HAL Id: hal-01137018
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Submitted on 8 Mar 2017
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Genomics based approach to identify the genes involved in ipu mineralization in sphingomonas sp.sh
Sabir Hussain, Marion Devers-Lamrani, Fabrice Martin
To cite this version:
Sabir Hussain, Marion Devers-Lamrani, Fabrice Martin. Genomics based approach to identify the genes involved in ipu mineralization in sphingomonas sp.sh. 8. Congrès National de la Société Française de Microbiologie, Jun 2010, Marseille, France. n.p. �hal-01137018�
GENOMICS BASED APPROACH TO IDENTIFY THE GENES INVOLVED IN IPU MINERALIZATION IN SPHINGOMONAS SP. SH
Sabir Hussain, Marion Devers-Lamrani, and Fabrice Martin-Laurent
INRA, Université de Bourgogne, UMR MSE, 17 rue Sully, BP 86510, F- 21065 Dijon Cedex, France.
Abstract
Phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralised in a French agricultural soil previously exposed to IPU. A bacterial strain able to metabolise IPU was isolated from this soil adapted to IPU mineralization. Based on 16S rDNA sequence analysis, the strain was found to be belonging to a new species of the genus Sphingomonas (96% similarity with Sphingomonas sp. JEM-14, AB219361) and was designated as Sphingomonas sp. SH. It had the ability to mineralize only IPU and its known metabolites including 4-isopropylaniline but it could not degrade other structurally related phenylurea hebicides i.e. diuron, linuron, monolinuron and chlorotoluron as well as their aniline derivatives suggesting that the catabolic abilities of the strain SH are highly specific for IPU metabolism. IPU degrading ability of the strain SH was strongly influenced by the pH with the optimal degradation taking place at pH 7.5. A significant reduction in the maximum rate of degradation (µm) was observed at the pH values over and below 7.5. In order to search for the genes coding for IPU degrading enzymes, a BAC clone library was established from the genomic DNA of the strain SH. Functional screening of 3000 BAC clones was carried out to identify the BACs able to degrade IPU and its known metabolites i.e. MDIPU, DDIPU and 4-IA. Unfortunately, we were not able to identify any BAC clone able to degrade these compounds by this functional screening. However, PCR based genomic screening led to the identification of three positive BAC clones harbouring catA gene coding for 1,2-dioxygenase enzyme involved in the degradation of catechol which is considered as a key intermediate during the phenyl-ring cleavage of IPU as well as most of the aromatic hydrocarbons. Partial sequencing of the BACs confirmed the presence of catA sequences. The positive BACs (about 20 kb in length) were fully sequenced by pyrosequencing using the Genome Sequencer FLX Titanium SystemTM (Beckman Genomics, USA) to target the gene clusters involved in biodegradation process. Annotation of the sequences using the bioinformatics tools is going on.
Key words Isoproturon, Sphingomonas sp. SH, Mineralization, Phenylurea herbicides, BAC library, catA gene
