Molecular characterization of an ice nucleation protein variant (inaQ) from Pseudomonas syringae and the analysis of its transmembrane transport activity in Escherichia coli

Surface display provides an efficient expression system for production of recombinant proteins and bacterial whole cell biosensor in E. coli

A novel bacterial display vector based on Escherichia coli has been engineered for recombinant protein production and purification. Accordingly, a construct harboring the enhanced green fluorescent protein (EGFP) and the ice nucleation protein (INP) was designed to produce EGFP via the surface display in E. coli cells. The fusion EGFP-expressed cells were then investigated using fluorescence measurement, SDS- and native-PAGE before and after TEV protease digestion. The displayed EGFP was obtained with a recovery of 57.7 % as a single band on SDS-PAGE. Next, the efficiency of the cell surface display for mutant EGFP (EGFP S202H/Q204H) was examined in sensing copper ions. Under optimal conditions, a satisfactorily linear range for copper ions concentrations up to 10 nM with a detection limit of 0.073 nM was obtained for cell-displayed mutant EGFP (mEGFP). In the presence of bacterial cell lysates and purified mEGFP, response to copper was linear in the 2-10 nM and 0.1-2 μM concentration range, respectively, with a 1.3 nM and 0.14 μM limit of detection. The sensitivity of bacterial cell lysates and surface-displayed mEGFP in the detection of copper ions is higher than the purified mEGFP.

Probiotics in addressing heavy metal toxicities in fish farming: Current progress and perspective

Heavy metal contamination of aquatic environments adversely affects the health of aquatic organisms and consumption of fish contaminated with heavy metals poses serious health risks to humans. Among various strategies, probiotics (living microorganisms known to have beneficial effects on the host), which have been extensively applied in the aquaculture industry, could be helpful for heavy metal detoxification and remediation. Several probiotics, including Lactobacillus strains, exhibit heavy metal binding, high heavy metal tolerance, and other beneficial characteristics for the host. Notably, numerous probiotics have been reported to bind heavy metals and excrete them from the host. Various probiotic strains (Lactobacillus, Bacillus, Lactococcus, etc.) show beneficial effects in alleviating heavy metal toxicity in cultured fish species. Certain probiotic bacteria reduce the absorption and bioavailability of heavy metals by enhancing heavy metal detoxification and sequestration while preserving gut barrier function. This review summarises the toxic effects of selected heavy metals on the health of farmed fish and discusses the role of probiotic strains in remediating the consequential exposure-induced immune toxicity and oxidative stress. Moreover, we discussed the protective strategies of probiotics against heavy metal accumulation in various tissues and gut dysbiosis in fish to alleviate heavy metal toxicity in fish farming, thereby promoting a sustainable blue economy worldwide.

Exploiting bacteria for cancer immunotherapy

Immunotherapy has revolutionized the treatment of cancer but continues to be constrained by limited response rates, acquired resistance, toxicities and high costs, which necessitates the development of new, innovative strategies. The discovery of a connection between the human microbiota and cancer dates back 4,000 years, when local infection was observed to result in tumour eradication in some individuals. However, the true oncological relevance of the intratumoural microbiota was not recognized until the turn of the twentieth century. The intratumoural microbiota can have pivotal roles in both the pathogenesis and treatment of cancer. In particular, intratumoural bacteria can either promote or inhibit cancer growth via remodelling of the tumour microenvironment. Over the past two decades, remarkable progress has been made preclinically in engineering bacteria as agents for cancer immunotherapy; some of these bacterial products have successfully reached the clinical stages of development. In this Review, we discuss the characteristics of intratumoural bacteria and their intricate interactions with the tumour microenvironment. We also describe the many strategies used to engineer bacteria for use in the treatment of cancer, summarizing contemporary data from completed and ongoing clinical trials. The work described herein highlights the potential of bacteria to transform the landscape of cancer therapy, bridging ancient wisdom with modern scientific innovation.

T6SS nuclease effectors in Pseudomonas syringae act as potent antimicrobials in interbacterial competition

Type VI secretion system (T6SS) is a potent weapon employed by various Pseudomonas species to compete with neighboring microorganisms for limited nutrients and ecological niches. However, the involvement of T6SS effectors in interbacterial competition within the phytopathogen Pseudomonas syringae remains unknown. In this study, we examined two T6SS clusters in a wild-type P. syringae MB03 and verified the involvement of one cluster, namely, T6SS-1, in interbacterial competition. Additionally, our results showed that two T6SS DNase effectors, specifically Tde1 and Tde4, effectively outcompeted antagonistic bacteria, with Tde4 playing a prominent role. Furthermore, we found several cognate immunity proteins, including Tde1ia, Tde1ib, and Tde4i, which are located in the downstream loci of their corresponding effector protein genes and worked synergistically to protect MB03 cells from self-intoxication. Moreover, expression of either Tde1 or C-terminus of Tde4 in Escherichia coli cells induced DNA degradation and changes in cell morphology. Thus, our results provide new insights into the role of the T6SS effectors of P. syringae in the interbacterial competition in the natural environment.

IMPORTANCE

The phytopathogen Pseudomonas syringae employs an active type VI secretion system (T6SS) to outcompete other microorganisms in the natural environment, particularly during the epiphytic growth in the phyllosphere. By examining two T6SS clusters in P. syringae MB03, T6SS-1 is found to be effective in killing Escherichia coli cells. We highlight the excellent antibacterial effect of two T6SS DNase effectors, namely, Tde1 and Tde4. Both of them function as nuclease effectors, leading to DNA degradation and cell filamentation in prey cells, ultimately resulting in cell death. Our findings deepen our understanding of the T6SS effector repertoires used in P. syringae and will facilitate the development of effective antibacterial strategies.

Nematicidal activity and action mode of a methyl-accepting chemotaxis protein from Pseudomonas syringae against Caenorhabditis elegans

The conventional phytopathogen Pseudomonas syringae reportedly possesses several virulence determinants against Caenorhabditis elegans; however, their action mechanisms remain elusive. This study reports the nematicidal activity and action receptor of a methyl-accepting chemotaxis protein (MCP03) of a wild-type P. syringae MB03 against C. elegans. Purified MCP03 exhibited nematicidal toxicity against C. elegans at a half-lethal concentration of 124.4 μg mL-1, alongside detrimental effects on the growth and brood size of C. elegans. Additionally, MCP03-treated worms exhibited severe pathological destruction of the intestine and depressed wrinkles of the cuticle. Yeast two-hybrid assays identified a subunit of COP9 signalosome, namely CSN-5, which functioned as an MCP03 action receptor. In vitro pull-down verified the binding interaction between MCP03 and CSN-5. RNA interference assays confirmed that MCP03 antagonizes CSN-5, thereby adversely affecting the brood size and cuticle integrity of C. elegans. Following MCP03 infection, the expression of genes related to reproduction, growth, and cuticle formation, such as kgb-1, unc-98, and col-117, was considerably downregulated, indicating pathological changes in MCP03-treated nematodes. Therefore, we proposed that MCP03 antagonizes CSN-5, causing lethality as well as detrimental effects on the fertility, growth, and morphogenesis of C. elegans, which can provide new insights into the signaling pathways and mechanisms underlying the nematicidal action of MCP03 toward C. elegans.

Aeromicrobiology: A global review of the cycling and relationships of bioaerosols with the atmosphere

Airborne microorganisms and biological matter (bioaerosols) play a key role in global biogeochemical cycling, human and crop health trends, and climate patterns. Their presence in the atmosphere is controlled by three main stages: emission, transport, and deposition. Aerial survival rates of bioaerosols are increased through adaptations such as ultra-violet radiation and desiccation resistance or association with particulate matter. Current research into modern concerns such as climate change, global gene transfer, and pathogenicity often neglects to consider atmospheric involvement. This comprehensive review outlines the transpiring of bioaerosols across taxa in the atmosphere, with significant focus on their interactions with environmental elements including abiotic factors (e.g., atmospheric composition, water cycle, and pollution) and events (e.g., dust storms, hurricanes, and wildfires). The aim of this review is to increase understanding and shed light on needed research regarding the interplay between global atmospheric phenomena and the aeromicrobiome. The abundantly documented bacteria and fungi are discussed in context of their cycling and human health impacts. Gaps in knowledge regarding airborne viral community, the challenges and importance of studying their composition, concentrations and survival in the air are addressed, along with understudied plant pathogenic oomycetes, and archaea cycling. Key methodologies in sampling, collection, and processing are described to provide an up-to-date picture of ameliorations in the field. We propose optimization to microbiological methods, commonly used in soil and water analysis, that adjust them to the context of aerobiology, along with other directions towards novel and necessary advancements. This review offers new perspectives into aeromicrobiology and calls for advancements in global-scale bioremediation, insights into ecology, climate change impacts, and pathogenicity transmittance.

Ice nucleation proteins self-assemble into large fibres to trigger freezing at near 0 °C

In nature, frost can form at a few degrees below 0 °C. However, this process requires the assembly of tens of thousands of ice-like water molecules that align together to initiate freezing at these relatively high temperatures. Water ordering on this scale is mediated by the ice nucleation proteins (INPs) of common environmental bacteria like Pseudomonas syringae and Pseudomonas borealis. However, individually, these 100 kDa proteins are too small to organize enough water molecules for frost formation, and it is not known how giant, megadalton-sized multimers, which are crucial for ice nucleation at high sub-zero temperatures, form. The ability of multimers to self-assemble was suggested when the transfer of an INP gene into Escherichia coli led to efficient ice nucleation. Here, we demonstrate that a positively charged subdomain at the C-terminal end of the central β-solenoid of the INP is crucial for multimerization. Truncation, relocation, or change of the charge of this subdomain caused a catastrophic loss of ice nucleation ability. Cryo-electron tomography of the recombinant E. coli showed that the INP multimers form fibres that are ~5 nm across and up to 200 nm long. A model of these fibres as an overlapping series of antiparallel dimers can account for all their known properties and suggests a route to making cell-free ice nucleators for biotechnological applications.

Ice nucleation proteins self-assemble into large fibres to trigger freezing at near 0 °C

In nature, frost can form at a few degrees below 0 °C. However, this process requires the assembly of tens of thousands of ice-like water molecules that align together to initiate freezing at these relatively high temperatures. Water ordering on this scale is mediated by the ice nucleation proteins of common environmental bacteria like Pseudomonas syringae and P. borealis. However, individually, these 100-kDa proteins are too small to organize enough water molecules for frost formation, and it is not known how giant, megadalton-sized multimers, which are crucial for ice nucleation at high sub-zero temperatures, form. The ability of multimers to self-assemble was suggested when the transfer of an ice nucleation protein gene into Escherichia coli led to efficient ice nucleation. Here we demonstrate that a positively-charged sub-domain at the C-terminal end of the central beta-solenoid of the ice nucleation protein is crucial for multimerization. Truncation, relocation, or change of the charge of this subdomain caused a catastrophic loss of ice nucleation ability. Cryo-electron tomography of the recombinant E. coli showed that the ice nucleation protein multimers form fibres that are ~ 5 nm across and up to 200 nm long. A model of these fibres as an overlapping series of antiparallel dimers can account for all their known properties and suggests a route to making cell-free ice nucleators for biotechnological applications.

Detection, Diagnosis, and Preventive Management of the Bacterial Plant Pathogen Pseudomonas syringae

Plant diseases caused by the pathogen Pseudomonas syringae are serious problems for various plant species worldwide. Accurate detection and diagnosis of P. syringae infections are critical for the effective management of these plant diseases. In this review, we summarize the current methods for the detection and diagnosis of P. syringae, including traditional techniques such as culture isolation and microscopy, and relatively newer techniques such as PCR and ELISA. It should be noted that each method has its advantages and disadvantages, and the choice of each method depends on the specific requirements, resources of each laboratory, and field settings. We also discuss the future trends in this field, such as the need for more sensitive and specific methods to detect the pathogens at low concentrations and the methods that can be used to diagnose P. syringae infections that are co-existing with other pathogens. Modern technologies such as genomics and proteomics could lead to the development of new methods of highly accurate detection and diagnosis based on the analysis of genetic and protein markers of the pathogens. Furthermore, using machine learning algorithms to analyze large data sets could yield new insights into the biology of P. syringae and novel diagnostic strategies. This review could enhance our understanding of P. syringae and help foster the development of more effective management techniques of the diseases caused by related pathogens.

Functionalization of OMVs for Biocatalytic Applications

Outer membrane vesicles (OMVs) are miniature versions of gram-negative bacteria that contain almost the same content as their parent cells, particularly in terms of membrane composition. Using OMVs as biocatalysts is a promising approach due to their potential benefits, including their ability to be handled similarly to bacteria while lacking potentially pathogenic organisms. To employ OMVs as biocatalysts, they must be functionalized with immobilized enzymes to the OMV platform. Various enzyme immobilization techniques are available, including surface display and encapsulation, each with advantages and disadvantages depending on the objectives. This review provides a concise yet comprehensive overview of these immobilization techniques and their applications in utilizing OMVs as biocatalysts. Specifically, we discuss the use of OMVs in catalyzing the conversion of chemical compounds, their role in polymer degradation, and their performance in bioremediation.

Life Cycle Assessment of Functionalized Bionanocompounds with Ice Nucleation Protein for Freezing Applications

The objective of this study was to assess the effectiveness of functionalized bionanocompounds with ice nucleation protein (INP) as a novel approach for freezing applications in terms of how much energy is used during each step of freezing when water bionanocompound solutions were compared with pure water. According to the results of the manufacturing analysis, water required 28 times less energy than the silica + INA bionanocompound and 14 times less than the magnetite + INA bionanocompound. These findings showed that water used the least energy during the manufacturing process. In order to determine the associated environmental implications, an analysis of the operating stage was also conducted, taking the defrosting time of each bionanocompound during a 4 h work cycle into account. Our results showed that bionanocompounds may substantially reduce the environmental effects by achieving a 91% reduction in the impact after their use during all four work cycles in the operation stage. Additionally, given the energy and raw materials needed in this process, this improvement was more significant than at the manufacturing stage. The results from both stages indicated that, when compared with water, the magnetite + INA bionanocompound and the silica + INA bionanocompound would save an estimated 7% and 47% of total energy, respectively. The study’s findings also demonstrated the great potential for using bionanocompounds in freezing applications to reduce the effects on the environment and human health.

Water-organizing motif continuity is critical for potent ice nucleation protein activity

Bacterial ice nucleation proteins (INPs) can cause frost damage to plants by nucleating ice formation at high sub-zero temperatures. Modeling of Pseudomonas borealis INP by AlphaFold suggests that the central domain of 65 tandem sixteen-residue repeats forms a beta-solenoid with arrays of outward-pointing threonines and tyrosines, which may organize water molecules into an ice-like pattern. Here we report that mutating some of these residues in a central segment of P. borealis INP, expressed in Escherichia coli, decreases ice nucleation activity more than the section’s deletion. Insertion of a bulky domain has the same effect, indicating that the continuity of the water-organizing repeats is critical for optimal activity. The ~10 C-terminal coils differ from the other 55 coils in being more basic and lacking water-organizing motifs; deletion of this region eliminates INP activity. We show through sequence modifications how arrays of conserved motifs form the large ice-nucleating surface required for potency.

Ice nucleation proteins have the same tandemly arrayed water-organizing motifs seen in some antifreeze proteins, but on a larger scale. The authors show that mutation, interruption, and truncation of these arrays reduce ice nucleation activity indicating that the two protein types share a common mechanism.

RsmA3 modulates RpoS through the RetS-Gac-Rsm signaling pathway in response to H2 O2 stress in the phytopathogen Pseudomonas syringae

Reactive oxygen species are a fatal challenge to the plant pathogenic bacterium Pseudomonas syringae. In this study, we reveal that the global regulatory protein RsmA3 from the RetS-Gac/Rsm signaling pathway modulates RpoS in the early-log growth phase in the P. syringae wild-type strain MB03, thereby regulating oxidative tolerance to H₂ O₂ and ultimately affecting pathogenicity to the host plant. Following increased H₂ O₂ by external addition or endogenous induction by menadione, the resistance of the mutant strain ΔretS to H₂ O₂ is significantly enhanced due to rapid increases in the transcription of Rsm-related non-coding small RNAs (nc sRNAs), a sigma factor RpoS, and H₂ O₂ -detoxifying enzymes. Moreover, the ΔretS mutant is significantly less pathogenic in cucumber leaves. Seven Rsm-related nc sRNAs (namely, rsmZ, rsmY, and rsmX_1-5 ) show functional redundancy in the RetS-Gac-Rsm signaling pathway. External addition of H₂ O₂ stimulates increases in the transcription of both rsmY and rsmZ. Thus, we propose a regulatory model of the RetS-Gac-Rsm signaling pathway in P. syringae MB03 for the regulation of H₂ O₂ tolerance and phytopathogenicity in the host plant.

Nematicidal effects of a peptidase (NlpC/P60) from the phytopathogen Pseudomonas syringae MB03 on the model nematode Caenorhabditis elegans and plant-parasitic Meloidogyne incognita

BACKGROUND

Plant-parasitic nematodes (PPNs) are severe threats to agricultural yields and continue to be challenging to treat in several crops worldwide. Microbial-based control has been suggested as a better alternative to chemical control. In this study, we aimed to identify and characterize nematicidal virulence factors of a common phytopathogenic bacterium, Pseudomonas syringae, mainly focusing on the nematicidal and suppressive activities of an NlpC/P60 family peptidase, namely, Peptidase03, against the model nematode Caenorhabditis elegans and an agriculturally important PPN, Meloidogyne incognita.

METHODS AND RESULTS

Genome-wide virulence factor prediction of the P. syringae wild-type strain MB03 revealed numerous nematode pathogenic determinants. We selected 11 predicted nematicidal genes for cloning and induced expression in an Escherichia coli expression system and then performed comparative nematicidal bioassays on the model nematode C. elegans. The recombinant strain expressing Peptidase03 showed the highest level of toxicity against C. elegans, with 75.9% mortality, compared to the other tested strains. Purified Peptidase03 showed significant toxicity against C. elegans and M. incognita, with half lethal concentration (LC50) values of 147.9 µg/mL and 211.50 µg/mL, respectively. We also demonstrated that Peptidase03 could damage the intestinal tissues of C. elegans and exhibit detrimental effects on its growth, brood size, and locomotion.

CONCLUSIONS

The Peptidase03 protein from P. syringae MB03 had significant nematicidal and suppressive activities against C. elegans and M. incognita, thereby showing potential for the development of an effective PPN-controlling agent for use in agricultural practice.

Identification of the Genes of the Plant Pathogen Pseudomonas syringae MB03 Required for the Nematicidal Activity Against Caenorhabditis elegans Through an Integrated Approach

Nematicidal potential of the common plant pathogen Pseudomonas syringae has been recently identified against Caenorhabditis elegans. The current study was designed to investigate the detailed genetic mechanism of the bacterial pathogenicity by applying comparative genomics, transcriptomics, mutant library screening, and protein expression. Results showed that P. syringae strain MB03 could kill C. elegans in the liquid assay by gut colonization. The genome of P. syringae MB03 was sequenced and comparative analysis including multi locus sequence typing, and genome-to-genome distance placed MB03 in phylogroup II of P. syringae. Furthermore, comparative genomics of MB03 with nematicidal strains of Pseudomonas aeruginosa (PAO1 and PA14) predicted 115 potential virulence factors in MB03. However, genes for previously reported nematicidal metabolites, such as phenazine, pyochelin, and pyrrolnitrin, were found absent in the MB03 genome. Transcriptomics analysis showed that the growth phase of the pathogen considerably affected the expression of virulence factors, as genes for the flagellum, glutamate ABC transporter, phoP/phoQ, fleS/fleR, type VI secretion system, and serralysin were highly up-regulated when stationary phase MB03 cells interacted with C. elegans. Additionally, screening of a transposon insertion mutant library led to the identification of other nematicidal genes such as acnA, gltP, oprD, and zapE. Finally, the nematicidal activity of selected proteins was confirmed by heterologous expression in Escherichia coli.

Life from a Snowflake: Diversity and Adaptation of Cold-Loving Bacteria among Ice Crystals

Incredible as it is, researchers have now the awareness that even the most extreme environment includes special habitats that host several forms of life. Cold environments cover different compartments of the cryosphere, as sea and freshwater ice, glaciers, snow, and permafrost. Although these are very particular environmental compartments in which various stressors coexist (i.e., freeze–thaw cycles, scarce water availability, irradiance conditions, and poorness of nutrients), diverse specialized microbial communities are harbored. This raises many intriguing questions, many of which are still unresolved. For instance, a challenging focus is to understand if microorganisms survive trapped frozen among ice crystals for long periods of time or if they indeed remain metabolically active. Likewise, a look at their site-specific diversity and at their putative geochemical activity is demanded, as well as at the equally interesting microbial activity at subzero temperatures. The production of special molecules such as strategy of adaptations, cryoprotectants, and ice crystal-controlling molecules is even more intriguing. This paper aims at reviewing all these aspects with the intent of providing a thorough overview of the main contributors in investigating the microbial life in the cryosphere, touching on the themes of diversity, adaptation, and metabolic potential.

An Escherichia coli carrier vaccine with surface-displayed protein MAP3061c elicits protective immunity against Mycobacterium paratuberculosis in mice

Johne's disease, or paratuberculosis, is a chronic granulomatous enteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). This disease occurs worldwide and results in considerable economic losses in the livestock industry. There are no effective treatments for Johne's disease, so there is an urgent need to develop an efficient, economical, and stable vaccine for MAP control. Here, a live Escherichia coli (E. coli) surface display vaccine harboring the MAP3061c gene was developed through an ice nucleation protein (INP) surface display system. The experimental data demonstrated that MAP3061c has strong immunogenicity and that the surface displayed vaccine can stimulate mice to produce high levels of antibodies. Both CD4⁺ and CD8⁺ T cell counts as well as several cytokines - including IFN-γ, IL-4, IL-10, IL-17A and IL-23 - were significantly increased in the display vaccine group. Post-vaccination challenge with MAP in mice resulted in improved fitness of the mice as demonstrated by a lack of weight loss. Pathological results revealed that the surface display vaccine could reduce the degree of pathological damage and slowed the course of disease. Taken together, our data suggests that the E. coli carrier vaccine with surface-displayed MAP3061c elicits protective immunity against MAP, providing new insights into the development of a MAP vaccine.

Nematicidal effects of 2-methyl-aconitate isomerase from the phytopathogen Pseudomonas syringae MB03 on the model nematode Caenorhabditis elegans

The pathogenicity of a common phytopathogenic bacterium, Pseudomonas syringae, against animal model hosts, such as mice and Caenorhabditis elegans, has been recently revealed. However, most of the virulence determinants associated with pathogenesis remain elusive. In the current study, we performed predictive analysis of virulence factors against C. elegans in the genome of the wild-type P. syringae strain MB03. Nine predicted nematicidal proteins were expressed and purified in recombinant Escherichia coli strains and were evaluated to define their toxicity against C. elegans in liquid killing assays. Next, we focused on one essential 2-methyl citrate cycle protein, PrpF03, which showed the highest lethal activity against C. elegans compared to the other tested proteins with a half lethal concentration (LC₅₀) of 155.3 (123.4-176.6) µg mL^-1 and a half lethal time (LT₅₀) of 3.72 (1.64-4.85) days. Purified PrpF03 also caused adverse effects on the brood size, growth, and motility of C. elegans. Moreover, the PrpF03 protein exhibited pathological activity towards the intestinal tract of C. elegans. We surmise that the PrpF03 protein functions as a virulence factor when it blocks the average circulation of the 2-methyl citrate cycle of C. elegans by accumulating 2-methyl citrate in the gut of C. elegans, which damages and restrains the growth of intestinal tissues that ultimately kill C. elegans. The discovery of specific nematicidal activities of PrpF03 provides a better understanding of the mechanisms of phytopathogenic P. syringae against nematodes and could aid in developing nematode pest-controlling agents in agriculture.

alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria

Alfalfa has emerged as one of the most important forage crops, owing to its wide adaptation and high biomass production worldwide. In the last decade, the emergence of bacterial stem blight (caused by Pseudomonas syringae pv. syringae ALF3) in alfalfa has caused around 50% yield losses in the United States. Studies are being conducted to decipher the roles of the key genes and pathways regulating the disease, but due to the sparse knowledge about the infection mechanisms of Pseudomonas, the development of resistant cultivars is hampered. The database alfaNET is an attempt to assist researchers by providing comprehensive Pseudomonas proteome annotations, as well as a host–pathogen interactome tool, which predicts the interactions between host and pathogen based on orthology. alfaNET is a user-friendly and efficient tool and includes other features such as subcellular localization annotations of pathogen proteins, gene ontology (GO) annotations, network visualization, and effector protein prediction. Users can also browse and search the database using particular keywords or proteins with a specific length. Additionally, the BLAST search tool enables the user to perform a homology sequence search against the alfalfa and Pseudomonas proteomes. With the successful implementation of these attributes, alfaNET will be a beneficial resource to the research community engaged in implementing molecular strategies to mitigate the disease. alfaNET is freely available for public use at http://bioinfo.usu.edu/alfanet/.

Gut Escherichia coli expressing Pb2+-adsorption protein reduces lead accumulation in grass carp, Ctenopharyngodon idellus

Lead (Pb²⁺) is easy to accumulate in fish which become a major source of Pb²⁺ exposure to humans. In this study, a recombinant Escherichia coli strain expressing Pb²⁺-specific surface-binding protein anchored by the ice nucleation protein was introduced into grass carp (Ctenopharyngodon idellus) gut to investigate its protective effect against dietary Pb²⁺ exposure. Pb²⁺ mostly precipitated on the surface of the engineered strain through Pb²⁺-specific surface-binding protein, with a maximum adsorption efficiency of 73% and an adsorption capacity of 163 μmol/g dry cells. The Pb²⁺ concentration in engineered bacteria-fed grass carp was reduced significantly, and the residual level of Pb²⁺ in feces was increased by 76%, compared with the control group. Meantime, the engineered bacteria were able to mitigate the oxidative stress and histological alterations of intestines and dysbiosis of gut microbiota induced by Pb²⁺exposure. Thus, the engineered bacterium that can effectively reduce Pb²⁺ residue in grass carp might be a useful tool for decontamintion of lead in aquatic organisms.

A Microfluidic Device for Automated High Throughput Detection of Ice Nucleation of Snomax®

Measurement of ice nucleation (IN) temperature of liquid solutions at sub-ambient temperatures has applications in atmospheric, water quality, food storage, protein crystallography and pharmaceutical sciences. Here we present details on the construction of a temperature-controlled microfluidic platform with multiple individually addressable temperature zones and on-chip temperature sensors for high-throughput IN studies in droplets. We developed, for the first time, automated droplet freezing detection methods in a microfluidic device, using a deep neural network (DNN) and a polarized optical method based on intensity thresholding to classify droplets without manual counting. This platform has potential applications in continuous monitoring of liquid samples consisting of aerosols to quantify their IN behavior, or in checking for contaminants in pure water. A case study of the two detection methods was performed using Snomax® (Snomax International, Englewood, CO, USA), an ideal ice nucleating particle (INP). Effects of aging and heat treatment of Snomax® were studied with Fourier transform infrared (FTIR) spectroscopy and a microfluidic platform to correlate secondary structure change of the IN protein in Snomax® to IN temperature. It was found that aging at room temperature had a mild impact on the ice nucleation ability but heat treatment at 95 °C had a more pronounced effect by reducing the ice nucleation onset temperature by more than 7 °C and flattening the overall frozen fraction curve. Results also demonstrated that our setup can generate droplets at a rate of about 1500/min and requires minimal human intervention for DNN classification.

Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water

Ice-nucleation active (INA) bacteria can promote the growth of ice more effectively than any other known material. Using specialized ice-nucleating proteins (INPs), they obtain nutrients from plants by inducing frost damage and, when airborne in the atmosphere, they drive ice nucleation within clouds, which may affect global precipitation patterns. Despite their evident environmental importance, the molecular mechanisms behind INP-induced freezing have remained largely elusive. We investigate the structural basis for the interactions between water and the ice-nucleating protein InaZ from the INA bacterium Pseudomonas syringae. Using vibrational sum-frequency generation (SFG) and two-dimensional infrared spectroscopy, we demonstrate that the ice-active repeats of InaZ adopt a β-helical structure in solution and at water surfaces. In this configuration, interaction between INPs and water molecules imposes structural ordering on the adjacent water network. The observed order of water increases as the interface is cooled to temperatures close to the melting point of water. Experimental SFG data combined with molecular-dynamics simulations and spectral calculations show that InaZ reorients at lower temperatures. This reorientation can enhance water interactions, and thereby the effectiveness of ice nucleation.

Ice-nucleating proteins promote ice formation at high sub-zero temperatures, but the mechanism is still unclear. The authors investigate a model ice-nucleating protein at the air-water interface using vibrational sum frequency generation spectroscopy and simulations, revealing its reorientation at low temperatures, which increases contact with water molecules and promotes their ordering.

Decorating the surface of Escherichia coli with bacterial lipoproteins: a comparative analysis of different display systems

Background

The display of recombinant proteins on cell surfaces has a plethora of applications including vaccine development, screening of peptide libraries, whole-cell biocatalysts and biosensor development for diagnostic, industrial or environmental purposes. In the last decades, a wide variety of surface display systems have been developed for the exposure of recombinant proteins on the surface of Escherichia coli, such as autotransporters and outer membrane proteins.

Results

In this study, we assess three approaches for the surface display of a panel of heterologous and homologous mature lipoproteins in E. coli: four from Neisseria meningitidis and four from the host strain that are known to be localised in the inner leaflet of the outer membrane. Constructs were made carrying the sequences coding for eight mature lipoproteins, each fused to the delivery portion of three different systems: the autotransporter adhesin involved in diffuse adherence-I (AIDA-I) from enteropathogenic E. coli, the Lpp’OmpA chimaera and a truncated form of the ice nucleation protein (INP), InaK-NC (N-terminal domain fused with C-terminal one) from Pseudomonas syringae. In contrast to what was observed for the INP constructs, when fused to the AIDA-I or Lpp’OmpA, most of the mature lipoproteins were displayed on the bacterial surface both at 37 and 25 °C as demonstrated by FACS analysis, confocal and transmission electron microscopy.

Conclusions

To our knowledge this is the first study that compares surface display systems using a number of passenger proteins. We have shown that the experimental conditions, including the choice of the carrier protein and the growth temperature, play an important role in the translocation of mature lipoproteins onto the bacterial surface. Despite all the optimization steps performed with the InaK-NC anchor motif, surface exposure of the passenger proteins used in this study was not achieved. For our experimental conditions, Lpp’OmpA chimaera has proved to be an efficient surface display system for the homologous passenger proteins although cell lysis and phenotype heterogeneity were observed. Finally, AIDA-I was found to be the best surface display system for mature lipoproteins (especially heterologous ones) in the E. coli host strain with no inhibition of growth and only limited phenotype heterogeneity.

Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop

Medicago sativa (also known as alfalfa), a forage legume, is widely cultivated due to its high yield and high-value hay crop production. Infectious diseases are a major threat to the crops, owing to huge economic losses to the agriculture industry, worldwide. The protein-protein interactions (PPIs) between the pathogens and their hosts play a critical role in understanding the molecular basis of pathogenesis. Pseudomonas syringae pv. syringae ALF3 suppresses the plant's innate immune response by secreting type III effector proteins into the host cell, causing bacterial stem blight in alfalfa. The alfalfa-P. syringae system has little information available for PPIs. Thus, to understand the infection mechanism, we elucidated the genome-scale host-pathogen interactions (HPIs) between alfalfa and P. syringae using two computational approaches: interolog-based and domain-based method. A total of ∼14 M putative PPIs were predicted between 50,629 alfalfa proteins and 2,932 P. syringae proteins by combining these approaches. Additionally, ∼0.7 M consensus PPIs were also predicted. The functional analysis revealed that P. syringae proteins are highly involved in nucleotide binding activity (GO:0000166), intracellular organelle (GO:0043229), and translation (GO:0006412) while alfalfa proteins are involved in cellular response to chemical stimulus (GO:0070887), oxidoreductase activity (GO:0016614), and Golgi apparatus (GO:0005794). According to subcellular localization predictions, most of the pathogen proteins targeted host proteins within the cytoplasm and nucleus. In addition, we discovered a slew of new virulence effectors in the predicted HPIs. The current research describes an integrated approach for deciphering genome-scale host-pathogen PPIs between alfalfa and P. syringae, allowing the researchers to better understand the pathogen's infection mechanism and develop pathogen-resistant lines.

Pyoverdine-Mediated Killing of Caenorhabditis elegans by Pseudomonas syringae MB03 and the Role of Iron in Its Pathogenicity

The pathogenicity of the common phytopathogenic bacterium Pseudomonas syringae toward Caenorhabditis elegans has been recently demonstrated. However, the major virulence factors involved in this interaction remain unknown. In this study, we investigated the nematocidal activity of P. syringae against C. elegans under iron-sufficient/limited conditions, primarily focusing on the role of the ferric chelator pyoverdine in a P. syringae–C. elegans liquid-based pathogenicity model. Prediction-based analysis of pyoverdine-encoding genes in the genome of the wild-type P. syringae strain MB03 revealed that the genes are located in one large cluster. Two non-ribosomal peptide synthetase genes (pvdD and pvdJ) were disrupted via a Rec/TE recombination system, resulting in mutant strains with abrogated pyoverdine production and attenuated virulence against C. elegans. When used alone, pure pyoverdine also showed nematocidal activity. The role of iron used alone or with pyoverdine was further investigated in mutant and MB03-based bioassays. The results indicated that pyoverdine in P. syringae MB03 is a robust virulence factor that promotes the killing of C. elegans. We speculate that pyoverdine functions as a virulence determinant by capturing environmentally available iron for host bacterial cells, by limiting its availability for C. elegans worms, and by regulating and/or activating other intracellular virulence factors that ultimately kills C. elegans worms.

Ice Binding Proteins: Diverse Biological Roles and Applications in Different Types of Industry

More than 80% of Earth’s surface is exposed periodically or continuously to temperatures below 5 °C. Organisms that can live in these areas are called psychrophilic or psychrotolerant. They have evolved many adaptations that allow them to survive low temperatures. One of the most interesting modifications is production of specific substances that prevent living organisms from freezing. Psychrophiles can synthesize special peptides and proteins that modulate the growth of ice crystals and are generally called ice binding proteins (IBPs). Among them, antifreeze proteins (AFPs) inhibit the formation of large ice grains inside the cells that may damage cellular organelles or cause cell death. AFPs, with their unique properties of thermal hysteresis (TH) and ice recrystallization inhibition (IRI), have become one of the promising tools in industrial applications like cryobiology, food storage, and others. Attention of the industry was also caught by another group of IBPs exhibiting a different activity—ice-nucleating proteins (INPs). This review summarizes the current state of art and possible utilizations of the large group of IBPs.

An AGT-based protein-tag system for the labelling and surface immobilization of enzymes on E. coli outer membrane

The use of natural systems, such as outer membrane protein A (OmpA), phosphoporin E (PhoE), ice nucleation protein (INP), etc., has been proved very useful for the surface exposure of proteins on the outer membrane of Gram-negative bacteria. These strategies have the clear advantage of unifying in a one-step the production, the purification and the in vivo immobilisation of proteins/biocatalysts onto a specific biological support. Here, we introduce the novel Anchoring-and-Self-Labelling-protein-tag (ASLtag), which allows the in vivo immobilisation of enzymes on E. coli surface and the labelling of the neosynthesised proteins with the engineered alkylguanine-DNA-alkyl-transferase (H5) from Sulfolobus solfataricus. Our results demonstrated that this tag enhanced the overexpression of thermostable enzymes, such as the carbonic anhydrase (SspCA) from Sulfurihydrogenibium yellowstonense and the β-glycoside hydrolase (SsβGly) from S. solfataricus, without affecting their folding and catalytic activity, proposing a new tool for the improvement in the utilisation of biocatalysts of biotechnological interest.

An Effective Platform for Exploring Rotavirus Receptors by Bacterial Surface Display System

Rotavirus (RV) is a major foodborne pathogen. For RV prevention and control, it is a key to uncover the interaction mechanism between virus and its receptors. However, it is hard to specially purify the viral receptors, including histo-blood group antigens (HBGAs). Previously, the protruding domain protein (P protein) of human norovirus (genotype II.4) was displayed on the surface of Escherichia coli, and it specifically recognized and captured the viral ligands. In order to further verify the feasibility of the system, P protein was replaced by VP8* of RV (G9P[8]) in this study. In the system, VP8* could be correctly released by thrombin treatment with antigenicity retaining, which was confirmed by Western blot and Enzyme-Linked Immunosorbent Assays. Type A HBGAs from porcine gastric mucin (PGM) were recognized and captured by this system. From saliva mixture, the captured viral receptor bound with displayed VP8* was confirmed positive with monoclonal antibody against type A HBGAs. It indicated that the target ligands could be easily separated from the complex matrix. These results demonstrate that the bacterial surface display system will be an effective platform to explore viral receptors/ligands from cell lines or food matrix.

Applying<i> In Silico</i> Approaches for Designing a Chimeric InaV/N-DFPase Protein and Evaluating its Binding with Diisopropyl-Fluorophosphate

The N-terminal domain of the ice-nucleation protein InaV (InaV-N) ofPseudomonas syringaewas applied to display the DFPase on the cell surface.In silicotechniques were used to generate a model in order to examine the possibility of DFPase exhibition on the cell surface. The secondary and tertiary structures of a chimeric protein were determined and then, the predicted model was subjected to several repeated cycles of stereochemical evaluation and energy minimization. The homology-modeled structure of the InaV/N-DFPase protein was docked to DFP. The optimizedinaV/N-dfpasegene was translated to 519 amino acids. The minimum free energy of the best-predicted secondary structures was formed by RNA molecules (-215.45 kcal/mol). SOPMA analysis results showed that the main helix peak corresponded to the anchor fragment. Validation of the 3D model indicated that 86.1% of amino acid residues were incorporated into the favored regions. The moldock score was 360.22 for DFP. Results of this study indicated that according toin silicoanalysis, all of these findings were effective in targeting DFPase.

The Nif3-Family Protein YqfO03 from Pseudomonas syringae MB03 Has Multiple Nematicidal Activities against Caenorhabditis elegans and Meloidogyne incognita

The nematicidal activity of the common plant-pathogenic bacterium Pseudomonas syringae against certain nematodes has been recently identified, but little is known about its virulence factors. In the current study, predictive analysis of nematode-virulent factors in the genome of a P. syringae wild-type strain MB03 revealed a variety of factors with the potential to be pathogenic against nematodes. One of these virulence factors that was predicted with a high score, namely, YqfO03, was a protein with structural domains that are similar to the Nif3 superfamily. This protein was expressed and purified in Escherichia coli, and was investigated for nematicidal properties against the model nematode Caenorhabditis elegans and an agriculturally important pest Meloidogyne incognita. Our results showed that YqfO03 exhibits lethal activity toward C. elegans and M. incognita worms, and it also caused detrimental effects on the growth, brood size, and motility of C. elegans worms. However, C. elegans worms were able to defend themselves against YqfO03 via a physical defense response by avoiding contact with the protein. Discovery of the diverse nematicidal activities of YqfO03 provides new knowledge on the biological function of a bacterial Nif3-family protein and insight into the potential of this protein as a specific means of controlling agricultural nematode pests.

Chromosomal expression of CadR on Pseudomonas aeruginosa for the removal of Cd(II) from aqueous solutions

Genetically engineered bacteria for pollution control of heavy metal have been widely studied, however, using Pseudomonas aeruginosa (P. aeruginosa) that can adapt to various circumstances to remediate heavy metal pollution is rarely reported. In this study, we employed CadR, a cadmium (Cd)-specific binding protein, displaying on the surface of P. aeruginosa with chromosomal expression. The genetically engineered (GE) P. aeruginosa still flourished in the 30th generation in the LB broth which contained 100 μM Cd(II), exhibiting an excellent genetic stability. Chromosomally expressed P. aeruginosa showed an adsorption capacity of up to 131.9 μmol/g of Cd(II). In addition, the low concentration of the coexisting two valence ions has no significant effect on adsorption capacity of Cd(II). This study provides a direction for application of P. aeruginosa in environment remediation.

Detection of catechol using an electrochemical biosensor based on engineered Escherichia coli cells that surface-display laccase

In this study, we report an electrochemical microbial biosensor that was made by immobilizing a bacterial laccase on the surface of Escherichia coli cells followed by adsorption of modified live cells onto a glassy-carbon electrode. Expression and surface localization of laccase on target cells were confirmed by Western blotting, flow cytometry assays and immunofluorescence microscopy observation. Increased tandem-aligned anchors with three repeats of the N-terminal domain of an ice nucleation protein were used to construct a highly active E. coli whole cell laccase-based catalytic system. When the proposed biosensor was used to detect catechol, the electrochemical response under optimized pH conditions was linear within a concentration range of 0.5 μM-300.0 μM catechol. Metal ions (Mn²⁺, Fe³⁺, Cu²⁺, Mg²⁺, Al³⁺ and Zn²⁺) at concentrations from 1 to 10 mg L^-1, bovine serum albumin and glucose at concentrations from 0.1 to 10 g L^-1, and ascorbic acid at concentrations from 0.01 to 0.1 g L^-1 did not cause a noticeable interference effect. The detection limit of 0.1 μM catechol was comparable to those of other biosensors based on purified chemically modified laccases. When used to detect catechol in real red wine and tea samples, the biosensor offered a considerable level of accuracy comparable to the HPLC method as well as high recovery rates (98.2%-103.8%) towards all of the tested samples. Moreover, the developed system also exhibited high stability and reproducibility.

Bacillus Cellulase Molecular Cloning, Expression, and Surface Display on the Outer Membrane of Escherichia coli

One of the main challenges of using recombinant enzymes is that they are derived from genetically-modified microorganisms commonly located in the intracellular region. The use of these recombinant enzymes for commercial purposes requires the additional processes of cell disruption and purification, which may result in enzyme loss, denaturation, and increased total production cost. In this study, the cellulase gene of Bacillus licheniformis ATCC 14580 was cloned, over-expressed, and surface displayed in recombinant Escherichia coli using an ice-nucleation protein (INP). INP, an outer membrane-bound protein from Pseudomonas syringae, was utilized as an anchor linker, which was cloned with a foreign cellulase gene into the pET21a vector to develop a surface display system on the outer membrane of E. coli. The resulting strain successfully revealed cellulase on the host cell surface. The over-expressed INP-cellulase fusion protein was confirmed via staining assay for determining the extracellular cellulase and Western blotting method for the molecular weight (MW) of cellulase, which was estimated to be around 61.7 kDa. Cell fractionation and localization tests demonstrated that the INP-cellulase fusion protein was mostly present in the supernatant (47.5%) and outer membrane (19.4%), while the wild-type strain intracellularly retained enzymes within cytosol (>61%), indicating that the INP gene directed the cellulase expression on the bacteria cell surface. Further studies of the optimal enzyme activity were observed at 60 °C and pH 7.0, and at least 75% of maximal enzyme activity was preserved at 70 °C.

Engineered commensal microbes for diet-mediated colorectal-cancer chemoprevention

Chemoprevention-the use of medication to prevent cancer-can be augmented by the consumption of produce enriched with natural metabolites. However, chemopreventive metabolites are typically inactive and have low bioavailability and poor host absorption. Here, we show that engineered commensal microbes can prevent carcinogenesis and promote the regression of colorectal cancer through a cruciferous vegetable diet. The engineered commensal Escherichia coli bound specifically to the heparan sulphate proteoglycan on colorectal cancer cells and secreted the enzyme myrosinase to transform host-ingested glucosinolates-natural components of cruciferous vegetables-to sulphoraphane, an organic small molecule with known anticancer activity. The engineered microbes coupled with glucosinolates resulted in >95% proliferation inhibition of murine, human and colorectal adenocarcinoma cell lines in vitro. We also show that murine models of colorectal carcinoma fed with the engineered microbes and the cruciferous vegetable diet displayed significant tumour regression and reduced tumour occurrence.

A Bacterial Surface Display System Expressing Cleavable Capsid Proteins of Human Norovirus: A Novel System to Discover Candidate Receptors

Human noroviruses (HuNoVs) are the dominant cause of food-borne outbreaks of acute gastroenteritis. However, fundamental researches on HuNoVs, such as identification of viral receptors have been limited by the currently immature system to culture HuNoVs and the lack of efficient small animal models. Previously, we demonstrated that the recombinant protruding domain (P domain) of HuNoVs capsid proteins were successfully anchored on the surface of Escherichia coli BL21 cells after the bacteria were transformed with a plasmid expressing HuNoVs P protein fused with bacterial transmembrane anchor protein. The cell-surface-displayed P proteins could specifically recognize and bind to histo-blood group antigens (HBGAs, receptors of HuNoVs). In this study, an upgraded bacterial surface displayed system was developed as a new platform to discover candidate receptors of HuNoVs. A thrombin-susceptible “linker” sequence was added between the sequences of bacterial transmembrane anchor protein and P domain of HuNoV (GII.4) capsid protein in a plasmid that displays the functional P proteins on the surface of bacteria. In this new system, the surface-displayed HuNoV P proteins could be released by thrombin treatment. The released P proteins self-assembled into small particles, which were visualized by electron microscopy. The bacteria with the surface-displayed P proteins were incubated with pig stomach mucin which contained HBGAs. The bacteria-HuNoV P proteins-HBGAs complex could be collected by low speed centrifugation. The HuNoV P proteins-HBGAs complex was then separated from the recombinant bacterial surface by thrombin treatment. The released viral receptor was confirmed by using the monoclonal antibody against type A HBGA. It demonstrated that the new system was able to capture and easily isolate receptors of HuNoVs. This new strategy provides an alternative, easier approach for isolating unknown receptors/ligands of HuNoVs from different samples including mammalian cell lines, oysters, and fresh produce.

Bacterial Surface-Displayed GII.4 Human Norovirus Capsid Proteins Bound to HBGA-Like Molecules in Romaine Lettuce

Human Noroviruses (HuNoVs) are the main cause of non-bacterial gastroenteritis. Contaminated produce is a main vehicle for dissemination of HuNoVs. In this study, we used an ice nucleation protein mediated surface display system to present the protruding domain of GII.4 HuNoV capsid protein on bacterial surface and used it as a new strategy to explore interaction between HuNoV protein and receptor candidates from romaine lettuce. The surface-displayed HuNoV proteins were confirmed on the surface of the transformed bacteria by an immunofluorescence assay. The distribution patterns of the surface-displayed HuNoV proteins in romaine lettuce were identified through a confocal immunofluorescence assay. The surface-displayed HuNoV proteins could be found in the stomata, and the surfaces of vein and leaf of romaine lettuce. The surface-displayed HuNoV proteins could be captured by an ELISA assay utilizing extract from leaf (LE) or vein (VE). The binding of the surface-displayed HuNoV proteins to LE or VE could be competitively blocked by histo-blood group antigens from human saliva. In addition, the binding of the surface-displayed HuNoV proteins to LE or VE could also be attenuated by heat denaturation of lettuce proteins, and abolished by oxidation of lettuce carbohydrates. The results indicated that histo-blood group antigen-like molecules in LE or VE were involved in the binding of the surface-displayed HuNoV proteins to romaine lettuce. All data demonstrated that the surface-displayed HuNoV proteins could be utilized in a new and simple system for investigation of the interaction between the HuNoVs and their candidate ligands.

Poly-γ-glutamic acid coupled Pseudomonas putida cells surface-displaying metallothioneins: composited copper(ii) biosorption and inducible flocculation in aqueous solution

Schematic illustration of the preparation, biosorption, and induced flocculation of the biocomposite MB546-PGA.

Surface Immobilization of Human Arginase-1 with an Engineered Ice Nucleation Protein Display System in E. coli

Ice nucleation protein (INP) is frequently used as a surface anchor for protein display in gram-negative bacteria. Here, MalE and TorA signal peptides, and three charged polypeptides, 6×Lys, 6×Glu and 6×Asp, were anchored to the N-terminus of truncated INP (InaK-N) to improve its surface display efficiency for human Arginase1 (ARG1). Our results indicated that the TorA signal peptide increased the surface translocation of non-protein fused InaK-N and human ARG1 fused InaK-N (InaK-N/ARG1) by 80.7% and 122.4%, respectively. Comparably, the MalE signal peptide decreased the display efficiencies of both the non-protein fused InaK-N and InaK-N/ARG1. Our results also suggested that the 6×Lys polypeptide significantly increased the surface display efficiency of K6-InaK-N/ARG1 by almost 2-fold, while also practically abolishing the surface translocation of non-protein fused InaK-N, indicating the interesting roles of charged polypeptides in bacteria surface display systems. Cell surface-immobilized K6-InaK-N/ARG1 presented an arginase activity of 10.7 U/OD600 under the optimized conditions of 40°C, pH 10.0 and 1 mM Mn2+, which could convert more than 95% of L-Arginine (L-Arg) to L-Ornithine (L-Orn) in 16 hours. The engineered InaK-Ns expanded the INP surface display system, which aided in the surface immobilization of human ARG1 in E. coli cells.

Genome-sequence analysis of Acinetobacter johnsonii MB44 reveals potential nematode-virulent factors

Acinetobacter johnsonii is generally recognized as a nonpathogenic bacterium although it is often found in hospital environments. However, a newly identified isolate of this species from a frost-plant-tissue sample, namely, A. johnsonii MB44, showed significant nematicidal activity against the model organism Caenorhabditis elegans. To expand our understanding of this bacterial species, we generated a draft genome sequence of MB44 and analyzed its genomic features related to nematicidal attributes. The 3.36 Mb long genome contains 3636 predicted protein-coding genes and 95 RNA genes (including 14 rRNA genes), with a G + C content of 41.37 %. Genomic analysis of the prediction of nematicidal proteins using the software MP3 revealed a total of 108 potential virulence proteins. Some of these proteins were homologous to the known virulent proteins identified from Acinetobacter baumannii, a pathogenic species of the genus Acinetobacter. These virulent proteins included the outer membrane protein A, the phospholipase D, and penicillin-binding protein 7/8. Moreover, one siderophore biosynthesis gene cluster and one capsular polysaccharide gene cluster, which were predicted to be important virulence factors for C. elegans, were identified in the MB44 genome. The current study demonstrated that A. johnsonii MB44, with its nematicidal activity, could be an opportunistic pathogen to animals.

The Pathogenicity of Pseudomonas syringae MB03 against Caenorhabditis elegans and the Transcriptional Response of Nematicidal Genes upon Different Nutritional Conditions

Different species of the Pseudomonas genus have been reported for their pathogenic potential against animal cells. However, the pathogenicity of Pseudomonas syringae against Caenorhabditis elegans has never been reported. In this study, the interaction of P. syringae MB03 with C. elegans was studied. Different bioassays such as killing assay, lawn leaving assay, food preference assay, L4 growth assay and newly developed “secretion assay” were performed to evaluate the pathogenic potential of P. syringae on different growth media. The results of the killing assay showed that P. syringae MB03 was able to kill C. elegans under specific conditions, as the interaction between the host and the pathogen varied from non-pathogenic (assay on NGM medium) to pathogenic (assay on PG medium). The lawn leaving assay and the food preference assay illustrated that C. elegans identified P. syringae MB03 as a pathogen when assays were performed on PG medium. Green fluorescent protein was used as the reporter protein to study gut colonization by P. syringae MB03. Our results suggested that MB03 has the ability to colonize the gut of C. elegans. Furthermore, to probe the role of selected virulence determinants, qRT-PCR was used. The genes for pyoverdine, phoQ/phoP, phoR/phoB, and flagella were up regulated during the interaction of P. syringae MB03 and C. elegans on PG medium. Other than these, the genes for some proteases, such as pepP, clpA, and clpS, were also up regulated. On the other hand, kdpD and kdpB were down regulated more than threefold in the NGM – C. elegans interaction model. The deletion of the kdpD and kdpE genes altered the pathogenicity of the bacterial strain against C. elegans. Overall, our results suggested that the killing of C. elegans by P. syringae requires a prolonged interaction between the host and pathogen in an agar-based assay. Moreover, it seemed that some toxic metabolites were secreted by the bacterial strain that were sensed by C. elegans. Previously, it was believed that P. syringae could not damage animal cells. However, this study provides evidence of the pathogenic behavior of P. syringae against C. elegans.

Draft Genome Sequence of Acinetobacter johnsonii MB44, Exhibiting Nematicidal Activity against Caenorhabditis elegans

Acinetobacter johnsonii MB44 was isolated from a frost-plant-tissue sample, which showed noteworthy nematicidal activity against the model organism Caenorhabditis elegans. Here, we report the 3.4 Mb draft genome of A. johnsonii MB44, which will help in understanding the molecular mechanism of its ability to infect nematodes.

Engineering Bacterial Surface Displayed Human Norovirus Capsid Proteins: A Novel System to Explore Interaction Between Norovirus and Ligands

Human noroviruses (HuNoVs) are major contributors to acute nonbacterial gastroenteritis outbreaks. Many aspects of HuNoVs are poorly understood due to both the current inability to culture HuNoVs, and the lack of efficient small animal models. Surrogates for HuNoVs, such as recombinant viral like particles (VLPs) expressed in eukaryotic system or P particles expressed in prokaryotic system, have been used for studies in immunology and interaction between the virus and its receptors. However, it is difficult to use VLPs or P particles to collect or isolate potential ligands binding to these recombinant capsid proteins. In this study, a new strategy was used to collect HuNoVs binding ligands through the use of ice nucleation protein (INP) to display recombinant capsid proteins of HuNoVs on bacterial surfaces. The viral protein-ligand complex could be easily separated by a low speed centrifugation step. This system was also used to explore interaction between recombinant capsid proteins of HuNoVs and their receptors. In this system, the VP1 capsid encoding gene (ORF2) and the protruding domain (P domain) encoding gene (3′ terminal fragment of ORF2) of HuNoVs GI.1 and GII.4 were fused with 5′ terminal fragment of INP encoding gene (inaQn). The results demonstrated that the recombinant VP1 and P domains of HuNoVs were expressed and anchored on the surface of Escherichia coli BL21 cells after the bacteria were transformed with the corresponding plasmids. Both cell surface displayed VP1 and P domains could be recognized by HuNoVs specific antibodies and interact with the viral histo-blood group antigens receptors. In both cases, displayed P domains had better binding abilities than VP1. This new strategy of using displayed HuNoVs capsid proteins on the bacterial surface could be utilized to separate HuNoVs binding components from complex samples, to investigate interaction between the virus and its receptors, as well as to develop an oral vaccine for HuNoVs.

Oral immunization with recombinant hepatitis E virus antigen displayed on the Lactococcus lactis surface enhances ORF2-specific mucosal and systemic immune responses in mice

Hepatitis E virus (HEV) as a recognized zoonotic pathogen has posed global burden on public health, which is exacerbated by lack of efficient vaccine. In this study, we constructed a recombinant (inaQ-ORF2 gene fusion) Lactococcus lactis (L. lactis) strain NZ3900 that expresses and displays the hepatitis E virus antigen ORF2 utilizing an ice uncleation protein-based anchor system. After oral vaccination of BALB/c mice, significantly higher levels of ORF2-specific mucosal IgA and serum IgG were detected and cellular immunity was also induced. These findings further support that L. lactis-based HEV antigen vaccines could be used for human and animal protection against infection.

Expression and localization of an ice nucleating protein from a soil bacterium, Pseudomonas borealis

An ice nucleating protein (INP) coding region with 66% sequence identity to the INP of Pseudomonas syringae was previously cloned from P. borealis, a plant beneficial soil bacterium. Ice nucleating activity (INA) in the P. borealis DL7 strain was highest after transfer of cultures to temperatures just above freezing. The corresponding INP coding sequence (inaPb or ina) was used to construct recombinant plasmids, with recombinant expression visualized using a green fluorescent protein marker (gfp encoding GFP). Although the P. borealis strain was originally isolated by ice-affinity, bacterial cultures with membrane-associated INP-GFP did not adsorb to pre-formed ice. Employment of a shuttle vector allowed expression of ina-gfp in both Escherichia coli and Pseudomonas cells. At 27 °C, diffuse fluorescence appeared throughout the cells and was associated with low INA. However, after transfer of cultures to 4 °C, the protein localized to the poles coincident with high INA. Transformants with truncated INP sequences ligated to either gfp, or an antifreeze protein-gfp fusion showed that the repetitive ice-nucleation domain was not necessary for localization. Such localization is consistent with the flanking residues of the INP associating with a temperature-dependent secretion apparatus. A polar location would facilitate INP-INP interactions resulting in the formation of larger aggregates, serving to increase INA. Expression of INPs by P. borealis could function as an efficient atmospheric dispersal mechanism for these soil bacteria, which are less likely to use these proteins for nutrient procurement, as has been suggested for P. syringae.