Ontology highlight
ABSTRACT:
PROVIDER: PRJNA738185 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR15143039.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
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Project description:Paenarthrobacter strains effectively degrade the fungicide iprodione, exhibiting a specialization rarely seen amongst bacteria. The transformation of iprodione is controlled by an amidase, a deacetylase and a hydrolase encoded by ipaH, ddaH and duaH respectively. We aimed to elucidate the mechanisms of this catabolic specialization and its evolution in Paenarthrobacters. The genomes of two new iprodione-degrading Paenarthrobacter strains TA1.8 and C1 were sequenced and analyzed comparatively with the genomes of two other iprodione-degrading Paenarthrobacter strains YJN-5 and YJN-D. Comparative genomics revealed different gene organization motifs amongst strains which suggest that the strains are at different stages of pathway evolution, in accord with their prior exposure to iprodione. Strains TA1.8, YJN-5 and YJN-D, all isolated from soils heavily exposed to iprodione, carried multiple copies of ipaH, ddaH and duaH in their chromosomes and plasmids that were assigned to two distinct phylogenetic clusters based on genome topology. Conversely, strain C1, isolated from a pristine soil, carried ipaH, ddaH and duaH in the chromosome. Pangenome analysis of the genus Paenarthrobacter placed ipaH and duaH in the core genome reinforcing their specialization in the degradation of iprodione as they need to acquire only ddaH, the sole gene of the pathway associated with transposable elements in strains C1 and TA1.8, to complete the pathway. We propose an evolution route of the iprodione transformation pathway which involves acquisition of ddaH through horizontal gene transfer, gene duplication of the chromosomally encoded ipaH and ddaH, and further genetic rearrangements for pathway optimization, complementing duaH, a core gene in Paenarthrobacters. Transcriptomic analysis of strain TA1.8 verified the involvement of all copies of ipaH, ddaH and duaH in the transformation of iprodione, and identified hydantoinases, upregulated during iprodione degradation, as potential facilitators of the transformation of the hydantoin-containing intermediate N-(3,-5-dichlorophenyl)- 2,4-dioxoimida-zolidine, a step mediated by DdaH.
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Project description:Levoglucosan is produced in the pyrolysis of cellulose and starch, including from bushfires or the burning of biofuels, and is deposited from the atmosphere across the surface of the earth. We describe two levoglucosan degrading Paenarthrobacter spp. (Paenarthrobacter nitrojuajacolis LG01 and Paenarthrobacter histidinolovorans LG02) that were isolated by metabolic enrichment on levoglucosan as sole carbon source. Genome sequencing and proteomics analysis revealed expression of a series of gene clusters encoding known levoglucosan degrading enzymes, levoglucosan dehydrogenase (LGDH, LgdA), 3-keto-levoglucosan b-eliminase (LgdB1) and glucose 3-dehydrogenase (LgdC), along with an ABC transporter cassette and associated solute binding protein. However, no homologues of 3-ketoglucose dehydratase (LgdB2) were evident. The expressed gene clusters contained a range of putative sugar phosphate isomerase/xylose isomerases with weak similarity to LgdB2. Sequence similarity network analysis of genome neighbors revealed that homologues of LgdA, LgdB1 and LgdC are generally conserved in a range of bacteria in the phyla Firmicutes, Actinobacteria and Proteobacteria. One sugar phosphate isomerase/xylose isomerase cluster (LgdB3) was identified with limited distribution mutually exclusive with LgdB2. LgdB1, LgdB2 and LgdB3 adopt similar predicted 3D folds suggesting overlapping function in processing intermediates in LG metabolism. Our findings highlight the diversity within the LGDH pathway through which bacteria utilize levoglucosan as a nutrient source.
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