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Extremophiles : Life Under Extreme... Nov 2019Glycoside hydrolases, particularly cellulases, xylanases and mannanases, are essential for the depolymerisation of lignocellulosic substrates in various industrial...
Glycoside hydrolases, particularly cellulases, xylanases and mannanases, are essential for the depolymerisation of lignocellulosic substrates in various industrial bio-processes. In the present study, a novel glycoside hydrolase from Paenibacillus mucilaginosus (PmGH) was expressed in E. coli, purified and characterised. Functional analysis indicated that PmGH is a 130 kDa thermophilic multi-modular and multi-functional enzyme, comprising a GH5, a GH6 and two CBM3 domains and exhibiting cellulase, mannanase and xylanase activities. The enzyme displayed optimum hydrolytic activities at pH 6 and 60 °C and moderate thermostability. Homology modelling of the full-length protein highlighted the structural and functional novelty of native PmGH, with no close structural homologs identified. However, homology modelling of the individual GH5, GH6 and the two CBM3 domains yielded excellent models based on related structures from the Protein Data Bank. The catalytic GH5 and GH6 domains displayed a (β/α) and a distorted seven stranded (β/α) fold, respectively. The distinct homology at the domain level but low homology of the full-length protein suggests that this protein evolved by exogenous gene acquisition and recombination.
Topics: Bacterial Proteins; Glycoside Hydrolases; Hot Temperature; Hydrogen-Ion Concentration; Models, Molecular; Paenibacillus; Protein Domains; Protein Structure, Secondary
PubMed: 31372752
DOI: 10.1007/s00792-019-01121-8 -
Molecular Phylogenetics and Evolution Dec 2022Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond...
Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.
Topics: Nitrogen Fixation; Nitrogenase; Paenibacillus; Phylogeny
PubMed: 36084857
DOI: 10.1016/j.ympev.2022.107624 -
International Journal of Systematic and... Aug 2020Bacteria of the genus are relevant to humans, animals and plants. The species and are Gram-stain-positive and endospore-forming bacilli isolated from a blood culture...
Bacteria of the genus are relevant to humans, animals and plants. The species and are Gram-stain-positive and endospore-forming bacilli isolated from a blood culture of a leukemia patient and from soil of a ginseng field, respectively. Comparative analyses of their 16S rRNA genes revealed that the two species could be synonyms (99.3% sequence identity). In the present study we performed different genomic analyses in order to evaluate the phylogenetic relationship of these micro-organisms. DSM 16942 and DSM 21345 presented a difference in their G+C content lower than 1 mol%, overall genome relatedness index values higher than the species circumscription thresholds (average nucleotide identity, 95.57 %; genome-wide ANI, =96.51 %; and orthologous ANI, 96.25 %), and a monophyletic grouping pattern in the phylogenies of the 16S rRNA gene and the proteome core. Considering that these strains present differential biochemical capabilities and that their computed digital DNA-DNA hybridization value is lower than the cut-off for bacterial subspecies circumscription, we suggest that each of them form different subspecies of , subsp. subsp. nov. (type strain DSM 21345) and subsp. subsp. nov. (type strain DSM 16942).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Genes, Bacterial; Nucleic Acid Hybridization; Paenibacillus; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 32692645
DOI: 10.1099/ijsem.0.004328 -
International Journal of Systematic and... Jan 2018A bacterial strain designated YYJ7-1 was isolated from farmland soil in China and characterized using a polyphasic taxonomic approach. Cells of strain YYJ7-1 were...
A bacterial strain designated YYJ7-1 was isolated from farmland soil in China and characterized using a polyphasic taxonomic approach. Cells of strain YYJ7-1 were Gram-staining-positive, aerobic or facultatively anaerobic, rod-shaped, motile and endospore-forming. Growth occurred at 18-42 °C (optimum at 35 °C), at pH 6.0-8.0 (optimum at pH 7.5) and with 0.0-4.0 % NaCl (optimum with 0.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Paenibacillus and showed high levels of sequence similarity with respect to Paenibacillus provencensis 4401170 (98.6 %) and Paenibacillus urinalis 5402403 (98.4 %), while lower 16S rRNA gene sequence similarities were observed with all other type strains (97.0 %). However, strain YYJ7-1 showed low DNA-DNA relatedness with P. provencensis 4401170 48.7±4.5 % (43.6±7.1 % in a reciprocal experiment), and P. urinalis 5402403 38.9±5.7 % (35.6±6.8 %). The major cellular fatty acids (>10.0 %) of strain YYJ7-1 were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The polar lipid profile consisted of phospholipids, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major isoprenoid quinone was MK-7. The DNA G+C content was 39.4 mol%. Based on these results, it is concluded that strain YYJ7-1 represents a novel species of the genus Paenibacillus, for which the name Paenibacillus shunpengii sp. nov. is proposed, with YYJ7-1 (=ACCC 19965=KCTC 33849) as the type strain.
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Farms; Fatty Acids; Paenibacillus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2
PubMed: 29134934
DOI: 10.1099/ijsem.0.002484 -
Life Science Alliance Oct 2020is an agriculturally important plant growth-promoting rhizobacterium. Many species are known to be engaged in complex bacteria-bacteria and bacteria-host interactions,...
is an agriculturally important plant growth-promoting rhizobacterium. Many species are known to be engaged in complex bacteria-bacteria and bacteria-host interactions, which in other species were shown to necessitate quorum sensing communication. However, to date, no quorum sensing systems have been described in Here, we show that the type strain ATCC 842 encodes at least 16 peptide-based communication systems. Each of these systems is comprised of a pro-peptide that is secreted to the growth medium and processed to generate a mature short peptide. Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of communication peptides leads to reprogramming of the transcriptional response. We found that these quorum sensing systems are conserved across hundreds of species belonging to the family, with some species encoding more than 25 different peptide-receptor pairs, representing a record number of quorum sensing systems encoded in a single genome.
Topics: Bacterial Proteins; Genome, Bacterial; Genomics; Paenibacillus; Paenibacillus polymyxa; Plant Development; Quorum Sensing
PubMed: 32764104
DOI: 10.26508/lsa.202000847 -
Scientific Reports Feb 2020Microbial flocculant (MBF), an environmentally friendly water treatment agent, can be widely used in various water treatments. However, its use is limited by low yield...
Microbial flocculant (MBF), an environmentally friendly water treatment agent, can be widely used in various water treatments. However, its use is limited by low yield and high cost. This problem can be solved by clarifying its biosynthesis mechanism and regulating it. Paenibacillus shenyangensis A9, a flocculant-producing bacterium, was used to produce polysaccharide-type MBFA9 by regulating the nitrogen source (nitrogen adequacy/nitrogen deficiency). In this study, RNA-Seq high-throughput sequencing technology and bioinformatic approaches were used to investigate the fermentation and biosynthesis of polysaccharide-type MBFA9 by regulating the nitrogen source (high nitrogen/low nitrogen) in the flocculant-producing bacteria Paenibacillus shenyangensis A9. Differentially expressed genes, functional clustering, and functional annotation of key genes were assessed. Then the MBFA9 biosynthesis and metabolic pathway were reconstructed. Our results showed that when cultured under different nitrogen conditions, bacterial strain A9 had a greater ability to synthesize polysaccharide-type MBFA9 under low nitrogen compared to high nitrogen conditions, with the yield of MBFA9 reaching 4.2 g/L at 36 h of cultivation. The quality of transcriptome sequencing data was reliable, with a matching rate of 85.38% and 85.48% when L36/H36 was mapped to the reference genome. The total expressed genes detected were 4719 and 4730, with 265 differentially expressed genes. The differentially expressed genes were classified into 3 categories: molecular function (MF), cell component (CC), and biological process (BP), and can be further divided into 22 subcategories. There were 192 upregulated genes and 73 downregulated genes, with upregulation being predominant under low nitrogen. UDP-Gal, UDP-Glc, UDP-GlcA, and UDP-GlcNAc, which are in the polysaccharide metabolic pathway, could all be used as precursors for MBFA9 biosynthesis, and murA, wecB, pgm, galU/galF, fcl, gmd, and glgC were the main functional genes capable of affecting the growth of bacteria and the biosynthesis of MBF. Results from this study provide evidence that high-level expression of key genes in MBFA9 biosynthesis, regulation, and control can achieve MBFA9 directional synthesis for large-scale applications.
Topics: Biosynthetic Pathways; Carbon; Flocculation; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Gene Ontology; Genes, Bacterial; Nitrogen; Paenibacillus; Polysaccharides
PubMed: 32075995
DOI: 10.1038/s41598-020-59114-z -
Current Microbiology Jan 2022Two bacterial strains were isolated and identified using microbial culturomics and characterised according to the taxono-genomics strategy. The strictly anaerobic...
Two bacterial strains were isolated and identified using microbial culturomics and characterised according to the taxono-genomics strategy. The strictly anaerobic strain, Marseille-P3773, forms smooth and translucent colonies consisting of Gram-stain negative, non-motile and non-spore-forming rod-shaped cells. Strain Marseille-P3787 consists of Gram-stain positive, motile and spore-forming cells resulting in grey and translucent colonies. The phylogenetic analysis of the 16S rRNA gene of strains Marseille-P3773 and Marseille-P3787 revealed a 96.9% similarity level with Lachnotalea glycerini strain DLD10 and 97% identity with Paenibacillus uliginis strain N3/975, respectively. The genome of strain Marseille-P3773 is 4,260,534 bp long with a 40.3 mol% G + C content and includes 3879 predicted genes of which 3769 are protein-coding genes, 76 RNAs and 34 are pseudo-genes. Strain Marseille-P3787 had a genome size of 4,833,032 bp with a 47.9 mol% G + C and has 4481 predicted genes of which 4265 are protein-coding genes, 101 RNAs and 115 are pseudo-genes. According to the data collected on these strains and, more specifically to the genomic comparison, we suggest the creation of a new genus and species, Konateibacter massiliensis gen. nov., sp. nov. with strain Marseille-P3773 (=CSURP3773 and CCUG71331) as its type strain within the Lachnospiraceae family, as well as a new species, Paenibacillus faecalis sp. nov. with strain Marseille-P3787 (=CSURP3787 and CCUG71650) as its type strain within the Paenibacillus genus.
Topics: DNA, Bacterial; Humans; Paenibacillus; Phylogeny; Protein-Energy Malnutrition; RNA, Ribosomal, 16S
PubMed: 35059831
DOI: 10.1007/s00284-021-02757-6 -
Antonie Van Leeuwenhoek Jan 2022A Gram-positive, nitrogen-fixing and endospore-forming strain, designated P121, was isolated from the gut of the armored catfish (Parotocinclus maculicauda) and...
A Gram-positive, nitrogen-fixing and endospore-forming strain, designated P121, was isolated from the gut of the armored catfish (Parotocinclus maculicauda) and identified as a member of the genus Paenibacillus based on the sequences of the 16S rRNA encoding gene, rpoB, gyrB and nifH genes and phenotypic analyses. The most closely related species to strain P121 were Paenibacillus rhizoplanae DSM 103993, Paenibacillus silagei DSM 101953 and Paenibacillus borealis DSM 13188, with similarity values of 98.9, 98.3 and 97.6%, respectively, based on 16S rRNA gene sequences. Genome sequencing revealed a genome size of 7,513,698 bp, DNA G + C content of 53.9 mol% and the presence of the structural nitrogenase encoding genes (nifK, nifD and nifH) and of other nif genes necessary for nitrogen fixation. Digital DNA-DNA hybridization (dDDH) experiments and average nucleotide identity (ANI) analyses between strain P121 and the type strains of the closest species demonstrated that the highest values were below the thresholds of 70% dDDH (42.3% with P. borealis) and 95% ANI (84.28% with P. silagei) for bacterial species delineation, indicating that strain P121 represents a distinct species. Its major cellular fatty acid was anteiso-C (42.4%), and the major isoprenoid quinone was MK-7. Based on physiological, genomic, biochemical and chemotaxonomic characteristics, we propose that strain P121 represents a novel species for which the name Paenibacillus piscarius sp. nov. is proposed (type strain = DSM 25072 = LFB-Fiocruz 1636).
Topics: Animals; Catfishes; DNA, Bacterial; Nitrogen; Paenibacillus; Phylogeny; RNA, Ribosomal, 16S
PubMed: 34993761
DOI: 10.1007/s10482-021-01694-5 -
Current Microbiology Sep 2015Amoebae of the genus Acanthamoeba occur worldwide and in addition to being pathogens, are important vehicles for microorganisms with clinical and environmental...
Amoebae of the genus Acanthamoeba occur worldwide and in addition to being pathogens, are important vehicles for microorganisms with clinical and environmental importance. This study aimed to evaluate the profiling of endosymbionts in 12 isolates of Acanthamoeba using V3 region of 16S rDNA denaturing gradient gel electrophoresis (DGGE) and sequencing. The DGGE enabled us to characterize the endosymbionts diversity in isolates of Acanthamoeba, and to identify Paenibacillus sp., an emerging pathogen, as an amoebic endosymbiont. The results of this study demonstrated that Acanthamoeba is capable of transporting a large number of endosymbionts. This is the first study that reports, the presence of Paenibacillus sp. as amebic symbiont.
Topics: Acanthamoeba; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Denaturing Gradient Gel Electrophoresis; Molecular Sequence Data; Paenibacillus; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Symbiosis
PubMed: 26159775
DOI: 10.1007/s00284-015-0869-8 -
Marine Drugs Jan 2022As a low molecular weight alginate, alginate oligosaccharides (AOS) exhibit improved water solubility, better bioavailability, and comprehensive health benefits. In...
As a low molecular weight alginate, alginate oligosaccharides (AOS) exhibit improved water solubility, better bioavailability, and comprehensive health benefits. In addition, their biocompatibility, biodegradability, non-toxicity, non-immunogenicity, and gelling capability make them an excellent biomaterial with a dual curative effect when applied in a drug delivery system. In this paper, a novel alginate lyase, Algpt, was cloned and characterized from a marine bacterium, sp. LJ-23. The purified enzyme was composed of 387 amino acid residues, and had a molecular weight of 42.8 kDa. The optimal pH of Algpt was 7.0 and the optimal temperature was 45 °C. The analysis of the conserved domain and the prediction of the three-dimensional structure indicated that Algpt was a novel alginate lyase. The dominant degradation products of Algpt on alginate were AOS dimer to octamer, depending on the incubation time, which demonstrated that Algpt degraded alginate in an endolytic manner. In addition, Algpt was a salt-independent and thermo-tolerant alginate lyase. Its high stability and wide adaptability endow Algpt with great application potential for the efficient preparation of AOS with different sizes and AOS-based products.
Topics: Alginates; Animals; Aquatic Organisms; China; Cloning, Molecular; Drug Delivery Systems; Lyases; Paenibacillus
PubMed: 35049921
DOI: 10.3390/md20010066