-
BMC Microbiology Jun 2024Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer...
BACKGROUND
Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paenibacillus genomes encompass a considerable array of antibiotic biosynthetic gene clusters (BGCs), rendering these species as good candidates for genome-driven novel antibiotic exploration. Nevertheless, BGCs within Paenibacillus genomes have not been extensively studied.
RESULTS
We conducted an analysis of 554 Paenibacillus genome sequences, sourced from the National Center for Biotechnology Information database, with a focused investigation involving 89 of these genomes via antiSMASH. Our analysis unearthed a total of 848 BGCs, of which 716 (84.4%) were classified as unknown. From the initial pool of 554 Paenibacillus strains, we selected 26 available in culture collections for an in-depth evaluation. Genomic scrutiny of these selected strains unveiled 255 BGCs, encoding non-ribosomal peptide synthetases, polyketide synthases, and bacteriocins, with 221 (86.7%) classified as unknown. Among these strains, 20 exhibited antimicrobial activity against the gram-positive bacterium Micrococcus luteus, yet only six strains displayed activity against the gram-negative bacterium Escherichia coli. We proceeded to focus on Paenibacillus brasilensis, which featured five new BGCs for further investigation. To facilitate detailed characterization, we constructed a mutant in which a single BGC encoding a novel antibiotic was activated while simultaneously inactivating multiple BGCs using a cytosine base editor (CBE). The novel antibiotic was found to be localized to the cell wall and demonstrated activity against both gram-positive bacteria and fungi. The chemical structure of the new antibiotic was elucidated on the basis of ESIMS, 1D and 2D NMR spectroscopic data. The novel compound, with a molecular weight of 926, was named bracidin.
CONCLUSIONS
This study outcome highlights the potential of Paenibacillus species as valuable sources for novel antibiotics. In addition, CBE-mediated dereplication of antibiotics proved to be a rapid and efficient method for characterizing novel antibiotics from Paenibacillus species, suggesting that it will greatly accelerate the genome-based development of new antibiotics.
Topics: Paenibacillus; Anti-Bacterial Agents; Multigene Family; Genome, Bacterial; Peptide Synthases; Polyketide Synthases; Bacteriocins; Biosynthetic Pathways; Bacterial Proteins; Drug Discovery
PubMed: 38937695
DOI: 10.1186/s12866-024-03375-5 -
Applied and Environmental Microbiology Nov 2021PcAxy43B is a modular protein comprising a catalytic domain of glycoside hydrolase family 43 (GH43), a family 6 carbohydrate-binding module (CBM6), and a family 36...
A Novel Multifunctional Arabinofuranosidase/Endoxylanase/β-Xylosidase GH43 Enzyme from Paenibacillus curdlanolyticus B-6 and Its Synergistic Action To Produce Arabinose and Xylose from Cereal Arabinoxylan.
PcAxy43B is a modular protein comprising a catalytic domain of glycoside hydrolase family 43 (GH43), a family 6 carbohydrate-binding module (CBM6), and a family 36 carbohydrate-binding module (CBM36) and found to be a novel multifunctional xylanolytic enzyme from Paenibacillus curdlanolyticus B-6. This enzyme exhibited α-l-arabinofuranosidase, endoxylanase, and β-d-xylosidase activities. The α-l-arabinofuranosidase activity of PcAxy43B revealed a new property of GH43, via the release of both long-chain cereal arabinoxylan and short-chain arabinoxylooligosaccharide (AXOS), as well as release from both the C(O) and C(O) positions of AXOS, which is different from what has been seen for other arabinofuranosidases. PcAxy43B liberated a series of xylooligosaccharides (XOSs) from birchwood xylan and xylohexaose, indicating that PcAxy43B exhibited endoxylanase activity. PcAxy43B produced xylose from xylobiose and reacted with -nitrophenyl-β-d-xylopyranoside as a result of β-xylosidase activity. PcAxy43B effectively released arabinose together with XOSs and xylose from the highly arabinosyl-substituted rye arabinoxylan. Moreover, PcAxy43B showed significant synergistic action with the trifunctional endoxylanase/β-xylosidase/α-l-arabinofuranosidase PcAxy43A and the endoxylanase Xyn10C from strain B-6, in which almost all products produced from rye arabinoxylan by these combined enzymes were arabinose and xylose. In addition, the presence of CBM36 was found to be necessary for the endoxylanase property of PcAxy43B. PcAxy43B is capable of hydrolyzing untreated cereal biomass, corn hull, and rice straw into XOSs and xylose. Hence, PcAxy43B, a significant accessory multifunctional xylanolytic enzyme, is a potential candidate for application in the saccharification of cereal biomass. Enzymatic saccharification of cereal biomass is a strategy for the production of fermented sugars from low-price raw materials. In the present study, PcAxy43B from B-6 was found to be a novel multifunctional α-l-arabinofuranosidase/endoxylanase/β-d-xylosidase enzyme of glycoside hydrolase family 43. It is effective in releasing arabinose, xylose, and XOSs from the highly arabinosyl-substituted rye arabinoxylan, which is usually resistant to hydrolysis by xylanolytic enzymes. Moreover, almost all products produced from rye arabinoxylan by the combination of PcAxy43B with the trifunctional xylanolytic enzyme PcAxy43A and the endoxylanase Xyn10C from strain B-6 were arabinose and xylose, which can be used to produce several value-added products. In addition, PcAxy43B is capable of hydrolyzing untreated cereal biomass into XOSs and xylose. Thus, PcAxy43B is an important multifunctional xylanolytic enzyme with high potential in biotechnology.
Topics: Arabinose; Bacterial Proteins; Edible Grain; Endo-1,4-beta Xylanases; Glycoside Hydrolases; Multifunctional Enzymes; Paenibacillus; Xylans; Xylose; Xylosidases
PubMed: 34613758
DOI: 10.1128/AEM.01730-21 -
Iranian Journal of Biotechnology 2017A number of microorganisms and their enzymes have been reported as xanthan depolymerizers. species are well-known polysaccharide hydrolyzing bacteria. However, and...
A number of microorganisms and their enzymes have been reported as xanthan depolymerizers. species are well-known polysaccharide hydrolyzing bacteria. However, and sp. XD are the only species in the genus which are now known to degrade xanthan. Complete biodegradation of the xanthan exopolysaccharide is a rarely found capability among microorganisms. The aim of this study is to survey xanthanase producing bacteria with an appropriate bioactivity for the biopolymer degradation under different environmental conditions. The bacteria were isolated based on viscosity reduction of the xanthan solution. Bacterial isolates were identified using rep-PCR (repetitive element-based genomic fingerprinting) and 16S rDNA sequencing. Xanthanases were identified using rep-PCR (repetitive element-based genomic fingerprinting) and 16S rDNA sequencing. Xanthanases were characterized by measuring their activity at different temperatures, pH values, and NaCl concentrations. Degradation of other polysaccharides and xanthan degradation products were investigated based on the screening plate method and TLC (thin-layer chromatography), respectively. :Six isolates from different species with a complete xanthan degrading capability were isolated from Urmia Lake. Phylogenetic analysis placed these strains within the genus with the closest relatives that were found to be , and . These isolates displayed different levels of the xanthan biodegradation activity in temperatures ranging from 15 to 55°C and pH values from 4 to 11. Xanthanolytic activity was generally prevented in presence of NaCl (> 0.1 mol.L-1). Furthermore, the isolated spp. could degrade several other polysaccharides including xylan, CMC (carboxymethyl cellulose), starch, alginate, and pectin. Novel strains of the six different species that were introduced in the present study are able to produce xanthanases with interesting characteristics. In light of the results from this study, special applications, particularly in healthcare, medicine, and the environment is hereby proposed for these enzymes.
PubMed: 29845059
DOI: 10.15171/ijb.1477 -
The Journal of General and Applied... Sep 2022Paenibacillus polymyxa is a spore-forming Gram-positive bacterial species. Both its sporulation process and the spore properties are poorly understood. Here, we...
Paenibacillus polymyxa is a spore-forming Gram-positive bacterial species. Both its sporulation process and the spore properties are poorly understood. Here, we investigated sporulation in P. polymyxa ATCC39564. When cultured at 37℃ for 24 h in sporulation medium, more than 80% of the total cells in the culture were spores. Time-lapse imaging revealed that cellular morphological changes during sporulation of P. polymyxa were highly similar to those of B. subtilis. We demonstrated that genetic deletion of spo0A, sigE, sigF, sigG, or sigK, which are highly conserved transcriptional regulators in spore forming bacteria, abolished spore formation. In P. polymyxa, spo0A was required for cell growth in sporulation medium, as well as for the initiation of sporulation. The sigE and sigF mutants formed abnormal multiple asymmetric septa during the early stage of sporulation. The sigG and sigK mutants formed forespores in the sporangium, but they did not become mature. Moreover, fluorescence reporter analysis confirmed compartment-specific gene expression of spoIID and spoVFA in the mother cell and spoIIQ and sspF in the forespore. Transmission electron microscopy imaging revealed that P. polymyxa produces multilayered endospores but lacking a balloon-shaped exosporium. Our results indicate that spore morphogenesis is conserved between P. polymyxa and B. subtilis. However, P. polymyxa genomes lack many homologues encoding spore-coat proteins that are found in B. subtills, suggesting that there are differences in the spore coat composition and surface structure between P. polymyxa and B. subtilis.
Topics: Bacillus subtilis; Bacterial Proteins; Gene Expression Regulation, Bacterial; Morphogenesis; Paenibacillus polymyxa; Spores, Bacterial; Transcription Factors
PubMed: 35418538
DOI: 10.2323/jgam.2021.10.006 -
Poultry Science Oct 2019This study aimed to investigate the effects of Lactobacillus plantarum 16 (Lac16) and Paenibacillus polymyxa 10 (BSC10) on intestinal barrier function, antioxidative...
Effects of probiotics Lactobacillus plantarum 16 and Paenibacillus polymyxa 10 on intestinal barrier function, antioxidative capacity, apoptosis, immune response, and biochemical parameters in broilers.
This study aimed to investigate the effects of Lactobacillus plantarum 16 (Lac16) and Paenibacillus polymyxa 10 (BSC10) on intestinal barrier function, antioxidative capacity, apoptosis, immune response, and biochemical parameters in broilers. A total of 540 one-day-old broiler chicks (Cobb500) were randomly allocated to three groups of 180 birds, and fed either a basal diet or a basal diet supplemented with 108 colony-forming units Lac16 or BSC10 per kilogram feed for 21 D. The results revealed that both Lac16 and BSC10 maintained ileal mucosal morphology, and BSC10 regulated the expression of barrier function-related genes. Birds fed with probiotics decreased malondialdehyde level in jejunal mucosa and serum, and the increased activities of hepatic GSH-Px and jejunal CAT were observed in BSC10 group (P < 0.05). Immunohistochemistry of Bax, Bcl-2 and proliferating cell nuclear antigen and TUNEL-immunofluorescence assay demonstrated that Lac16 and BSC10 exerted beneficial effects on cell apoptosis and proliferation, as indicated by the gene expression of down-regulated Bax and p53 as well as a significant upregulation of Bcl-2 (P < 0.05). In addition, Lac16 and BSC10 significantly increased NO production and iNOS activity in liver and jejunal mucosa, and gene expression of IFN-γ (P < 0.01), IL-6 (P < 0.05), and IL-10 (P < 0.05 and P < 0.01, respectively) in ileum mucosa, whereas markedly decreased the expression of Cox2 (P < 0.05). Furthermore, it was found that Lac16 and BSC10 significantly reduced levels of alkaline phosphatase (P < 0.05 and P < 0.01, respectively) and creatine kinase (P < 0.05). Moreover, BSC10 significantly reduced uric acid (P < 0.05) and low-density lipoprotein levels (P < 0.01). Taken together, Lac16 and BSC10 could improve intestinal and body health status of broilers by increasing intestinal barrier function, anti-oxidative capacity and immunity, and decreasing cell apoptosis with strain-specificity.
Topics: Animal Feed; Animal Nutritional Physiological Phenomena; Animals; Antioxidants; Apoptosis; Chickens; Diet; Immunity, Innate; Intestines; Lactobacillus plantarum; Paenibacillus polymyxa; Probiotics; Random Allocation
PubMed: 31064013
DOI: 10.3382/ps/pez226 -
Bioscience Reports Jan 2021C3larvinA was recently described as a mono-ADP-ribosyltransferase (mART) toxin from the enterobacterial repetitive intergenic consensus (ERIC) III genotype of the...
C3larvinA was recently described as a mono-ADP-ribosyltransferase (mART) toxin from the enterobacterial repetitive intergenic consensus (ERIC) III genotype of the agricultural pathogen, Paenibacillus larvae. It was shown to be the full-length, functional version of the previously described C3larvintrunc toxin, due to a 33-residue extension of the N-terminus of the protein. In the present study, a series of deletions and substitutions were made to the N-terminus of C3larvinA to assess the contribution of the α1-helix to toxin structure and function. Catalytic characterization of these variants identified Asp23 and Ala31 residues as supportive to enzymatic function. A third residue, Lys36, was also found to contribute to the catalytic activity of the enzyme. Analysis of the C3larvinA homology model revealed that these three residues were participating in a series of interactions to properly orient both the Q-X-E and S-T-S motifs. Ala31 and Lys36 were found to associate with a structural network of residues previously identified in silico, whereas Asp23 forms novel interactions not previously described. At last, the membrane translocation activity into host target cells of each variant was assessed, highlighting a possible relationship between protein dipole and target cell entry.
Topics: ADP Ribose Transferases; Animals; Bacterial Proteins; Catalysis; Cell Line; Kinetics; Mice; Models, Molecular; Paenibacillus larvae; Protein Conformation
PubMed: 33289829
DOI: 10.1042/BSR20203727 -
Microbiology Spectrum Jun 2023The role of microbial volatile organic compounds (MVOCs) in promoting plant growth has received much attention. We isolated Paenibacillus peoriae from mangrove...
The role of microbial volatile organic compounds (MVOCs) in promoting plant growth has received much attention. We isolated Paenibacillus peoriae from mangrove rhizosphere soil, which can produce VOCs to promote the growth of Arabidopsis thaliana seedlings, increase the aboveground biomass of , and increase the number of lateral roots of . The effects of different inoculation amounts and different media on the composition of MVOCs were studied by solid-phase microextraction/gas chromatography-mass spectrometry (SPME/GC-MS) and headspace sampler/GC-MS. We found that the growth medium influences the function and composition of MVOCs. To survey the growth-promoting functions, the transcriptome of the receptor was then determined. We also verified the inhibitory effect of the soluble compounds produced by on the growth of 10 pathogenic fungi. The ability of to produce volatile and soluble compounds to promote plant growth and disease resistance has shown great potential for application in the sustainability of agricultural production. Microbial volatile organic compounds (MVOCs) have great potential as "gas fertilizers" for agricultural applications, and it is a promising research direction for the utilization of microbial resources. This study is part of the field of interactions between microorganisms and plants. To study the function and application of microorganisms from the perspective of VOCs is helpful to break the bottleneck of traditional microbial application. At present, the study of MVOCs is lacking; there is a lack of functional strains, especially with plant-protective functions and nonpathogenic application value. The significance of this study is that it provides Paenibacillus peoriae, which produces VOCs with plant growth-promoting effects and broad-spectrum antifungal activity against plant-pathogenic fungi. Our study provides a more comprehensive, new VOC component analysis method and explains how MVOCs promote plant growth through transcriptome analysis. This will greatly increase our understanding of MVOC applications as a model for other MVOC research.
Topics: Volatile Organic Compounds; Arabidopsis; Plant Development; Paenibacillus; Fungi
PubMed: 36988498
DOI: 10.1128/spectrum.04346-22 -
The Journal of Veterinary Medical... Mar 2022Paenibacillus larvae and Melissococcus plutonius are the causative agents of American and European foulbroods of honey bees, respectively. Since their virulence and...
A novel multiplex PCR assay to detect and distinguish between different types of Paenibacillus larvae and Melissococcus plutonius, and a survey of foulbrood pathogen contamination in Japanese honey.
Paenibacillus larvae and Melissococcus plutonius are the causative agents of American and European foulbroods of honey bees, respectively. Since their virulence and resistance to disinfectants differ depending on the genotypes/phenotypes of the strains, the discrimination of strain types is important for the effective control of these diseases. Methods to detect and differentiate pathogens in honey are useful for surveying the contamination status of beehives/apiaries. In the present study, we selected a sequence (GenBank accession no. FI763267) as the specific target for enterobacterial repetitive intergenic consensus (ERIC) II-type P. larvae strains for the first time and developed a novel multiplex PCR assay that precisely distinguishes between the major types of foulbrood pathogens (ERIC I and II P. larvae and typical and atypical M. plutonius) in one reaction. In addition, we found that commercially available kits designed for DNA extraction from Mycobacterium in feces efficiently extracted DNA from foulbrood pathogens in honey. Using the multiplex PCR assay and DNA extraction kits, all the targeted types of P. larvae and M. plutonius were detected in honey spiked with the pathogens at a concentration of 100 bacterial cells/strain/ml. Moreover, 94% of the Japanese honey samples examined in the present study were contaminated with one or more types of the foulbrood pathogens. These results indicate that the newly developed methods are useful for detecting foulbrood pathogens in honey. The epidemiological information obtained by these methods will contribute to the effective control of foulbroods in apiaries.
Topics: Animals; Bees; Enterococcaceae; Japan; Larva; Multiplex Polymerase Chain Reaction; Paenibacillus larvae; United States
PubMed: 35082220
DOI: 10.1292/jvms.21-0629 -
Brazilian Journal of Microbiology :... Sep 2022Previous studies carried out in our laboratory described the antimicrobial activity of the whole hexanic extract (HE) of Achyrocline satureioides (Lam.) DC against...
Previous studies carried out in our laboratory described the antimicrobial activity of the whole hexanic extract (HE) of Achyrocline satureioides (Lam.) DC against Paenibacillus larvae, the causal agent of American Foulbrood (AFB) a disease of the honey bee larvae. In this study, the HE was partitioned into five main fractions by chromatographic techniques leading to the isolation of four known compounds: two prenylated phloroglucinol α-pyrones (1 and 3), 5,7-dihydroxy-3,8-dimethoxyflavone (gnaphaliin A) (2), and 23-methyl-6-O-demethylauricepyrone (4). Isolated compounds were further analyzed towards structural elucidation using H RMN and C RMN spectroscopic techniques. For the first time, the antimicrobial activity of the isolated compounds was evaluated against P. larvae strains by broth microdilution method and compared with that of the whole HE. Compounds 1-4 displayed minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values ranging between 0.07 and 62.5 μg/mL and 0.26 and 12.5 μg/mL, respectively. The lowest MIC and MBC values were obtained with compounds 3 and 4, respectively. The antimicrobial activity of each single compound and the combination of them showed that the presence of all compounds is needed for the antimicrobial efficacy of whole HE.
Topics: Achyrocline; Animals; Anti-Infective Agents; Bees; Hexanes; Larva; Microbial Sensitivity Tests; Paenibacillus; Paenibacillus larvae; United States
PubMed: 35349126
DOI: 10.1007/s42770-022-00736-y -
The ISME Journal Nov 2018Microbial communities primarily consist of multiple species that affect one another's fitness both directly and indirectly. This study showed that the cocultivation of...
Microbial communities primarily consist of multiple species that affect one another's fitness both directly and indirectly. This study showed that the cocultivation of Paenibacillus amylolyticus and Xanthomonas retroflexus exhibited facultative mutualistic interactions in a static environment, during the course of which a new adapted phenotypic variant of X. retroflexus appeared. Although the emergence of this variant was not directly linked to the presence of P. amylolyticus, its establishment in the coculture enhanced the productivity of both species due to mutations that stimulated biofilm formation. The mutations were detected in genes encoding a diguanylate cyclase predicted to synthesise cyclic-di-GMP. Examinations of the biofilm formed in cocultures of P. amylolyticus and the new variant of X. retroflexus revealed a distinct spatial organisation: P. amylolyticus only resided in biofilms in association with X. retroflexus and occupied the outer layers. The X. retroflexus variant therefore facilitated increased P. amylolyticus growth as it produced more biofilm biomass. The increase in X. retroflexus biomass was thus not at the expense of P. amylolyticus, demonstrating that interspecies interactions can shape diversification in a mutualistic coculture and reinforce these interactions, ultimately resulting in enhanced communal performance.
Topics: Biofilms; Cyclic GMP; Escherichia coli Proteins; Paenibacillus; Phenotype; Phosphorus-Oxygen Lyases; Symbiosis; Xanthomonas
PubMed: 29977009
DOI: 10.1038/s41396-018-0165-2