NOVELTY - A naphthalene dioxygenase (NDO) or NDO related complex (I) comprising several polypeptides which contain an alpha subunit that contains substituted amino acids at specific positions is new.    USE - The polypeptides and host cells are useful for preparing (-)-(1S,2R)-cis-napththalene dihydrodiol, (- or +)-cis-biphenyl-3,4-dihydrodiol, (1S,2R)-cis-phenanthrene-1,2-dihydrodiol, cis-1,2-dihydroxyindan, 1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, which involves contacting them with naphthalene, biphenyl, phenanthrene, indene, and 1,2-dihydronaphthalene respectively. The polypeptides and the host cells are also useful for preparing 1,2-dihydroxy-1,2-dihydrophenanthrene or 3,4-dihydroxy-3,4-dihydrophenanthrene which involves contacting them with phenanthrene. The polypeptides and the host cells are also used in bioremediation in which they oxidize an aromatic compound such as indene, 1,2-dihydronaphthalene, benzocyclohelpt-1-ene, anthracene, phenanthrene, dibenzo(1,4)dioxan, acenaphthylene, naphthalene, biphenyl, fluorene, dibenzofuran, dibenzothiophene, 9,10-dihydroanthracene, or 9,10-dihydrophenanthrene a corresponding dihydro dihydroxy compound (claimed). The polypeptide and the host cell are also useful for preparing an optically active cis-cyclohexadiene of formula (1) R1 and R2 = hydrogen; other = phenyl, 2-phenylvinyl, 2-phenylethynyl, or vinyl, in which any phenyl ring may optionally be substituted with 1, 2 or 3 substituents independently selected from the group consisting of hydroxy, halo, carboxy, cyano, nitro, trifluoromethyl, amino (C1-C6)alkyl, (C1-C6)alkoxycarbonyl, and (C1-C6)alkoxy which involves contacting a corresponding compound of formula (2) in which R1 is phenyl or 4-hydroxy phenyl. The method may optionally comprise dehydrating the resulting compound of formula (1). The polypeptides and the host cells are useful for preparing chiral diols for use in the polymer, resin, pharmaceutical or rubber industry. The compound (-)-cis-3,4-dihydroxy-3,4-dihydrobiphenyl can be dehydrated to provide 4-hydroxybiphenyl, which is useful for the manufacture of rubber and resins. The polypeptides provide a biosynthetic route to either enantiomer of cis-naphthalene dihydrodiol, cis-biphenyl-3,4-dihydrodiol, and cis-phenanthrene-1,2-dihydrodiol. These products can be used in the synthesis of new polymers and pharmaceutical products. For example, arene cis-diols are useful starting materials for stereospecific organic synthesis and to prepare a variety of synthetic products that are not readily obtainable by conventional chemical synthesis. Examples include conduritols, inositol phosphates, pinitol enantiomers, prostanoid and terpene synthons, and complex natural products such as (-)-zeylena and (+)-lycoricidine.    DETAILED DESCRIPTION - A new naphthalene dioxygenase (NDO) or NDO related complex (I) comprises several polypeptides which contain an alpha subunit that contains a substituted amino acid at the position corresponding to 352 in NDO and/or a substituted amino acid at the position corresponding to position 201, 202, 260, 316, 351, 358, 362 or 366 in NDO or its catalytically active fragment.    INDEPENDENT CLAIMS are also included for the following:    (1) an isolated and purified DNA segment (II) comprising a DNA sequence encoding (I);    (2) an expression cassette comprising a promoter operably linked to (II);    (3) a host cell (III), the genome of which is augmented by (II); and    (4) an oligonucleotide comprising any one of: ttcagcgaac ggtcgggcct gc; gaggcacccg cggaagcttt tgtgggagat gca; gcacccgcgg aacaatttgt gggagatgca; ccgcggaaag ctttgtggga g; ccgcggaaaa gcttgtggga gatg; cgcggaaacc gttgtgggag atg; atattcaggt gcgcatagcg cag; ggacggatat tcagggctcc atagcgcaga cttg; gacggatatt caggtaacca tagcgcagac ttg; ggtgttttca aagtcgcgaa cccgatcgac; ctgttcagcg aaacttcggg cctgct; ctgttcagcg aaggttcggg cctgct; ctgttcagcg aagcttcggg cctgct; ttcagcgaac gctcgggcct gc; ggcctgctgg cttcgcggaa agcgacgaca; gaaagcgacg ccaatgacaa t; and acgacaatga caattgggaa acagcttcgc.