Direct Control of Type IIA Topoisomerase Activity by a Chromosomally Encoded Regulatory Protein
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Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein Seychelle M. Vos,1,4 Artem Y. Lyubimov,1,5 David M. Hershey,2 Allyn J. Schoeffler,1,6 Sugopa Sengupta,3,7 Valakunja Nagaraja,3 and James M. Berger1,8,9 1Department of Molecular and Cell Biology, 2Deparment of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720, USA; 3Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India Precise control of supercoiling homeostasis is critical to DNA-dependent processes such as gene expression, replication, and damage response. Topoisomerases are central regulators of DNA supercoiling commonly thought to act independently in the recognition and modulation of chromosome superstructure; however, recent evidence has indicated that cells tightly regulate topoisomerase activity to support chromosome dynamics, transcriptional response, and replicative events. How topoisomerase control is executed and linked to the internal status of a cell is poorly understood. To investigate these connections, we determined the structure of Escherichia coli gyrase, a type IIA topoisomerase bound to YacG, a recently identified chromosomally encoded inhibitor protein. Phylogenetic analyses indicate that YacG is frequently associated with coenzyme A (CoA) production enzymes, linking the protein to metabolism and stress. The structure, along with supporting solution studies, shows that YacG represses gyrase by sterically occluding the principal DNA-binding site of the enzyme. Unexpectedly, YacG acts by both engaging two spatially segregated regions associated with small-molecule inhibitor interactions (fluoroquinolone antibiotics and the newly reported antagonist GSK299423) and remodeling the gyrase holoenzyme into an inactive, ATP-trapped configuration. This study establishes a new mechanism for the protein-based control of topoisomerases, an approach that may be used to alter supercoiling levels for responding to changes in cellular state. [Keywords: gyrase; DNA topology; YacG; type II topoisomerase; transcription; metabolism] Supplemental material is available for this article. Received March 21, 2014; revised version accepted May 30, 2014. The ability to rapidly alter the production and activity of Although difficult to monitor directly, chromosome proteins associated with housekeeping and proliferative topology also serves a central part in homeotic control processes is essential to allow cells to respond to envi- and response (Higgins et al. 1988; Dorman et al. 1990; ronmental and developmental cues. Appropriate regula- Stewart et al. 1990; Merino et al. 1993; Pedersen et al. tion of gene expression and cell growth can occur through 2012; King et al. 2013). Chromosome topology is main- a variety of mechanisms, including transcription factor tained by a variety of factors, including DNA-bending/ activity, second messenger metabolites, and pathways wrapping proteins and DNA supercoiling (Luijsterburg such as RNAi (de Nadal et al. 2011; Castel and Martienssen et al. 2008). Topoisomerases are a ubiquitous class of 2013). enzymes that play a key role in controlling topological status, supporting essential DNA transactions such as replication, transcription, and repair (Vos et al. 2011). Topoisomerases alter supercoiling levels and resolve chro- Present addresses: 4Department of Molecular Biology, Max-Planck-Institute mosomal tangles by transiently breaking, moving, and 5 for Biophysical Chemistry, 37077 Go¨ttingen, Germany; The James H Clark rejoining different DNA segments with respect to each Center, Stanford School of Medicine, Stanford, California 94305 USA; 6Department of Early Discovery Biochemistry, Genentech, South San other (Schoeffler and Berger 2008). In turn, topoisomerase Francisco, CA 94080 USA; 7Department of Molecular Biology, Presidency University, Kolkata, India; 8Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD Ó 2014 Vos et al. This article is distributed exclusively by Cold Spring 21205, USA Harbor Laboratory Press for the first six months after the full-issue 9Corresponding author publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). E-mail [email protected] After six months, it is available under a Creative Commons License Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.241984. (Attribution-NonCommercial 4.0 International), as described at http:// 114. creativecommons.org/licenses/by-nc/4.0/. GENES & DEVELOPMENT 28:1485–1497 Published by Cold Spring Harbor Laboratory Press; ISSN 0890-9369/14; www.genesdev.org 1485 Vos et al. expression levels and activities are reciprocally influ- ical experiments confirm the importance of the observed enced by DNA supercoiling and the metabolic status of interactions to YacG binding and function and show that the cell (Menzel and Gellert 1983; Tse-Dinh and Beran inhibition by YacG is specific to its cognate gyrase. A 1988; Hsieh et al. 1991; van Workum et al. 1996; C-terminal peptide encompassing both binding epitopes Schneider et al. 1999; Champion and Higgins 2007; of YacG is sufficient to inhibit gyrase, while small-angle Rovinskiy et al. 2012). Due to their requisite action in X-ray scattering (SAXS) experiments indicate that full- preserving and maintaining the flow of genetic informa- length YacG further remodels the gyrase holoenzyme to tion, topoisomerases have served as the successful targets enforce closure of its distal ATPase regions. Bioinformatic of a number of cell-killing agents, often with significant analyses of ORFs that neighbor yacG genes in different therapeutic benefit (Nitiss 2009b; Pommier et al. 2010; bacterial species suggest that the protein regulates gyrase Collin et al. 2011). in response to specific metabolic signals linked to cell As their nucleic acid substrates frequently bear dis- growth and/or stress. Together, our study defines a novel tinctive biophysical properties and/or shapes (Schoeffler protein-based mechanism for controlling gyrase that and Berger 2008), topoisomerases are frequently depicted exploits demonstrated drug-binding loci and provides as ‘‘stand-alone’’ actors that rely solely on topological a new framework for considering how bacteria might features in DNA to direct their time and place of work. reconfigure topoisomerase activity to suit specific cellu- However, many studies have called this picture into lar needs. question, revealing that in cells, topoisomerases are actually subject to multiple levels of control such as protein–protein interactions and post-translational mod- Results ifications (for review, see Vos et al. 2011). At present, it YacG preferentially binds to the C terminus of GyrB has yet to be established how the vast majority of these regulatory factors and marks modulate topoisomerase Gyrase is a heterotetrameric (GyrA2•GyrB2) enzyme that activity. How topoisomerase control mechanisms are in uses three reversibly associable dimer interfaces (or turn integrated with feedback systems to fine-tune tran- ‘‘gates’’) to coordinate the transient, ATP-dependent scriptional output for altering metabolic state or respond- breakage of one DNA duplex and the passage of a second ing to cellular environment is similarly unknown. duplex through the break. YacG is a member of the treble In bacteria, both transcription and the initiation of clef and FCS zinc finger motif families that mediate DNA replication are highly sensitive to the steady-state diverse functions, including protein•protein and nucleic levels of DNA underwinding or overwinding (Bramhill acid interactions (Grishin 2001; Krishna et al. 2003). To and Kornberg 1988; Higgins et al. 1988). Supercoiling determine how Escherichia coli YacG and gyrase interact, equilibrium is determined in part by RNA polymerase we cloned, purified, and performed fluorescence anisot- activity (Gamper and Hearst 1982; Rovinskiy et al. 2012) ropy-based binding experiments with various gyrase along with two topoisomerases, topo IA and gyrase constructs and a fluorescently labeled construct of the (Sternglanz et al. 1981; DiNardo et al. 1982; Pruss et al. inhibitor. Consistent with a previous limited proteolysis 1982; Zechiedrich et al. 2000), which counterbalance study suggesting that YacG binds primarily to the C each other by adding (gyrase) or subtracting (topo IA) terminus of GyrB (Sengupta and Nagaraja 2008), we negative supercoils to and from DNA (Wang 1971; Gellert observed that YacG associated robustly with the full- et al. 1976). To date, a number of distinct proteins and length gyrase tetramer, the individual GyrB subunit, and pharmaceutical agents have been discovered that either the isolated topoisomerase/primase (TOPRIM) domain of generally inhibit gyrase in response to specific toxins or GyrB (with Kd,app values ranging from 30 to 45 nM) (Fig. environmental cues or trap gyrase in a covalent complex 1A,B). In contrast, no binding was evident when YacG with DNA to directly induce cell death (Collin et al. was incubated with the GyrB ATPase domain. Tests using 2011). While significant strides have been made in un- a GyrB•GyrA fusion protein (GyrBA) that lacks both an derstanding how small-molecule inhibitors interfere with auxiliary C-terminal domain (CTD) of GyrA and the GyrB topoisomerase function (Pommier et al. 2010; Collin et al. ATPase domain (Fig. 1A), but is still competent to bind 2011), how proteinaceous inhibitors of these enzymes and cleave DNA (Schoeffler et al.