Pseudomonas abietaniphila
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA275816 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR030175.fastq.gz | Fastqsanger.gz | |||
| DRR030176_1.fastq.gz | Fastqsanger.gz | |||
| DRR030176_2.fastq.gz | Fastqsanger.gz | |||
| DRR030177_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 17 |
Similar Datasets
Project description:Pseudomonas abietaniphila strain:BHJ04 Genome sequencing
| PRJNA1110075 | ENA
Project description:Pseudomonas abietaniphila LMG 20220 genome sequencing
| PRJNA319561 | ENA
Project description:Grey mould is an important necrotrophic fungal pathogen that causes huge economic losses in agriculture. Many types of bacteria are used for biological control of grey mould via competition for space or nutrients and/or the production of antifungal metabolites. Oxalate is a key component of virulent necrotic fungal pathogens. In this study, we isolated non-antifungal oxalate-degrading bacteria (ODB) from the surfaces of oxalate-rich spinach and strawberries to investigate their ability to control necrotic fungal pathogens such as grey mould. A total of 36 bacteria grown on oxalate minimal (OM) agar plates were tested for oxalate-degrading activity. Five isolates exhibiting the highest oxalate degradation activity were subjected to molecular identification using 16S rRNA gene sequencing. Two isolates exhibiting non-antifungal activity were subjected to disease suppression assays using Arabidopsis-Botrytis systems. The isolate Pseudomonas abietaniphila ODB36, which exhibited significant plant protective ability, was finally selected for further investigation. Based on whole-genome information, the pseudomonad oxalate degrading (podA) gene, which encodes formyl-CoA transferase, was analysed. The podA- mutant did not inhibit Botrytis infection and oxalate toxicity; the defects were recovered by podA complementation. Purified PodA-His converted oxalate to formate and eliminated oxalate toxicity. These results indicate that P. abietaniphila ODB36 and PodA enzyme are associated with various aspects of grey mould disease inhibitory effects.
| S-EPMC6994688 | biostudies-literature
Project description:Pseudomonas abietaniphila BKME-9 is able to degrade dehydroabietic acid (DhA) via ring hydroxylation by a novel dioxygenase. The ditA1, ditA2, and ditA3 genes, which encode the alpha and beta subunits of the oxygenase and the ferredoxin of the diterpenoid dioxygenase, respectively, were isolated and sequenced. The ferredoxin gene is 9. 2 kb upstream of the oxygenase genes and 872 bp upstream of a putative meta ring cleavage dioxygenase gene, ditC. A Tn5 insertion in the alpha subunit gene, ditA1, resulted in the accumulation by the mutant strain BKME-941 of the pathway intermediate, 7-oxoDhA. Disruption of the ferredoxin gene, ditA3, in wild-type BKME-9 by mutant-allele exchange resulted in a strain (BKME-91) with a phenotype identical to that of the mutant strain BKME-941. Sequence analysis of the putative ferredoxin indicated that it is likely to be a [4Fe-4S]- or [3Fe-4S]-type ferredoxin and not a [2Fe-2S]-type ferredoxin, as found in all previously described ring-hydroxylating dioxygenases. Expression in Escherichia coli of ditA1A2A3, encoding the diterpenoid dioxygenase without its putative reductase component, resulted in a functional enzyme. The diterpenoid dioxygenase attacks 7-oxoDhA, and not DhA, at C-11 and C-12, producing 7-oxo-11, 12-dihydroxy-8,13-abietadien acid, which was identified by 1H nuclear magnetic resonance, UV-visible light, and high-resolution mass spectrometry. The organization of the genes encoding the various components of the diterpenoid dioxygenase, the phylogenetic distinctiveness of both the alpha subunit and the ferredoxin component, and the unusual Fe-S cluster of the ferredoxin all suggest that this enzyme belongs to a new class of aromatic ring-hydroxylating dioxygenases.
| S-EPMC93704 | biostudies-literature
Project description:Diterpenoids are naturally occurring plant compounds which have pharmaceutical properties. We have sequenced a 10.4-kbp extension of the dit cluster in Pseudomonas abietaniphila BKME-9, containing genes involved in abietane diterpenoid biodegradation. The ditQ gene was found to encode a cytochrome P450 monooxygenase, P450dit, and to be homologous to the tdtD gene of Pseudomonas diterpeniphila A19-6a. Knocking out ditQ had little effect on growth of BKME-9 on abietic acid but severely impaired growth on dehydroabietic acid (DhA) and palustric acid (PaA), increasing doubling times from 3.8 to 15 h on DhA and from 5.6 to 18.5 h on PaA. A xylE transcriptional fusion showed that transcription of ditQ was induced by a range of diterpenoids. Substrate binding assays of P450dit expressed in Escherichia coli revealed that DhA binds to the enzyme and yields a type I binding spectrum with a Kd of 0.4 microM. These results indicate that P450dit is involved in the metabolism of DhA and PaA and are consistent with its putative role in converting DhA to 7-hydroxy-DhA. Finally, an amino acid sequence identity of greater than 72% and conserved gene arrangement support the hypothesis that the dit gene cluster of P. abietaniphila BKME-9 and the tdt cluster of P. diterpeniphila A19-6a contain functional homologues.
| S-EPMC415779 | biostudies-literature
Project description:ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by DAP-seq in Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.
2019-12-20 | GSE137648 | GEO
Project description:We have cloned and sequenced the dit gene cluster encoding enzymes of the catabolic pathway for abietane diterpenoid degradation by Pseudomonas abietaniphila BKME-9. The dit gene cluster is located on a 16.7-kb DNA fragment containing 13 complete open reading frames (ORFs) and 1 partial ORF. The genes ditA1A2A3 encode the alpha and beta subunits and the ferredoxin of the dioxygenase which hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8, 13-abietadien acid. The dioxygenase mutant strain BKME-941 (ditA1::Tn5) did not grow on nonaromatic abietanes, and transformed palustric and abietic acids to 7-oxodehydroabietic acid in cell suspension assays. Thus, nonaromatic abietanes are aromatized prior to further degradation. Catechol 2,3-dioxygenase activity of xylE transcriptional fusion strains showed induction of ditA1 and ditA3 by abietic, dehydroabietic, and 7-oxodehydroabietic acids, which support the growth of strain BKME-9, as well as by isopimaric and 12, 14-dichlorodehydroabietic acids, which are diterpenoids that do not support the growth of strain BKME-9. In addition to the aromatic-ring-hydroxylating dioxygenase genes, the dit cluster includes ditC, encoding an extradiol ring cleavage dioxygenase, and ditR, encoding an IclR-type transcriptional regulator. Although ditR is not strictly required for the growth of strain BKME-9 on abietanes, a ditR::Km(r) mutation in a ditA3::xylE reporter strain demonstrated that it encodes an inducer-dependent transcriptional activator of ditA3. An ORF with sequence similarity to genes encoding permeases (ditE) is linked with genes involved in abietane degradation.
| S-EPMC94551 | biostudies-literature