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<i>Staphylococcus aureus</i> inactivates daptomycin by releasing membrane phospholipids

Nature Microbiology, Published online: 24 October 2016; doi:10.1038/nmicrobiol.2016.194

Staphylococcus aureus releases phospholipid membranes to inactivate daptomycin.

Single-molecule imaging reveals modulation of cell wall synthesis dynamics in live bacterial cells

Nature Communications, Published online: 24 October 2016; doi:10.1038/ncomms13170

The bacterial cell wall is important for cell shape and stability, but how the activities of the biosynthetic machinery are coordinated are not clear. Here the authors use single-molecule imaging and chemical perturbations to determine factors that affect the localization dynamics of penicillin-binding proteins (PBP)1A and PBP1B.

Abstract

Nature advance online publication 24 October 2016. doi:10.1038/nature20124

Authors: Kaihang Wang, Julius Fredens, Simon F. Brunner, Samuel H. Kim, Tiongsun Chia & Jason W. Chin

ABSTRACT

The ability of Gram-negative bacteria to carefully modulate outer membrane (OM) composition is essential to their survival. However, the asymmetric and heterogeneous structure of the Gram-negative OM poses unique challenges to the cell’s successful adaption to rapid environmental transitions. Although mechanisms to recycle and degrade OM phospholipid material exist, there is no known mechanism by which to remove unfavorable lipopolysaccharide (LPS) glycoforms, except slow dilution through cell growth. As all Gram-negative bacteria constitutively shed OM vesicles (OMVs), we propose that cells may utilize OMV formation as a way to selectively remove environmentally disadvantageous LPS species. We examined the native kinetics of OM composition during physiologically relevant environmental changes in Salmonella enterica, a well-characterized model system for activation of PhoP/Q and PmrA/B two-component systems (TCSs). In response to acidic pH, toxic metals, antimicrobial peptides, and lack of divalent cations, these TCSs modify the LPS lipid A and core, lengthen the O antigen, and upregulate specific OM proteins. An environmental change to PhoP/Q- and PmrA/B-activating conditions simultaneously induced the addition of modified species of LPS to the OM, downregulation of previously dominant species of LPS, greater OMV production, and increased OMV diameter. Comparison of the relative abundance of lipid A species present in the OM and the newly budded OMVs following two sets of rapid environmental shifts revealed the retention of lipid A species with modified phosphate moieties in the OM concomitant with the selective loss of palmitoylated species via vesiculation following exposure to moderately acidic environmental conditions.

IMPORTANCE All Gram-negative bacteria alter the structural composition of LPS present in their OM in response to various environmental stimuli. We developed a system to track the native dynamics of lipid A change in Salmonella enterica serovar Typhimurium following an environmental shift to PhoP/Q- and PmrA/B-inducing conditions. We show that growth conditions influence OMV production, size, and lipid A content. We further demonstrate that the lipid A content of OMVs does not fit a stochastic model of content selection, revealing the significant retention of lipid A species containing covalent modifications that mask their 1- and 4'-phosphate moieties under host-like conditions. Furthermore, palmitoylation of the lipid A to form hepta-acylated species substantially increases the likelihood of its incorporation into OMVs. These results highlight a role for the OMV response in OM remodeling and maintenance processes in Gram-negative bacteria.

Nature Chemical Biology 12, 902 (2016). doi:10.1038/nchembio.2176

Authors: Laura K Stone, Michael Baym, Tami D Lieberman, Remy Chait, Jon Clardy & Roy Kishony

We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline.

Nature Chemistry. doi:10.1038/nchem.2635

Authors: Leanna R. Staben, Stefan G. Koenig, Sophie M. Lehar, Richard Vandlen, Donglu Zhang, Josefa Chuh, Shang-Fan Yu, Carl Ng, Jun Guo, Yanzhou Liu, Aimee Fourie-O'Donohue, MaryAnn Go, Xin Linghu, Nathaniel L. Segraves, Tao Wang, Jinhua Chen, BinQing Wei, Gail D. Lewis Phillips, Keyang Xu, Katherine R. Kozak, Sanjeev Mariathasan, John A. Flygare & Thomas H. Pillow

Many drugs contain tertiary and heteroaryl amines; however, these functional groups are difficult to reversibly crosslink to a carrier protein. Now, a method for conjugating anticancer and antibiotic drugs to antibodies via a quaternary ammonium salt has been developed. Cleavage of the linker results in the traceless release of the free dug and subsequent therapeutic activity.

Metabolomic and proteomic profiling unveil intracellular L-arginine as a crucial regulator of metabolic fitness, survival capacity, and anti-tumor activity of central memory T cells.

Abstract

ABSTRACT

Peptidoglycan recycling is a metabolic process by which Gram-negative bacteria reutilize up to half of their cell wall within one generation during vegetative growth. Whether peptidoglycan recycling also occurs in Gram-positive bacteria has so far remained unclear. We show here that three Gram-positive model organisms, Staphylococcus aureus, Bacillus subtilis, and Streptomyces coelicolor, all recycle the sugar N-acetylmuramic acid (MurNAc) of their peptidoglycan during growth in rich medium. They possess MurNAc-6-phosphate (MurNAc-6P) etherase (MurQ in E. coli) enzymes, which are responsible for the intracellular conversion of MurNAc-6P to N-acetylglucosamine-6-phosphate and d-lactate. By applying mass spectrometry, we observed accumulation of MurNAc-6P in MurNAc-6P etherase deletion mutants but not in either the isogenic parental strains or complemented strains, suggesting that MurQ orthologs are required for the recycling of cell wall-derived MurNAc in these bacteria. Quantification of MurNAc-6P in murQ cells of S. aureus and B. subtilis revealed small amounts during exponential growth phase (0.19 nmol and 0.03 nmol, respectively, per ml of cells at an optical density at 600 nm [OD₆₀₀] of 1) but large amounts during transition (0.56 nmol and 0.52 nmol) and stationary (0.53 nmol and 1.36 nmol) phases. The addition of MurNAc to murQ cultures greatly increased the levels of intracellular MurNAc-6P in all growth phases. The murQ mutants of S. aureus and B. subtilis showed no growth deficiency in rich medium compared to the growth of the respective parental strains, but intriguingly, they had a severe survival disadvantage in late stationary phase. Thus, although peptidoglycan recycling is apparently not essential for the growth of Gram-positive bacteria, it provides a benefit for long-term survival.

IMPORTANCE The peptidoglycan of the bacterial cell wall is turned over steadily during growth. As peptidoglycan fragments were found in large amounts in spent medium of exponentially growing Gram-positive bacteria, their ability to recycle these fragments has been questioned. We conclusively showed recycling of the peptidoglycan component MurNAc in different Gram-positive model organisms and revealed that a MurNAc-6P etherase (MurQ or MurQ ortholog) enzyme is required in this process. We further demonstrated that recycling occurs predominantly during the transition to stationary phase in S. aureus and B. subtilis, explaining why peptidoglycan fragments are found in the medium during exponential growth. We quantified the intracellular accumulation of recycling products in MurNAc-6P etherase gene mutants, revealing that about 5% and 10% of the MurNAc of the cell wall per generation is recycled in S. aureus and B. subtilis, respectively. Importantly, we showed that MurNAc recycling and salvaging does not sustain growth in these bacteria but is used to enhance survival during late stationary phase.

The generation of strain-specific neutralizing antibodies against influenza A virus is known to confer potent protection against homologous infections. The majority of these antibodies bind to the hemagglutinin (HA) head domain and function by blocking the receptor binding site, preventing infection of host cells. Recently, elicitation of broadly neutralizing antibodies...

Natural enzymes contain highly evolved active sites that lead to fast rates and high selectivities. Although artificial metalloenzymes have been developed that catalyze abiological transformations with high stereoselectivity, the activities of these artificial enzymes are much lower than those of natural enzymes. Here, we report a reconstituted artificial metalloenzyme containing an iridium porphyrin that exhibits kinetic parameters similar to those of natural enzymes. In particular, variants of the P450 enzyme CYP119 containing iridium in place of iron catalyze insertions of carbenes into C–H bonds with up to 98% enantiomeric excess, 35,000 turnovers, and 2550 hours−1 turnover frequency. This activity leads to intramolecular carbene insertions into unactivated C–H bonds and intermolecular carbene insertions into C–H bonds. These results lift the restrictions on merging chemical catalysis and biocatalysis to create highly active, productive, and selective metalloenzymes for abiological reactions. Authors: P. Dydio, H. M. Key, A. Nazarenko, J. Y.-E. Rha, V. Seyedkazemi, D. S. Clark, J. F. Hartwig

Abstract

ABSTRACT

The Gram-negative outer membrane is an important barrier that provides protection against toxic compounds, which include antibiotics and host innate immune molecules such as cationic antimicrobial peptides. Recently, significant research progress has been made in understanding the biogenesis, regulation, and functioning of the outer membrane, including a recent paper from the laboratory of Dr. Brett Finlay at the University of British Columbia (J. van der Heijden et al., mBio 7:e01238-16, 2016, http://dx.doi.org/10.1128/mBio.01541-16). These investigators demonstrate that toxic oxygen radicals, such as those found in host tissues, regulate outer membrane permeability by altering the outer membrane porin protein channels to regulate the influx of oxygen radicals as well as β-lactam antibiotics. This commentary provides context about this interesting paper and discusses the prospects of utilizing increased knowledge of outer membrane biology to develop new antibiotics for antibiotic-resistant Gram-negative bacteria.

Abstract

A quorum-sensing signal promotes host tolerance training through HDAC1-mediated epigenetic reprogramming

Nature Microbiology, Published online: 3 October 2016; doi:10.1038/nmicrobiol.2016.174

The Pseudomonas aeruginosa quorum-sensing molecule 2-aminoacetophenone (2-AA) upregulates HDAC1 to reduce acetylation at cytokine promoters and promote host tolerance during infection.

Nature advance online publication 28 September 2016. doi:10.1038/nature19799

Authors: Liang Tao, Jie Zhang, Paul Meraner, Alessio Tovaglieri, Xiaoqian Wu, Ralf Gerhard, Xinjun Zhang, William B. Stallcup, Ji Miao, Xi He, Julian G. Hurdle, David T. Breault, Abraham L. Brass & Min Dong

Nature Medicine. doi:10.1038/nm.4174

Authors: Joseph P Zackular, Jessica L Moore, Ashley T Jordan, Lillian J Juttukonda, Michael J Noto, Maribeth R Nicholson, Jonathan D Crews, Matthew W Semler, Yaofang Zhang, Lorraine B Ware, M Kay Washington, Walter J Chazin, Richard M Caprioli & Eric P Skaar

Clostridium difficile is the most commonly reported nosocomial pathogen in the United States and is an urgent public health concern worldwide. Over the past decade, incidence, severity and costs associated with C. difficile infection (CDI) have increased dramatically. CDI is most commonly initiated by antibiotic-mediated disruption of the gut microbiota; however, non-antibiotic-associated CDI cases are well documented and on the rise. This suggests that unexplored environmental, nutrient and host factors probably influence CDI. Here we show that excess dietary zinc (Zn) substantially alters the gut microbiota and, in turn, reduces the minimum amount of antibiotics needed to confer susceptibility to CDI. In mice colonized with C. difficile, excess dietary Zn severely exacerbated C. difficile–associated disease by increasing toxin activity and altering the host immune response. In addition, we show that the Zn-binding S100 protein calprotectin has antimicrobial effects against C. difficile and is an essential component of the innate immune response to CDI. Taken together, these data suggest that nutrient Zn levels have a key role in determining susceptibility to CDI and severity of disease, and that calprotectin-mediated metal limitation is an important factor in the host immune response to C. difficile.

Combatting antimicrobial resistance globally

Nature Microbiology, Published online: 27 September 2016; doi:10.1038/nmicrobiol.2016.187

The threat of antimicrobial resistance causing drug-resistant infections and the escalating health, social and economic consequences are now becoming visible at a global level. Here, we discuss the economic and political considerations for creating a truly global and effective response to antimicrobial resistance.

Abstract

Structure–function insights reveal the human ribosome as a cancer target for antibiotics

Nature Communications, Published online: 26 September 2016; doi:10.1038/ncomms12856

The ribosome of bacteria and other unicellular pathogens is a common target for antibiotic drugs. Here the authors determine a structure of the human ribosome bound to the translation inhibitor cycloheximide, and provide evidence that targeting the ribosome is a promising avenue for cancer therapy.

Abstract

The intestinal microbiome modulates host susceptibility to enteric pathogens, but the specific protective factors and mechanisms of individual bacterial species are not fully characterized. We show that secreted antigen A (SagA) from Enterococcus faecium is sufficient to protect Caenorhabditis elegans against Salmonella pathogenesis by promoting pathogen tolerance. The NlpC/p60 peptidoglycan hydrolase activity of SagA is required and generates muramyl-peptide fragments that are sufficient to protect C. elegans against Salmonella pathogenesis in a tol-1–dependent manner. SagA can also be heterologously expressed and secreted to improve the protective activity of probiotics against Salmonella pathogenesis in C. elegans and mice. Our study highlights how protective intestinal bacteria can modify microbial-associated molecular patterns to enhance pathogen tolerance. Authors: Kavita J. Rangan, Virginia A. Pedicord, Yen-Chih Wang, Byungchul Kim, Yun Lu, Shai Shaham, Daniel Mucida, Howard C. Hang