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Insights Into Histidine Kinase Activation Mechanisms from the Monomeric Blue Light Sensor EL346

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Insights Into Histidine Kinase Activation Mechanisms from the Monomeric Blue Light Sensor EL346 Insights into histidine kinase activation mechanisms from the monomeric blue light sensor EL346 Igor Dikiya, Uthama R. Edupugantia,b, Rinat R. Abzalimova, Peter P. Borbatc,d, Madhur Srivastavad,e, Jack H. Freedc,d, and Kevin H. Gardnera,f,g,1 aStructural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031; bBiochemistry Ph.D. Program, Graduate Center, City University of New York, New York, NY 10016; cDepartment of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; dNational Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, NY 14853; eMeinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853; fBiochemistry, Chemistry, and Biology Ph.D. Programs, Graduate Center, City University of New York, New York, NY 10016; and gDepartment of Chemistry and Biochemistry, City College of New York, New York, NY 10031 Edited by Sean Crosson, University of Chicago, Chicago, IL, and accepted by Editorial Board Member Michael A. Marletta January 24, 2019 (received for review August 9, 2018) Translation of environmental cues into cellular behavior is a motions alternatively described as piston-like motions, scissoring, necessary process in all forms of life. In bacteria, this process or helical rotations (12), to the DHp helices. The CA domain frequently involves two-component systems in which a sensor then catalyzes the transfer of a phosphoryl group from the bound histidine kinase (HK) autophosphorylates in response to a stimulus ATP substrate to the phosphoacceptor histidine located on the before subsequently transferring the phosphoryl group to a first DHp helix. We term this process, consisting of the two steps response regulator that controls downstream effectors. Many of (i) stimulus detection and (ii) increase of autophosphorylation details of the molecular mechanisms of HK activation are still enzymatic activity, HK “activation.” The molecular details of this unclear due to complications associated with the multiple signal- process are somewhat unclear due to the disparate truncated ing states of these large, multidomain proteins. To address these protein constructs used in different studies, although it is ap- challenges, we combined complementary solution biophysical parent that activation is associated with breaking the dimeric approaches to examine the conformational changes upon activa- symmetry observed in inactive states (14, 15). tion of a minimal, blue-light–sensing histidine kinase from Eryth- In contrast, the soluble, minimal HK EL346 consists simply of BIOPHYSICS AND robacter litoralis HTCC2594, EL346. Our data show that multiple a sensor domain [a Light-Oxygen-Voltage (LOV) domain that COMPUTATIONAL BIOLOGY conformations coexist in the dark state of EL346 in solution, which responds to blue light] and kinase domain (10, 16). Since may explain the enzyme’s residual dark-state activity. We also EL346 contains only the minimum modules needed to sense and observe that activation involves destabilization of the helices in respond to its stimulus, and light is easy to apply in a laboratory the dimerization and histidine phosphotransfer-like domain, where the phosphoacceptor histidine resides, and their interac- setting, this protein is well-suited for mechanistic studies of sig- tions with the catalytic domain. Similar light-induced changes oc- nal transduction. In addition, from the sensor point of view, one well-established mechanism of LOV domain signaling involves cur to some extent even in constitutively active or inactive – mutants, showing that light sensing can be decoupled from acti- release of a C-terminal helix (17 19). Interestingly, the EL346 vation of kinase activity. These structural changes mirror those kinase functions as a monomer, with the standard DHp dimer- inferred by comparing X-ray crystal structures of inactive and ac- ization interface blocked by a direct interaction with the sensor tive HK fragments, suggesting that they are at the core of confor- mational changes leading to HK activation. More broadly, our Significance findings uncover surprising complexity in this simple system and allow us to outline a mechanism of the multiple steps of HK All living things must sense and react to their environment. activation. Many single-celled organisms do so by using two-component systems, most simply consisting of a sensor histidine kinase sensor histidine kinase | HDX-MS | ESR spectroscopy | two-component and a response regulator. These systems are involved in system | photoreceptor pathogenicity pathways and can be targeted by new antibi- otics. However, the molecular mechanisms used by histidine hile all living things sense and respond to their environ- kinases to translate sensing into responses are not well un- Wment, this process is especially important to single-celled derstood. To probe this general question, we apply a combi- organisms. To do so, these organisms often use two-component nation of biophysical techniques to a monomeric histidine systems, consisting of a sensor histidine kinase (HK), which kinase that senses blue light to determine the structural autophosphorylates in response to specific stimuli, and a re- changes occurring upon activation. We find these changes to sponse regulator (RR), which is then phosphorylated by the HK be similar to those predicted for the common dimeric histidine and activates downstream responses (1, 2). Despite recent kinases, illustrating that the mechanism of activation is con- structural studies of HKs motivated by general interest in signal served regardless of oligomeric state. transduction mechanisms and more specific goals of designing Author contributions: I.D., R.R.A., P.P.B., M.S., J.H.F., and K.H.G. designed research; I.D., new antibiotic/antifungal agents (3, 4), the detailed mechanisms U.R.E., R.R.A., and P.P.B. performed research; I.D., U.R.E., and M.S. contributed new of HK activation have been inferred chiefly from static snapshots reagents/analytic tools; I.D., U.R.E., R.R.A., P.P.B., M.S., J.H.F., and K.H.G. analyzed data; of active and inactive states (5–9). and I.D. and K.H.G. wrote the paper. Aside from notable exceptions (10, 11), HKs are canonically The authors declare no conflict of interest. viewed as dimeric proteins with modular architecture that in- This article is a PNAS Direct Submission. S.C. is a guest editor invited by the Editorial cludes an extracytoplasmic sensor region, transmembrane (TM) Board. helices, various signal transduction domains, and a kinase do- Published under the PNAS license. main consisting of dimerization and histidine phosphotransfer 1To whom correspondence should be addressed. Email: [email protected]. (DHp) and catalytic ATP-binding (CA) subdomains (12, 13). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. After the sensor detects its stimulus, the signal propagates 1073/pnas.1813586116/-/DCSupplemental. through the TM and other intervening domains via a variety of Published online February 26, 2019. www.pnas.org/cgi/doi/10.1073/pnas.1813586116 PNAS | March 12, 2019 | vol. 116 | no. 11 | 4963–4972 Downloaded by guest on September 29, 2021 LOV domain in the dark, inactive state (10) (Fig. 1). Another useful feature of this kinase is a collection of point mutations that alter dark and light state activity, including constitutively A ATP inactive (V119A) and active (V115A) mutants, which tune the α1 α2 lid basal dark-state activity of EL346 by modulating of the LOV- LOV DHpL CA DHpL interface (10). 8 125129 188 196 338 These practical advantages of EL346 make it an ideal system AMP-PNP to probe the conformational changes that accompany HK acti- B vation in a natural, full-length context. Thus, we studied the α2 gripper conformations of this enzyme in solution in the dark state, upon light sensing, and as a result of ATP hydrolysis. To do so, we Arg175 applied biophysical methods that are especially useful for highly dynamic systems, such as hydrogen-deuterium exchange by mass Val115 spectrometry (HDX-MS) and pulsed electron spin resonance (ESR) spectroscopy. Intriguingly, we found that, in the dark state, the enzyme exists in both inactive and active conforma- tions, a balance that is shifted during activation. In agreement Val119 with our proposed model (10), we found that light-induced changes in the sensor domain are propagated to the kinase do- main via a disruption of direct interactions between the domains. His142 Finally, we directly detect the destabilization of the central α1 DHpL helices upon illumination and loss of their interaction with the gripper helix (15) in the catalytic domain upon ATP LOV DHpL CA hydrolysis, confirming and more fully characterizing previously inferred HK activation-induced changes. C α2 Results ATP EL346 Is Monomeric Regardless of Illumination State. We subjected R gripper EL346, without and with prior illumination, to size-exclusion LC- FMN MS in nondenaturing conditions (20, 21). Both unilluminated and illuminated proteins eluted at times corresponding to a 39- EL346 H kDa globular protein (consistent with monomeric EL346) with- Minimal Monomeric α out sign of dimers or higher-order oligomers in any of the 1 chromatograms. However, illumination resulted in a small but LOV sensor DHpL CA reproducible shift in elution time and broadening of the elution peak (SI Appendix,Fig.S1A). This shift may suggest a change in conformation or a decrease in number of conformations sam- Sensor pled. The mass spectra of unilluminated and illuminated pro- tein samples were almost identical, with charge states and m/z values corresponding to monomeric protein, as well as low- Sensor intensity dimers and trimers (SI Appendix,Fig.S1B). Since these oligomers coelute with monomeric protein, they likely result from nonspecific protein association in the electrospray droplets (20, 22). The masses of the major peaks match the Transmembrane predicted molecular weight of EL346 plus that of the flavin chromophores riboflavin (RBF), FMN, and FAD (SI Appendix, Domains Fig. S1C). Other Domains e.g. HAMP DHpL α1 and α2 Helices Are Exposed upon Activation by Light.
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