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Genome Biology Aug 2018Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer,...
BACKGROUND
Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesize that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from 33 controls and 143 cancer cases, we conduct 16S ribosomal RNA (rRNA) bacterial gene sequencing, with RNA-sequencing data from lung cancer cases in The Cancer Genome Atlas serving as the validation cohort.
RESULTS
Overall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma specifically, a separate group of taxa are identified, in which Acidovorax is enriched in smokers. Acidovorax temporans is identified within tumor sections by fluorescent in situ hybridization and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibit higher abundance among the subset of squamous cell carcinoma cases with TP53 mutations, an association not seen in adenocarcinomas.
CONCLUSIONS
The results of this comprehensive study show both microbiome-gene and microbiome-exposure interactions in squamous cell carcinoma lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can impair epithelial function, have a unique bacterial consortium that is higher in relative abundance in smoking-associated tumors of this type. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection.
Topics: Adult; Aged; Biodiversity; Comamonadaceae; Female; Humans; Lung Neoplasms; Male; Microbiota; Middle Aged; Mutation; Neoplasms, Squamous Cell; Proteobacteria; Reproducibility of Results; Smokers; Tumor Suppressor Protein p53
PubMed: 30143034
DOI: 10.1186/s13059-018-1501-6 -
Revista Chilena de Infectologia :... Apr 2020
Topics: Bacterial Typing Techniques; Comamonas; DNA, Bacterial
PubMed: 32730480
DOI: 10.4067/s0716-10182020000200147 -
Microbial Genomics Dec 2021Beta-proteobacteria belonging to the genus have been described from various environments. Many strains can interact with a range of hosts, including humans and plants,...
Beta-proteobacteria belonging to the genus have been described from various environments. Many strains can interact with a range of hosts, including humans and plants, forming neutral, beneficial or detrimental associations. In the frame of this study, we investigated the genomic properties of 52 bacterial strains of the genus , isolated from healthy roots of with the intent of identifying traits important for effective plant-growth promotion. Based on single-strain inoculation bioassays with , performed in a gnotobiotic system, we distinguished seven robust plant-growth promoting strains from strains with no significant effects on plant-growth. We showed that the genomes of the two groups differed prominently in protein families linked to sensing and transport of organic acids, production of phytohormones, as well as resistance and production of compounds with antimicrobial properties. In a second step, we compared the genomes of the tested isolates with those of plant pathogens and free-living strains of the genus sourced from public repositories. Our pan-genomics comparison revealed features correlated with commensal and pathogenic lifestyle. We showed that commensals and pathogens differ mostly in their ability to use plant-derived lipids and in the type of secretion-systems being present. Most free-living strains did not harbour any secretion-systems. Overall, our data indicate that strains undergo extensive adaptations to their particular lifestyle by horizontal uptake of novel genetic information and loss of unnecessary genes.
Topics: Bacterial Proteins; Comamonadaceae; Genome, Bacterial; Genomics; High-Throughput Nucleotide Sequencing; Lotus; Phylogeny; Plant Diseases; Sequence Analysis, DNA; Symbiosis
PubMed: 34889729
DOI: 10.1099/mgen.0.000666 -
Functional and structural characterization of AntR, an Sb(III) responsive transcriptional repressor.Molecular Microbiology Aug 2021The ant operon of the antimony-mining bacterium Comamonas testosterone JL40 confers resistance to Sb(III). The operon is transcriptionally regulated by the product of...
The ant operon of the antimony-mining bacterium Comamonas testosterone JL40 confers resistance to Sb(III). The operon is transcriptionally regulated by the product of the first gene in the operon, antR. AntR is a member of ArsR/SmtB family of metal/metalloid-responsive repressors resistance. We purified and characterized C. testosterone AntR and demonstrated that it responds to metalloids in the order Sb(III) = methylarsenite (MAs(III) >> As(III)). The protein was crystallized, and the structure was solved at 2.1 Å resolution. The homodimeric structure of AntR adopts a classical ArsR/SmtB topology architecture. The protein has five cysteine residues, of which Cys103 from one monomer and Cys113 from the other monomer, are proposed to form one Sb(III) binding site, and Cys113 and Cys103 forming a second binding site. This is the first report of the structure and binding properties of a transcriptional repressor with high selectivity for environmental antimony.
Topics: Amino Acid Sequence; Antimony; Arsenic; Arsenicals; Binding Sites; Comamonas testosteroni; Gene Expression Regulation, Bacterial; Protein Conformation; Repressor Proteins; Transcription Factors; Transcription, Genetic
PubMed: 33786926
DOI: 10.1111/mmi.14721 -
BMC Microbiology Aug 2012Two important plant pathogenic bacteria Acidovorax oryzae and Acidovorax citrulli are closely related and often not easy to be differentiated from each other, which...
BACKGROUND
Two important plant pathogenic bacteria Acidovorax oryzae and Acidovorax citrulli are closely related and often not easy to be differentiated from each other, which often resulted in a false identification between them based on traditional methods such as carbon source utilization profile, fatty acid methyl esters, and ELISA detection tests. MALDI-TOF MS and Fourier transform infrared (FTIR) spectra have recently been successfully applied in bacterial identification and classification, which provide an alternate method for differentiating the two species.
RESULTS
Characterization and comparison of the 10 A. oryzae strains and 10 A. citrulli strains were performed based on traditional bacteriological methods, MALDI-TOF MS, and FTIR spectroscopy. Our results showed that the identity of the two closely related plant pathogenic bacteria A. oryzae and A. citrulli was able to be confirmed by both pathogenicity tests and species-specific PCR, but the two species were difficult to be differentiated based on Biolog and FAME profile as well as 16 S rRNA sequence analysis. However, there were significant differences in MALDI-TOF MS and FTIR spectra between the two species of Acidovorax. MALDI-TOF MS revealed that 22 and 18 peaks were specific to A. oryzae and A. citrulli, respectively, while FTIR spectra of the two species of Acidovorax have the specific peaks at 1738, 1311, 1128, 1078, 989 cm(-1) and at 1337, 968, 933, 916, 786 cm(-1), respectively.
CONCLUSIONS
This study indicated that MALDI-TOF MS and FTIR spectra may give a new strategy for rapid bacterial identification and differentiation of the two closely related species of Acidovorax.
Topics: Comamonadaceae; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Spectroscopy, Fourier Transform Infrared
PubMed: 22900823
DOI: 10.1186/1471-2180-12-182 -
The Science of the Total Environment Feb 2021Antimony, like arsenic, is a toxic metalloid widely distributed in the environment. Microbial detoxification of antimony has recently been identified. Here we describe a...
Antimony, like arsenic, is a toxic metalloid widely distributed in the environment. Microbial detoxification of antimony has recently been identified. Here we describe a novel bacterial P-type antimonite (Sb(III))-translocating ATPase from the antimony-mining bacterium Comamonas testosterone JL40 that confers resistance to Sb(III). In a comparative proteomics analysis of strain JL40, an operon (ant operon) was up-regulated by Sb(III). The ant operon includes three genes, antR, antC and antA. AntR belongs to the ArsR/SmtB family of metalloregulatory proteins that regulates expression of the ant operon. AntA belongs to the P family of the P-type cation-translocating ATPases. It has both similarities to and differences from other members of the P subfamily and appears to be the first identified member of a distinct subfamily that we designate P. Expression AntA in E. coli AW3110 (Δars) conferred resistance to Sb(III) and reduced the intracellular concentration of Sb(III) but not As(III) or other metals. Everted membrane vesicles from cells expressing antA accumulated Sb(III) but not As(III), where uptake in everted vesicles reflects efflux from cells. AntC is a small protein with a potential Sb(III) binding site, and co-expression of AntC with AntA increased resistance to Sb(III). We propose that AntC functions as an Sb(III) chaperone to AntA, augmenting Sb(III) efflux. The identification of a novel Sb(III)-translocating ATPase enhances our understanding of the biogeochemical cycling of environmental antimony by bacteria.
Topics: Adenosine Triphosphatases; Antimony; Comamonas testosteroni; Escherichia coli; P-type ATPases
PubMed: 33254899
DOI: 10.1016/j.scitotenv.2020.142393 -
Journal of Oleo Science Apr 2021A total of 100 environmental samples were investigated for their ability to degrade 1 g/L surfactin as a substrate. Among them, two enrichment cultures, which exhibited...
A total of 100 environmental samples were investigated for their ability to degrade 1 g/L surfactin as a substrate. Among them, two enrichment cultures, which exhibited microbial growth as well as surfactin degradation, were selected and further investigated. After several successive cultivations, nanopore sequencing of full-length 16S rRNA genes with MinION was used to analyze the bacterial species in the enrichment cultures. Variovorax spp., Caulobacter spp., Sphingopyxis spp., and Pseudomonas spp. were found to be dominant in these surfactin-degrading mixed cultures. Finally, one strain of Pseudomonas putida was isolated as a surfactin-degrading bacterium. This strain degraded 1 g/L surfactin below a detectable level within 14 days, and C surfactin was degraded faster than C surfactin.
Topics: Biodegradation, Environmental; Caulobacter; Comamonadaceae; Lipopeptides; Peptides, Cyclic; Pseudomonas putida; Sphingomonadaceae; Surface-Active Agents
PubMed: 33692244
DOI: 10.5650/jos.ess20331 -
Applied and Environmental Microbiology Apr 2022Halonitrobenzenes are toxic chemical intermediates used widely for industrial synthesis of dyes and pesticides. Bacteria able to degrade 2- and 4-chloronitrobenzene have...
Halonitrobenzenes are toxic chemical intermediates used widely for industrial synthesis of dyes and pesticides. Bacteria able to degrade 2- and 4-chloronitrobenzene have been isolated and characterized; in contrast, no natural isolate has been reported to degrade -halonitrobenzenes. In this study, sp. strain JS3051, previously reported to degrade 2,3-dichloronitrobenzene, grew readily on 3-chloronitrobenzene and 3-bromonitrobenzene, but not on 3-fluoronitrobenzene, as sole sources of carbon, nitrogen, and energy. A Rieske nonheme iron dioxygenase (DcbAaAbAcAd) catalyzed the dihydroxylation of 3-chloronitrobenzene and 3-bromonitrobenzene, resulting in the regiospecific production of ring-cleavage intermediates 4-chlorocatechol and 4-bromocatechol. The lower activity and relaxed regiospecificity of DcbAaAbAcAd toward 3-fluoronitrobenzene is likely due to the higher electronegativity of the fluorine atom, which hinders it from interacting with E204 residue at the active site. DccA, a chlorocatechol 1,2-dioxygenase, converts 4-chlorocatechol and 4-bromocatechol into the corresponding halomuconic acids with high catalytic efficiency, but with much lower / values for fluorocatechol analogues. The results indicate that the Dcb and Dcc enzymes of sp. strain JS3051 can catalyze the degradation of 3-chloro- and 3-bromonitrobenzene in addition to 2,3-dichloronitrobenzene. The ability to utilize multiple substrates would provide a strong selective advantage in a habitat contaminated with mixtures of chloronitrobenzenes. Halonitroaromatic compounds are persistent environmental contaminants, and some of them have been demonstrated to be degraded by bacteria. Natural isolates that degrade 3-chloronitrobenzene and 3-bromonitrobenzene have not been reported. In this study, we report that sp. strain JS3051 can degrade 2,3-dichloronitrobenzene, 3-chloronitrobenzene, and 3-bromonitrobenzene using the same catabolic pathway, whereas it is unable to grow on 3-fluoronitrobenzene. Based on biochemical analyses, it can be concluded that the initial dioxygenase and lower pathway enzymes are inefficient for 3-fluoronitrobenzene and even misroute the intermediates, which is likely responsible for the failure to grow. These results advance our understanding of how the broad substrate specificities of catabolic enzymes allow bacteria to adapt to habitats with mixtures of xenobiotic contaminants.
Topics: Biodegradation, Environmental; Comamonadaceae; Dioxygenases; Nitrobenzenes
PubMed: 35343758
DOI: 10.1128/aem.02437-21 -
International Journal of Molecular... Aug 2022A type VI secretion system (T6SS) gene cluster has been reported in . Research on the activation conditions, functions, and the interactions between key elements in ....
Hcp of the Type VI Secretion System (T6SS) in Group II Strain Aac5 Has a Dual Role as a Core Structural Protein and an Effector Protein in Colonization, Growth Ability, Competition, Biofilm Formation, and Ferric Iron Absorption.
A type VI secretion system (T6SS) gene cluster has been reported in . Research on the activation conditions, functions, and the interactions between key elements in . T6SS is lacking. Hcp (Hemolysin co-regulated protein) is both a structural protein and a secretion protein of T6SS, which makes it a special element. The aims of this study were to determine the role of Hcp and its activated conditions to reveal the functions of T6SS. In virulence and colonization assays of deletion mutant strain Δ, (type VI secretion system membrane subunit) deletion mutant strain Δ and double mutant ΔΔ, population growth was affected but not virulence after injection of cotyledons and seed-to-seedling transmission on watermelon. The population growth of Δ and Δ were lower than wild type strain Aac5 of group II at early stage but higher at a later stage. Deletion of also affected growth ability in different culture media, and the decline stage of Δ was delayed in KB medium. Biofilm formation ability of Δ, Δ and ΔΔ was lower than Aac5 with competition by prey bacteria but higher in KB and M9-Fe medium. Deletion of reduced the competition and survival ability of Aac5. Based on the results of Western blotting and qRT-PCR analyses, Hcp is activated by cell density, competition, ferric irons, and the host plant. The expression levels of genes related to bacterial secretion systems, protein export, and several other pathways, were significantly changed in the Δ mutant compared to Aac5 when T6SS was activated at high cell density. Based on transcriptome data, we found that a few candidate effectors need further identification. The phenotypes, activated conditions and transcriptome data all supported the conclusion that although there is only one T6SS gene cluster present in the . group II strain Aac5, it related to multiple biological processes, including colonization, growth ability, competition and biofilm formation.
Topics: Bacterial Proteins; Biofilms; Biological Phenomena; Comamonadaceae; Iron; Type VI Secretion Systems
PubMed: 36077040
DOI: 10.3390/ijms23179632 -
Systematic and Applied Microbiology Sep 2018Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina,...
Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina, USA, characterized, and their genomes sequenced. Their 16S rRNA genes were highly similar to those previously recovered during stable-isotope probing (SIP) of one of the soils with the polycyclic aromatic hydrocarbon (PAH) phenanthrene. Heterotrophic growth of all strains occurred with a number of organic acids, as well as phenanthrene, but no other tested PAHs. Optimal growth occurred aerobically under mesophilic temperature, neutral pH, and low salinity conditions. Predominant fatty acids were Cω7c/Cω6c, C, and Cω7c, and were consistent with the genus. Genomic G+C contents ranged from 63.6 to 64.2%. A combination of whole genome comparisons and physiological analyses indicated that these four strains likely represent a single species within the Acidovorax genus. Chromosomal genes for phenanthrene degradation to phthalate were nearly identical to highly conserved regions in phenanthrene-degrading Delftia, Burkholderia, Alcaligenes, and Massilia species in regions flanked by transposable or extrachromosomal elements. The lower degradation pathway for phenanthrene metabolism was inferred by comparisons to described genes and proteins. The novel species Acidovorax carolinensis sp. nov. is proposed, comprising the four strains described in this study with strain NA3 as the type strain (=LMG 30136, =DSM 105008).
Topics: Biodegradation, Environmental; Comamonadaceae; DNA, Bacterial; Genes, Bacterial; Genome, Bacterial; Metabolic Networks and Pathways; North Carolina; Phenanthrenes; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Soil Pollutants
PubMed: 29937052
DOI: 10.1016/j.syapm.2018.06.001