbiol.", volume = "18", pages = "301--311", pmid = "8709849", year = "1995"} @article{Brent.Ptashne1981, author = "R. Brent and M. Ptashne", title = "Mechanism of action of the {{\em lexA}} gene product", journal = "Proc. Natl. Acad. Sci. USA", volume = "78", pages = "4204--4208", comment = "original name: Brent1981", year = "1981"} @article{Courcelle.Hanawalt2001, author = "J. Courcelle and A. Khodursky and B. Peter and P. O. Brown and P. C. Hanawalt", title = "{Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient \emph{Escherichia coli}}", journal = "Genetics", volume = "158", pages = "41--64", pmid = "11333217", pmcid = "PMC1461638", year = "2001"} @article{Easton.Kushner1983, author = "A. M. Easton and S. R. Kushner", title = "{Transcription of the \emph{uvrD} gene of \emph{Escherichia coli} is controlled by the \emph{lexA} repressor and by attenuation}", journal = "Nucleic Acids Res.", volume = "11", pages = "8625--8640", pmid = "6324092", pmcid = "PMC326612", year = "1983"} @article{FernandezDeHenestrosa.Woodgate2000, author = "A. R. {Fernandez De Henestrosa} and T. Ogi and S. Aoyagi and D. Chafin and J. J. Hayes and H. Ohmori and R. Woodgate", title = "{Identification of additional genes belonging to the LexA regulon in \emph{Escherichia coli}}", journal = "Mol. Microbiol.", volume = "35", pages = "1560--1572", pmid = "10760155", year = "2000"} Fernandez_De_Henestrosa.Woodgate2000 not found in /Users/schneidt/papers/references/all.bib @article{Kitagawa.Kato1985, author = "Y. Kitagawa and E. Akaboshi and H. Shinagawa and T. Horii and H. Ogawa and T. Kato", title = "{Structural analysis of the \emph{umu} operon required for inducible mutagenesis in \emph{Escherichia coli}}", journal = "Proc. Natl. Acad. Sci. USA", volume = "82", pages = "4336--4340", pmid = "2989817", pmcid = "PMC390408", note = "\url {https://doi.org/10.1073/pnas.82.13.4336}", comment = "2021/06/06 21:55:47 formerly Kitagawa1985", year = "1985"} @article{Kuhner.Gaub2004, author = "F. {K\"{u}hner} and L. T. Costa and P. M. Bisch and S. Thalhammer and W. M. Heckl and H. E. Gaub", title = "{LexA-DNA bond strength by single molecule force spectroscopy}", journal = "Biophys J", volume = "87", pages = "2683--2690", pmid = "15454462", pmcid = "PMC1304687", year = "2004"} @article{Lewis.Mount1992b, author = "L. K. Lewis and D. W. Mount", title = "{Interaction of LexA repressor with the asymmetric \emph{dinG} operator and complete nucleotide sequence of the gene}", journal = "J. Bacteriol.", volume = "174", pages = "5110--5116", pmid = "1629168", pmcid = "PMC206328", year = "1992"} @article{Lewis.Mount1994, author = "L. K. Lewis and G. R. Harlow and L. A. Gregg-Jolly and D. W. Mount", title = "{Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in \emph{Escherichia coli}}", journal = "J. Mol. Biol.", volume = "241", pages = "507--523", pmid = "8057377", note = "\url {https://doi.org/10.1006/jmbi.1994.1528}", comment = "2008Apr17_18:34:420 from pdf date", year = "1994"} @article{Little.Yanisch-Perron1981, author = "J. W. Little and D. W. Mount and C. R. Yanisch-Perron", title = "{Purified \emph{lexA} protein is a repressor of the \emph{recA} and \emph{lexA} genes}", journal = "Proc. Natl. Acad. Sci. USA", volume = "78", pages = "4199--4203", pmid = "7027255", pmcid = "PMC319756", year = "1981"} @article{Lomba.de_Almeida1997, author = "M. R. Lomba and A. T. Vasconcelos and A. B. Pacheco and D. F. {de Almeida}", title = "{Identification of \emph{yebG} as a DNA damage-inducible \emph{Escherichia coli} gene}", journal = "FEMS Microbiol. Lett.", volume = "156", pages = "119--122", pmid = "9368369", year = "1997"} @article{Mizusawa.Gottesman1983, author = "S. Mizusawa and D. Court and S. Gottesman", title = "{Transcription of the \emph{sulA} gene and repression by LexA}", journal = "J. Mol. Biol.", volume = "171", pages = "337--343", pmid = "6317868", year = "1983"} @article{Ohmori.Nagai1995, author = "H. Ohmori and M. Saito and T. Yasuda and T. Nagata and T. Fujii and M. Wachi and K. Nagai", title = "{The \emph{pcsA} gene is identical to \emph{dinD} in \emph{Escherichia coli}}", journal = "J. Bacteriol.", volume = "177", pages = "156--165", pmid = "8002613", pmcid = "PMC176568", year = "1995"} @article{Robison.Church1998, author = "K. Robison and A. M. McGuire and G. M. Church", title = "{A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete \emph{Escherichia coli} K-12 genome}", journal = "J. Mol. Biol.", volume = "284", pages = "241--254", pmid = "9813115", note = "http://arep.med.harvard.edu/dpinteract/", year = "1998"} @article{Rostas.Lloyd1987, author = "K. Rostas and S. J. Morton and S. M. Picksley and R. G. Lloyd", title = "{Nucleotide sequence and LexA regulation of the \emph{Escherichia coli} \emph{recN} gene}", journal = "Nucleic Acids Res.", volume = "15", pages = "5041--5049", pmid = "3037486", pmcid = "PMC305946", year = "1987"} @article{Sancar.Mount1982, author = "A. Sancar and G. B. Sancar and W. D. Rupp and J. W. Little and D. W. Mount", title = "{LexA protein inhibits transcription of the \emph{E. coli} \emph{uvrA} gene \emph{in vitro}}", journal = "Nature", volume = "298", pages = "96--98", pmid = "6283374", year = "1982"} @article{Sancar.Rupp1982, author = "G. B. Sancar and A. Sancar and J. W. Little and W. D. Rupp", title = "{The \emph{uvrB} gene of \emph{Escherichia coli} has both \emph{lexA}-repressed and \emph{lexA}-independent promoters}", journal = "Cell", volume = "28", pages = "523--530", pmid = "6280873", year = "1982"} @article{Schnarr.Granger-Schnarr1991, author = "M. Schnarr and P. Oertel-Buchheit and M. Kazmaier and M. Granger-Schnarr", title = "{DNA binding properties of the LexA repressor}", journal = "Biochimie", volume = "73", pages = "423--431", pmid = "1911942", year = "1991"} @article{Sharma.Moses1986, author = "S. Sharma and T. F. Stark and W. G. Beattie and R. E. Moses", title = "{Multiple control elements for the \emph{uvrC} gene unit of \emph{Escherichia coli}}", journal = "Nucleic Acids Res.", volume = "14", pages = "2301--2318", pmid = "3515318", pmcid = "PMC339659", year = "1986"} @article{Shinagawa.Nakata1988, author = "H. Shinagawa and K. Makino and M. Amemura and S. Kimura and H. Iwasaki and A. Nakata", title = "{Structure and regulation of the \emph{Escherichia coli} \emph{ruv} operon involved in DNA repair and recombination}", journal = "J. Bacteriol.", volume = "170", pages = "4322--4329", pmid = "2842314", pmcid = "PMC211445", year = "1988"} @article{Stark.Moses1989, author = "T. Stark and R. E. Moses", title = "{Interaction of the LexA repressor and the \emph{uvrC} regulatory region}", journal = "FEBS Lett", volume = "258", pages = "39--41", pmid = "2556297", year = "1989"} @article{Yasuda.Ohmori1996, author = "T. Yasuda and T. Nagata and H. Ohmori", title = "{Multicopy suppressors of the cold-sensitive phenotype of the \emph{pcsA68} (\emph{dinD68}) mutation in \emph{Escherichia coli}}", journal = "J. Bacteriol.", volume = "178", pages = "3854--3859", pmid = "8682790", pmcid = "PMC232646", year = "1996"} *)