TY - JOUR
T1 - Application of bioinformatics tools and databases in microbial dehalogenation research
T2 - A review
AU - Satpathy, R.
AU - Konkimalla, V. B.
AU - Ratha, J.
N1 - Publisher Copyright:
© 2015, Pleiades Publishing, Inc.
PY - 2015
Y1 - 2015
N2 - Microbial dehalogenation is a biochemical process in which the halogenated substances are catalyzed enzymatically in to their non-halogenated form. The microorganisms have a wide range of organohalogen degradation ability both explicit and non-specific in nature. Most of these halogenated organic compounds being pollutants need to be remediated; therefore, the current approaches are to explore the potential of microbes at a molecular level for effective biodegradation of these substances. Several microorganisms with dehalogenation activity have been identified and characterized. In this aspect, the bioinformatics plays a key role to gain deeper knowledge in this field of dehalogenation. To facilitate the data mining, many tools have been developed to annotate these data from databases. Therefore, with the discovery of a microorganism one can predict a gene/protein, sequence analysis, can perform structural modelling, metabolic pathway analysis, biodegradation study and so on. This review highlights various methods of bioinformatics approach that describes the application of various databases and specific tools in the microbial dehalogenation fields with special focus on dehalogenase enzymes. Attempts have also been made to decipher some recent applications of in silico modeling methods that comprise of gene finding, protein modelling, Quantitative Structure Biodegradibility Relationslup (QSBR) study and reconstruction of metabolic pathways employed in dehalogenation research area.
AB - Microbial dehalogenation is a biochemical process in which the halogenated substances are catalyzed enzymatically in to their non-halogenated form. The microorganisms have a wide range of organohalogen degradation ability both explicit and non-specific in nature. Most of these halogenated organic compounds being pollutants need to be remediated; therefore, the current approaches are to explore the potential of microbes at a molecular level for effective biodegradation of these substances. Several microorganisms with dehalogenation activity have been identified and characterized. In this aspect, the bioinformatics plays a key role to gain deeper knowledge in this field of dehalogenation. To facilitate the data mining, many tools have been developed to annotate these data from databases. Therefore, with the discovery of a microorganism one can predict a gene/protein, sequence analysis, can perform structural modelling, metabolic pathway analysis, biodegradation study and so on. This review highlights various methods of bioinformatics approach that describes the application of various databases and specific tools in the microbial dehalogenation fields with special focus on dehalogenase enzymes. Attempts have also been made to decipher some recent applications of in silico modeling methods that comprise of gene finding, protein modelling, Quantitative Structure Biodegradibility Relationslup (QSBR) study and reconstruction of metabolic pathways employed in dehalogenation research area.
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U2 - 10.1134/S0003683815010147
DO - 10.1134/S0003683815010147
M3 - Review article
AN - SCOPUS:84925438462
SN - 0003-6838
VL - 51
SP - 11
EP - 20
JO - Applied Biochemistry and Microbiology
JF - Applied Biochemistry and Microbiology
IS - 1
ER -