Marcos Pires

A Western-style, high-fat diet promotes cardiovascular disease, in part because it is rich in choline, which is converted to trimethylamine (TMA) by the gut microbiota. However, whether diet-induced changes in intestinal physiology can alter the metabolic capacity of the microbiota remains unknown. Using a mouse model of diet-induced obesity, we show that chronic exposure to a high-fat diet escalates Escherichia coli choline catabolism by altering intestinal epithelial physiology. A high-fat diet impaired the bioenergetics of mitochondria in the colonic epithelium to increase the luminal bioavailability of oxygen and nitrate, thereby intensifying respiration-dependent choline catabolism of E. coli. In turn, E. coli choline catabolism increased levels of circulating trimethlamine N-oxide, which is a potentially harmful metabolite generated by gut microbiota.

Lewis and Harthorn et al. demonstrate a platform to discover protein-small molecule hybrids that merge pharmacophore activity with engineerable proteins to achieve potency and specificity superior to those of either component alone. Hybrids with multiple linker lengths, conjugation sites, and protein sequences against two enzymes reveal platform flexibility and design impacts.

Gut microbiota generate circadian rhythms in innate immunity that synchronize with feeding and anticipate exogenous microbial exposure.

Activation of cell-autonomous defense by the immune cytokine interferon- (IFN-) is critical to the control of life-threatening infections in humans. IFN- induces the expression of hundreds of host proteins in all nucleated cells and tissues, yet many of these proteins remain uncharacterized. We screened 19,050 human genes by CRISPR-Cas9 mutagenesis and identified IFN-–induced apolipoprotein L3 (APOL3) as a potent bactericidal agent protecting multiple non–immune barrier cell types against infection. Canonical apolipoproteins typically solubilize mammalian lipids for extracellular transport; APOL3 instead targeted cytosol-invasive bacteria to dissolve their anionic membranes into human-bacterial lipoprotein nanodiscs detected by native mass spectrometry and visualized by single-particle cryo–electron microscopy. Thus, humans have harnessed the detergent-like properties of extracellular apolipoproteins to fashion an intracellular lysin, thereby endowing resident nonimmune cells with a mechanism to achieve sterilizing immunity.

A prospective randomized multiomics study in humans investigating the longitudinal effects of a high-fiber or fermented-food diet shows their differential effects on the diversity of the microbiome, with the latter having a noticeable impact on reducing inflammatory markers and modulating immune responses.

Nature Microbiology, Published online: 08 July 2021; doi:10.1038/s41564-021-00927-7

Several Fusobacterium species, such as Fusobacterium nucleatum, have been associated with cancer. Here, using differential RNA-sequencing, the authors provide high-resolution global RNA maps for five clinically relevant fusobacterial strains, elucidating basic aspects of fusobacterial gene expression and identifying multiple non-coding RNAs, including an oxygen-induced small RNA, FoxI, which represses the major outer membrane porin FomA.

Nature Microbiology, Published online: 05 July 2021; doi:10.1038/s41564-021-00920-0

Direct gut sampling shows that probiotics reduce the number of antibiotic resistance genes in the gut of colonization-permissive and antibiotic-naïve individuals. However, when given after antibiotic treatment, probiotics can expand the gut resistome via a bloom of indigenous strains carrying vancomycin resistance genes, rather than antibiotic resistance genes carried by the probiotics themselves.

Neutrophils communicate with each other to form swarms in infected organs. Coordination of this population response is critical for the elimination of bacteria and fungi. Using transgenic mice, we found that neutrophils have evolved an intrinsic mechanism to self-limit swarming and avoid uncontrolled aggregation during inflammation. G protein–coupled receptor (GPCR) desensitization acts as a negative feedback control to stop migration of neutrophils when they sense high concentrations of self-secreted attractants that initially amplify swarming. Interference with this process allows neutrophils to scan larger tissue areas for microbes. Unexpectedly, this does not benefit bacterial clearance as containment of proliferating bacteria by neutrophil clusters becomes impeded. Our data reveal how autosignaling stops self-organized swarming behavior and how the finely tuned balance of neutrophil chemotaxis and arrest counteracts bacterial escape.

Zhu et al. demonstrate via gut microbial transplantation studies that stroke severity is transmissible; specifically, the metaorganismal TMAO pathway was found to impact infarct size and functional impairment in mice. Gut microbial CutC increased host TMAO generation, cerebral infarct size, and post-stroke functional deficits.

A multifunctional peptide–colistin conjugate for the treatment of bacterial infections has been synthesized. The conjugate binds to E. coli bacteria by an all-d sequence of the human peptide ubiquicidin_29–41. Host immune cells, activated upon infection, secrete the enzyme neutrophil elastase that cleaves an optimized linker sequence to release free colistin, a potent antibiotic that kills the bacteria.

Abstract

In order to render potent, but toxic antibiotics more selective, we have explored a novel conjugation strategy that includes drug accumulation followed by infection-triggered release of the drug. Bacterial targeting was achieved using a modified fragment of the human antimicrobial peptide ubiquicidin, as demonstrated by fluorophore-tagged variants. To limit the release of the effector colistin only to infection-related situations, we introduced a linker that was cleaved by neutrophil elastase (NE), an enzyme secreted by neutrophil granulocytes at infection sites. The linker carried an optimized sequence of amino acids that was required to assure sufficient cleavage efficiency. The antibacterial activity of five regioisomeric conjugates prepared by total synthesis was masked, but was released upon exposure to recombinant NE when the linker was attached to amino acids at the 1- or the 3-position of colistin. A proof-of-concept was achieved in co-cultures of primary human neutrophils and Escherichia coli that induced the secretion of NE, the release of free colistin, and an antibacterial efficacy that was equal to that of free colistin.

Nature Chemical Biology, Published online: 27 May 2021; doi:10.1038/s41589-021-00803-9

Glycerol phosphate modifications of cell wall carbohydrates localize regulators of cell division in Streptococcus mutans.

During infection, intracellular bacterial pathogens translocate a variety of effectors into host cells that modify host membrane trafficking for their benefit. We found a self-organizing system consisting of a bacterial phosphoinositide kinase and its opposing phosphatase that formed spatiotemporal patterns, including traveling waves, to remodel host cellular membranes. The Legionella effector MavQ, a phosphatidylinositol (PI) 3-kinase, was targeted to the endoplasmic reticulum (ER). MavQ and the Legionella PI 3-phosphatase SidP, even in the absence of other bacterial components, drove rapid PI 3-phosphate turnover on the ER and spontaneously formed traveling waves that spread along ER subdomains inducing vesicle and tubule budding. Thus, bacteria can exploit a self-organizing membrane-targeting mechanism to hijack host cellular structures for survival.

Repurposing a cell death mechanism for antibacterial defense, human immune cells combat infection by punching holes in bacterial membranes. A human pathogen has evolved a way to fight back.

Identification of stable mammalian RNAs decorated with glycan structures opens up a new dimension for regulatory control of RNA localization and function by post-transcriptional modification.

by Marisela M. Davis, Aaron M. Brock, Tanner G. DeHart, Brittany P. Boribong, Katherine Lee, Mecaila E. McClune, Yunjie Chang, Nicholas Cramer, Jun Liu, Caroline N. Jones, Brandon L. Jutras

The bacterial pathogen responsible for causing Lyme disease, Borrelia burgdorferi, is an atypical Gram-negative spirochete that is transmitted to humans via the bite of an infected Ixodes tick. In diderms, peptidoglycan (PG) is sandwiched between the inner and outer membrane of the cell envelope. In many other Gram-negative bacteria, PG is bound by protein(s), which provide both structural integrity and continuity between envelope layers. Here, we present evidence of a peptidoglycan-associated protein (PAP) in B. burgdorferi. Using an unbiased proteomics approach, we identified Neutrophil Attracting Protein A (NapA) as a PAP. Interestingly, NapA is a Dps homologue, which typically functions to bind and protect cellular DNA from damage during times of stress. While B. burgdorferi NapA is known to be involved in the oxidative stress response, it lacks the critical residues necessary for DNA binding. Biochemical and cellular studies demonstrate that NapA is localized to the B. burgdorferi periplasm and is indeed a PAP. Cryo-electron microscopy indicates that mutant bacteria, unable to produce NapA, have structural abnormalities. Defects in cell-wall integrity impact growth rate and cause the napA mutant to be more susceptible to osmotic and PG-specific stresses. NapA-linked PG is secreted in outer membrane vesicles and augments IL-17 production, relative to PG alone. Using microfluidics, we demonstrate that NapA acts as a molecular beacon—exacerbating the pathogenic properties of B. burgdorferi PG. These studies further our understanding of the B. burgdorferi cell envelope, provide critical information that underlies its pathogenesis, and highlight how a highly conserved bacterial protein can evolve mechanistically, while maintaining biological function.

Nature, Published online: 28 April 2021; doi:10.1038/s41586-021-03502-6

RNA-sequencing experiments determine that sorbitol, a metabolite produced by the host enzyme aldose reductase, is exploited by Clostridium difficile in its adaptation to inflammatory conditions in the gut.

by Yue Chen, Sean M. Vargas, Trever C. Smith II, Sai Lakshmi Rajasekhar Karna, Taylor MacMackin Ingle, Karen L. Wozniak, Floyd L. Wormley Jr., Janakiram Seshu

The Peptidoglycan (PG) cell wall of the Lyme disease (LD) spirochete, Borrelia burgdorferi (Bb), contributes to structural and morphological integrity of Bb; is a persistent antigen in LD patients; and has a unique pentapeptide with L-Ornithine as the third amino acid that cross-links its glycan polymers. A borrelial homolog (BB_0167) interacted specifically with borrelilal PG via its peptidoglycan interacting motif (MHELSEKRARAIGNYL); was localized to the protoplasmic cylinder of Bb; and was designated as Borrelia peptidoglycan interacting Protein (BpiP). A bpiP mutant displayed no defect under in vitro growth conditions with similar levels of several virulence-related proteins. However, the burden of bpiP mutant in C3H/HeN mice at day 14, 28 and 62 post-infection was significantly lower compared to control strains. No viable bpiP mutant was re-isolated from any tissues at day 62 post-infection although bpiP mutant was able to colonize immunodeficient SCID at day 28 post-infection. Acquisition or transmission of bpiP mutant by Ixodes scapularis larvae or nymphs respectively, from and to mice, was significantly lower compared to control strains. Further analysis of bpiP mutant revealed increased sensitivity to vancomycin, osmotic stress, lysosomal extracts, human antimicrobial peptide cathelicidin-LL37, complement-dependent killing in the presence of day 14 post-infection mouse serum and increased internalization of CFSC-labeled bpiP mutant by macrophages and dendritic cells compared to control strains. These studies demonstrate the importance of accessory protein/s involved in sustaining integrity of PG and cell envelope during different phases of Bb infection.

Nature Communications, Published online: 21 April 2021; doi:10.1038/s41467-021-22634-x

Von Willebrand factor (VWF) is a large glycoprotein in the blood secreted from endothelial cells lining the blood vessel and activation of VWF leads to formation of VWF-platelet complexes or thrombi. Here authors use single-molecule force measurement, X-ray crystallography and functional measurements to monitor the activation of VWF via mechanical unfolding of the autoinhibitory module (AIM).

Nature Chemistry, Published online: 15 April 2021; doi:10.1038/s41557-021-00661-x

Robust delivery of proteins into cells is challenging, but it has now been shown that by conjugating arginine-rich cell-penetrating peptides to the surface of cells, proteins containing a cell-penetrating peptide can be delivered efficiently into them. Using a thiol-reactive cell-penetrating peptide enables thiol-containing proteins to be delivered by simple co-incubation.

Nature, Published online: 14 April 2021; doi:10.1038/s41586-021-03455-w

Structural studies resolve how the antibiotic darobactin inhibits the bacterial BAM insertase.

A longitudinal analysis of 338 individuals across 4 years characterizes the temporal stability and diversity of human gut microbiome, linking the microbial profile with individual-specific host phenotypes and suggesting the role of plasma metabolites in mediating the impact of microbiome on host physiology.