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A novel Gram-stain-negative, strictly aerobic, rod-shaped, light-yellow-pigmented, and chemo-organoheterotrophic bacterium, designated DF-77T, was isolated from dense mats of filamentous algae collected in March 2004 at Okinawa in Japan. The microorganism grew at 0-2.0% NaCl concentrations (w/v), pH 6.0-9.0, and 20-30 °C. The 16S rRNA gene sequence-based phylogenetic tree demonstrated that the strain DF-77T is a novel member of the family Flavobacteriaceae and was greatly related to Flagellimonas nanhaiensis SM1704T with sequence similarity of 95.5%. The main fatty acids were iso-C15:1 G, iso-C15:0, and iso-C17:0 3-OH, and the only isoprenoid quinone was menaquinone-6. The dominant polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phosphoaminolipid, and four unidentified lipids. The genome size of strain DF-77T was 3.60 Mbp with a DNA G + C content of 47.5%. The average nucleotide identity (ANI) value between the genomes of strain DF-77T and its closely related species was 69.8-70.7%. The digital DNA - DNA hybridization (dDDH) value of strain DF-77T with the strain of F. nanhaiensis SM1704T was 16.8%. The genome of the strain DF-77T revealed that it encoded several genes involved in bio-macromolecule degradation, indicating a high potential for producing industrially useful enzymes. Consequently, the strain is described as a new species in the genus Flagellimonas, for which the name Flagellimonas algarum sp. nov., is proposed with the type strain DF-77T (= KCTC 72791T = NBRC 114251T).
- MeSH
- DNA bakterií genetika chemie MeSH
- Flavobacteriaceae * klasifikace izolace a purifikace genetika MeSH
- fosfolipidy analýza MeSH
- fylogeneze MeSH
- genom bakteriální MeSH
- hybridizace nukleových kyselin MeSH
- mastné kyseliny analýza MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- techniky typizace bakterií MeSH
- vitamin K 2 analýza analogy a deriváty MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Japonsko MeSH
Halophilic bacteria are extremophiles that thrive in saline environment. Their ability to withstand such harsh conditions makes them an ideal choice for industrial applications such as lignocellulosic biomass degradation. In this study, a halophilic bacterium with the ability to produce extracellular cellulases and hemicellulases, designated as Nesterenkonia sp. CL21, was isolated from mangrove sediment in Tanjung Piai National Park, Malaysia. Thus far, studies on lignocellulolytic enzymes concerning bacterial species under this genus are limited. To gain a comprehensive understanding of its lignocellulose-degrading potential, the whole genome was sequenced using the Illumina NovaSeq 6000 platform. The genome of strain CL21 was assembled into 25 contigs with 3,744,449 bp and a 69.74% GC content and was predicted to contain 3,348 coding genes. Based on taxonomy analysis, strain CL21 shares 73.8 to 82.0% average nucleotide identity with its neighbouring species, below the 95% threshold, indicating its possible status as a distinct species in Nesterenkonia genus. Through in-depth genomic mining, a total of 81 carbohydrate-active enzymes were encoded. Among these, 24 encoded genes were identified to encompass diverse cellulases (GH3), xylanases (GH10, GH11, GH43, GH51, GH127 and CE4), mannanases (GH38 and GH106) and pectinases (PL1, PL9, and PL11). The production of lignocellulolytic enzymes was tested in the presence of several substrates. This study revealed that strain CL21 can produce a diverse array of enzymes which are active at different time points. By combining experimental data with genomic information, the ability of strain CL21 to produce lignocellulolytic enzymes has been elucidated, with potential applications in biorefinery industry.
- MeSH
- bakteriální proteiny genetika metabolismus MeSH
- celulasy genetika metabolismus MeSH
- fylogeneze * MeSH
- genom bakteriální * MeSH
- genomika * MeSH
- geologické sedimenty mikrobiologie MeSH
- glykosidhydrolasy * genetika metabolismus MeSH
- lignin * metabolismus MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenování celého genomu MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
Pseudomonas mandelii SW-3, isolated from the Napahai plateau wetland, can survive in cold environments. The mechanisms underlying the survival of bacteria in low temperatures and high altitudes are not yet fully understood. In this study, the whole genome of SW-3 was sequenced to identify the genomic features that may contribute to survival in cold environments. The results showed that the genome size of strain SW-3 was 6,538,059 bp with a GC content of 59%. A total of 67 tRNAs, a 34,110 bp prophage sequence, and a large number of metabolic genes were found. Based on 16S rRNA gene phylogeny and average nucleotide identity analysis among P. mandelii, SW-3 was identified as a strain belonging to P. mandelii. In addition, we clarified the mechanisms by which SW-3 survived in a cold environment, providing a basis for further investigation of host-phage interaction. P. mandelii SW-3 showed stress resistance mechanisms, including glycogen and trehalose metabolic pathways, and antisense transcriptional silencing. Furthermore, cold shock proteins and glucose 6-phosphate dehydrogenase may play pivotal roles in facilitating adaptation to cold environmental conditions. The genome-wide analysis provided us with a deeper understanding of the cold-adapted bacterium.
- MeSH
- DNA bakterií genetika MeSH
- fylogeneze * MeSH
- fyziologická adaptace * genetika MeSH
- genom bakteriální * MeSH
- nízká teplota * MeSH
- profágy genetika MeSH
- Pseudomonas * genetika klasifikace MeSH
- RNA ribozomální 16S * genetika MeSH
- sekvenování celého genomu MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
Three closely related, aerobic, Gram-stain-negative, motile, rod-shaped bacterial strains (PS-2T, PS-17, and PS-19) were isolated from the skin of freshwater pufferfish (Tetraodon cutcutia). Colonies are pinkish-colored. The optimum growth occurred at 28-30 °C, and the pH was 6.5-7. The major cellular fatty acids were C16:1 ω7c, iso-C15.0, C17:1 ω8c, C18:1 ω7c, and C16:0. The predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and amino lipids. The genome size of strain PS-2T is 4.8 Mbp, and the G + C content was 46.0%. The major fraction of genes were associated with biological processes (45.64%), followed by molecular function (29.86%) and cellular components (24.49%). The unique genes identified in strain PS-2T secreted cyanophycinase, UDP-N-acetylglucosamine 2-epimerase, methyltransferase, kynureninase, ADA regulatory protein, biphenyl degradation, thermostable carboxypeptidase 1, tetrathionate respiration, etc. In addition, alanine and glutamate racemases were present. The 16S rRNA gene sequences shared 98.83-99.24% similarity with the closely related type strains of Shewanella. The ANI and AAI of strain PS-2T with reference type strains of the genus Shewanella were below 95-96%, and the corresponding dDDH values were below 70%. A phylogenetic tree based on 16S rRNA gene sequences and genome-wide core genes revealed that strain PS-2T clustered with Shewanella oneidensis LMG 19005T in both phylogenetic trees. Based on the polyphasic analysis, the new isolates (PS-2T, PS-17, and PS-19) represent a novel species of Shewanella, for which Shewanella cutis sp. nov. is proposed. The type strain is PS-2T (= TBRC 15838T = NBRC 115342T).
- MeSH
- DNA bakterií * genetika MeSH
- fosfolipidy analýza MeSH
- fylogeneze * MeSH
- genom bakteriální * MeSH
- genomika MeSH
- kůže mikrobiologie MeSH
- mastné kyseliny * analýza MeSH
- RNA ribozomální 16S * genetika MeSH
- sekvenční analýza DNA MeSH
- Shewanella * genetika izolace a purifikace klasifikace MeSH
- sladká voda mikrobiologie MeSH
- techniky typizace bakterií MeSH
- Tetraodontiformes * mikrobiologie MeSH
- zastoupení bazí * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
The genomic signature of an organism captures the characteristics of repeated oligonucleotide patterns in its genome 1, such as oligomer frequencies, GC content, and differences in codon usage. Viruses, however, are obligate intracellular parasites that are dependent on their host cells for replication, and information about genomic signatures in viruses has hitherto been sparse.Here, we investigate the presence and specificity of genomic signatures in 2,768 eukaryotic viral species from 105 viral families, aiming to illuminate dependencies and selective pressures in viral genome evolution. We demonstrate that most viruses have highly specific genomic signatures that often also differ significantly between species within the same family. The species-specificity is most prominent among dsDNA viruses and viruses with large genomes. We also reveal consistent dissimilarities between viral genomic signatures and those of their host cells, although some viruses present slight similarities, which may be explained by genetic adaptation to their native hosts. Our results suggest that significant evolutionary selection pressures act upon viral genomes to shape and preserve their genomic signatures, which may have implications for the field of synthetic biology in the construction of live attenuated vaccines and viral vectors.
The taxonomic position of three actinobacterial strains, BCCO 10_0061T, BCCO 10_0798T, and BCCO 10_0856T, recovered from bare soil in the Sokolov Coal Basin, Czech Republic, was established using a polyphasic approach. The multilocus sequence analysis based on 100 single-copy genes positioned BCCO 10_0061T in the same cluster as Lentzea waywayandensis, strain BCCO 10_0798T in the same cluster as Lentzea flaviverrucosa, Lentzea californiensis, Lentzea violacea, and Lentzea albidocapillata, and strain BCCO 10_0856T clustered together with Lentzea kentuckyensis and Lentzea alba. Morphological and chemotaxonomic characteristics of these strains support their assignment to the genus Lentzea. In all three strains, MK-9(H4) accounted for more than 80 % of the isoprenoid quinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The whole-cell sugars were rhamnose, ribose, mannose, glucose, and galactose. The major fatty acids (>10 %) were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and C16 : 0. The polar lipids were diphosphatidylglycerol, methyl-phosphatidylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol. The genomic DNA G+C content of strains (mol%) was 68.8 for BCCO 10_0061T, 69.2 for BCCO 10_0798T, and 68.5 for BCCO 10_0856T. The combination of digital DNA-DNA hybridization results, average nucleotide identity values and phenotypic characteristics of BCCO 10_0061T, BCCO 10_0798T, and BCCO 10_0856T distinguishes them from their closely related strains. Bioinformatic analysis of the genome sequences of the strains revealed several biosynthetic gene clusters (BGCs) with identities >50 % to already known clusters, including BGCs for geosmin, coelichelin, ε-poly-l-lysine, and erythromycin-like BGCs. Most of the identified BGCs showed low similarity to known BGCs (<50 %) suggesting their genetic potential for the biosynthesis of novel secondary metabolites. Based on the above results, each strain represents a novel species of the genus Lentzea, for which we propose the name Lentzea sokolovensis sp. nov. for BCCO 10_0061T (=DSM 116175T), Lentzea kristufekii sp. nov. for BCCO 10_0798T (=DSM 116176T), and Lentzea miocenica sp. nov. for BCCO 10_0856T (=DSM 116177T).
- MeSH
- Actinobacteria * MeSH
- Actinomycetales * MeSH
- Bacteria MeSH
- DNA bakterií genetika MeSH
- fosfatidylethanolaminy MeSH
- fylogeneze MeSH
- mastné kyseliny chemie MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- techniky typizace bakterií MeSH
- uhlí MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
To explore the mechanism whereby cGAS-STING pathway regulates the pyroptosis of cryptorchidism cells, with a view to finding a new strategy for clinically treating cryptorchidism-induced infertility. Spermatogonial GC-1 cells were heat stimulated to simulate the heat hurt microenvironment of cryptorchidism. The cell viability was assayed by CCK-8, and cellular DNA damage was detected by gamma-H2AX immunofluo-rescence assay. Flow cytometry was employed to assess pyroptosis index, while western blot, ELISA and PCR were used to examine the expressions of pyroptosis-related proteins (Caspase-1, IL-1beta, NLRP3) and cGAS-STING pathway proteins (cGAS, STING). After STING silencing by siRNA, the expressions of pyroptosis-related proteins were determined. Pyroptosis occurred after heat stimulation of cells. Morphological detection found cell swelling and karyopyknosis. According to the gamma-H2AX immunofluorescence (IFA) assay, the endonuclear green fluorescence was significantly enhanced, the gamma-H2AX content markedly increased, and the endonuclear DNA was damaged. Flow cytometry revealed a significant increase in pyroptosis index. Western blot and PCR assays showed that the expressions of intracellular pyrogenic proteins like Caspase-1, NLRP3 and GSDMD were elevated. The increased STING protein and gene expressions in cGAS-STING pathway suggested that the pathway was intracellularly activated. Silencing STING protein in cGAS-STING pathway led to significantly inhibited pyroptosis. These results indicate that cGAS-STING pathway plays an important role in heat stress-induced pyroptosis of spermatogonial cells. After heat stimulation of spermatogonial GC-1 cells, pyroptosis was induced and cGAS-STING pathway was activated. This study can further enrich and improve the molecular mechanism of cryptorchidism.
Phoenix sylvestris Roxb. (Arecaceae) seeds are used in the treatment of diabetes in the traditional system of medicine. The present study evaluated antihyperglycemic and antioxidant activities as well as the total phenolic and flavonoid content of the methanol extract of P. sylvestris seeds (MEPS). The constituents of the extract were identified by GC-MS analysis. MEPS demonstrated strong antioxidant activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH) (IC50 = 162.70 ± 14.99 μg) and nitric oxide (NO) (IC50 = 101.56 ± 9.46 μg/ml) free radicals. It also possesses a substantial amount of phenolics and flavonoids. It significantly (p < .05) reduced blood glucose levels in glucose-loaded and alloxan-induced diabetic mice at the doses of 150 and 300 mg/kg b.w., respectively. A total of 46 compounds were detected and identified by gas chromatography-mass spectroscopy (GC-MS) analysis, among which 8-methylisoquinoline N-oxide (32.82%) was predominant. The phytochemical study by GC-MS revealed that the MEPS possesses compounds which could be related to its antidiabetic and antioxidant activities. To recapitulate, P. sylvestris seeds can be a very good option for antidiabetic and antioxidant activity though further studies are still recommended to figure out the responsible phytochemicals and establish their exact mechanism of action.
- Publikační typ
- časopisecké články MeSH
Bacillus species as fungal antagonistic agents have been widely used in the agriculture and considered as safe products for the management of plant pathogens. In this study, we reported the whole genome sequence of strain LJBV19 isolated from grapevine rhizosphere soil. Strain LJBV19 was identified as Bacillus velezensis through morphological, physicochemical, molecular analysis and genome comparison. Bacillus velezensis LJBV19 had a significant inhibitory effect on the growth of Magnaporthe oryzae with an inhibition ratio up to 75.55% and showed broad spectrum of activity against fungal phytopathogens. The 3,973,013-bp circular chromosome with an average GC content of 46.5% consisted of 3993 open reading frames (ORFs), and 3308 ORFs were classified into 19 cluster of orthologous groups of proteins (COG) categories. Genes related to cell wall degrading enzymes were predicted by Carbohydrate-Active enZYmes (CAZy) database and validated at the metabolic level, producing 0.53 ± 0.00 U/mL cellulose, 0.14 ± 0.01 U/mL chitinase, and 0.11 ± 0.01 U/mL chitosanase. Genome comparison confirmed the taxonomic position of LJBV19, conserved genomic structure, and genetic homogeneity. Moreover, 13 gene clusters for biosynthesis of secondary metabolites in LJBV19 genome were identified and two unique clusters (clusters 2 and 12) shown to direct an unknown compound were only present in strain LJBV19. In general, our results will provide insights into the antifungal mechanisms of Bacillus velezensis LJBV19 and further application of the strain.
- MeSH
- antifungální látky chemie MeSH
- Bacillus * MeSH
- genom bakteriální * MeSH
- genomika MeSH
- Publikační typ
- časopisecké články MeSH
Approximately 13% of the human genome at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity of polymerases and helicases. Because sequencing technologies use these enzymes, they might possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif types but were increased for G-quadruplexes and Z-DNA in all three technologies. Deletion errors were increased for all non-B types but Z-DNA in Illumina and HiFi, as well as only for G-quadruplexes in ONT. Insertion errors for non-B motifs were highly, moderately, and slightly elevated in Illumina, HiFi, and ONT, respectively. Additionally, we developed a probabilistic approach to determine the number of false positives at non-B motifs depending on sample size and variant frequency, and applied it to publicly available data sets (1000 Genomes, Simons Genome Diversity Project, and gnomAD). We conclude that elevated sequencing errors at non-B DNA motifs should be considered in low-read-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA.
