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The emergence and rapid spread of methicillin-resistant Staphylococcus aureus (MRSA) poses a serious threat to public health. New antibiotics and strategies are urgently needed to combat S. aureus associated infections. Bacaucin, a novel cyclic lipopeptide from Bacillus subtilis CAU21, is reported. Bacaucin shows broad antibacterial activity against Gram-positive bacteria, but is also hemolytic and cytotoxic. However, bacaucin-1, a bacaucin-inspired ring-opened heptapeptide, shows specific antibacterial activity against MRSA by a membrane-disruptive mechanism without detectable toxicity to mammalian cells or induction of bacterial resistance. Bacaucin-1 was efficient in preventing infections in both in vitro and in vivo models and is a valuable prototype antibiotic with high potential against S. aureus infections.

Pandora's box with hope: A natural cytotoxic antibiotic bacaucin (see picture; red), a cyclic lipopeptide from Bacillus subtilis, is presented. The safe bacaucin-inspired synthetic derivative bacaucin-1 (blue) shows specific antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), and is efficient in preventing infections in vitro and in vivo.

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The binding kinetics of various β-lactam antibiotics were investigated on Ldt_Mt2, an essential l,d-transpeptidase from Mycobacterium tuberculosis. Faropenem, a classical penem-type compound showed the highest rate in adduct formation. Mass spectrometry and crystal structure analysis revealed a small well-shielded fragment of faropenem bound as covalent adduct. The high stability of this dead-end complex was observed in biochemical assays.

Therapeutic applications of peptides are currently limited by their proteolytic instability and impermeability to the cell membrane. A general, reversible bicyclization strategy is now reported to increase both the proteolytic stability and cell permeability of peptidyl drugs. A peptide drug is fused with a short cell-penetrating motif and converted into a conformationally constrained bicyclic structure through the formation of a pair of disulfide bonds. The resulting bicyclic peptide has greatly enhanced proteolytic stability as well as cell-permeability. Once inside the cell, the disulfide bonds are reduced to produce a linear, biologically active peptide. This strategy was applied to generate a cell-permeable bicyclic peptidyl inhibitor against the NEMO-IKK interaction.

In the loop: Peptide bicyclization by a pair of disulfide bonds increases its proteolytic stability and cell permeability. This method also allows for regeneration of the functional linear peptide once inside the cytosol of the cell. CPP=cell-penetrating peptide.

The development of fluorogenic reactions which lead to the formation of fluorescent products from two nonfluorescent starting materials is highly desirable, but challenging. Reported herein is a new concept of fluorescent product formation upon the inverse electron-demand Diels–Alder reaction of 1,2,4,5-tetrazines with particular trans-cyclooctene (TCO) isomers. In sharp contrast to known fluorogenic reagents the presented chemistry leads to the rapid formation of unprecedented fluorescent 1,4-dihydropyridazines so that the fluorophore is built directly upon the chemical reaction. Attachment of an extra fluorophore moiety is therefore not needed. The photochemical properties of the resulting dyes can be easily tuned by changing the substitution pattern of the starting 1,2,4,5-tetrazine. We support the claim with NMR measurements and rationalize the data by computational study. Cell-labeling experiments were performed to demonstrate the potential of the fluorogenic reaction for bioimaging.

Click-in color: A conceptually new approach enables the formation of fluorescent 1,4-dihydropyridazine products upon reaction of various 1,2,4,5-tetrazines with particular trans-cyclooctene isomers. The chemistry was applied for rapid fluorogenic labeling of subcellular compartments in live cells.

Metabolic adaptation is a key feature for the virulence of pathogenic intracellular bacteria. Nevertheless, little is known about the pathways in adapting the bacterial metabolism to multiple carbon sources available from the host cell. To analyze the metabolic adaptation of the obligate intracellular human pathogen Chlamydia trachomatis, we labeled infected HeLa or Caco-2 cells with ¹³C-marked glucose, glutamine, malate or a mix of amino acids as tracers. Comparative GC-MS-based isotopologue analysis of protein-derived amino acids from the host cell and the bacterial fraction showed that C. trachomatis efficiently imported amino acids from the host cell for protein biosynthesis. FT-ICR-MS analyses also demonstrated that label from exogenous ¹³C-glucose was efficiently shuffled into chlamydial lipopolysaccharide probably via glucose 6-phosphate of the host cell. Minor fractions of bacterial Ala, Asp, and Glu were made de novo probably using dicarboxylates from the citrate cycle of the host cell. Indeed, exogenous ¹³C-malate was efficiently taken up by C. trachomatis and metabolized into fumarate and succinate when the bacteria were kept in axenic medium containing the malate tracer. Together, the data indicate co-substrate usage of intracellular C. trachomatis in a stream-lined bipartite metabolism with host cell-supplied amino acids for protein biosynthesis, host cell-provided glucose 6-phosphate for cell wall biosynthesis, and, to some extent, one or more host cell-derived dicarboxylates, e.g. malate, feeding the partial TCA cycle of the bacterium. The latter flux could also support the biosynthesis of meso-2,6-diaminopimelate required for the formation of chlamydial peptidoglycan.

In a bipartite metabolism the obligate intracellular human pathogen Chlamydia trachomatis uses host cell derived amino acids and glucose-6-phosphate for feeding protein biosynthesis and cell wall biosynthesis, respectively. Host dicarboxylates, e.g. malate are used for supplementing the chlamydial partial TCA cycle and may support peptidoglycan formation.

Most commonly studied bacteria grow symmetrically and divide by binary fission, generating two siblings of equal morphology. An exception to this rule are budding bacteria, in which new offspring emerges de novo from a morphologically invariant mother cell. Although this mode of proliferation is widespread in diverse bacterial lineages, the underlying mechanisms are still incompletely understood. Here, we report the first molecular-level analysis of growth and morphogenesis in the stalked budding alphaproteobacterium Hyphomonas neptunium. Peptidoglycan labeling shows that, in this species, buds originate from a stalk-like extension of the mother cell whose terminal segment is gradually remodeled into a new cell compartment. As a first step toward identifying the machinery mediating the budding process, we performed comprehensive mutational and localization studies of predicted peptidoglycan biosynthetic proteins in H. neptunium. These analyses identify factors that localize to distinct zones of dispersed and zonal growth, and they suggest a critical role of the MreB-controlled elongasome in cell morphogenesis. Collectively, our work shows that the mechanism of growth in H. neptunium is distinct from that in related, polarly growing members of the order Rhizobiales, setting the stage for in-depth analyses of the molecular principles regulating the fascinating developmental cycle of this species.

The stalked budding bacterium Hyphomonas neptunium grows by generating buds at the tip of a stalk-like cellular extension. This study reports the first molecular-level analysis of cell wall biosynthesis in this species. We show that its mode of growth differs significantly from that in related polarly growing species and identify factors critical to proper morphogenesis. These findings set the stage for in-depth mechanistic studies of a fascinating but poorly understood mode of bacterial proliferation.

Affinity-based protein profiling (AfBPP) is a widely applied method for the target identification of bioactive molecules. Probes containing photocrosslinkers, such as benzophenones, diazirines, and aryl azides, irreversibly link the molecule of interest to its target protein upon irradiation with UV light. Despite their prevalent application, little is known about photocrosslinker-specific off-targets, affecting the reliability of results. Herein, we investigated background protein labeling by gel-free quantitative proteomics. Characteristic off-targets were identified for each photoreactive group and compiled in a comprehensive inventory. In a proof-of-principle study, H8, a protein kinase A inhibitor, was equipped with a diazirine moiety. Application of this photoprobe revealed, by alignment with the diazirine background, unprecedented insight into its in situ proteome targets. Taken together, our findings guide the identification of biologically relevant binders in photoprobe experiments.

In affinity-based protein profiling, small molecules are equipped with a photocrosslinker for irreversible binding to a protein target. The background protein labeling observed with such photocrosslinkers was analyzed by gel-free quantitative proteomics, and characteristic off-targets were identified for each photoreactive group. This is of importance for the reliable identification of biologically relevant binders in photoprobe experiments.

Advances in automated fluorescence microscopy have made snapshot and time-lapse imaging of bacterial cells commonplace, yet fundamental challenges remain in analysis. The vast quantity of data collected in high-throughput experiments requires a fast and reliable automated method to analyze fluorescence intensity and localization, cell morphology and proliferation as well as other descriptors. Inspired by effective yet tractable methods of population-level analysis using flow cytometry, we have developed a framework and tools for facilitating analogous analyses in image cytometry. These tools can both visualize and gate (generate subpopulations) more than 70 cell descriptors, including cell size, age and fluorescence. The method is well suited to multi-well imaging, analysis of bacterial cultures with high cell density (thousands of cells per frame) and complete cell cycle imaging. We give a brief description of the analysis of four distinct applications to emphasize the broad applicability of the tool.

In this paper, we have described a framework (Clist) and tools (gateTool) for visualizing and analyzing image cytometry data, inspired by the standard tools used for flow cytometry. This approach facilitates efficient analysis of subpopulations defined by cell descriptors such as fluorescence intensity and localization, cell morphology and growth rate. We provided four representative examples relevant to bacterial cell biology.