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Title (Primary) An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene
Author Cárdenas Espinosa, M.J.; Schmidgall, T.; Wagner, G.; Kappelmeyer, U.; Schreiber, S.; Heipieper, H.J.; Eberlein, C.
Journal PLOS ONE
Year 2021
Department UBT; MOLSYB; BIOINF
Volume 16
Issue 11
Page From e0260002
Language englisch
Topic T7 Bioeconomy
T9 Healthy Planet
Supplements https://doi.org/10.1371/journal.pone.0260002.s001
https://doi.org/10.1371/journal.pone.0260002.s002
https://doi.org/10.1371/journal.pone.0260002.s003
https://doi.org/10.1371/journal.pone.0260002.s004
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.
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=25352
Cárdenas Espinosa, M.J., Schmidgall, T., Wagner, G., Kappelmeyer, U., Schreiber, S., Heipieper, H.J., Eberlein, C. (2021):
An optimized method for RNA extraction from the polyurethane oligomer degrading strain Pseudomonas capeferrum TDA1 growing on aromatic substrates such as phenol and 2,4-diaminotoluene
PLOS One 16 (11), e0260002