title: The organization of naphthalene degradation genes in Pseudomonas putida strain AK5.
abstract: The Pseudomonas putida АК5 that was isolated from the slime pit of a Nizhnekamsk oil chemical factory can metabolize naphthalene via salicylate and gentisate. Catabolic genes are localized on non-conjugative IncP-7 plasmid pAK5 of about 115 kb in size. The "classical"nah-1 operon and the novel sgp-operon (salicylate-gentisate pathway) are both involved in naphthalene degradation by P. putida АК5, that was first described for Pseudomonas. The sgp-operon includes six open reading frames (ORFs) (sgpAIKGHB). The four ORFs code for the entire salicylate 5-hydroxylase - oxidoreductase component (sgpA), large and small subunits of the oxigenase component (sgpG and sgpH) and 2Fe-2S ferredoxin (sgpB). Genes for gentisate 1, 2-dioxygenase (sgpI) and fumarylpyruvate hydrolase (sgpK) are located in salicylate 5-hydroxylase genes clustering between sgpA and sgpG. The putative positive regulator for the sgp-operon (sgpR) was found upstream of the sgpA gene and oriented in the opposite direction from sgpA. The putative maleylacetoacetate isomerase gene is located apart, directly downstream from the sgp-operon. The sgp-operon organization and phylogenetic analysis of deduced amino acid sequences indicate that this operon has a mosaic structure according to the modular theory of the evolution of modern catabolic pathways.
authors.affiliation: Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia. tatiz@ibpm.pushchino.ru
authors.forename: Tatyana Yu
authors.initials: TY
authors.lastname: Izmalkova
authors.forename: Olesya I
authors.initials: OI
authors.lastname: Sazonova
authors.forename: Maxim O
authors.initials: MO
authors.lastname: Nagornih
authors.forename: Sergei L
authors.initials: SL
authors.lastname: Sokolov
authors.forename: Irina A
authors.initials: IA
authors.lastname: Kosheleva
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Boronin
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D049308:Dioxygenases / Q000737:chemistry / Q000235:genetics; D005841:Gentisates / Q000737:chemistry / Q000378:metabolism; D006867:Hydrolases / Q000737:chemistry / Q000235:genetics; D006899:Mixed Function Oxygenases / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D009281:Naphthalenes / Q000378:metabolism*; D016366:Open Reading Frames / Q000235:genetics; D009876:Operon; D010088:Oxidoreductases / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny; D016958:Pseudomonas putida / Q000201:enzymology* / Q000235:genetics*; D012459:Salicylates / Q000737:chemistry / Q000378:metabolism; D019745:cis-trans-Isomerases / Q000737:chemistry / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D005841:Gentisates; D009281:Naphthalenes; D012459:Salicylates; C112535:SgpA protein, bacterial; C112537:SgpB protein, bacterial; C031721:naphthalene; D006899:Mixed Function Oxygenases; D010088:Oxidoreductases; D049308:Dioxygenases; C026247:gentisate 1,2-dioxygenase; C099614:salicylic acid 5-hydroxylase; D006867:Hydrolases; C026249:fumarylpyruvate hydrolase; D019745:cis-trans-Isomerases; C021531:maleylacetoacetate isomerase