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Applied Microbiology and Biotechnology Oct 2023Cyclodextrin glucanotransferase (CGTase) is an extracellular enzyme of the GH13 α-amylase family that catalyzes a unique intramolecular reaction known as cyclization to... (Review)
Review
Cyclodextrin glucanotransferase (CGTase) is an extracellular enzyme of the GH13 α-amylase family that catalyzes a unique intramolecular reaction known as cyclization to transform α-1, 4-glucans and similar starches into cyclodextrins. They also catalyze intermolecular transglycosylation reactions namely coupling, disproportionation, and some hydrolyzing effects on starch. The monomeric structures of the CGTase exhibit five domains (A, B, C, D, and E domains) with different molecular weights and amino acid sequences depending on the source. Among bacteria, Bacillus genus covers approximately 90% of the CGTase producers, while other genera like Klebsiella, Paenibacillus, and Thermoanaerobacter also shown decent contributions in recent studies. CGTase production is highly supported by alkaliphilic bacteria under submerged fermentation rather than solid-state fermentation. The bacterial sources, biochemical properties, production conditions, and structure of CGTases are compiled in this review. Cyclodextrins have the unique property of making inclusion complexes with various compounds, hence widely used in the food, pharmaceutical, cosmetics, laundry, and chemical sectors. This review presents a comprehensive view of CGTase produced by Bacillus spp., and other bacterial genera like Klebsiella, Paenibacillus, and Microbacterium. It also gives insight of the properties and recent biotechnological applications of cyclodextrins. KEY POINTS: • Transglycosylation reactions catalyzed by CGTase and their structural properties. • Comparative data of CGTase production by various genera and Bacillus spp. • Structures, properties, and applications of different cyclodextrins.
Topics: Cyclodextrins; Amino Acid Sequence; Glucans; Glucosyltransferases; Bacillus; Starch
PubMed: 37548666
DOI: 10.1007/s00253-023-12708-9 -
Nature Communications Sep 2023The cell walls of pathogenic and acidophilic bacteria, such as Mycobacterium tuberculosis and Mycobacterium leprae, contain lipoarabinomannan and arabinogalactan. These...
The cell walls of pathogenic and acidophilic bacteria, such as Mycobacterium tuberculosis and Mycobacterium leprae, contain lipoarabinomannan and arabinogalactan. These components are composed of D-arabinose, the enantiomer of the typical L-arabinose found in plants. The unique glycan structures of mycobacteria contribute to their ability to evade mammalian immune responses. In this study, we identified four enzymes (two GH183 endo-D-arabinanases, GH172 exo-α-D-arabinofuranosidase, and GH116 exo-β-D-arabinofuranosidase) from Microbacterium arabinogalactanolyticum. These enzymes completely degraded the complex D-arabinan core structure of lipoarabinomannan and arabinogalactan in a concerted manner. Furthermore, through biochemical characterization using synthetic substrates and X-ray crystallography, we elucidated the mechanisms of substrate recognition and anomer-retaining hydrolysis for the α- and β-D-arabinofuranosidic bonds in both endo- and exo-mode reactions. The discovery of these D-arabinan-degrading enzymes, along with the understanding of their structural basis for substrate specificity, provides valuable resources for investigating the intricate glycan architecture of mycobacterial cell wall polysaccharides and their contribution to pathogenicity.
Topics: Animals; Female; Humans; Galactans; Lipopolysaccharides; Mycobacterium tuberculosis; Endometriosis; Mammals
PubMed: 37726269
DOI: 10.1038/s41467-023-41431-2 -
Archives of Microbiology Feb 2024Three Gram-reaction-positive bacterial strains, designated KSW-18, KSW2-22, and KSW4-11, were isolated from seawater, and two dried seaweed samples collected at Gwakji...
Three Gram-reaction-positive bacterial strains, designated KSW-18, KSW2-22, and KSW4-11, were isolated from seawater, and two dried seaweed samples collected at Gwakji Beach in Jeju, Republic of Korea, respectively, and their taxonomic positions were examined by a polyphasic approach. The 16S rRNA gene phylogeny showed that strain KSW4-11 was tightly associated with Microbacterium oleivorans NBRC 103075, while strains KSW-18 and KSW2-22 formed a distinctive subline at the base of a clade including the above two strains. The three isolates showed high sequence similarity with one another (99.7-99.9%; 1-4 nt differences) and Microbacterium oleivorans (99.8-99.9%; 1-3 nt differences). The chemotaxonomic features were typical for the genus Microbacterium; Lysine as the diagnostic diamino acid and N-glycolylated muramic acid of the peptidoglycans, the predominant menaquinones of MK-11, MK-10 and MK-12, the major fatty acids of anteiso-C and anteiso-C, and the major polar lipids including diphosphatidylglycerol, phosphatidylglycerol, and two or three unidentified glycolipids. In core genome-based phylogenetic tree, strains KSW-18 and KSW2-22 were closely associated with Microbacterium oleivorans NBRC 103075, while strain KSW4-11 formed a distinctive subline at the base of a clade including the above three strains, in contrast to the 16S rRNA gene tree. Strains KSW-18 and KSW2-22 shared an OrthoANIu of 98.6% and a digital DNA-DNA hybridization of 87.6% with each other, representing that they were strains of a species, while the OrthoANIu and digital DNA-DNA hybridization values between strains KSW-18 and KSW4-11, and between both of these isolates and all members of the genus Microbacterium were ≤86.5% and ≤30.7%, respectively. The analyses of overall genomic relatedness indices and phenotypic distinctness support that the three isolates represent two new species of the genus Microbacterium. Based on the results obtained here, Microbacterium aquilitoris sp. nov. (type strain KSW-18 = KCTC 49623 = NBRC 115222) and Microbacterium gwkjiense sp. nov. (type strain KSW4-11 = KACC 23321 = DSM 116380) are proposed.
Topics: Microbacterium; Phylogeny; RNA, Ribosomal, 16S; Actinomycetales; DNA
PubMed: 38353773
DOI: 10.1007/s00203-023-03804-5 -
International Journal of Systematic and... Nov 2023Two novel plant growth-promoting, rod-shaped, Gram-positive and non-motile rhizobacteria, W1N and W2R, were isolated from wetland plants and respectively, in China....
Two novel plant growth-promoting, rod-shaped, Gram-positive and non-motile rhizobacteria, W1N and W2R, were isolated from wetland plants and respectively, in China. The results of the 16S rRNA sequence alignment analysis showed that they were related to , with the highest similarity to (98.7 %) and (98.5 %) for strain W1N, and to (98.1 %) and (98.0 %) for strain W2R. Phylogenetic analyses based on 16S rRNA gene sequences and 92 conserved concatenated proteins suggested that the two strains belong to the genus and were placed in two separate novel phylogenetic clades. The genome sizes of the two strains were 3.2 and 3.7 Mb, and the G+C contents were 71.7 and 68.5 mol%, respectively. The comparative genome results showed that the average nucleotide identity values between W1N and W2R and other species ranged from 73.5 to 83.6 %, and the digital DNA-DNA hybridization values ranged from 19.7 to 26.8 %. These two strains show physiological and biochemical features that differ from those of closely related species. Rhamnose, galactose and glucose were present in the characteristic sugar fractions of strains W1N and W2R. The peptidoglycan of strains W1N and W2R contained the amino acids ornithine, alanine and aspartic acid. C anteiso, C anteiso and C iso were the predominant cellular fatty acids in W1N and W2R. Phosphatidylglycerol and diphosphatidylglycerol are major polar lipid components. Strain W1N not only formed bacterial biofilms but also had the ability to solubilize phosphorus and produce indole-3-acetic acid. Strain W2R had siderophore-producing and lignin-degrading properties. Based on their genetic and phenotypic characteristics, strains W1N and W2R were classified as novel bacteria in the genus and designated as sp. nov. (type strain W1N=ACCC 61807=GDMCC 1.2966=JCM 35339) and sp. nov. (type strain W2R=ACCC 61808=GDMCC 1.2967=JCM 35340).
Topics: Base Composition; Fatty Acids; Microbacterium; Phylogeny; RNA, Ribosomal, 16S; Wetlands; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; China; Actinomycetales
PubMed: 37917000
DOI: 10.1099/ijsem.0.006121 -
Frontiers in Microbiology 2023The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA...
The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a clade and distributed further into four subclusters in the core genome-based phylogenetic tree. phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA-DNA hybridization supported that the study strains constituted four new species of the genus . In addition, some type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, sp. nov., sp. nov., sp. nov., and sp. nov., are described, along with the proposal of gen. nov. containing five reclassified species from the " clade", with gen. nov., comb. nov. as the type species.
PubMed: 38164402
DOI: 10.3389/fmicb.2023.1299950 -
International Journal of Systematic and... Sep 2023Four Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped, motile endophytic bacterial strains, designated NM3R9, NE1TT3, NE2TL11 and NE2HP2, were isolated...
Four Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped, motile endophytic bacterial strains, designated NM3R9, NE1TT3, NE2TL11 and NE2HP2, were isolated from the inner tissues (leaf and stem) of and roots of . They were characterized using a polyphasic approach, which revealed that they represent two novel species. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the species closest to NE2HP2 was DSM 20754 (99.6 %) and that closest to NM3R9, NE2TL11 and NE2TT3 was NBRC 103075 (97.4 %). The whole-genome average nucleotide identity value between strain NM3R9 and DSM 20530 was 90.91 %, and that between strain NE2HP2 and DSM 20754 was 91.03 %. Digital DNA-DNA hybridization showed values of less than 70 % with the type strains of related species. The polar lipids present in both strains included diphosphatidylglycerol, phosphatidylglycerol, glycolipids and unidentified lipids, whereas the major fatty acids included anteiso-C, anteiso-C, iso-C and C. Whole-cell sugars included mannose, rhamnose and galactose. Strains NM3R9 and NE2HP2 showed physiological characteristics different from those present in closely related species. According to the taxonomic analysis, both strains belong to two novel species. The name sp. nov. is proposed for strain NE2HP2 (=LMG 30875=CCBAU 101117) and sp. nov. for strains NM3R9 (=LMG 30873=CCBAU 101116), NE1TT3 (=CCBAU 101114) and NE2TL11 (=CCBAU 101115).
Topics: Fatty Acids; Phospholipids; Prosopis; Microbacterium; Phylogeny; RNA, Ribosomal, 16S; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Sequence Analysis, DNA; Vitamin K 2; Actinomycetales
PubMed: 37754346
DOI: 10.1099/ijsem.0.006052 -
Journal of Agricultural and Food... Oct 2023Semiochemicals produced by microbes in hemipteran honeydew play an important role in mediating the ant-hemipteran interaction. However, the specific volatile compounds...
Semiochemicals produced by microbes in hemipteran honeydew play an important role in mediating the ant-hemipteran interaction. However, the specific volatile compounds and their origins remain unclear. Here, we found that honeydew produced by exhibited strong attractiveness to fire ant workers, but sterilized honeydew was much less attractive. Four compounds were identified from the honeydew volatiles, including 1-octen-3-ol, limonene, phenylethyl alcohol, and 2,4-di-butylphenol. All the identified compounds triggered strong electroantennography response of fire ants and showed repellence at relatively high concentrations while attractiveness at low concentrations to fire ant workers. Furthermore, six bacterial isolates were identified based on 16S rRNA sequencing, namely, , , , , , and . Fire ants exhibited a strong preference for , , and , suggesting that these bacterial isolates are involved in the attracting effect of honeydew. Both limonene and phenylethyl alcohol were detected from , while limonene was only detected from and phenylethyl alcohol was exclusively detected from . Reinoculation of these bacteria restored the attractiveness of honeydew to fire ants, and the active compounds, limonene and phenylethyl alcohol, were detectable in bacteria-reinoculated honeydew. Collectively, our results reveal the active compounds in hemipteran honeydew and their association with honeydew bacteria. The findings will contribute to the development of novel attractants for efficient monitoring of fire ants.
Topics: Animals; Ants; Pheromones; Limonene; Phenylethyl Alcohol; RNA, Ribosomal, 16S; Symbiosis; Bacteria
PubMed: 37843466
DOI: 10.1021/acs.jafc.3c04444 -
Foods (Basel, Switzerland) Nov 2023The microbial community in donkey milk and its impact on the nutritional value of donkey milk are still unclear. We evaluated the effects of different lactation stages...
The microbial community in donkey milk and its impact on the nutritional value of donkey milk are still unclear. We evaluated the effects of different lactation stages on the composition and function of donkey milk microbiota. The milk samples were collected at 1, 30, 60, 90, 120, 150, and 180 days post-delivery. The result showed that the microbial composition and functions in donkey milk were significantly affected by different lactation stages. The dominant bacterial phyla in donkey milk are (60%) and (22%). (39%), (4%), and (2%) were the predominant bacterial genera detected in all milk samples. In the mature milk, the abundance of lactic acid bacteria (7%) was higher. (5%) and (3%) were more plentiful in milk samples from middle and later lactation stages (90-180 d). Furthermore, the pathogens and and thermoduric bacteria , , and were also detected. Donkey milk is rich in beneficial bacteria and also poses a potential health risk. The above findings have improved our understanding of the composition and function changes of donkey milk microbiota, which is beneficial for the rational utilization of donkey milk.
PubMed: 38231735
DOI: 10.3390/foods12234272 -
Marine Drugs Oct 2023Dextranase, also known as glucanase, is a hydrolase enzyme that cleaves α-1,6 glycosidic bonds. In this study, a dextranase-producing strain was isolated from water...
Dextranase, also known as glucanase, is a hydrolase enzyme that cleaves α-1,6 glycosidic bonds. In this study, a dextranase-producing strain was isolated from water samples of the Qingdao Sea and identified as sp. This strain was further evaluated for growth conditions, enzyme-producing conditions, enzymatic properties, and hydrolysates. Yeast extract and sodium chloride were found to be the most suitable carbon and nitrogen sources for strain growth, while sucrose and ammonium sodium were found to be suitable carbon and nitrogen sources for fermentation. The optimal pH was 7.5, with a culture temperature of 40 °C and a culture time of 48 h. Dextranase produced by strain XD05 showed good thermal stability at 40 °C by retaining more than 70% relative enzyme activity. The pH stability of the enzyme was better under a weak alkaline condition (pH 6.0-8.0). The addition of NH increased dextranase activity, while Co and Mn had slight inhibitory effects on dextranase activity. In addition, high-performance liquid chromatography showed that dextran is mainly hydrolyzed to maltoheptanose, maltohexanose, maltopentose, and maltootriose. Moreover, it can form corn porous starch. Dextranase can be used in various fields, such as food, medicine, chemical industry, cosmetics, and agriculture.
Topics: Microbacterium; Dextranase; Hydrogen-Ion Concentration; Starch; Carbon; Nitrogen
PubMed: 37888463
DOI: 10.3390/md21100528 -
International Journal of Systematic and... Mar 2024Two Gram-positive, non-motile, short rod-shaped actinomycete strains, designated as A18JL241 and Y20, were isolated from deep-sea sediment samples collected from the...
Two Gram-positive, non-motile, short rod-shaped actinomycete strains, designated as A18JL241 and Y20, were isolated from deep-sea sediment samples collected from the Southwest Indian Ocean and Western Pacific Ocean, respectively. Both of the isolates were able to grow within the temperature range of 5-40 °C, NaCl concentration range of 0-7 % (w/v) and at pH 6.0-12.0. The two most abundant cellular fatty acids of both strains were anteiso-C and anteiso-C. The major polar lipid contents of the two strains were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified glycolipid. These two strains shared common chemotaxonomic features comprising MK-10 and MK-12 as the respiratory quinones. The genomic DNA G+C contents of the two strains were 68.1 and 70.4 mol%, respectively. The 16S rRNA gene phylogeny showed that the novel strains formed two distinct sublines within the genus . Strain A18JL241 was most closely related to the type strain of KCTC 49593 (98.8 % sequence similarity), whereas strain Y20 formed a tight cluster with the type strain of NBRC 15075 (99.0 %). The orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the type strains of related species were in the range of 74.1-89.1 % and 19.4-36.9 %, respectively, which were below the recognized thresholds of 95-96 % ANI and 70 % dDDH for species definition. Based on the results obtained here, it can be concluded that strains A18JL241 and Y20 represent two novel species of the genus , for which the names sp. nov. (type strain A18JL241=JCM 33956=MCCC 1A16622) and sp. nov. (type strain Y20=JCM 33960=MCCC 1A16747) are proposed.
Topics: Microbacterium; Base Composition; Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Nucleotides
PubMed: 38526416
DOI: 10.1099/ijsem.0.006299