Streptomyces-based whole-cell biosensors for detecting diverse cell envelope-targeting antibiotics

Cell envelope-targeting antibiotics are potent therapeutic agents against various bacterial infections. The emergence of multiple antibiotic-resistant strains underscores the significance of identifying potent antimicrobials specifically targeting the cell envelope. However, current drug screening approaches are tedious and lack sufficient specificity and sensitivity, warranting the development of more efficient methods. Genetic circuit-based whole-cell biosensors hold great promise for targeted drug discovery from natural products. Here, we performed comparative transcriptomic analysis of Streptomyces coelicolor M1146 exposed to diverse cell envelope-targeting antibiotics, aiming to identify regulatory elements involved in perceiving and responding to these compounds. Differential gene expression analysis revealed significant activation of VanS/R two-component system in response to the glycopeptide class of cell envelope-acting antibiotics. Therefore, we engineered a pair of VanS/R-based biosensors that exhibit functional complementarity and possess exceptional sensitivity and specificity for glycopeptides detection. Additionally, through promoter screening and characterization, we expanded the biosensor's detection range to include various cell envelope-acting antibiotics beyond glycopeptides. Our genetically engineered biosensor exhibits superior performance, including a dynamic range of up to 887-fold for detecting subtle antibiotic concentration changes in a rapid 2-h response time, enabling high-throughput screening of natural product libraries for antimicrobial agents targeting the bacterial cell envelope.

Effects of the antimicrobial glabridin on membrane integrity and stress response activation in Listeria monocytogenes

Glabridin is a prenylated isoflavan which can be extracted from liquorice roots and has shown antimicrobial activity against foodborne pathogens and spoilage microorganisms. However, its application may be hindered due to limited information about its mode of action. In this study, we aimed to investigate the mode of action of glabridin using a combined phenotypic and proteomic approach on Listeria monocytogenes. Fluorescence and transmission electron microscopy of cells exposed to glabridin showed membrane permeabilization upon treatment with lethal concentrations of glabridin. Comparative proteomics analysis of control cells and cells exposed to sub-lethal concentrations of glabridin showed upregulation of proteins related to the two-component systems LiaSR and VirRS, confirming cell envelope damage during glabridin treatment. Additional upregulation of SigmaB regulon members signified activation of the general stress response in L. monocytogenes during this treatment. In line with the observed upregulation of cell envelope and general stress response proteins, sub-lethal treatment of glabridin induced (cross)protection against lethal heat and low pH stress and against antimicrobials such as nisin and glabridin itself. Overall, this study sheds light on the mode of action of glabridin and activation of the main stress responses to this antimicrobial isoflavan and highlights possible implications of its use as a naturally derived antimicrobial compound.

Professor David Minnikin Memorial Lecture: An era of the mycobacterial cell wall lipid biomarkers

This paper is dedicated to the memory of Professor David Ernest Minnikin (1939-2021). David was one of the key scientists who pioneered the field of Mycobacterium tuberculosis cell envelope research for over half a century. From the classification, identification, and extraction of the unusual lipids of the mycobacterial cell wall, to exploiting them as characteristic lipid biomarkers for sensitive detection, his ideas enlightened a whole world of possibilities within the tuberculosis (TB) field. In addition, his definition of the intricate models now forms a key milestone in our understanding of the M. tuberculosis cell envelope and has resolved many unanswered questions on the evolution of M. tuberculosis.

Issues with the current drugs for Mycobacterium tuberculosis cure and potential of cell envelope proteins for new drug discovery

Mycobacterium tuberculosis has been the smartest pathogen ever and a challenge to drug development. Its replicative machinery is unique, so targeting the same for killing the pathogen remains a challenge. Our body typically throws out the drugs before they see the bacterium multiply. The pathogen has also learned how to remove drugs from its internal chambers and not allow them to reach their targets. Another strategy for Mtb is the mutation of the targets to reject drug binding and bypass the drug's inhibitory actions. In this review, we tried to explore possible targets on the outer side of the bacterial cell. We have also explored if those targets are promising enough and if there are drugs or inhibitors available. We also discuss the essential proteins and why they remain to be a good target. We concluded that the cell envelope has got a few proteins that can be targeted in isolation or maybe along with other machinery while making the outer environment more conducive for penetration of current drugs or newly proposed drugs.

Making a chink in their armor: Current and next-generation antimicrobial strategies against the bacterial cell envelope

Gram-negative bacteria are uniquely equipped to defeat antibiotics. Their outermost layer, the cell envelope, is a natural permeability barrier that contains an array of resistance proteins capable of neutralizing most existing antimicrobials. As a result, its presence creates a major obstacle for the treatment of resistant infections and for the development of new antibiotics. Despite this seemingly impenetrable armor, in-depth understanding of the cell envelope, including structural, functional and systems biology insights, has promoted efforts to target it that can ultimately lead to the generation of new antibacterial therapies. In this article, we broadly overview the biology of the cell envelope and highlight attempts and successes in generating inhibitors that impair its function or biogenesis. We argue that the very structure that has hampered antibiotic discovery for decades has untapped potential for the design of novel next-generation therapeutics against bacterial pathogens.

Targeting LPS biosynthesis and transport in gram-negative bacteria in the era of multi-drug resistance

Gram-negative bacteria pose a major threat to human health in an era fraught with multi-drug resistant bacterial infections. Despite extensive drug discovery campaigns over the past decades, no new antibiotic target class effective against gram-negative bacteria has become available to patients since the advent of the carbapenems in 1985. Antibiotic discovery efforts against gram-negative bacteria have been hampered by limited intracellular accumulation of xenobiotics, in large part due to the impermeable cell envelope comprising lipopolysaccharide (LPS) in the outer leaflet of the outer membrane, as well as a panoply of efflux pumps. The biosynthesis and transport of LPS are essential to the viability and virulence of most gram-negative bacteria. Thus, both LPS biosynthesis and transport are attractive pathways to target therapeutically. In this review, we summarize the LPS biosynthesis and transport pathways and discuss efforts to find small molecule inhibitors against targets within these pathways.

Antagonist Impact of Selenium-Based Nanoparticles Against Mycobacterium tuberculosis

One of the cardinal causes of global deaths from a single-point infectious agent has been reported to be tuberculosis (or TB). At present times, the incidence of TB cases occurs mostly due to multi-drug resistance, which is expected to boost further in the upcoming times. Accordingly, the development of alternative treatment methodologies has received significant research interest. In this regard, the application of nanoparticles has notable cognizance. The literature suggested that nanoparticles have substantial potential to be used as the delivery medium for drug injection as well as they also serve as a potential bactericidal agent. In this present study, the efficacy of the selenium nanoparticles against the inhibition of growth of Mycobacterium tuberculosis was evaluated. The obtained results indicated that the synthesized selenium nanoparticles have notable cognizance towards the inhibition of growth of Mycobacterium tuberculosis by disrupting the integrity of their cell envelope. This study thus proposes a novel approach and opens new dimensional avenues in the field of nanoparticle-induced cell disruption strategies.

Characterizing the role of phosphatidylglycerol-phosphate phosphatases in Acinetobacter baumannii cell envelope biogenesis and antibiotic resistance

The dissemination of multi-drug resistant Acinetobacter baumannii threatens global healthcare systems and necessitates the development of novel therapeutic options. The Gram-negative bacterial cell envelope provides a first defensive barrier against antimicrobial assault. Essential components of this multi-layered complex are the phospholipid-rich membranes. Phosphatidylglycerol phosphate (PGP) phosphatases are responsible for a key step in the biosynthesis of a major phospholipid species, phosphatidylglycerol (PG), but these enzymes have also been implicated in the biogenesis of other cell envelope components. Our bioinformatics analyses identified two putative PGP candidates in the A. baumannii genome, PgpA and PgpB. Phospholipid analyses of isogenic pgpA mutants in two distinct A. baumannii strains revealed a shift in the desaturation levels of phosphatidylethanolamine (PE) phospholipid species, possibly due to the activation of the phospholipid desaturase DesA. We also investigated the impact of the inner membrane phosphatases on other cell envelope components, which revealed a role of PgpB in the maintenance of the A. baumannii peptidoglycan layer, and consequently carbapenem resistance. Collectively, this work provides novel insights into the roles of PGP phosphatases on the global lipidomic landscape of A. baumannii and their interconnectivity with the biogenesis of other cell envelope components. The non-essentiality of these candidates exemplifies metabolic versatility of A. baumannii, which is believed to be key to its success as global pathogen.

Small protein Cgl2215 enhances phenolic tolerance by promoting MytA activity in Corynebacterium glutamicum

Corynebacterium glutamicum is a promising chassis microorganism for the bioconversion of lignocellulosic biomass owing to its good tolerance and degradation of the inhibitors generated in lignocellulosic pretreatments. Among the identified proteins encoded by genes within the C. glutamicum genome, nearly 400 are still functionally unknown. Based on previous transcriptome analysis, we found that the hypothetical protein gene cgl2215 was highly upregulated in response to phenol, ferulic acid, and vanillin stress. The cgl2215 deletion mutant was shown to be more sensitive than the parental strain to phenolic compounds as well as other environmental factors such as heat, ethanol, and oxidative stresses. Cgl2215 interacts with C. glutamicum mycoloyltransferase A (MytA) and enhances its in vitro esterase activity. Sensitivity assays of the ΔmytA and Δcgl2215ΔmytA mutants in response to phenolic stress established that the role of Cgl2215 in phenolic tolerance was mediated by MytA. Furthermore, transmission electron microscopy (TEM) results showed that cgl2215 and mytA deletion both led to defects in the cell envelope structure of C. glutamicum, especially in the outer layer (OL) and electron-transparent layer (ETL). Collectively, these results indicate that Cgl2215 can enhance MytA activity and affect the cell envelope structure by directly interacting with MytA, thus playing an important role in resisting phenolic and other environmental stresses.

Isolation and characterization of a main porin from the outer membrane of Salinibacter ruber

Salinibacter ruber is an extremophilic bacterium able to grow in high-salts environments, such as saltern crystallizer ponds. This halophilic bacterium is red-pigmented due to the production of several carotenoids and their derivatives. Two of these pigment molecules, salinixanthin and retinal, are reported to be essential cofactors of the xanthorhodopsin, a light-driven proton pump unique to this bacterium. Here, we isolate and characterize an outer membrane porin-like protein that retains salinixanthin. The characterization by mass spectrometry identified an unknown protein whose structure, predicted by AlphaFold, consists of a 8 strands beta-barrel transmembrane organization typical of porins. The protein is found to be part of a functional network clearly involved in the outer membrane trafficking. Cryo-EM micrographs showed the shape and dimensions of a particle comparable with the ones of the predicted structure. Functional implications, with respect to the high representativity of this protein in the outer membrane fraction, are discussed considering its possible role in primary functions such as the nutrients uptake and the homeostatic balance. Finally, also a possible involvement in balancing the charge perturbation associated with the xanthorhodopsin and ATP synthase activities is considered.

Bacterial cell wall material properties determine E. coli resistance to sonolysis

The applications of bacterial sonolysis in industrial settings are plagued by the lack of the knowledge of the exact mechanism of action of sonication on bacterial cells, variable effectiveness of cavitation on bacteria, and inconsistent data of its efficiency. In this study we have systematically changed material properties of E. coli cells to probe the effect of different cell wall layers on bacterial resistance to ultrasonic irradiation (20 kHz, output power 6,73 W, horn type, 3 mm probe tip diameter, 1 ml sample volume). We have determined the rates of sonolysis decay for bacteria with compromised major capsular polymers, disrupted outer membrane, compromised peptidoglycan layer, spheroplasts, giant spheroplasts, and in bacteria with different cell physiology. The non-growing bacteria were 5-fold more resistant to sonolysis than growing bacteria. The most important bacterial cell wall structure that determined the outcome during sonication was peptidoglycan. If peptidoglycan was remodelled, weakened, or absent the cavitation was very efficient. Cells with removed peptidoglycan had sonolysis resistance equal to lipid vesicles and were extremely sensitive to sonolysis. The results suggest that bacterial physiological state as well as cell wall architecture are major determinants that influence the outcome of bacterial sonolysis.

Architects of their own environment: How membrane proteins shape the Gram-negative cell envelope

Gram-negative bacteria are surrounded by a complex multilayered cell envelope, consisting of an inner and an outer membrane, and separated by the aqueous periplasm, which contains a thin peptidoglycan cell wall. These bacteria employ an arsenal of highly specialized membrane protein machineries to ensure the correct assembly and maintenance of the membranes forming the cell envelope. Here, we review the diverse protein systems, which perform these functions in Escherichia coli, such as the folding and insertion of membrane proteins, the transport of lipoproteins and lipopolysaccharide within the cell envelope, the targeting of phospholipids, and the regulation of mistargeted envelope components. Some of these protein machineries have been known for a long time, yet still hold surprises. Others have only recently been described and some are still missing pieces or yet remain to be discovered.

Shotgun Bacterial Lipid A Analysis Using Routine MALDI-TOF Mass Spectrometry

Detection of bacterial lipids and particularly the lipid A, the lipid anchor of the lipopolysaccharide, can be very challenging and requires a certain level of expertise. Here, this chapter describes a straightforward and simple method for the analysis of bacterial lipid A. In addition, such approach, lipid fingerprint, has the potential to be applied to other bacteria such as mycobacteria.

Cell wall polysaccharides of Gram positive ovococcoid bacteria and their role as bacteriophage receptors

Gram-positive bacterial cell walls are characterised by the presence of a thick peptidoglycan layer which provides protection from extracellular stresses, maintains cell integrity and determines cell morphology, while it also serves as a foundation to anchor a number of crucial polymeric structures. For ovococcal species, including streptococci, enterococci and lactococci, such structures are represented by rhamnose-containing cell wall polysaccharides, which at least in some instances appear to serve as a functional replacement for wall teichoic acids. The biochemical composition of several streptococcal, lactococcal and enterococcal rhamnose-containing cell wall polysaccharides have been elucidated, while associated functional genomic analyses have facilitated the proposition of models for individual biosynthetic pathways. Here, we review the genomic loci which encode the enzymatic machinery to produce rhamnose-containing, cell wall-associated polysaccharide (Rha cwps) structures of the afore-mentioned ovococcal bacteria with particular emphasis on gene content, biochemical structure and common biosynthetic steps. Furthermore, we discuss the role played by these saccharidic polymers as receptors for bacteriophages and the important role phages play in driving Rha cwps diversification and evolution.

Tanshinones from Salvia miltiorrhiza inhibit Mycobacterium tuberculosis via disruption of the cell envelope surface and oxidative stress

The unique structure of Mycobacterium tuberculosis cell envelope provides impermeable barrier against environmental stimuli. In the situation that this barrier is disturbed Mycobacteria react at the transcriptional and translational level to redirect metabolic processes and to maintain integrity of the cell. In this work we aimed to explore the early metabolic response of M. tuberculosis to tanshinones, which are active antimycobacterial compounds of Salvia miltiorrhiza Bunge root. The investigation of the expression of sigma factors revealed the significant shifts in the general bacterial regulatory network, whereas LC-MS metabolomics evidenced the changes in the composition of bacterial cell envelope and indicated altered metabolic pathways. Tanshinones acted via the disruption of the cell envelope surface and generation of reactive oxygen species. Bacteria responded with overproduction of inner region of outer membrane, fluctuations in the production of glycerophosphoinositolglycans, as well as changes in the levels of mycobactins, accompanied by enrichment of metabolic pathways related to redox balance and repair of damages caused by tanshinones.

Chemical probes for tagging mycobacterial lipids

Mycobacteria, which cause tuberculosis and related diseases, possess a diverse set of complex envelope lipids that provide remarkable tolerance to antibiotics and are major virulence factors that drive pathogenesis. Recently, metabolic labeling and bio-orthogonal chemistry have been harnessed to develop chemical probes for tagging specific lipids in live mycobacteria, enabling a range of new basic and translational research avenues. A toolbox of probes has been developed for labeling mycolic acids and their derivatives, including trehalose-, arabinogalactan-, and protein-linked mycolates, as well as newer probes for labeling phthiocerol dimycocerosates (PDIMs) and potentially other envelope lipids. These lipid-centric tools have yielded fresh insights into mycobacterial growth and host interactions, provided new avenues for drug target discovery and characterization, and inspired innovative diagnostic and therapeutic strategies.

The impact of cell structure, metabolism and group behavior for the survival of bacteria under stress conditions

Microbes from diverse types of habitats are continuously exposed to external challenges, which may include acidic, alkaline, and toxic metabolites stress as well as nutrient deficiencies. To promote their own survival, bacteria have to rapidly adapt to external perturbations by inducing particular stress responses that typically involve genetic and/or cellular changes. In addition, pathogenic bacteria need to sense and withstand these environmental stresses within a host to establish and maintain infection. These responses can be, in principle, induced by changes in bacterial cell structure, metabolism and group behavior. Bacterial nucleic acids may serve as the core part of the stress response, and the cell envelope and ribosomes protect genetic structures from damage. Cellular metabolism and group behavior, such as quorum sensing system, can play a more important role in resisting stress than we have now found. Since bacteria survival can be only appreciated if we better understand the mechanisms behind bacterial stress response, here we review how morphological and physiological features may lead to bacterial resistance upon exposure to particular stress-inducing factors.

Effect of lipid A aminoarabinosylation on Pseudomonas aeruginosa colistin resistance and fitness

Colistin represents the last-line treatment option against many multidrug-resistant Gram-negative pathogens. Several lines of evidence indicate that aminoarabinosylation of the lipid A moiety of lipopolysaccharide (LPS) is an essential step for the development of colistin resistance in Pseudomonas aeruginosa. However, whether it is sufficient to confer resistance in this bacterium remains unclear. The aim of this work was to investigate the specific contribution of lipid A aminoarabinosylation to colistin resistance in P. aeruginosa and evaluate the effect of this resistance mechanism on bacterial fitness. Recombinant strains constitutively expressing the enzymes for lipid A aminoarabinosylation were generated in a small collection of reference and clinical isolates and verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR), lipid A extraction and mass spectrometry. The effect of aminoarabinosylated lipid A on colistin resistance was found to be strain- and culture condition-dependent. Higher levels of resistance were generally obtained in the presence of divalent cations, which appear to be important for aminoarabinosylation-mediated colistin resistance. High colistin resistance was also observed for most strains in human serum and in artificial sputum medium, which should partly mimic growth conditions during infection. The results of growth, biofilm, cell envelope integrity and Galleria mellonella infection assays indicate that lipid A aminoarabinosylation does not cause relevant fitness costs in P. aeruginosa.

The role of bacterial cell envelope structures in acid stress resistance in E. coli

Acid resistance (AR) is an indispensable mechanism for the survival of neutralophilic bacteria, such as Escherichia coli (E. coli) strains that survive in the gastrointestinal tract. E. coli acid tolerance has been extensively studied during past decades, with most studies focused on gene regulation and mechanisms. However, the role of cell membrane structure in the context of acid stress resistance has not been discussed in depth. Here, we provide a comprehensive review of the roles and mechanisms of the E. coli cell envelope from different membrane components, such as membrane proteins, fatty acids, chaperones, and proton-consuming systems, and particularly focus on the innovative effects revealed by recent studies. We hope that the information guides us to understand the bacterial survival strategies under acid stress and to further explore the AR regulatory mechanisms to prevent or treat E. coli and other related Gram-negative bacteria infection, or to enhance the AR of engineering E. coli.

Complex Diffusion in Bacteria

Diffusion within bacteria is often thought of as a "simple" random process by which molecules collide and interact with each other. New research however shows that this is far from the truth. Here we shed light on the complexity and importance of diffusion in bacteria, illustrating the similarities and differences of diffusive behaviors of molecules within different compartments of bacterial cells. We first describe common methodologies used to probe diffusion and the associated models and analyses. We then discuss distinct diffusive behaviors of molecules within different bacterial cellular compartments, highlighting the influence of metabolism, size, crowding, charge, binding, and more. We also explicitly discuss where further research and a united understanding of what dictates diffusive behaviors across the different compartments of the cell are required, pointing out new research avenues to pursue.

The effects of the Ncw2 protein of Saccharomyces cerevisiae on the positioning of chitin in response to cell wall damage

The recently described NCW2 gene encodes a protein that is assumed to be located in the cell wall (CW). This protein was proposed to participate in the repair of CW damages induced by polyhexamethylene biguanide (PHMB). However, much of the information on the biological function(s) of Ncw2p still remains unclear. In view of this, this study seeks to extend the analysis of this gene in light of the way its protein functions in the Cell Wall Integrity (CWI) mechanism. Deletion of the NCW2 gene led to constitutive overexpression of some key CWI genes and increased chitin deposition in the walls of cells exposed to PHMB. This means the lack of Ncw2p might activate a compensatory mechanism that upregulates glucan CWI genes for cell protection by stiffening the CW. This condition seems to alleviate the response through the HOG pathway and makes cells sensitive to osmotic stress. However, Ncw2p may not have been directly involved in tolerance to osmotic stress itself. The results obtained definitely place the NCW2 gene in the list of CWI genes of S. cerevisiae and indicate that its protein has an auxiliary function in the maintenance of the glucan/chitin balance and ensuring the correct structure of the yeast cell wall.

Role of the Streptomyces spore wall synthesizing complex SSSC in differentiation of Streptomyces coelicolor A3(2)

A crucial stage of the Streptomyces life cycle is the sporulation septation, a process were dozens of cross walls are synchronously formed in the aerial hyphae in a highly coordinated manner. This process includes the remodeling of the spore envelopes to make Streptomyces spores resistant to detrimental environmental conditions. Sporulation septation and the synthesis of the thickened spore envelope in S. coelicolor A3(2) involves the Streptomyces spore wall synthesizing complex SSSC. The SSSC is a multi-protein complex including proteins directing peptidoglycan synthesis (MreBCD, PBP2, Sfr, RodZ) and cell wall glycopolymer synthesis (PdtA). It also includes two eukaryotic like serin/threonine protein kinases (eSTPK), PkaI and PkaH, which were shown to phosphorylate MreC. Since unbalancing phosphorylation activity by either deleting eSTPK genes or by expressing a second copy of an eSTPK gene affected proper sporulation, a model was developed, in which the activity of the SSSC is controlled by protein phosphorylation.

BamA is a pivotal protein in cell envelope synthesis and cell division in Deinococcus radiodurans

The beta-barrel assembly machinery (BAM) is an indispensable complex for protein transportation located at the outer membrane of bacteria. BAM is composed of five subunits (BamA-E) in the model bacterium Escherichia coli. DR_0379 is a BamA homolog in Deinococcus radiodurans, but the other subunits have not been detected in this species. In the present study, deletion of bamA resulted in decreased growth rate and altered morphology of D. radiodurans. ΔbamA cells underwent abnormal cell division, leading to aggregated bacteria of diverse size and shape, and the cell envelope was detached from the cell surface, resulting in reduced resistance to high ionic strength. Oxidative stress resistance was significantly enhanced in the mutant, which may be attributed to increased manganese ion concentration and Mn/Fe ratio. Numerous proteins were released into the medium from ΔbamA cells, including surface layer (S-layer) proteins and various transporters located in the periplasm and outer membrane. These results indicate that BamA affects the synthesis and assembly of the outer membrane and S-layer, and thereby influences material transport and cell division. The findings highlight the special functions of BamA in D. radiodurans, and promote our understanding of the multi-layer structure of the D. radiodurans cell envelope.

Psychrophilic lifestyles: mechanisms of adaptation and biotechnological tools

Cold-adapted microorganisms inhabiting permanently low-temperature environments were initially just a biological curiosity but have emerged as rich sources of numerous valuable tools for application in a broad spectrum of innovative technologies. To overcome the multiple challenges inherent to life in their cold habitats, these microorganisms have developed a diverse array of highly sophisticated synergistic adaptations at all levels within their cells: from cell envelope and enzyme adaptation, to cryoprotectant and chaperone production, and novel metabolic capabilities. Basic research has provided valuable insights into how these microorganisms can thrive in their challenging habitat conditions and into the mechanisms of action of the various adaptive features employed, and such insights have served as a foundation for the knowledge-based development of numerous novel biotechnological tools. In this review, we describe the current knowledge of the adaptation strategies of cold-adapted microorganisms and the biotechnological perspectives and commercial tools emerging from this knowledge. Adaptive features and, where possible, applications, in relation to membrane fatty acids, membrane pigments, the cell wall peptidoglycan layer, the lipopolysaccharide component of the outer cell membrane, compatible solutes, antifreeze and ice-nucleating proteins, extracellular polymeric substances, biosurfactants, chaperones, storage materials such as polyhydroxyalkanoates and cyanophycins and metabolic adjustments are presented and discussed.

Phenotypic MicroArray Screening of Neisseria gonorrhoeae in Chemically Defined Liquid Medium

Phenotype MicroArrays (PMs) provide a considerable benefit to the evaluation of potential vaccine/drug targets and the assessment of hypothetical protein function. Nearly 2000 conditions can be screened relatively quickly either to search for phenotypes associated with the loss of a protein or to understand metabolic differences between closely related bacterial isolates. The fastidious organism Neisseria gonorrhoeae presents an experimental challenge for phenotypic screening due to its nutrient restrictions and its autolytic activity upon reaching the stationary phase of growth. These limitations can be mitigated by modulating screening parameters. In this chapter, we describe a technique optimized for the phenotypic screening of N. gonorrhoeae FA1090 and isogenic mutant strains. Inoculum size and culturing times have been adjusted for growth in chemically defined, protein-free Graver-Wade liquid medium in the 96-well microtiter plate format employed by the PMs. With the conditions presented, highly reproducible gonococcal growth is achieved, and autolysis prior to the experimental endpoint is minimized.

Cell Walls and Membranes of Actinobacteria

Actinobacteria is a group of diverse bacteria. Most species in this class of bacteria are filamentous aerobes found in soil, including the genus Streptomyces perhaps best known for their fascinating capabilities of producing antibiotics. These bacteria typically have a Gram-positive cell envelope, comprised of a plasma membrane and a thick peptidoglycan layer. However, there is a notable exception of the Corynebacteriales order, which has evolved a unique type of outer membrane likely as a consequence of convergent evolution. In this chapter, we will focus on the unique cell envelope of this order. This cell envelope features the peptidoglycan layer that is covalently modified by an additional layer of arabinogalactan . Furthermore, the arabinogalactan layer provides the platform for the covalent attachment of mycolic acids , some of the longest natural fatty acids that can contain ~100 carbon atoms per molecule. Mycolic acids are thought to be the main component of the outer membrane, which is composed of many additional lipids including trehalose dimycolate, also known as the cord factor. Importantly, a subset of bacteria in the Corynebacteriales order are pathogens of human and domestic animals, including Mycobacterium tuberculosis. The surface coat of these pathogens are the first point of contact with the host immune system, and we now know a number of host receptors specific to molecular patterns exposed on the pathogen's surface, highlighting the importance of understanding how the cell envelope of Actinobacteria is structured and constructed. This chapter describes the main structural and biosynthetic features of major components found in the actinobacterial cell envelopes and highlights the key differences between them.

Purification and partial characterization of LdtP, a cell envelope modifying enzyme in Liberibacter asiaticus

Background

The aggressive spread of Liberibacter asiaticus, a bacterium closely associated with citrus greening, has given rise to an acute crisis in the citrus industry, making it imperative to expand the scientific knowledge base regarding L. asiaticus. Despite several endeavors to culture L. asiaticus, this bacterium has yet to be maintained in axenic culture, rendering identification and analysis of potential treatment targets challenging. Accordingly, a thorough understanding of biological mechanisms involved in the citrus host-microbe relationship is critical as a means of directing the search for future treatment targets. In this study, we evaluate the biochemical characteristics of CLIBASIA_01175, renamed LdtP (L,D-transpeptidase). Surrogate strains were used to evaluate its potential biological significance in gram-negative bacteria. A strain of E. coli carrying quintuple knock-outs of all genes encoding L,D-transpeptidases was utilized to demonstrate the activity of L. asiaticus LdtP.

Results

This complementation study demonstrated the periplasmic localization of mature LdtP and provided evidence for the biological role of LdtP in peptidoglycan modification. Further investigation highlighted the role of LdtP as a periplasmic esterase involved in modification of the lipid A moiety of the lipopolysaccharide. This work described, for the first time, an enzyme of the L,D-transpeptidase family with moonlighting enzyme activity directed to the modification of the bacterial cell wall and LPS.

Conclusions

Taken together, the data indicates that LdtP is a novel protein involved in an alternative pathway for modification of the bacterial cell, potentially affording L. asiaticus a means to survive within the host.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1348-8) contains supplementary material, which is available to authorized users.

The singular Corynebacterium glutamicum Emb arabinofuranosyltransferase polymerises the α(1 → 5) arabinan backbone in the early stages of cell wall arabinan biosynthesis

The arabinan-containing polysaccharides, arabinogalactan (AG) and lipoarabinomannan (LAM), are key cell wall components of the Corynebacterineae, which include Corynebacteria, Norcadia and Mycobacteria. Both AG and LAM contain elaborate arabinan domains composed of distinct structural motifs. Mycobacterial EmbA, EmbB and EmbC, collectively known as the Emb proteins, have been identified as arabinosyltransferases (ArafTs), which are targeted by the front-line anti-tubercular drug ethambutol. Previous studies have established that EmbA and EmbB play a role in the synthesis of the characteristic terminal hexa-arabinosuranosyl motif, whilst EmbC is involved exclusively in the biosynthesis of LAM. Herein, we have investigated the role of the singular Emb protein from Corynebacterium glutamicum through the detailed biochemical and chemical analysis of a double ΔaftAΔemb mutant, where the priming Cg-AftA protein, which generates the substrate for Cg-Emb has been deleted. Analysis of its cell wall revealed a complete absence of arabinose resulting in a truncated cell wall containing only a galactan backbone accompanied with complete loss of cell wall bound mycolates. In vitro cell-free assays using C. glutamicumΔaftA, C. glutamicumΔemb, C. glutamicumΔaftAΔemb and C. glutamicumΔaftBΔaftD and two synthetic acceptors, which mimick the arabinofuranose (Araf) “primed” galactan chain, demonstrated that Cg-Emb is able to transfer an Araf residue to the C5 of the Araf positioned on the synthetic acceptor(s). These results indicate that Cg-Emb acts as an α(1 → 5) ArafT and elongates the arabinan core during the early stages of arabinan biosynthesis in C. glutamicum.

Proteomics of Vibrio cholerae

Combining high-throughput mass spectrometry with isobaric tags for relative and absolute quantification (iTRAQ) allows for the identification and relative quantification of proteins from multiple samples. Furthermore, low-abundance proteins that are usually not detected can be enriched by using only the relevant fraction of the proteome, e.g., cytoplasmic, membrane proteins, or secreted proteins. Described here is a workflow for isolation and enrichment of secreted and membrane proteins that is compatible with mass spectrometry. Isolated proteins are reduced, alkylated, and digested with trypsin, and obtained peptides are labeled with iTRAQ reagent and separated by strong cation exchange to reduce the complexity. Finally, the peptides are separated by reverse-phase chromatography, spotted on a MALDI target plate, and analyzed by MALDI TOF-TOF.

Defining Lipoprotein Localisation by Fluorescence Microscopy

In recent years it has become evident that lipoproteins play crucial roles in the assembly of bacterial envelope-embedded nanomachineries and in the processes of protein export/secretion. In this chapter we describe a method to determine their precise localisation, for example inner versus outer membrane, in Gram-negative bacteria using human opportunistic pathogen Pseudomonas aeruginosa as a model. A fusion protein between a given putative lipoprotein and the red fluorescent protein mCherry must be created and expressed in a strain expressing cytoplasmic green fluorescent protein (GFP). Then the peripheral localisation of the fusion protein in the cell can be examined by treating cells with lysozyme to create spheroplasts and monitoring fluorescence under a confocal microscope. Mutants in the signal peptide can be engineered to study the association with the membrane and efficiency of transport. This protocol can be adapted to monitor lipoprotein localisation in other Gram-negative bacteria.

Green Fluorescent Protein as a protein localization and topological reporter in mycobacteria

The cell envelope-associated proteins of Mycobacterium species play critical functions in the physiology and pathogenicity of these microorganisms. Because the determination of their subcellular localization and transmembrane topology is often critical to the understanding of their function, we investigated whether the Green Fluorescent Protein (GFP) could be used as a reporter to probe protein localization and map the topology of inner membrane proteins directly in intact mycobacterial cells. To this end, two GFP-based mycobacterial reporter plasmids were engineered and their functionality validated using a variety of membrane-associated, exported and cytosolic proteins.

Impact of defined cell envelope mutations in Escherichia coli on the in vitro antibacterial activity of avibactam/β-lactam combinations

Avibactam is a novel non-β-lactam β-lactamase inhibitor being developed in combination with ceftazidime, ceftaroline and aztreonam for the treatment of infections caused by Gram-negative bacteria. Avibactam protects the antibacterial activity of these antibiotics by inhibiting Ambler classes A and C and some class D β-lactamases. The Gram-negative cell envelope presents a complex barrier to hydrophilic solutes and contains multiple molecular determinants of antibiotic susceptibility and resistance. To investigate the role of some of these determinants in the activity of avibactam and its partner antibiotics in Escherichia coli, an isogenic panel with deletions in specific components of the cell envelope was constructed in an E. coli W3110 strain background. The mutant constructs were also engineered to express the β-lactamase CTX-M-15 as a tool to enable assessment of the activity of avibactam. Mutations to shorten the lipopolysaccharide (LPS), to reduce efflux from the basal (i.e. non-upregulated) level or to alter the outer membrane porin composition did not have appreciable effects on the in vitro activity of ceftazidime, ceftaroline or aztreonam alone or in combination with avibactam. In conclusion, in this susceptible strain background, none of the β-lactams nor avibactam was measurably subject to efflux based on evaluating minimum inhibitory concentrations (MICs). None of the porin single or double mutations caused a decrease in susceptibility to the test compounds, implying that the compounds do not possess a strong porin preference, but instead can pass the outer membrane through a variety of routes.

Changes in the Vibrio harveyi Cell Envelope Subproteome During Permanence in Cold Seawater

Previous work demonstrated that physiological, morphological, and gene expression changes as well as the time-dependent entry into the viable but not culturable (VBNC) state are used by Vibrio species to survive and cope with diverse stress conditions including seasonal temperature downshifts and starvation. To learn more about the nature and specific contribution of membrane proteins to cell adaptation and survival, we analyzed variations in the protein composition of cell envelope and related them to morphological and physiological changes that were taking place during the long-term permanence of Vibrio harveyi in seawater microcosm at 4 °C. We found that after 21 days of permanence, nearly all population (ca. 99 %) of V. harveyi acquired the VBNC phenotype. Although the size of V. harveyi cells gradually decreased during the incubation time, we found that this morphological change was not directly related to their entry into the VBNC state. Our proteomic study revealed that the level of membrane proteins playing key roles in cellular transport, maintenance of cell structure, and in bioenergetics processes remained unchanged along starvation at low temperature, thus suggesting that V. harveyi might need these proteins for the long-term survival and/or for the resuscitation process. On a contrary, the level of two proteins, elongation factor Tu (EF-TU) and bacterioferritin, greatly increased reaching the maximal values by the end of the incubation period. We further discuss the above data with respect to the putative roles likely exerted by membrane proteins during transition to and maintaining of the VBNC state.

Quantitative proteomic analysis of cell envelope preparations under iron starvation stress in Aeromonas hydrophila

Background

Iron homeostasis is an essential process over the entire lives of both hosts and bacterial pathogens, and also plays roles in many other metabolic functions. Currently, knowledge is limited on the iron scavenging mechanism of the cell envelope in the aquatic pathogen, Aeromonas hydrophila. To understand the iron homeostasis mechanism in A. hydrophila, a dimethyl labelling based quantitative proteomics method was used to compare the differential expression of cell envelope proteins under iron starvation.

Results

A total of 542 cell envelope proteins were identified by LC-MS/MS, with 66 down-regulated and 104 up-regulated proteins. Bioinformatics analysis showed that outer membrane siderophores, heme and iron receptors, periplasmic iron binding proteins, inner membrane ABC transporters and H⁺-ATP synthase subunits increased in abundance while iron-cluster proteins, electron transport chain and redox proteins were down-regulated. Further q-PCR validation, in vivo addition of exogenous metabolites, and an enzyme inhibition assay revealed that redox, the energy generation process, and ATP synthase elevated the susceptibility of A. hydrophila to iron starvation.

Conclusions

Our study demonstrates that the redox and energy generation process, and ATP synthase in A. hydrophila may play critical roles in iron acquisition under conditions of iron-stress. An understanding of the iron scavenging mechanism may be helpful for the development of strategies for preventing and treating A. hydrophila infection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0769-5) contains supplementary material, which is available to authorized users.

BEEP: An assay to detect bio-energetic and envelope permeability alterations in Pseudomonas aeruginosa

We developed an effective and rapid assay to detect both bio-energetic and envelope permeability (BEEP) alterations of Pseudomonas aeruginosa. The assay is based on quantification of extracellular ATP in bacterial cultures using luciferase as a reporter. To demonstrate the validity of our assay we conducted a biased screen of a transposon insertion library in P. aeruginosa strain PAO1 in order to expedite the isolation of mutants with defects in bioenergetic pathways. We successfully isolated insertion mutants that were reduced for extracellular ATP accumulation and identified the corresponding mutations that caused the phenotype. Most of the genes identified from this analysis were associated with energy metabolism and several appeared to be potentially novel bioenergetic targets. In addition, we show that treatment of P. aeruginosa strain PAO1 with antibiotics that disrupt the bacterial cell envelope leads to greater extracellular ATP accumulation. In summary, increases in extracellular ATP accumulation above wild type levels indicated a perturbation of membrane permeability while decreases in extracellular ATP accumulation indicated defects in bioenergetics.

Identifying novel mycobacterial stress associated genes using a random mutagenesis screen in Mycobacterium smegmatis

Cell envelope associated components of Mycobacterium tuberculosis (M.tb) have been implicated in stress response, immune modulation and in vivo survival of the pathogen. Although many such factors have been identified, there is a large disparity between the number of genes predicted to be involved in functions linked to the envelope and those described in the literature. To identify and characterise novel stress related factors associated with the mycobacterial cell envelope, we isolated colony morphotype mutants of Mycobacterium smegmatis (M. smegmatis), based on the hypothesis that mutants with unusual colony morphology may have defects in the biosynthesis of cell envelope components. On testing their susceptibility to stress conditions relevant to M.tb physiology, multiple mutants were found to be sensitive to Isoniazid, Diamide and H2O2, indicative of altered permeability due to changes in cell envelope composition. Two mutants showed defects in biofilm formation implying possible roles for the target genes in antibiotic tolerance and/or virulence. These assays identified novel stress associated roles for several mycobacterial genes including sahH, tatB and aceE. Complementation analysis of selected mutants with the M. smegmatis genes and their M.tb homologues showed phenotypic restoration, validating their link to the observed phenotypes. A mutant carrying an insertion in fhaA encoding a forkhead associated domain containing protein, showed reduced survival in THP-1 macrophages, providing in vivo validation to this screen. Taken together, these results suggest that the M.tb homologues of a majority of the identified genes may play significant roles in the pathogenesis of tuberculosis.

Free nitrous acid serving as a pretreatment method for alkaline fermentation to enhance short-chain fatty acid production from waste activated sludge

Alkaline condition (especially pH 10) has been demonstrated to be a promising method for short-chain fatty acid (SCFA) production from waste activated sludge anaerobic fermentation, because it can effectively inhibit the activities of methanogens. However, due to the limit of sludge solubilization rate, long fermentation time is required but SCFA yield is still limited. This paper reports a new pretreatment method for alkaline fermentation, i.e., using free nitrous acid (FNA) to pretreat sludge for 2 d, by which the fermentation time is remarkably shortened and meanwhile the SCFA production is significantly enhanced. Experimental results showed the highest SCFA production of 370.1 mg COD/g VSS (volatile suspended solids) was achieved at 1.54 mg FNA/L pretreatment integration with 2 d of pH 10 fermentation, which was 4.7- and 1.5-fold of that in the blank (uncontrolled) and sole pH 10 systems, respectively. The total time of this integration system was only 4 d, whereas the corresponding time was 15 d in the blank and 8 d in the sole pH 10 systems. The mechanism study showed that compared with pH 10, FNA pretreatment accelerated disruption of both extracellular polymeric substances and cell envelope. After FNA pretreatment, pH 10 treatment (1 d) caused 38.0% higher substrate solubilization than the sole FNA, which indicated that FNA integration with pH 10 could cause positive synergy on sludge solubilization. It was also observed that this integration method benefited hydrolysis and acidification processes. Therefore, more SCFA was produced, but less fermentation time was required in the integrated system.

Genetic, Biochemical, and Structural Analyses of Bacterial Surface Polysaccharides

Surface polysaccharides are an often essential component of the outer surface of bacteria. They may serve to protect organisms from harsh environmental conditions and to increase virulence. The focus of this review will be to introduce polysaccharide biosynthesis and export from the cell, and the associated techniques used to determine these glycostructures. Protein interactions and proteomics will then be discussed while introducing systems biology approaches used to determine protein-protein and protein-polysaccharide interactions. The final section will address related screening methods used to study gene regulation in bacteria relating to polysaccharide gene clusters and their associated regulators. The goal of this review will be to highlight key studies that have increased our knowledge of glycobiology and discuss novel methods that examine this field at the cellular level using systems biology.

RND transporters protect Corynebacterium glutamicum from antibiotics by assembling the outer membrane

Corynebacterium-Mycobacterium-Nocardia (CMN) group are the causative agents of a broad spectrum of diseases in humans. A distinctive feature of these Gram-positive bacteria is the presence of an outer membrane of unique structure and composition. Recently, resistance-nodulation-division (RND) transporters (nicknamed MmpLs, Mycobacterial membrane protein Large) have emerged as major contributors to the biogenesis of the outer membranes in mycobacteria and as promising drug targets. In this study, we investigated the role of RND transporters in the physiology of Corynebacterium glutamicum and analyzed properties of these proteins. Our results show that in contrast to Gram-negative species, in which RND transporters actively extrude antibiotics from cells, in C. glutamicum and relatives these transporters protect cells from antibiotics by playing essential roles in the biogenesis of the low-permeability barrier of the outer membrane. Conditional C. glutamicum mutants lacking RND proteins and with the controlled expression of either NCgl2769 (CmpL1) or NCgl0228 (CmpL4) are hypersusceptible to multiple antibiotics, have growth deficiencies in minimal medium and accumulate intracellularly trehalose monocorynomycolates, free corynomycolates, and the previously uncharacterized corynomycolate-containing lipid. Our results also suggest that similar to other RND transporters, Corynebacterial membrane proteins Large (CmpLs) functions are dependent on a proton-motive force.

High resolution clear native electrophoresis is a good alternative to blue native electrophoresis for the characterization of the Escherichia coli membrane complexes

Blue native electrophoresis (BNE) has become the most popular method for the global analysis of membrane protein complexes. Although it has been shown to be very useful for that purpose, it can produce the dissociation of complexes with weak interactions and, due to the use of Coomassie Brilliant Blue, does not allow the subsequent application of fluorimetric and/or enzymatic techniques. Recently, we have successfully used the high resolution clear native electrophoresis (hrCNE) for the analysis of Neisseria meningitidis outer membrane porin complexes. The aim of this study was to determine the composition of the complexome of the Escherichia coli envelope by using hrCNE and to compare our results with those previously obtained using BNE. The bidimensional electrophoresis approaches used, hrCN/hrCNE and hrCN/SDS-PAGE, coupled to mass spectrometry allowed a detailed analysis of the complexome of E. coli membranes. For the first time, the three subunits of the formate dehydrogenase FDH-O were identified forming a single complex and hrCNE also allowed the identification of both the HflK and HflC proteins as components of the HflA complex. This technique also allowed us to suggest a relationship between OmpF and DLDH and, although OmpA is considered to be monomeric in vivo, we found this protein structured as homodimers. Thus hrCNE provides a good tool for future analyses of bacterial membrane proteins and complexes and is an important alternative to the commonly used BNE.

Subcellular protein localization (cell envelope) in Phaeobacter inhibens DSM 17395

Phaeobacter inhibens DSM 17395 is a metabolically versatile, secondary metabolite producing and surface colonizing member of the alphaproteobacterial Roseobacter clade. Proteins compartmentalized across the Gram-negative cell envelope are expected to be relevant for the habitat success of P. inhibens DSM 17395. Subcellular fractionation was followed by gel- or nano-LC-based separation of proteins and peptides, respectively. Subsequent MS-based identification of in total 1187 proteins allowed allocation to cytoplasm (303 proteins), cytoplasmic membrane (346), periplasm (325), outer membrane (76), and extracellular milieu (22). Multidimensional scaling was used to visualize the spreading of heuristically allocated proteins across the five different compartments. Experimentally inferred subcellular protein localization was compared with PSORTb prediction of protein secretion and membrane localization. Determined subcellular localizations of identified proteins were interpreted to reconstruct the functional traits of the different cell envelope compartments, in particular protein secretion and sorting, direct effector molecule transit, and cell envelope biogenesis. From a proteogenomic perspective, functional prediction of 74 genes (including 17 coding for proteins of hitherto unknown function) could be refined.