ABSTRACT
The stereoselective synthesis of meso-diaminopimelic acid (meso-DAP), the key cross-linking amino acid of the peptidoglycan cell wall layer in Gram-negative bacteria, and its biological precursor, l,l-DAP, is described. The key step involved stereoselective reduction of a common enone-derived amino acid by substrate- or reagent-based control. Overman rearrangement of the resulting allylic alcohols, concurrent alkene hydrogenation and trichloroacetamide reduction, and subsequent ruthenium-catalyzed arene oxidation completed the synthesis of each stereoisomer. The synthetic utility of this approach was demonstrated with the efficient preparation of an l,l-DAP-derived dipeptide.
Subject(s)
Diaminopimelic Acid , Stereoisomerism , Diaminopimelic Acid/chemistry , Diaminopimelic Acid/chemical synthesis , Amino Acids/chemistry , Amino Acids/chemical synthesis , Molecular Structure , Catalysis , Oxidation-Reduction , Ketones/chemistryABSTRACT
A Gram-stain-positive, rod-shaped, aerobic, motile bacterium, J379T, was isolated from radioactive water spring C1, located in a former silver-uranium mine in the Czech Republic. This slow-growing strain exhibited optimal growth at 24-28â°C on solid media with <1â% salt concentration and alkaline pH 8-10. The only respiratory quinone found in strain J379T was MK-7(H4). C18â:â1 ω9c (60.9â%), C18â:â0 (9.4â%), C16â:â0 and alcohol-C18â:â0 (both 6.2â%) were found to be the major fatty acids. The peptidoglycan contained directly cross-linked meso-diaminopimelic acid. Phylogenetic reconstruction based on the 16S rRNA gene sequences and the core-genome analysis revealed that strain J379T forms a separate phylogenetic lineage within the recently amended order Solirubrobacterales. A comparison of the 16S rRNA gene sequences between strain J379T and other members of the order Solirubrobacterales showed <96â% similarity. This analysis revealed that the closest type strains were Parviterribacter kavangonensis D16/0 /H6T (95.2â%), Capillimicrobium parvum 0166_1T (94.9â%) and Conexibacter arvalis KV-962T (94.5â%). Whole-genome analysis showed that the closest type strain was Baekduia soli BR7-21T with an average nucleotide identity of 78â%, average amino acid identity of 63.2â% and percentage of conserved proteins of 48.2â%. The G+C content of the J379T genomic DNA was 71.7âmol%. Based on the phylogenetic and phylogenomic data, as well as its physiological characteristics, strain J379T is proposed to represent a type strain (DSM 113746T=CCM 9300T) of Svornostia abyssi gen. nov. sp. nov. within the family Baekduiaceae.
Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Mining , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , RNA, Ribosomal, 16S/genetics , Fatty Acids/chemistry , Fatty Acids/analysis , DNA, Bacterial/genetics , Czech Republic , Peptidoglycan , Diaminopimelic Acid/analysis , Vitamin K 2/analogs & derivatives , Vitamin K 2/analysis , Silver , Water MicrobiologyABSTRACT
The lung is prone to infections from respiratory viruses such as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). A challenge in combating these infections is the difficulty in targeting antiviral activity directly at the lung mucosal tract. Boosting the capability of the respiratory mucosa to trigger a potent immune response at the onset of infection could serve as a potential strategy for managing respiratory infections. This study focused on screening immunomodulators to enhance innate immune response in lung epithelial and immune cell models. Through testing various subfamilies and pathways of pattern recognition receptors (PRRs), the nucleotide-binding and oligomerization domain (NOD)-like receptor (NLR) family was found to selectively activate innate immunity in lung epithelial cells. Activation of NOD1 and dual NOD1/2 by the agonists TriDAP and M-TriDAP, respectively, increased the number of IL-8+ cells by engaging the NF-κB and interferon response pathways. Lung epithelial cells showed a stronger response to NOD1 and dual NOD1/2 agonists compared to control. Interestingly, a less-pronounced response to NOD1 agonists was noted in PBMCs, indicating a tissue-specific effect of NOD1 in lung epithelial cells without inducing widespread systemic activation. The specificity of the NOD agonist pathway was confirmed through gene silencing of NOD1 (siRNA) and selective NOD1 and dual NOD1/2 inhibitors in lung epithelial cells. Ultimately, activation induced by NOD1 and dual NOD1/2 agonists created an antiviral environment that hindered SARS-CoV-2 replication in vitro in lung epithelial cells.
Subject(s)
COVID-19 , Epithelial Cells , Lung , Nod1 Signaling Adaptor Protein , SARS-CoV-2 , Humans , A549 Cells , Antiviral Agents/pharmacology , COVID-19/immunology , COVID-19/virology , COVID-19 Drug Treatment , Diaminopimelic Acid/analogs & derivatives , Diaminopimelic Acid/pharmacology , Epithelial Cells/virology , Epithelial Cells/metabolism , Epithelial Cells/drug effects , Epithelial Cells/immunology , Immunity, Innate/drug effects , Interleukin-8/metabolism , Lung/immunology , Lung/virology , Lung/metabolism , NF-kappa B/metabolism , Nod1 Signaling Adaptor Protein/metabolism , Nod1 Signaling Adaptor Protein/agonists , Nod2 Signaling Adaptor Protein/agonists , Nod2 Signaling Adaptor Protein/metabolism , SARS-CoV-2/physiology , SARS-CoV-2/immunology , Signal Transduction/drug effectsABSTRACT
Strain HUAS 3-15T was isolated from the leaves of Cathaya argyrophylla collected from Chenzhou, Hunan Province, PR China. The main fatty acids (>5.0â%) of the strain were anteiso-C15â:â0, C16â:â0, C18â:â1 ω9c, iso-C16â:â0, summed feature 5 (C18â:â2 ω6,9c/C18â:â0 ante), iso-C15â:â0 and anteiso-C17â:â0. MK-9(H6), MK-9(H8) and MK-9(H4) were detected as respiratory quinones. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. Galactose, glucose and ribose were also present in the cell wall. The major polar lipids consisted of diphosphatidylglycerol, phosphatidyl ethanolamine, phosphatidylinositol mannosides and unidentified phospholipids. The DNA G+C content of the genome sequence, consisting of 8â860â963 bp, is 72.4âmol%. blast analysis based on 16S rRNA gene sequences revealed that the strain belongs to the genus Kitasatospora, with 99.37, 99.03, 98.95, 98.68 and 98.67â% sequence similarity to Kitasatospora aureofaciens ATCC 10762T, Kitasatospora viridis DSM 44826T, Kitasatospora xanthocidica NBRC 13469T, Kitasatospora aburaviensis NRRL B-2218T and Kitasatospora kifunensis IFO 15206T, respectively. Phylogenetic trees based on 16S rRNA gene and whole-genome sequences demonstrated that strain HUAS 3-15T formed a well-supported cluster with K. aureofaciens ATCC 10762T. Further genomic characterization through average nucleotide identity (ANIb/m) and digital DNA-DNA hybridization analysis between strain HUAS 3-15T and K. aureofaciens ATCC 10762T showed values of 90.62/92.55â% and 45.3â%, respectively, lower than the 95-96â% ANI threshold and 70.0â% cutoff used as guideline values for species delineation in bacteria. Furthermore, the differences between the strain and its phylogenomic neighbour in terms of physiological (e.g. sole carbon source growth) and chemotaxonomic (e.g. cellular fatty composition) characteristics further supported this conclusion. Consequently, we concluded that strain HUAS 3-15T represents a novel species of the genus Kitasatospora, for which the name Kitasatospora cathayae sp. nov. is proposed. The type strain is HUAS 3-15T (=MCCC 1K08542T=JCM 36274T).
Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Endophytes , Fatty Acids , Phospholipids , Phylogeny , Plant Leaves , RNA, Ribosomal, 16S , Sequence Analysis, DNA , RNA, Ribosomal, 16S/genetics , Fatty Acids/chemistry , Plant Leaves/microbiology , DNA, Bacterial/genetics , China , Endophytes/isolation & purification , Endophytes/genetics , Endophytes/classification , Phospholipids/chemistry , Vitamin K 2/analogs & derivatives , Cell Wall/chemistry , Diaminopimelic Acid , Nucleic Acid Hybridization , Actinomycetales/isolation & purification , Actinomycetales/genetics , Actinomycetales/classificationABSTRACT
A Gram-stain-positive actinomycete, designated REN17T, was isolated from fermented grains of Baijiu collected from Sichuan, PR China. It exhibited branched substrate mycelia and a sparse aerial mycelium. The optimal growth conditions for REN17T were determined to be 28â°C and pH 7, with a NaCl concentration of 0â% (w/v). ll-Diaminopimelic acid was the diagnostic amino acid of the cell-wall peptidoglycan and the polar lipids were composed of phosphatidylethanolamine, phosphatidylinositol, an unidentified phospholipid, two unidentified lipids and four unidentified glycolipids. The predominant menaquinone was MK-9 (H2), MK-9 (H4), MK-9 (H6) and MK-9 (H8). The major fatty acids were iso-C16 : 0. The 16S rRNA sequence of REN17T was most closely related to those of Streptomyces apricus SUN 51T (99.8â%), Streptomyces liliiviolaceus BH-SS-21T (99.6â%) and Streptomyces umbirnus JCM 4521T (98.9â%). The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identify values between REN17T and its closest replated strain, of S. apricus SUN 51T, were 35.9, 88.9 and 87.3â%, respectively. Therefore, REN17T represents a novel species within the genus Streptomyces, for which the name Streptomyces beigongshangae sp. nov. is proposed. The type strain is REN17T (=GDMCC 4.193T=JCM 34712T). While exploring the function of the strain, REN17T was found to possess the ability to transform major ginsenosides of Panax notoginseng (Burk.) F.H. Chen (Araliaceae) into minor ginsenoside through HPLC separation, which was due to the presence of ß-glucosidase. The recombinant ß-glucosidase was constructed and purified, which could produce minor ginsenosides of Rg3 and C-K. Finally, the enzymatic properties were characterized.
Subject(s)
Bacterial Typing Techniques , DNA, Bacterial , Fatty Acids , Fermentation , Ginsenosides , Nucleic Acid Hybridization , Panax notoginseng , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , Streptomyces , Vitamin K 2 , RNA, Ribosomal, 16S/genetics , Fatty Acids/chemistry , Streptomyces/isolation & purification , Streptomyces/genetics , Streptomyces/classification , Vitamin K 2/analogs & derivatives , DNA, Bacterial/genetics , China , Panax notoginseng/microbiology , Ginsenosides/metabolism , Peptidoglycan , Edible Grain/microbiology , Diaminopimelic Acid , Phospholipids/chemistry , Base CompositionABSTRACT
Fish rely on innate immune system for immunity, and nucleotide-binding oligomerization domain-like receptors (NLRs) are a vital group of receptor for recognition. In the present study, NOD1 gene was cloned and characterized from golden pompano Trachinotus ovatus, a commercially important aquaculture fish species. The ORF of T. ovatus NOD1 was 2820 bp long, encoding 939 amino acid residues with a highly conserved domains containing CARD-NACHT-LRRs. Phylogenetic analysis revealed that the T. ovatus NOD1 clustered with those of fish and separated from those of birds and mammals. T. ovatus NOD1 has wide tissue distribution with the highest expression in gills. Bacterial challenges (Streptococcus agalactiae and Vibrio alginolyticus) significantly up-regulated the expression of NOD1 with different response time. The results of T. ovatus NOD1 ligand recognition and signaling pathway analysis revealed that T. ovatus NOD1 could recognize iE-DAP at the concentration of ⧠100 ng/mL and able to activate NF-κB signaling pathway. This study confirmed that NOD1 play a crucial role in the innate immunity of T. ovatus. The findings of this study improve our understanding on the immune function of NOD1 in teleost, especially T. ovatus.
Subject(s)
Amino Acid Sequence , Fish Diseases , Fish Proteins , Immunity, Innate , Nod1 Signaling Adaptor Protein , Phylogeny , Sequence Alignment , Vibrio alginolyticus , Animals , Nod1 Signaling Adaptor Protein/genetics , Nod1 Signaling Adaptor Protein/immunology , Nod1 Signaling Adaptor Protein/chemistry , Fish Proteins/genetics , Fish Proteins/immunology , Fish Proteins/chemistry , Immunity, Innate/genetics , Fish Diseases/immunology , Sequence Alignment/veterinary , Vibrio alginolyticus/physiology , Streptococcal Infections/immunology , Streptococcal Infections/veterinary , Streptococcus agalactiae/physiology , Gene Expression Regulation/immunology , Gene Expression Profiling/veterinary , Vibrio Infections/immunology , Vibrio Infections/veterinary , Diaminopimelic Acid/chemistry , Diaminopimelic Acid/analogs & derivatives , Perciformes/immunology , Perciformes/genetics , Fishes/immunology , Fishes/geneticsABSTRACT
Strain Odt1-22T, an insect-derived actinomycete was isolated from a termite (Odontotermes formosanus) that was collected from Chanthaburi province, Thailand. Strain Odt1-22T was aerobic, Gram-stain-positive, and produced bud-like spore chain on the substrate hypha. According to chemotaxonomic analysis, strain Odt1-22T contained meso-diaminopimelic acid in peptidoglycan and the whole-cell hydrolysates contained arabinose, galactose, glucose, and ribose. The major menaquinone was MK-8(H4). The diagnostic phospholipids were diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis based on 16 S rRNA gene sequence revealed that strain Odt1-22T was identified to the genus Actinomycetospora and showed high similarity values with A. chiangmaiensis DSM 45062 T (99.24%), A. soli SF1T (99.24%) and A. corticicola 014-5 T (98.17%). The genomic size of strain Odt1-22T was 6.6 Mbp with 73.8% G + C content and 6355 coding sequences (CDSs). The genomic analysis, strain Odt1-22T and closely related species A. chiangmaiensis DSM 45062 T, A. soli SF1T and A. corticicola DSM 45772 T displayed the values of average nucleotide identity-blast (ANIb) at 83.7-84.1% and MUMmer (ANIm) at 86.6-87.0%. Moreover, the results of digital DNA-DNA hybridization values between strain Odt1-22T and related Actinomycetospora species were 45.8-50.5% that lower than the threshold value of commonly used to delineate separated species level. On the basis of phenotypic, chemotaxonomic, and genotypic data, strain Odt1-22T represented a novel species within the genus Actinomycetospora, for which the name Actinomycetospora termitidis sp. nov. is proposed. The type strain of the species is Odt1-22T (= TBRC 16192 T = NBRC 115965 T).
Subject(s)
Isoptera , Phylogeny , RNA, Ribosomal, 16S , Animals , Isoptera/microbiology , RNA, Ribosomal, 16S/genetics , Thailand , DNA, Bacterial/genetics , Actinobacteria/genetics , Actinobacteria/isolation & purification , Actinobacteria/classification , Diaminopimelic Acid , Vitamin K 2/chemistry , Base Composition , Phospholipids/chemistry , Sequence Analysis, DNAABSTRACT
OBJECTIVES: During innate immune defense, host pattern recognition receptors, including toll-like receptors and nucleotide-binding oligomerization domain-like receptors (NLRs), can activate downstream pathways by recognizing pathogen-associated molecular patterns produced by microorganisms, triggering immune responses. NOD1, an important cell membrane protein in the NLR-like receptor protein family, exerts anti-infective effects through γ-D-glutamyl-meso-diaminopimelic acid (iE-DAP) recognition. Oral epithelial cells resist bacterial invasion through iE-DAP-induced interleukin (IL)-8 production, recruiting neutrophils to sites of inflammation in response to bacterial threats to periodontal tissues. To date, the regulatory mechanisms of iE-DAP in gingival epithelial cells (GECs) are poorly understood. This study was conducted to investigate the role of the NOD1 pathway in the development of periodontitis by examining the effect of iE-DAP on IL-8 production in Ca9-22 cells. METHODS: IL-8 production by iE-DAP-stimulated-Ca9-22 cells was assessed using an enzyme-linked immunosorbent assay. Phosphorylation levels of intracellular signaling molecules were evaluated using western blot analyses. RESULTS: iE-DAP induced NOD1 receptor expression in Ca9-22 cells. Additionally, iE-DAP induced expression of pro-IL-1ß protein without extracellular secretion. Our results suggest that iE-DAP regulates IL-8 production by activating p38 mitogen-activated protein kinase (MAPK) and ERK1/2 signaling pathways. iE-DAP also promoted nuclear factor kappa-B p65 phosphorylation, facilitating its nuclear translocation. Notably, p38 MAPK and ERK1/2 inhibitors suppressed iE-DAP-stimulated IL-8 production, suggesting that JNK is not involved in this mechanism. CONCLUSIONS: Our results indicate that p38 MAPK and ERK1/2, but not JNK, are involved in innate immune responses in GECs.
Subject(s)
Diaminopimelic Acid/analogs & derivatives , Interleukin-8 , Periodontitis , Humans , Nucleotides , p38 Mitogen-Activated Protein KinasesABSTRACT
In this study, two novel alkalitolerant strains (FJAT-53046T and FJAT-53715T) were isolated from sediment samples collected in Zhangzhou, PR China. Phylogeny based on 16S rRNA gene sequences suggested that strains FJAT-53046T and FJAT-53715T were new members of the genus Pseudalkalibacillus. The two novel strains showed the highest 16S rRNA gene sequence similarity to Pseudalkalibacillus hwajinpoensis DSM 16206T, with values of 97.4 and 97.6â%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains and the reference strain were 77.2 and 79.6â%, 20.9 and 30.2â%, respectively, which were below the prokaryotic species delineation thresholds. The ANI and dDDH values between strains FJAT-53046T and FJAT-53715T were 86.0 and 30.2â%, respectively, suggesting that they belonged to different species in the genus Pseudalkalibacillus. The major respiratory quinone in both strains was MK-7 and the major cellular fatty acids were anteiso-C15â:â0 and anteiso-C17â:â0. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids in both novel strains. Combined with results stemming from the determination of physical and biochemical characteristics, chemical properties, and genome analysis, strains FJAT-53046T and FJAT-53715T are proposed to represent two novel species of the genus Pseudalkalibacillus, for which the names Pseudalkalibacillus spartinae sp. nov. and Pseudalkalibacillus sedimenti sp. nov. are proposed. The type strains are FJAT-53046T (=GDMCC 1.3077T=JCM 35611T) and FJAT-53715T (=GDMCC 1.3076T=JCM 35610T), respectively.
Subject(s)
Bacillus , Fatty Acids , Fatty Acids/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Phylogeny , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Sequence Analysis, DNA , Soil Microbiology , Cell Wall/chemistry , Diaminopimelic Acid/chemistry , Peptidoglycan/chemistry , Vitamin K 2/chemistryABSTRACT
NOD1 and NOD2 sense small bacterial peptidoglycan fragments, often called muropeptides, that access the cytosol. These muropeptides include iE-DAP and MDP, the minimal agonists for NOD1 and NOD2, respectively. Here, we synthesized and validated alkyne-modified muropeptides, iE-DAP-Alk and MDP-Alk, for use in click-chemistry reactions. While it has long been known that many cell types respond to extracellular exposure to muropeptides, it is unclear how these innate immune activators access their cytosolic innate immune receptors, NOD1 and NOD2. The subcellular trafficking and transport mechanisms by which muropeptides access these cytosolic innate immune receptors are a major gap in our understanding of these critical host responses. The click-chemistry-enabled agonists developed here will be particularly powerful to decipher the underlying cell biology and biochemistry of NOD1 and NOD2 innate immune sensing.
Subject(s)
Nod1 Signaling Adaptor Protein , Receptor Protein-Tyrosine Kinases , Diaminopimelic Acid/metabolism , Receptor Protein-Tyrosine Kinases/metabolism , Nod1 Signaling Adaptor Protein/metabolism , Nod2 Signaling Adaptor Protein/genetics , Nod2 Signaling Adaptor Protein/metabolismABSTRACT
A novel actinobacterium, designated as strain WRP15-2T, was isolated from rhizosphere soil of rice plant (Oryza rufipogon). The strain was Gram-stain-positive, aerobic, and non-motile. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain WRP15-2T fell into the genus Saccharopolyspora. The strain shared the highest 16S rRNA gene sequence similarity with the type strains Saccharopolyspora kobensis JCM 9109T (99.1%), Saccharopolyspora indica VRC122T (98.9%), and Saccharopolyspora antimicrobica DSM 45119T (98.7%). However, the digital DNA-DNA hybridization and average nucleotide identity values among these strains confirmed that the microorganism represented a novel member of the genus Saccharopolyspora. Chemotaxonomic data revealed that strain WRP15-2T possessed MK-9(H4) as the predominant menaquinone. It contained meso-diaminopimelic acid as the diagnostic diaminopimelic acid and arabinose, galactose, and ribose as predominant whole-cell sugars. The detected phospholipids were dominated by phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxy-phosphatidylmethylethanolamine, and phosphatidylcholine. The predominant cellular fatty acids were iso-C16:0, C16:0, and iso-C15:0. The G + C content of the genomic DNA was 69.5%. Based on these genotypic and phenotypic data, it is supported that strain WRP15-2T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora oryzae sp. nov. is proposed. The type strain is WRP15-2T ( = TBRC 15728T = NBRC 115560T).
Subject(s)
Oryza , Saccharopolyspora , Phosphatidylethanolamines , Saccharopolyspora/genetics , Rhizosphere , Phylogeny , RNA, Ribosomal, 16S/genetics , Diaminopimelic Acid , DNA, Bacterial/genetics , Fatty Acids , Sequence Analysis, DNA , Bacterial Typing TechniquesABSTRACT
Growing antibiotic resistance by pathogenic bacteria has led to a global crisis. The bacterial enzyme N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) provides a very attractive target for the discovery of a new class of antibiotics, as it resides exclusively in many pathogenic bacterial strains and is a key enzyme in the lysine biosynthetic pathway. This pathway is responsible for the production of lysine as well as meso-diaminopimelate (m-DAP), both of which are required for peptidoglycan cell-wall synthesis, and lysine for peptide synthesis. The enzyme DapE catalyzes the hydrolysis of N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) to succinate and l,l-diaminopimelic acid (l,l-DAP), and due to its absence in humans, inhibition of DapE avoids mechanism-based side effects. We have executed the asymmetric synthesis of N,N-dimethyl-SDAP, an l,l-SDAP substrate analog and an analog of the synthetic substrate of our previously described DapE assay. Previous modeling studies advocated that N,N-dimethyl-SDAP might function as an inhibitor, however the compound behaves as a substrate, and we have demonstrated the use of N,N-dimethyl-SDAP as the substrate in a modified ninhydrin-based DapE assay. Thermal shift experiments of DapE in the presence of N,N-dimethyl-SDAP are consistent with a melt temperature (Tm) shifted by succinate, the product of enzymatic hydrolysis.
Subject(s)
Lysine , Succinates , Humans , Diaminopimelic Acid/chemistry , Diaminopimelic Acid/metabolism , Drug Resistance, BacterialABSTRACT
An isolation effort focused on sporogenous Actinomycetota from the Tagus estuary in Alcochete, Portugal, yielded a novel actinomycetal strain, designated MTZ3.1T, which was subjected to a polyphasic taxonomic study. MTZ3.1T is characterised by morphology typical of members of the genus Streptomyces, with light beige coloured substrate mycelium, which does not release pigments to the culture medium and with helicoidal aerial hyphae that differentiate into spores with a light-grey colour. The phylogeny of MTZ3.1T, based on the full 16S rRNA gene sequence, indicated that its closest relatives were Streptomyces alkaliterrae OF1T (98.48â%), Streptomyces chumphonensis KK1-2T (98.41â%), Streptomyces albofaciens JCM 4342T (98.34â%), Streoptomyces paromomycinus NBRC 15454T (98.34â%) and Streptomyces chrestomyceticus NRBC 13444T (98.34â%). Moreover, average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridisation (dDDH) are below the species cutoff values (ANI 67.70 and 68.35â%, AAI 77.06 and 76.71â% and dDDH 22.10 and 21.50â% for S. alkaliterrae OF1T and S. chumphonensis KK1-2T, respectively). Whole genome sequencing revealed that MTZ3.1T has a genome of 5 644 485 bp with a DNA G+C content of 71.29 mol% and 5044 coding sequences. Physiologically, MTZ3.1T is strictly aerobic, able to grow at 15-37 °C, optimally at 25 °C and between pH5 and 8 and showed high salinity tolerance, growing with 0-10â%(w/v) NaCl. Major cellular fatty acids are C15â:â0, iso-C15â:â0, anteiso-C15â:â0 and iso-C16â:â0. Furthermore, it was able to utilise a variety of nitrogen and carbon sources. Antimicrobial screening indicated that MTZ3.1T has potent anti-Staphylococcus aureus activity. On the basis of the polyphasic data, MTZ3.1T is proposed to represent a novel species, Streptomyces meridianus sp. nov. (= CECT 30416T = DSM 114037T=LMG 32463T).
Subject(s)
Fatty Acids , Streptomyces , Fatty Acids/chemistry , RNA, Ribosomal, 16S/genetics , Portugal , Estuaries , Sequence Analysis, DNA , Phylogeny , Base Composition , DNA, Bacterial/genetics , Bacterial Typing Techniques , Diaminopimelic Acid/chemistry , Saline Waters , Phospholipids/chemistryABSTRACT
Streptomyces albulus NBRC14147 produces a homopoly(amino acid), ε-poly-L-lysine (ε-PL). Due to its antibiotic activity, thermostability, biodegradability, and non-toxicity to humans, ε-PL is used as a food preservative. In this study, homology searches of diaminopimelate (DAP) pathway genes (dapB and dapE), in an S. albulus genome database, were shown to encode predicted enzymes using dapB or dapE in Escherichia coli strain complementation assays. We observed that dapB and dapE transcriptional levels were weak during ε-PL production stages. Therefore, we strengthened this expression using an ermE constitutive promoter. Engineered strains generated faster growth and ε-PL production rates when compared with the control strain. Moreover, maximum ε-PL yields in S. albulus, where dapB was constitutively expressed, were approximately 14% higher when compared with the control strain. These findings showed that enhanced lysine biosynthetic gene expression generated faster and higher ε-PL production levels.
Subject(s)
Polylysine , Streptomyces , Humans , Fermentation , Gene Expression , Polylysine/genetics , Polylysine/metabolism , Streptomyces/metabolism , Diaminopimelic Acid/metabolismABSTRACT
Three Gram-positive-staining strains FJAT-49754T, FJAT-49682 and FJAT-49731 were isolated from the citrus rhizosphere soil sample. These strains showed the highest 16S rRNA gene sequence similarity with the type strain of Lederbergia panacisoli (97.8-97.9â%). The 16S rRNA gene sequence similarities between strains FJAT-49754T, FJAT-49682, and FJAT-49731 were 99.9â%. The average nucleotide identity (ANI) values between strains FJAT-49754T, FJAT-49682 and FJAT-49731 were above 96â%, while the ANI values with the members of the genus Lederbergia were below 95â%, which were below the cut-off level for prokaryotic species delineation. The above results suggest that strains FJAT-49754T, FJAT-49682 and FJAT-49731 belong to a novel species of the genus Lederbergia. Growth of strain FJAT-49754T was observed at 10-40 °C (optimum at 30 °C, pH 6.0-10.0 (optimum at pH 8.0), and NaCl tolerance up to 7â% (w/v) (optimum at 1â%). MK-7 was the only menaquinone detected in strain FJAT-49754T, and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids of strain FJAT-49754T were anteiso-C15â:â0, iso-C15â:â0, and C16â:â0. The genomic DNA G+C content of strain FJAT-49754T was 38.7â%. Based on the above results, strain FJAT-49754T represents a novel species of the genus Lederbergia, for which the name Lederbergia citrea sp. nov., is proposed. The type strain is FJAT-49754T (=CCTCC AB 2019211T=LMG 31589T).
Subject(s)
Fatty Acids , Rhizosphere , Fatty Acids/chemistry , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Nucleic Acid Hybridization , Base Composition , Phylogeny , Soil Microbiology , Bacterial Typing Techniques , Diaminopimelic Acid/chemistry , Sequence Analysis, DNA , Cell Wall/chemistry , Peptidoglycan/chemistryABSTRACT
An actinomycete strain, AA8T, which produced a long straight chain of spores (verticillati type), was isolated from the rhizosphere soil of Mangifera indica in Bangkok, Thailand. A polyphasic taxonomic study was carried out to establish the taxonomic position of the strain. Strain AA8T formed a tight taxonomic position in the 16S rRNA gene tree with Streptomyces roseifaciens MBT76T. In contrast, the genome-based taxonomic analysis showed that strain AA8T shared low average nucleotide identity-BLAST (94.1%), the digital DNA-DNA hybridization (58.2%), and the average amino acid identity (93.6%) values with S. roseifaciens MBT76T. Moreover, a combination of physiological and biochemical properties indicated that strain AA8T was distinguished from all Streptomyces species with effectively published names. Strain AA8T, therefore, represents a novel species of Streptomyces, and the name Streptomyces telluris is proposed for the strain. The type strain is AA8T (= TBRC 8483T = NBRC 113461T). The chemical investigation led to the isolation of nine known compounds (compounds 1-9). Among these compounds, compound 7 (3,4-dihydroxybenzaldehyde) possesses strong antioxidant activity equal to ascorbic acid, a powerful antioxidative agent.
Subject(s)
Streptomyces , Fatty Acids/chemistry , Phospholipids/chemistry , Antioxidants , Sequence Analysis, DNA , RNA, Ribosomal, 16S/genetics , Diaminopimelic Acid/chemistry , Phylogeny , DNA, Bacterial/genetics , Bacterial Typing Techniques , Base Composition , Soil Microbiology , ThailandABSTRACT
A white-coloured, rod-shaped, motile, aerobic, and Gram-stain-positive bacterial strain S3N08T was isolated from agricultural soil. The strain grew at temperature 10-40 °C, at 0-1.0% (w/v) NaCl concentration, and at pH 6.5-8.0. Catalase was negative and oxidase was positive. The phylogenetic analysis inferred that the strain S3N08T belonged to the genus Paenibacillus, with the closest relative being Paenibacillus periandrae PM10T (95.6% 16S rRNA gene sequence similarity). The only menaquinone was MK-7 and the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylglycerol, and phosphatidylethanolamine. The predominant fatty acids were antiso-C15:0, C16:0, and iso-C15:0. The DNA G + C content was 45.1%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain S3N08T and with closest members were < 72.0% and < 19.0%, respectively. Altogether, the phylogenetic, genomics, phenotypic, and chemotaxonomic evidence illustrated in this study suggested that strain S3N08T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus agricola sp. nov. is proposed. The type strain is S3N08T (= KACC 19666 T = NBRC 113430 T).
Subject(s)
Paenibacillus , Phospholipids , Phospholipids/chemistry , Soil , Phylogeny , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Sequence Analysis, DNA , Soil Microbiology , Bacterial Typing Techniques , Diaminopimelic Acid/chemistry , Fatty Acids/chemistryABSTRACT
A novel actinobacterium, designated strain SMC 277T, was isolated from the clay soil in paddy field of Chonburi Province, Thailand, and characterized using polyphasic taxonomy. Strain SMC 277T formed straight chains of nonmotile cylindrical spores with smooth surface developed on aerial mycelia. The typical chemotaxonomic properties of members of the genus Streptomyces were observed in strain SMC 277T, e.g., cell wall peptidoglycan, whole cell sugars, major menaquinones, cellular fatty acids, and polar lipids. Chemotaxonomic data combined with mycelium and spore morphologies supported the assignment of strain SMC 277T to the genus Streptomyces. The results of comparative analysis of the 16S rRNA gene sequences confirmed that strain SMC 277T represented a member of the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMC 277T shared the highest sequence similarity with Streptomyces bambusae NBRC 110903T (98.8%). Genome sequencing revealed a genome size of 6.55 Mbp and a digital G+C content of 73.4 mol%. In addition to the differences in phenotypic characteristics (morphology and physiology), values of ANI (ANIb and ANIm), AAI and dDDH between strain SMC 277T and its closest relative S. bambusae NBRC 110903T were 81.84, 86.77, 76.91 and 26.1%, respectively. Genome annotation and secondary metabolite gene cluster analysis predicted that SMC 277T contained 35 biosynthetic gene clusters encoding diverse bioactive secondary metabolites. It is in agreement with observed antimicrobial activity against drug-resistant bacteria associated with nosocomial infections (methicillin-resistant Staphylococcus aureus, extended-spectrum ß-lactamase producing Klebsiella pneumoniae, and multidrug-resistant Acinetobacter baumannii). On the basis of these genotypic and phenotypic characteristics, strain SMC 277T can be characterized to represent a novel species of the genus Streptomyces, for which the name Streptomyces antimicrobicus is proposed. The type strain is SMC 277T (= TBRC 15568T = NBRC 115422T).
Subject(s)
Actinobacteria , Anti-Infective Agents , Methicillin-Resistant Staphylococcus aureus , Streptomyces , Phospholipids/metabolism , Clay , Soil , Phylogeny , RNA, Ribosomal, 16S/genetics , RNA, Ribosomal, 16S/metabolism , Methicillin-Resistant Staphylococcus aureus/genetics , Diaminopimelic Acid/metabolism , Thailand , Streptomyces/metabolism , Fatty Acids/metabolism , Actinobacteria/genetics , Anti-Infective Agents/pharmacology , Anti-Infective Agents/metabolism , DNA, Bacterial/genetics , Sequence Analysis, DNA , Bacterial Typing TechniquesABSTRACT
An endophytic actinobacterium, strain PIP175T, was isolated from the root sample of a native apricot tree (Pittosporum angustifolium) growing on the Bedford Park campus of Flinders University, Adelaide, South Australia. This strain is a Gram stain-positive, aerobic actinobacterium with well-developed substrate mycelia. Aerial mycelia rarely produce spores and the spore chain is spiral. Strain PIP175T showed the highest 16S rRNA gene sequence similarity to Streptomyces aculeolatus DSM 41644T (99.4â%). Other closely related phylogenetic representatives include Streptomyces synnematoformans DSM 41902T (98.3â%), Streptomyces albospinus NBRC 13846T (97.6â%), Streptomyces cacaoi subsp. cacaoi NRRL B-1220T (97.5â%) and Streptomyces ruber NBRC 14600T (97.4â%). The major cellular fatty acid of this strain was iso-C16â:â0 and the major menaquinone was MK-9(H6). The whole-cell sugar contained galactose, glucose and mannose. Chemotaxonomic data confirmed that strain PIP175T belonged to the genus Streptomyces. Digital DNA-DNA hybridization, average nucleotide identity based on blast and OrthoANIu results between strain PIP175T and S. aculeolatus DSM 41644T were 60.0, 94.1 and 94.9â%, respectively. Genotypic and phenotypic data and genome analysis results allowed the differentiation of strain PIP175T from its closest species with validly published names. Strain PIP175T showed good activity against methicillin-resistant Staphylococcus aureus 03120385. Genome mining of strain PIP175T revealed biosynthetic genes encoding proteins relating to antibiotic production, plant growth promotion and biodegradation enzymes. The name proposed for the new species is Streptomyces phytophilus sp. nov. The type strain is PIP175T (=DSM 103379T=TBRC 6026T).
Subject(s)
Actinobacteria , Methicillin-Resistant Staphylococcus aureus , Streptomyces , Humans , Fatty Acids/chemistry , Phospholipids/analysis , Phylogeny , RNA, Ribosomal, 16S/genetics , Anti-Bacterial Agents , Methicillin-Resistant Staphylococcus aureus/genetics , Diaminopimelic Acid/analysis , Sequence Analysis, DNA , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/geneticsABSTRACT
PURPOSE: Duodenal-jejunal bypass (DJB) has a definite hypoglycemic effect; however, the intrinsic mechanisms remain unclear. The purpose of this study was to determine whether DJB may cause changes in the gut microbiota and metabolite of portal venous blood and to explore the effects of DJB on blood glucose metabolism. METHODS: T2DM was induced in rats with a high-fat diet and a low dose of streptozotocin, which were randomly divided into two groups: Sham operation and DJB. RESULTS: DJB significantly improved several diabetic parameters. 16S rRNA analyses showed that the compositions of the gut microbiota were significantly different between the two groups. The results of metabolomics showed that DJB could significantly regulate the metabolites, among which diaminopimelic acid and isovaleric acid had a significant down-regulation in the DJB group. Transcriptomic analysis showed that DJB can regulate the expression of hepatic genes related to abnormal glucose metabolism, such as Ltc4s, Alox15, Ggt1, Gpat3, and Cyp2c24. Correlation analyses showed that diaminopimelic acid was positively associated with Allobaculum, Serratia, and Turicibacter. There was a significant correlation between diaminopimelic acid and Gpat3, and its Spearman correlation coefficient was the highest among metabolite-DEG pairs (ρ=0.97). DISCUSSIONS: These results suggest an important cue of the relation between the diaminopimelic acid, Gpat3, and gut microbiome in the mechanism by which DJB can improve glucose metabolism.