Poster abstracts
Poster number 115 submitted by Sandeepani Ranaweera
Genome-wide effects of NusA and NusG on intrinsic termination in Escherichia coli
Sandeepani Ranaweera (Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802), Jan G. Kosiski (Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty ofBiology, Adam Mickiewicz University in Pozna, Pozna, 61-614, Poland), Alexander V Yakhnin (NCI RNA Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD 21702), Marek ywicki (Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty ofBiology, Adam Mickiewicz University in Pozna, Pozna, 61-614, Poland), Mikhail Kashlev (NCI RNA Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD 21702), Paul Babitzke (Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802)
Abstract:
Bacterial transcription termination has historically been described as occurring via two distinct mechanisms triggered either by motifs in the nascent RNA (intrinsic termination) or by the motor protein Rho (Rho-dependent termination). Intrinsic termination was considered as a factor-independent mechanism that relied on intrinsic terminator features consisting of an RNA hairpin followed by a U-rich tract. Our previous genome-wide 3’ end mapping strategy (Term-seq) together with in vitro studies identified both NusA and NusG as vital intrinsic termination factors that work both alone and cooperatively to facilitate efficient intrinsic termination in Bacillus subtilis. Rho was also identified as an intrinsic termination factor. However, the global impact of these proteins in Escherichia coli is not known. By sequencing released transcript using a method called Term-seq on wild type and engineered NusA and NusG depletion strains led to the identification of 946 intrinsic terminators in the E. coli genome, 500 of which met our thresholding criteria for further analysis. We sub-categorized these terminators as factor stimulated, factor independent or factor inhibited based on the change in percent termination (%T) upon depletion of NusA or NusG (delta%T). This analysis determined that NusA and NusG stimulated termination at 9% and 7% of the 500 intrinsic terminators, respectively. Importantly, the weak suboptimal terminators needed the support from NusA or NusG for efficient termination. However, the effects of these proteins on intrinsic termination in E. coli is relatively low compared to B. subtilis.
Keywords: Intrinsic termination, NusA , NusG