Ring-Hydroxylating Oxygenase database: a database of bacterial aromatic ring-hydroxylating oxygenases in the management of bioremediation and biocatalysis of aromatic compounds Joydeep Chakraborty, 1† Tanmoy Jana, 2† Sudipto Saha 2 and Tapan K. Dutta 1 * 1 Department of Microbiology and 2 Centre for Excellence in Bioinformatics, Bose Institute, Kolkata 700054, India. Summary Bacterial Rieske-type aromatic ring-hydroxylating oxygenases (RHOs) constitute a large family of enzymes, primarily involved in bioremediation of diverse aromatic compounds in the environment. In the present study, we have designed a manually curated database, Ring-Hydroxylating Oxygenase database (RHObase), which provides comprehensive information on all biochemically characterized bacte- rial RHOs. It consists of ∼ 1000 entries including 196 oxygenase α-subunits, 153 oxygenase β-subunits, 92 ferredoxins and 110 reductases, distributed among 131 different bacterial strains implementing a total of 318 oxygenation reactions. For each protein, users can get detailed information about its structure and conserved domain(s) with motif signature. RHObase allows users to search a query, based on organism, oxygenase, substrate, or protein structure. In addi- tion, this resource provides analysis tools to perform blast search against RHObase for prediction of puta- tive substrate(s) for the query oxygenase and its phylogenetic affiliation. Furthermore, there is an integrated cheminformatics tool to search for struc- turally similar compound(s) in the database vis-a-vis RHO(s) capable of transforming those compound(s). Resources in the RHObase and multiple search/ display options therein are intended to provide oxygenase-related requisite information to research- ers, especially working in the field of environmental microbiology and biocatalysis to attain difficult chem- istry of biotechnological importance. Introduction Human activities have influenced the environment with the release of various toxic and/or carcinogenic aromatic compounds. Many of these are recalcitrant in nature and appear to inflict growing environmental problems of catastrophic magnitude. This has gradually led to development of remediation techniques to combat the threats posed by such pollutants. One of the most effi- cient and cost-effective techniques identified so far is bioremediation, which involves harnessing the catabolic potential of microorganisms against such toxic com- pounds (Prasad and Prasad, 2012). Bacterial Rieske-type aromatic ring-hydroxylating oxygenases (RHOs) consti- tute a large family of enzymes, which have potential utility in bioremediation of diverse aromatic compounds in the environment. Degradation by RHO is the committed step of the major route by which a wide range of aromatic compounds (primarily composed of benzene ring(s), the most abundant unit of chemical structure in nature next to glucosyl residue) are mineralized in the environment (Gibson and Subramanian, 1984; Lau and De Lorenzo, 1999; Gibson and Parales, 2000; Mallick et al., 2011). These compounds include linked and fused aromatics such as polychlorinated biphenyls and polycyclic aromatic hydrocarbons, heteroaromatics, substituted aromatics and aliphatic olefins, many of which are known to be toxic and/or carcinogenic in nature (McKinney et al., 1985; van den Berg et al., 1998). The multicomponent RHO system comprises of one or two soluble electron transport (ET) proteins (viz. ferredoxins and reductases) and a terminal oxygenase that may either be a homo-multimer (α n) or a hetero-multimer (αnβn), where α and β are the large (cata- lytic) and small (structural) subunits respectively (Mason and Butler, 1997; Nojiri et al., 2005). Transfer of electrons by the ET proteins from nicotinamide adenine dinucleotide phosphate (NAD(P)H) to the terminal oxygenase indeed contributes to the overall activity of the RHO (Kauppi et al., 1998; Wolfe et al., 2001). RHOs catalyze regio- and stereo-specific addition of molecular oxygen to the otherwise inert aromatic nuclei, making them prone to further transformation and mineralization. Apart from being the rate-limiting step in biodegradation process, Received 13 February, 2014; accepted 27 May, 2014. *For corre- spondence. E-mail tapan@jcbose.ac.in; Tel. (+91) 33 2569 3241; Fax (+91) 33 2355 3886. † Both the authors contributed equally. Environmental Microbiology Reports (2014) doi:10.1111/1758-2229.12182 © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd