Biology subjects

Mekalanos, J. J.

Publications and source records attributed to Mekalanos, J. J..

8 recordsLinked to original sources

bioRxiv2026

Antibody-recruiting molecules based on mimotope fusion peptides and a dimeric antibiotic

New therapeutic approaches are needed to treat infections due to multidrug resistant (MDR) Gram-negative bacteria. The use of antibody-recruiting molecules (ARMs) is a promising approach to address the MDR problem given their potential to engage both the adaptive and innate immune systems to treat bacterial infections. Here we present two new strategies to create ARMs. First, we show that a 9-mer antimicrobial peptide (K6) can be fused to a 11-mer mimotope peptide recognized by antibodies targeting the Vibrio cholerae O1 O-antigen to produce an ARM peptide (FZ5) that can render E. coli more sensitive to complement killing in the presence of antibodies that recognize this mimotope. FZ5 can drive killing by complement in the presence of rabbit antibodies raised against O1 serogroup V. cholerae as well as antibodies present in human sera elicited by immunization with the live attenuated cholera vaccine PanChol. We also describe a strategy that combines bacterial surface binding with hapten display through the use of homodimers of the antibiotic streptomycin (Str) and anti-Str antibodies elicited by Str-protein conjugate vaccines. When combined with dimeric Str derivatives and human complement, polyclonal anti-streptomycin antisera kills E. coli by targeting the Str hapten. Dimeric forms of Str also significantly enhanced killing of a Str-resistant P. aeruginosa clinical isolate dependent on low levels of human complement and polyclonal anti-Str antibody. Together these data suggest that anti-bacterial ARM molecules based on mimotope display through simple synthetic fusion peptides, or dimeric haptens have promise as new approaches for the treatment of MDR bacterial infections.

microbiology↗

bioRxiv2026

An Aeromonad selectively removes a class of pathogens from shrimp, prevents disease and preserves a healthy commensal microbiome

On their own, probiotics do not entirely eliminate pathogens during infection and disease. Instead, they often serve as adjuncts that rely on distinct mechanisms to reduce the presence of harmful bacteria. Our prior research indicates that an isolated Aeromonas dhakensis strain A603 kills pathogenic Vibrio strains through two antibacterial mechanisms: the type VI secretion system (T6SS) and phenazine (AdPhen). Here, we investigate A603 as a standalone probiotic for a shrimp disease model. This study shows that A603 prevents mortality from acute hepatopancreatic necrosis disease (AHPND) in shrimp caused by pathogenic Vibrio spp. that produce the PirAB toxin. AHPND infection alters the shrimp microbiota by increasing pathogen abundance and decreasing beneficial bacterial abundance prior to death. As both a prophylactic and treatment, A603 removes pathogenic Vibrio from shrimp and reverses such alterations in the microbiota using both T6SS and AdPhen. Collectively, our findings show that A603 antibacterial mechanisms prevent AHPND.

microbiology↗

bioRxiv2023

Microbiome induced complement synthesized in the gut protects against enteric infections

Canonically, complement is a serum-based host defense system that protects against systemic microbial invasion. Little is known about the production and function of complement components on mucosal surfaces. Here we show gut complement component 3 (C3), central to complement function, is regulated by the composition of the microbiota in healthy humans and mice, leading to host-specific gut C3 levels. Stromal cells in intestinal lymphoid follicles (LFs) are the predominant source of intestinal C3. During enteric infection with Citrobacter rodentium or enterohemorrhagic Escherichia coli, luminal C3 levels increase significantly and are required for protection. C. rodentium is remarkably more invasive to the gut epithelium of C3-deficient mice than of wild-type mice. In the gut, C3-mediated phagocytosis of C. rodentium functions to clear pathogens. Our study reveals that variations in gut microbiota determine individuals intestinal mucosal C3 levels, dominantly produced by LF stromal cells, which directly correlate with protection against enteric infection. HighlightsO_LIGut complement component 3 (C3) is induced by the microbiome in healthy humans and mice at a microbiota-specific level. C_LIO_LIGut stromal cells located in intestinal lymphoid follicles are a major source of luminal C3 C_LIO_LIDuring enteric infections with Citrobacter rodentium or enterohemorrhagic Escherichia coli, gut luminal C3 levels increase and are required for protection. C_LIO_LIC. rodentium is significantly more invasive of the gut epithelium in C3-deficient mice when compared to WT mice. C_LIO_LIIn the gut, C3-mediated opsonophagocytosis of C. rodentium functions to clear pathogens. C_LI

immunology↗

bioRxiv2022

Cell density-dependent death triggered by viral palindromic DNA sequences

Defense systems that recognize viruses have provided not only the tools of molecular biology but also important insights into other mechanisms that can induce immunity to these or other infectious agents including transmissible plasmids and chromosomal genetic elements. Several systems that trigger cell death upon viral infection have recently been recognized but the signals that activate these abortive infection systems remain largely unknown. Here we characterize one such system in Vibrio cholerae that we found was responsible for triggering cell-density dependent death (CDD) of bacterial cells in response to the presence of certain genetic elements. The key components of the CDD system include quorum-regulated components DdmABC and the host factor PriA. Our analysis indicates that the plasmid and phage signals that trigger CDD were palindromic DNA sequences that are predicted to form stem-loop hairpin structures from single-stranded DNA during stalled replication. Our results further suggest that other agents that generate damaged DNA can also trigger DdmABC/PriA activation and cell death probably through activation of a nuclease domain present in the DdmA protein. Thus, any infectious process that results in damaged DNA, particularly during DNA replication, can in theory trigger cell death through the DdmABC/PriA abortive infection system.

microbiology↗

bioRxiv2022

Covariance predicts conserved protein residue interactions important to the emergence and continued evolution of SARS-CoV-2 as a human pathogen

SARS-CoV-2 is one of three recognized coronaviruses (CoVs) that have caused epidemics or pandemics in the 21st century and that likely emerged from animal reservoirs. Differences in nucleotide and protein sequence composition within related {beta}-coronaviruses are often used to better understand CoV evolution, host adaptation, and their emergence as human pathogens. Here we report the comprehensive analysis of amino acid residue changes that have occurred in lineage B {beta}-coronaviruses that show covariance with each other. This analysis revealed patterns of covariance within conserved viral proteins that potentially define conserved interactions within and between core proteins encoded by SARS-CoV-2 related {beta}-coranaviruses. We identified not only individual pairs but also networks of amino acid residues that exhibited statistically high frequencies of covariance with each other using an independent pair model followed by a tandem model approach. Using 149 different CoV genomes that vary in their relatedness, we identified networks of unique combinations of alleles that can be incrementally traced genome by genome within different phylogenic lineages. Remarkably, covariant residues and their respective regions most abundantly represented are implicated in the emergence of SARS-CoV-2 are also enriched in dominant SARS-CoV-2 variants.

microbiology↗

bioRxiv2020

Protein covariance networks reveal interactions important to the emergence of SARS coronaviruses as human pathogens

SARS-CoV-2 is one of three recognized coronaviruses (CoVs) that have caused epidemics or pandemics in the 21st century and that have likely emerged from animal reservoirs based on genomic similarities to bat and other animal viruses. Here we report the analysis of conserved interactions between amino acid residues in proteins encoded by SARS-CoV-related viruses. We identified pairs and networks of residue variants that exhibited statistically high frequencies of covariance with each other. While these interactions are likely key to both protein structure and other protein-protein interactions, we have also found that they can be used to provide a new computational approach (CoVariance-based Phylogeny Analysis) for understanding viral evolution and adaptation. Our data provide evidence that the evolutionary processes that converted a bat virus into human pathogen occurred through recombination with other viruses in combination with new adaptive mutations important for entry into human cells.

bioinformatics↗

bioRxiv2019

Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity

Bacteria possess an array of defenses against foreign invaders, including diverse nucleases that target and destroy the genome of an invading bacteriophage or foreign DNA element. A recently-described bacteriophage immunity pathway employs a cGAS/DncV-like nucleotidyltransferase to produce a cyclic tri-AMP second messenger, which activates the DNA endonuclease effector NucC. Here, we show that NucC is related to restriction enzymes but uniquely assembles into a homotrimer in solution. cAAA binding in a conserved allosteric pocket promotes assembly of two NucC trimers into a homohexamer competent for double-strand DNA cleavage. We propose that NucC mediates bacteriophage immunity either through global activation, causing altruistic cell death and abortive infection, or through local activation and targeted phage genome destruction. Finally, we identify NucC homologs in type III CRISPR-Cas systems, where they likely function as accessory nucleases activated by cyclic oligoadenylate second messengers synthesized by these systems effector complexes.

biochemistry↗

bioRxiv2018

Structure and mutagenic analysis of the lipid II flippase MurJ from Escherichia coli

The peptidoglycan cell wall provides an essential protective barrier in almost all bacteria, defining cellular morphology and conferring resistance to osmotic stress and other environmental hazards. The precursor to peptidoglycan, lipid II, is assembled on the inner leaflet of the plasma membrane. However, peptidoglycan polymerization occurs on the outer face of the plasma membrane, and lipid II must be flipped across the membrane by the MurJ protein prior to its use in peptidoglycan synthesis. Due to its central role in cell wall assembly, MurJ is of fundamental importance in microbial cell biology and is a prime target for novel antibiotic development. However, relatively little is known regarding the mechanisms of MurJ function, and structural data are only available for MurJ from the extremophile Thermosipho africanus. Here, we report the crystal structure of substrate-free MurJ from the Gram-negative model organism Escherichia coli, revealing an inward-open conformation. Taking advantage of the genetic tractability of E. coli, we performed high-throughput mutagenesis and next-generation sequencing to assess mutational tolerance at every amino acid in the protein, providing a detailed functional and structural map for the enzyme and identifying sites for inhibitor development. Finally, through the use of sequence co-evolution analysis we identify functionally important interactions in the outward-open state of the protein, supporting a rocker-switch model for lipid II transport.

biochemistry↗