Proc Natl Acad Sci U S A. 2018 Dec
Dietary sugar silences a colonization factor in a mammalian gut symbiont.
Dietary components are believed to influence the composition of the gut microbiota by serving as nutrients to a subset of microbes, thereby favoring their expansion. However, we now report that dietary fructose and glucose, which are prevalent in the Western diet, specifically silence a protein that is necessary for gut colonization, but not for utilization of these sugars, by the human gut commensal Bacteroides thetaiotaomicron. Our findings underscore a role for dietary sugars that escape absorption by the host intestine and reach the microbiota: regulation of gut colonization by beneficial microbes independently of supplying nutrients to the microbiota.
PLoS Biol. 2018 Nov
Cryo-electron tomography of periplasmic flagella in Borrelia burgdorferi reveals a distinct cytoplasmic ATPase complex.
Periplasmic flagella are essential for the distinct morphology and motility of spirochetes. Our studies provide structural insights into the unique mechanisms underlying assembly and rotation of the periplasmic flagella and may provide the basis for the development of novel therapeutic strategies against several pathogenic spirochetes.
Science. 2018 Nov
De novo design of self-assembling helical protein filaments.
Shen H1,2,3, Fallas JA4,2, Lynch E2, Sheffler W1,2, Parry B5,6, Jannetty N6,7, Decarreau J8, Wagenbach M8, Vicente JJ8, Chen J9,10, Wang L10,11, Dowling Q2,12, Oberdorfer G1,2, Stewart L1, Wordeman L8, De Yoreo J9,10, Jacobs-Wagner C6,7,13, Kollman J2, Baker D4,2,14.
We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.
J Surg Res. 2018 Nov
Mucosal homeostasis is altered in the ileum of gnotobiotic mice.
Single-organism gnotobiotic mice demonstrate enhanced morphometric parameters compared with mice with CF and show differences in growth patterns among bacterial species. These findings suggest unique interactions between individual bacteria and the host animal which hold potential for future therapeutic strategies aimed at mucosal restoration. The mechanisms involved in this process therefore warrant further study.
Mol Microbiol. 2018 Nov
A tetratricopeptide repeat domain protein has profound effects on assembly of periplasmic flagella, morphology and motility of the lyme disease spirochete Borrelia burgdorferi.
Spirochetes possess a unique periplasmic flagellar motor component called the collar. To identify a collar protein, we have inactivated almost all genes annotated as motility-related in the Borrelia burgdorferi genome and identified only FlbB, which comprises the base of the collar. Using various comprehensive approaches, we identified a tetratricopeptide repeat protein BB0236 as a potential candidate for the collar. Biochemical assays indicated that FlbB interacts with BB0236. Furthermore, ∆bb0236 mutant analyses indicated that BB0236 is crucial for collar structure assembly, cellular morphology, motility, orientation of periplasmic flagella and assembly of other flagellar structures. Together, our studies provide new insights into the organization and the complex assembly inherent to the unique spirochetal collar structure.
Proc Natl Acad Sci U S A. 2018 Oct
On the deformability of an empirical fitness landscape by microbial evolution.
A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining evolutionary trajectories and the predictability of evolution. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium Escherichia coli. Our results suggest that, even in situations in which mutations have strong environmental effects, fitness landscapes may retain their power to forecast evolution over small mutational distances despite the potential attenuation of that power over longer evolutionary trajectories. Our methods and results provide an avenue for integrating adaptive and eco-evolutionary dynamics with complex genetics and genomics.
Elife. 2018 Oct
Visualization of the type III secretion mediated Salmonella-host cell interface using cryo-electron tomography.
Many important gram-negative bacterial pathogens use highly sophisticated type III protein secretion systems (T3SSs) to establish complex host-pathogen interactions. Here, we use high-throughput cryo-electron tomography (cryo-ET) to visualize the T3SS-mediated Salmonella-host cell interface. Our analysis reveals the intact translocon at an unprecedented level of resolution, its deployment in the host cell membrane, and the establishment of an intimate association between the bacteria and the target cells, which is essential for effector translocation. Our studies provide critical data supporting the long postulated direct injection model for effector translocation.
Appl Environ Microbiol. 2018 Oct
Characterization of fluorescent proteins, promoters, and selectable markers for applications in the Lyme disease spirochete Borrelia burgdorferi.
Genetic manipulation of the Lyme disease spirochete B. burgdorferi remains cumbersome, despite significant progress in the field. Of interest, B. burgdorferi displays complex cellular organization features that have yet to be understood. Here, we complement and expand the array of molecular tools available for use in B. burgdorferi by generating and characterizing multiple fluorescent proteins, antibiotic selection markers, and promoters of varied strengths. These tools will facilitate investigations in this important human pathogen, as exemplified by the polar and midcell localization of the cell envelope regulator BB0323, which we uncovered using these reagents.
Curr Top Microbiol Immunol. 2018 Sep
Activity-Based Protein Profiling at the Host-Pathogen Interface.
Activity-based protein profiling (ABPP) is a technique for selectively detecting reactive amino acids in complex proteomes with the aid of chemical probes. Using probes that target catalytically active enzymes, ABPP can rapidly define the functional proteome of a biological system. In recent years, this approach has been increasingly applied to globally profile enzymes active at the host-pathogen interface of microbial infections. From in vitro co-culture systems to animal models of infection, these studies have revealed enzyme-mediated mechanisms of microbial pathogenicity, host immunity, and metabolic adaptation that dynamically shape pathogen interactions with the host.
Human gut Bacteroides capture vitamin B12 via cell surface-exposed lipoproteins.
Human gut Bacteroides use surface-exposed lipoproteins to bind and metabolize complex polysaccharides. Although vitamins and other nutrients are also essential for commensal fitness, much less is known about how commensal bacteria compete with each other or the host for these critical resources. Our studies suggest that Bacteroides use surface-exposed lipoproteins not only for capturing polysaccharides, but also to acquire key vitamins in the gut.
Science. 2018 Aug
Emergent simplicity in microbial community assembly.
A major unresolved question in microbiome research is whether the complex taxonomic architectures observed in surveys of natural communities can be explained and predicted by fundamental, quantitative principles. Bridging theory and experiment is hampered by the multiplicity of ecological processes that simultaneously affect community assembly in natural ecosystems. We addressed this challenge by monitoring the assembly of hundreds of soil- and plant-derived microbiomes in well-controlled minimal synthetic media. Both the community-level function and the coarse-grained taxonomy of the resulting communities are highly predictable and governed by nutrient availability, despite substantial species variability. By generalizing classical ecological models to include widespread nonspecific cross-feeding, we show that these features are all emergent properties of the assembly of large microbial communities, explaining their ubiquity in natural microbiomes.
EMBO J. 2018 Jul
A protein that controls the onset of a Salmonella virulence program.
The mechanism of action and contribution to pathogenesis of many virulence genes are understood. By contrast, little is known about anti-virulence genes, which contribute to the start, progression, and outcome of an infection. We now report how an anti-virulence factor in Salmonella enterica serovar Typhimurium dictates the onset of a genetic program that governs metabolic adaptations and pathogen survival in host tissues.
Cell Host Microbe. 2018 Jul
The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut.
In the mammalian gut, bacteria compete for resources to maintain their populations, but the factors determining their success are poorly understood. We report that the human gut bacterium Bacteroides thetaiotaomicron relies on the stringent response, an intracellular signaling pathway that allocates resources away from growth, to survive carbon starvation and persist in the gut.
Mol Syst Biol. 2018 Jun
Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli.
Cell size, cell growth, and cell cycle events are necessarily intertwined to achieve robust bacterial replication. Yet, a comprehensive and integrated view of these fundamental processes is lacking. Here, we describe an image-based quantitative screen of the single-gene knockout collection of Escherichia coli and identify many new genes involved in cell morphogenesis, population growth, nucleoid (bulk chromosome) dynamics, and cell division.
Nat Microbiol. 2018 Jun
A unique cytoplasmic ATPase complex defines the Legionella pneumophila type IV secretionchannel.
Type IV secretion systems (T4SSs) are complex machines used by bacteria to deliver protein and DNA complexes into target host cells1-5. Conserved ATPases are essential for T4SS function, but how they coordinate their activities to promote substrate transfer remains poorly understood. Here, we show that the DotB ATPase associates with the Dot-Icm T4SS at the Legionella cell pole through interactions with the DotO ATPase.
Proc Natl Acad Sci U S A. 2018 May
Reduction in adaptor amounts establishes degradation hierarchy among protease substrates.
ATP-dependent proteases control critical cellular processes, including development, physiology, and virulence. A given protease may recognize a substrate directly via an unfoldase domain or subunit or indirectly via an adaptor that delivers the substrate to the unfoldase. We now report that cells achieve differential stability among substrates of a given protease by modulating adaptor amounts.
Biophys J. 2018 May
Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells.
Transcription is the dominant point of control of gene expression. Biochemical studies have revealed key molecular components of transcription and their interactions, but the dynamics of transcription initiation in cells is still poorly understood. This state of affairs is being remedied with experiments that observe transcriptional dynamics in single cells using fluorescent reporters.
Nat Microbiol. 2018 May
Topical application of aminoglycoside antibiotics enhances host resistance to viral infections in a microbiota-independent manner.
Antibiotics are widely used to treat infections in humans. However, the impact of antibiotic use on host cells is understudied. Here we identify an antiviral effect of commonly used aminoglycoside antibiotics. We show that topical mucosal application of aminoglycosides prophylactically increased host resistance to a broad range of viral infections including herpes simplex viruses, influenza A virus and Zika virus.
Cell. 2018 Mar
Subcellular Organization: A Critical Feature of Bacterial Cell Replication.
Spatial order is required for faithful and efficient cellular replication and offers a powerful means for the development of unique biological properties. Here, we discuss organizational features of bacterial cells and highlight how bacteria have evolved diverse spatial mechanisms to overcome challenges cells face as self-replicating entities.
Cell. 2017 Oct
Ferroptosis: A Regulated Cell Death Nexus Linking Metabolism, Redox Biology, and Disease.
Stockwell BR1, Friedmann Angeli JP2, Bayir H3, Bush AI4, Conrad M2, Dixon SJ5, Fulda S6, Gascón S7, Hatzios SK8, Kagan VE9, Noel K10, Jiang X11, Linkermann A12, Murphy ME13, Overholtzer M11, Oyagi A14, Pagnussat GC15, Park J16, Ran Q17, Rosenfeld CS10, Salnikow K18, Tang D19, Torti FM20, Torti SV21, Toyokuni S22, Woerpel KA23, Zhang DD24.
Ferroptosis is a form of regulated cell death characterized by the iron-dependent accumulation of lipid hydroperoxides to lethal levels. Emerging evidence suggests that ferroptosis represents an ancient vulnerability caused by the incorporation of polyunsaturated fatty acids into cellular membranes, and cells have developed complex systems that exploit and defend against this vulnerability in different contexts.
Proc Natl Acad Sci U S A. 2017 Oct
Molecular architecture of the sheathed polar flagellum in Vibrio alginolyticus.
Vibrio species are Gram-negative rod-shaped bacteria that are ubiquitous and often highly motile in aqueous environments. Vibrio swimming motility is driven by a polar flagellum covered with a membranous sheath, but this sheathed flagellum is not well understood at the molecular level because of limited structural information. Here, we use Vibrio alginolyticus as a model system to study the sheathed flagellum in intact cells by combining cryoelectron tomography (cryo-ET) and subtomogram analysis with a genetic approach.
Cell Syst. 2017 Jan
Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle.
Cells decide when, where, and to what level to express their genes by “computing” information from transcription factors (TFs) binding to regulatory DNA. How is the information contained in multiple TF-binding sites integrated to dictate the rate of transcription? The dominant conceptual and quantitative model is that TFs combinatorially recruit one another and RNA polymerase to the promoter by direct physical interactions. Here, we develop a quantitative framework to explore kinetic control, an alternative model in which combinatorial gene regulation can result from TFs working on different kinetic steps of the transcription cycle.
MBio. 2017 Jan
Expressing the Geobacter metallireducens PilA in Geobacter sulfurreducens Yields Pili with Exceptional Conductivity.
The electrically conductive pili (e-pili) of Geobacter sulfurreducens serve as a model for a novel strategy for long-range extracellular electron transfer. e-pili are also a new class of bioelectronic materials. However, the only other Geobacter pili previously studied, which were from G. uraniireducens, were poorly conductive. In order to obtain more information on the range of pili conductivities in Geobacter species, the piliof G. metallireducens were investigated….. The G. metallireducens pili represent the most highly conductive pilifound to date and suggest strategies for designing synthetic pili with even higher conductivities.