Marcos Pires

Certain Escherichia coli strains residing in the human gut produce colibactin, a small-molecule genotoxin implicated in colorectal cancer pathogenesis. However, colibactin’s chemical structure and the molecular mechanism underlying its genotoxic effects have remained unknown for more than a decade. Here we combine an untargeted DNA adductomics approach with chemical synthesis to identify and characterize a covalent DNA modification from human cell lines treated with colibactin-producing E. coli. Our data establish that colibactin alkylates DNA with an unusual electrophilic cyclopropane. We show that this metabolite is formed in mice colonized by colibactin-producing E. coli and is likely derived from an initially formed, unstable colibactin-DNA adduct. Our findings reveal a potential biomarker for colibactin exposure and provide mechanistic insights into how a gut microbe may contribute to colorectal carcinogenesis.

In this work, Xie et al. report the structure of a chimeric protein containing the complete HK module of AgrC, the histidine kinase involved in S. aureus agr quorum sensing. Structure-guided biochemical analysis reveals that activation of AgrC involves disruption of an intrasteric inhibitory docking interaction in the AgrC dimer.

Commensal and pathogenic bacteria hydrolyze host lipid substrates with secreted lipases and phospholipases for nutrient acquisition, colonization, and infection. Bacterial lipase activity on mammalian lipids and phospholipids can promote release of free fatty acids from lipid stores, detoxify antimicrobial lipids, and facilitate membrane dissolution. The gram-positive bacterium Staphylococcus aureus secretes...

α‐Gal–antibody (Ab) conjugates have been developed that can dramatically increase cellular cytotoxicity by recruiting natural Abs through the interaction between α‐gal and anti‐gal Abs. The potency of the α‐gal–Ab conjugates increased with the amount of α‐gal conjugated to the Ab. The method developed here will enable the re‐development of Abs to improve their potency.

Abstract

Cancer treatment with antibodies (Abs) is one of the most successful therapeutic strategies for obtaining high selectivity. In this study, α‐gal–Ab conjugates were developed that dramatically increased cellular cytotoxicity by recruiting natural Abs through the interaction between α‐gal and anti‐gal Abs. The potency of the α‐gal–Ab conjugates depended on the amount of α‐gal conjugated to the antibody: the larger the amount of α‐gal introduced, the higher the level of cytotoxicity observed. The conjugation of antibodies with an α‐gal dendrimer allowed the introduction of large amounts of α‐gal to the Ab, without loss of affinity for the target cell. The method described here will enable the re‐development of Abs to improve their potency.

Staphylococcus aureus is a notorious human bacterial pathogen with considerable capacity to develop antibiotic resistance. We have observed that human infections caused by highly drug-resistant S. aureus are more prolonged, complicated, and difficult to eradicate. Here we describe a metabolic adaptation strategy used by clinical S. aureus strains that leads...

Nε-lysine acetylation is an abundant and dynamic regulatory posttranslational modification that remains poorly characterized in bacteria. In bacteria, hundreds of proteins are known to be acetylated, but the biological significance of the majority of these events remains unclear. Previously, we characterized the Bacillus subtilis acetylome and found that the essential...

The enzymes Csd6 and Pgp2 are peptidoglycan (PG) proteases found in the pathogenic bacteria Helicobacter pylori and Campylobacter jejuni, respectively. These enzymes are involved in the trimming of uncrosslinked PG sidechains and catalyze the cleavage of the bond between meso‐diaminopimelic acid (meso‐Dap) and D‐alanine, thus converting a PG‐tetrapeptide into a PG‐tripeptide. They are known to be cell shape‐determining enzymes, since deletion of the corresponding genes result in mutant strains that have lost the normal helical phenotype and instead possess a straight rod morphology. In this work, we report two approaches towards the synthesis of a tripeptide substrate, Ac‐iso‐D‐Glu‐meso‐oxa‐Dap‐D‐Ala, that serves as a mimic of the terminus of an uncrosslinked PG‐tetrapeptide substrate. The isosteric analog meso‐oxa‐Dap is utilized in place of meso‐Dap to simply the synthetic procedure. The more efficient synthesis involves the ring opening of a peptide‐embedded aziridine by a serine‐based nucleophile. A branched tetrapeptide is also prepared as a mimic of the terminus of a crosslinked PG‐tetrapeptide. We use a mass spectral analysis to demonstrate that the tripeptide serves as a substrate for both Csd6 and Pgp2, and that the branched tetrapeptide serves as a substrate for Pgp2, albeit at a significantly slower rate.

The alarming rise of antimicrobial resistance (AMR) imposes severe burdens on health care systems and the economy worldwide, urgently calling for the development of novel antibiotics. Antimicrobial peptides could be ideal templates for next‐generation antibiotics due to their low propensity to develop resistance. An especially promising branch of antimicrobial peptides target Lipid II, the precursor of the bacterial peptidoglycan network. In order to develop these peptides into clinically applicable compounds, detailed information on their pharmacologically relevant modes of action is of critical importance. Here, we review the current understanding on the binding mode of a selection of Lipid II targeting peptides, and we highlight shortcomings in our molecular understanding that, at least partly, relate to the widespread use of artificial membrane mimics for structural studies of membrane‐active antibiotics. In particular, we showcase on the example of the antimicrobial peptide nisin that the native cellular membrane environment can be critical to understand the physiologically relevant binding mode.

The neuroactive potential of the human gut microbiota in quality of life and depression

The neuroactive potential of the human gut microbiota in quality of life and depression, Published online: 04 February 2019; doi:10.1038/s41564-018-0337-x

Correlation of microbiome features with host quality of life and depression identified specific taxa and microbial pathways in two independent, large population cohorts, identifying links between microbial neuroactive potential and depression.

Lung cancer development is associated with increased bacterial burden and altered bacterial composition in the lung. Depletion of microbiota or blockade of the downstream cellular or molecular immune mediators significantly suppress lung tumor growth.

Mycobacterium tuberculosis (Mtb) is the leading infectious cause of death in humans. Synthesis of lipids critical for Mtb’s cell wall and virulence depends on phosphopantetheinyl transferase (PptT), an enzyme that transfers 4'-phosphopantetheine (Ppt) from coenzyme A (CoA) to diverse acyl carrier proteins. We identified a compound that kills Mtb by binding and partially inhibiting PptT. Killing of Mtb by the compound is potentiated by another enzyme encoded in the same operon, Ppt hydrolase (PptH), that undoes the PptT reaction. Thus, loss-of-function mutants of PptH displayed antimicrobial resistance. Our PptT-inhibitor cocrystal structure may aid further development of antimycobacterial agents against this long-sought target. The opposing reactions of PptT and PptH uncover a regulatory pathway in CoA physiology.

Reaching new depths: Polymer–peptide conjugates (PPCs) designed to undergo an acid‐induced increase in hydrophobicity with a narrow pH‐response range (from pH 7.4 to 6.5) underwent in vivo self‐assembly in the tumor microenvironment (see picture). The PPCs in single‐chain form can penetrate deeply into the tumor and self‐assemble into nanoaggregates at molecular concentrations around the IC₅₀ values of the PPCs for enhanced cancer therapy.

Abstract

In cancer treatment, the unsatisfactory solid‐tumor penetration of nanomaterials limits their therapeutic efficacy. We employed an in vivo self‐assembly strategy and designed polymer–peptide conjugates (PPCs) that underwent an acid‐induced hydrophobicity increase with a narrow pH‐response range (from 7.4 to 6.5). In situ self‐assembly in the tumor microenvironment at appropriate molecular concentrations (around the IC₅₀ values of PPCs) enabled drug delivery deeper into the tumor. A cytotoxic peptide KLAK, decorated with the pH‐sensitive moiety cis‐aconitic anhydride (CAA), and a cell‐penetrating peptide TAT were conjugated onto poly(β‐thioester) backbones to produce PT‐K‐CAA, which can penetrate deeply into solid tumors owing to its small size as a single chain. During penetration in vivo, CAA responds to the weak acid, leading to the self‐assembly of PPCs and the recovery of therapeutic activity. Therefore, a deep‐penetration ability for enhanced cancer therapy is provided by this in vivo assembly strategy.

ABSTRACT

Streptococcus pneumoniae is a leading killer of infants and immunocompromised adults and has become increasingly resistant to major antibiotics. Therefore, the development of new antibiotic strategies is desperately needed. Targeting bacterial cell division is one such strategy, specifically by targeting proteins that are essential for the synthesis and breakdown of peptidoglycan. One complex important to this process is FtsEX. FtsEX comprises a cell division-regulating integral membrane protein (FtsX) and a cytoplasmic ATPase (FtsE) that resembles an ATP-binding cassette (ABC) transporter. Here, we present nuclear magnetic resonance (NMR) solution structural and crystallographic models of the large extracellular domain of FtsX, denoted extracellular loop 1 (ECL1). The structure of ECL1 reveals an upper extended β-hairpin and a lower α-helical lobe, each extending from a mixed α-β core. The helical lobe mediates a physical interaction with the peptidoglycan hydrolase PcsB via the coiled-coil domain of PcsB (PscB_CC). Characterization of S. pneumoniae strain D39-derived strains harboring mutations in the α-helical lobe shows that this subdomain is essential for cell viability and required for proper cell division of S. pneumoniae.

IMPORTANCE FtsX is a ubiquitous bacterial integral membrane protein involved in cell division that regulates the activity of peptidoglycan (PG) hydrolases. FtsX is representative of a large group of ABC3 superfamily proteins that function as "mechanotransmitters," proteins that relay signals from the inside to the outside of the cell. Here, we present a structural characterization of the large extracellular loop, ECL1, of FtsX from the opportunistic human pathogen S. pneumoniae. We show the molecular nature of the direct interaction between the peptidoglycan hydrolase PcsB and FtsX and demonstrate that this interaction is essential for cell viability. As such, FtsX represents an attractive, conserved target for the development of new classes of antibiotics.

FtsW is a peptidoglycan polymerase that is functional only in complex with its cognate penicillin-binding protein

FtsW is a peptidoglycan polymerase that is functional only in complex with its cognate penicillin-binding protein, Published online: 28 January 2019; doi:10.1038/s41564-018-0345-x

Classically, peptidoglycan (PG) synthesis was thought to be mediated solely by class A penicillin-binding proteins (PBPs) and related enzymes, a view changed by the identification of RodA as a PG polymerase. Now FtsW is also shown to polymerize PG, in a process that requires complex formation with a partner class B PBP.

Metabolic rewiring of macrophages by CpG potentiates clearance of cancer cells and overcomes tumor-expressed CD47−mediated ‘don’t-eat-me’ signal

Metabolic rewiring of macrophages by CpG potentiates clearance of cancer cells and overcomes tumor-expressed CD47−mediated ‘don’t-eat-me’ signal, Published online: 21 January 2019; doi:10.1038/s41590-018-0292-y

Macrophages have important antitumor functions but can be evaded by tumor-expressed CD47-dependent ‘don’t-eat-me’ signals. Beatty and colleagues demonstrate that the Toll-like receptor 9 ligand CpG metabolically reprograms macrophages to overcome don’t-eat-me signals.

The human microbiome harbors many unidentified species. By large-scale metagenomic assembly of samples from diverse populations, we uncovered >150,000 microbial genomes that are recapitulated in 4,930 species. Many species (77%) were never described before, increase the mappability of metagenomes, and expand our understanding of global body-wide human microbiomes.

Oh et al. discover that the central carbon metabolism of the gut symbiont Lactobacillus reuteri is intimately connected to phage production. Dietary fructose or exposure to SCFAs activates the Ack pathway in Lactobacillus reuteri, which evokes a global stress response in the bacterium that consequently leads to increased phage production.

Koliaraki et al. show that MyD88 in mesenchymal cells is responsible for its tumor-promoting role in the Apcmin/+ model. They further show that this is a TLR4-mediated mechanism that leads to the production of pro-tumorigenic molecules, also identified in human CAFs.

Translation control of the immune checkpoint in cancer and its therapeutic targeting

Translation control of the immune checkpoint in cancer and its therapeutic targeting, Published online: 14 January 2019; doi:10.1038/s41591-018-0321-2

Oncogene cooperation enhances PD-L1 translation to promote immune evasion and metastasis in a novel model of liver cancer.

Blood–brain barrier breakdown is an early biomarker of human cognitive dysfunction

Blood–brain barrier breakdown is an early biomarker of human cognitive dysfunction, Published online: 14 January 2019; doi:10.1038/s41591-018-0297-y

Neuroimaging and cerebrospinal fluid analyses in humans reveal that loss of blood–brain barrier integrity and brain capillary pericyte damage are early biomarkers of cognitive impairment that occur independently of changes in amyloid-β and tau.

Exploring the vast chemical space for immunotherapeutic agent discovery requires robust technologies that recapitulate the tumor-immune microenvironment. Mo et al. developed an HTiP platform that models the KRAS mutation-driven immunosuppressive phenotype. The identification of IAP inhibitors with known anti-tumor immunity activity supports the utility of HTiP to uncover small-molecule anti-cancer immunomodulators.

Cytopenias are an important clinical problem associated with inflammatory disease and infection. We show that specialized phagocytes that internalize red blood cells develop in Toll-like receptor 7 (TLR7)–driven inflammation. TLR7 signaling caused the development of inflammatory hemophagocytes (iHPCs), which resemble splenic red pulp macrophages but are a distinct population derived from Ly6C^hi monocytes. iHPCs were responsible for anemia and thrombocytopenia in TLR7-overexpressing mice, which have a macrophage activation syndrome (MAS)–like disease. Interferon regulatory factor 5 (IRF5), associated with MAS, participated in TLR7-driven iHPC differentiation. We also found iHPCs during experimental malarial anemia, in which they required endosomal TLR and MyD88 signaling for differentiation. Our findings uncover a mechanism by which TLR7 and TLR9 specify monocyte fate and identify a specialized population of phagocytes responsible for anemia and thrombocytopenia associated with inflammation and infection.

A genetics-free method for high-throughput discovery of cryptic microbial metabolites

A genetics-free method for high-throughput discovery of cryptic microbial metabolites, Published online: 07 January 2019; doi:10.1038/s41589-018-0193-2

A combination of elicitor screening to induce expression of silent biosynthetic gene clusters with imaging mass spectrometry to visualize the resulting metabolome enables the discovery of nine cryptic natural products.

Calibration of CAR activation potential directs alternative T cell fates and therapeutic potency

Calibration of CAR activation potential directs alternative T cell fates and therapeutic potency, Published online: 17 December 2018; doi:10.1038/s41591-018-0290-5

A novel chimeric antigen receptor (CAR) T cell design improves therapeutic efficacy by balancing effector and memory profiles.