Nicotine-degradation related gene clusters identification

Fragments containing the Nic-like gene clusters in strain JY-Q, involved in the nicotine-degradation, were identified through literature curation and data mining for gene clusters and cognate protein sequences of P. putida KT2440 and S16. Two Nic homology gene clusters and one NA-like genetic locus were characterized by in silico analyses (Figure ​(Figure2).2). Several homologous genetic loci similar to Nic in P. putida S16 were also identified in the customized Pseudomonas genome databases, as exemplified in Figure ​Figure2.2. The Nic-like gene clusters discovered generally encoded five enzymes that could step-by-step convert 6-hydroxy-3-succinoylpyridine (HSP) to fumaric acid, formic acid and ammonia.

Schematic representation for genetic organization and immediate vicinity of putative nicotine-degradation gene clusters of Pseudomonas sp. JY-Q compared with the similar gene cluster from Pseudomonas putida S16, KT2440 (A) and HZN6 (B). HspB, HSP hydroxylase; Iso, maleate isomerase; Nfo, NFM deformylase; Hpo, DHP dioxygenase; Ami, maleamate amidase; Hna, 6-hydroxynicotine 3-monooxygenase; Nox, nicotine oxidase; Pao, pseudooxynicotine amine oxidase; Sap, NADP⁺-dependent 3-succinoylsemialdehyde-pyridine dehydrogenase; Orf, no predicted function. The numbers within the arrows indicate the percent amino acid sequence identity with the orthologous gene product from Pseudomonas putida S16 and sp. HZN6.