Structural basis of transcription activation by Rob, a pleiotropic AraC/XylS family regulator.
AraC Transcription Factor
/ genetics
Bacterial Proteins
/ metabolism
Cytarabine
/ metabolism
DNA
/ chemistry
DNA-Binding Proteins
/ metabolism
DNA-Directed RNA Polymerases
/ genetics
Escherichia coli
/ genetics
Escherichia coli Proteins
/ metabolism
Gene Expression Regulation, Bacterial
Transcriptional Activation
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
10 06 2022
10 06 2022
Historique:
accepted:
09
05
2022
revised:
14
04
2022
received:
14
11
2021
pubmed:
1
6
2022
medline:
11
6
2022
entrez:
31
5
2022
Statut:
ppublish
Résumé
Rob, which serves as a paradigm of the large AraC/XylS family transcription activators, regulates diverse subsets of genes involved in multidrug resistance and stress response. However, the underlying mechanism of how it engages bacterial RNA polymerase and promoter DNA to finely respond to environmental stimuli is still elusive. Here, we present two cryo-EM structures of Rob-dependent transcription activation complex (Rob-TAC) comprising of Escherichia coli RNA polymerase (RNAP), Rob-regulated promoter and Rob in alternative conformations. The structures show that a single Rob engages RNAP by interacting with RNAP αCTD and σ70R4, revealing their generally important regulatory roles. Notably, by occluding σ70R4 from binding to -35 element, Rob specifically binds to the conserved Rob binding box through its consensus HTH motifs, and retains DNA bending by aid of the accessory acidic loop. More strikingly, our ligand docking and biochemical analysis demonstrate that the large Rob C-terminal domain (Rob CTD) shares great structural similarity with the global Gyrl-like domains in effector binding and allosteric regulation, and coordinately promotes formation of competent Rob-TAC. Altogether, our structural and biochemical data highlight the detailed molecular mechanism of Rob-dependent transcription activation, and provide favorable evidences for understanding the physiological roles of the other AraC/XylS-family transcription factors.
Identifiants
pubmed: 35641097
pii: 6596093
doi: 10.1093/nar/gkac433
pmc: PMC9178005
doi:
Substances chimiques
AraC Transcription Factor
0
AraC protein, E coli
0
Bacterial Proteins
0
DNA-Binding Proteins
0
Escherichia coli Proteins
0
Rob protein, E coli
0
Cytarabine
04079A1RDZ
DNA
9007-49-2
DNA-Directed RNA Polymerases
EC 2.7.7.6
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5974-5987Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Annu Rev Microbiol. 2013;67:113-39
pubmed: 23768203
Nucleic Acids Res. 2019 Sep 26;47(17):9423-9432
pubmed: 31392983
J Mol Biol. 2010 Aug 6;401(1):13-32
pubmed: 20595001
Nucleic Acids Res. 2020 Sep 25;48(17):9931-9942
pubmed: 32785630
Curr Opin Microbiol. 2001 Apr;4(2):132-7
pubmed: 11282467
J Bacteriol. 1996 May;178(9):2507-13
pubmed: 8626315
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
pubmed: 20124702
Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10413-8
pubmed: 9724717
Mol Cell. 2020 Apr 16;78(2):275-288.e6
pubmed: 32160514
Nat Commun. 2018 Feb 13;9(1):656
pubmed: 29440634
J Mol Biol. 2011 Oct 7;412(5):754-71
pubmed: 21371479
Nucleic Acids Res. 2002 Jan 1;30(1):318-21
pubmed: 11752325
J Mol Biol. 2009 May 8;388(3):415-30
pubmed: 19289129
Mol Cell. 2021 Jul 15;81(14):2875-2886.e5
pubmed: 34171296
Int J Biotechnol Wellness Ind. 2013;2(3):101-124
pubmed: 24860636
Adv Sci (Weinh). 2022 Feb;9(4):e2103669
pubmed: 34761556
Nat Rev Microbiol. 2021 Feb;19(2):95-109
pubmed: 33122819
J Struct Biol. 2015 Nov;192(2):216-21
pubmed: 26278980
Nat Commun. 2019 Jul 2;10(1):2925
pubmed: 31266960
Cell. 2011 Dec 9;147(6):1257-69
pubmed: 22136875
Mol Microbiol. 2003 Jun;48(6):1609-19
pubmed: 12791142
Mol Microbiol. 1996 Jun;20(5):937-45
pubmed: 8809747
Science. 1993 Nov 26;262(5138):1407-13
pubmed: 8248780
Appl Environ Microbiol. 1995 Jun;61(6):2302-7
pubmed: 7793951
J Mol Biol. 2001 Oct 12;313(1):1-12
pubmed: 11601842
PLoS Biol. 2020 Apr 20;18(4):e3000706
pubmed: 32310937
J Comput Chem. 2009 Dec;30(16):2785-91
pubmed: 19399780
Biochemistry. 2016 Aug 30;55(34):4850-63
pubmed: 27505298
J Bacteriol. 2002 Mar;184(5):1407-16
pubmed: 11844771
FEMS Microbiol Rev. 2021 Sep 8;45(5):
pubmed: 33837749
J Biol Chem. 1999 Nov 12;274(46):33105-13
pubmed: 10551881
RNA. 2016 Dec;22(12):1884-1892
pubmed: 27777365
EMBO J. 1998 Jun 15;17(12):3439-47
pubmed: 9628879
J Mol Biol. 2012 Jun 8;419(3-4):139-57
pubmed: 22465792
Cell. 1991 Jun 14;65(6):1015-22
pubmed: 1646077
J Struct Biol. 2005 Oct;152(1):36-51
pubmed: 16182563
Nucleic Acids Res. 2018 Jul 2;46(W1):W363-W367
pubmed: 29860391
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
pubmed: 15572765
Annu Rev Microbiol. 2014;68:357-76
pubmed: 25002089
Methods Mol Biol. 2015;1276:13-29
pubmed: 25665556
Nat Commun. 2020 Dec 8;11(1):6284
pubmed: 33293519
J Bacteriol. 1995 Apr;177(7):1655-61
pubmed: 7896685
Elife. 2015 Sep 08;4:
pubmed: 26349032
J Mol Biol. 2004 Oct 22;343(3):513-32
pubmed: 15465042
Mol Cell. 2015 May 7;58(3):534-40
pubmed: 25866247
Nat Rev Microbiol. 2016 Oct;14(10):638-50
pubmed: 27498839
Science. 2016 Jun 10;352(6291):1330-3
pubmed: 27284196
Nat Methods. 2017 Apr;14(4):331-332
pubmed: 28250466
J Biol Chem. 1993 Mar 15;268(8):5365-70
pubmed: 8449900
Nat Commun. 2021 May 11;12(1):2702
pubmed: 33976201
J Phys Chem B. 2021 Jul 1;125(25):6791-6806
pubmed: 34137249
Science. 2017 Nov 17;358(6365):947-951
pubmed: 29146813
J Biol Chem. 2018 May 11;293(19):7367-7375
pubmed: 29581236
Mol Microbiol. 2004 Oct;54(1):45-59
pubmed: 15458404
Nat Struct Biol. 2000 May;7(5):424-30
pubmed: 10802742
Microbiol Mol Biol Rev. 1997 Dec;61(4):393-410
pubmed: 9409145
Nucleic Acids Res. 2021 Oct 11;49(18):10756-10769
pubmed: 34530448
Trends Microbiol. 1996 Jun;4(6):214-6
pubmed: 8795154
J Struct Biol. 2012 Dec;180(3):519-30
pubmed: 23000701