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ELife Jan 2018The functions of most proteins are yet to be determined. The function of an enzyme is often defined by its interacting partners, including its substrate and product, and...
The functions of most proteins are yet to be determined. The function of an enzyme is often defined by its interacting partners, including its substrate and product, and its role in larger metabolic networks. Here, we describe a computational method that predicts the functions of orphan enzymes by organizing them into a linear metabolic pathway. Given candidate enzyme and metabolite pathway members, this aim is achieved by finding those pathways that satisfy structural and network restraints implied by varied input information, including that from virtual screening, chemoinformatics, genomic context analysis, and ligand -binding experiments. We demonstrate this integrative pathway mapping method by predicting the L-gulonate catabolic pathway in Rd KW20. The prediction was subsequently validated experimentally by enzymology, crystallography, and metabolomics. Integrative pathway mapping by satisfaction of structural and network restraints is extensible to molecular networks in general and thus formally bridges the gap between structural biology and systems biology.
Topics: Computational Biology; Enzymes; Haemophilus influenzae; Metabolic Networks and Pathways; Systems Biology
PubMed: 29377793
DOI: 10.7554/eLife.31097 -
Molecular Oral Microbiology Jun 2020Aggregatibacter actinomycetemcomitans is a Gram-negative bacterium associated with localized aggressive periodontitis, as well as other systemic diseases. This organism... (Review)
Review
Aggregatibacter actinomycetemcomitans is a Gram-negative bacterium associated with localized aggressive periodontitis, as well as other systemic diseases. This organism produces a number of virulence factors, all of which provide some advantage to the bacterium. Several studies have demonstrated that clinical isolates from diseased patients, particularly those of African descent, frequently belong to specific clones of A. actinomycetemcomitans that produce significantly higher amounts of a protein exotoxin belonging to the repeats-in-toxin (RTX) family, leukotoxin (LtxA), whereas isolates from healthy patients harbor minimally leukotoxic strains. This finding suggests that LtxA might play a key role in A. actinomycetemcomitans pathogenicity. Because of this correlation, much work over the past 30 years has been focused on understanding the mechanisms by which LtxA interacts with and kills host cells. In this article, we review those findings, highlight the remaining open questions, and demonstrate how knowledge of these mechanisms, particularly the toxin's interactions with lymphocyte function-associated antigen-1 (LFA-1) and cholesterol, enables the design of targeted anti-LtxA strategies to prevent/treat disease.
Topics: Aggregatibacter actinomycetemcomitans; Exotoxins; Humans; Lymphocyte Function-Associated Antigen-1; Virulence Factors
PubMed: 32061022
DOI: 10.1111/omi.12284 -
Scientific Reports Aug 2023Bovine respiratory disease (BRD) is a significant health issue in the North American feedlot industry, causing substantial financial losses due to morbidity and...
Bovine respiratory disease (BRD) is a significant health issue in the North American feedlot industry, causing substantial financial losses due to morbidity and mortality. A lack of effective vaccines against BRD pathogens has resulted in antibiotics primarily being used for BRD prevention. The aim of this study was to develop a mucosal vaccine against the BRD pathogen, Mannheimia haemolytica, using Bacillus subtilis spores as an adjuvant. A chimeric protein (MhCP) containing a tandem repeat of neutralizing epitopes from M. haemolytica leukotoxin A (NLKT) and outer membrane protein PlpE was expressed to produce antigen for adsorption to B. subtilis spores. Adsorption was optimized by comparing varying amounts of antigen and spores, as well as different buffer pH and reaction temperatures. Using the optimal adsorption parameters, spore-bound antigen (Spore-MhCP) was prepared and administered to mice via two mucosal routes (intranasal and intragastric), while intramuscular administration of free MhCP and unvaccinated mice were used as positive and negative control treatments, respectively. Intramuscular administration of MhCP elicited the strongest serum IgG response. However, intranasal immunization of Spore-MhCP generated the best secretory IgA-specific response against both PlpE and NLKT in all samples evaluated (bronchoalveolar lavage, saliva, and feces). Since proliferation of M. haemolytica in the respiratory tract is a prerequisite to lung infection, this spore-based vaccine may offer protection in cattle by limiting colonization and subsequent infection, and Spore-MhCP warrants further evaluation in cattle as a mucosal vaccine against M. haemolytica.
Topics: Cattle; Animals; Mice; Mannheimia haemolytica; Spores, Bacterial; Respiratory System; Bacterial Vaccines; Cattle Diseases
PubMed: 37563163
DOI: 10.1038/s41598-023-29732-4 -
TheScientificWorldJournal 2024species are frequently encountered as serious diseases in small ruminants. It is the main cause of respiratory pasteurellosis in sheep and goats of all age groups.
BACKGROUND
species are frequently encountered as serious diseases in small ruminants. It is the main cause of respiratory pasteurellosis in sheep and goats of all age groups.
METHODS
The cross-sectional study was conducted from December 2022 to April 2023 in Haramaya district, eastern Ethiopia, to isolate and identify and and estimate their prevalence, associated risk factors, and antimicrobial sensitivity of isolates in small ruminants using a purposive sampling method. A total of 384 samples (156 nasal swabs from clinic cases and 228 lung swabs from abattoir cases) were collected. STATA 14 software was used to analyze the data. In addition, multivariable logistic regression analysis was performed to assess an association of risk factors.
RESULTS
Out of the 384 samples examined, 164 were positive for pasteurellosis, resulting in a 42.70% prevalence. Similarly, 63 (38.4%) of the 164 positive results were from nasal swabs, while 101 (61.6%) came from lung samples. accounted for 126 (76.82%) of the isolates, while accounted for 38 (23.17%). Of the 63 nasal swab isolates, 33 (37%) were from goats and 30 (42.8%) were from sheep. And 17 (10.89%) and 46 (29.58%), respectively, were and . Of the 46 (40%) of the 101 (44.3%) isolates of the pneumonic lung, samples were from goats, while 55 (48.47%) were from sheep. In this study, the risk factors (species, age, and body condition score) were found to be significant ( < 0.05). isolates evaluated for antibiotic susceptibility were highly resistant to oxacillin (90.90%), followed by gentamycin (72.72%), and penicillin (63.63%). However, the isolates were highly sensitive to chloramphenicol (90.90%), followed by tetracycline (63.63%), and ampicillin (54.54%).
CONCLUSION
This study showed that and are the common causes of mannheimiosis and pasteurellosis in small ruminants, respectively, and isolates were resistant to commonly used antibiotics in the study area. Thus, an integrated vaccination strategy, antimicrobial resistance monitoring, and avoidance of stress-inducing factors are recommended.
Topics: Animals; Pasteurella multocida; Mannheimia haemolytica; Ethiopia; Sheep; Goats; Anti-Bacterial Agents; Cross-Sectional Studies; Microbial Sensitivity Tests; Sheep Diseases; Goat Diseases; Prevalence; Risk Factors; Pasteurella Infections
PubMed: 38655561
DOI: 10.1155/2024/5605552 -
Journal of Veterinary Internal Medicine May 2021Nicoletella semolina was identified in the airways of horses and its low prevalence could be because of its difficult differentiation from other Pasteurellaceae.
BACKGROUND
Nicoletella semolina was identified in the airways of horses and its low prevalence could be because of its difficult differentiation from other Pasteurellaceae.
OBJECTIVES
To develop a molecular method for the identification of N. semolina and to evaluate its prevalence in the mouth and the airways of healthy and severe asthmatic horses.
ANIMALS
Six healthy and 6 severely asthmatic horses in phase I, 10 severely asthmatic horses in phase II, and 10 healthy horses in phase III.
METHODS
Cohort (phases I and II) and cross-sectional (phase III) studies. Quantitative polymerase chain reaction primers targeting the sodA gene were optimized. N. semolina was quantified in oral and nasal washes and in bronchoalveolar lavage fluid (BALF; phase I, sampled twice), in nasal washes and BALF (phase II, sampled twice), and in nasal washes (phase III).
RESULTS
N. semolina was found in the nose of 5, 10, and 9 horses in phases I, II, and III, respectively (first sampling for phases I and II). Six BALF from 5 different horses were positive for N. semolina in phase II. In phase I, there was no significant difference in the nasal loads of healthy horses (median (range): 2.04 × 10 copies/mL (0-2.44 × 10 )) and asthmatic horses in exacerbation (3.75 × 10 (0-4.84 × 10 ); Wilcoxon's rank sum test, P = .57).
CONCLUSIONS AND CLINICAL IMPORTANCE
N. semolina is commonly found in the airways of horses. The potential pathogenicity of N. semolina remains to be elucidated, but the molecular technique we developed will facilitate future studies.
Topics: Animals; Asthma; Bronchoalveolar Lavage Fluid; Cross-Sectional Studies; Horse Diseases; Horses; Pasteurellaceae
PubMed: 33942932
DOI: 10.1111/jvim.16140 -
Molecular Oral Microbiology Jun 2016Aggregatibacter actinomycetemcomitans is a perio-pathogenic bacteria that has long been associated with localized aggressive periodontitis. The mechanisms of its... (Review)
Review
Aggregatibacter actinomycetemcomitans is a perio-pathogenic bacteria that has long been associated with localized aggressive periodontitis. The mechanisms of its pathogenicity have been studied in humans and preclinical experimental models. Although different serotypes of A. actinomycetemcomitans have differential virulence factor expression, A. actinomycetemcomitans cytolethal distending toxin (CDT), leukotoxin, and lipopolysaccharide (LPS) have been most extensively studied in the context of modulating the host immune response. Following colonization and attachment in the oral cavity, A. actinomycetemcomitans employs CDT, leukotoxin, and LPS to evade host innate defense mechanisms and drive a pathophysiologic inflammatory response. This supra-physiologic immune response state perturbs normal periodontal tissue remodeling/turnover and ultimately has catabolic effects on periodontal tissue homeostasis. In this review, we have divided the host response into two systems: non-hematopoietic and hematopoietic. Non-hematopoietic barriers include epithelium and fibroblasts that initiate the innate immune host response. The hematopoietic system contains lymphoid and myeloid-derived cell lineages that are responsible for expanding the immune response and driving the pathophysiologic inflammatory state in the local periodontal microenvironment. Effector systems and signaling transduction pathways activated and utilized in response to A. actinomycetemcomitans will be discussed to further delineate immune cell mechanisms during A. actinomycetemcomitans infection. Finally, we will discuss the osteo-immunomodulatory effects induced by A. actinomycetemcomitans and dissect the catabolic disruption of balanced osteoclast-osteoblast-mediated bone remodeling, which subsequently leads to net alveolar bone loss.
Topics: Aggregatibacter actinomycetemcomitans; Aggressive Periodontitis; Alveolar Bone Loss; Homeostasis; Host-Pathogen Interactions; Humans; Immunity, Innate; Inflammasomes; Pasteurellaceae Infections; Signal Transduction; Virulence Factors
PubMed: 26197893
DOI: 10.1111/omi.12119 -
Virulence Feb 2017
Topics: Aggregatibacter actinomycetemcomitans; Bacterial Outer Membrane Proteins; Humans; Periodontal Diseases; Virulence Factors
PubMed: 27623711
DOI: 10.1080/21505594.2016.1235128 -
Biochemical and Biophysical Research... Mar 2022L-enantiomers of antimicrobial peptides (AMPs) are sensitive to proteolytic degradation; however, D-enantiomers of AMPs are expected to provide improved proteolytic... (Comparative Study)
Comparative Study
L-enantiomers of antimicrobial peptides (AMPs) are sensitive to proteolytic degradation; however, D-enantiomers of AMPs are expected to provide improved proteolytic resistance. The present study aimed to comparatively investigate the in vitro antibacterial activity, trypsin and serum stability, toxicity, and in vivo antibacterial activity of L-enantiomeric bovine NK2A (L-NK2A) and its D-enantiomeric NK2A (D-NK2A). Circular dichroism spectroscopy of D-NK2A and L-NK2A in anionic liposomes showed α-helical structures and the α-helical conformation of D-NK2A was a mirror image of L-NK2A. Both D-NK2A and L-NK2A displayed minimal in vitro and in vivo toxicities. RP-HPLC and mass spectrometry analyses revealed that D-NK2A, but not L-NK2A, was resistant to trypsin digestion. D-NK2A and L-NK2A showed similar in vitro bacterial killing activities against Histophilus somni. Slightly reduced antibacterial activity was observed when D-NK2A and L-NK2A were pre-incubated with serum. Confocal and transmission electron microscopic findings confirmed that both peptides induced disruption of bacterial inner- and outer-membranes. Improved survivals with D-NK2A treatment were observed when compared to L-NK2A in a murine model of acute H. somni septicemia. We conclude that antibacterial activity and mode of action of NK2A are not chiral specific. With further optimization, D-NK2A may be a viable AMP candidate to combat bacterial infections.
Topics: Animals; Anti-Bacterial Agents; Antimicrobial Peptides; Cattle; Circular Dichroism; Kaplan-Meier Estimate; Mice; Microscopy, Electron, Transmission; Pasteurellaceae; Pasteurellaceae Infections; Protein Stability; Protein Structure, Secondary; Proteolipids; Stereoisomerism
PubMed: 35101666
DOI: 10.1016/j.bbrc.2022.01.071 -
FEBS Open Bio Dec 2022Nontypeable Haemophilus influenzae (NTHi) has emerged as a dominant mucosal pathogen causing acute otitis media (AOM) in children, acute sinusitis in children and...
Nontypeable Haemophilus influenzae (NTHi) has emerged as a dominant mucosal pathogen causing acute otitis media (AOM) in children, acute sinusitis in children and adults, and acute exacerbations of chronic bronchitis in adults. Consequently, there is an urgent need to develop a vaccine to protect against NTHi infection. A multi-component vaccine will be desirable to avoid emergence of strains expressing modified proteins allowing vaccine escape. Protein D (PD), outer membrane protein (OMP) 26, and Protein 6 (P6) are leading protein vaccine candidates against NTHi. In pre-clinical research using mouse models, we found that recombinantly expressed PD, OMP26, and P6 induce robust antibody responses after vaccination as individual vaccines, but when PD and OMP26 were combined into a single vaccine formulation, PD antibody levels were significantly lower. We postulated that PD and OMP26 physiochemically interacted to mask PD antigenic epitopes resulting in the observed effect on antibody response. However, column chromatography and mass spectrometry analysis did not support our hypothesis. We postulated that the effect might be in vivo through the mechanism of protein vaccine immunologic antigenic competition. We found when PD and OMP26 were injected into the same leg or separate legs of mice, so that antigens were immunologically processed at the same or different regional lymph nodes, respectively, antibody levels to PD were significantly lower with same leg vaccination. Different leg vaccination produced PD antibody levels quantitatively similar to vaccination with PD alone. We conclude that mixing PD and OMP26 into a single vaccine formulation requires further formulation studies.
Topics: Mice; Animals; Haemophilus Vaccines; Bacterial Outer Membrane Proteins; Antibodies, Bacterial; Immunoglobulin G; Haemophilus influenzae
PubMed: 36263849
DOI: 10.1002/2211-5463.13498 -
Bioresource Technology Jan 2022Succinic acid (SA) is a top platform chemical obtainable from biomass. The current study evaluated the potential of Actinobacillus succinogenes for SA production using...
Succinic acid (SA) is a top platform chemical obtainable from biomass. The current study evaluated the potential of Actinobacillus succinogenes for SA production using xylose-rich hemicellulosic fractions of two important lignocellulosic feedstocks, olive pits (OP) and sugarcane bagasse (SCB) and the results were compared with pure xylose. Initial experiments were conducted in shake flask followed by batch and fed-batch cultivation in bioreactor. Further separation of SA from the fermented broth was carried out by adapting direct crystallisation method. During fed-batch culture, maximum SA titers of 36.7, 33.6, and 28.7 g/L was achieved on pure xylose, OP and SCB hydrolysates, respectively, with same conversion yield of 0.27 g/g. The recovery yield of SA accumulated on pure xylose, OP and SCB hydrolysates was 79.1, 76.5, and 75.2%, respectively. The results obtained are of substantial value and pave the way for development of sustainable SA biomanufacturing in an integrated biorefinery.
Topics: Actinobacillus; Fermentation; Succinic Acid; Xylose
PubMed: 34751156
DOI: 10.1016/j.biortech.2021.126224