TY  - JOUR
A1  - Benina, Maria
A1  - Ribeiro, Dimas Mendes
A1  - Gechev, Tsanko S.
A1  - Müller-Röber, Bernd
A1  - Schippers, Jos H. M.
T1  - A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves
JF  - Plant, cell & environment : cell physiology, whole-plant physiology, community physiology
N2  - Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5-untranslated region (5-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress.
 The study illustrates the response of different Arabidopsis thaliana leaf cells and tissues to oxidative stress at the translational level, an aspect of reactive oxygen species (ROS) biology that has been little studied in the past. Our data reveal insights into how translational regulation of ROS-responsive genes is fine-tuned at the cellular level, a phenomenon contributing to the integrated physiological response of leaves to stresses involving changes in ROS levels.
KW  - Arabidopsis
KW  - gene regulation
KW  - oxidative stress
KW  - tissue-specific
KW  - translation
Y1  - 2015
U6  - https://doi.org/10.1111/pce.12355
SN  - 0140-7791
SN  - 1365-3040
VL  - 38
IS  - 2
SP  - 349
EP  - 363
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Hoffmann, Stefan A.
A1  - Hao, Nan
A1  - Shearwin, Keith E.
A1  - Arndt, Katja Maren
T1  - Characterizing transcriptional interference between converging genes in bacteria
JF  - ACS synthetic biology
N2  - Antisense transcription is common in naturally occurring genomes and is increasingly being used in synthetic genetic circuitry as a tool for gene expression control. Mutual influence on the expression of convergent genes can be mediated by antisense RNA effects and by transcriptional interference (TI). We aimed to quantitatively characterize long-range TI between convergent genes with untranslated intergenic spacers of increasing length. After controlling for antisense RNA-mediated effects, which contributed about half of the observed total expression inhibition, the TI effect was modeled. To achieve model convergence, RNA polymerase processivity and collision resistance were assumed to be modulated by ribosome trailing. The spontaneous transcription termination rate in regions of untranslated DNA was experimentally determined. Our modeling suggests that an elongating RNA polymerase with a trailing ribosome is about 13 times more likely to resume transcription than an opposing RNA polymerase without a trailing ribosome, upon head-on collision of the two.
KW  - gene regulation
KW  - antisense transcription
KW  - transcriptional interference
KW  - mathematical modeling
KW  - Escherichia coli
Y1  - 2019
U6  - https://doi.org/10.1021/acssynbio.8b00477
SN  - 2161-5063
VL  - 8
IS  - 3
SP  - 466
EP  - 473
PB  - American Chemical Society
CY  - Washington
ER  -