Bacterial transmembrane signalling systems and their engineering for biosensing

In Staphylococcus aureus, the acyl-CoA synthetase MbcS supports branched-chain fatty acid synthesis from carboxylic acid and aldehyde precursors

In the human pathogen Staphylococcus aureus, branched-chain fatty acids (BCFAs) are the most abundant fatty acids in membrane phospholipids. Strains deficient for BCFAs synthesis experience auxotrophy in laboratory culture and attenuated virulence during infection. Furthermore, the membrane of S. aureus is among the main targets for antibiotic therapy. Therefore, determining the mechanisms involved in BCFAs synthesis is critical to manage S. aureus infections. Here, we report that the overexpression of SAUSA300_2542 (annotated to encode an acyl-CoA synthetase) restores BCFAs synthesis in strains lacking the canonical biosynthetic pathway catalyzed by the branched-chain α-keto acid dehydrogenase (BKDH) complex. We demonstrate that the acyl-CoA synthetase activity of MbcS activates branched-chain carboxylic acids (BCCAs), and is required by S. aureus to utilize the isoleucine derivative 2-methylbutyraldehyde to restore BCFAs synthesis in S. aureus. Based on the ability of some staphylococci to convert branched-chain aldehydes into their respective BCCAs and our findings demonstrating that branched-chain aldehydes are in fact BCFAs precursors, we propose that MbcS promotes the scavenging of exogenous BCCAs and mediates BCFA synthesis via a de novo alternative pathway.

Antibody Nanotweezer Constructing Bivalent Transistor-Biomolecule Interface with Spatial Tolerance

Establishing a multivalent interface between the biointerface of a living system and electronic device is vital to building intelligent bioelectronic systems. How to achieve multivalent binding with spatial tolerance at the nanoscale remains challenging. Here, we report an antibody nanotweezer that is a self-adaptive bivalent nanobody enabling strong and resilient binding between transistor and envelope proteins at biointerfaces. The antibody nanotweezer is constructed by a DNA framework, where the nanoscale patterning of nanobodies along with their local spatial adaptivity enables simultaneous recognition of target epitopes without binding stress. As such, effective binding affinity increases by 1 order of magnitude compared with monovalent antibody. The antibody nanotweezer operating on transistor offers enhanced signal transduction, which is implemented to detect clinical pathogens, showing ∼100% overall agreement with PCR results. This work provides a perspective of engineering multivalent interfaces between biosystems with solid-state devices, holding great potential for organoid intelligence on a chip.

A critical role for iron and zinc homeostatic systems in the evolutionary adaptation of Escherichia coli to metal restriction

Host nutritional immunity utilizes metal deprivation to help prevent microbial infection. To investigate bacterial adaptation to such restrictive conditions, we conducted experimental evolution with two metal sequestering agents. Ethylenediaminetetraacetic acid (EDTA) and diethylenetriamine pentamethylene phosphonic acid (DTPMP) were selected as ligands because they differentially affect cellular levels of iron, manganese and zinc in Escherichia coli. Mutants of E. coli strain BW25113 were isolated after cultivation at sub-minimum inhibitory concentration (MIC) chelant levels and genetic changes potentially responsible for tolerance were identified by whole-genome sequencing. In EDTA-selected strains, mutations in the promoter region of yeiR resulted in elevated gene expression. The yeiR product, a zinc-specific metallochaperone, was confirmed to be primarily responsible for EDTA resistance. Similarly, in two of the DTPMP-selected strains, a promoter mutation increased expression of the fepA-entD operon, which encodes components of the ferric-enterobactin uptake pathway. However, in this case improved DTPMP tolerance was only detectable following overexpression of FepA or EntD in trans. Additional mutations in the cadC gene product, an acid-response regulator, preserved the neutrality of the growth medium by constitutively activating expression of the cadAB regulon. This study uncovers specific resistance mechanisms for zinc and iron starvation that could emerge by selection against host nutritional immunity or competition with heterologous metallophores. It also provides insight into the specific metals affected by these two widely used chelators critical for their antibacterial mode of action.

TetR and OmpR family regulators in natural product biosynthesis and resistance

This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.

A closed-loop catalytic nanoreactor system on a transistor

Precision chemistry demands miniaturized catalytic systems for sophisticated reactions with well-defined pathways. An ideal solution is to construct a nanoreactor system functioning as a chemistry laboratory to execute a full chemical process with molecular precision. However, existing nanoscale catalytic systems fail to in situ control reaction kinetics in a closed-loop manner, lacking the precision toward ultimate reaction efficiency. We find an inter-electrochemical gating effect when operating DNA framework-constructed enzyme cascade nanoreactors on a transistor, enabling in situ closed-loop reaction monitoring and modulation electrically. Therefore, a comprehensive system is developed, encapsulating nanoreactors, analyzers, and modulators, where the gate potential modulates enzyme activity and switches cascade reaction "ON" or "OFF." Such electric field-effect property enhances catalytic efficiency of enzyme by 343.4-fold and enables sensitive sarcosine assay for prostate cancer diagnoses, with a limit of detection five orders of magnitude lower than methodologies in clinical laboratory. By coupling with solid-state electronics, this work provides a perspective to construct intelligent nano-systems for precision chemistry.

Trends in the two-component system's role in the synthesis of antibiotics by Streptomyces

Despite the advances in understanding the regulatory networks for secondary metabolite production in Streptomyces, the participation of the two-component systems (TCS) in this process still requires better characterization. These sensing systems and their responses to environmental stimuli have been described by evaluating mutant strains with techniques that allow in-depth regulatory responses. However, defining the stimulus that triggers their activation is still a task. The transmembrane nature of the sensor kinases and the high content of GC in the streptomycetes represent significant challenges in their study. In some examples, adding elements to the assay medium has determined the respective ligand. However, a complete TCS description and characterization requires specific amounts of the involved proteins that are most difficult to obtain. The availability of enough sensor histidine kinase concentrations could facilitate the identification of the ligand-protein interaction, and besides would allow the establishment of its phosphorylation mechanisms and determine their tridimensional structure. Similarly, the advances in the development of bioinformatics tools and novel experimental techniques also promise to accelerate the TCSs description and provide knowledge on their participation in the regulation processes of secondary metabolite formation. This review aims to summarize the recent advances in the study of TCSs involved in antibiotic biosynthesis and to discuss alternatives to continue their characterization. KEY POINTS: • TCSs are the environmental signal transducers more abundant in nature. • The Streptomyces have some of the highest number of TCSs found in bacteria. • The study of signal transduction between SHKs and RRs domains is a big challenge.

Compartmentalized Cell-Free Expression Systems for Building Synthetic Cells

One of the grand challenges in bottom-up synthetic biology is the design and construction of synthetic cellular systems. One strategy toward this goal is the systematic reconstitution of biological processes using purified or non-living molecular components to recreate specific cellular functions such as metabolism, intercellular communication, signal transduction, and growth and division. Cell-free expression systems (CFES) are in vitro reconstitutions of the transcription and translation machinery found in cells and are a key technology for bottom-up synthetic biology. The open and simplified reaction environment of CFES has helped researchers discover fundamental concepts in the molecular biology of the cell. In recent decades, there has been a drive to encapsulate CFES reactions into cell-like compartments with the aim of building synthetic cells and multicellular systems. In this chapter, we discuss recent progress in compartmentalizing CFES to build simple and minimal models of biological processes that can help provide a better understanding of the process of self-assembly in molecularly complex systems.

BosR: A novel biofilm-specific regulator in Pseudomonas aeruginosa

Biofilms are the most common cause of bacterial infections in humans and notoriously hard to treat due to their ability to withstand antibiotics and host immune defenses. To overcome the current lack of effective antibiofilm therapies and guide future design, the identification of novel biofilm-specific gene targets is crucial. In this regard, transcriptional regulators have been proposed as promising targets for antimicrobial drug design. Therefore, a Transposon insertion sequencing approach was employed to systematically identify regulators phenotypically affecting biofilm growth in Pseudomonas aeruginosa PA14 using the TnSeq analysis tools Bio-TraDIS and TRANSIT. A screen of a pool of 300,000 transposon insertion mutants identified 349 genes involved in biofilm growth on hydroxyapatite, including 47 regulators. Detection of 19 regulatory genes participating in well-established biofilm pathways validated the results. An additional 28 novel prospective biofilm regulators suggested the requirement for multiple one-component transcriptional regulators. Biofilm-defective phenotypes were confirmed for five one-component transcriptional regulators and a protein kinase, which did not affect motility phenotypes. The one-component transcriptional regulator bosR displayed a conserved role in P. aeruginosa biofilm growth since its ortholog in P. aeruginosa strain PAO1 was also required for biofilm growth. Microscopic analysis of a chromosomal deletion mutant of bosR confirmed the role of this regulator in biofilm growth. Overall, our results highlighted that the gene network driving biofilm growth is complex and involves regulators beyond the primarily studied groups of two-component systems and cyclic diguanylate signaling proteins. Furthermore, biofilm-specific regulators, such as bosR, might constitute prospective new drug targets to overcome biofilm infections.

The fciTABC and feoABI systems contribute to ferric citrate acquisition in Stenotrophomonas maltophilia

Background

Stenotrophomonas maltophilia, a member of γ-proteobacteria, is a ubiquitous environmental bacterium that is recognized as an opportunistic nosocomial pathogen. FecABCD system contributes to ferric citrate acquisition in Escherichia coli. FeoABC system, consisting of an inner membrane transporter (FeoB) and two cytoplasmic proteins (FeoA and FeoC), is a well-known ferrous iron transporter system in γ-proteobacteria. As revealed by the sequenced genome, S. maltophilia appears to be equipped with several iron acquisition systems; however, the understanding of these systems is limited. In this study, we aimed to elucidate the ferric citrate acquisition system of S. maltophilia.

Methods

Candidate genes searching and function validation are the strategy for elucidating the genes involved in ferric citrate acquisition. The candidate genes responsible for ferric citrate acquisition were firstly selected using FecABCD of E. coli as a reference, and then revealed by transcriptome analysis of S. maltophilia KJ with and without 2,2′-dipyridyl (DIP) treatment. Function validation was carried out by deletion mutant construction and ferric citrate utilization assay. The bacterial adenylate cyclase two-hybrid system was used to verify intra-membrane protein–protein interaction.

Results

Smlt2858 and Smlt2356, the homologues of FecA and FecC/D of E. coli, were first considered; however, deletion mutant construction and functional validation ruled out their involvement in ferric citrate acquisition. FciA (Smlt1148), revealed by its upregulation in DIP-treated KJ cells, was the outer membrane receptor for ferric citrate uptake. The fciA gene is a member of the fciTABC operon, in which fciT, fciA, and fciC participated in ferric citrate acquisition. Uniquely, the Feo system of S. maltophilia is composed of a cytoplasmic protein FeoA, an inner membrane transporter FeoB, and a predicted inner membrane protein FeoI. The intra-membrane protein–protein interaction between FeoB and FeoI may extend the substrate profile of FeoB to ferric citrate. FeoABI system functioned as an inner membrane transporter of ferric citrate.

Conclusions

The FciTABC and FeoABI systems contribute to ferric citrate acquisition in S. maltophilia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12929-022-00809-y.

Division of labor and collective functionality in Escherichia coli under acid stress

The acid stress response is an important factor influencing the transmission of intestinal microbes such as the enterobacterium Escherichia coli. E. coli activates three inducible acid resistance systems - the glutamate decarboxylase, arginine decarboxylase, and lysine decarboxylase systems to counteract acid stress. Each system relies on the activity of a proton-consuming reaction catalyzed by a specific amino acid decarboxylase and a corresponding antiporter. Activation of these three systems is tightly regulated by a sophisticated interplay of membrane-integrated and soluble regulators. Using a fluorescent triple reporter strain, we quantitatively illuminated the cellular individuality during activation of each of the three acid resistance (AR) systems under consecutively increasing acid stress. Our studies highlight the advantages of E. coli in possessing three AR systems that enable division of labor in the population, which ensures survival over a wide range of low pH values.

The Regulatory Hierarchy Following Signal Integration by the CbrAB Two-Component System: Diversity of Responses and Functions

CbrAB is a two-component system, unique to bacteria of the family Pseudomonaceae, capable of integrating signals and involved in a multitude of physiological processes that allow bacterial adaptation to a wide variety of varying environmental conditions. This regulatory system provides a great metabolic versatility that results in excellent adaptability and metabolic optimization. The two-component system (TCS) CbrA-CbrB is on top of a hierarchical regulatory cascade and interacts with other regulatory systems at different levels, resulting in a robust output. Among the regulatory systems found at the same or lower levels of CbrAB are the NtrBC nitrogen availability adaptation system, the Crc/Hfq carbon catabolite repression cascade in Pseudomonas, or interactions with the GacSA TCS or alternative sigma ECF factor, such as SigX. The interplay between regulatory mechanisms controls a number of physiological processes that intervene in important aspects of bacterial adaptation and survival. These include the hierarchy in the use of carbon sources, virulence or resistance to antibiotics, stress response or definition of the bacterial lifestyle. The multiple actions of the CbrAB TCS result in an important competitive advantage.

Allostery and protein plasticity: the keystones for bacterial signaling and regulation

Bacteria sense intracellular and environmental signals using an array of proteins as antennas. The information is transmitted from such sensory modules to other protein domains that act as output effectors. Sensor and effector can be part of the same polypeptide or instead be separate diffusible proteins that interact specifically. The output effector modules regulate physiologic responses, allowing the cells to adapt to the varying conditions. These biological machineries are known as signal transduction systems (STSs). Despite the captivating architectural diversity exhibited by STS proteins, a universal feature is their allosteric regulation: signal binding at one site modifies the activity at a physically distant site. Allostery requires protein plasticity, precisely encoded within their 3D structures, and implicating programmed molecular motions. This review summarizes how STS proteins connect stimuli to specific responses by exploiting allostery and protein plasticity. Illustrative examples spanning a wide variety of protein folds will focus on one- and two-component systems (TCSs). The former encompass the entire transmission route within a single polypeptide, whereas TCSs have evolved as separate diffusible proteins that interact specifically, sometimes including additional intermediary proteins in the pathway. Irrespective of their structural diversity, STS proteins are able to modulate their own molecular motions, which can be relatively slow, rigid-body movements, all the way to fast fluctuations in the form of macromolecular flexibility, thus spanning a continuous protein dynamics spectrum. In sum, STSs rely on allostery to steer information transmission, going from simple two-state switching to rich multi-state conformational order/disorder transitions.

Strategic traits of bacteria and archaea vary widely within substrate-use groups

Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.

Programmable receptors enable bacterial biosensors to detect pathological biomarkers in clinical samples

Bacterial biosensors, or bactosensors, are promising agents for medical and environmental diagnostics. However, the lack of scalable frameworks to systematically program ligand detection limits their applications. Here we show how novel, clinically relevant sensing modalities can be introduced into bactosensors in a modular fashion. To do so, we have leveraged a synthetic receptor platform, termed EMeRALD (Engineered Modularized Receptors Activated via Ligand-induced Dimerization) which supports the modular assembly of sensing modules onto a high-performance, generic signaling scaffold controlling gene expression in E. coli. We apply EMeRALD to detect bile salts, a biomarker of liver dysfunction, by repurposing sensing modules from enteropathogenic Vibrio species. We improve the sensitivity and lower the limit-of-detection of the sensing module by directed evolution. We then engineer a colorimetric bactosensor detecting pathological bile salt levels in serum from patients having undergone liver transplant, providing an output detectable by the naked-eye. The EMeRALD technology enables functional exploration of natural sensing modules and rapid engineering of synthetic receptors for diagnostics, environmental monitoring, and control of therapeutic microbes.

Engineered acetoacetate-inducible whole-cell biosensors based on the AtoSC two-component system

Whole-cell biosensors hold potential in a variety of industrial, medical, and environmental applications. These biosensors can be constructed through the repurposing of bacterial sensing mechanisms, including the common two-component system (TCS). Here we report on the construction of a range of novel biosensors that are sensitive to acetoacetate, a molecule that plays a number of roles in human health and biology. These biosensors are based on the AtoSC TCS. An ordinary differential equation model to describe the action of the AtoSC TCS was developed and sensitivity analysis of this model used to help inform biosensor design. The final collection of biosensors constructed displayed a range of switching behaviours at physiologically relevant acetoacetate concentrations and can operate in several Escherichia coli host strains. It is envisaged that these biosensor strains will offer an alternative to currently available commercial strip tests and, in future, may be adopted for more complex in vivo or industrial monitoring applications.

Understanding D-xylonic acid accumulation: a cornerstone for better metabolic engineering approaches

The xylose oxidative pathway (XOP) has been engineered in microorganisms for the production of a wide range of industrially relevant compounds. However, the performance of metabolically engineered XOP-utilizing microorganisms is typically hindered by D-xylonic acid accumulation. It acidifies the media and perturbs cell growth due to toxicity, thus curtailing enzymatic activity and target product formation. Fortunately, from the growing portfolio of genetic tools, several strategies that can be adapted for the generation of efficient microbial cell factories have been implemented to address D-xylonic acid accumulation. This review centers its discussion on the causes of D-xylonic acid accumulation and how to address it through different engineering and synthetic biology techniques with emphasis given on bacterial strains. In the first part of this review, the ability of certain microorganisms to produce and tolerate D-xylonic acid is also tackled as an important aspect in developing efficient microbial cell factories. Overall, this review could shed some insights and clarity to those working on XOP in bacteria and its engineering for the development of industrially applicable product-specialist strains. KEY POINTS: D-Xylonic acid accumulation is attributed to the overexpression of xylose dehydrogenase concomitant with basal or inefficient expression of enzymes involved in D-xylonic acid assimilation. Redox imbalance and insufficient cofactors contribute to D-xylonic acid accumulation. Overcoming D-xylonic acid accumulation can increase product formation among engineered strains. Engineering strategies involving enzyme engineering, evolutionary engineering, coutilization of different sugar substrates, and synergy of different pathways could potentially address D-xylonic acid accumulation.

Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity

Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.

Proline codon pair selection determines ribosome pausing strength and translation efficiency in bacteria

The speed of mRNA translation depends in part on the amino acid to be incorporated into the nascent chain. Peptide bond formation is especially slow with proline and two adjacent prolines can even cause ribosome stalling. While previous studies focused on how the amino acid context of a Pro-Pro motif determines the stalling strength, we extend this question to the mRNA level. Bioinformatics analysis of the Escherichia coli genome revealed significantly differing codon usage between single and consecutive prolines. We therefore developed a luminescence reporter to detect ribosome pausing in living cells, enabling us to dissect the roles of codon choice and tRNA selection as well as to explain the genome scale observations. Specifically, we found a strong selective pressure against CCC/U-C, a sequon causing ribosomal frameshifting even under wild-type conditions. On the other hand, translation efficiency as positive evolutionary driving force led to an overrepresentation of CCG. This codon is not only translated the fastest, but the corresponding prolyl-tRNA reaches almost saturating levels. By contrast, CCA, for which the cognate prolyl-tRNA amounts are limiting, is used to regulate pausing strength. Thus, codon selection both in discrete positions but especially in proline codon pairs can tune protein copy numbers.

Distinctive features of the Gac-Rsm pathway in plant-associated Pseudomonas

Productive plant-bacteria interactions, either beneficial or pathogenic, require that bacteria successfully sense, integrate and respond to continuously changing environmental and plant stimuli. They use complex signal transduction systems that control a vast array of genes and functions. The Gac-Rsm global regulatory pathway plays a key role in controlling fundamental aspects of the apparently different lifestyles of plant beneficial and phytopathogenic Pseudomonas as it coordinates adaptation and survival while either promoting plant health (biocontrol strains) or causing disease (pathogenic strains). Plant-interacting Pseudomonas stand out for possessing multiple Rsm proteins and Rsm RNAs, but the physiological significance of this redundancy is not yet clear. Strikingly, the components of the Gac-Rsm pathway and the controlled genes/pathways are similar, but the outcome of its regulation may be opposite. Therefore, identifying the target mRNAs bound by the Rsm proteins and their mode of action (repression or activation) is essential to explain the resulting phenotype. Some technical considerations to approach the study of this system are also given. Overall, several important features of the Gac-Rsm cascade are now understood in molecular detail, particularly in Pseudomonas protegens CHA0, but further questions remain to be solved in other plant-interacting Pseudomonas.

Dynamics of chromosomal target search by a membrane-integrated one-component receptor

Membrane proteins account for about one third of the cellular proteome, but it is still unclear how dynamic they are and how they establish functional contacts with cytoplasmic interaction partners. Here, we consider a membrane-integrated one-component receptor that also acts as a transcriptional activator, and analyze how it kinetically locates its specific binding site on the genome. We focus on the case of CadC, the pH receptor of the acid stress response Cad system in E. coli. CadC is a prime example of a one-component signaling protein that directly binds to its cognate target site on the chromosome to regulate transcription. We combined fluorescence microscopy experiments, mathematical analysis, and kinetic Monte Carlo simulations to probe this target search process. Using fluorescently labeled CadC, we measured the time from activation of the receptor until successful binding to the DNA in single cells, exploiting that stable receptor-DNA complexes are visible as fluorescent spots. Our experimental data indicate that CadC is highly mobile in the membrane and finds its target by a 2D diffusion and capture mechanism. DNA mobility is constrained due to the overall chromosome organization, but a labeled DNA locus in the vicinity of the target site appears sufficiently mobile to randomly come close to the membrane. Relocation of the DNA target site to a distant position on the chromosome had almost no effect on the mean search time, which was between four and five minutes in either case. However, a mutant strain with two binding sites displayed a mean search time that was reduced by about a factor of two. This behavior is consistent with simulations of a coarse-grained lattice model for the coupled dynamics of DNA within a cell volume and proteins on its surface. The model also rationalizes the experimentally determined distribution of search times. Overall our findings reveal that DNA target search does not present a much bigger kinetic challenge for membrane-integrated proteins than for cytoplasmic proteins. More generally, diffusion and capture mechanisms may be sufficient for bacterial membrane proteins to establish functional contacts with cytoplasmic targets.

Adaptation to changing environments is vital to bacteria and is enabled by sophisticated signal transduction systems. While signal transduction by two-component systems is well studied, the signal transduction of membrane-integrated one-component systems, where one protein performs both sensing and response regulation, are insufficiently understood. How can a membrane-integrated protein bind to specific sites on the genome to regulate transcription? Here, we study the kinetics of this process, which involves both protein diffusion within the membrane and conformational fluctuations of the genomic DNA. A well-suited model system for this question is CadC, the signaling protein of the E. coli Cad system involved in pH stress response. Fluorescently labeled CadC forms visible spots in single cells upon stable DNA-binding, marking the end of the protein-DNA search process. Moreover, the start of the search is triggered by a medium shift exposing cells to pH stress. We probe the underlying mechanism by varying the number and position of DNA target sites. We combine these experiments with mathematical analysis and kinetic Monte Carlo simulations of lattice models for the search process. Our results suggest that CadC diffusion in the membrane is pivotal for this search, while the DNA target site is just mobile enough to reach the membrane.

Bacterial flagellar motor as a multimodal biosensor

Bacterial Flagellar Motor is one of nature's rare rotary molecular machines. It enables bacterial swimming and it is the key part of the bacterial chemotactic network, one of the best studied chemical signalling networks in biology, which enables bacteria to direct its movement in accordance with the chemical environment. The network can sense down to nanomolar concentrations of specific chemicals on the time scale of seconds. Motor's rotational speed is linearly proportional to the electrochemical gradients of either proton or sodium driving ions, while its direction is regulated by the chemotactic network. Recently, it has been discovered that motor is also a mechanosensor. Given these properties, we discuss the motor's potential to serve as a multifunctional biosensor and a tool for characterising and studying the external environment, the bacterial physiology itself and single molecular motor biophysics.

Two-Component Signal Transduction Systems in the Human Pathogen Streptococcus agalactiae

Streptococcus agalactiae (group B Streptococcus [GBS]) is an important cause of invasive infection in newborns, maternal women, and older individuals with underlying chronic illnesses. GBS has many mechanisms to adapt and survive in its host, and these mechanisms are often controlled via two-component signal transduction systems. In GBS, more than 20 distinct two-component systems (TCSs) have been classified to date, consisting of canonical TCSs as well as orphan and atypical sensors and regulators. These signal transducing systems are necessary for metabolic regulation, resistance to antibiotics and antimicrobials, pathogenesis, and adhesion to the mucosal surfaces to colonize the host. This minireview discusses the structures of these TCSs in GBS as well as how selected systems regulate essential cellular processes such as survival and colonization. GBS contains almost double the number of TCSs compared to the closely related Streptococcus pyogenes and Streptococcus pneumoniae, and while research on GBS TCSs has been increasing in recent years, no comprehensive reviews of these TCSs exist, making this review especially relevant.

Host stimuli and operator binding sites controlling protein interactions between virulence master regulator ToxR and ToxS in Vibrio cholerae

Protein-protein interactions (PPIs) are key mechanisms in the maintenance of biological regulatory networks. Herein, we characterize PPIs within ToxR and its co-activator, ToxS, to understand the mechanisms of ToxR transcription factor activation. ToxR is a key transcription activator that is supported by ToxS for virulence gene regulation in Vibrio cholerae. ToxR comprises a cytoplasmic DNA-binding domain that is linked by a transmembrane domain to a periplasmic signal receiver domain containing two cysteine residues. ToxR-ToxR and ToxR-ToxS PPIs were detected using an adenylate-cyclase-based bacterial two-hybrid system approach in Escherichia coli. We found that the ToxR-ToxR PPIs are significantly increased in response to ToxR operators, the co-activator ToxS and bile salts. We suggest that ToxS and bile salts promote the interaction between ToxR molecules that ultimately results in dimerization. Upon binding of operators, ToxR-ToxR PPIs are found at the highest frequency. Moreover, disulfide-bond-dependent interaction in the periplasm results in homodimer formation that is promoted by DNA binding. The formation of these homodimers and the associated transcriptional activity of ToxR were strongly dependent on the oxidoreductases DsbA/DsbC. These findings show that protein and non-protein partners, that either transiently or stably interact with ToxR, fine-tune ToxR PPIs, and its associated transcriptional activity in changing environments.

Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting

Extracting structural information from sequence co-variation has become a common computational biology practice in the recent years, mainly due to the availability of large sequence alignments of protein families. However, identifying features that are specific to sub-classes and not shared by all members of the family using sequence-based approaches has remained an elusive problem. We here present a coevolutionary-based method to differentially analyze subfamily specific structural features by a continuous sequence reweighting (SR) approach. We introduce the underlying principles and test its predictive capabilities on the Response Regulator family, whose subfamilies have been previously shown to display distinct, specific homo-dimerization patterns. Our results show that this reweighting scheme is effective in assigning structural features known a priori to subfamilies, even when sequence data is relatively scarce. Furthermore, sequence reweighting allows assessing if individual structural contacts pertain to specific subfamilies and it thus paves the way for the identification specificity-determining contacts from sequence variation data.

A pH-responsive genetic sensor for the dynamic regulation of D-xylonic acid accumulation in Escherichia coli

The xylose oxidative pathway (XOP) is continuously gaining prominence as an alternative for the traditional pentose assimilative pathways in prokaryotes. It begins with the oxidation of D-xylose to D-xylonic acid, which is further converted to α-ketoglutarate or pyruvate + glycolaldehyde through a series of enzyme reactions. The persistent drawback of XOP is the accumulation of D-xylonic acid intermediate that causes culture media acidification. This study addresses this issue through the development of a novel pH-responsive synthetic genetic controller that uses a modified transmembrane transcription factor called CadCΔ. This genetic circuit was tested for its ability to detect extracellular pH and to control the buildup of D-xylonic acid in the culture media. Results showed that the pH-responsive genetic sensor confers dynamic regulation of D-xylonic acid accumulation, which adjusts with the perturbation of culture media pH. This is the first report demonstrating the use of a pH-responsive transmembrane transcription factor as a transducer in a synthetic genetic circuit that was designed for XOP. This may serve as a benchmark for the development of other genetic controllers for similar pathways that involve acidic intermediates.

What do archaeal and eukaryotic histidine kinases sense?

Signal transduction systems configured around a core phosphotransfer step between a histidine kinase and a cognate response regulator protein occur in organisms from all domains of life. These systems, termed two-component systems, constitute the majority of multi-component signaling pathways in Bacteria but are less prevalent in Archaea and Eukarya. The core signaling domains are modular, allowing versatility in configuration of components into single-step phosphotransfer and multi-step phosphorelay pathways, the former being predominant in bacteria and the latter in eukaryotes. Two-component systems regulate key cellular regulatory processes that provide adaptive responses to environmental stimuli and are of interest for the development of antimicrobial therapeutics, biotechnology applications, and biosensor engineering. In bacteria, two-component systems have been found to mediate responses to an extremely broad array of extracellular and intracellular chemical and physical stimuli, whereas in archaea and eukaryotes, the use of two-component systems is more limited. This review summarizes recent advances in exploring the repertoire of sensor histidine kinases in the Archaea and Eukarya domains of life.

Exceptionally versatile – arginine in bacterial post-translational protein modifications

Post-translational modifications (PTM) are the evolutionary solution to challenge and extend the boundaries of genetically predetermined proteomic diversity. As PTMs are highly dynamic, they also hold an enormous regulatory potential. It is therefore not surprising that out of the 20 proteinogenic amino acids, 15 can be post-translationally modified. Even the relatively inert guanidino group of arginine is subject to a multitude of mostly enzyme mediated chemical changes. The resulting alterations can have a major influence on protein function. In this review, we will discuss how bacteria control their cellular processes and develop pathogenicity based on post-translational protein-arginine modifications.

Unraveling the role of the CbrA histidine kinase in the signal transduction of the CbrAB two-component system in Pseudomonas putida

The histidine kinase CbrA of the CbrAB two-component system of Pseudomonas putida is a key element to recognise the activating signal and mediate auto- and trans-phosphorylation of the response element CbrB. CbrA is encoded by the gene cbrA which is located downstream of a putative open reading frame we have named cbrX. We describe the role of the CbrX product in the expression of CbrA and show there is translational coupling of the genes. We also explore the role of the transmembrane (TM) and PAS domains of CbrA in the signal recognition. A ΔcbrXA mutant lacking its TM domains is uncoupled in its growth in histidine and citrate as carbon sources, but its overexpression restores the ability to grow in such carbon sources. In these conditions ΔTM-CbrA is able to respond to carbon availability, thus suggesting an intracellular nature for the signal sensed.

DNA-binding directs the localization of a membrane-integrated receptor of the ToxR family

All living cells have a large number of proteins that are anchored with one transmembrane helix in the cytoplasmic membrane. Almost nothing is known about their spatiotemporal organization in whole cells. Here we report on the localization and dynamics of one representative, the pH sensor and transcriptional regulator CadC in Escherichia coli. Fluorophore-tagged CadC was detectable as distinct cluster only when the receptor was activated by external stress, which results in DNA-binding. Clusters immediately disappeared under non-stress conditions. CadC variants that mimic the active state of CadC independent of environmental stimuli corroborated the correlation between CadC clustering and binding to the DNA, as did altering the number or location of the DNA-binding site(s) in whole cells. These studies reveal a novel diffusion-and-capture mechanism to organize a membrane-integrated receptor dependent on the DNA in a rod-shaped bacterium.