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Antioxidants (Basel, Switzerland) Feb 2021PON1, PON2, and PON3 belong to a family of lactone hydrolyzing enzymes endowed with various substrate specificities. Among PONs, PON2 shows the highest hydrolytic... (Review)
Review
PON1, PON2, and PON3 belong to a family of lactone hydrolyzing enzymes endowed with various substrate specificities. Among PONs, PON2 shows the highest hydrolytic activity toward many acyl-homoserine lactones (acyl-HL) involved in bacterial quorum-sensing signaling. Accordingly, defense against pathogens, such as (), was postulated to be the principal function of PON2. However, recent findings have highlighted the importance of PON2 in oxidative stress control, inhibition of apoptosis, and the progression of various types of malignancies. This review focuses on all of these aspects of PON2.
PubMed: 33562328
DOI: 10.3390/antiox10020256 -
Viruses Apr 2024Previous studies have identified diverse bacteriophages that infect strain CB15 ranging from small RNA phages to four genera of jumbo phages. In this study, we focus on...
Previous studies have identified diverse bacteriophages that infect strain CB15 ranging from small RNA phages to four genera of jumbo phages. In this study, we focus on 20 bacteriophages whose genomes range from 40 to 60 kb in length. Genome comparisons indicated that these diverse phages represent six phage genera and one additional genus that includes both and phages. Within species, comparisons revealed that both single base changes and inserted or deleted genetic material cause the genomes of closely related phages to diverge. Among genera, the basic gene order and the orientation of key genes were retained with most of the observed variation occurring at ends of the genomes. We hypothesize that the nucleotide sequences of the ends of these phage genomes are less important than the need to maintain the size of the genome and the stability of the corresponding mRNAs.
Topics: Genome, Viral; Bacteriophages; Caulobacter; Phylogeny; Evolution, Molecular; Gene Order
PubMed: 38675982
DOI: 10.3390/v16040641 -
The EMBO Journal Mar 2023Glycosylation of surface structures diversifies cells chemically and physically. Nucleotide-activated sialic acids commonly serve as glycosyl donors, particularly...
Glycosylation of surface structures diversifies cells chemically and physically. Nucleotide-activated sialic acids commonly serve as glycosyl donors, particularly pseudaminic acid (Pse) and its stereoisomer legionaminic acid (Leg), which decorate eubacterial and archaeal surface layers or protein appendages. FlmG, a recently identified protein sialyltransferase, O-glycosylates flagellins, the subunits of the flagellar filament. We show that flagellin glycosylation and motility in Caulobacter crescentus and Brevundimonas subvibrioides is conferred by functionally insulated Pse and Leg biosynthesis pathways, respectively, and by specialized FlmG orthologs. We established a genetic glyco-profiling platform for the classification of Pse or Leg biosynthesis pathways, discovered a signature determinant of eubacterial and archaeal Leg biosynthesis, and validated it by reconstitution experiments in a heterologous host. Finally, by rewiring FlmG glycosylation using chimeras, we defined two modular determinants that govern flagellin glycosyltransferase specificity: a glycosyltransferase domain that either donates Leg or Pse and a specialized flagellin-binding domain that identifies the acceptor.
Topics: Flagellin; Stereoisomerism; Bacteria; Glycosyltransferases; Sialyltransferases; Archaea; Flagella; Bacterial Proteins
PubMed: 36636824
DOI: 10.15252/embj.2022112880 -
Frontiers in Microbiology 2023Microbial inoculation with plant growth-promoting microorganisms (PGPMs) is one of the most promising technologies to solve the current global challenges. Co-inoculants...
Microbial inoculation with plant growth-promoting microorganisms (PGPMs) is one of the most promising technologies to solve the current global challenges. Co-inoculants is more efficient and stable than mono-inoculants. However, the growth promoting mechanism of co-inoculants in complex soil system is still poorly understood. In this study, the effects on rice, soil and the microbiome of the mono-inoculant FH-1 (F) and NYM3 (N) and the co-inoculant FN obtained in previous works were compared. Correlation analysis and PLS-PM were used to explore the primary mechanism of different inoculants promoting rice growth. We hypothesized that inoculants promoted plant growth (i) by themselves, (ii) by improving soil nutrient availability or (iii) by regulating the rhizosphere microbiome in complex soil system. We also assumed that different inoculants had different ways of promoting plant growth. The results showed that FN significantly promoted rice growth and nitrogen absorption and slightly increased soil total nitrogen and microbial network complexity compared with F, N and the control (CK). FH-1 and NYM3 interfered with each other's colonization in FN. FN increased the complexity of the microbial network compared to F and N. The bacterial community of FN was quite different from CK and N, while the fungal community was not significantly different from other treatments. The species and functions enriched or inhibited by FN are part of F. The correlation analysis and PLS-PM results showed that inoculants (F/N/FN) promoted the growth of rice mainly by regulating the rhizosphere microbiome rather than by themselves or by improving soil nutrient availability. Co-inoculant FN promotes rice growth specifically by enhancing microbial nitrification function through enriching related species compared with F or N. This may provide theoretical guidance for the construction and application of co-inoculants in the future.
PubMed: 36846752
DOI: 10.3389/fmicb.2023.1101773 -
PeerJ 2022Dental unit waterlines (DUWLs) provide water for handpieces, air/water syringes, and mouth-rinse water outlets. DUWL contamination can negatively affect the operating...
BACKGROUND
Dental unit waterlines (DUWLs) provide water for handpieces, air/water syringes, and mouth-rinse water outlets. DUWL contamination can negatively affect the operating environment and public health. Therefore, it is important to elucidate the bacterial concentrations and microbial composition in the DUWLs from different dental specialties.
METHODS
We collected 350 5-mL dental water samples (from high-speed handpieces, air/water syringes, and mouth-rinse water outlets) from 60 dental chair units (DCUs) at a dental hospital to determine the bacterial concentrations by culture methods. Meanwhile, to investigate the diversity and community structure of microbe in the DUWLs, 17 high-quality DNA from 60 250-mL air/water syringe water samples, which were collected from the same 60 DCUs, were analyzed using 16S rDNA high-throughput sequencing.
RESULTS
The median bacterial concentration was 166 (31.5, 672.5) CFU/mL and the range was 0-3,816,000 CFU/mL. Only 42.6% of the water samples had bacterial concentrations below 100 CFU/mL. The Kruskal-Wallis -test revealed that the water samples from three dental specialties had significantly different bacterial concentrations ( = 27.441, < 0.01). High-throughput sequencing results showed significant differences in bacterial community structure between periodontics and the other two dental specialties. In the samples from three dental specialties, 508 OTUs were detected, with 160, 182 and 176 OTUs unique to the periodontics, endodontics and prosthodontics specialties, respectively. Linear discriminant analysis (LDA) effect size (LEfSe) suggested that Hydrocarboniphaga, Zoogloea, Aquabacterium, and Hydrogenophaga were enriched in the periodontics specialty; Acinetobacter, Geothrix, and Desulfovibrio were enriched in the prosthodontics specialty; and Alistipes, Clostridium XIVa, and Serratia were enriched in the endodontics specialty. Seven potentially human-pathogenic genera (Pseudomonas, Acinetobacter, Sphingomonas, Ochrobactrum, Rhizobium, Brevundimonas, and Methylobacterium) with relative abundance exceeding 1% were also detected in the DUWLs.
CONCLUSIONS
The bacterial concentrations and microbial composition were influenced by different dental specialties, so a validated disinfection protocol should be used to control DUWL contamination in different dental specialties.
Topics: Humans; Equipment Contamination; Bacteria; Disinfection; Microbiota; Biofilms
PubMed: 35036099
DOI: 10.7717/peerj.12723 -
Marine Drugs 2011Marine bacteria belonging to genera Paracoccus and Brevundimonas of the α-Proteobacteria class can produce C₄₀-type dicyclic carotenoids containing two β-end... (Review)
Review
Marine bacteria belonging to genera Paracoccus and Brevundimonas of the α-Proteobacteria class can produce C₄₀-type dicyclic carotenoids containing two β-end groups (β rings) that are modified with keto and hydroxyl groups. These bacteria produce astaxanthin, adonixanthin, and their derivatives, which are ketolated by carotenoid β-ring 4(4')-ketolase (4(4')-oxygenase; CrtW) and hydroxylated by carotenoid β-ring 3(3')-hydroxylase (CrtZ). In addition, the genus Brevundimonas possesses a gene for carotenoid β-ring 2(2')-hydroxylase (CrtG). This review focuses on these carotenoid β-ring-modifying enzymes that are promiscuous for carotenoid substrates, and pathway engineering for the production of xanthophylls (oxygen-containing carotenoids) in Escherichia coli, using these enzyme genes. Such pathway engineering researches are performed towards efficient production not only of commercially important xanthophylls such as astaxanthin, but also of xanthophylls minor in nature (e.g., β-ring(s)-2(2')-hydroxylated carotenoids).
Topics: Alphaproteobacteria; Genetic Engineering; Mixed Function Oxygenases; Oxygenases; Water Microbiology; Xanthophylls
PubMed: 21673887
DOI: 10.3390/md9050757 -
International Journal of Environmental... Mar 2022Lake Vostok is the deepest lake of Antarctica but has poor accessibility for study due to a thick glacial cover, however, water samples of this lake have become...
Lake Vostok is the deepest lake of Antarctica but has poor accessibility for study due to a thick glacial cover, however, water samples of this lake have become available for study just recently. Previously, only the microbiome of the ice cover samples was characterized. Here we report results of bacteriological seeding with subsequent identification of the heterotrophic microorganisms (bacteria and micellar fungi) present by 16S rDNA sequencing as well as results of a direct molecular study of the water microbiome. Surprisingly, the data obtained gave evidence of a predominant occurrence of common chemoorganotrophs that were rather psychrotolerant than psychrophilic. We isolated and described strains belonging to eight heterotrophic microbial species able to grow in a rich medium: six bacterial strains belonging to the species and , , , sp. and ; and two fungal strains belonging to sp. and . Direct study of 16S rDNA purified water samples confirmed the predominance of the , , and () .
Topics: Antarctic Regions; DNA, Ribosomal; Lakes; Microbiota; Sphingomonadaceae; Water; Water Microbiology
PubMed: 35409708
DOI: 10.3390/ijerph19074025 -
MSystems Jan 2021Pullorum disease is one of the most common diarrhea-related diseases caused by subspecies serovar Gallinarum biovar Pullorum ( Pullorum); it negatively affects the...
Pullorum disease is one of the most common diarrhea-related diseases caused by subspecies serovar Gallinarum biovar Pullorum ( Pullorum); it negatively affects the poultry industry. However, limited studies have explored the association between the gut microbiota and Pullorum infection in chickens. In the present study, we performed a microbiome comparison and a microbiome genome-wide association study (mGWAS) to investigate the association among the host genetics, the gut microbiota, and pullorum disease in chickens. We found that Pullorum infection in chickens could alter the abundance of 39 bacterial genera (0.05). The altered structure and composition of the gut microbiota were also detected in the offspring. mGWAS results revealed host genetic variants to be prominently associated with gut microbial diversity and individual microbes. The pathogens and , which had a high abundance in positive parent chickens and their offspring, were significantly associated with several genetic mutations in immunity-related genes, such as , , and This finding explained why and were heritable in Pullorum-infected chickens. The heritable gut microbes and identified genetic variants could provide references for the selection of resistant chickens and the elimination of pullorum disease. The present study investigated the association among the host genome, the gut microbiome, and Pullorum infection in chickens. The results suggested that the gut microbial structure is altered in Pullorum-infected chickens. The diversity and abundance of the gut microbiota remarkably differed between the offspring coming from Pullorum-positive and Pullorum-negative chickens. Heritable gut microbiota were detected in the offspring. Moreover, host genetic variants were associated with microbial diversity and individual gut microbes. The pathogens and , which exhibited a high heritability in Pullorum-positive parents and their offspring, were associated with several genetic mutations in immunity-related genes.
PubMed: 33402350
DOI: 10.1128/mSystems.01192-20 -
BMC Microbiology May 2023Arsenic (As) with various chemical forms, including inorganic arsenic and organic arsenic, is the most prevalent water and environmental toxin. This metalloid occurs...
BACKGROUND
Arsenic (As) with various chemical forms, including inorganic arsenic and organic arsenic, is the most prevalent water and environmental toxin. This metalloid occurs worldwide and many of its forms, especially arsenite [As(III)], cause various diseases including cancer. Organification of arsenite is an effective way for organisms to cope with arsenic toxicity. Microbial communities are vital contributors to the global arsenic biocycle and represent a promising way to reduce arsenite toxicity.
METHODS
Brevundimonas sp. M20 with arsenite and roxarsone resistance was isolated from aquaculture sewage. The arsHRNBC cluster and the metRFHH operon of M20 were identified by sequencing. The gene encoding ArsR/methyltransferase fusion protein, arsR, was amplified and expressed in Escherichia coli BL21 (DE3), and this strain showed resistance to arsenic in the present of 0.25-6 mM As(III), aresenate, or pentavalent roxarsone. The methylation activity and regulatory action of ArsR were analyzed using Discovery Studio 2.0, and its functions were confirmed by methyltransferase activity analysis and electrophoretic mobility shift assays.
RESULTS
The minimum inhibitory concentration of the roxarsone resistant strain Brevundimonas sp. M20 to arsenite was 4.5 mM. A 3,011-bp arsenite resistance ars cluster arsHRNBC and a 5649-bp methionine biosynthesis met operon were found on the 3.315-Mb chromosome. Functional prediction analyses suggested that ArsR is a difunctional protein with transcriptional regulation and methyltransferase activities. Expression of ArsR in E. coli increased its arsenite resistance to 1.5 mM. The arsenite methylation activity of ArsR and its ability to bind to its own gene promoter were confirmed. The As(III)-binding site (ABS) and S-adenosylmethionine-binding motif are responsible for the difunctional characteristic of ArsR.
CONCLUSIONS
We conclude that ArsR promotes arsenite methylation and is able to bind to its own promoter region to regulate transcription. This difunctional characteristic directly connects methionine and arsenic metabolism. Our findings contribute important new knowledge about microbial arsenic resistance and detoxification. Future work should further explore how ArsR regulates the met operon and the ars cluster.
Topics: Arsenic; Arsenites; Base Sequence; Escherichia coli; Methylation; Roxarsone; Bacterial Proteins; Arsenicals; Operon; Methyltransferases; Methionine; Gene Expression Regulation, Bacterial; Trans-Activators
PubMed: 37193944
DOI: 10.1186/s12866-023-02876-z -
International Journal of Molecular... May 2022Arsenic (As), distributed widely in the natural environment, is a toxic substance which can severely impair the normal functions in living cells. Research on the genetic...
Arsenic (As), distributed widely in the natural environment, is a toxic substance which can severely impair the normal functions in living cells. Research on the genetic determinants conferring functions in arsenic resistance and metabolism is of great importance for remediating arsenic-contaminated environments. Many organisms, including bacteria, have developed various strategies to tolerate arsenic, by either detoxifying this harmful element or utilizing it for energy generation. More and more new arsenic resistance () determinants have been identified to be conferring resistance to diverse arsenic compounds and encoded in operons. There is a hazard in mobilizing arsenic during gold-mining activities due to gold- and arsenic-bearing minerals coexisting. In this study, we isolated 8 gold enrichment strains from the Zijin gold and copper mine (Longyan, Fujian Province, China) wastewater treatment site soil, at an altitude of 192 m. We identified two strains, Au-Bre29 and Au-Bre30, among these eight strains, having a high minimum inhibitory concentration (MIC) for As(III). These two strains contained the same operons but displayed differences regarding secretion of extra-polymeric substances (EPS) upon arsenite (As(III)) stress. Au-Bre29 contained one extra plasmid but without harboring any additional genes compared to Au-Bre30. We optimized the growth conditions for strains Au-Bre29 and Au-Bre30. Au-Bre30 was able to tolerate both a lower pH and slightly higher concentrations of NaCl. We also identified , a folate synthesis gene, in the operon of these two strains. In most organisms, folate synthesis begins with a FolE (GTP-Cyclohydrolase I)-type enzyme, and the corresponding gene is typically designated (in bacteria) or (in mammals). Heterologous expression of , cloned from Au-Bre30, in the arsenic-hypersensitive strain AW3110, conferred resistance to As(III), arsenate (As(V)), trivalent roxarsone (Rox(III)), pentavalent roxarsone (Rox(V)), trivalent antimonite (Sb(III)), and pentavalent antimonate (Sb(V)), indicating that folate biosynthesis is a target of arsenite toxicity and increased production of folate confers increased resistance to oxyanions. Genes encoding Acr3 and ArsH were shown to confer resistance to As(III), Rox(III), Sb(III), and Sb(V), and ArsH also conferred resistance to As(V). Acr3 did not confer resistance to As(V) and Rox(V), while ArsH did not confer resistance to Rox(V).
Topics: Arsenic; Arsenites; Bacteria; Bacterial Proteins; Caulobacteraceae; Escherichia coli; Folic Acid; Gold; Roxarsone
PubMed: 35628430
DOI: 10.3390/ijms23105619