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

Ohgew Kweon^*¹ , Seong-Jae Kim^*¹ , Songjoon Baek^*² , Jong-Chan Chae^*³ , Michael D Adjei⁴ , Dong-Heon Baek⁵ , Young-Chang Kim⁶ and Carl E Cerniglia¹

¹Microbiology Division, National Center for Toxicological Research/U.S. FDA, Jefferson, AR 72079, USA

²Division of Personalized Nutrition & Medicine, National Center for Toxicological Research/U.S. FDA, Jefferson, AR 72079, USA

³Biotechnology Center for Agriculture and the Environment, Cook College, Rutgers University, New Brunswick, NJ 08901, USA

⁴Department of Health Norfolk Department of Public Health Bureau of Laboratories, Norfolk, VA 23510, USA

⁵Department of Oral Microbiology and Immunology, School of Dentistry, Dankook University, Chonan 330-714, Republic of Korea

⁶School of Life Science, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea

author email corresponding author email* Contributed equally

BMC Biochemistry 2008, 9:11doi:10.1186/1471-2091-9-11


Published:	3 April 2008

Abstract

Background

Rieske 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.

Result

We 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 FNR_C-type reductase. Type II contains other two-component RHO systems that consist of an oxygenase and an FNR_N-type reductase. Type III represents a group of three-component RHO systems that consist of an oxygenase, a [2Fe-2S]-type ferredoxin and an FNR_N-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.

Conclusion

The 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.