Abstract
Bacterial degradation of xenobiotic compounds is an intense field of research already for decades. Lately, this research is complemented by downstream applications including Next Generation Sequencing (NGS), RT-PCR, qPCR, and RNA-seq. For most of these molecular applications, high-quality RNA is a fundamental necessity. However, during the degradation of aromatic substrates, phenolic or polyphenolic compounds such as polycatechols are formed and interact irreversibly with nucleic acids, making RNA extraction from these sources a major challenge. Therefore, we established a method for total RNA extraction from the aromatic degrading Pseudomonas capeferrum TDA1 based on RNAzol® RT, glycogen and a final cleaning step. It yields a high-quality RNA from cells grown on TDA1 and on phenol compared to standard assays conducted in the study. To our knowledge, this is the first report tackling the problem of polyphenolic compound interference with total RNA isolation in bacteria. It might be considered as a guideline to improve total RNA extraction from other bacterial species.
Highlights
IntroductionVarious microorganisms have evolved metabolic pathways to degrade environmental pollutants derived from anthropogenic activities (e.g. agriculture, solid waste, untreated industrial effluents, oil and solvent industry, etc.) which are present in different habitats [1]
During several decades, various microorganisms have evolved metabolic pathways to degrade environmental pollutants derived from anthropogenic activities which are present in different habitats [1]
Five RNA isolation methods were compared in order to obtain high-quality RNA from Pseudomonas capeferrum TDA1 growing on aromatic compounds and succinate
Summary
Various microorganisms have evolved metabolic pathways to degrade environmental pollutants derived from anthropogenic activities (e.g. agriculture, solid waste, untreated industrial effluents, oil and solvent industry, etc.) which are present in different habitats [1]. Aromatic compounds belong to the most persistent and hazardous pollutants, causing deleterious effects on human and animal health [2,3]. Their biodegradation has been intensely studied, the removal of organic compounds has been focused on the role of bacteria due to their quick adaptation, metabolic versatility and genetic plasticity. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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