Jaiswal Shweta, Singh Dileep Kumar, Shukla Pratyoosh
Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India.
Soil Microbial Ecology and Environmental Toxicology Laboratory, Department of Zoology, University of Delhi, New Delhi, India.
Front Microbiol. 2019 Feb 13;10:87. doi: 10.3389/fmicb.2019.00087. eCollection 2019.
Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.
生物修复是指微生物将周围环境中的复杂化合物异化的降解潜力。数据集中生物降解过程的遗传学和生物化学为系统生物学开辟了道路。系统生物学有助于研究系统中相互作用的部分。系统生物学的关键要素是生物降解网络、计算生物学和组学方法。生物降解网络由所有有助于辅助微生物在生物修复过程中的降解和分解潜力的数据库和数据集组成。本综述解读了生物降解网络,即有助于辅助微生物在生物修复过程中的降解和分解潜力的数据库和数据集(UM-BBD、PAN、PTID等)、计算生物学以及宏基因组学、基因组学、转录组学、蛋白质组学和代谢组学等多组学方法,以实现高效的功能基因挖掘及其在生物修复实验中的验证。此外,本综述还描述了基因编辑工具,如CRISPR Cas、TALEN和ZFNs,这些工具可能用于设计具有感兴趣功能基因的微生物,以降解特定的难降解物质,从而改善生物修复效果。