A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases

Abstract

BackgroundRieske non-heme iron aromatic ring-hydroxylating oxygenases (RHOs) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. Since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many RHOs have been discovered, which do not belong to any group in the previous classification. Here, we present a scheme for classification of RHOs reflecting new sequence information and interactions between RHO enzyme components.ResultWe have analyzed a total of 130 RHO enzymes in which 25 well-characterized RHO enzymes were used as standards to test our hypothesis for the proposed classification system. From the sequence analysis of electron transport chain (ETC) components of the standard RHOs, we extracted classification keys that reflect not only the phylogenetic affiliation within each component but also relationship among components. Oxygenase components of standard RHOs were phylogenetically classified into 10 groups with the classification keys derived from ETC components. This phylogenetic classification scheme was converted to a new systematic classification consisting of 5 distinct types. The new classification system was statistically examined to justify its stability. Type I represents two-component RHO systems that consist of an oxygenase and an FNRC-type reductase. Type II contains other two-component RHO systems that consist of an oxygenase and an FNRN-type reductase. Type III represents a group of three-component RHO systems that consist of an oxygenase, a [2Fe-2S]-type ferredoxin and an FNRN-type reductase. Type IV represents another three-component systems that consist of oxygenase, [2Fe-2S]-type ferredoxin and GR-type reductase. Type V represents another different three-component systems that consist of an oxygenase, a [3Fe-4S]-type ferredoxin and a GR-type reductase.ConclusionThe new classification system provides the following features. First, the new classification system analyzes RHO enzymes as a whole. RwithSecond, the new classification system is not static but responds dynamically to the growing pool of RHO enzymes. Third, our classification can be applied reliably to the classification of incomplete RHOs. Fourth, the classification has direct applicability to experimental work. Fifth, the system provides new insights into the evolution of RHO systems based on enzyme interaction.

Semirational Engineering of the Naphthalene Dioxygenase from Pseudomonas sp. NCIB 9816‐4 towards Selective Asymmetric Dihydroxylation

“…[3,4] Representing ab iocatalytic alternative to asymmetricd ihydroxylation with toxic transition-metal catalysts, ROs also exhibit ab road substrate scope.…”

“…[2] In ROs, categorized as types III and IV,t he reductase obtains electrons from the naturalc osubstrate NAD(P)H,a nd a ferredoxin component shuttles electrons from the reductase to the oxygenase active site, at which actual oxygen activation and substrate hydroxylation occur. [3,4] Representing ab iocatalytic alternative to asymmetricd ihydroxylation with toxic transition-metal catalysts, ROs also exhibit ab road substrate scope. [5] Over 300 diverse substrates ranging from polyaromatic hydrocarbons such as phenanthracene to halogenated ethylenes and flavonoid structures were reportedt ob eh ydroxylated with these enzymes.…”

Pleiotropic and Epistatic Behavior of a Ring-Hydroxylating Oxygenase System in the Polycyclic Aromatic Hydrocarbon Metabolic Network from Mycobacterium vanbaalenii PYR-1

“…7) reveals, of 21 RHO genes in the M. vanbaalenii PYR-1 genome (17, 28), about 10 RHO systems respond dynamically to PAH substrates (23). Among them, the type V RHO systems are mostly active for PAH hydroxylation in the PAH-MN, due mainly to their type V ETC requirement (23,32). In Kweon's RHO classification reflecting functional interactions between oxygenase components and ETCs (32), the Pdo system is a type V RHO system and is functionally compatible with type V ETC components.…”

“…As the RHO-centric anthracene, phenanthrene, fluoranthene, and pyrene degradation on the basis of their ETC compatibility, substrate specificity, and protein abundance. RHO enzymes were classified according to Kweon's RHO scheme (32). The ETC compatibility of an RHO enzyme was calculated from its RHO classification.…”

“…These endeavors have allowed evidence-based annotation of RHOs for the hydroxylation of HMW PAHs and also a better understanding of the effects of genetic perturbation and responses at a network level (25). A type V RHO (32), like the phenanthrene dioxygenase of Nocardioides sp. KP7, consists of an oxygenase, a [3Fe-4S]-type ferredoxin, and a glutathione-type reductase.…”