Integration of bioinformatics to biodegradation
- PDF / 415,867 Bytes
- 10 Pages / 595.28 x 793.7 pts Page_size
- 9 Downloads / 203 Views
Biological Procedures Online
REVIEW
Open Access
Integration of bioinformatics to biodegradation Pankaj Kumar Arora and Hanhong Bae*
Abstract Bioinformatics and biodegradation are two primary scientific fields in applied microbiology and biotechnology. The present review describes development of various bioinformatics tools that may be applied in the field of biodegradation. Several databases, including the University of Minnesota Biocatalysis/Biodegradation database (UM-BBD), a database of biodegradative oxygenases (OxDBase), Biodegradation Network-Molecular Biology Database (Bionemo) MetaCyc, and BioCyc have been developed to enable access to information related to biochemistry and genetics of microbial degradation. In addition, several bioinformatics tools for predicting toxicity and biodegradation of chemicals have been developed. Furthermore, the whole genomes of several potential degrading bacteria have been sequenced and annotated using bioinformatics tools.
Background Millions of toxic chemicals have been produced for use in a variety of industries [1]. These chemicals have often been released into the environment due to anthropogenic activities, where they contaminate soil and water [2]. Furthermore, many chemicals persist in the environment, causing severe problems to living organisms; accordingly, it is crucial that these compounds be removed from the environment [2]. Biodegradation is the break-down of chemicals or xenobiotic compounds by microbes and plants [3]. Biodegrading microbes degrade toxic chemicals via either mineralization or co-metabolism [4]. In the process of mineralization, microbes completely degrade toxic chemicals by utilizing them as carbon and energy sources, whereas co-metabolism results in biotransformation of toxic compounds into less toxic compounds [4,5]. Microbial remediation is an emerging technology for the removal of toxic chemicals from the environment [4-6]. A large number of microbes capable of utilizing toxic chemicals as their sole sources of carbon and energy have been isolated, many of which break complex chemical compounds down to carbon dioxide and water through a series of chemical reactions catalyzed by microbial enzymes [5-8], such as monooxygenases, dioxygenases, reductases, deaminases, and dehalogenases. The genes encoding these enzymes have been identified in a variety of microbes and cloned into bacteria to increase * Correspondence: [email protected] School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Republic of Korea
the efficiency of bioremediation. The degradation of a specific toxic chemical requires a specific microbe that depends on the structure of that chemical and the presence of the enzyme systems in bacteria for degradation of the compound. Therefore, knowledge regarding chemicals (classification, identification, environmental properties, toxicity, distribution, and associated risks) as well as their microbial biodegradation (xenobiotics degrading bacteria, enzymes, genes, proteins) can improve bioremediation process. Bioinfo
Data Loading...
