Project description:A novel Paenarthrobacter ilicis 6C isolate from soil found in Bielefeld, Germany, was sequenced and characterized by proteome analysis to provide the first clear look at a novel genus in the realm of xanthan degrading microorganisms. This research provides additional groundwork for the ongoing characterization of Paenarthrobacter, as well as widening the understanding of xanthan degrading microorganisms.
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.
