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

Journal Article · · BMC Biochemistry (Online)
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [2]
  1. U.S. Food and Drug Administration (FDA), Jefferson, AR (United States). National Center for Toxicological Research. Microbiology Division; DOE/OSTI
  2. U.S. Food and Drug Administration (FDA), Jefferson, AR (United States). National Center for Toxicological Research. Microbiology Division
  3. U.S. Food and Drug Administration (FDA), Jefferson, AR (United States). National Center for Toxicological Research. Division of Personalized Nutrition & Medicine
  4. Rutgers Univ., New Brunswick, NJ (United States). Cook College. Biotechnology Center for Agriculture and the Environment
  5. Norfolk Department of Public Health, Norfolk, VA (United States). Dept. of Health. Bureau of Labs
  6. Dankook Univ., Chonan (Korea, Republic of). School of Dentistry. Dept. of Oral Microbiology and Immunology
  7. Chungbuk National Univ. (Korea, Republic of). School of Life Science
+ Show Author Affiliations
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 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. 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.
Research Organization:
Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; USFDA
OSTI ID:
1629839
Journal Information:
BMC Biochemistry (Online), Journal Name: BMC Biochemistry (Online) Journal Issue: 1 Vol. 9; ISSN 1471-2091
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

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From Functional Potential of Soil Bacterial Communities Towards Petroleum Hydrocarbons Bioremediation journal May 2019
Artifizielle Lichtsammelkomplexe ermöglichen Rieske‐Oxygenase‐ katalysierte Hydroxylierungen in nicht‐photosynthetischen Zellen journal January 2020
Artificial Light‐Harvesting Complexes Enable Rieske Oxygenase Catalyzed Hydroxylations in Non‐Photosynthetic cells journal January 2020
Dihydroxylation of four- and five-ring aromatic hydrocarbons by the naphthalene dioxygenase from Sphingomonas CHY-1 journal October 2015
Starvation- and xenobiotic-related transcriptomic responses of the sulfanilic acid-degrading bacterium, Novosphingobium resinovorum SA1 journal October 2017
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Identification of a multi-component berberine 11-hydroxylase from Burkholderia sp. strain CJ1 journal June 2020
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Characterization of Novel Polycyclic Aromatic Hydrocarbon Dioxygenases from the Bacterial Metagenomic DNA of a Contaminated Soil journal August 2014
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Characterization of a Novel Rieske-Type Alkane Monooxygenase System in Pusillimonas sp. Strain T7-7 journal May 2013
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Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia journal May 2012
Role of oxygenases in guiding diverse metabolic pathways in the bacterial degradation of low-molecular-weight polycyclic aromatic hydrocarbons: A review journal September 2010
Identification of a multi-component berberine 11-hydroxylase from Burkholderia sp. strain CJ1 text January 2020
An insight into the origin and functional evolution of bacterial aromatic ring-hydroxylating oxygenases text January 2012
An insight into the origin and functional evolution of bacterial aromatic ring-hydroxylating oxygenases text January 2012

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