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

Kweon O, Kim SJ, Baek S, Chae JC, Adjei MD, Baek DH, Kim YC, Cerniglia CE - BMC Biochem. (2008)

Bottom Line: Type II contains other two-component RHO systems that consist of an oxygenase 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microbiology Division, National Center for Toxicological Research/US FDA, Jefferson, AR 72079, USA. oh-gew.kweon@fda.hhs.gov

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 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.

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Grouping of reductase components from 25 standard RHO enzymes with schematic representation of the conserved domain structures. The names of bacterial strains are indicated after the enzyme names. GR-type, FNRC-type, and FNRN-type reductases are shown in the boxes with black, gray, and white background, respectively. Designations: FAD-Flavin adenine dinucleotide; NAD-Nicotinamide adenine dinucleotide.
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Figure 2: Grouping of reductase components from 25 standard RHO enzymes with schematic representation of the conserved domain structures. The names of bacterial strains are indicated after the enzyme names. GR-type, FNRC-type, and FNRN-type reductases are shown in the boxes with black, gray, and white background, respectively. Designations: FAD-Flavin adenine dinucleotide; NAD-Nicotinamide adenine dinucleotide.

Mentions: The phenogram with the domain arrangements of reductases is presented in Figure 2. The 25 reductases were divided into three groups, Rd-I, Rd-II and Rd-III, based on the conserved domain arrangements. When grouped with PD value of 0.85, the 25 reductases can also be grouped into the same three groups. Therefore, the PD values obtained by using Gonnet weight matrix were less than 0.85 within each group which has the same arrangement of conserved domains. Group Rd-I consists of glutathione reductase (GR) type reductases that show over 28% amino acid identity to one another, while groups Rd-II and Rd-III include the ferredoxin-NADP+ reductase (FNR) type reductases that show over 15 and 23% amino acid identity within each group, respectively. Groups Rd-II and Rd-III share the same three domains for flavin, NAD and [2Fe-2S] binding, but show different domain arrangements. In group Rd-II, the [2Fe-2S] ferredoxin domains are connected to the C-terminus of NAD domains, but to the N-terminus of flavin-binding domains in group Rd-III. The overall degree of sequence identity between the Group Rd-II and Rd-III is generally no more than 14%. Accordingly, group Rd-I, Rd-II and Rd-III are designated as GR-type, FNRC-type and FNRN-type reductases, respectively, and were selected as classification keys for the reductase components of RHO enzymes.


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

Kweon O, Kim SJ, Baek S, Chae JC, Adjei MD, Baek DH, Kim YC, Cerniglia CE - BMC Biochem. (2008)

Grouping of reductase components from 25 standard RHO enzymes with schematic representation of the conserved domain structures. The names of bacterial strains are indicated after the enzyme names. GR-type, FNRC-type, and FNRN-type reductases are shown in the boxes with black, gray, and white background, respectively. Designations: FAD-Flavin adenine dinucleotide; NAD-Nicotinamide adenine dinucleotide.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2358900&req=5

Figure 2: Grouping of reductase components from 25 standard RHO enzymes with schematic representation of the conserved domain structures. The names of bacterial strains are indicated after the enzyme names. GR-type, FNRC-type, and FNRN-type reductases are shown in the boxes with black, gray, and white background, respectively. Designations: FAD-Flavin adenine dinucleotide; NAD-Nicotinamide adenine dinucleotide.
Mentions: The phenogram with the domain arrangements of reductases is presented in Figure 2. The 25 reductases were divided into three groups, Rd-I, Rd-II and Rd-III, based on the conserved domain arrangements. When grouped with PD value of 0.85, the 25 reductases can also be grouped into the same three groups. Therefore, the PD values obtained by using Gonnet weight matrix were less than 0.85 within each group which has the same arrangement of conserved domains. Group Rd-I consists of glutathione reductase (GR) type reductases that show over 28% amino acid identity to one another, while groups Rd-II and Rd-III include the ferredoxin-NADP+ reductase (FNR) type reductases that show over 15 and 23% amino acid identity within each group, respectively. Groups Rd-II and Rd-III share the same three domains for flavin, NAD and [2Fe-2S] binding, but show different domain arrangements. In group Rd-II, the [2Fe-2S] ferredoxin domains are connected to the C-terminus of NAD domains, but to the N-terminus of flavin-binding domains in group Rd-III. The overall degree of sequence identity between the Group Rd-II and Rd-III is generally no more than 14%. Accordingly, group Rd-I, Rd-II and Rd-III are designated as GR-type, FNRC-type and FNRN-type reductases, respectively, and were selected as classification keys for the reductase components of RHO enzymes.

Bottom Line: Type II contains other two-component RHO systems that consist of an oxygenase 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microbiology Division, National Center for Toxicological Research/US FDA, Jefferson, AR 72079, USA. oh-gew.kweon@fda.hhs.gov

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 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.

Show MeSH