Bacterial Energy Sensor Aer Modulates the Activity of the Chemotaxis Kinase CheA Based on the Redox State of the Flavin Cofactor

The VanS sensor histidine kinase from type-B VRE recognizes vancomycin directly

V ancomycin- r esistant e nterococci (VRE) are among the most common causes of nosocomial infections and have been prioritized as targets for new therapeutic development. Many genetically distinct types of VRE have been identified; however, they all share a common suite of resistance genes that function together to confer resistance to vancomycin. Expression of the resistance phenotype is controlled by the VanRS two-component system. This system senses the presence of the antibiotic, and responds by initiating transcription of resistance genes. VanS is a transmembrane sensor histidine kinase, and plays a fundamental role in antibiotic resistance by detecting vancomycin or its effects; it then transduces this signal to the VanR transcription factor, thereby alerting the organism to the presence of the antibiotic. Despite the critical role played by VanS, fundamental questions remain about its function, and in particular about how it senses vancomycin. Here, we focus on a purified VanRS system from one of the most clinically prevalent forms of VRE, type B. We show that in a native-like membrane environment, the autokinase activity of type-B VanS is strongly stimulated by vancomycin. We additionally demonstrate that this effect is mediated by a direct physical interaction between the antibiotic and the type-B VanS protein, and localize the interacting region to the protein's periplasmic domain. This represents the first time that a direct sensing mechanism has been confirmed for any VanS protein.

Significance Statement

When v ancomycin- r esistant e nterococci (VRE) sense the presence of vancomycin, they remodel their cell walls to block antibiotic binding. This resistance phenotype is controlled by the VanS protein, a histidine kinase that senses the antibiotic or its effects and signals for transcription of resistance genes. However, the mechanism by which VanS detects the antibiotic has remained unclear, with no consensus emerging as to whether the protein interacts directly with vancomycin, or instead detects some downstream consequence of vancomycin's action. Here, we show that for one of the most clinically relevant types of VRE, type B, VanS is activated by direct binding of the antibiotic. Such mechanistic insights will likely prove useful in circumventing vancomycin resistance.

Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid

The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.

Molecular insights into RmcA-mediated c-di-GMP consumption: Linking redox potential to biofilm morphogenesis in Pseudomonas aeruginosa

The ability of many bacteria to form biofilms contributes to their resilience and makes infections more difficult to treat. Biofilm growth leads to the formation of internal oxygen gradients, creating hypoxic subzones where cellular reducing power accumulates, and metabolic activities can be limited. The pathogen Pseudomonas aeruginosa counteracts the redox imbalance in the hypoxic biofilm subzones by producing redox-active electron shuttles (phenazines) and by secreting extracellular matrix, leading to an increased surface area-to-volume ratio, which favors gas exchange. Matrix production is regulated by the second messenger bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP) in response to different environmental cues. RmcA (Redox modulator of c-di-GMP) from P. aeruginosa is a multidomain phosphodiesterase (PDE) that modulates c-di-GMP levels in response to phenazine availability. RmcA can also sense the fermentable carbon source arginine via a periplasmic domain, which is linked via a transmembrane domain to four cytoplasmic Per-Arnt-Sim (PAS) domains followed by a diguanylate cyclase (DGC) and a PDE domain. The biochemical characterization of the cytoplasmic portion of RmcA reported in this work shows that the PAS domain adjacent to the catalytic domain tunes RmcA PDE activity in a redox-dependent manner, by differentially controlling protein conformation in response to FAD or FADH2. This redox-dependent mechanism likely links the redox state of phenazines (via FAD/FADH2 ratio) to matrix production as indicated by a hyperwrinkling phenotype in a macrocolony biofilm assay. This study provides insights into the role of RmcA in transducing cellular redox information into a structural response of the biofilm at the population level. Conditions of resource (i.e. oxygen and nutrient) limitation arise during chronic infection, affecting the cellular redox state and promoting antibiotic tolerance. An understanding of the molecular linkages between condition sensing and biofilm structure is therefore of crucial importance from both biological and engineering standpoints.

Bacterial chemotaxis in human diseases

To infect and cause disease, bacterial pathogens must localize to specific regions of the host where they possess the metabolic and defensive acumen for survival. Motile flagellated pathogens exercise control over their localization through chemotaxis to direct motility based on the landscape of exogenous nutrients, toxins, and molecular cues sensed within the host. Here, we review advances in understanding the roles chemotaxis plays in human diseases. Chemotaxis drives pathogen colonization to sites of inflammation and injury and mediates fitness advantages through accessing host-derived nutrients from damaged tissue. Injury tropism may worsen clinical outcomes through instigating chronic inflammation and subsequent cancer development. Inhibiting bacterial chemotactic systems could act synergistically with antibacterial medicines for more effective and specific eradication.

Endophytes and their potential in biotic stress management and crop production

Biotic stress is caused by harmful microbes that prevent plants from growing normally and also having numerous negative effects on agriculture crops globally. Many biotic factors such as bacteria, fungi, virus, weeds, insects, and nematodes are the major constrains of stress that tends to increase the reactive oxygen species that affect the physiological and molecular functioning of plants and also led to the decrease in crop productivity. Bacterial and fungal endophytes are the solution to overcome the tasks faced with conventional farming, and these are environment friendly microbial commodities that colonize in plant tissues without causing any damage. Endophytes play an important role in host fitness, uptake of nutrients, synthesis of phytohormone and diminish the injury triggered by pathogens via antibiosis, production of lytic enzymes, secondary metabolites, and hormone activation. They are also reported to help plants in coping with biotic stress, improving crops and soil health, respectively. Therefore, usage of endophytes as biofertilizers and biocontrol agent have developed an eco-friendly substitute to destructive chemicals for plant development and also in mitigation of biotic stress. Thus, this review highlighted the potential role of endophytes as biofertilizers, biocontrol agent, and in mitigation of biotic stress for maintenance of plant development and soil health for sustainable agriculture.

Redox properties and PAS domain structure of the Escherichia coli energy sensor Aer indicate a multistate sensing mechanism

The Per-Arnt-Sim (PAS; named for the representative proteins: Period, Aryl hydrocarbon receptor nuclear translocator protein and Single-minded) domain of the dimeric Escherichia coli aerotaxis receptor Aer monitors cellular respiration through a redox-sensitive flavin adenine dinucleotide (FAD) cofactor. Conformational shifts in the PAS domain instigated by the oxidized FAD (FAD_OX)/FAD anionic semiquinone (FAD_ASQ) redox couple traverse the HAMP (histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and kinase control domains of the Aer dimer to regulate CheA kinase activity. The PAS domain of Aer is unstable and has not been previously purified. Here, residue substitutions that rescue FAD binding in an FAD binding-deficient full-length Aer variant were used in combination to stabilize the Aer PAS domain. We solved the 2.4 Å resolution crystal structure of this variant, Aer-PAS-GVV, and revealed a PAS fold that contains distinct features associated with FAD-based redox sensing, such as a close contact between the Arg115 side chain and N5 of the isoalloxazine ring and interactions of the flavin with the side chains of His53 and Asn85 that are poised to convey conformational signals from the cofactor to the protein surface. In addition, we determined the FAD_ox/FAD_ASQ formal potentials of Aer-PAS-GVV and full-length Aer reconstituted into nanodiscs. The Aer redox couple is remarkably low at -289.6 ± 0.4 mV. In conclusion, we propose a model for Aer energy sensing based on the low potential of Aer-PAS-FAD_ox/FAD_ASQ couple and the inability of Aer-PAS to bind to the fully reduced FAD hydroquinone.

Endophytism: A Multidimensional Approach to Plant-Prokaryotic Microbe Interaction

Plant growth and development are positively regulated by the endophytic microbiome via both direct and indirect perspectives. Endophytes use phytohormone production to promote plant health along with other added benefits such as nutrient acquisition, nitrogen fixation, and survival under abiotic and biotic stress conditions. The ability of endophytes to penetrate the plant tissues, reside and interact with the host in multiple ways makes them unique. The common assumption that these endophytes interact with plants in a similar manner as the rhizospheric bacteria is a deterring factor to go deeper into their study, and more focus was on symbiotic associations and plant–pathogen reactions. The current focus has shifted on the complexity of relationships between host plants and their endophytic counterparts. It would be gripping to inspect how endophytes influence host gene expression and can be utilized to climb the ladder of “Sustainable agriculture.” Advancements in various molecular techniques have provided an impetus to elucidate the complexity of endophytic microbiome. The present review is focused on canvassing different aspects concerned with the multidimensional interaction of endophytes with plants along with their application.

Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins

Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.

Redox Titration of Flavoproteins: An Overview

Redox titration of flavoproteins allows to detect and analyze (1) the determinants of the stabilization of individual redox forms of the flavin by the protein; (2) the binding of the redox-active cofactor to the protein; (3) the effects of other components of the systems (such as micro- or macromolecular interactors) on parameters 1 and 2; (4) the pattern of electron flow to and from the flavin cofactor to other redox-active chemical species, including those present in the protein itself or in its physiological partners. This overview presents and discusses the fundamentals of the methodological approaches most commonly used for these purposes, and illustrates how data may be obtained in a reliable way, and how they can be read and interpreted.

Electrolocation? The evidence for redox-mediated taxis in Shewanella oneidensis

Shewanella oneidensis is a dissimilatory metal reducing bacterium and model for extracellular electron transfer (EET), a respiratory mechanism in which electrons are transferred out of the cell. In the last 10 years, migration to insoluble electron acceptors for EET has been shown to be nonrandom and tactic, seemingly in the absence of molecular or energy gradients that typically allow for taxis. As the ability to sense, locate, and respire electrodes has applications in bioelectrochemical technology, a better understanding of taxis in S. oneidensis is needed. While the EET conduits of S. oneidensis have been studied extensively, its taxis pathways and their interplay with EET are not yet understood, making investigation into taxis phenomena nontrivial. Since S. oneidensis is a member of an EET-encoding clade, the genetic circuitry of taxis to insoluble acceptors may be conserved. We performed a bioinformatic analysis of Shewanella genomes to identify S. oneidensis chemotaxis orthologs conserved in the genus. In addition to the previously reported core chemotaxis gene cluster, we identify several other conserved proteins in the taxis signaling pathway. We present the current evidence for the two proposed models of EET taxis, "electrokinesis" and flavin-mediated taxis, and highlight key areas in need of further investigation.

Phylogenetic characterization of the energy taxis receptor Aer in Pseudomonas and phenotypic characterization in Pseudomonas pseudoalcaligenes KF707

Chemotaxis allows bacteria to sense gradients in their environment and respond by directing their swimming. Aer is a receptor that, instead of responding to a specific chemoattractant, allows bacteria to sense cellular energy levels and move towards favourable environments. In Pseudomonas, the number of apparent Aer homologues differs between the only two species it has been characterized in, Pseudomonas aeruginosa and Pseudomonas putida. Here we combined bioinformatic approaches with deletional mutagenesis in Pseudomonas pseudoalcaligenes KF707 to further characterize Aer. It was determined that the number of Aer homologues varies between zero and four throughout the genus Pseudomonas, and they were phylogenetically classified into five subgroups. We also used sequence analysis to show that these homologous receptors differ in their HAMP signal transduction domains. Genetic analysis also indicated that some Aer homologues have likely been subject to horizontal transfer. P. pseudoalcaligenes KF707 was unique among strains for having three Aer homologues as well as the receptors CttP and McpB. Phenotypic characterization in this strain showed that the most prevalent homologue of Aer was key, but not essential, for energy taxis. This study demonstrates that energy taxis in Pseudomonas varies between species and provides a new naming convention and associated phylogenetic details for Aer chemoreceptors.

Protein Activity Sensing in Bacteria in Regulating Metabolism and Motility

Bacteria have evolved complex sensing and signaling systems to react to their changing environments, most of which are present in all domains of life. Canonical bacterial sensing and signaling modules, such as membrane-bound ligand-binding receptors and kinases, are very well described. However, there are distinct sensing mechanisms in bacteria that are less studied. For instance, the sensing of internal or external cues can also be mediated by changes in protein conformation, which can either be implicated in enzymatic reactions, transport channel formation or other important cellular functions. These activities can then feed into pathways of characterized kinases, which translocate the information to the DNA or other response units. This type of bacterial sensory activity has previously been termed protein activity sensing. In this review, we highlight the recent findings about this non-canonical sensory mechanism, as well as its involvement in metabolic functions and bacterial motility. Additionally, we explore some of the specific proteins and protein-protein interactions that mediate protein activity sensing and their downstream effects. The complex sensory activities covered in this review are important for bacterial navigation and gene regulation in their dynamic environment, be it host-associated, in microbial communities or free-living.

Global transcriptomic analysis of Cronobacter sakazakii CICC 21544 by RNA-seq under inorganic acid and organic acid stresses

Cronobacter sakazakii is a common foodborne pathogen that can tolerate various stress conditions. Acidic environment is a common stress condition encountered by bacteria in food processing and gastrointestinal digestion, including both inorganic and organic acids. In order to elucidate the Acid Tolerance Response (ATR) of C. sakazakii, we performed high-throughput RNA-seq to compare gene expression under hydrochloric acid and citric acid stresses. In this study, 107 differentially expressed genes (DEGs) were identified in both acids, of which 85 DEGs were functionally related to the regulation of acid tolerance. Multiple layers of mechanisms may be applied by C. sakazakii in response to acid stress: Firstly, in order to reduce excessive intracellular protons, C. sakazakii pumps them out through trans-membrane proteins or consumes them through metabolic reactions. Secondly, under acidic conditions, a large amount of reactive oxygen species and hydroxyl radicals accumulate in the cells, resulting in oxidative damage. C. sakazakii protects cells by up-regulating the antioxidant stress genes such as soxS and madB. Thirdly, C. sakazakii chooses energy efficient metabolic pathways to reduce energy consumption and maintain necessary processes. Finally, genes involved in chemotaxis and motility were differentially expressed to respond to different acidic conditions. This study systematically analyzed the acid-resistant mechanism of C. sakazakii under the stress of organic and inorganic acids, and provided a theoretical basis for better control of its contamination in food.

Regulation of the chemotaxis histidine kinase CheA: A structural perspective

Bacteria sense and respond to their environment through a highly conserved assembly of transmembrane chemoreceptors (MCPs), the histidine kinase CheA, and the coupling protein CheW, hereafter termed "the chemosensory array". In recent years, great strides have been made in understanding the architecture of the chemosensory array and how this assembly engenders sensitive and cooperative responses. Nonetheless, a central outstanding question surrounds how receptors modulate the activity of the CheA kinase, the enzymatic output of the sensory system. With a focus on recent advances, we summarize the current understanding of array structure and function to comment on the molecular mechanism by which CheA, receptors and CheW generate the high sensitivity, gain and dynamic range emblematic of bacterial chemotaxis. The complexity of the chemosensory arrays has motivated investigation with many different approaches. In particular, structural methods, genetics, cellular activity assays, nanodisc technology and cryo-electron tomography have provided advances that bridge length scales and connect molecular mechanism to cellular function. Given the high degree of component integration in the chemosensory arrays, we ultimately aim to understand how such networked molecular interactions generate a whole that is truly greater than the sum of its parts. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.

Physical methods for studying flavoprotein photoreceptors

Molecular mechanisms of dark-to-light state transitions in flavoprotein photoreceptors have been the subject of intense investigation. Blue-light sensing flavoproteins fall into three general classes that share aspects of their activation processes: LOV domains, BLUF proteins, and cryptochromes. In all cases, light-induced changes in flavin redox, protonation, and bonding states result in hydrogen-bond and conformational rearrangements important for regulation of downstream targets. Physical characterization of these flavoprotein states can provide valuable insights into biological function, but clear conclusions are often challenging to draw owing to complexities of data collection and interpretation. In this chapter, we briefly review the three classes of flavoprotein photoreceptors and provide methods for their recombinant production, reconstitution with flavin cofactor, and characterization. We then relate best practices and special considerations for the application of several types of spectroscopies, redox potential measurements, and X-ray scattering experiments to photosensitive flavoproteins. The methods presented are generally accessible to most laboratories.

Thermotaxis in Chlamydomonas is brought about by membrane excitation and controlled by redox conditions

Temperature is physiologically critical for all living organisms, which cope with temperature stress using metabolic and behavioral responses. In unicellular and some multicellular organisms, thermotaxis is a behavioral response to avoid stressful thermal environments and promote accumulation in an optimal thermal environment. In this study, we examined whether Chlamydomonas reinhardtii, a unicellular green alga, demonstrated thermotaxis. We found that between 10 °C and 30 °C, Chlamydomonas cells migrated toward lower temperatures independent of cultivation temperature. Interestingly, when we applied reagents to change intracellular reduction-oxidation (redox) conditions, we saw that thermotaxis was enhanced, suppressed, or reversed, depending on the redox conditions and cultivation temperature. Thermotaxis was almost absent in ppr2 and ppr3 mutants, which cannot swim backward because of a defect in generating calcium current in flagella. The frequency of spontaneous backward swimming was lower at more favorable temperature, suggesting a pivotal role of spontaneous backward swimming generated by flagellar membrane excitation.

mcp, aer, cheB, and cheV contribute to the regulation of Vibrio alginolyticus (ND-01) adhesion under gradients of environmental factors

Adhesion is a key virulence factor of pathogens and can be affected by the environment. Our previously research with RNA-seq indicated that mcp, aer, cheB, and cheV might play roles in the regulation of adhesion in Vibrio alginolyticus (ND-01). In order to determine whether and how environmental factors affect adhesion through these genes, gene silencing was performed followed by quantitative real-time PCR (qRT-PCR), RNAi, transmission electron microscopy, and adhesion, capillary, and motility assays to verify how these genes influence adhesion. Silencing these genes led to deficiencies in adhesion, chemotaxis, flagellar assembly, and motility. The expression levels of cheA, cheW, and cheY, which are important genes closely related to the functions of mcp, aer, cheV, and cheB, were significantly downregulated in all of the RNAi groups. The expression of mcp, aer, cheV, and cheB under different gradients of temperature, pH, and salinity and after starvation for various durations was also detected, which showed that these genes were sensitive to certain environmental stresses, particularly pH and starvation. Our results indicated that mcp, aer, cheB, and cheV: (1) are necessary for ND-01 adhesion; (2) play key roles in the bacterial chemotaxis pathway by controlling the expression of downstream genes; (3) might affect adhesion by impacting motility, though motility is not the only route through which adhesion is affected; and (4) contribute to the regulation of ND-01 adhesion in natural environments with different temperatures, pH levels, and salinities as well as after various starvation periods.

Sensory Repertoire of Bacterial Chemoreceptors

Chemoreceptors in bacteria detect a variety of signals and feed this information into chemosensory pathways that represent a major mode of signal transduction. The five chemoreceptors from Escherichia coli have served as traditional models in the study of this protein family. Genome analyses revealed that many bacteria contain much larger numbers of chemoreceptors with broader sensory capabilities. Chemoreceptors differ in topology, sensing mode, cellular location, and, above all, the type of ligand binding domain (LBD). Here, we highlight LBD diversity using well-established and emerging model organisms as well as genomic surveys. Nearly a hundred different types of protein domains that are found in chemoreceptor sequences are known or predicted LBDs, but only a few of them are ubiquitous. LBDs of the same class recognize different ligands, and conversely, the same ligand can be recognized by structurally different LBDs; however, recent studies began to reveal common characteristics in signal-LBD relationships. Although signals can stimulate chemoreceptors in a variety of different ways, diverse LBDs appear to employ a universal transmembrane signaling mechanism. Current and future studies aim to establish relationships between LBD types, the nature of signals that they recognize, and the mechanisms of signal recognition and transduction.