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The Enzymes 2020Choline oxidase catalyzes the four-electron, two-step, flavin-mediated oxidation of choline to glycine betaine. The enzyme is important both for medical and... (Review)
Review
Choline oxidase catalyzes the four-electron, two-step, flavin-mediated oxidation of choline to glycine betaine. The enzyme is important both for medical and biotechnological reasons, because glycine betaine is one among a limited number of compatible solutes used by cells to counteract osmotic pressure. From a fundamental standpoint, choline oxidase has emerged as one of the paradigm enzymes for the oxidation of alcohols catalyzed by flavoproteins. Mechanistic, structural, and computational studies have elucidated the mechanism of action of the enzyme from Arthrobacter globiformis at the molecular level. Both choline and oxygen access to the active site cavity are gated and tightly controlled. Amino acid residues involved in substrate binding, and their contribution, have been identified. The mechanism of choline oxidation, with a hydride transfer reaction, an asynchronous transition state, the formation and stabilization of an alkoxide transient species, and a quantum mechanical mode of reaction, has been elucidated. The importance of nonpolar side chains for oxygen localization and of the positive charge harbored on the substrate for activation of oxygen for reaction with the reduced flavin have been recognized. Interesting phenomena, like the formation of a metastable photoinduced flavin-protein adduct, the reversible formation of a bicovalent flavoprotein, and the trapping of the enzyme in inactive conformations, have been described. This review summarizes the current status of our understanding on the structure-function-dynamics of choline oxidase.
Topics: Alcohol Oxidoreductases; Arthrobacter; Bacterial Proteins; Catalysis; Choline; Kinetics; Oxygen
PubMed: 32951822
DOI: 10.1016/bs.enz.2020.05.004 -
Frontiers in Microbiology 2023Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an...
Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an in-depth analysis of microbial diversity that no other approach allows. Bearing in mind that culture-dependent approaches cannot replace culture-independent approaches, we have improved an original method for isolating strains consisting of "culturing" grains of sand directly on Petri dishes (grain-by-grain method). This method allowed to cultivate up to 10% of the bacteria counted on the surface of grains of the three sites studied in the Great Western Erg in Algeria (Timoudi, Béni Abbès, and Taghit), knowing that on average about 10 bacterial cells colonize each grain. The diversity of culturable bacteria (collection of 290 strains) predicted by 16S rRNA gene sequencing revealed that , , , , and are the dominant species. The comparison of the culture-dependent and -independent (16S rRNA gene metabarcoding) approaches at the Timoudi site revealed 18 bacterial genera common to both approaches with a relative overestimation of the genera / and , and a relative underestimation of the genera and by the bacterial culturing approach. The bacterial isolates will allow further study on the mechanisms of tolerance to desiccation, especially in ().
PubMed: 37113232
DOI: 10.3389/fmicb.2023.1098150 -
International Journal of Systematic and... Feb 2022Four novel bacterial strains (zg-ZUI122/zg-ZUI10 and zg-ZUI227/zg-ZUI100) were isolated from the intestinal contents of and characterized using a polyphasic approach....
Four novel bacterial strains (zg-ZUI122/zg-ZUI10 and zg-ZUI227/zg-ZUI100) were isolated from the intestinal contents of and characterized using a polyphasic approach. Cells were Gram-stain- and catalase-positive, urease- and oxidase-negative. Strains grew optimally at 28-30 °C, pH 7.0, with 0.5 % NaCl (w/v). A comparative analysis of 16S rRNA gene sequences revealed that strain pairs zg-ZUI122/zg-ZUI10 and zg-ZUI227/zg-ZUI100 belonged to the genus and were most closely related to DSM 20133, with similarities of 99.6 and 99.5 %, respectively. This was further confirmed by phylogenetic analyses based on the 16S rRNA gene and genome sequences. The digital DNA-DNA hybridization and average nucleotide identity values between the two new type strains (zg-ZUI122 and zg-ZUI227) and other species in the genus were 20.0-24.4/77.2-83.4% and 19.9-25.1/77.1-83.4%, all below the thresholds. The major cellular fatty acids detected in the two novel species included -C and -C; the predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. MK-8(H) (77.3%) was the predominant respiratory quinone detected in strain zg-ZUI122, while MK-8(H) (53.7%) and MK-9(H) (46.3%) were detected in strain zg-ZUI227. The shared cell-wall amino acids detected in the two novel species were alanine, glutamic acid and lysine; the shared whole cell wall sugars consisted of galactose, mannose and ribose. All these analyses concluded that these four strains represent two different novel species in the genus , for which the names sp. nov. (zg-ZUI122 = GDMCC 1.2502 = KCTC 49677) and sp. nov. (zg-ZUI227 = GDMCC 1.2500 = KCTC 49676) are proposed.
Topics: Animals; Arthrobacter; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Intestines; Marmota; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2
PubMed: 35103585
DOI: 10.1099/ijsem.0.005181 -
International Journal of Systematic and... Nov 2023Four yellow-coloured strains (zg-Y815/zg-Y108 and zg-Y859/zg-Y826) were isolated from the intestinal contents of and assigned to the ' group'. The four strains grew...
Four yellow-coloured strains (zg-Y815/zg-Y108 and zg-Y859/zg-Y826) were isolated from the intestinal contents of and assigned to the ' group'. The four strains grew optimally on brain heart infusion agar with 5 % defibrinated sheep blood plate at 30 °C, pH 7.0 and with 0.5 % NaCl (w/v). Comparative analysis of their 16S rRNA genes indicated that the two strain pairs belong to the genus , showing the highest similarity to 785 (99.52 %), which was further confirmed by the 16S rRNA gene and genome-based phylogenetic analysis. The comparative genomic analysis [digital DNA-DNA hybridization, (dDDH) and average nucleotide identity (ANI)] proved that the four strains are two different species (zg-Y815/zg-Y108, 71.7 %/96.8 %; zg-Y859/zg-Y826, 87.3 %/98.5 %) and differ from other known species within the genus (zg-Y815, 19.6-32.3 %/77.2-88.0 %; zg-Y859, 19.5-29.3 %/77.4-86.3 %). Strain pairs zg-Y815/zg-Y108 and zg-Y859/zg-Y826 had the same major cellular fatty acids (iso-C and anteiso-C), with MK-8(H) as their dominant respiratory quinone (70.6 and 61.7 %, respectively). The leading polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol. The detected amino acids and cell-wall sugars of the two new species were identical (amino acids: alanine, glutamic acid, and lysine; sugars: rhamnose, galactose, mannose, glucose, and ribose). According to the phylogenetic, phenotypic, and chemotaxonomic analyses, we concluded that the four new strains represented two different novel species in the genus , for which the names sp. nov. (zg-Y815= GDMCC 1.3494 = JCM 35821) and sp. nov. (zg-Y859 = GDMCC 1.3493 = JCM 35822) are proposed.
Topics: Animals; Sheep; Arthrobacter; Fatty Acids; Phospholipids; Marmota; Phylogeny; RNA, Ribosomal, 16S; Vitamin K 2; Base Composition; DNA, Bacterial; Sequence Analysis, DNA; Bacterial Typing Techniques; Amino Acids; Comparative Genomic Hybridization; Sugars
PubMed: 38018813
DOI: 10.1099/ijsem.0.006168 -
International Journal of Systematic and... Dec 2021Two Gram-stain-positive, aerobic, rod-shaped, pink and light pink colony-forming bacteria, designated as Hz2 and MDT2-14, respectively, were isolated from glacier...
Two Gram-stain-positive, aerobic, rod-shaped, pink and light pink colony-forming bacteria, designated as Hz2 and MDT2-14, respectively, were isolated from glacier cryoconite samples. Comparisons based on 16S rRNA gene sequences showed that strains Hz2 and MDT2-14 take KR32 and J391 as their closest neighbours, respectively. The average nucleotide identity values between the two novel strains and their closest relatives were 83.56 and 93.06 %, respectively. The two strains contain MK-9(H) as their predominant menaquinone. The polar lipids of both strains were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The major fatty acids of strain Hz2 were anteiso-C, summed feature 3 (comprising C 7 and/or C 6) and iso-C, while the major fatty acids of strain MDT2-14 were anteiso-C and anteiso-C. Based on these data, we propose two novel species, sp. nov. (Hz2 = CGMCC 1.9262=NBRC 113086) and sp. nov. (MDT2-14=CGMCC 1.9882=NBRC 113089).
Topics: Arthrobacter; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Ice Cover; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2
PubMed: 34919039
DOI: 10.1099/ijsem.0.005177 -
International Journal of Systematic and... Apr 2023Six aerobic or facultative anaerobic, motile, Gram-stain-positive, catalase-positive and oxidase-negative strains (zg-Y453, zg-Y324, zg-Y462, zg-Y411, zg-Y809 and...
Six aerobic or facultative anaerobic, motile, Gram-stain-positive, catalase-positive and oxidase-negative strains (zg-Y453, zg-Y324, zg-Y462, zg-Y411, zg-Y809 and zg-Y786) were isolated from different faecal samples of from the Qinghai-Tibet Plateau. Pale yellow, round, raised and moist colonies appeared 48 h after incubation at 28 °C on brain-heart infusion plates supplemented with 5 % defibrinated sheep blood. According to the 16S rRNA gene sequence alignment, two strain pairs (zg-Y453/zg-Y324 and zg-Y462/zg-Y411) shared the highest similarities to (99.5 and 99.2 %), and the other one (zg-Y809/zg-Y786) to (99.5 %). Results of phylogenetic analysis based on the 16S rRNA gene and genome sequences showed that these six strains represented three separate species within the genus . The average nucleotide identity and digital DNA-DNA hybridization values between the three novel type strains (zg-Y453/zg-Y462/zg-Y809) and other known species in this genus were all below respective thresholds (70.2-81.5/19.6-24.2 %, 70.6-81.8/19.8-25.0 %, and 70.4-88.2/19.9-35.3 %). Although phylogenetically related, there were obvious chemotaxonomic and phenotypic differences: strain pair zg-Y462/zg-Y411 had C as the only major fatty acid; the three novel species had different dominant quinones, MK-8(H) in strains zg-Y462/zg-Y809 (74.8/81.1 %) and MK-8(H)/MK-9(H) (43.1/53.0 %) in zg-Y453; similarly, the ability to reduce nitrate in strains zg-Y453 and zg-Y462 could differentiate them from zg-Y809. All strains had diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, but differed slightly in the types of unidentified glycolipids, phospholipids and lipids. Based on the results of these polyphasic taxonomic analyses, three novel species within the genus are proposed, namely sp. nov. (type strain, zg-Y453=GDMCC 1.2809=JCM 35173), sp. nov. (type strain, zg-Y462=GDMCC 1.2880=JCM 35170) and sp. nov. (type strain, zg-Y809=GDMCC 1.2808=JCM 35168).
Topics: Animals; Sheep; Tibet; Arthrobacter; Fatty Acids; Marmota; Phylogeny; RNA, Ribosomal, 16S; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Sequence Analysis, DNA; Vitamin K 2; Feces
PubMed: 37042839
DOI: 10.1099/ijsem.0.005742 -
Current Microbiology Feb 2023A Gram-staining-positive, catalase positive and oxidase negative, non-motile, non-flagellated, and oval-shaped bacterium, was designated as I2-34, isolated from wetland...
A Gram-staining-positive, catalase positive and oxidase negative, non-motile, non-flagellated, and oval-shaped bacterium, was designated as I2-34, isolated from wetland in Soul South Korea. Colonies were round, entire, raised, and cream colored after two days of incubation on R2A agar plates at 25 °C. Based on genomes (both 16S rRNA gene and draft genome) sequence analysis, strain I2-34 belongs to the genus Arthrobacter and was most closely related to Arthrobacter deserti YIM CS25 (98.0%). The strain I2-34 had a circular genome with length of 5,186,447 base pairs (67 contigs) and 4830 total genes. Out of 4696 were protein-coding genes, 54 tRNA and 4 rRNA genes. The chemotaxonomic analysis indicates iso-C, anteiso-C, and anteisoC as major fatty acids, phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and two unidentified glycolipids (GL1, GL2) as major polar lipids. The predominant quinone was MK-8(H). The peptidoglycan type was A3α with an. L-Lys-L-Ala interpeptide bridge. Thus, the experimental data demonstrated here show that the novel isolate shares the similar major fatty acids, major polar lipid PG, DPG, and GLs, major and major quinone MK8-(H) with the described members of the genus Arthrobacter. However, the low 16S rRNA gene sequence (98.0%), and some physiological and biochemical characteristics differentiate the I2-34 from its closest phylogenetic neighbors. As a result, the isolate represents a novel species in within the genus Arthrobacter and family Micrococcaceae for which the name Arthrobacter hankyongi sp. nov. is proposed. The type strain is I2-34 (= KACC 22217, LMG 32197).
Topics: Arthrobacter; Phylogeny; RNA, Ribosomal, 16S; Base Composition; Nucleic Acid Hybridization; DNA, Bacterial; Bacterial Typing Techniques; Sequence Analysis, DNA; Vitamin K 2; Fatty Acids; Phospholipids
PubMed: 36725813
DOI: 10.1007/s00284-022-03162-3 -
International Journal of Systematic and... Oct 2020Four unknown strains belonging to the genus were isolated from plateau wildlife on the Qinghai-Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene...
Four unknown strains belonging to the genus were isolated from plateau wildlife on the Qinghai-Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785 and 208) had the greatest 16S rRNA gene sequence similarity to (98.6 and 98.7 %, respectively), (98.0 and 98.1%, respectively), (97.9 and 98.0 %, respectively) and (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391 and J915) had the highest sequence similarity to (98.6 and 98.3 %, respectively) and (98.1 and 97.9 %, respectively). Average nucleotide identity and the digital DNA-DNA hybridization values illustrated that the two type strains, 785 and J391, represented two separate novel species that are distinct from all currently recognized species in the genus . These strains had DNA G+C contents of 66.0-66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785 and J391 were in line with those of the genus : anteiso-C (79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H) (65.8 %) or MK-9(H) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3 or A4 as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus are proposed, namely sp. nov. (type strain, 785=CGMCC 1.16725=GDMCC 1.1592=JCM 33491) and sp. nov. (type strain, J391=CGMCC 1.17382=GDMCC 1.1667=JCM 33841).
Topics: Animals; Arthrobacter; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Ducks; Equidae; Fatty Acids; Feces; Lagomorpha; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vitamin K 2
PubMed: 32841110
DOI: 10.1099/ijsem.0.004414 -
Foods (Basel, Switzerland) Mar 2023Milk is naturally a rich source of many essential nutrients; therefore, it is quite a suitable medium for bacterial growth and serves as a reservoir for bacterial... (Review)
Review
Milk is naturally a rich source of many essential nutrients; therefore, it is quite a suitable medium for bacterial growth and serves as a reservoir for bacterial contamination. The genus is a food-related bacterial group commonly present as a contaminant in milk and dairy products as primary and secondary microflora. bacteria frequently demonstrate the nutritional versatility to degrade different compounds even in extreme environments. As a result of their metabolic diversity, species have long been of interest to scientists for application in various industry and biotechnology sectors. In the dairy industry, strains from the genus are part of the microflora of raw milk known as an indicator of hygiene quality. Although they cause spoilage, they are also regarded as important strains responsible for producing fermented milk products, especially cheeses. Several spp. have reported their significance in the development of cheese color and flavor. Furthermore, based on the data obtained from previous studies about its thermostability, and thermoacidophilic and thermoresistant properties, the genus promisingly provides advantages for use as a potential producer of β-galactosidases to fulfill commercial requirements as its enzymes allow dairy products to be treated under mild conditions. In light of these beneficial aspects derived from spp. including pigmentation, flavor formation, and enzyme production, this bacterial genus is potentially important for the dairy industry.
PubMed: 36981196
DOI: 10.3390/foods12061270 -
Ecotoxicology and Environmental Safety Sep 2023Cadmium (Cd) removal from soil to reduce Cd accumulation in plants is essential for agroecology, food safety, and human health. Cd enters plants from soil and affects...
Cadmium (Cd) removal from soil to reduce Cd accumulation in plants is essential for agroecology, food safety, and human health. Cd enters plants from soil and affects plant growth and development. Hydrogels can easily combine with Cd, thereby altering its bioavailability in soil. However, few studies have evaluated the effects of hydrogel on the complex phytotoxicity caused by Cd uptake in plants and the microbial community structure. Herein, a new poly (acrylic acid)-grafted starch and potassium humate composite (S/K/AA) hydrogel was added to soil to evaluate its impact on tobacco growth and the soil microenvironment. The results indicate that the addition of S/K/AA hydrogel can significantly improve the biomass, chlorophyll (Chl) content, and photosynthetic capacity of tobacco plants during Cd stress conditions, and decrease Cd concentration, probably by affecting Cd absorption through the expression of Cd absorption transporters (e.g., NRAMP5, NRAMP3, and IRT1). Moreover, the application of S/K/AA hydrogel not only reduced the accumulation of reactive oxygen species (ROS), but also reduced the antioxidant activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT), suggesting that S/K/AA hydrogel alleviates Cd toxicity via a non-antioxidant pathway. Notably, we further analyzed the effectiveness of the hydrogel on microbial communities in Cd-contaminated soil and found that it increased the Cd-tolerant microbial community (Arthrobacter, Massilia, Streptomyces), enhancing the remediation ability of Cd-contaminated soil and helping tobacco plants to alleviate Cd toxicity. Overall, our study provides primary insights into how S/K/AA hydrogel affects Cd bioavailability and alleviates Cd toxicity in plants.
Topics: Humans; Cadmium; Biological Availability; Nicotiana; Hydrogels; Arthrobacter
PubMed: 37597289
DOI: 10.1016/j.ecoenv.2023.115361