Structural insights into functional amyloid inhibition in Gram -ve bacteria

Biofilm Biology to Brain Health: Harnessing Microbial Wisdom to Uncover Amyloid Dissociating Bifunctional Nano Chaperones for Alzheimer's Therapeutics

Microbial infections have long been implicated in the gut-brain link to Alzheimer's disease (AD). These infections may influence AD development either directly, through brain invasion, or indirectly via bacterial metabolites crossing the blood-brain-barrier (BBB) or interacting with the enteric nervous system (ENS). Such findings have inspired clinicians to repurpose antimicrobial drugs for AD, yielding promising results. However, the sole bacterial link to AD may be insufficiently understood. Bacterial amyloid presence in biofilms is well-documented, with certain bacterial proteins exacerbating amyloid formation while others inhibit it. For instance, Curli-specific gene protein C (CsgC) in E. coli suppresses curli amyloid formation. This review investigates the possibility of human CsgC-like proteins, identifying beta-2 microglobulin (β2M) and E3 ubiquitin ligases (E3s) as potential analogs that may influence amyloid degradation. We propose that nanoparticles (NPs) could serve as platforms to anchor these proteins, forming Amyloid Dissociating Bifunctional NanoChaperones (ADBiNaCs) with enhanced antiamyloidogenic activity. This innovative approach holds promise for novel AD treatment strategies, meriting further investigation into the role of bacterial and human amyloid-modulating proteins in AD pathology.

Ochoa S, Xicohtencatl-Cortes J. Pathogenesis and Immunomodulation of Urinary Tract Infections Caused by Uropathogenic Escherichia coli

Urinary tract infections (UTIs) are a leading cause of illness in children and adults of all ages, with uropathogenic Escherichia coli (UPEC) being the primary agent responsible. During colonization and subsequent infection of the urinary tract (UT), UPEC requires the expression of genes associated with virulence, such as those that encode the fimbrial adhesins FimH, PapG, and CsgA, as well as the presence of the TosA protein and the flagellar appendages of the bacteria. However, for colonization and infection to be successful, UPEC must overcome the host's immunological barriers, such as physical barriers, expressed peptides and proteins, and immune cells found in the UT. In this context, the UT functions as an integral system where these factors act to prevent the colonization of uropathogens. Significant genetic diversity exists among UPEC strains, and the clonal complex ST131 represents one of the key lineages. This lineage has a high content of virulence genes, multiple mechanisms of antibiotic resistance, and a high frequency of extended-spectrum β-lactamases (ESBLs). New knowledge regarding protein structures known as adhesins and their role in the infection process can help identify therapeutic targets and aid in the design of vaccines. These vaccines could be based on the development of chimeric fusion proteins (FimH + CsgA + PapG), which may significantly reduce the incidence of UTIs in pediatric and adult patients.

Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality

Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.

Exploiting pilus-mediated bacteria-host interactions for health benefits

Surface pili (or fimbriae) are an important but conspicuous adaptation of several genera and species of Gram-negative and Gram-positive bacteria. These long and non-flagellar multi-subunit adhesins mediate the initial contact that a bacterium has with a host or environment, and thus have come to be regarded as a key colonization factor for virulence activity in pathogens or niche adaptation in commensals. Pili in pathogenic bacteria are well recognized for their roles in the adhesion to host cells, colonization of tissues, and establishment of infection. As an 'anti-adhesive' ploy, targeting pilus-mediated attachment for disruption has become a potentially effective alternative to using antibiotics. In this review, we give a description of the several structurally distinct bacterial pilus types thus far characterized, and as well offer details about the intricacy of their individual structure, assembly, and function. With a molecular understanding of pilus biogenesis and pilus-mediated host interactions also provided, we go on to describe some of the emerging new approaches and compounds that have been recently developed to prevent the adhesion, colonization, and infection of piliated bacterial pathogens.

The Role of Gram-Negative Bacteria in Urinary Tract Infections: Current Concepts and Therapeutic Options

Urinary tract infections (UTIs) are some of the most common infections in human medicine worldwide, recognized as an important public health concern to healthcare systems around the globe. In addition, urine specimens are one of the most frequently submitted samples for culture to the clinical microbiology laboratory, exceeding the number of most of the other sample types. The epidemiology, species-distribution and susceptibility-patterns of uropathogens vary greatly in a geographical and time-dependent manner and it also strongly correlated with the reported patient population studied. Nevertheless, many studies highlight the fact that the etiological agents in UTIs have changed considerably, both in nosocomial and community settings, with a shift towards "less common" microorganisms having more pronounced roles. There is increasing demand for further research to advance diagnostics and treatment options, and to improve care of the patients. The aim of this review paper was to summarize current developments in the global burden of UTI, the diagnostic aspects of these infectious pathologies, the possible etiological agents and their virulence determinants (with a special focus on the members of the Enterobacterales order), current guidelines and quality indicators in the therapy of UTIs and the emergence of multidrug resistance in urinary pathogens.

Enhanced expression of recombinant proteins in Escherichia coli by co-expression with Vibrio parahaemolyticus CsgG, a pore-forming protein of the curli biogenesis pathway

AIM

To test whether engineered nanopores on the outer membrane (OM) of Escherichia coli can increase expression of heterologous proteins by making additional nutrients available to the host.

METHODS AND RESULTS

Outer membrane nanopores were generated by expressing recombinant Vibrio parahaemolyticus CsgG (rVpCsgG), which spontaneously assembles into a pore-forming channel on the OM, allowing spontaneous diffusion of small chemical entities from the exterior. Protein expression was probed using a reporter protein, sfGFP, expressed on a second compatible plasmid. OM pore formation was shown by acquired erythromycin sensitivity in cells transformed with rVpCsgG, influx of propidium iodide as well as by surface localization of recombinant CsgG by immunogold-labeled transmission electron microscopy. Expression of recombinant CsgG showed increased growth and also enhanced expression of sfGFP in minimal medium and is due to both enhanced transcription as well as translation. Similar enhancement of expression was also observed for a number of different proteins of different origin, sizes and nature.

CONCLUSIONS

Our findings clearly demonstrate that engineered nanopores on the OM of E. coli enhance expression of different heterologous proteins in minimal medium.

SIGNIFICANCE AND IMPACT OF THE STUDY

Vibrio parahaemolyticus CsgG β-nanopore mediated co-expression strategy to improve recombinant protein expression is fully compatible with other methods of protein expression enhancement, and therefore can be a useful tool in biotechnology particularly for whole-cell bio-transformations for production of secondary metabolite.

Quantitating denaturation by formic acid: imperfect repeats are essential to the stability of the functional amyloid protein FapC

Bacterial functional amyloids are evolutionarily optimized to aggregate, so much so that the extreme robustness of functional amyloid makes it very difficult to examine their structure-function relationships in a detailed manner. Previous work has shown that functional amyloids are resistant to conventional chemical denaturants, but they dissolve in formic acid (FA) at high concentrations. However, systematic investigation requires a quantitative analysis of FA's ability to denature proteins. Amyloid formed by Pseudomonas sp. protein FapC provides an excellent model to investigate FA denaturation. It contains three imperfect repeats, and stepwise removal of these repeats slows fibrillation and increases fragmentation during aggregation. However, the link to stability is unclear. We first calibrated FA denaturation using three small, globular, and acid-resistant proteins. This revealed a linear relationship between the concentration of FA and the free energy of unfolding with a slope of mFA+pH (the combined contribution of FA and FA-induced lowering of pH), as well as a robust correlation between protein size and mFA+pH We then measured the solubilization of fibrils formed from different FapC variants with varying numbers of repeats as a function of the concentration of FA. This revealed a decline in the number of residues driving amyloid formation upon deleting at least two repeats. The midpoint of denaturation declined with the removal of repeats. Complete removal of all repeats led to fibrils that were solubilized at FA concentrations 2-3 orders of magnitude lower than the repeat-containing variants, showing that at least one repeat is required for the stability of functional amyloid.

The FapF Amyloid Secretion Transporter Possesses an Atypical Asymmetric Coiled Coil

Gram-negative bacteria possess specialized biogenesis machineries that facilitate the export of amyloid subunits, the fibers of which are key components of their biofilm matrix. The secretion of bacterial functional amyloid requires a specialized outer-membrane protein channel through which unfolded amyloid substrates are translocated. We previously reported the crystal structure of the membrane-spanning domain of the amyloid subunit transporter FapF from Pseudomonas. However, the structure of the periplasmic domain, which is essential for amyloid transport, is yet to be determined. Here, we present the crystal structure of the N-terminal periplasmic domain at 1.8-Å resolution. This domain forms a novel asymmetric trimeric coiled coil that possesses a single buried tyrosine residue as well as an extensive hydrogen-bonding network within a glutamine layer. This new structural insight allows us to understand this newly described functional amyloid secretion system in greater detail.

Ecology and Biogenesis of Functional Amyloids in Pseudomonas

Functional amyloids can be found in the extracellular matrix produced by many bacteria during biofilm growth. They mediate the initial attachment of bacteria to surfaces and provide stability and functionality to mature biofilms. Efficient amyloid biogenesis requires a highly coordinated system of amyloid subunits, molecular chaperones and transport systems. The functional amyloid of Pseudomonas (Fap) represents such a system. Here, we review the phylogenetic diversification of the Fap system, its potential ecological role and the dedicated machinery required for Fap biogenesis, with a particular focus on the amyloid exporter FapF, the structure of which has been recently resolved. We also present a sequence covariance-based in silico model of the FapC fiber-forming subunit. Finally, we highlight key questions that remain unanswered and we believe deserve further attention by the scientific community.

In-silico screening and experimental validation reveal L-Adrenaline as anti-biofilm molecule against biofilm-associated protein (Bap) producing Acinetobacter baumannii

Acinetobacter baumannii, an ESKAPE pathogen, causes various nosocomial infections and has capacity to produce biofilm. Biofilm produced by this bacterium is highly tolerant to environmental factors and different antibiotics. Biofilm-associated protein (Bap) plays a significant role in the biofilm formation by A. baumannii and found in the extra cellular matrix of the biofilm. Therefore, it becomes essential to find a potential drug against Bap that has capacity to inhibit biofilm formation by A. baumannii. In-silico screening, molecular mechanics and molecular dynamics studies identified ZINC00039089 (L-Adrenaline) as an inhibitor for Bap of A. baumannii. Recently, it is reported that Bap can form amyloid like structure; hence we have created dimer of Bap protein. This inhibitor can bind to dimeric Bap with good affinity. It confirms that ZINC00039089 (L-Adrenaline) can bind with Bap monomer as well as oligomeric Bap, responsible for amyloid formation and biofilm formation. Hence, we have tested Adrenaline as an anti-biofilm molecule and determined its IC₅₀ value against biofilm. The result showed Adrenaline has anti-biofilm activity with IC₅₀ value of 75μg/ml. Therefore; our finding suggests that L-Adrenaline can be developed to inhibit biofilm formation by carbapenem resistant strain of Acinetobacter baumannii.

Nucleation and growth of a bacterial functional amyloid at single-fiber resolution

Curli are functional amyloids produced by proteobacteria like Escherichia coli as part of the extracellular matrix that holds cells together into biofilms. The molecular events that occur during curli nucleation and fiber extension remain largely unknown. Combining observations from curli amyloidogenesis in bulk solutions with real-time in situ nanoscopic imaging at the single-fiber level, we show that curli display polar growth, and we detect two kinetic regimes of fiber elongation. Single fibers exhibit stop-and-go dynamics characterized by bursts of steady-state growth alternated with periods of stagnation. At high subunit concentrations, fibers show constant, unperturbed burst growth. Curli follow a one-step nucleation process in which monomers contemporaneously fold and oligomerize into minimal fiber units that have growth characteristics identical to those of the mature fibrils. Kinetic data and interaction studies of curli fibrillation in the presence of the natural inhibitor CsgC show that the inhibitor binds curli fibers and predominantly acts at the level of fiber elongation.