Fluorene Degradation Pathway Map

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This pathway was contributed by Dr. Anna Maria Solanas, University of Barcelona, completed by Jingfeng Feng, University of Minnesota, and up-dated by Carla Essenberg and Lynda Ellis, University of Minnesota.

Fluorene, a tricyclic aromatic hydrocarbon, contains a five-membered ring. It is a major component of fossil fuels and their derivatives and is also a byproduct of coal-conversion and energy-related industries. It is commonly found in vehicle exhaust emissions, crude oils, motor oils, coal and oil combustion products, waste incineration, and industrial effluents. Fluorene is one of the compounds on the EPA Priority Pollutants List. This naphthenoaromatic compound bears structural relationships to other chemicals of concern (carbazoles, dibenzothiophenes, dibenzofurans, and dibenzodioxins) and is thus a useful model for biodegradation studies.

The chemical structure of fluorene, including aromatic and alicyclic moieties, offers a variety of possibilities for biochemical attack. Two pathways for fluorene metabolism in Arthrobacter sp. strain F101 were suggested by Casellas et al., 1997. Compounds in brackets were not identified but postulated based on other experiments. A nonproductive route, initiated by monooxygenation at C-9, leads to the accumulation of 9-fluorenone. An alternative pathway is initiated by dioxygenation at C-1, C-2 or at C-3, C-4. The corresponding cis-dihydrodiols undergo dehydrogenation and then meta-cleavage which is catalyzed by an extradiol dioxygenase. After the aldolase reaction and decarboxylation of the fission product, the resulting indanones are substrates for a biological Baeyer-Villiger reaction, yielding the aromatic lactones 3-isochromanone and 3,4-dihydrocoumarin. 1-Indanone also appears to be a substrate for aromatic hydroxylation yielding 3-hydroxy-1-indanone, probably a dead-end product. Arene dioxygenases have been reported to act as monooxygenases hydroxylating methylene groups (Wackett et al., 1988).

Another pathway, observed in Sphingomonas sp. LB126, Brevibacterium sp. DPO1361, and Pseudomonas sp. F274, was reported by Wattiau et. al, 2001. In this pathway, fluorene is converted to phthalic acid and 2-hydroxypenta-2,4-dienoate by way of 9-fluorenone and a biphenyl intermediate.

Other organisms which can metabolize fluorene include Pseudomonas sp. strain NCIB 9816/11 (Resnick et al., 1996), Pseudomonas cepacia F297 (Grifoll et al., 1995), and Staphylococcus auricularis strain DBF63 (Monna et al., 1993). Naphthalene dioxygenase, the enzyme which initiates fluorene metabolism in Ps. strain NCIB 9816/11, is used in a biotechnological process to synthesize the blue jean dye indigo. This versatile enzyme has many other catalytic abilities, which are documented in a table of the Reactions of Naphthalene 1,2-Dioxygenase.

The following is a text-format fluorene pathway map. Some organisms which can initiate the pathway are given, but other organisms may also carry out some later steps. Follow the links for more information on compounds or reactions.

|------------Graphical Map (20K)-----------|------------Graphical Map (13K)-----------|-----Graphical Map (20K)-----|

                 Fluorene               Fluorene                        Fluorene               Fluorene
          Arthrobacter sp. F101   Pseudomonas sp. NCIB 9816/11    Arthrobacter sp. F101    Arthrobacter sp. F101
                     |             Pseudomonas cepacia F297   Staphylococcus auricularis DBF63     |
                     |                   |   |                  Sphingomonas sp. LB126             |
                     |                   |   |                Brevibacterium sp. DPO1361           |
                     |                   |   |                   Pseudomonas sp. F274              |
                     |                   |   |                             |                       |
                     |               NDO |   |naphthalene                  |                       |
                     |                   |   |1,2-dioxygenase              |                       |              
                     |                   |   |(NDO)                        |                       |
                     |                   |   +--------------------------+  |                       |
                     |                   V                              |  |                       |
                     V A          (+)-(3S,4R)-cis-                      |  | fluorene              V E
                     |             3,4-Dihydroxy-                       |  | oxygenase             |
                     |          3,4-dihydrofluorene                     |  |                       |
                     |                   |                              |  |                       |
                     |                   | 3,4-dihydroxy-               |  |                       |
                     |                   | 3,4-dihydrofluorene          |  |                       |
                     |                   | dehydrogenase                |  |                       |
                     V                   |                              V  V                       V
          [3,4-Dihydroxyfluorene] <------+                           9-Fluorenol        [1,2-Dihydroxyfluorene]
                     |                                                     |                       |
                     | 3,4-dihydroxyfluorene                               |                       | 1,2-dihydroxy-
                     | 4,4a-dioxygenase                                    | 9-fluorenol           | fluorene
                     |                                                     | dehydrogenase         | 1,1a-dioxygenase
                     V                                                     |                       |
          [2-Hydroxy-4-(1-oxo-1,3-                                         |                       V
         dihydro-2H-inden-2-ylidene)-                                      V             [2-Hydroxy-4-(2-oxo-1,3-
              but-2-enoate]                   +-----------------------9-Fluorenone       dihydro-2H-inden-1-ylidene)-
                     |                        |                            |               but-2-enoic acid]
                     | 2-hydroxy-4-(1-oxo-    |                            |                       |
                     | 1,3-dihydro-2H-inden-  | 9-fluorenone               | 9-fluorenone          | 2-hydroxy-4-(2-oxo-
                     | -2-ylidene)-but-2-     | 3,4-dioxygenase            | dioxygenase           | 1,3-dihydro-2H-inden-
                     | enoate hydratase       |                            |                       | -1-ylidene)-but-2-
                     |                        |                            |                       | enoate hydratase
                     V                        V                            V                       V
           2-Formyl-1-indanone    1-Hydro-1,1a-dihydroxy-     [(3S,4R)-3,4-Dihydroxy-3,4-   1-Formyl-2-indanone
                     |                  9-fluorenone               dihydro-9-fluorenone]           |
                     |                        |                            |                       |
                     |                        | 1-hydro-1,1a-              |                       |
                     V C                      | dihydroxy-                 | I                     V G
                     |                        | 9-fluorenone               |                       |
                     |                        | dehydrogenase              |                       |
                     V                        V                            V                       V
    +------------1-Indanone            2,3-Dihydroxy-           4-Hydroxy-9-fluorenone        2-Indanone
    |                |               2'-carboxybiphenyl                                            |
    |                |                        |                                                    |
    |                |                        | 2,3-dihydroxy-                                     | 
    | 1-indanone     | 1-indanone             | 2'-carboxybiphenyl                                 | 2-indanone
    | dioxygenase    | monooxygenase          | 1,2-dioxygenase                                    | monooxygenase
    V                |                        |                                                    |
3-Hydroxy-           |                        |                                                    |
1-indanone           |                        V                                                    |
                     V                2-Hydroxy-6-oxo-6-                                           V
           3,4-Dihydrocoumarin        (2-carboxyphenyl)-                                    3-Isochromanone
                     |                 hexa-2,4-dienoate                                           |
                     |                        |                                                    |
                     | 3,4-dihydro-           | 2-hydroxy-6-oxo-6-                                 |
                     | coumarin               | (2-carboxyphenyl)-                                 V H
                     | hydrolase              | hexa-2,4-dienoate                                  |
                     |                        | hydrolase                                          |
                     |                        |                                                    |
                     V                        V                                                    V
           3-(2-Hydroxyphenyl)-    Phthalate  +  cis-2-Hydroxypenta-                            Catechol
               propionate              |            2,4-dienoate                                   |
                     |                 |                  |                                        |
                     |                 |                  |                                        |
                     V D               |                  |                                        |
                     |                 |                  |                                        |
                     |                 V                  V                                        V 
                     V              to the              to the                                Intermediary
                Salicylate     Phthalate Family    4-Chlorobiphenyl                            Metabolism
                     |             Pathway             Pathway                                   (KEGG)
                     |            
                     |
                     V
                   to the
                Naphthalene
                  Pathway

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Page Author(s): Jingfeng Feng and Carla Essenberg

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