Regulating exopolysaccharide gene wcaF allows control of Escherichia coli biofilm formation

Targeting bacterial biofilm-related genes with nanoparticle-based strategies

Persistent infection caused by biofilm is an urgent in medicine that should be tackled by new alternative strategies. Low efficiency of classical treatments and antibiotic resistance are the main concerns of the persistent infection due to biofilm formation which increases the risk of morbidity and mortality. The gene expression patterns in biofilm cells differed from those in planktonic cells. One of the promising approaches against biofilms is nanoparticle (NP)-based therapy in which NPs with multiple mechanisms hinder the resistance of bacterial cells in planktonic or biofilm forms. For instance, NPs such as silver (Ag), zinc oxide (ZnO), titanium dioxide (TiO2), copper oxide (Cu), and iron oxide (Fe3O4) through the different strategies interfere with gene expression of bacteria associated with biofilm. The NPs can penetrate into the biofilm structure and affect the expression of efflux pump, quorum-sensing, and adhesion-related genes, which lead to inhibit the biofilm formation or development. Therefore, understanding and targeting of the genes and molecular basis of bacterial biofilm by NPs point to therapeutic targets that make possible control of biofilm infections. In parallel, the possible impact of NPs on the environment and their cytotoxicity should be avoided through controlled exposure and safety assessments. This study focuses on the biofilm-related genes that are potential targets for the inhibition of bacterial biofilms with highly effective NPs, especially metal or metal oxide NPs.

Enterobacterales Biofilm-Specific Genes and Antimicrobial and Anti-Inflammatory Biomarkers in the Blood of Patients with Ischemic Heart Disease

BACKGROUND

Ischemic heart disease (IHD) is the most prevalent type of cardiovascular disease. The main cause of IHD is atherosclerosis, which is a multifactorial inflammatory disease of blood vessels. Studies show that bacteria might have a significant impact on the pathogenesis of atherosclerosis and plaque rupture. This study aimed to evaluate the complexity of interactions between bacteria and the human body concerning metabolites and bacterial genes in patients with ischemic heart disease.

METHODS

Bacterial 16S rDNA and wcaF, papC, and sdhC genes were detected in whole blood using a real-time PCR methodology. An enzyme-linked immunosorbent assay was used to measure the concentration of the LL-37 protein. An analysis of ARA in blood plasma was performed.

RESULTS

Bacterial 16S rDNA was detected in 31% of the study patients, and the genes wcaF and sdhC in 20%. Enterobacterales genes were detected more frequently in patients younger than 65 years than in patients aged 65 years and older (p = 0.018) and in patients with type 2 diabetes (p = 0.048). Concentrations of the human antimicrobial peptide LL-37 and 12S-HETE concentrations were determined to be higher if patients had 16S rDNA and biofilm-specific genes.

CONCLUSIONS

The results of this study enhance the understanding that Enterobacterales bacteria may participate in the pathogenesis of atherosclerosis and IHD. Bacterial DNA and host metabolites in higher concentrations appear to be detected.

Driving forces shaping the microbial ecology in meat packing plants

Meat production is a complex system, continually receiving animals, water, air, and workers, all of which serve as carriers of bacteria. Selective pressures involved in different meat processing stages such as antimicrobial interventions and low temperatures, may promote the accumulation of certain residential microbiota in meat cutting facilities. Bacteria including human pathogens from all these sources can contaminate meat surfaces. While significant advancements have been made in enhancing hygienic standards and pathogen control measures in meat plants, resulting in a notable reduction in STEC recalls and clinical cases, STEC still stands as a predominant contributor to foodborne illnesses associated with beef and occasionally with pork. The second-and third-generation sequencing technology has become popular in microbiota related studies and provided a better image of the microbial community in the meat processing environments. In this article, we reviewed the potential factors influencing the microbial ecology in commercial meat processing facilities and conducted a meta-analysis on the microbiota data published in the last 10 years. In addition, the mechanisms by which bacteria persist in meat production environments have been discussed with a focus on the significant human pathogen E. coli O157:H7 and generic E. coli, an indicator often used for the hygienic condition in food production.

Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells

Introduction

Adherent-invasive Escherichia coli (AIEC) is strongly associated with the pathogenesis of Crohn's disease (CD). However, no molecular markers currently exist for AIEC identification. This study aimed to identify differentially expressed genes (DEGs) between AIEC and non-AIEC strains that may contribute to AIEC pathogenicity and to evaluate their utility as molecular markers.

Methods

Comparative transcriptomics was performed on two closely related AIEC/non-AIEC strain pairs during Intestine-407 cell infection. DEGs were quantified by RT-qPCR in the same RNA extracts, as well as in 14 AIEC and 23 non-AIEC strains to validate the results across a diverse strain collection. Binary logistical regression was performed to identify DEGs whose quantification could be used as AIEC biomarkers.

Results

Comparative transcriptomics revealed 67 differences in expression between the two phenotypes in the strain pairs, 50 of which (81.97%) were corroborated by RT-qPCR. When explored in the whole strain collection, 29 DEGs were differentially expressed between AIEC and non-AIEC phenotypes (p-value < 0.042), and 42 genes between the supernatant fraction of infected cell cultures and the cellular fraction containing adhered and intracellular bacteria (p-value < 0.049). Notably, six DEGs detected in the strain collection were implicated in arginine biosynthesis and five in colanic acid synthesis. Furthermore, two biomarkers based on wzb and cueR gene expression were proposed with an accuracy of ≥ 85% in our strain collection.

Discussion

This is the first transcriptomic study conducted using AIEC-infected cell cultures. We have identified several genes that may be involved in AIEC pathogenicity, two of which are putative biomarkers for identification.

Advances in mechanisms and engineering of electroactive biofilms

Electroactive biofilms (EABs) are electroactive microorganisms (EAMs) encased in conductive polymers that are secreted by EAMs and formed by the accumulation and cross-linking of extracellular polysaccharides, proteins, nucleic acids, lipids, and other components. EABs are present in the form of multicellular aggregates and play a crucial role in bioelectrochemical systems (BESs) for diverse applications, including biosensors, microbial fuel cells for renewable bioelectricity production and remediation of wastewaters, and microbial electrosynthesis of valuable chemicals. However, naturally occurred EABs are severely limited owing to their low electrical conductivity that seriously restrict the electron transfer efficiency and practical applications. In the recent decade, synthetic biology strategies have been adopted to elucidate the regulatory mechanisms of EABs, and to enhance the formation and electrical conductivity of EABs. Based on the formation of EABs and extracellular electron transfer (EET) mechanisms, the synthetic biology-based engineering strategies of EABs are summarized and reviewed as follows: (i) Engineering the structural components of EABs, including strengthening the synthesis and secretion of structural elements such as polysaccharides, eDNA, and structural proteins, to improve the formation of biofilms; (ii) Enhancing the electron transfer efficiency of EAMs, including optimizing the distribution of c-type cytochromes and conducting nanowire assembly to promote contact-based EET, and enhancing electron shuttles' biosynthesis and secretion to promote shuttle-mediated EET; (iii) Incorporating intracellular signaling molecules in EAMs, including quorum sensing systems, secondary messenger systems, and global regulatory systems, to increase the electron transfer flux in EABs. This review lays a foundation for the design and construction of EABs for diverse BES applications.

Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives

Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.

Synthetic phosphoethanolamine-modified oligosaccharides reveal the importance of glycan length and substitution in biofilm-inspired assemblies

Bacterial biofilm matrices are nanocomposites of proteins and polysaccharides with remarkable mechanical properties. Efforts understanding and tuning the protein component have been extensive, whereas the polysaccharide part remained mostly overlooked. The discovery of phosphoethanolamine (pEtN) modified cellulose in E. coli biofilms revealed that polysaccharide functionalization alters the biofilm properties. To date, the pattern of pEtN cellulose and its mode of interactions with proteins remains elusive. Herein, we report a model system based on synthetic epitomes to explore the role of pEtN in biofilm-inspired assemblies. Nine pEtN-modified oligosaccharides were synthesized with full control over the length, degree and pattern of pEtN substitution. The oligomers were co-assembled with a representative peptide, triggering the formation of fibers in a length dependent manner. We discovered that the pEtN pattern modulates the adhesion of biofilm-inspired matrices, while the peptide component controls its stiffness. Unnatural oligosaccharides tune or disrupt the assembly morphology, revealing interesting targets for polysaccharide engineering to develop tunable bio-inspired materials.

Bioactive properties of ZnO nanoparticles synthesized using Cocos nucifera leaves

Biosynthesis of zinc oxide nanoparticles has been reported using Cocos nucifera leaf (CNL) extract along with estimation of their antimicrobial potential before and after calcination using different micro-organisms. UV-visible spectra of ZnO nanoparticles showed absorption maxima at 383 nm and 363 nm, respectively, with 3.237 eV and 3.416 eV, respectively, as the corresponding band gap energies. FESEM and TEM images showed spherical morphologies of ZnO nanoparticles within the size range 109-215 nm. XRD analysis confirmed the formation of hexagonal wurtzite structures. ATR-IR spectra revealed the presence of stretching vibrations of N-H, O-H, C=C, C=O and NH2 groups along with C-H and N-H deformation involving biomolecules from CNL extract responsible for reduction and stabilization of ZnO nanoparticles. Uncalcinated ZnO nanoparticles displayed antibacterial activities only against S. aureus and P. aeruginosa whereas calcinated ZnO nanoparticles did not show antibacterial activities against E. coli, S. aureus, P. aeruginosa and B. subtilis. ZnO nanoparticles were not active against Penicillium spp., Fusarium oxysporum, Aspergillus flavus, Rhizoctonia solani as well as HCT-116 cancer cells before as well as after calcination. Antimicrobial nature and biocompatibility of ZnO nanoparticles were influenced by different parameters of the nanoparticles along with micro-organisms and the human cells. Non-antimicrobial properties of ZnO nanoparticles can be treated as a pre-requisite for its biocompatibility due to its inert nature. These ZnO nanoparticles can serve a dual purpose by facilitating use as antibacterial agent against susceptible micro-organisms as well as a biocompatible carrier molecule in drug delivery applications.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-022-03110-9.

Repurposing CRISPR-Cas Systems as Genetic Tools for the Enterobacteriales

Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative "repurposing" of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses. The main objective of this review is to describe the development and current state-of-the-art use of CRISPR-Cas techniques specifically as it is applied to members of the Enterobacteriales. While many of the applications covered have been initially developed in Escherichia coli, we also highlight the potential, along with the limitations, of this technology for expanding the availability of genetic tools in less-well-characterized non-model species, including bacterial pathogens.

Microbial biofilms in biorefinery - Towards a sustainable production of low-value bulk chemicals and fuels

Harnessing the potential of biocatalytic conversion of renewable biomass into value-added products is still hampered by unfavorable process economics. This has promoted the use of biofilms as an alternative to overcome the limitations of traditional planktonic systems. In this paper, the benefits and challenges of biofilm fermentations are reviewed with a focus on the production of low-value bulk chemicals and fuels from waste biomass. Our study demonstrates that biofilm fermentations can potentially improve productivities and product yields by increasing biomass retention and allowing for continuous operation at high dilution rates. Furthermore, we show that biofilms can tolerate hazardous environments, which improve the conversion of crude biomass under substrate and product inhibitory conditions. Additionally, we present examples for the improved conversion of pure and crude substrates into bulk chemicals by mixed microbial biofilms, which can benefit from microenvironments in biofilms for synergistic multi-species reactions, and improved resistance to contaminants. Finally, we suggest the use of mathematical models as useful tools to supplement experimental insights related to the effects of physico-chemical and biological phenomena on the process. Major challenges for biofilm fermentations arise from inconsistent fermentation performance, slow reactor start-up, biofilm carrier costs and carrier clogging, insufficient biofilm monitoring and process control, challenges in reactor sterilization and scale-up, and issues in recovering dilute products. The key to a successful commercialization of the technology is likely going to be an interdisciplinary approach. Crucial research areas might include genetic engineering combined with the development of specialized biofilm reactors, biofilm carrier development, in-situ biofilm monitoring, model-based process control, mixed microbial biofilm technology, development of suitable biofilm reactor scale-up criteria, and in-situ product recovery.

Epidemiologic and molecular characterization of β-lactamase-producing multidrug-resistant uropathogenic Escherichia coli isolated from asymptomatic hospitalized patients

Uropathogenic Escherichia coli (UPECs) are the predominant cause of asymptomatic bacteriuria (ABU) and symptomatic UTI. In this study, multidrug-resistant (MDR) ABU-UPECs from hospitalized patients of Kolkata, India, were characterized with respect to their ESBL phenotype, acquisition of β-lactamase genes, mobile genetic elements (MGEs), phylotype property, ERIC-PCR profile, sequence types (STs), clonal complexes (CCs) and evolutionary and quantitative relationships and compared to the symptomatic ones to understand their epidemiology and evolutionary origin. Statistically significant incidence of ESBL producers, β-lactamase genes, MGEs and novel phylotype property (NPP) among ABU-UPECs similar to the symptomatic ones indicated the probable incidence of chromosomal plasticity on resistance gene acquisition through MGEs due to indiscriminate drug usage. ERIC-PCR typing and MLST analysis showed clonal heterogeneity and predominance of ST940 (CC448) among asymptomatic isolates akin to symptomatic ones along with the evidence of zoonotic transmissions. Minimum spanning tree analysis showed a close association between ABU-UPEC with known and unidentified STs having NPPs with isolates that belonged to phylogroups clade I, D, and B2. This is the first study that reported the occurrence of MGEs and NPPs among ABU-UPECs with the predominance of ESBL production which displayed the deleterious effect of MDR among this pathogen demanding alternative therapeutic interventions. Moreover, this study for the first time attempted to introduce a new approach to ascertain the phylotype property of unassigned UPECs. Withal, increased recognition, proper understanding and characterization of ABU-UPECs with the implementation of appropriate therapeutic measures against them when necessary are the need of the era which otherwise might lead to serious complications in the vulnerable population.

Insights into the structure of Escherichia coli outer membrane as the target for engineering microbial cell factories

Escherichia coli is generally used as model bacteria to define microbial cell factories for many products and to investigate regulation mechanisms. E. coli exhibits phospholipids, lipopolysaccharides, colanic acid, flagella and type I fimbriae on the outer membrane which is a self-protective barrier and closely related to cellular morphology, growth, phenotypes and stress adaptation. However, these outer membrane associated molecules could also lead to potential contamination and insecurity for fermentation products and consume lots of nutrients and energy sources. Therefore, understanding critical insights of these membrane associated molecules is necessary for building better microbial producers. Here the biosynthesis, function, influences, and current membrane engineering applications of these outer membrane associated molecules were reviewed from the perspective of synthetic biology, and the potential and effective engineering strategies on the outer membrane to improve fermentation features for microbial cell factories were suggested.

Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

BACKGROUND

Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules.

METHODS

To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively.

RESULTS

The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction.

CONCLUSIONS

These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

Controlling biofilms using synthetic biology approaches

Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of biofilms due to the non-growing nature of biofilm bacteria and the physical barrier provided by the extracellular matrix, eradicating biofilms is a very difficult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling biofilms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate biofilms via protein engineering of biofilm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables beneficial applications of biofilms through the production of biomaterials and patterning biofilms with specific temporal and spatial structures. Advances in synthetic biology will add novel biofilm functionalities for future therapeutic, biomanufacturing, and environmental applications.

Pyruvate Substitutions on Glycoconjugates

Glycoconjugates are the most diverse biomolecules of life. Mostly located at the cell surface, they translate into cell-specific "barcodes" and offer a vast repertoire of functions, including support of cellular physiology, lifestyle, and pathogenicity. Functions can be fine-tuned by non-carbohydrate modifications on the constituting monosaccharides. Among these modifications is pyruvylation, which is present either in enol or ketal form. The most commonly best-understood example of pyruvylation is enol-pyruvylation of N-acetylglucosamine, which occurs at an early stage in the biosynthesis of the bacterial cell wall component peptidoglycan. Ketal-pyruvylation, in contrast, is present in diverse classes of glycoconjugates, from bacteria to algae to yeast-but not in humans. Mild purification strategies preventing the loss of the acid-labile ketal-pyruvyl group have led to a collection of elucidated pyruvylated glycan structures. However, knowledge of involved pyruvyltransferases creating a ring structure on various monosaccharides is scarce, mainly due to the lack of knowledge of fingerprint motifs of these enzymes and the unavailability of genome sequences of the organisms undergoing pyruvylation. This review compiles the current information on the widespread but under-investigated ketal-pyruvylation of monosaccharides, starting with different classes of pyruvylated glycoconjugates and associated functions, leading to pyruvyltransferases, their specificity and sequence space, and insight into pyruvate analytics.

Identification of the Functional Roles of Six Key Proteins in the Biosynthesis of Enterobacteriaceae Colanic Acid

When subjected to harsh conditions such as low pH, pathogenic Escherichia coli can secrete colanic acid to establish a protective barrier between the organism and the acidic environment. The colanic acid consists of a six-sugar repeating unit polymer comprised of glucose, fucose, galactose, and glucuronic acid. The region of the E. coli genome that encodes colanic acid biosynthesis has been reported, and the first enzyme in the biosynthesis pathway has been biochemically characterized. However, the specific roles of the remaining genes required for colanic acid biosynthesis have not been identified. Here we report the in vitro reconstitution of the next six steps in the assembly of the colanic acid repeating unit. To do this, we have cloned and overexpressed each gene within the colanic acid biosynthesis operon. We then tested the activity of the protein product of these genes using high-performance liquid chromatography analysis and a fluorescent analogue of the isoprenoid anchor bactoprenyl diphospho-glucose as a starting substrate. To ensure that retention time changes were associated with varying sugar additions or modifications, we developed a liquid chromatography-mass spectrometry method for analysis of the products produced by each enzyme. We have identified the function of all but one encoded glycosyltransferase and have identified the function of two acetyltransferases. This work demonstrates the centrality of acetylation in the biosynthesis of colanic acid and provides insight into the activity of key proteins involved in the production of an important and highly conserved bacterial glycopolymer.