Glutamine Amide Flip Elicits Long Distance Allosteric Responses in the LOV Protein Vivid

Light-oxygen-voltage (LOV) domains sense blue light through the photochemical formation of a cysteinyl-flavin covalent adduct. Concurrent protonation at the flavin N5 position alters the hydrogen bonding interactions of an invariant Gln residue that has been proposed to flip its amide side chain as a critical step in the propagation of conformational change. Traditional molecular dynamics (MD) and replica-exchange MD (REMD) simulations of the well-characterized LOV protein Vivid (VVD) demonstrate that the Gln182 amide indeed reorients by ∼180° in response to either adduct formation or reduction of the isoalloxazine ring to the neutral semiquinone, both of which involve N5 protonation. Free energy simulations reveal that the relative free energies of the flipped Gln conformation and the flipping barrier are significantly lower in the light-adapted state. The Gln182 flip stabilizes an important hinge-bβ region between the PAS β-sheet and the N-terminal cap helix that in turn destabilizes an N-terminal latch region against the PAS core. Release of the latch, observed both experimentally and in the simulations, is known to mediate light-induced VVD dimerization. This computational study of a LOV protein, unprecedented in its agreement with experiment, provides an atomistic view of long-range allosteric coupling in a photoreceptor

Light-Induced Subunit Dissociation by a Light–Oxygen–Voltage Domain Photoreceptor from <i>Rhodobacter sphaeroides</i>

Light–oxygen–voltage (LOV) domains bind a flavin chromophore to serve as blue light sensors in a wide range of eukaryotic and prokaryotic proteins. LOV domains are associated with a variable effector domain or a separate protein signaling partner to execute a wide variety of functions that include regulation of kinases, generation of anti-sigma factor antagonists, and regulation of circadian clocks. Here we present the crystal structure, photocycle kinetics, association properties, and spectroscopic features of a full-length LOV domain protein from <i>Rhodobacter sphaeroides</i> (RsLOV). RsLOV exhibits N- and C-terminal helical extensions that form an unusual helical bundle at its dimer interface with some resemblance to the helical transducer of sensory rhodopsin II. The blue light-induced conformational changes of RsLOV revealed from a comparison of light- and dark-state crystal structures support a shared signaling mechanism of LOV domain proteins that originates with the light-induced formation of a flavin–cysteinyl photoadduct. Adduct formation disrupts hydrogen bonding in the active site and propagates structural changes through the LOV domain core to the N- and C-terminal extensions. Single-residue variants in the active site and dimer interface of RsLOV alter photoadduct lifetimes and induce structural changes that perturb the oligomeric state. Size exclusion chromatography, multiangle light scattering, small-angle X-ray scattering, and cross-linking studies indicate that RsLOV dimerizes in the dark but, upon light excitation, dissociates into monomers. This light-induced switch in oligomeric state may prove to be useful for engineering molecular associations in controlled cellular settings

Defining a Key Receptor–CheA Kinase Contact and Elucidating Its Function in the Membrane-Bound Bacterial Chemosensory Array: A Disulfide Mapping and TAM-IDS Study

The three core components of the ubiquitous bacterial chemosensory array  the transmembrane chemoreceptor, the histidine kinase CheA, and the adaptor protein CheW  assemble to form a membrane-bound, hexagonal lattice in which receptor transmembrane signals regulate kinase activity. Both the regulatory domain of the kinase and the adaptor protein bind to overlapping sites on the cytoplasmic tip of the receptor (termed the protein interaction region). Notably, the kinase regulatory domain and the adaptor protein share the same fold constructed of two SH3-like domains. The present study focuses on the structural interface between the receptor and the kinase regulatory domain. Two models have been proposed for this interface: Model 1 is based on the crystal structure of a homologous Thermotoga complex between a receptor fragment and the CheW adaptor protein. This model has been used in current models of chemosensory array architecture to build the receptor–CheA kinase interface. Model 2 is based on a newly determined crystal structure of a homologous Thermotoga complex between a receptor fragment and the CheA kinase regulatory domain. Both models present unique strengths and weaknesses, and current evidence is unable to resolve which model best describes contacts in the native chemosensory arrays of <i>Escherichia coli</i>, <i>Salmonella typhimurium</i>, and other bacteria. Here we employ disulfide mapping and tryptophan and alanine mutation to identify docking sites (TAM-IDS) to test Models 1 and 2 in well-characterized membrane-bound arrays formed from <i>E. coli</i> and <i>S. typhimurium</i> components. The results reveal that the native array interface between the receptor protein interaction region and the kinase regulatory domain is accurately described by Model 2, but not by Model 1. In addition, the results show that the interface possesses both a structural function that contributes to stable CheA kinase binding in the array and a regulatory function central to transmission of the activation signal from receptor to CheA kinase. On–off switching alters the disulfide formation rates of specific Cys pairs at the interface, but not most Cys pairs, indicating that signaling perturbs localized regions of the interface. The findings suggest a simple model for the rearrangement of the interface triggered by the attractant signal and for longer range transmission of the signal in the chemosensory array

Multiple sequence alignment analysis (MSA) of <i>Treponema</i> spp. that contain a single CheA isoform.

(A) MSA of Treponema spp. CheA P2 domain sequences. BbCheA1 and BbCheA2 sequences are included for comparison. The location of BbCheA2 P2α is marked with a black box. (B) MSA of Treponema spp. CheA P3 domain sequences. BbCheA1 and BbCheA2 sequences are included for comparison. The location of BbCheA2 P3 domain is marked with a black box. Sequences collected using Annotree [1], MSA files generated using Clustal Omega [6]. (TIFF)</p

Distance-Independent Charge Recombination Kinetics in Cytochrome <i>c</i>–Cytochrome <i>c</i> Peroxidase Complexes: Compensating Changes in the Electronic Coupling and Reorganization Energies

Charge recombination rate constants vary no more than 3-fold for interprotein ET in the Zn-substituted wild type (WT) cytochrome <i>c</i> peroxidase (CcP):cytochrome <i>c</i> (<i>Cc</i>) complex and in complexes with four mutants of the <i>Cc</i> protein (i.e., F82S, F82W, F82Y, and F82I), despite large differences in the ET distance. Theoretical analysis indicates that charge recombination for all complexes involves a combination of tunneling and hopping via Trp191. For three of the five structures (WT and F82S­(W)), the protein favors hopping more than that in the other two structures that have longer heme → ZnP distances (F82Y­(I)). Experimentally observed biexponential ET kinetics is explained by the complex locking in alternative coupling pathways, where the acceptor hole state is either primarily localized on ZnP (slow phase) or on Trp191 (fast phase). The large conformational differences between the CcP:<i>Cc</i> interface for the F82Y­(I) mutants compared to that the WT and F82S­(W) complexes are predicted to change the reorganization energies for the CcP:<i>Cc</i> ET reactions because of changes in solvent exposure and interprotein ET distances. Since the recombination reaction is likely to occur in the inverted Marcus regime, an increased reorganization energy compensates the decreased role for hopping recombination (and the longer transfer distance) in the F82Y­(I) mutants. Taken together, coupling pathway and reorganization energy effects for the five protein complexes explain the observed insensitivity of recombination kinetics to donor–acceptor distance and docking pose and also reveals how hopping through aromatic residues can accelerate long-range ET

<i>cheA₁^mut</i> is attenuated in causing systemic infection in immunodeficient mice.

To determine if CheA1 is required for B. burgdorferi immune evasion, needle infection study was repeated using severe combined immunodeficiency (SCIDs) mice. For this study, 105 of WT, cheA1mut and cheA1com strains were subcutaneously inoculated into SCID mice and sacrificed three weeks after infection. Skin tissues around and distal from the injection site were harvested along with tissues from the ear, joint, heart and spleen to assess for borrelial burden using qRT-PCR as described [17]. The data are presented as mean flaB transcript copies over 105 of mouse β-actin ± SEM. *, significant difference (P < 0.05).</p

Oligonucleotide primers used in this study.

As an enzootic pathogen, the Lyme disease bacterium Borrelia burgdorferi possesses multiple copies of chemotaxis proteins, including two chemotaxis histidine kinases (CHK), CheA1 and CheA2. Our previous study showed that CheA2 is a genuine CHK that is required for chemotaxis; however, the role of CheA1 remains mysterious. This report first compares the structural features that differentiate CheA1 and CheA2 and then provides evidence to show that CheA1 is an atypical CHK that controls the virulence of B. burgdorferi through modulating the stability of RpoS, a key transcriptional regulator of the spirochete. First, microscopic analyses using green-fluorescence-protein (GFP) tags reveal that CheA1 has a unique and dynamic cellular localization. Second, loss-of-function studies indicate that CheA1 is not required for chemotaxis in vitro despite sharing a high sequence and structural similarity to its counterparts from other bacteria. Third, mouse infection studies using needle inoculations show that a deletion mutant of CheA1 (cheA1mut) is able to establish systemic infection in immune-deficient mice but fails to do so in immune-competent mice albeit the mutant can survive at the inoculation site for up to 28 days. Tick and mouse infection studies further demonstrate that CheA1 is dispensable for tick colonization and acquisition but essential for tick transmission. Lastly, mechanistic studies combining immunoblotting, protein turnover, mutagenesis, and RNA-seq analyses reveal that depletion of CheA1 affects RpoS stability, leading to reduced expression of several RpoS-regulated virulence factors (i.e., OspC, BBK32, and DbpA), likely due to dysregulated clpX and lon protease expression. Bulk RNA-seq analysis of infected mouse skin tissues further show that cheA1mut fails to elicit mouse tnf-α, il-10, il-1β, and ccl2 expression, four important cytokines for Lyme disease development and B. burgdorferi transmigration. Collectively, these results reveal a unique role and regulatory mechanism of CheA1 in modulating virulence factor expression and add new insights into understanding the regulatory network of B. burgdorferi.</div

CheA₁ is not required for <i>B</i>. <i>burgdorferi</i> acquisition and survival in tick but necessary for transmission.

(A) Detection of spirochete burdens in microinjected nymphal ticks after feeding. RNA samples were extracted from whole fed ticks (after repletion; 5 to 7 days) and subjected to qRT-PCR analysis. The bacterial burdens in ticks were measured by the number of copies of flaB transcript compared to the number of copies of tick β-actin transcript as previously described [17]. The data are presented as the means of relative levels of flaB transcript ± SEM for each strain (WT, cheA1mut, and cheA1com). (B) Detection of spirochete burdens in mice infected via tick bite. At day 14 after tick feeding, mice were sacrificed and tissues from the skin, heart, joint, and bladder were harvested for qRT-PCR analysis as previously documented [17,107]. No trace of flaB transcript was detected in the mouse tissues fed upon by cheA1mut infected ticks while 1 in 3 mice fed upon by cheA1com showed positive results at the skin and heart tissues. *, significant difference (P (C) Detection of spirochete burdens in naïve nymphal ticks fed on infected mice. C3H mice were artificially infected with WT or cheA1mut strain via needle inoculation. Naïve nymphal ticks were confined to the injection site and allowed to feed to repletion. After 72 hours, fed nymphs were collected and individually tested for the presence of flaB via qPCR. Experiments were repeated twice and data are presented as mean flaB copies per fed nymph from both data sets ± SEM.</p

CheA₁ has a unique polar localization when cultivated under tick-like condition.

(A)In vitro localization of CheA1. To localize CheA1, a CheA1-GFP reporter construct (S3 Fig) was used to complement cheA1mut. The obtained cells were cultivated under unfed tick (UF) condition at 23°C/pH 7.6 or routine laboratory culture condition at 34°C/pH 7.6. Cells were monitored for the presence of GFP signal and images were taken at early log phase at ×200 magnification using a Zeiss Axiostar Plus microscope. Scale bars represent 10 μm. A cheA1mut carrying a GFP reporter construct was used as a control to confirm that the polar localization seen in CheA1-GFP complemented strain is due to CheA1 and not an artifact from GFP protein. (B) Time course images of CheA1-GFP strain cultivated under UF condition. 105 cells/ml of CheA1-GFP strain was inoculated into 10 ml fresh BSK-II and cultivated under UF condition. Images were taken every 2 days to monitor the localization of CheA1-GFP signals. As cells entered late log to early stationary phase, increasing numbers of discrete bright puncta were observed evenly distributed along the cell body, coincided with the zones of new peptidoglycan formation that mark the division sites for daughter cells [106].</p

<i>B. burgdorferi</i> RNA-seq analysis.

As an enzootic pathogen, the Lyme disease bacterium Borrelia burgdorferi possesses multiple copies of chemotaxis proteins, including two chemotaxis histidine kinases (CHK), CheA1 and CheA2. Our previous study showed that CheA2 is a genuine CHK that is required for chemotaxis; however, the role of CheA1 remains mysterious. This report first compares the structural features that differentiate CheA1 and CheA2 and then provides evidence to show that CheA1 is an atypical CHK that controls the virulence of B. burgdorferi through modulating the stability of RpoS, a key transcriptional regulator of the spirochete. First, microscopic analyses using green-fluorescence-protein (GFP) tags reveal that CheA1 has a unique and dynamic cellular localization. Second, loss-of-function studies indicate that CheA1 is not required for chemotaxis in vitro despite sharing a high sequence and structural similarity to its counterparts from other bacteria. Third, mouse infection studies using needle inoculations show that a deletion mutant of CheA1 (cheA1mut) is able to establish systemic infection in immune-deficient mice but fails to do so in immune-competent mice albeit the mutant can survive at the inoculation site for up to 28 days. Tick and mouse infection studies further demonstrate that CheA1 is dispensable for tick colonization and acquisition but essential for tick transmission. Lastly, mechanistic studies combining immunoblotting, protein turnover, mutagenesis, and RNA-seq analyses reveal that depletion of CheA1 affects RpoS stability, leading to reduced expression of several RpoS-regulated virulence factors (i.e., OspC, BBK32, and DbpA), likely due to dysregulated clpX and lon protease expression. Bulk RNA-seq analysis of infected mouse skin tissues further show that cheA1mut fails to elicit mouse tnf-α, il-10, il-1β, and ccl2 expression, four important cytokines for Lyme disease development and B. burgdorferi transmigration. Collectively, these results reveal a unique role and regulatory mechanism of CheA1 in modulating virulence factor expression and add new insights into understanding the regulatory network of B. burgdorferi.</div