TY  - JOUR
A1  - Bartholomäus, Alexander
A1  - Fedyunin, Ivan
A1  - Feist, Peter
A1  - Sin, Celine
A1  - Zhang, Gong
A1  - Valleriani, Angelo
A1  - Ignatova, Zoya
T1  - Bacteria differently regulate mRNA abundance to specifically respond to various stresses
JF  - Geology
N2  - Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up-and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs.
KW  - transcription
KW  - translation
KW  - deep sequencing
KW  - Escherichia coli
KW  - copy numbers
Y1  - 2016
U6  - https://doi.org/10.1098/rsta.2015.0069
SN  - 1364-503X
SN  - 1471-2962
VL  - 374
PB  - Royal Society
CY  - London
ER  - 
TY  - JOUR
A1  - Lukoszek, Radoslaw
A1  - Feist, Peter
A1  - Ignatova, Zoya
T1  - Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq
JF  - BMC plant biology
N2  - Background: Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different levels of gene expression. Results: Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of Arabidopsis thaliana to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are likely candidates to play a role in regulating translation of those genes. Conclusions: Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids is maintained upon heat exposure.
KW  - Translation
KW  - Ribosome profiling
KW  - Transcription
KW  - RNA-Seq
KW  - Secondary structure
KW  - G-quadruplexes
KW  - Heat stress response
Y1  - 2016
U6  - https://doi.org/10.1186/s12870-016-0915-0
SN  - 1471-2229
VL  - 16
PB  - BioMed Central
CY  - London
ER  - 
TY  - GEN
A1  - Lukoszek, Radoslaw
A1  - Feist, Peter
A1  - Ignatova, Zoya
T1  - Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq
T2  - BMC plant biology
N2  - Background:
Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize
survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different
levels of gene expression.
Results:
Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of
Arabidopsis  thaliana
to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is
modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of
genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are
likely candidates to play a role in regulating translation of those genes.
Conclusions:
Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids
is maintained upon heat exposure.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 438 
KW  - translation
KW  - ribosome profiling
KW  - transcription
KW  - RNA-Seq
KW  - secondary structure
KW  - G-quadruplexes,
KW  - heat stress response
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407262
ER  -