Marcos Pires

Teng et al. show that exosome-like nanoparticles (ELNs) from edible plants such as ginger are preferentially taken up by gut bacteria in an ELN lipid-dependent manner. ELN RNAs regulate gut microbiota composition and localization as well as host physiology, notably enhancing gut barrier function to alleviate colitis.

Bacterial pathogens can invade the protected intracellular space, potentially evading host immune function. Abuaita et al. show that macrophage infection by methicillin-resistant Staphylococcus aureus activates host stress response pathways that trigger innate intracellular defense mechanisms. Infection stimulates delivery of antimicrobial-containing mitochondria-derived vesicles to phagosomes to participate in bacterial killing.

Imidazole propionate, a metabolite produced by the gut microbiota, is elevated in type 2 diabetes and can directly impair glucose tolerance and insulin signaling.

Mammals house a diversity of bacteria that affect health in various ways, but the routes by which bacterial lineages are transmitted between hosts remain poorly understood. We experimentally determined microbiota transmission modes by deriving 17 inbred mouse lines from two wild populations and monitoring their gut microbiotas for up to 11 host generations. Individual- and population-level microbiota compositions were maintained within mouse lines throughout the experiment, indicating predominantly vertical inheritance of the microbiota. However, certain bacterial taxa tended to be exchanged horizontally between mouse lines. Consistent with evolutionary theory, the degree of horizontal transmission predicted bacterial genera with pathogenic representatives responsible for human infections and hospitalizations.

Breaching the wall

Breaching the wall, Published online: 24 October 2018; doi:10.1038/s41564-018-0279-3

Protein translocation across bacterial membranes can take many routes through dedicated transport machines. A new study finds that Salmonella Typhi utilizes a distinct pathway to translocate typhoid toxin across the peptidoglycan layer and prime the bacterium for host intoxication.

ABSTRACT

A central question in mechanobiology is how cellular-scale structures are established and regulated. In bacteria, the cell envelope is essential for mechanical integrity, protecting against environmental stresses and bearing the load from high turgor pressures. Trivedi et al. (mBio 9:e01340-18, 2018, https://doi.org/10.1128/mBio.01340-18) screened a Pseudomonas aeruginosa transposon library and identified genes that influence cell stiffness by measuring cell growth while cells were embedded in an agarose gel. Their findings provide a broad knowledge base for how biochemical pathways regulate cellular mechanical properties in this pathogen. Dozens of genes across diverse functional categories were implicated, suggesting that cellular mechanics is a systems-level emergent property. Furthermore, changes in d-alanine levels in a dadA (d-alanine dehydrogenase) mutant resulted in decreases in the expression of cell wall enzymes, cross-linking density, and cell stiffness. These insights into the biochemical and mechanical roles of dadA highlight the importance of systems-level investigations into the physical properties of cells.

ABSTRACT

Posttranslational modifications, such as N-lysine acetylation, regulate protein function. N-lysine acetylation can occur either nonenzymatically or enzymatically. The nonenzymatic mechanism uses acetyl phosphate (AcP) or acetyl coenzyme A (AcCoA) as acetyl donor to modify an N-lysine residue of a protein. The enzymatic mechanism uses N-lysine acetyltransferases (KATs) to specifically transfer an acetyl group from AcCoA to N-lysine residues on proteins. To date, only one KAT (YfiQ, also known as Pka and PatZ) has been identified in Escherichia coli. Here, we demonstrate the existence of 4 additional E. coli KATs: RimI, YiaC, YjaB, and PhnO. In a genetic background devoid of all known acetylation mechanisms (most notably AcP and YfiQ) and one deacetylase (CobB), overexpression of these putative KATs elicited unique patterns of protein acetylation. We mutated key active site residues and found that most of them eliminated enzymatic acetylation activity. We used mass spectrometry to identify and quantify the specificity of YfiQ and the four novel KATs. Surprisingly, our analysis revealed a high degree of substrate specificity. The overlap between KAT-dependent and AcP-dependent acetylation was extremely limited, supporting the hypothesis that these two acetylation mechanisms play distinct roles in the posttranslational modification of bacterial proteins. We further showed that these novel KATs are conserved across broad swaths of bacterial phylogeny. Finally, we determined that one of the novel KATs (YiaC) and the known KAT (YfiQ) can negatively regulate bacterial migration. Together, these results emphasize distinct and specific nonenzymatic and enzymatic protein acetylation mechanisms present in bacteria.

IMPORTANCE N-Lysine acetylation is one of the most abundant and important posttranslational modifications across all domains of life. One of the best-studied effects of acetylation occurs in eukaryotes, where acetylation of histone tails activates gene transcription. Although bacteria do not have true histones, N-lysine acetylation is prevalent; however, the role of these modifications is mostly unknown. We constructed an E. coli strain that lacked both known acetylation mechanisms to identify four new N-lysine acetyltransferases (RimI, YiaC, YjaB, and PhnO). We used mass spectrometry to determine the substrate specificity of these acetyltransferases. Structural analysis of selected substrate proteins revealed site-specific preferences for enzymatic acetylation that had little overlap with the preferences of the previously reported acetyl-phosphate nonenzymatic acetylation mechanism. Finally, YiaC and YfiQ appear to regulate flagellum-based motility, a phenotype critical for pathogenesis of many organisms. These acetyltransferases are highly conserved and reveal deeper and more complex roles for bacterial posttranslational modification.

Therapeutic treatment of Zika virus infection using a brain-penetrating antiviral peptide

Therapeutic treatment of Zika virus infection using a brain-penetrating antiviral peptide, Published online: 22 October 2018; doi:10.1038/s41563-018-0194-2

The Zika virus infects the central nervous system and results in severe brain malformation. An amphiphatic peptide is now shown to penetrate the blood–brain barrier, reducing viral loads due to its activity against Zika and other mosquito-borne viruses.

by Matthias I. Gröschel, Timothy M. Walker, Tjip S. van der Werf, Christoph Lange, Stefan Niemann, Matthias Merker

A widely conserved toxin for interbacterial competition targets proteins for ADP-ribosylation, while antitoxins fight back using dual mechanisms of active site occlusion and enzymatic reversal of the modification, conferring broad immunity to diverse toxins.

In most well studied rod-shaped bacteria, peptidoglycan is primarily crosslinked by penicillin-binding proteins (PBPs). However, in mycobacteria, crosslinks formed by L,D-transpeptidases (LDTs) are highly abundant. To elucidate the role of these unusual crosslinks, we characterized Mycobacterium smegmatis cells lacking all LDTs. We find that crosslinks generate by LDTs are required for rod shape maintenance specifically at sites of aging cell wall, a byproduct of polar elongation. Asymmetric polar growth leads to a non-uniform distribution of these two types of crosslinks in a single cell. Consequently, in the absence of LDT-mediated crosslinks, PBP-catalyzed crosslinks become more important. Because of this, Mycobacterium tuberculosis (Mtb) is more rapidly killed using a combination of drugs capable of PBP- and LDT- inhibition. Thus, knowledge about the spatial and genetic relationship between drug targets can be exploited to more effectively treat this pathogen.

Extracellular vesicles (EVs) contain protein and RNA cargo that can be transferred between cells. Hinger et al. identify distinct subsets of cellular coding and long noncoding RNAs that are enriched in EVs that can be functionally transferred between cells, supporting a regulated form of cell-cell communication.

ABSTRACT

Pathogens are exposed to toxic levels of copper during infection, and copper tolerance may be a general virulence mechanism used by bacteria to resist host defenses. In support of this, inactivation of copper exporter genes has been found to reduce the virulence of bacterial pathogens in vivo. Here we investigate the role of copper hypertolerance in methicillin-resistant Staphylococcus aureus (MRSA). We show that a copper hypertolerance operon (copB-mco), carried on a mobile genetic element (MGE), is prevalent in a collection of invasive S. aureus strains and more widely among clonal complex 22, 30, and 398 strains. The copB and mco genes encode a copper efflux pump and a multicopper oxidase, respectively. Isogenic mutants lacking copB or mco had impaired growth in subinhibitory concentrations of copper. Transfer of a copB-mco-carrying plasmid to a naive clinical isolate resulted in a gain of copper hypertolerance and enhanced bacterial survival inside primed macrophages. The copB and mco genes were upregulated within infected macrophages, and their expression was dependent on the copper-sensitive operon repressor CsoR. Isogenic copB and mco mutants were impaired in their ability to persist intracellularly in macrophages and were less resistant to phagocytic killing in human blood than the parent strain. The importance of copper-regulated genes in resistance to phagocytic killing was further elaborated using mutants expressing a copper-insensitive variant of CsoR. Our findings suggest that the gain of mobile genetic elements carrying copper hypertolerance genes contributes to the evolution of virulent strains of S. aureus that are better equipped to resist killing by host immune cells.

IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) poses a substantial threat to human health worldwide and evolves rapidly by acquiring mobile genetic elements, such as plasmids. Here we investigate how the copB-mco copper hypertolerance operon carried on a mobile genetic element contributes to the virulence potential of clinical isolates of MRSA. Copper is a key component of innate immune bactericidal defenses. Here we show that copper hypertolerance genes enhance the survival of S. aureus inside primed macrophages and in whole human blood. The copB and mco genes are carried by clinical isolates responsible for invasive infections across Europe, and more broadly among three successful clonal lineages of S. aureus. Our findings show that a gain of copper hypertolerance genes increases the resistance of MRSA to phagocytic killing by host immune cells and imply that acquisition of this mobile genetic element can contribute to the success of MRSA.

Lipopolysaccharide-affinity copolymer senses the rapid motility of swarmer bacteria to trigger antimicrobial drug release

Lipopolysaccharide-affinity copolymer senses the rapid motility of swarmer bacteria to trigger antimicrobial drug release, Published online: 15 October 2018; doi:10.1038/s41467-018-06729-6

Urinary tract infections are a common side effect of urethral catheters. Here, the authors report on the development of antibiotic loaded NPs with functional polymer coatings which attach too and are removed by motile bacteria to trigger the release of antibiotic.

Targeted killing of tumor cells with antibody–drug conjugates (ADCs) utilizing kinesin spindle protein inhibitor payloads is described in the Communication by Lerchen et al. on https://doi.org/10.1002/anie.201807619page 15243 ff. Upon binding of the armed antibody to tumor‐specific antigens, the ADC is internalized into lysosomal compartments, where the active metabolite is released. Subsequent inhibition of KSP, an ATP‐dependent motor protein involved in the generation of bipolar spindles, finally leads to apoptosis. (Artwork by The New Atlantic, Cologne.)

by Jonathan Dworkin

Cas12a (Cpf1) is a CRISPR-associated nuclease with broad utility for synthetic genome engineering, agricultural genomics, and biomedical applications. Although bacteria harboring CRISPR-Cas9 or CRISPR-Cas3 adaptive immune systems sometimes acquire mobile genetic elements encoding anti-CRISPR proteins that inhibit Cas9, Cas3, or the DNA-binding Cascade complex, no such inhibitors have been found for CRISPR-Cas12a. Here we use a comprehensive bioinformatic and experimental screening approach to identify three different inhibitors that block or diminish CRISPR-Cas12a–mediated genome editing in human cells. We also find a widespread connection between CRISPR self-targeting and inhibitor prevalence in prokaryotic genomes, suggesting a straightforward path to the discovery of many more anti-CRISPRs from the microbial world.

No washing required: A photoswitchable protein/chromophore complex enables control of the ON‐ and OFF‐emitting state of a protein‐bound fluorophore, with emission in the far‐red region of the spectrum. The genetically coded protein‐based fluorophore can be used as a no‐wash imaging system.

Abstract

FR‐1V, a fluorene‐based aldehydic chromophore, binds its target protein as an imine to yield a highly bathochromic pigment, CF‐2, a prototypic protein–dye tagging system whose NIR emission can be spatiotemporally switched ON by rapid UV‐light activation. This is achieved through photoisomerization of the imine and its subsequent protonation. We demonstrate a no‐wash protocol for live cell imaging of subcellular compartments in a variety of mammalian cell lines with minimal fluorescence background.

Host-associated niche metabolism controls enteric infection through fine-tuning the regulation of type 3 secretion

Host-associated niche metabolism controls enteric infection through fine-tuning the regulation of type 3 secretion, Published online: 10 October 2018; doi:10.1038/s41467-018-06701-4

Infection of mice with Citrobacter rodentium is a common model of infection with attaching-and-effacing pathogens. Here, Connolly et al. analyse the transcriptome of C. rodentium during mouse infection, showing host-induced coordinated upregulation of virulence factors and 1,2-propanediol metabolism.

Angewandte Chemie International Edition, EarlyView.

Extracellular vesicles exchange protein and lipid signals between endothelial cells and adipocytes conveying information about nutrient state changes from the blood in adipose tissues.