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Microbiology Resource Announcements Jun 2024Janeemi is a bacteriophage that infects B-2880, which was isolated from soil collected in New York City. The genome has a length of 43,877 bp and contains 69 predicted...
Janeemi is a bacteriophage that infects B-2880, which was isolated from soil collected in New York City. The genome has a length of 43,877 bp and contains 69 predicted genes. Based on gene content similarity to phages in the actinobacteriophage database, Janeemi is assigned to phage cluster AZ1.
PubMed: 38860811
DOI: 10.1128/mra.00177-24 -
Cell Reports Apr 2024Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost...
Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.
Topics: Sorghum; Striga; Plant Roots; Microbiota; Soil Microbiology; Metabolome; Plant Diseases
PubMed: 38537644
DOI: 10.1016/j.celrep.2024.113971 -
Marine Drugs Feb 2024Sulfation is gaining increased interest due to the role of sulfate in the bioactivity of many polysaccharides of marine origin. Hence, sulfatases, enzymes that control...
Sulfation is gaining increased interest due to the role of sulfate in the bioactivity of many polysaccharides of marine origin. Hence, sulfatases, enzymes that control the degree of sulfation, are being more extensively researched. In this work, a novel sulfatase (SulA1) encoded by the gene was characterized. The -gene is located upstream of a chondroitin lyase encoding gene in the genome of the marine Arthrobacter strain (MAT3885). The sulfatase was produced in . Based on the primary sequence, the enzyme is classified under sulfatase family 1 and the two catalytic residues typical of the sulfatase 1 family-Cys57 (post-translationally modified to formyl glycine for function) and His190-were conserved. The enzyme showed increased activity, but not improved stability, in the presence of Ca, and conserved residues for Ca binding were identified (Asp17, Asp18, Asp277, and Asn278) in a structural model of the enzyme. The temperature and pH activity profiles (screened using -nitrocatechol sulfate) were narrow, with an activity optimum at 40-50 °C and a pH optimum at pH 5.5. The was significantly higher (67 °C) than the activity optimum. Desulfation activity was not detected on polymeric substrates, but was found on GalNAc4S, which is a sulfated monomer in the repeated disaccharide unit (GlcA-GalNAc4S) of, e.g., chondroitin sulfate A. The position of the sulA1 gene upstream of a chondroitin lyase gene and combined with the activity on GalNAc4S suggests that there is an involvement of the enzyme in the chondroitin-degrading cascade reaction, which specifically removes sulfate from monomeric GalNAc4S from chondroitin sulfate degradation products.
Topics: Sulfates; Acetylgalactosamine; Arthrobacter; Sulfatases; Escherichia coli; Galactosamine; Chondroitin Lyases; Cloning, Molecular
PubMed: 38535445
DOI: 10.3390/md22030104 -
Microbiology Resource Announcements Mar 2024Here, we present the genomes of two soil actinobacteria: sp. strain AZCC_0090 and sp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern...
Here, we present the genomes of two soil actinobacteria: sp. strain AZCC_0090 and sp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern Arizona, USA.
PubMed: 38376218
DOI: 10.1128/mra.01089-23 -
Heliyon Feb 2024Taking rural dispersed sewage for research objects, the treatment effect and microbial community structure characteristics of a bio filter (BF) reactor was studied. At...
Taking rural dispersed sewage for research objects, the treatment effect and microbial community structure characteristics of a bio filter (BF) reactor was studied. At fixed time and location, the removal efficiencies of common pollutants were investigated. By using high-throughput sequencing method, the heterogeneities of microbial community structure in fillers and plant roots were analyzed. The results showed that the average annual removal rates of COD, NH-N, TN, and TP by the BF were 83.10 %, 65.67 %, 60.25 %, and 80.32 % respectively, and the effluent could reach the first grade of the water pollutant discharge standard of rural sewage treatment facility (DB51/2626-2019). During the sewage treatment process, Scindapsus could effectively establish complex and stable microbial communities, and could better degrade pollutants, especially nitrogen removal. The dominant microbial communities were more than 11 phyla and 19 classes. At the genus level, the dominant bacteria included , etc.
PubMed: 38317885
DOI: 10.1016/j.heliyon.2024.e25301 -
Foods (Basel, Switzerland) Apr 2024The qualities of precooked foods can be significantly changed by the microorganisms produced during room temperature storage. This work assessed the effects of different...
The qualities of precooked foods can be significantly changed by the microorganisms produced during room temperature storage. This work assessed the effects of different antibacterial treatments (CK, without any treatment; microwave treatment, MS; microwave treatment and biological preservatives, MSBP) on the physicochemical properties and microbial communities of precooked crayfish tails during room temperature storage. Only the combination of microwave sterilization and biological preservatives significantly inhibited spoilage, as evidenced by the total viable count (4.15 log CFU/g) after 3 days of room temperature storage, which satisfied the transit time of most logistics companies in China. Changes in pH and TVB-N were also significantly inhibited in the MSBP group compared with those in the CK and MS groups. More than 30 new volatile compounds were produced in the CK groups during room temperature storage. However, in the MSBP groups, the volatile compounds were almost unchanged. The correlations between the microbial composition and volatile compounds suggested that specific bacterial species with metabolic activities related to amino acid, energy, cofactor, and vitamin metabolism, as well as xenobiotics biodegradation and metabolism, were responsible for the changes in volatile compounds. These bacteria included , , , , , , , , and . Overall, our findings provide a foundation for the development of strategies to inhibit spoilage in precooked crayfish tails stored at room temperature.
PubMed: 38672928
DOI: 10.3390/foods13081256 -
Microbiology Resource Announcements Apr 2024In the present work, we present the draft genome sequence of a new putative species associated with the tomato rhizosphere.
In the present work, we present the draft genome sequence of a new putative species associated with the tomato rhizosphere.
PubMed: 38517186
DOI: 10.1128/mra.01220-23 -
Data in Brief Feb 2024sp. EM1 is a cold-adapted bacterium isolated from the Antarctic region, which was known to exhibit mannan-degrading activity. Accordingly, this strain not only promises...
sp. EM1 is a cold-adapted bacterium isolated from the Antarctic region, which was known to exhibit mannan-degrading activity. Accordingly, this strain not only promises a cell factory for mannan-degrading enzymes, widely used in industry but also serves as a model organism to decipher its cold adaptation mechanism. Accordingly, whole genome sequencing of the EM1 strain was performed via Single Molecule Real Time sequencing under the PacBio platform, followed by genome HGAP de novo assembly and genome annotation through Rapid Annotation System Technology (RAST) server. The chromosome of this strain is 3,885,750 bp in size with a GC content of 65.8. The annotation predicted a total of 3607 protein-coding genes and 65 RNA genes, which were classified under 398 subsystems. The subsystem with the highest number of genes is carbohydrate metabolism (397 genes), which includes two genes encoding mannan-degrading enzymes (endoglucanase and α-mannosidase). This confirmed that the EM1 strain is able to produce cold-adapted mannan degrading enzymes. The complete genome sequence data have been submitted to the National Center for Biotechnology Information (NCBI) and have been deposited at GenBank (Bioproject ID Accession Number: PRJNA963062; Biosample ID Accession Number: SAMN34434776; GenBank: CP124836.1; https://www.ncbi.nlm.nih.gov/nuccore/CP124836).
PubMed: 38146304
DOI: 10.1016/j.dib.2023.109841 -
Journal, Genetic Engineering &... Mar 2024Choline oxidase, a flavoprotein, is an enzyme that catalyzes the reaction which converts choline into glycine betaine. Choline oxidase started its journey way back in...
BACKGROUND
Choline oxidase, a flavoprotein, is an enzyme that catalyzes the reaction which converts choline into glycine betaine. Choline oxidase started its journey way back in 1933. However, the impact of the high temperature on its structure has not been explored despite the long history and availability of its crystal structure. Both choline oxidase and its product, glycine betaine, have enormous applications spanning across multiple industries. Understanding how the 3D structure of the enzyme will change with the temperature change can open new ways to make it more stable and useful for industry.
PROCESS
This research paper presents the in-silico study and analysis of the structural changes of A. globiformis choline oxidase at temperatures from 25 °C to 60 °C. A step-wise process is depicted in Fig. 1.
RESULTS
Multiple sequence alignment (MSA) of 11 choline oxidase sequences from different bacteria vs Arthrobacter globiformis choline oxidase showed that active site residues are highly conserved. The available crystal structure of A. globiformis choline oxidase with cofactor Flavin Adenine Dinucleotide (FAD) in the dimeric state (PDB ID: 4MJW) was considered for molecular dynamics simulations. A simulated annealing option was used to gradually increase the temperature of the system from 25 °C to 60 °C. Analysis of the conserved residues, as well as residues involved in Flavin Adenine Dinucleotide (FAD) binding, substrate binding, substate gating, and dimer formationwas done. At high temperatures, the formation of the inter-chain salt bridge between Arg50 and Glu63 was a significant observation near the active site of choline oxidase.
CONCLUSION
Molecular dynamics studies suggest that an increase in temperature has a significant impact on the extended Flavin Adenine Dinucleotide (FAD) binding region. These changes interfere with the entry of substrate to the active site of the enzyme and make the enzyme inactive.
PubMed: 38494262
DOI: 10.1016/j.jgeb.2023.100348