The Mechanism of E. Coli RNA Polymerase Regulation by PpGpp is Suggested by the Structure of Their Complex

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2013 Apr 30

PMID 23623685

Citations 116

Authors

Yuhong Zuo

Yeming Wang

Thomas A Steitz

Affiliations

Soon will be listed here.

Abstract

Guanosine tetraphosphate (ppGpp) is an alarmone that enables bacteria to adapt to their environment. It has been known for years that ppGpp acts directly on RNA polymerase (RNAP) to alter the rate of transcription, but its exact target site is still under debate. Here we report a crystal structure of Escherichia coli RNAP holoenzyme in complex with ppGpp at 4.5 Å resolution. The structure reveals that ppGpp binds at an interface between the shelf and core modules on the outer surface of RNAP, away from the catalytic center and the nucleic acid binding path. Bound ppGpp connects these two pivotal modules that may restrain the opening of the RNAP cleft. A detailed mechanism of action of ppGpp is proposed in which ppGpp prevents the closure of the active center that is induced by the binding of NTP, which could slow down nucleotide addition cycles and destabilize the initial transcription complexes.

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References

Murshudov G, Skubak P, Lebedev A, Pannu N, Steiner R, Nicholls R . REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 2011; 67(Pt 4):355-67. PMC: 3069751. DOI: 10.1107/S0907444911001314. View

Perederina A, Svetlov V, Vassylyeva M, Tahirov T, Yokoyama S, Artsimovitch I . Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Cell. 2004; 118(3):297-309. DOI: 10.1016/j.cell.2004.06.030. View

Rymer R, Solorio F, Tehranchi A, Chu C, Corn J, Keck J . Binding mechanism of metal⋅NTP substrates and stringent-response alarmones to bacterial DnaG-type primases. Structure. 2012; 20(9):1478-89. PMC: 3438381. DOI: 10.1016/j.str.2012.05.017. View

Tagami S, Sekine S, Kumarevel T, Hino N, Murayama Y, Kamegamori S . Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein. Nature. 2010; 468(7326):978-82. DOI: 10.1038/nature09573. View

Trinh V, Langelier M, Archambault J, Coulombe B . Structural perspective on mutations affecting the function of multisubunit RNA polymerases. Microbiol Mol Biol Rev. 2006; 70(1):12-36. PMC: 1393249. DOI: 10.1128/MMBR.70.1.12-36.2006. View

Magnusson L, Gummesson B, Joksimovic P, Farewell A, Nystrom T . Identical, independent, and opposing roles of ppGpp and DksA in Escherichia coli. J Bacteriol. 2007; 189(14):5193-202. PMC: 1951846. DOI: 10.1128/JB.00330-07. View

Barker M, Gaal T, Josaitis C, Gourse R . Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J Mol Biol. 2001; 305(4):673-88. DOI: 10.1006/jmbi.2000.4327. View

Buglino J, Shen V, Hakimian P, Lima C . Structural and biochemical analysis of the Obg GTP binding protein. Structure. 2002; 10(11):1581-92. DOI: 10.1016/s0969-2126(02)00882-1. View

Travers A . Promoter sequence for stringent control of bacterial ribonucleic acid synthesis. J Bacteriol. 1980; 141(2):973-6. PMC: 293725. DOI: 10.1128/jb.141.2.973-976.1980. View

10.

Cramer P, Bushnell D, Kornberg R . Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science. 2001; 292(5523):1863-76. DOI: 10.1126/science.1059493. View

11.

McCoy A, Grosse-Kunstleve R, Adams P, Winn M, Storoni L, Read R . Phaser crystallographic software. J Appl Crystallogr. 2009; 40(Pt 4):658-674. PMC: 2483472. DOI: 10.1107/S0021889807021206. View

12.

Dalebroux Z, Svensson S, Gaynor E, Swanson M . ppGpp conjures bacterial virulence. Microbiol Mol Biol Rev. 2010; 74(2):171-99. PMC: 2884408. DOI: 10.1128/MMBR.00046-09. View

13.

Winn M, Ballard C, Cowtan K, Dodson E, Emsley P, Evans P . Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr. 2011; 67(Pt 4):235-42. PMC: 3069738. DOI: 10.1107/S0907444910045749. View

14.

Vrentas C, Gaal T, Ross W, Ebright R, Gourse R . Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA. Genes Dev. 2005; 19(19):2378-87. PMC: 1240046. DOI: 10.1101/gad.1340305. View

15.

Niu W, Kim Y, Tau G, Heyduk T, Ebright R . Transcription activation at class II CAP-dependent promoters: two interactions between CAP and RNA polymerase. Cell. 1996; 87(6):1123-34. PMC: 4430116. DOI: 10.1016/s0092-8674(00)81806-1. View

16.

Paul B, Barker M, Ross W, Schneider D, Webb C, Foster J . DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell. 2004; 118(3):311-22. DOI: 10.1016/j.cell.2004.07.009. View

17.

Vrentas C, Gaal T, Berkmen M, Rutherford S, Haugen S, Vassylyev D . Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation. J Mol Biol. 2008; 377(2):551-64. PMC: 2317782. DOI: 10.1016/j.jmb.2008.01.042. View

18.

Artsimovitch I, Patlan V, Sekine S, Vassylyeva M, Hosaka T, Ochi K . Structural basis for transcription regulation by alarmone ppGpp. Cell. 2004; 117(3):299-310. DOI: 10.1016/s0092-8674(04)00401-5. View

19.

Minakhin L, Bhagat S, Brunning A, Campbell E, Darst S, Ebright R . Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. Proc Natl Acad Sci U S A. 2001; 98(3):892-7. PMC: 14680. DOI: 10.1073/pnas.98.3.892. View

20.

Toulokhonov I, Shulgina I, Hernandez V . Binding of the transcription effector ppGpp to Escherichia coli RNA polymerase is allosteric, modular, and occurs near the N terminus of the beta'-subunit. J Biol Chem. 2000; 276(2):1220-5. DOI: 10.1074/jbc.M007184200. View