Bacterial permeases

Cytoplasmic Accumulation and Permeability of Antibiotics in Gram Positive and Gram Negative Bacteria Visualized in Real-Time via a Fluorogenic Tagging Strategy

In this study, we describe the first real-time live cell assay for compound accumulation and permeability in both Gram positive and Gram negative bacteria. The assay utilizes a novel fluorogenic tagging strategy that permits direct visualization of compound accumulation dynamics in the cytoplasm of live cells, unobscured by washing or other processing steps. Quantitative differences could be reproducibly measured by flow cytometry at compound concentrations below the limit of detection for MS-based approaches. We establish the fluorogenic assay in E. coli and B. subtilis and compare the intracellular accumulation of two antibiotics, ciprofloxacin and ampicillin, with related pharmacophores in these bacteria.

Cracking outer membrane biogenesis

The outer membrane is a distinguishing feature of the Gram-negative envelope. It lies on the external face of the peptidoglycan sacculus and forms a robust permeability barrier that protects extracytoplasmic structures from environmental insults. Overcoming the barrier imposed by the outer membrane presents a significant hurdle towards developing novel antibiotics that are effective against Gram-negative bacteria. As the outer membrane is an essential component of the cell, proteins involved in its biogenesis are themselves promising antibiotic targets. Here, we summarize key findings that have built our understanding of the outer membrane. Foundational studies describing the discovery and composition of the outer membrane as well as the pathways involved in its construction are discussed.

How Escherichia coli Became the Flagship Bacterium of Molecular Biology

Escherichia coli is likely the most studied organism and was instrumental in developing many fundamental concepts in biology. But why E. coli? In the 1940s, E. coli was well suited for the biochemical and genetic research that blended to become the seminal field of biochemical genetics and led to the realization that processes already known to occur in complex organisms were conserved in bacteria. This now-obvious concept, combined with the advantages offered by its easy cultivation, ultimately drove many researchers to shift from the complexity of eukaryotic models to the simpler bacterial system, which eventually led to the development of molecular biology. As knowledge and experimental tools amassed, a positive-feedback loop fixed the central role of E. coli in research. However, given the vast diversity among bacteria and even among E. coli strains, it was by many fortuitous events that E. coli rose to the top as an experimental model. Here, we share how serendipity and its own biology selected E. coli as the flagship bacterium of molecular biology.

The β-galactosidase assay in perspective: Critical thoughts for biosensor development

Recently, the β-galactosidase assay has become a key component in the development of assays and biosensors for the detection of enterobacteria and E. coli in water quality monitoring. The assay has often performed below its maximum potential, mainly due to a poor choice of conditions. In this study we establish a set of optimal conditions and provide a rough estimate of how departure from optimal values reduces the output of the assay potentially decreasing its sensitivity. We have established that maximum response for detecting low cell concentrations requires an induction of the samples using IPTG at a concentration of 0.2 mM during 180 min. Permeabilization of the samples is mandatory as lack of it results in an almost 60% reduction in assay output. The choice of enzyme substrate is critical as different substrates yield products with different extinction coefficients or fluorescence yields. The concentration of substrate used must be high enough (around 3 to 4 times K_m) to ensure that the activity measured is not substrate limited. Finally, as the color/fluorescence of the reaction products is highly dependent on pH, care must be taken to ensure that pH at the time of reading is high enough to provide maximum signal.

The biological Maxwell's demons: exploring ideas about the information processing in biological systems

This work is based on ideas supported by some of the biologists who discovered foundational facts of twentieth-century biology and who argued that Maxwell's demons are physically implemented by biological devices. In particular, JBS Haldane first, and later J. Monod, A, Lwoff and F. Jacob argued that enzymes and molecular receptors implemented Maxwell's demons that operate in systems far removed from thermodynamic equilibrium and that were responsible for creating the biological order. Later, these ideas were extended to other biological processes. In this article, we argue that these biological Maxwell's demons (BMD) are systems that have information processing capabilities that allow them to select their inputs and direct their outputs toward targets. In this context, we propose the idea that these BMD are information catalysts in which the processed information has broad thermodynamic consequences.

Omnipresent Maxwell's demons orchestrate information management in living cells

The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information-managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers.

Regulation of Camphor Metabolism: Induction and Repression of Relevant Monooxygenases in Pseudomonas putida NCIMB 10007

For the first time, the differential rates of synthesis of all the key monooxygenases involved in the catabolism by Pseudomonas putida NCIMB 10007 of bicyclic (rac)-camphor to ∆2,5-3,4,4-trimethylpimelyl-CoA, the first aliphatic pathway intermediate, have been determined to help establish the relevant induction profile of each of the oxygen-dependent enzymes. The efficacy of both relevant substrates and pathway metabolites as inducers has been established. Further, inhibitors with characterised functionality have been used to indicate that the pertinent regulatory controls operate at the level of transcription of the corresponding genes.

Tribute to Marcelle Grenson (1925-1996), A Pioneer in the Study of Amino Acid Transport in Yeast

The year 2016 marked the 20th anniversary of the death of Marcelle Grenson and the 50th anniversary of her first publication on yeast amino acid transport, the topic to which, as Professor at the Free University of Brussels (ULB), she devoted the major part of her scientific career. M. Grenson was the first scientist in Belgium to introduce and apply genetic analysis in yeast to dissect the molecular mechanisms that were underlying complex problems in biology. Today, M. Grenson is recognized for the pioneering character of her work on the diversity and regulation of amino acid transporters in yeast. The aim of this tribute is to review the major milestones of her forty years of scientific research that were conducted between 1950 and 1990.

Once upon a time the cell membranes: 175 years of cell boundary research

All modern cells are bounded by cell membranes best described by the fluid mosaic model. This statement is so widely accepted by biologists that little attention is generally given to the theoretical importance of cell membranes in describing the cell. This has not always been the case. When the Cell Theory was first formulated in the XIX(th) century, almost nothing was known about the cell membranes. It was not until well into the XX(th) century that the existence of the plasma membrane was broadly accepted and, even then, the fluid mosaic model did not prevail until the 1970s. How were the cell boundaries considered between the articulation of the Cell Theory around 1839 and the formulation of the fluid mosaic model that has described the cell membranes since 1972? In this review I will summarize the major historical discoveries and theories that tackled the existence and structure of membranes and I will analyze how these theories impacted the understanding of the cell. Apart from its purely historical relevance, this account can provide a starting point for considering the theoretical significance of membranes to the definition of the cell and could have implications for research on early life.

Gene network requirements for regulation of metabolic gene expression to a desired state

Gene circuits that control metabolism should restore metabolic functions upon environmental changes. Whether gene networks are capable of steering metabolism to optimal states is an open question. Here we present a method to identify such optimal gene networks. We show that metabolic network optimisation over a range of environments results in an input-output relationship for the gene network that guarantees optimal metabolic states. Optimal control is possible if the gene network can achieve this input-output relationship. We illustrate our approach with the best-studied regulatory network in yeast, the galactose network. We find that over the entire range of external galactose concentrations, the regulatory network is able to optimally steer galactose metabolism. Only a few gene network parameters affect this optimal regulation. The other parameters can be tuned independently for optimisation of other functions, such as fast and low-noise gene expression. This study highlights gene network plasticity, evolvability, and modular functionality.

The nicotinic acetylcholine receptor: the founding father of the pentameric ligand-gated ion channel superfamily

A critical event in the history of biological chemistry was the chemical identification of the first neurotransmitter receptor, the nicotinic acetylcholine receptor. Disciplines as diverse as electrophysiology, pharmacology, and biochemistry joined together in a unified and rational manner with the common goal of successfully identifying the molecular device that converts a chemical signal into an electrical one in the nervous system. The nicotinic receptor has become the founding father of a broad family of pentameric membrane receptors, paving the way for their identification, including that of the GABA(A) receptors.

Catabolic Activities of Neisseria meningitidis: Utilization of Succinate

When resting cells of Neisseria meningitidis group B were incubated with either succinate, fumarate, or malate, respiration and CO(2) production were not significantly stimulated. These dicarboxylic acids were readily utilized, however, when they were added in association with a combination of alpha-ketoglutarate and aspartate or with glucose or with glutamate. The amounts of these substrates required for exogenous succinate utilization were relatively large. Both the alpha-ketoglutarate-aspartate combination and glutamate greatly stimulated succinate uptake into the cells, but glutamate was far more effective than the alpha-ketoglutarate-aspartate combination in eliciting exogenous succinate utilization. This difference is explained on the basis of evidence reported in another article that succinate derived from the alpha-ketoglutarate-aspartate mixture is metabolized more rapidly-and thus more rapidly dilutes the specific activity of added succinate-than the succinate derived from glutamate.

Bacterial adaptation through distributed sensing of metabolic fluxes

We present a large-scale differential equation model of E. coli's central metabolism and its enzymatic, transcriptional, and posttranslational regulation. This model reproduces E. coli's known physiological behavior.

We found that the interplay of known interactions in E. coli's central metabolism can indirectly recognize the presence of extracellular carbon sources through measuring intracellular metabolic flux patterns.

We found that E. coli's system-level adaptations between glycolytic and gluconeogenic carbon sources are realized on the molecular level by global feedback architectures that overarch the enzymatic and transcriptional regulatory layers.

We found that the capability for closed-loop self-regulation can emerge within metabolism itself and therefore, metabolic operation may adapt itself autonomously to changing carbon sources (not requiring upstream sensing and signaling).

Adaptations to fluctuating carbon source availability are of particular importance for bacteria. To understand these adaptations, it needs to be understood how a system's behavior emerges from the interactions between the characterized molecules (Kitano, 2002b). To attain such a system understanding of bacterial metabolic adaptations to carbon source availability, the coupling between the recognition and adjustment aspects and between the enzymatic and genetic regulatory layers must be understood. For many carbon sources, neither transmembrane sensors nor regulatory proteins with sensing function have been identified. Also, it remains unclear how multiple local regulations work together to accomplish a coherent adjustment on the systems level. In this paper, we show that (1) the interplay of the known interactions in E. coli's central metabolism is capable of recognizing carbon sources indirectly, and that (2) these molecular interactions can adjust E. coli's metabolic operation between growth on glycolytic and gluconeogenic carbon sources, and that (3) this adaptation is governed by general principles.

We hypothesized that the system-level adaptations between growth on glycolytic and gluconeogenic carbon sources are accomplished by a system-wide regulation architecture that emerges when the known enzymatic and transcriptional regulations become coupled through five transcription factor (TF)–metabolite interactions. To (1) assess whether such coupled molecular interactions can indeed work together to adapt metabolic operation, and if yes, (2) to understand this system-level adaptation in molecular-level detail, we constructed a large-scale differential equation model. The model topology comprises the Embden–Meyerhoff pathway, the tricarboxylic acid (TCA) cycle, the glyoxylate (GLX) shunt, the anaplerotic reactions, the diversion of carbon flux to the GLX shunt, the uptake of glucose, the uptake and excretion of acetate, enzymatic regulation, transcriptional regulation by four TFs, and the regulation of these TFs' activities through TF–metabolite interactions. We translated the topology into differential equations by assigning the most appropriate rate law to each interaction. The kinetic model comprises 47 ordinary differential equations and 193 parameters. Parameter values were estimated through application of the ‘divide-and-conquer approach' (Kotte and Heinemann, 2009) on published experimental steady state-omics data sets.

Model simulations reproduce E. coli's known physiological behavior in an environment with fluctuating carbon source availability. But how does the in silico cell recognize acetate without a transmembrane sensor for extracellular acetate or a TF binding to intracellular acetate? Similarly, it is unclear whether the glucose sensing function of the phosphotransferase system is the exclusive mechanism to recognize glucose, or whether this sensing function is integrated into a larger sensing architecture. The model suggests that the recognition is performed indirectly through a mechanism we termed distributed sensing of intracellular metabolic fluxes. This mechanism uses two distinct motifs, which we termed pathway usage and flux direction, to establish defined correlations between metabolic fluxes and the levels of certain, here termed flux-signaling metabolites. The binding of these metabolites to TFs propagates the flux information to the transcriptional regulatory layer. A molecular sensor for intracellular metabolic flux is thus defined as a system of regulations and enzyme kinetics, comprising (1) either of the two motifs pathway usage or flux direction and (2) the binding of the thus established flux-signaling metabolites to TF(s).

As the in silico cell establishes and uses sensors for several intracellular metabolic fluxes, the overall sensing architecture infers the present carbon sources from a pattern of metabolic fluxes and is as such of a distributed nature. The core of this sensing architecture is formed not by transmembrane sensors but by four flux sensors, which establish flux-signaling metabolites according to the two proposed general motifs. These flux sensors use intracellular metabolic flux as a means to correlate the presence of extracellular carbon sources with the levels of intracellular metabolites. The recognition of glucose through the PTS transmembrane complex is embedded as one flux sensor in this distributed sensing architecture; the other three flux sensors function without the help of transmembrane complexes.

The in silico cell achieves the coupling between recognition and adjustment through its TFs, whose activities respond to the available carbon sources and at the same time regulate the expression of target genes. This combined recognition and adjustment, centered on the four TFs, closes four global feedback loops that overarch the metabolic and genetic layers as illustrated in Figure 6. The adaptation of the in silico cell arises from the global feedback loop-embedded, flux sensor-adjusted transcriptional regulation of the four TFs, with each TF performing one part of the overall adaptation. This adaptation incorporates both the influence of the metabolic on the genetic layer, achieved through TF–metabolite interactions, and of the genetic on the metabolic layer, achieved through the impact of adjusted enzyme levels on metabolic fluxes.

The existence of the global feedback architectures challenges the conventional view that top-level regulatory proteins recognize environmental conditions and adjust downstream metabolic operation. It suggests that the capability for closed-loop self-regulation can emerge within metabolism itself and therefore, metabolic operation may adapt itself autonomously (not requiring upstream sensing and regulation) to changing carbon sources.

To conclude, the presented differential equation model of E. coli's central metabolism offers a consistent explanation of how a multitude of known molecular interactions fit into a coherent systems picture; the interactions work together like gear wheels that mesh with one another to adapt central metabolism between growth on the glycolytic substrate glucose and the gluconeogenic substrate acetate. The deduced general functional principles provide the missing link to understand system-level adaptations to carbon sources in molecular-level detail. The proposed principles fall under the umbrella of distributed flux sensing. The flux sensing mechanism entails the binding of TFs to flux-signaling metabolites, which are established through the motifs signaling of pathway usage and signaling of flux direction, and are embedded in global feedback loop architectures. These principles allow an autonomous adaptation of metabolic operation to growth in fluctuating environments.

The recognition of carbon sources and the regulatory adjustments to recognized changes are of particular importance for bacterial survival in fluctuating environments. Despite a thorough knowledge base of Escherichia coli's central metabolism and its regulation, fundamental aspects of the employed sensing and regulatory adjustment mechanisms remain unclear. In this paper, using a differential equation model that couples enzymatic and transcriptional regulation of E. coli's central metabolism, we show that the interplay of known interactions explains in molecular-level detail the system-wide adjustments of metabolic operation between glycolytic and gluconeogenic carbon sources. We show that these adaptations are enabled by an indirect recognition of carbon sources through a mechanism we termed distributed sensing of intracellular metabolic fluxes. This mechanism uses two general motifs to establish flux-signaling metabolites, whose bindings to transcription factors form flux sensors. As these sensors are embedded in global feedback loop architectures, closed-loop self-regulation can emerge within metabolism itself and therefore, metabolic operation may adapt itself autonomously (not requiring upstream sensing and signaling) to fluctuating carbon sources.

A stochastic single-molecule event triggers phenotype switching of a bacterial cell

By monitoring fluorescently labeled lactose permease with single-molecule sensitivity, we investigated the molecular mechanism of how an Escherichia coli cell with the lac operon switches from one phenotype to another. At intermediate inducer concentrations, a population of genetically identical cells exhibits two phenotypes: induced cells with highly fluorescent membranes and uninduced cells with a small number of membrane-bound permeases. We found that this basal-level expression results from partial dissociation of the tetrameric lactose repressor from one of its operators on looped DNA. In contrast, infrequent events of complete dissociation of the repressor from DNA result in large bursts of permease expression that trigger induction of the lac operon. Hence, a stochastic single-molecule event determines a cell's phenotype.

Characterization of Sec-translocon-dependent extracytoplasmic proteins of Rickettsia typhi

As obligate intracellular, vector-borne bacteria, rickettsiae must adapt to both mammalian and arthropod host cell environments. Deciphering the molecular mechanisms of the interactions between rickettsiae and their host cells has largely been hindered by the genetic intractability of these organisms; however, research in other gram-negative pathogens has demonstrated that many bacterial determinants of attachment, entry, and pathogenesis are extracytoplasmic proteins. The annotations of several rickettsial genomes indicate the presence of homologs of the Sec translocon, the major route for bacterial protein secretion from the cytoplasm. For Rickettsia typhi, the etiologic agent of murine typhus, homologs of the Sec-translocon-associated proteins LepB, SecA, and LspA have been functionally characterized; therefore, the R. typhi Sec apparatus represents a mechanism for the secretion of rickettsial proteins, including virulence factors, into the extracytoplasmic environment. Our objective was to characterize such Sec-dependent R. typhi proteins in the context of a mammalian host cell infection. By using the web-based programs LipoP, SignalP, and Phobius, a total of 191 R. typhi proteins were predicted to contain signal peptides targeting them to the Sec translocon. Of these putative signal peptides, 102 were tested in an Escherichia coli-based alkaline phosphatase (PhoA) gene fusion system. Eighty-four of these candidates exhibited signal peptide activity in E. coli, and transcriptional analysis indicated that at least 54 of the R. typhi extracytoplasmic proteins undergo active gene expression during infections of HeLa cells. This work highlights a number of interesting proteins possibly involved in rickettsial growth and virulence in mammalian cells.

LOOKING BACK

My encounter with Jacques Monod has shaped my scientific career. After a short incursion in the biochemistry of strict anaerobes, and after elucidating the biosynthetic pathway leading from aspartate to threonine in Escherichia coli, I joined his laboratory. With him and Howard Rickenberg, I discovered the stereospecific permeability of galactosides and amino acids (permeases). After this intermezzo, I returned to the analysis of biosynthetic pathways and of their regulation by allosteric feedback inhibition and repression in E. coli. Among others, my studies led to the discovery of the tryptophan and methionine repressors, to the incorporation of amino acid analogues in proteins, including selenomethionine (which much later led to progress in protein crystallography), to the definition of isofunctional and multifunctional enzymes, and to the elucidation of the primary structure of most of the enzymes leading to threonine and methionine.

Bacterial choices for the consumption of multiple resources for current and future needs

Microorganisms differ in their effectiveness in uptake and selection of substances that they bring in from the environment. They also differ in how they balance the allocation of nutrients for immediate and for delayed use. Moreover, they may not take up resources as fast as they seemingly could, and they may extrude derivatives of substances just pumped in. A good deal of these apparent choices must reside in the uptake systems and the linkage of these with the cell's intermediate metabolism. An important feature is that a resource may vary in concentration from time to time, nutrient to nutrient, and habitat to habitat. This variation must have been critical to the evolution of regulatory processes. Some possibilities for the combined uptake and consumption are considered for substrates serving the same (homologous) and different (heterologous) roles for the bacterium. From the membrane transport processes diagrammed in Fig. 1c and Fig. 2 and corresponding computer program given in Appendix A, the combined effect of uptake processes and cell growth can be studied. The model can be modified for various alternate models to study the possible control of cellular uptake and metabolism for the range of ecological roles of the bacterium.

Gleanings of a chemiosmotic eye

In 1961, an inventive Englishman, named Peter Mitchell, proposed a radically novel hypothesis to explain how energy is conserved during respiration and photosynthesis, and applied to the generation of ATP and other kinds of functional work. The chemiosmotic hypothesis sparked an intense controversy that lasted for 15 years. Today, Mitchell's conception of proton currents and their role in phosphorylation and active transport is generally accepted, and has ramified into many corners of cellular physiology. His most profound contribution may have been to introduce spatial direction into biochemistry, and thereby transform our perception of the relationship between molecules and cells.

A functional-phylogenetic classification system for transmembrane solute transporters

A comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the International Union of Biochemistry and Molecular Biology. This system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. Almost all of the more than 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters, and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Transport mode and energy coupling prove to be relatively immutable characteristics and therefore provide primary bases for classification. Phylogenetic grouping reflects structure, function, mechanism, and often substrate specificity and therefore provides a reliable secondary basis for classification. Substrate specificity and polarity of transport prove to be more readily altered during evolutionary history and therefore provide a tertiary basis for classification. With very few exceptions, a phylogenetic family of transporters includes members that function by a single transport mode and energy coupling mechanism, although a variety of substrates may be transported, sometimes with either inwardly or outwardly directed polarity. In this review, I provide cross-referencing of well-characterized constituent transporters according to (i) transport mode, (ii) energy coupling mechanism, (iii) phylogenetic grouping, and (iv) substrates transported. The structural features and distribution of recognized family members throughout the living world are also evaluated. The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects.

The French school of genetics: from physiological and population genetics to regulatory molecular genetics

French genetics had unusual beginnings. There are clear indications that the French biological establishment resisted Mendelian genetics strenuously from about 1910 to 1940. From about 1930 to 1950 several unconventional research programs with a strongly physiological orientation paved the way for the full entrance of French biology into genetics after World War II. This review examines some salient features of this history to clarify the strengths, weaknesses, and distinctive features of French genetics until about 1965. We suggest that after that data French genetics slowly merged into the international mainstream as genetics has become a largely molecular discipline.

Potassium accumulation and sodium efflux by Porphyra perforata tissues in lithium and magnesium sea water

Cells of Porphyra perforata, a red marine alga, accumulate K in the absence of concomitant Na or Li extrusion while immersed in Li- or Mg-sea waters lacking Na. This suggests that the coupling observed between K and Na transport is facultative. No evidence is obtained for net extrusion of Li. Na efflux, with the concentration gradient, is facilitated by K and is proportional to the cellular Na content. Either Na efflux does not involve an ion carrier or the number of Na sites is large. Because K accumulation has been observed in the absence of Na extrusion, but not vice versa, it seems that K uptake is the primary secretory event, with Na extrusion a secondary process dependent upon K accumulation.

Mechanism of arabinose transport in Tertahymena pyriformis

Cirillo, Vincent P. (Seton Hall College of Medicine and Dentistry, Jersey City, N.J.). Mechanism of arabinose transport in Tetrahymena pyriformis. J. Bacteriol. 84:754-758. 1962.-The mechanism of sugar transport was studied in Tetrahymena pyriformis, using the nonmetabolizable sugar, l-arabinose. Arabinose transport does not result in accumulation against a concentration difference but shows a high Q(10) and is competitively inhibited by glucose. The addition of glucose to arabinose-equilibrated cells results in arabinose efflux against a concentration difference. These results are discussed in terms of carrier-mediated transport.