A comprehensive guide to pilus biogenesis in Gram-negative bacteria

Enhancing the persistence of engineered biotherapeutics in the gut: Adhesion, glycan metabolism, and environmental resistance

Engineered live biotherapeutic products (eLBPs) are receiving increasing attention as next-generation therapeutics to treat a variety of diseases with high specificity and effectiveness. Despite their potential, eLBPs face challenges, such as limited colonization, competition with native microbiota, nutrient depletion, and susceptibility to gastrointestinal stresses, which ultimately reduce their persistence in the gut and hinder their therapeutic efficacy. This review examines the key strategies to enhance the persistence and activity of eLBPs in the gut environment. First, methods to strengthen the adhesion capacity of eLBPs are discussed, including genetic engineering to express adhesins and chemical surface modifications to improve their binding to mucus and epithelial cells. Second, strategies to improve the ability of eLBPs to efficiently use mucin-derived sugars, which are continuously secreted by intestinal epithelial cells, were highlighted. These strategies involve the introduction and optimization of glycan-degrading enzymes and metabolic pathways for key mucin sugars, such as N-acetylglucosamine, galactose, and sialic acid, to support sustained energy production and enhance gut colonization. Third, strategies to improve the resistance of eLBPs against environmental stress are discussed, including genetic modifications to stabilize cell membranes, enhancement of ion pump activity, overexpression of stress-response proteins, and encapsulation techniques to provide protection. The implementation of these strategies can address challenges related to gut colonization by eLBPs, thereby enhancing their metabolic activity and enabling sustained and efficient secretion of therapeutic molecules. This review offers a comprehensive framework for developing and optimizing eLBPs, paving the way for their successful clinical application with enhanced effectiveness in treating gastrointestinal and systemic diseases.

Nitazoxanide inhibits pili assembly by targeting BamB to synergize with polymyxin B against drug-resistant Escherichia coli

Gram-negative bacteria rely on pili assembly for pathogenicity, with the chaperone-usher (CU) pathway regulating pilus biogenesis. Nitazoxanide (NTZ) inhibits CU pathway-mediated P pilus biogenesis by specifically interfering with the proper folding of the outer membrane protein (OMP) usher, primarily mediated by the β-barrel assembly machinery (BAM) complex. In this study, we identified the BAM complex components BamB and the BamA POTRA2 domain as key binding targets for NTZ. Molecular dynamics simulations and Bio-Layer Interferometry revealed that BamB residues S61 and R195 are critical for NTZ binding. NTZ activated the Cpx two-component system and induced inner membrane perturbations, which resulted from the accumulation of misfolded P pilus subunits. Upregulation of the ibpAB gene, which protects the bacteria against NTZ-induced oxidative stress, was also observed. Importantly, NTZ combined with polymyxin B enhanced the latter's antibacterial activity against both susceptible and MCR-positive E. coli strains. This enhancement was achieved through NTZ-induced increases in inner membrane permeability, oxidative stress, and inhibition of efflux pump activity and biofilm formation. This study provides new insights into the antimicrobial mechanism of NTZ and highlights its potential as an antibiotic adjuvant by targeting BamB to inhibit the CU pathway, restoring the efficacy of polymyxin B against multidrug-resistant bacteria.

Structures of the Escherichia coli type 1 pilus during pilus rod assembly and after assembly termination

Uropathogenic Escherichia coli strains use filamentous type 1 pili to adhere to and invade uroepithelial cells. The pilus consists of a flexible tip fibrillum, formed by the adhesin FimH and the subunits FimG and FimF. The pilus rod is a helical assembly of up to 3000 copies of the main subunit FimA, terminated by a single copy of the subunit FimI that anchors the rod to the assembly platform FimD in the outer membrane. Although type 1 pilus assembly can be completely reconstituted in vitro, the precise mechanism of assembly termination on FimD is still unknown. Here, we present cryo-electron microscopy structures of the fully assembled pilus with all its components prior to and after incorporation of FimI, capped with the assembly chaperone FimC. The structures reveal that FimD positions the proximal end of the pilus rod at an angle of ca. 50 degrees relative to the plane of the outer membrane. Specific interactions between FimI and FimC, absent in the equivalent FimA-FimC interface of the non-terminated pilus, stabilize the assembly-terminated state. In addition, we present structures of the transition region between the tip fibrillum and the helical rod, showing how FimF aligns the tip fibrillum along the rod axis.

Tad pili with adaptable tips mediate contact-dependent killing during bacterial predation

The predatory bacterium, Myxococcus xanthus, kills its prey by contact, using a putative Tight Adherence pilus, known as the Kil system, along with a protein complex resembling the basal body a type-III secretion system, named the "needleless" T3SS*. In this work, we provide direct evidence that Myxococcus polymerizes a Kil pilus at the prey contact site, which is constituted by the major pilin KilP. We also genetically demonstrate that the predation function of this pilus is linked to four different minor pilin complexes, which work in specific combinations to detect and kill phylogenetically diverse bacterial species. Structural models of the Kil pilus suggest that these minor pilin complexes form interchangeable "Tips", exposing variable domains at the extremity of the pilus to interact with prey cells. Remarkably, the activity of these Tips also depends on the T3SS*, revealing a tight functional connection between the Kil system and the T3SS*. While these Tips are mostly restricted to predatory bacteria, genomic and structural analyses suggest that in other bacteria, including pathogens, Tad pili are also customized and functionalized by similar minor pilin complexes exposing variable domains.

Cryo-Electron Microscopy of BfpB Reveals a Type IVb Secretin Multimer Adapted to Accommodate the Exceptionally Wide Bundle-Forming Pilus

Type IV pili (T4Ps) are multifunctional surface fibers essential for bacterial motility, adhesion, and virulence, found across Gram-negative and Gram-positive bacteria and archaea. Detailed descriptions of T4P structural biology are allowing progress in understanding T4P biogenesis. Secretins, large outer membrane channels, are crucial for T4P extrusion in Gram-negative bacteria. Using cryo-EM and AlphaFold, we modeled the structure of BfpB, the secretin of the Bundle-Forming Pilus (BFP) of enteropathogenic Escherichia coli. BfpB exhibits a unique 17-fold symmetry, correlating with the thicker BFP filaments, and diverging from the 12-15 subunits typical of T4P, type 2 secretion (T2S), and type 3 secretion (T3S) systems. Additionally, we identified an extended β-hairpin loop in the N3 domain, resembling features of distantly related T3SS secretins, and an N-terminal helix where a C-terminal S-domain is seen in some T2S and T3S secretins. These findings reveal evolutionary parallels and structural adaptations in secretins, highlighting the link between oligomerization and pilus structure. This work advances our understanding of T4P biogenesis, secretin evolution, and bacterial secretion systems, offering insights into pathogenic diversity and future research directions.

Exposure and health risks of livestock air resistomes

Most of the global antibiotic consumption is by the livestock industry, making livestock farms a hotspot of antibiotic resistance genes (ARGs). Farm air poses direct ARG exposure to workers, but the health risks of air resistomes remain unclear. We evaluated the human exposure and health risks of air resistomes in pig and chicken farms and compared air resistomes in Chinese farms to those in European farms given their long-term restrictions on use of antibiotics in livestock. We found that livestock air was highly enriched in ARGs, with each cell harboring seven times more ARGs than urban air. The daily ARG inhalation of farm workers was equivalent to several years of ARG inhalation by urban residents. ARGs encoding resistance to last-resort antibiotics such as mcr-1 and tetX were detected in farm air, and tetX variants were prevalent in both Chinese and European farms. ARGs in livestock air were highly associated with mobile genetic elements, and conjugation experiments confirmed their cross-phyla transferability. The projected resistome risk of farm air was significantly higher than well-recognized ARG hotspots like air from hospitals, sewage treatment plants, and from animal manures. The diversity, abundance, and risk score of air resistomes in Chinese farms were significantly higher than those in European farms, suggesting that long-term restriction of antibiotic use mitigates antibiotic resistance in the livestock environment. Our results underscore the high exposure of farm workers to ARGs via farm air and highlight its role in ARG dissemination, supporting the importance of antibiotic stewardship practices in combating antibiotic resistance.

High-resolution cryo-EM analysis visualizes hydrated type I and IV pilus structures from enterotoxigenic Escherichia coli

Pathogenic bacteria utilize a variety of pilus filaments to colonize intestinal epithelia, including those synthesized by the chaperone-usher or type IV pilus assembly pathway. Despite the importance of these filaments as potential drug and vaccine targets, their large size and dynamic nature make high-resolution structure determination challenging. Here, we used cryo-electron microscopy (cryo-EM) and whole-genome sequencing to determine the structures of type I and IV pili expressed in enterotoxigenic Escherichia coli. Well-defined cryo-EM maps at resolutions of 2.2 and 1.8 Å for type I and IV pilus, respectively, facilitated the de novo structural modeling for these filaments, revealing side-chain structures in detail. We resolved thousands of hydrated water molecules around and within the inner core of the filaments, which stabilize the otherwise metastable quaternary subunit assembly. The high-resolution structures offer novel insights into subunit-subunit interactions, and provide important clues to understand pilus assembly, stability, and flexibility.

Type IV PilD mutant stimulates the formation of persister cells in Pseudomonas aeruginosa

BACKGROUND

Pseudomonas aeruginosa clinical isolates that lack motility do not express type IV pilin, yet the biological roles of this absence in the infection process remain poorly understood.

OBJECTIVES

We asked whether the absence of motility in these bacteria is associated with increased antibiotic persistence.

METHODS

In this study, we analysed type IV PilD protein sequences in the database and conducted antibiotic-tolerant persister cell assays.

RESULTS

We found that PilD variants were common in P. aeruginosa clinical isolates. Our results revealed that inactivation of PilD resulted in a significantly higher level of surviving persister cells following ciprofloxacin treatment. This PilD-mediated persistence did not involve previously described mechanisms, such as phenazine pyocyanin, biofilm or stringent response.

CONCLUSIONS

Our findings connect the non-motility of clinical P. aeruginosa isolates with the survival of persister cells, highlighting the clinical significance for the development of strategies to eradicate P. aeruginosa infections.

Phage therapy for Klebsiella pneumoniae: Understanding bacteria-phage interactions for therapeutic innovations

Klebsiella pneumoniae (KP) is a Gram-negative bacterium that commonly resides in the human gastrointestinal tract and can also act as an opportunistic pathogen and cause extra-intestinal infections. KP poses a global health threat because it causes both hospital- and community-acquired infections in immune-competent and immunocompromised hosts. These infections can be multidrug-resistant and/or hypervirulent, making KP infections difficult to treat and deadly. In the absence of effective treatments for recalcitrant KP infections, bacteriophage (phage) therapy is gaining attention as a promising alternative. In this review, we evaluate KP epidemiology and epitope diversity, discuss interactions between KP-targeting phages and their bacterial hosts from an eco-evolutionary perspective, and summarize recent efforts in phage therapy for treating KP infections. We also discuss novel approaches, including genetic engineering and machine learning, as initial steps toward developing KP-targeting phage therapy as a precision medicine approach for an emerging and dangerous pathogen.

Type IV Pili in Thermophilic Bacteria: Mechanisms and Ecological Implications

Type IV pili (T4P) machinery is critical for bacterial surface motility, protein secretion, and DNA uptake. This review highlights the ecological significance of T4P-dependent motility in Thermus thermophilus, a thermophilic bacterium isolated from hot springs. Unlike swimming motility, the T4P machinery enables bacteria to move over two-dimensional surfaces through repeated cycles of extension and retraction of pilus filaments. Notably, T. thermophilus exhibits upstream-directed migration under shear stress, known as rheotaxis, which appears to represent an adaptive strategy unique to thermophilic bacteria thriving in rapid water flows. Furthermore, T4P contributes to the capture of DNA and phages, indicating their multifunctionality in natural environments. Understanding the T4P dynamics provides insights into bacterial survival and evolution in extreme habitats.

Bacterial adhesion strategies and countermeasures in urinary tract infection

Urinary tract infections (UTIs) are compounded by antimicrobial resistance, which increases the risk of UTI recurrence and antibiotic treatment failure. This also intensifies the burden of disease upon healthcare systems worldwide, and of morbidity and mortality. Uropathogen adhesion is a critical step in the pathogenic process, as has been mainly shown for Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Streptococcus agalactiae, Proteus, Enterococcus and Staphylococcus species. Although many bacterial adhesion molecules from these uropathogens have been described, our understanding of their contributions to UTIs is limited. Here we explore knowledge gaps in the UTI field, as we discuss the broader repertoire of uropathogen adhesins, including their role beyond initial attachment and the counter-responses of the host immune system. Finally, we describe the development of therapeutic approaches that target uropathogenic adhesion strategies and provide potential alternatives to antibiotics.

Tat-fimbriae ("tafi"): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway

The surface structures of archaeal cells, many of which exist at high temperatures, high salinity, and non-physiological pH, are key factors for their adaptation to extreme living conditions. In the haloarchaeon Haloarcula hispanica, we have discovered a thin filamentous surface appendage called tat-fimbriae ("tafi"), which were identified to be composed of three protein subunits, TafA, TafC, and TafE, among which TafA is the major fimbrial subunit. Molecular genetic evidence demonstrates TafA was transported through the twin-arginine translocation pathway (Tat-pathway). Based on protein structure prediction (including AlphaFold 3), tafi exhibits a linear structure: TafC at the tip, TafE acting as an adapter, TafA forming the core filament, and they link the fourth subunit TafF, anchoring tafi to the cell wall. To our knowledge, this is the first case that the Tat-pathway has been linked to the secretion of protein subunits forming prokaryotic filamentous structures.

Stimulation of the Caulobacter crescentus surface sensing pathway by deletion of a specialized minor pilin-like gene

Bacteria colonize surfaces through complex mechanisms of surface sensing. Pili are dynamic bacterial appendages that play an important role in this process. In Caulobacter crescentus, tension on retracting, surface-bound pili triggers the rapid synthesis of the adhesive holdfast, which permanently attaches cells to surfaces. However, the detailed mechanisms of pilus-mediated surface sensing are unclear. In this study, we used a genetic screen to isolate mutants with altered pilus activity to identify genes that may be involved in pilus-mediated surface-sensing. This screen identified cpaL, whose deletion led to reduced piliation levels, and surprisingly, a threefold increase in surface adhesion due to increased holdfast production. To understand this finding, we compared holdfast synthesis in wild-type and cpaL mutant cells under conditions that block pilus retraction. While this treatment increased holdfast production in wild-type cells by triggering the surface-sensing pathway, no increase was observed in the cpaL mutant, suggesting that mutation of cpaL maximally stimulates surface-sensing. Furthermore, when the cpaL mutant was grown in a medium that blocks the surface sensing pathway, cells exhibited decreased surface attachment and holdfast production, consistent with a role for CpaL in pilus-dependent surface sensing in C. crescentus. To better understand the function of CpaL, we analyzed its predicted structure, which suggested that CpaL is a minor pilin fused to a mechanosensitive von Willebrand factor type A (vWA) domain that could be accommodated at the pilus tip. These results collectively position CpaL as a strong candidate for a mechanosensory element in pilus-mediated surface sensing.

Development of monoclonal antibodies against P. gingivalis Mfa1 and their protective capacity in an experimental periodontitis model

Porphyromonas gingivalis (P. gingivalis), a gram-negative, black-pigmented anaerobe, is a major etiological agent and a leading cause of periodontitis. Fimbriae protein Mfa1 is a key virulence factor of P. gingivalis and plays a crucial role in bacterial adhesion, colonization, biofilm formation, and persistent inflammation, making it a promising therapeutic target. However, the role of anti-Mfa1 antibodies and the underlying protective mechanisms remain largely unexplored. Here, we developed and characterized the monoclonal antibodies (mAbs) targeting the Mfa1 protein of P. gingivalis. Function analysis showed that anti-Mfa1 mAbs mediated bacterial agglutination and inhibited P. gingivalis adhesion to saliva-coated hydroxyapatite and host cells. Notably, anti-Mfa1 mAbs significantly reduced bacterial burden and alveolar bone loss in a P. gingivalis-induced experimental periodontitis model. These results show that anti-Mfa1 mAbs can be beneficial in alleviating P. gingivalis infections, and provide important insights for the development of adequate adjuvant treatment regimens for Mfa1-targeted therapeutics.

IMPORTANCE

Fimbriae (pili) play an important role in bacterial adhesion, invasion of host cells and tissues, and formation of biofilms. Studies have shown that two types of fimbriae of Porphyromonas gingivalis, FimA and Mfa1, are important for colonization and infection through their binding to host tissues and other bacteria. While anti-FimA antibodies have been shown to improve periodontitis, the effect of anti-Mfa1 antibodies on P. gingivalis infection and periodontitis was previously unknown. In this study, we report for the first time that anti-Mfa1 monoclonal antibodies can reduce P. gingivalis infection and improve periodontitis. These findings suggest that Mfa1 represents a promising therapeutic target, and the development of anti-Mfa1 mAbs holds a potential as essential diagnostic and adjunctive therapeutic tools for managing P. gingivalis-related diseases.

A Phage-Based Approach to Identify Antivirulence Inhibitors of Bacterial Type IV Pili

The increasing threat of antibiotic resistance underscores the urgent need for innovative strategies to combat infectious diseases, including the development of antivirulants. Microbial pathogens rely on their virulence factors to initiate and sustain infections. Antivirulants are small molecules designed to target virulence factors, thereby attenuating the virulence of infectious microbes. The bacterial type IV pilus (T4P), an extracellular protein filament that depends on the T4P machinery (T4PM) for its biogenesis, dynamics and function, is a key virulence factor in many significant bacterial pathogens. While the T4PM presents a promising antivirulence target, the systematic identification of inhibitors for its multiple protein constituents remains a considerable challenge. Here we report a novel high-throughput screening (HTS) approach for discovering T4P inhibitors. It uses Pseudomonas aeruginosa, a high-priority pathogen, in combination with its T4P-targeting phage, φKMV. Screening of a library of 2168 compounds using an optimised protocol led to the identification of tuspetinib, based on its deterrence of the lysis of P. aeruginosa by φKMV. Our findings show that tuspetinib also inhibits two additional T4P-targeting phages, while having no effect on a phage that recognises lipopolysaccharides as its receptor. Additionally, tuspetinib impedes T4P-mediated motility in P. aeruginosa and Acinetobacter species without impacting growth or flagellar motility. This bacterium-phage pairing approach is applicable to a broad range of virulence factors that are required for phage infection, paving ways for the development of advanced chemotherapeutics against antibiotic-resistant infections.

Architectural dissection of adhesive bacterial cell surface appendages from a "molecular machines" viewpoint

The ability of bacteria to interact with and respond to their environment is crucial to their lifestyle and survival. Bacterial cells routinely need to engage with extracellular target molecules, in locations spatially separated from their cell surface. Engagement with distant targets allows bacteria to adhere to abiotic surfaces and host cells, sense harmful or friendly molecules in their vicinity, as well as establish symbiotic interactions with neighboring cells in multicellular communities such as biofilms. Binding to extracellular molecules also facilitates transmission of information back to the originating cell, allowing the cell to respond appropriately to external stimuli, which is critical throughout the bacterial life cycle. This requirement of bacteria to bind to spatially separated targets is fulfilled by a myriad of specialized cell surface molecules, which often have an extended, filamentous arrangement. In this review, we compare and contrast such molecules from diverse bacteria, which fulfil a range of binding functions critical for the cell. Our comparison shows that even though these extended molecules have vastly different sequence, biochemical and functional characteristics, they share common architectural principles that underpin bacterial adhesion in a variety of contexts. In this light, we can consider different bacterial adhesins under one umbrella, specifically from the point of view of a modular molecular machine, with each part fulfilling a distinct architectural role. Such a treatise provides an opportunity to discover fundamental molecular principles governing surface sensing, bacterial adhesion, and biofilm formation.

Type IV pili of Enterobacteriaceae species

Type IV pili (T4Ps) are surface filaments widely distributed among bacteria and archaea. T4Ps are involved in many cellular functions and contribute to virulence in some species of bacteria. Due to the diversity of T4Ps, different properties have been observed for homologous proteins that make up T4Ps in various organisms. In this review, we highlight the essential components of T4Ps, their functions, and similarities to related systems. We emphasize the unique T4Ps of enteric pathogens within the Enterobacteriaceae family, which includes pathogenic strains of Escherichia coli and Salmonella. These include the bundle-forming pilus (BFP) of enteropathogenic E. coli (EPEC), longus (Lng) and colonization factor III (CFA/III) of enterotoxigenic E. coli (ETEC), T4P of Salmonella enterica serovar Typhi, Colonization Factor Citrobacter (CFC) of Citrobacter rodentium, T4P of Yersinia pseudotuberculosis, a ubiquitous T4P that was characterized in enterohemorrhagic E. coli (EHEC), and the R64 plasmid thin pilus. Finally, we highlight areas for further study.

P-type pilus PapG protein elicits toll-like receptor 2-mediated immune activation during cancer immunotherapy

The immune activation ability of FimH, an adhesion protein in pili of Escherichia coli (E. coli), has been recently reported. However, studies on the immune activity of PapG, another major pili terminal protein, have not been well explored. In this study, the immune stimulatory effect of purified recombinant PapG was evaluated. PapG treatment promoted dramatic changes in dendritic morphology of the bone marrow-derived dendritic cells (BMDCs) and induced upregulation of co-stimulatory molecule levels, major histocompatibility complex (MHC) I and II expression, and pro-inflammatory cytokine production in BMDCs. To identify the stimulatory receptor of PapG, an in silico study was performed. PapG exhibited strong binding affinity with murine toll-like receptor 2 (TLR2). In addition, PapG-induced activation of splenic DC and its subsets was unsuccessful in TLR2-knock out mice. Combination of PapG and ovalbumin (OVA) elicited OVA-specific T cell proliferation and cytokine production and cytotoxicity that consequently promoted anti-cancer immune responses against OVA-expressing B16 melanoma. Furthermore, PapG treatment induced activation of peripheral blood DCs and its subsets in humans in a TLR2 dependent manner. PapG-stimulated human conventional DC2 promoted syngeneic T cell proliferation and activation. The findings of this study demonstrated that PapG could be a useful immune stimulator for immunotherapy against cancer.

Structure of the Pseudomonas aeruginosa PAO1 Type IV pilus

Type IV pili (T4Ps) are abundant in many bacterial and archaeal species, where they play important roles in both surface sensing and twitching motility, with implications for adhesion, biofilm formation and pathogenicity. While Type IV pilus (T4P) structures from other organisms have been previously solved, a high-resolution structure of the native, fully assembled T4P of Pseudomonas aeruginosa, a major human pathogen, would be valuable in a drug discovery context. Here, we report a 3.2 Å-resolution structure of the P. aeruginosa PAO1 T4P determined by electron cryomicroscopy (cryo-EM). PilA subunits constituting the T4P exhibit a classical pilin fold featuring an extended N-terminal α-helix linked to a C-terminal globular β-sheet-containing domain, which are packed tightly along the pilus, in line with models derived from previous cryo-EM data of the P. aeruginosa PAK strain. The N-terminal helices constitute the pilus core where they stabilise the tubular assembly via hydrophobic interactions. The α-helical core of the pilus is surrounded by the C-terminal globular domain of PilA that coats the outer surface of the pilus, mediating interactions with the surrounding environment. Comparison of the P. aeruginosa PAO1 T4P with T4P structures from other organisms, both at the level of the pilin subunits and the fully assembled pili, confirms previously described common architectural principles whilst highlighting key differences between members of this abundant class of prokaryotic filaments. This study provides a structural framework for understanding the molecular and cell biology of these important cellular appendages mediating interaction of prokaryotes to surfaces.

Targeted protein evolution in the gut microbiome by diversity-generating retroelements

Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting they play adaptive roles in this environment. We identified >1,100 unique DGRs among human-associated Bacteroides species and discovered a subset that diversify adhesive components of Type V pili and related proteins. We show that Bacteroides DGRs are horizontally transferred across species, that some are highly active while others are tightly controlled, and that they preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched when Bacteroides strains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2,700 DGRs from diverse phyla in mother-infant pairs shows that Bacteroides DGRs are preferentially transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the roles of stochastic, targeted genome plasticity in shaping host-associated microbial communities.

Non-antibiotic compounds associated with humans and the environment can promote horizontal transfer of antimicrobial resistance genes

Horizontal gene transfer plays a key role in the global dissemination of antimicrobial resistance (AMR). AMR genes are often carried on self-transmissible plasmids, which are shared amongst bacteria primarily by conjugation. Antibiotic use has been a well-established driver of the emergence and spread of AMR. However, the impact of commonly used non-antibiotic compounds and environmental pollutants on AMR spread has been largely overlooked. Recent studies found common prescription and over-the-counter drugs, artificial sweeteners, food preservatives, and environmental pollutants, can increase the conjugative transfer of AMR plasmids. The potential mechanisms by which these compounds promote plasmid transmission include increased membrane permeability, upregulation of plasmid transfer genes, formation of reactive oxygen species, and SOS response gene induction. Many questions remain around the impact of most non-antibiotic compounds on AMR plasmid conjugation in clinical isolates and the long-term impact on AMR dissemination. By elucidating the role of routinely used pharmaceuticals, food additives, and pollutants in the dissemination of AMR, action can be taken to mitigate their impact by closely monitoring use and disposal. This review will discuss recent progress on understanding the influence of non-antibiotic compounds on plasmid transmission, the mechanisms by which they promote transfer, and the level of risk they pose.

Biogenesis and Functionality of Sortase-Assembled Pili in Gram-Positive Bacteria

A unique class of multimeric proteins made of covalently linked subunits known as pili, or fimbriae, are assembled and displayed on the gram-positive bacterial cell surface by a conserved transpeptidase enzyme named pilus-specific sortase. Sortase-assembled pili are produced by a wide range of gram-positive commensal and pathogenic bacteria inhabiting diverse niches such as the human oral cavity, gut, urogenital tract, and skin. These surface appendages serve many functions, including as molecular adhesins, immuno-modulators, and virulence determinants, that significantly contribute to both the commensal and pathogenic attributes of producer microbes. Intensive genetic, biochemical, physiological, and structural studies have been devoted to unveiling the assembly mechanism and functions, as well as the utility of these proteins in vaccine development and other biotechnological applications. We provide a comprehensive review of these topics and discuss the current status and future prospects of the field.

PlzR regulates type IV pili assembly in Pseudomonas aeruginosa via PilZ binding

Type IV pili (T4P) are thin, flexible filaments exposed on the cell surface of gram-negative bacteria and are involved in pathogenesis-related processes, including cell adsorption, biofilm formation, and twitching motility. Bacteriophages often use these filaments as receptors to infect host cells. Here, we describe the identification of a protein that inhibits T4P assembly in Pseudomonas aeruginosa, discovered during a screen for host factors influencing phage infection. We show that expression of PA2560 (renamed PlzR) in P. aeruginosa inhibits adsorption of T4P-dependent phages. PlzR does this by directly binding the T4P chaperone PilZ, which in turn regulates the ATPase PilB and results in disturbed T4P assembly. As the plzR promoter is induced by cyclic di-GMP, PlzR might play a role in coupling T4P function to levels of this second messenger.

The Combinatory Effects of Essential Oil from Lippia macrophylla on Multidrug Resistant Acinetobacter baumannii Clinical Isolates

To assess the antibacterial effectiveness of Lippia macrophylla essential oil (LMEO) against multidrug-resistant Acinetobacter baumannii isolates, both as a standalone treatment and in combination with conventional antibiotics. LMEO demonstrated a significant inhibitory effect on the growth of A. baumannii, with a minimum inhibitory concentration (MIC) below 500 μg/mL. Notably, LMEO was capable of reversing the antibiotic resistance of clinical isolates or reducing their MIC values when used in combination with antibiotics, showing synergistic (FICI≤0.5) or additive effects. The combination of LMEO and imipenem was particularly effective, displaying synergistic interactions for most isolates. Ultrastructural analyses supported these findings, revealing that the combination of LMEO+ceftazidime compromised the membrane integrity of the Acb35 isolate, leading to cytoplasmic leakage and increased formation of Outer Membrane Vesicles (OMVs). Taken together our results point for the use of LMEO alone or in combination as an antibacterial agent against A. baumannii. These findings offer promising avenues for utilizing LMEO as a novel antibacterial strategy against drug-resistant infections in healthcare settings, underscoring the potential of essential oils in enhancing antibiotic efficacy.

TasA Fibre Interactions Are Necessary for Bacillus subtilis Biofilm Structure

The extracellular matrix of biofilms provides crucial structural support to the community and protection from environmental perturbations. TasA, a key Bacillus subtilis biofilm matrix protein, forms both amyloid and non-amyloid fibrils. Non-amyloid TasA fibrils are formed via a strand-exchange mechanism, whereas the amyloid-like form involves non-specific self-assembly. We performed mutagenesis of the N-terminus to assess the role of non-amyloid fibrils in biofilm development. We find that the N-terminal tail is essential for the formation of structured biofilms, providing evidence that the strand-exchange fibrils are the active form in the biofilm matrix. Furthermore, we demonstrate that fibre formation alone is not sufficient to give structure to the biofilm. We build an interactome of TasA with other extracellular protein components, and identify important interaction sites. Our results provide insight into how protein-matrix interactions modulate biofilm development.

Molecular basis for sortase-catalyzed pilus tip assembly

During pilus assembly within the Gram-positive bacterial envelope, membrane-bound sortase enzymes sequentially crosslink specific pilus protein monomers through their cell wall sorting signals (CWSS), starting with a designated tip pilin, followed by the shaft made of another pilin, ultimately anchoring the fiber base pilin to the cell wall. To date, the molecular determinants that govern pilus tip assembly and the underlying mechanism remain unknown. Here, we addressed this in the model organism Actinomyces oris. This oral microbe assembles a pathogenically important pilus (known as type 2 fimbria) whose shafts, made of FimA pilins, display one of two alternate tip pilins-FimB or the coaggregation factor CafA-that share a markedly similar CWSS. We demonstrate that swapping the CWSS of CafA with that of FimB produces a functional hybrid, which localizes at the pilus tip and mediates polymicrobial coaggregation, whereas alanine-substitution of the conserved FLIAG motif within the CWSS hampers these processes. Remarkably, swapping the CWSS of the normal cell wall-anchored glycoprotein GspA with that of CafA promotes the assembly of hybrid GspA at the FimA pilus tip. Finally, exchanging the CWSS of the Corynebacterium diphtheriae shaft pilin SpaA with that of CafA leads to the FLIAG motif-dependent localization of the heterologous pilus protein SpaA at the FimA pilus tip in A. oris. Evidently, the CWSS and the FLIAG motif of CafA are both necessary and sufficient for its destination to the cognate pilus tip specifically assembled by a designated sortase in the organism.

IMPORTANCE

Gram-positive pili, whose precursors harbor a cell wall sorting signal (CWSS) needed for sortase-mediated pilus assembly, typically comprise a pilus shaft and a tip adhesin. How a pilin becomes a pilus tip, nevertheless, remains undetermined. We demonstrate here in Actinomyces oris that the CWSS of the tip pilin CafA is necessary and sufficient to promote pilus tip assembly, and this functional assembly involves a conserved FLIAG motif within the CWSS. This is evidenced by the fact that an A. oris cell-wall anchored glycoprotein, GspA, or a heterologous shaft pilin from Corynebacterium diphtheriae, SpaA, engineered to have the CWSS of CafA in place of their CWSS, localizes at the pilus tip in a process that requires the FLIAG motif. Our findings provide the molecular basis for sortase-catalyzed pilus tip assembly that is very likely employed by other Gram-positive bacteria and potential bioengineering applications to display antigens at controlled surface distance.

Type 1 fimbria and P pili: regulatory mechanisms of the prototypical members of the chaperone-usher fimbrial family

Adherence to both cellular and abiotic surfaces is a crucial step in the interaction of bacterial pathogens and commensals with their hosts. Bacterial surface structures known as fimbriae or pili play a fundamental role in the early colonization stages by providing specificity or tropism. Among the various fimbrial families, the chaperone-usher family has been extensively studied due to its ubiquity, diversity, and abundance. This family is named after the components that facilitate their biogenesis. Type 1 fimbria and P pilus, two chaperone-usher fimbriae associated with urinary tract infections, have been thoroughly investigated and serve as prototypes that have laid the foundations for understanding the biogenesis of this fimbrial family. Additionally, the study of the mechanisms regulating their expression has also been a subject of great interest, revealing that the regulation of the expression of the genes encoding these structures is a complex and diverse process, involving both common global regulators and those specific to each operon.

Tad pili contribute to the virulence and biofilm formation of virulent Aeromonas hydrophila

Type IV pili (T4P) are versatile proteinaceous protrusions that mediate diverse bacterial processes, including adhesion, motility, and biofilm formation. Aeromonas hydrophila, a Gram-negative facultative anaerobe, causes disease in a wide range of hosts. Previously, we reported the presence of a unique Type IV class C pilus, known as tight adherence (Tad), in virulent Aeromonas hydrophila (vAh). In the present study, we sought to functionalize the role of Tad pili in the pathogenicity of A. hydrophila ML09-119. Through a comprehensive comparative genomics analysis of 170 A. hydrophila genomes, the conserved presence of the Tad operon in vAh isolates was confirmed, suggesting its potential contribution to pathogenicity. Herein, the entire Tad operon was knocked out from A. hydrophila ML09-119 to elucidate its specific role in A. hydrophila virulence. The absence of the Tad operon did not affect growth kinetics but significantly reduced virulence in catfish fingerlings, highlighting the essential role of the Tad operon during infection. Biofilm formation of A. hydrophila ML09-119 was significantly decreased in the Tad operon deletant. Absence of the Tad operon had no effect on sensitivity to other environmental stressors, including hydrogen peroxide, osmolarity, alkalinity, and temperature; however, it was more sensitive to low pH conditions. Scanning electron microscopy revealed that the Tad mutant had a rougher surface structure during log phase growth than the wildtype strain, indicating the absence of Tad impacts the outer surface of vAh during cell division, of which the biological consequences are unknown. These findings highlight the role of Tad in vAh pathogenesis and biofilm formation, signifying the importance of T4P in bacterial infections.

The yad and yeh fimbrial loci influence gene expression and virulence in enterohemorrhagic Escherichia coli O157:H7

Fimbriae are essential virulence factors for many bacterial pathogens. Fimbriae are extracellular structures that attach bacteria to surfaces. Thus, fimbriae mediate a critical step required for any pathogen to establish infection by anchoring a bacterium to host tissue. The human pathogen enterohemorrhagic Escherichia coli (EHEC) O157:H7encodes 16 fimbriae that may be important for EHEC to initiate infection and allow for productive expression of virulence traits important in later stages of infection, including a type III secretion system (T3SS) and Shiga toxin; however, the roles of most EHEC fimbriae are largely uncharacterized. Here, we provide evidence that two EHEC fimbriae, Yad and Yeh, modulate expression of diverse genes including genes encoding T3SS and Shiga toxin and that these fimbriae are required for robust colonization of the gastrointestinal tract. These findings reveal a significant and previously unappreciated role for fimbriae in bacterial pathogenesis as important determinants of virulence gene expression.IMPORTANCEFimbriae are extracellular proteinaceous structures whose defining role is to anchor bacteria to surfaces. This is a fundamental step for bacterial pathogens to establish infection in a host. Here, we show that the contributions of fimbriae to pathogenesis are more complex. Specifically, we demonstrate that fimbriae influence expression of virulence traits essential for disease progression in the intestinal pathogen enterohemorrhagic Escherichia coli. Gram-positive and Gram-negative bacteria express multiple fimbriae; therefore, these findings may have broad implications for understanding how pathogens use fimbriae, beyond adhesion, to initiate infection and coordinate gene expression, which ultimately results in disease.

In silico analysis of Ffp1, an ancestral Porphyromonas spp. fimbrillin, shows differences with Fim and Mfa

Background. Scant information is available regarding fimbrillins within the genus Porphyromonas, with the notable exception of those belonging to Porphyromonas gingivalis, which have been extensively researched for several years. Besides fim and mfa, a third P. gingivalis adhesin called filament-forming protein 1 (Ffp1) has recently been described and seems to be pivotal for outer membrane vesicle (OMV) production. Objective. We aimed to investigate the distribution and diversity of type V fimbrillin, particularly Ffp1, in the genus Porphyromonas. Methods. A bioinformatics phylogenomic analysis was conducted using all accessible Porphyromonas genomes to generate a domain search for fimbriae, using hidden Markov model profiles. Results. Ffp1 was identified as the sole fimbrillin present in all analysed genomes. After manual verification (i.e. biocuration) of both structural and functional annotations and 3D modelling, this protein was determined to be a type V fimbrillin, with a closer structural resemblance to a Bacteroides ovatus fimbrillin than to FimA or Mfa1 from P. gingivalis. Conclusion. It appears that Ffp1 is an ancestral fimbria, transmitted through vertical inheritance and present across all Porphyromonas species. Additional investigations are necessary to elucidate the biogenesis of Ffp1 fimbriae and their potential role in OMV production and niche adaptation.

Catabolism and interactions of syntrophic propionate- and acetate oxidizing microorganisms under mesophilic, high-ammonia conditions

Microbial inhibition by high ammonia concentrations is a recurring problem that significantly restricts methane formation from intermediate acids, i.e., propionate and acetate, during anaerobic digestion of protein-rich waste material. Studying the syntrophic communities that perform acid conversion is challenging, due to their relatively low abundance within the microbial communities typically found in biogas processes and disruption of their cooperative behavior in pure cultures. To overcome these limitations, this study examined growth parameters and microbial community dynamics of highly enriched mesophilic and ammonia-tolerant syntrophic propionate and acetate-oxidizing communities and analyzed their metabolic activity and cooperative behavior using metagenomic and metatranscriptomic approaches. Cultivation in batch set-up demonstrated biphasic utilization of propionate, wherein acetate accumulated and underwent oxidation before complete degradation of propionate. Three key species for syntrophic acid degradation were inferred from genomic sequence information and gene expression: a syntrophic propionate-oxidizing bacterium (SPOB) "Candidatus Syntrophopropionicum ammoniitolerans", a syntrophic acetate-oxidizing bacterium (SAOB) Syntrophaceticus schinkii and a novel hydrogenotrophic methanogen, for which we propose the provisional name "Candidatus Methanoculleus ammoniitolerans". The results revealed consistent transcriptional profiles of the SAOB and the methanogen both during propionate and acetate oxidation, regardless of the presence of an active propionate oxidizer. Gene expression indicated versatile capabilities of the two syntrophic bacteria, utilizing both molecular hydrogen and formate as an outlet for reducing equivalents formed during acid oxidation, while conserving energy through build-up of sodium/proton motive force. The methanogen used hydrogen and formate as electron sources. Furthermore, results of the present study provided a framework for future research into ammonia tolerance, mobility, aggregate formation and interspecies cooperation.

Functional Analysis of the Major Pilin Proteins of Type IV Pili in Streptococcus sanguinis CGMH010

The pil gene cluster for Type IV pilus (Tfp) biosynthesis is commonly present and highly conserved in Streptococcus sanguinis. Nevertheless, Tfp-mediated twitching motility is less common among strains, and the factors determining twitching activity are not fully understood. Here, we analyzed the functions of three major pilin proteins (PilA1, PilA2, and PilA3) in the assembly and activity of Tfp in motile S. sanguinis CGMH010. Using various recombinant pilA deletion strains, we found that Tfp composed of different PilA proteins varied morphologically and functionally. Among the three PilA proteins, PilA1 was most critical in the assembly of twitching-active Tfp, and recombinant strains expressing motility generated more structured biofilms under constant shearing forces compared to the non-motile recombinant strains. Although PilA1 and PilA3 shared 94% identity, PilA3 could not compensate for the loss of PilA1, suggesting that the nature of PilA proteins plays an essential role in twitching activity. The single deletion of individual pilA genes had little effect on the invasion of host endothelia by S. sanguinis CGMH010. In contrast, the deletion of all three pilA genes or pilT, encoding the retraction ATPase, abolished Tfp-mediated invasion. Tfp- and PilT-dependent invasion were also detected in the non-motile S. sanguinis SK36, and thus, the retraction of Tfp, but not active twitching, was found to be essential for invasion.

Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus

Caulobacter crescentus Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in Escherichia coli, maintaining infectivity against C. crescentus, which presents promising applications, including RNA delivery and phage display.

Diverse and abundant phages exploit conjugative plasmids

Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.

The assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili

Type 1 pili are important virulence factors of uropathogenic Escherichia coli that mediate bacterial attachment to epithelial cells in the urinary tract. The pilus rod is comprised of thousands of copies of the main structural subunit FimA and is assembled in vivo by the assembly platform FimD. Although type 1 pilus rods can self-assemble from FimA in vitro, this reaction is slower and produces structures with lower kinetic stability against denaturants compared to in vivo-assembled rods. Our study reveals that FimD-catalysed in vitro-assembled type 1 pilus rods attain a similar stability as pilus rods assembled in vivo. Employing structural, biophysical and biochemical analyses, we show that in vitro assembly reactions lacking FimD produce pilus rods with structural defects, reducing their stability against dissociation. Overall, our results indicate that FimD is not only required for the catalysis of pilus assembly, but also to control the assembly of the most stable quaternary structure.

Understanding a Core Pilin of the Type IVa Pili of Acidithiobacillus thiooxidans, PilV

Pilins are protein subunits of pili. The pilins of type IV pili (T4P) in pathogenic bacteria are well characterized, but anything is known about the T4P proteins in acidophilic chemolithoautotrophic microorganisms such as the genus Acidithiobacillus. The interest in T4P of A. thiooxidans is because of their possible role in cell recruitment and bacterial aggregation on the surface of minerals during biooxidation of sulfide minerals. In this study we present a successful ad hoc methodology for the heterologous expression and purification of extracellular proteins such as the minor pilin PilV of the T4P of A. thiooxidans, a pilin exposed to extreme conditions of acidity and high oxidation-reduction potentials, and that interact with metal sulfides in an environment rich in dissolved minerals. Once obtained, the model structure of A. thiooxidans PilV revealed the core basic architecture of T4P pilins. Because of the acidophilic condition, we carried out in silico characterization of the protonation status of acidic and basic residues of PilV in order to calculate the ionization state at specific pH values and evaluated their pH stability. Further biophysical characterization was done using UV-visible and fluorescence spectroscopy and the results showed that PilV remains soluble and stable even after exposure to significant changes of pH. PilV has a unique amino acid composition that exhibits acid stability, with significant biotechnology implications such as biooxidation of sulfide minerals. The biophysics profiles of PilV open new paradigms about resilient proteins and stimulate the study of other pilins from extremophiles.

Pan-Genome Plasticity and Virulence Factors: A Natural Treasure Trove for Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative pathogen responsible for a variety of community- and hospital-acquired infections. It is recognized as a life-threatening pathogen among hospitalized individuals and, in particular, immunocompromised patients in many countries. A. baumannii, as a member of the ESKAPE group, encompasses high genomic plasticity and simultaneously is predisposed to receive and exchange the mobile genetic elements (MGEs) through horizontal genetic transfer (HGT). Indeed, A. baumannii is a treasure trove that contains a high number of virulence factors. In accordance with these unique pathogenic characteristics of A. baumannii, the authors aim to discuss the natural treasure trove of pan-genome and virulence factors pertaining to this bacterial monster and try to highlight the reasons why this bacterium is a great concern in the global public health system.

Structural and functional diversity of type IV secretion systems

Considerable progress has been made in recent years in the structural and molecular biology of type IV secretion systems in Gram-negative bacteria. The latest advances have substantially improved our understanding of the mechanisms underlying the recruitment and delivery of DNA and protein substrates to the extracellular environment or target cells. In this Review, we aim to summarize these exciting structural and molecular biology findings and to discuss their functional implications for substrate recognition, recruitment and translocation, as well as the biogenesis of extracellular pili. We also describe adaptations necessary for deploying a breadth of processes, such as bacterial survival, host-pathogen interactions and biotic and abiotic adhesion. We highlight the functional and structural diversity that allows this extremely versatile secretion superfamily to function under different environmental conditions and in different bacterial species. Additionally, we emphasize the importance of further understanding the mechanism of type IV secretion, which will support us in combating antimicrobial resistance and treating type IV secretion system-related infections.

What can molecular assembly learn from catalysed assembly in living organisms?

Molecular assembly is the process of organizing individual molecules into larger structures and complex systems. The self-assembly approach is predominantly utilized in creating artificial molecular assemblies, and was believed to be the primary mode of molecular assembly in living organisms as well. However, it has been shown that the assembly of many biological complexes is "catalysed" by other molecules, rather than relying solely on self-assembly. In this review, we summarize these catalysed-assembly (catassembly) phenomena in living organisms and systematically analyse their mechanisms. We then expand on these phenomena and discuss related concepts, including catalysed-disassembly and catalysed-reassembly. Catassembly proves to be an efficient and highly selective strategy for synergistically controlling and manipulating various noncovalent interactions, especially in hierarchical molecular assemblies. Overreliance on self-assembly may, to some extent, hinder the advancement of artificial molecular assembly with powerful features. Furthermore, inspired by the biological catassembly phenomena, we propose guidelines for designing artificial catassembly systems and developing characterization and theoretical methods, and review pioneering works along this new direction. Overall, this approach may broaden and deepen our understanding of molecular assembly, enabling the construction and control of intelligent assembly systems with advanced functionality.

Genetic Insights into Biofilm Formation by a Pathogenic Strain of Vibrio harveyi

The Vibrio genus includes bacteria widely distributed in aquatic habitats and the infections caused by these bacteria can affect a wide range of hosts. They are able to adhere to numerous surfaces, which can result in biofilm formation that helps maintain them in the environment. The involvement of the biofilm lifestyle in the virulence of Vibrio pathogens of aquatic organisms remains to be investigated. Vibrio harveyi ORM4 is a pathogen responsible for an outbreak in European abalone Haliotis tuberculata populations. In the present study, we used a dynamic biofilm culture technique coupled with laser scanning microscopy to characterize the biofilm formed by V. harveyi ORM4. We furthermore used RNA-seq analysis to examine the global changes in gene expression in biofilm cells compared to planktonic bacteria, and to identify biofilm- and virulence-related genes showing altered expression. A total of 1565 genes were differentially expressed, including genes associated with motility, polysaccharide synthesis, and quorum sensing. The up-regulation of 18 genes associated with the synthesis of the type III secretion system suggests that this virulence factor is induced in V. harveyi ORM4 biofilms, providing indirect evidence of a relationship between biofilm and virulence.

The basal and major pilins in the Corynebacterium diphtheriae SpaA pilus adopt similar structures that competitively react with the pilin polymerase

Many species of pathogenic gram-positive bacteria display covalently crosslinked protein polymers (called pili or fimbriae) that mediate microbial adhesion to host tissues. These structures are assembled by pilus-specific sortase enzymes that join the pilin components together via lysine-isopeptide bonds. The archetypal SpaA pilus from Corynebacterium diphtheriae is built by the Cd SrtA pilus-specific sortase, which crosslinks lysine residues within the SpaA and SpaB pilins to build the shaft and base of the pilus, respectively. Here, we show that Cd SrtA crosslinks SpaB to SpaA via a K139(SpaB)-T494(SpaA) lysine-isopeptide bond. Despite sharing only limited sequence homology, an NMR structure of SpaB reveals striking similarities with the N-terminal domain of SpaA (N SpaA) that is also crosslinked by Cd SrtA. In particular, both pilins contain similarly positioned reactive lysine residues and adjacent disordered AB loops that are predicted to be involved in the recently proposed "latch" mechanism of isopeptide bond formation. Competition experiments using an inactive SpaB variant and additional NMR studies suggest that SpaB terminates SpaA polymerization by outcompeting N SpaA for access to a shared thioester enzyme-substrate reaction intermediate.

Csu pili dependent biofilm formation and virulence of Acinetobacter baumannii

Acinetobacter baumannii has emerged as one of the most common extensive drug-resistant nosocomial bacterial pathogens. Not only can the bacteria survive in hospital settings for long periods, but they are also able to resist adverse conditions. However, underlying regulatory mechanisms that allow A. baumannii to cope with these conditions and mediate its virulence are poorly understood. Here, we show that bi-stable expression of the Csu pili, along with the production of poly-N-acetyl glucosamine, regulates the formation of Mountain-like biofilm-patches on glass surfaces to protect bacteria from the bactericidal effect of colistin. Csu pilus assembly is found to be an essential component of mature biofilms formed on glass surfaces and of pellicles. By using several microscopic techniques, we show that clinical isolates of A. baumannii carrying abundant Csu pili mediate adherence to epithelial cells. In addition, Csu pili suppressed surface-associated motility but enhanced colonization of bacteria into the lungs, spleen, and liver in a mouse model of systemic infection. The screening of c-di-GMP metabolizing protein mutants of A. baumannii 17978 for the capability to adhere to epithelial cells led us to identify GGDEF/EAL protein AIS_2337, here denoted PdeB, as a major regulator of Csu pili-mediated virulence and biofilm formation. Moreover, PdeB was found to be involved in the type IV pili-regulated robustness of surface-associated motility. Our findings suggest that the Csu pilus is not only a functional component of mature A. baumannii biofilms but also a major virulence factor promoting the initiation of disease progression by mediating bacterial adherence to epithelial cells.

The intracellular life of Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative opportunistic bacterium responsible for nosocomial and community-acquired infections. This pathogen is globally disseminated and associated with high levels of antibiotic resistance, which makes it an important threat to human health. Recently, new evidence showed that several A. baumannii isolates can survive and proliferate within eukaryotic professional and/or nonprofessional phagocytic cells, with in vivo consequences. This review provides updated information and describes the tools that A. baumannii possesses to adhere, colonize, and replicate in host cells. Additionally, we emphasize the high genetic and phenotypic heterogeneity detected amongst A. baumannii isolates and its impact on the bacterial intracellular features. We also discuss the need for standardized methods to characterize this pathogen robustly and consequently consider some strains as facultative intracellular bacteria.

Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids

Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.

Bacterial biofilms in the human body: prevalence and impacts on health and disease

Bacterial biofilms can be found in most environments on our planet, and the human body is no exception. Consisting of microbial cells encased in a matrix of extracellular polymers, biofilms enable bacteria to sequester themselves in favorable niches, while also increasing their ability to resist numerous stresses and survive under hostile circumstances. In recent decades, biofilms have increasingly been recognized as a major contributor to the pathogenesis of chronic infections. However, biofilms also occur in or on certain tissues in healthy individuals, and their constituent species are not restricted to canonical pathogens. In this review, we discuss the evidence for where, when, and what types of biofilms occur in the human body, as well as the diverse ways in which they can impact host health under homeostatic and dysbiotic states.

Extracellular transfer of a conserved polymerization factor for multi-flagellin filament assembly in Caulobacter

Unidirectional growth of filamentous protein assemblies including the bacterial flagellum relies on dedicated polymerization factors (PFs). The molecular determinants and structural transitions imposed by PFs on multi-subunit assembly are poorly understood. Here, we unveil FlaY from the polarized α-proteobacterium Caulobacter crescentus as a defining member of an alternative class of specialized flagellin PFs. Unlike the paradigmatic FliD capping protein, FlaY relies on a funnel-like β-propeller fold for flagellin polymerization. FlaY binds flagellin and is secreted by the flagellar secretion apparatus, yet it can also promote flagellin polymerization exogenously when donated from flagellin-deficient cells, serving as a transferable, extracellular public good. While the surge in FlaY abundance precedes bulk flagellin synthesis, FlaY-independent filament assembly is enhanced by mutation of a conserved region in multiple flagellin paralogs. We suggest that FlaYs are (multi-)flagellin PFs that evolved convergently to FliDs yet appropriated the versatile β-propeller fold implicated in human diseases for chaperone-assisted filament assembly.

Feature architecture aware phylogenetic profiling indicates a functional diversification of type IVa pili in the nosocomial pathogen Acinetobacter baumannii

The Gram-negative bacterial pathogen Acinetobacter baumannii is a major cause of hospital-acquired opportunistic infections. The increasing spread of pan-drug resistant strains makes A. baumannii top-ranking among the ESKAPE pathogens for which novel routes of treatment are urgently needed. Comparative genomics approaches have successfully identified genetic changes coinciding with the emergence of pathogenicity in Acinetobacter. Genes that are prevalent both in pathogenic and a-pathogenic Acinetobacter species were not considered ignoring that virulence factors may emerge by the modification of evolutionarily old and widespread proteins. Here, we increased the resolution of comparative genomics analyses to also include lineage-specific changes in protein feature architectures. Using type IVa pili (T4aP) as an example, we show that three pilus components, among them the pilus tip adhesin ComC, vary in their Pfam domain annotation within the genus Acinetobacter. In most pathogenic Acinetobacter isolates, ComC displays a von Willebrand Factor type A domain harboring a finger-like protrusion, and we provide experimental evidence that this finger conveys virulence-related functions in A. baumannii. All three genes are part of an evolutionary cassette, which has been replaced at least twice during A. baumannii diversification. The resulting strain-specific differences in T4aP layout suggests differences in the way how individual strains interact with their host. Our study underpins the hypothesis that A. baumannii uses T4aP for host infection as it was shown previously for other pathogens. It also indicates that many more functional complexes may exist whose precise functions have been adjusted by modifying individual components on the domain level.

Structural and antigenic characterization of a novel genotype of Mfa1 fimbriae in Porphyromonas gingivalis

Background

Mfa1 fimbriae of the periodontal pathogen Porphyromonas gingivalis are responsible for biofilm formation and comprise five proteins: Mfa1-5. Two major genotypes, mfa170 and mfa153, encode major fimbrillin. The mfa170 genotype is further divided into the mfa170A and mfa170B subtypes. The properties of the novel mfa170B remain unclear.

Methods

Fimbriae were purified from P. gingivalis strains JI-1 (mfa170A), 1439 (mfa170B), and Ando (mfa153), and their components and their structures were analyzed. Protein expression and variability in the antigenic specificity of fimbrillins were compared using Coomassie staining and western blotting using polyclonal antibodies against Mfa170A, Mfa170B, and Mfa153 proteins. Cell surface expression levels of fimbriae were analyzed by filtration enzyme-linked immunosorbent assays.

Results

The composition and structures of the purified Mfa1 fimbriae of 1439 was similar to that of JI-1. However, each Mfa1 protein of differential subtype/genotype was specifically detected by western blotting. Mfa170B fimbriae were expressed in several strains such as 1439, JKG9, B42, 1436, and Kyudai-3. Differential protein expression and antigenic heterogeneities were detected in Mfa2-5 between strains.

Conclusion

Mfa1 fimbriae from the mfa170A and mfa170B genotypes indicated an antigenic difference suggesting the mfa170B, is to be utilized for the novel classification of P. gingivalis.

Previously uncharacterized rectangular bacterial structures in the dolphin mouth

Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining revealed multiple paired bands within RBSs, suggesting the presence of cells dividing along the longitudinal axis. Cryogenic transmission electron microscopy and tomography showed parallel membrane-bound segments that are likely cells, encapsulated by an S-layer-like periodic surface covering. RBSs displayed unusual pilus-like appendages with bundles of threads splayed at the tips. We present multiple lines of evidence, including genomic DNA sequencing of micromanipulated RBSs, 16S rRNA gene sequencing, and fluorescence in situ hybridization, suggesting that RBSs are bacterial and distinct from the genera Simonsiella and Conchiformibius (family Neisseriaceae), with which they share similar morphology and division patterning. Our findings highlight the diversity of novel microbial forms and lifestyles that await characterization using tools complementary to genomics such as microscopy.

Bacterial secretion system functions: evidence of interactions and downstream implications

Unprecedented insights into the biology and functions of bacteria have been and continue to be gained through studying bacterial secretion systems in isolation. This method, however, results in our understanding of the systems being primarily based on the idea that they operate independently, ignoring the subtleties of downstream interconnections. Gram-negative bacteria are naturally able to adapt to and navigate their frequently varied and dynamic surroundings, mostly because of the covert connections between secretion systems. Therefore, to comprehend some of the linked downstream repercussions for organisms that follow this discourse, it is vital to have mechanistic insights into how the intersecretion system functions in bacterial rivalry, virulence, and survival, among other things. To that purpose, this paper discusses a few key instances of molecular antagonistic and interdependent relationships between bacterial secretion systems and their produced functional products.