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Microbiological Research Feb 2021Biological nitrogen fixation (BNF), performed by diazotrophic prokaryotes, is responsible for reducing dinitrogen (N) present in the biosphere into biologically...
Biological nitrogen fixation (BNF), performed by diazotrophic prokaryotes, is responsible for reducing dinitrogen (N) present in the biosphere into biologically available forms of nitrogen. Paenibacillus brasilensis PB24 is a diazotrophic Gram-positive bacterium and is considered ecologically and industrially important because it is able to produce antimicrobial substances and 2,3-butanediol. However, the genetics and regulation of its nitrogen fixing (nif) genes have never been assessed so far. Therefore, the present study aimed to (i) identify the structural and regulatory genes related to BNF in the PB24 genome, (ii) perform comparative genomics analysis of the nif operon among different Paenibacillus species and (iii) study the expression of these genes in the presence and absence of NH. Strain PB24 showed a nif operon composed of nine genes (nifBHDKENXhesAV), with a conserved synteny (with small variations) among the Paenibacillus species evaluated. BNF regulatory genes, glnK and amtB (encoding GlnK signal transduction protein and AmtB transmembrane protein, respectively) and glnR and glnA genes (encoding the transcription factor GlnR and glutamine synthetase) were found in the PB24 genome. Primers were designed for qPCR amplification of the nitrogenase structural (nifH, nifD and nifK) and regulatory (glnA and amtB) BNF genes. The structural gene expression in PB24 was up- and downregulated in the absence and presence of NH, respectively. The gene expression levels indicated a GlnR-mediated repression of genes associated with ammonium import (amtBglnK) and BNF (nif genes). Additionally, the regulatory mechanism of GlnR in P. brasilensis PB24 differed from the other Paenibacillus evaluated, considering the different distribution of binding sites recognized by GlnR.
Topics: Amino Acid Sequence; Bacterial Proteins; Binding Sites; Gene Expression Regulation, Bacterial; Nitrogen Fixation; Paenibacillus
PubMed: 33290933
DOI: 10.1016/j.micres.2020.126647 -
Biotechnology and Applied Biochemistry Feb 2021The chitinase-producing bacteria Paenibacillus sp. was isolated from soil samples. The chitinase was purified successively by ammonia sulfate fractional precipitation... (Review)
Review
The chitinase-producing bacteria Paenibacillus sp. was isolated from soil samples. The chitinase was purified successively by ammonia sulfate fractional precipitation followed by chromatography on DEAE 52-cellulose column and then on Sephadex G-75 column. The chitinase has a molecular weight of ca. 30 kDa as measured by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) electrophoresis. Its optimum pH is 4.5, and its optimum temperature is 50 °C with colloidal chitin as a substrate. The enzyme is stable below 45 °C and in pH ranges between 4.5 and 5.5. It is activated by glucosamine, glucose, N-acetylglucosamine, and metal ions including Ca , Fe , Fe , and Ni . It is inhibited by SDS, H O , ascorbic acid, Cu , Mg , Ba , Sn , Cr , and K . With colloidal chitin as substrate, the K and the V of the chitinase are 4.28 mg/mL and 14.29 μg/(Min·mL), respectively, whereas the end products of the enzymatic hydrolysis are 14.33% monomer and 85.67% dimer of N-acetylglucosamine. The viscosity of carboxymethyl chitin decreased rapidly at the initial stages when subjected to chitinase hydrolysis, which indicates that the chitinase acts in an endosplitting pattern.
Topics: Bacterial Proteins; Chitinases; Enzyme Stability; Paenibacillus
PubMed: 31957084
DOI: 10.1002/bab.1889 -
International Journal of Systematic and... Feb 2020Two Gram-positive, rod-shaped, motile, endospore-forming strains, SYSU K30003 and SYSU K30004, were isolated from cave soil sampled in Xingyi County, Guizhou Province,...
Two Gram-positive, rod-shaped, motile, endospore-forming strains, SYSU K30003 and SYSU K30004, were isolated from cave soil sampled in Xingyi County, Guizhou Province, south-west PR China. The 16S rRNA gene sequence results indicated that strains SYSU K30003 and SYSU K30004 had highest sequence similarities to DSM 26310 (93.2 %) and KCTC 33185 (97.8 %), respectively. Optimum growth for both strains occurred at pH 7.0 and 37 °C. Both strains contained -2,6-diaminopimelic acid in their cell-wall peptidoglycan and MK-7 was the only isoprenoid quinone detected. The polar lipid profile of strain SYSU K30004 consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, an unidentified glycolipid, unidentified phospholipids and two unidentified polar lipids. The polar lipid profile of strain SYSU K30003 contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified glycolipid. The major fatty acids (>5 %) of strain SYSU K30003 were anteiso-C C, anteiso-C and iso-C, while those of strain SYSU K30004 were anteiso-C, C, anteiso-C, iso-C, iso-C and iso-C. The genome G+C contents of strains SYSU K30003 and SYSU K30004 were 59.0 and 53.6 mol%, respectively. The average nucleotide identity values between strains SYSU K30003 and SYSU K30004 and other closely related members were below the cut-off level (95-96 %) for species identification. Based on the results of phenotypic, chemotaxonomic and genome analyses, strains SYSU K30003 and SYSU K30004 represent two novel species of the genus , for which the names sp. nov. and sp. nov. are proposed. The type strains are SYSU K30003 (=KCTC 33956=CGMCC 1.13505) and SYSU K30004 (=KCTC 33957=CGMCC 1.13872).
Topics: Bacterial Typing Techniques; Base Composition; Caves; Cell Wall; China; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Glycolipids; Nucleic Acid Hybridization; Paenibacillus; Peptidoglycan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2
PubMed: 31746729
DOI: 10.1099/ijsem.0.003870 -
Scientific Reports Nov 2022Antimicrobial resistance has been developing fast and incurring a loss of human life, and there is a need for new antimicrobial agents. Naturally occurring antimicrobial...
Antimicrobial resistance has been developing fast and incurring a loss of human life, and there is a need for new antimicrobial agents. Naturally occurring antimicrobial peptides offer the characteristics to counter AMR because the resistance development is low or no resistance. Antimicrobial peptides from Paenibacillus peoriae IBSD35 cell-free supernatant were salted out and purified using chromatography and characterized with liquid chromatography-tandem-mass spectrometry. The extract has shown a high and broad spectrum of antimicrobial activity. Combining the strain IBSD35 genome sequence with its proteomic data enabled the prediction of biosynthetic gene clusters by connecting the peptide from LC-MS/MS data to the gene that encode. Antimicrobial peptide databases offered a platform for the effective search, prediction, and design of AMPs and expanded the studies on their isolation, structure elucidation, biological evaluation, and pathway engineering. The genome-based taxonomy and comparisons have shown that P. peoriae IBSD35 is closely related to Paenibacillus peoriae FSL J3-0120. P. peoriae IBSD35 harbored endophytic trait genes and nonribosomal peptide synthases biosynthetic gene clusters. The comparative genomics revealed evolutionary insights and facilitated the discovery of novel SMs using proteomics from the extract of P. peoriae IBSD35. It will increase the potential to find novel bio-molecules to counter AMR.
Topics: Humans; Proteomics; Chromatography, Liquid; Tandem Mass Spectrometry; Paenibacillus; Anti-Infective Agents; Anti-Bacterial Agents; Genomics
PubMed: 36344671
DOI: 10.1038/s41598-022-23613-y -
International Journal of Systematic and... Nov 2023A novel bacterial strain, designated as PHS-Z3, was isolated from a marine sponge belonging to the genus on the Puerto Galera Deep Monkey, Philippines. Cells of PHS-Z3...
A novel bacterial strain, designated as PHS-Z3, was isolated from a marine sponge belonging to the genus on the Puerto Galera Deep Monkey, Philippines. Cells of PHS-Z3 were Gram-stain-positive, motile, oxidase- and catalase-positive, white-pigmented, spore-forming, short rods that could grow at 10-40 °C (optimum, 20 °C), pH 6.0-9.5 (optimum, pH 7.5) and with 2-16 % (w/v) NaCl (optimum, 7 %). The 16S rRNA gene sequence of PHS-Z3 showed 97.9 %, 96.7 %, and 96.2 % identities to C/2, DT7-4 and RC11, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PHS-Z3 formed an independent cluster with C/2. The total genome of PHS-Z3 was approximately 7 613 364 bp in size with a DNA G+C content of 51.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between PHS-Z3 and other type strains of species of the genus were 68.0-81.4 % [ANI by blast (ANIb)], 83.0-88.0 % [ANI by MUMmer (ANIm)] and 12.7-32.1 % (dDDH). The dDDH and ANI values were below the standard cut-off criteria for delineation of bacterial species. The percentage of conserved proteins (POCP) values between the genome of PHS-Z3 and those of members of the genus were 39.7-75.7 %, while the average amino acid identity (AAI) values were 55.9-83.7 %. The sole respiratory quinone in the strain was MK-7, and the predominant fatty acids were anteiso-C and C. The major polar lipids of PHS-Z3 consisted of diphosphatidylglycerol, phospholipid and phosphatidylglycerol. The characteristic amino acid in the cell wall of PHS-Z3 was diamino heptanoic acid (-DAP). On the basis of the molecular, physiological, biochemical and chemotaxonomic features, strain PHS-Z3 represents a novel species of the genus , for which the name sp. nov. is proposed, with the type strain PHS-Z3 (=MCCC 1K07848=KCTC 43443).
Topics: Animals; Theonella; Phylogeny; RNA, Ribosomal, 16S; Base Composition; Fatty Acids; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Paenibacillus; Amino Acids
PubMed: 37910170
DOI: 10.1099/ijsem.0.006122 -
Bioscience, Biotechnology, and... May 2021Chitin and its derivatives have valuable potential applications in various fields that include medicine, agriculture, and food industries. Paenibacillus sp. str. FPU-7... (Review)
Review
Chitin and its derivatives have valuable potential applications in various fields that include medicine, agriculture, and food industries. Paenibacillus sp. str. FPU-7 is one of the most potent chitin-degrading bacteria identified. This review introduces the chitin degradation system of P. str. FPU-7. In addition to extracellular chitinases, P. str. FPU-7 uses a unique multimodular chitinase (ChiW) to hydrolyze chitin to oligosaccharides on the cell surface. Chitin oligosaccharides are converted to N-acetyl-d-glucosamine by β-N-acetylhexosaminidase (PsNagA) in the cytosol. The functions and structures of ChiW and PsNagA are also summarized. The genome sequence of P. str. FPU-7 provides opportunities to acquire novel enzymes. Genome mining has identified a novel alginate lyase, PsAly. The functions and structure of PsAly are reviewed. These findings will inform further improvement of the sustainable conversion of polysaccharides to functional materials.
Topics: Chitin; Chitinases; Hydrolysis; Paenibacillus
PubMed: 33792636
DOI: 10.1093/bbb/zbab058 -
Antonie Van Leeuwenhoek Jan 2022Two strains HN-1 and 39 were isolated from rhizospheres of different plants grown in different regions of PR China. The two strains exhibited high nitrogenase activities...
Two strains HN-1 and 39 were isolated from rhizospheres of different plants grown in different regions of PR China. The two strains exhibited high nitrogenase activities and possessed almost identical 16S rRNA gene sequences. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 99.9 and 99.8%, respectively, suggesting that they belong to one species. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strains HN-1 and 39 are the members of the genus Paenibacillus and both strains exhibited 99.5% similarity to Paenibacillus stellifer DSM 14472 and the both strains represented a separate lineage from all other Paenibacillus species. However, the ANI of type strain HN-1 with P. stellifer DSM 14472 was 90.69, which was below the recommended threshold value (< 95-96% ANI). The dDDH showed 42.1% relatedness between strain HN-1 and P. stellifer DSM 14472, which was lower than the recommended threshold value (dDDH < 70%). The strain HN-1 contain anteiso-C as major fatty acids and MK-7 as predominant isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four aminophospholipids and an unidentified glycolipid. Unlike the most closely related P. stellifer DSM 14472, strain HN-1 or 39 was positive for catalase reaction. Distinct phenotypic and genomic characterisations from previously described taxa support the classification of strains HN-1 or 39 as representatives of a novel species of the genus Paenibacillus, for which the name Paenibacillus sinensis is proposed, with type strains HN-1 (=CGMCC 1.18902, JCM 34,620), and reference strain 39 (=CGMCC 1.18879, JCM 34,616), respectively.
Topics: Base Composition; DNA, Bacterial; Nitrogen; Paenibacillus; Phylogeny; RNA, Ribosomal, 16S; Rhizosphere
PubMed: 34718908
DOI: 10.1007/s10482-021-01677-6 -
Journal of Microbiology (Seoul, Korea) Oct 2020Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189 and 14171R-81 were isolated from the rhizosphere of tomato plants. The 16S rRNA...
Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189 and 14171R-81 were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189 and 14171R-81 were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01 (96.3% and 98.0%, respectively). The genome of strain 12200R-189 was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81 comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189, 14171R-81, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189 grew at a temperature range of 15-40°C, pH 6.0-9.0, and 0-3% NaCl (w/v), whereas strain 14171R-81 grew at a temperature range of 10-37°C, pH 6.0-8.0, and 0-1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C, anteiso-C, and iso-C. The polar lipids of strain 12200R-189 were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81 were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R-189 and 14171R-81 represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189 (= KACC 19916 = CCTCC AB 2020027) and 14171R-81 (= KACC 19915 = CCTCC AB 2020026).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genome, Bacterial; Solanum lycopersicum; Paenibacillus; Phylogeny; RNA, Ribosomal, 16S; Rhizosphere; Soil Microbiology; Vitamin K 2; Whole Genome Sequencing
PubMed: 32989640
DOI: 10.1007/s12275-020-0258-2 -
International Journal of Systematic and... Dec 2021A Gram-stain-positive, facultatively anaerobic, non-motile, endospore-forming and rod-shaped bacterium, occurring singly or in pairs, designated TB2019, was isolated...
A Gram-stain-positive, facultatively anaerobic, non-motile, endospore-forming and rod-shaped bacterium, occurring singly or in pairs, designated TB2019, was isolated from environmental monitoring samples of corridor air collected at the Tianjin Institute for Drug Control, Tianjin Province (PR China). The isolate was able to grow at 15-40 °C (optimum growth at 37 °C), pH 6.0-8.0 (pH 7.0) and in the presence of 0-2% (w/v) NaCl (0% NaCl). Comparison of 16S rRNA gene sequences indicated that TB2019 was most closely related to CGMCC 1.11012 (98.63%), Q4-3 (98.19%), DSM 13188 (97.55%), P26E (97.33%) and DSM 15391 (97.19%). The digital DNA-DNA hybridization and the average nucleotide identity values between TB2019 and the five type strains mentioned above ranged from 20.7 to 25.0% and 75.2 to 81.3%, respectively, and the genomic DNA G+C content was 49.52 mol%. The diagnostic cell-wall sugar was ribose, and the diagnostic amino acid was -diaminopimelic acid. The polar lipids of TB2019 included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. MK-7 was the predominant menaquinone, and anteiso-C (30.6%) was the major fatty acid. Based on the polyphasic taxonomic data, strain TB2019 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is TB2019 (=CICC 25065=JCM 34610).
Topics: Air Microbiology; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Paenibacillus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2
PubMed: 34908521
DOI: 10.1099/ijsem.0.005158 -
International Journal of Systematic and... Aug 2021A strict aerobic bacterium, strain JW14 was isolated from soil in the Republic of Korea. Cells were Gram-stain-positive, non-endospore-forming and motile rods showing...
A strict aerobic bacterium, strain JW14 was isolated from soil in the Republic of Korea. Cells were Gram-stain-positive, non-endospore-forming and motile rods showing catalase-positive and oxidase-negative activities. Growth of strain JW14 was observed at 20-37 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.0) and in the presence of 0-2.0% NaCl (optimum, 0%). Strain JW14 contained menaquinone-7 as the sole isoprenoid quinone, anteiso-C, C and iso-C as the major fatty acids (>10.0%), and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and an unidentified lipid as the major polar lipids. The cell-wall peptidoglycan of strain JW14 contained -diaminopimelic acid. The DNA G+C content of strain JW14 calculated from the whole genome sequence was 48.1 mol%. Strain JW14 was most closely related to DSM 15220 with 97.4% 16S rRNA gene sequence similarity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JW14 formed a distinct phyletic lineage from closely related type strains within the genus . Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain JW14 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is JW14 (=KACC 21840=JCM 34279).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Paenibacillus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2
PubMed: 34435945
DOI: 10.1099/ijsem.0.004981