Host manipulation by bacterial type III and type IV secretion system effector proteases

A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability

Antagonistic interactions play a key role in determining microbial community dynamics. Here, we report that one of the most widespread contact-dependent effectors in human gut microbiomes, Bte1, directly targets the PpiD-YfgM periplasmic chaperone complex in related microbes. Structural, biochemical, and genetic characterization of this interaction reveals that Bte1 reverses the activity of the chaperone complex, promoting substrate aggregation and toxicity. Using Bacteroides, we show that Bte1 is active in the mammalian gut, conferring a fitness advantage to expressing strains. Recipient cells targeted by Bte1 exhibit sensitivity to membrane-compromising conditions, and human gut microbes can use this effector to exploit pathogen-induced inflammation in the gut. Further, Bte1 allelic variation in gut metagenomes provides evidence for an arms race between Bte1-encoding and immunity-encoding strains in humans. Together, these studies demonstrate that human gut microbes alter the protein-folding capacity of neighboring cells and suggest strategies for manipulating community dynamics.

Cleavage of cell junction proteins as a host invasion strategy in leptospirosis

Infection and invasion are the prerequisites for developing the disease symptoms in a host. While the probable mechanism of host invasion and pathogenesis is known in many pathogens, very little information is available on Leptospira invasion/pathogenesis. For causing systemic infection Leptospira must transmigrate across epithelial barriers, which is the most critical and challenging step. Extracellular and membrane-bound proteases play a crucial role in the invasion process. An extensive search for the proteins experimentally proven to be involved in the invasion process through cell junction cleavage in other pathogens has resulted in identifying 26 proteins. The similarity searches on the Leptospira genome for counterparts of these 26 pathogenesis-related proteins identified at least 12 probable coding sequences. The proteins were either extracellular or membrane-bound with a proteolytic domain to cleave the cell junction proteins. This review will emphasize our current understanding of the pathogenic aspects of host cell junction-pathogenic protein interactions involved in the invasion process. Further, potential candidate proteins with cell junction cleavage properties that may be exploited in the diagnostic/therapeutic aspects of leptospirosis will also be discussed. KEY POINTS: • The review focussed on the cell junction cleavage proteins in bacterial pathogenesis • Cell junction disruptors from Leptospira genome are identified using bioinformatics • The review provides insights into the therapeutic/diagnostic interventions possible.

Virulence regulation in plant-pathogenic bacteria by host-secreted signals

Bacterial pathogens manipulate host signaling pathways and evade host defenses using effector molecules, coordinating their deployment to ensure successful infection. However, host-derived metabolites as signals, and their critical role in regulating bacterial virulence requires further insights. Effective regulation of virulence, which is essential for pathogenic bacteria, involves controlling factors that enable colonization, defense evasion, and tissue damage. This regulation is dynamic, influenced by environmental cues including signals from host plants like exudates. Plant exudates, comprising of diverse compounds released by roots and tissues, serve as rich chemical signals affecting the behavior and virulence of associated bacteria. Plant nutrients act as signaling molecules that are sensed through membrane-localized receptors and intracellular response mechanisms in bacteria. This review explains how different bacteria detect and answer to secreted chemical signals, regulating virulence gene expression. Our main emphasis is exploring the recognition process of host-originated signaling molecules through molecular sensors on cellular membranes and intracellular signaling pathways. This review encompasses insights into how bacterial strains individually coordinate their virulence in response to various distinct host-derived signals that can positively or negatively regulate their virulence. Furthermore, we explained the interruption of plant defense with the perception of host metabolites to dampen pathogen virulence. The intricate interplay between pathogens and plant signals, particularly in how pathogens recognize host metabolic signals to regulate virulence genes, portrays a crucial initial interaction leading to profound influences on infection outcomes. This work will greatly aid researchers in developing new strategies for preventing and treating infections.

Leptospira Leptolysin Contributes to Serum Resistance but Is Not Essential for Acute Infection

Previous in vitro works focusing on virulence determinants of the spirochete Leptospira implicated metalloproteinases as putative contributing factors to the pathogenicity of these bacteria. Those proteins have the capacity to degrade extracellular matrix components (ECM) and proteins of host's innate immunity, notably effectors of the complement system. In this study, we gained further knowledge on the role of leptolysin, one of the leptospiral-secreted metalloproteinases, previously described as having a broad substrate specificity. We demonstrated that a proportion of human patients with mild leptospirosis evaluated in the current study produced antibodies that recognize leptolysin, thus indicating that the protease is expressed during host infection. Using recombinant protein and a knockout mutant strain, Manilae leptolysin-, we determined that leptolysin contributes to Leptospira interrogans serum resistance in vitro, likely by proteolysis of complement molecules of the alternative, the classical, the lectin, and the terminal pathways. Furthermore, in a hamster model of infection, the mutant strain retained virulence; however, infected animals had lower bacterial loads in their kidneys. Further studies are necessary to better understand the role and potential redundancy of metalloproteinases on the pathogenicity of this important neglected disease.

RNA:DNA triplexes: a mechanism for epigenetic communication between hosts and microbes?

Molecular communication between host and microbe is mediated by the transfer of many different classes of macromolecules. Recently, the trafficking of RNA molecules between organisms has gained prominence as an efficient way to manipulate gene expression via RNA interference (RNAi). Here, we posit a new epigenetic control mechanism based on triple helix (triplex) structures comprising nucleic acids from both host and microbe. Indeed, RNA:DNA triplexes are known to regulate gene expression in humans, but it is unknown whether interkingdom triplexes are formed either to manipulate host processes during pathogenesis or as a host defense response. We hypothesize that a fraction of the extracellular RNAs commonly released by microbes (e.g., bacteria, fungi, and protists) and their hosts form triplexes with the genome of the other species, thereby impacting chromatin conformation and gene expression. We invite the field to consider interkingdom triplexes as unexplored weaponry in the arms race between host and microbe.

Primary architecture and energy requirements of Type III and Type IV secretion systems

Many pathogens use Type III and Type IV protein secretion systems to secrete virulence factors from the bacterial cytosol into host cells. These systems operate through a one-step mechanism. The secreted substrates (protein or nucleo-protein complexes in the case of Type IV conjugative systems) are guided to the base of the secretion channel, where they are directly delivered into the host cell in an ATP-dependent unfolded state. Despite the numerous disparities between these secretion systems, here we have focused on the structural and functional similarities between both systems. In particular, on the structural similarity shared by one of the main ATPases (EscN and VirD4 in Type III and Type IV secretion systems, respectively). Interestingly, these ATPases also exhibit a structural resemblance to F1-ATPases, which suggests a common mechanism for substrate secretion. The correlation between structure and function of essential components in both systems can provide significant insights into the molecular mechanisms involved. This approach is of great interest in the pursuit of identifying inhibitors that can effectively target these systems.

Unconventional structure and mechanisms for membrane interaction and translocation of the NF-κB-targeting toxin AIP56

Bacterial AB toxins are secreted key virulence factors that are internalized by target cells through receptor-mediated endocytosis, translocating their enzymatic domain to the cytosol from endosomes (short-trip) or the endoplasmic reticulum (long-trip). To accomplish this, bacterial AB toxins evolved a multidomain structure organized into either a single polypeptide chain or non-covalently associated polypeptide chains. The prototypical short-trip single-chain toxin is characterized by a receptor-binding domain that confers cellular specificity and a translocation domain responsible for pore formation whereby the catalytic domain translocates to the cytosol in an endosomal acidification-dependent way. In this work, the determination of the three-dimensional structure of AIP56 shows that, instead of a two-domain organization suggested by previous studies, AIP56 has three-domains: a non-LEE encoded effector C (NleC)-like catalytic domain associated with a small middle domain that contains the linker-peptide, followed by the receptor-binding domain. In contrast to prototypical single-chain AB toxins, AIP56 does not comprise a typical structurally complex translocation domain; instead, the elements involved in translocation are scattered across its domains. Thus, the catalytic domain contains a helical hairpin that serves as a molecular switch for triggering the conformational changes necessary for membrane insertion only upon endosomal acidification, whereas the middle and receptor-binding domains are required for pore formation.

Bacterial enzymes: powerful tools for protein labeling, cell signaling, and therapeutic discovery

Bacteria have evolved a diverse set of enzymes that enable them to subvert host defense mechanisms as well as to form part of the prokaryotic immune system. Due to their unique and varied biochemical activities, these bacterial enzymes have emerged as key tools for understanding and investigating biological systems. In this review, we summarize and discuss some of the most prominent bacterial enzymes used for the site-specific modification of proteins, in vivo protein labeling, proximity labeling, interactome mapping, signaling pathway manipulation, and therapeutic discovery. Finally, we provide a perspective on the complementary advantages and limitations of using bacterial enzymes compared with chemical probes for exploring biological systems.

Speaking the host language: how Salmonella effector proteins manipulate the host

Salmonella injects over 40 virulence factors, termed effectors, into host cells to subvert diverse host cellular processes. Of these 40 Salmonella effectors, at least 25 have been described as mediating eukaryotic-like, biochemical post-translational modifications (PTMs) of host proteins, altering the outcome of infection. The downstream changes mediated by an effector's enzymatic activity range from highly specific to multifunctional, and altogether their combined action impacts the function of an impressive array of host cellular processes, including signal transduction, membrane trafficking, and both innate and adaptive immune responses. Salmonella and related Gram-negative pathogens have been a rich resource for the discovery of unique enzymatic activities, expanding our understanding of host signalling networks, bacterial pathogenesis as well as basic biochemistry. In this review, we provide an up-to-date assessment of host manipulation mediated by the Salmonella type III secretion system injectosome, exploring the cellular effects of diverse effector activities with a particular focus on PTMs and the implications for infection outcomes. We also highlight activities and functions of numerous effectors that remain poorly characterized.

Evolution and Role of Proteases in Campylobacter jejuni Lifestyle and Pathogenesis

Infection with the main human food-borne pathogen Campylobacter jejuni causes campylobacteriosis that accounts for a substantial percentage of gastrointestinal infections. The disease usually manifests as diarrhea that lasts for up to two weeks. C. jejuni possesses an array of peptidases and proteases that are critical for its lifestyle and pathogenesis. These include serine proteases Cj1365c, Cj0511 and HtrA; AAA+ group proteases ClpP, Lon and FtsH; and zinc-dependent protease PqqE, proline aminopeptidase PepP, oligopeptidase PepF and peptidase C26. Here, we review the numerous critical roles of these peptide bond-dissolving enzymes in cellular processes of C. jejuni that include protein quality control; protein transport across the inner and outer membranes into the periplasm, cell surface or extracellular space; acquisition of amino acids and biofilm formation and dispersal. In addition, we highlight their role as virulence factors that inflict intestinal tissue damage by promoting cell invasion and mediating cleavage of crucial host cell factors such as epithelial cell junction proteins. Furthermore, we reconstruct the evolution of these proteases in 34 species of the Campylobacter genus. Finally, we discuss to what extent C. jejuni proteases have initiated the search for inhibitor compounds as prospective novel anti-bacterial therapies.

Emergence of a Novel NDM-5-Producing Sequence Type 4523 Klebsiella pneumoniae Strain Causing Bloodstream Infection in China

Klebsiella pneumoniae is a significant infectious pathogen that causes bloodstream infections. This study aimed to genetically characterize a novel sequence type 4523 (ST4523) multidrug-resistant (MDR) K. pneumoniae strain recovered from the blood of a 79-year-old Chinese female patient with severe pneumonia and chronic obstructive pulmonary disease who ultimately died of the infection. The susceptibility testing results showed that strain 18SHX180 is nonsusceptible to cephalosporin, carbapenems, combinations of β-lactam and β-lactamase inhibitors, levofloxacin, and colistin and is only susceptible to amikacin. The phylogenetic structure showed that strain 18SHX180 belongs to a novel sequence type, ST4523, and capsule serotype K111. ST4523 is closely related to ST11, the most dominant clone of clinical carbapenem-resistant K. pneumoniae in China. ST4523 has 2 single-base variants in mdh and phoE. 18SHX180 showed medium virulence in Galleria mellonella and a mouse intraperitoneal infection model. PacBio Sequel and Illumina sequencing were performed to analyze the genetic characterization of 18SHX180, which contains 2 plasmids (pSHX180-NDM5 and pSHX180-1). pSHX180-NDM5 exhibits 86% coverage and 100% identity with 3 blaNDM-5-carrying plasmids and contains an additional region coding for the frmRAB operon, which permits bacteria to sense and detoxify formaldehyde. pSHX180-1 is responsible for the MDR phenotype: it carries 11 categories of genes for antimicrobial resistance [aadA16, aph(3″)-Ib, aph(6)-Id, blaSHV-182, blaTEM-1A, qacE, aac(6')-Ib-cr, mph(A), floR, qnrB6, arr-3, sul, sul2], all of which are associated with transposons and integrons located in three accessory resistance regions. The novel ST4523 K. pneumoniae strain could threaten the control of antimicrobial resistance, and its discovery calls attention to the genetic evolution of bacteria. IMPORTANCE Klebsiella pneumoniae is a significant infectious pathogen causing bloodstream infections. Due to the dissemination of carbapenemase genes, the incidence of carbapenem-resistant K. pneumoniae (CRKP) has increased, with high morbidity and mortality rates in immunocompromised patients. Here, we reported a novel ST4523 blaNDM-5-bearing CRKP strain initially recovered from a 79-year-old female who died of both a lower respiratory tract infection and bloodstream infection. We also describe the genetic and phenotypic characteristics of this strain. This study provides important insights into the genetic evolution of ST11 K. pneumoniae.

Peptidomimetics as Potential Anti-Virulence Drugs Against Resistant Bacterial Pathogens

The uncontrollable spread of superbugs calls for new approaches in dealing with microbial-antibiotic resistance. Accordingly, the anti-virulence approach has arisen as an attractive unconventional strategy to face multidrug-resistant pathogens. As an emergent strategy, there is an imperative demand for discovery, design, and development of anti-virulence drugs. In this regard, peptidomimetic compounds could be a valuable source of anti-virulence drugs, since these molecules circumvent several shortcomings of natural peptide-based drugs like proteolytic instability, immunogenicity, toxicity, and low bioavailability. Some emerging evidence points to the feasibility of peptidomimetics to impair pathogen virulence. Consequently, in this review, we shed some light on the potential of peptidomimetics as anti-virulence drugs to overcome antibiotic resistance. Specifically, we address the anti-virulence activity of peptidomimetics against pathogens' secretion systems, biofilms, and quorum-sensing systems.