@phdthesis{Steffen2005, author = {Steffen, Jenny}, title = {Transkription von Markergenen an immbolisierten Nukleins{\"a}uren}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-10282}, school = {Universit{\"a}t Potsdam}, year = {2005}, abstract = {Die Etablierung der Transkription von kompletten Genen auf planaren Oberfl{\"a}chen soll eine Verbindung zwischen der Mikroarraytechnologie und der Transkriptomforschung herstellen. Dar{\"u}ber hinaus kann mit diesem Verfahren ein Br{\"u}ckenschlag zwischen der Synthese der Gene und ihrer kodierenden Proteine auf einer Oberfl{\"a}che erfolgen. Alle transkribierten RNAs wurden mittels RT-PCR in cDNA umgeschrieben und in einer genspezifischen PCR amplifiziert. Die PCR-Produkte wurden hierf{\"u}r entweder per Hand oder maschinell auf die Oberfl{\"a}che transferiert. {\"U}ber eine Oberfl{\"a}chen-PCR war es m{\"o}glich, die Gensequenz des Reportergens EGFP direkt auf der Oberfl{\"a}che zu synthetisieren und anschließend zu transkribieren. Somit war eine Transkription mit weniger als 1 ng an Matrize m{\"o}glich. Der Vorteil einer Oberfl{\"a}chen-Transkription gegen{\"u}ber der in L{\"o}sung liegt in der mehrfachen Verwendung der immobilisierten Matrize, wie sie in dieser Arbeit dreimal erfolgreich absolviert wurde. Die Oberfl{\"a}chen-Translation des EGFP-Gens konnte ebenfalls zweimal an einer immobilisierten Matrize gezeigt werden, wobei Zweifel {\"u}ber eine echte Festphasen-Translation nicht ausger{\"a}umt werden konnten. Zusammenfassend kann festgestellt werden, dass die Transkription und Translation von immobilisierten Gensequenzen auf planaren Oberfl{\"a}chen m{\"o}glich ist, wof{\"u}r die linearen Matrizen direkt auf der Oberfl{\"a}che synthetisiert werden k{\"o}nnen.}, subject = {Immobilisierung}, language = {de} } @misc{BenteleSaffertRauscheretal.2013, author = {Bentele, Kajetan and Saffert, Paul and Rauscher, Robert and Ignatova, Zoya and Bluethgen, Nils}, title = {Efficient translation initiation dictates codon usage at gene start}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {912}, issn = {1866-8372}, doi = {10.25932/publishup-44133}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441337}, pages = {12}, year = {2013}, abstract = {The genetic code is degenerate; thus, protein evolution does not uniquely determine the coding sequence. One of the puzzles in evolutionary genetics is therefore to uncover evolutionary driving forces that result in specific codon choice. In many bacteria, the first 5-10 codons of protein-coding genes are often codons that are less frequently used in the rest of the genome, an effect that has been argued to arise from selection for slowed early elongation to reduce ribosome traffic jams. However, genome analysis across many species has demonstrated that the region shows reduced mRNA folding consistent with pressure for efficient translation initiation. This raises the possibility that unusual codon usage is a side effect of selection for reduced mRNA structure. Here we discriminate between these two competing hypotheses, and show that in bacteria selection favours codons that reduce mRNA folding around the translation start, regardless of whether these codons are frequent or rare. Experiments confirm that primarily mRNA structure, and not codon usage, at the beginning of genes determines the translation rate.}, language = {en} } @article{BenteleSaffertRauscheretal.2013, author = {Bentele, Kajetan and Saffert, Paul and Rauscher, Robert and Ignatova, Zoya and Bluethgen, Nils}, title = {Efficient translation initiation dictates codon usage at gene start}, series = {Molecular systems biology}, volume = {9}, journal = {Molecular systems biology}, number = {6}, publisher = {Nature Publ. Group}, address = {New York}, issn = {1744-4292}, doi = {10.1038/msb.2013.32}, pages = {10}, year = {2013}, abstract = {The genetic code is degenerate; thus, protein evolution does not uniquely determine the coding sequence. One of the puzzles in evolutionary genetics is therefore to uncover evolutionary driving forces that result in specific codon choice. In many bacteria, the first 5-10 codons of protein-coding genes are often codons that are less frequently used in the rest of the genome, an effect that has been argued to arise from selection for slowed early elongation to reduce ribosome traffic jams. However, genome analysis across many species has demonstrated that the region shows reduced mRNA folding consistent with pressure for efficient translation initiation. This raises the possibility that unusual codon usage is a side effect of selection for reduced mRNA structure. Here we discriminate between these two competing hypotheses, and show that in bacteria selection favours codons that reduce mRNA folding around the translation start, regardless of whether these codons are frequent or rare. Experiments confirm that primarily mRNA structure, and not codon usage, at the beginning of genes determines the translation rate.}, language = {en} } @book{Mickiewicz2013, author = {Mickiewicz, Adam}, title = {Adam Mickiewicz}, series = {Potsdamer Beitr{\"a}ge zur Sorabistik}, journal = {Potsdamer Beitr{\"a}ge zur Sorabistik}, editor = {Norberg, Madlena and Kosta, Peter}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-205-6}, issn = {1615-2476}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-60508}, publisher = {Universit{\"a}t Potsdam}, pages = {235}, year = {2013}, abstract = {Die vorliegende Ausgabe der „Potsdamer Beitr{\"a}ge zur Sorabistik - Podstupimske pśinoski k Sorabistice" Adam Mickiewicz, Gedichte in sorbischer {\"U}bersetzung, zusammengestellt von Alfred Měškank stellt den Jubil{\"a}umsband Nr. 10 unserer Serie dar. Wir sind sehr stolz darauf, die Serie herausgeben zu d{\"u}rfen und vor allem darauf, das Jubil{\"a}um mit so einem w{\"u}rdigen Inhalt zu begehen. Adam Mickiewicz (1798-1855) gilt als der gr{\"o}ßte polnische Dichter, vergleichbar mit J. W. v. Goethe in Deutschland oder John Byron in England. Seine Werke sind in viele Sprachen {\"u}bersetzt und dadurch in der ganzen Welt bekannt geworden. Bedeutende sorbische Dichter und {\"U}bersetzer, wie z.B. Jakub Bart-Ćišinski und Otto Lehmann-Wićaz haben seine Gedichte auch ins Sorbische {\"u}bersetzt, doch diese {\"U}bersetzungen sind verstreut und dem heutigen Interessenten kaum zug{\"a}nglich. Einige seiner bedeutsamsten Werke, besonders sein Versepos „Pan Tadeusz", sowie Teile seines dramatischen Werkes „Dziady" fanden erst in neuerer Zeit einen {\"U}bersetzer. Die vorliegende Edition, die eine Zusammenstellung aller bisher ins Sorbische/Wendische {\"u}bersetzten Werke des großen polnischen Dichters der Romantik darstellt, schließt diese L{\"u}cke nun.}, language = {mul} } @article{KannanKanabarSchryeretal.2014, author = {Kannan, Krishna and Kanabar, Pinal and Schryer, David and Florin, Tanja and Oh, Eugene and Bahroos, Neil and Tenson, Tanel and Weissman, Jonathan S. and Mankin, Alexander S.}, title = {The general mode of translation inhibition by macrolide antibiotics}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {45}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1417334111}, pages = {15958 -- 15963}, year = {2014}, language = {en} } @misc{BeninaRibeiroGechevetal.2015, author = {Benina, Maria and Ribeiro, Dimas Mendes and Gechev, Tsanko S. and M{\"u}ller-R{\"o}ber, Bernd and Schippers, Jos H. M.}, title = {A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves}, series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, volume = {38}, journal = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0140-7791}, doi = {10.1111/pce.12355}, pages = {349 -- 363}, year = {2015}, abstract = {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.}, language = {en} } @misc{LukoszekFeistIgnatova2016, author = {Lukoszek, Radoslaw and Feist, Peter and Ignatova, Zoya}, title = {Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq}, series = {BMC plant biology}, journal = {BMC plant biology}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407262}, pages = {13}, year = {2016}, abstract = {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.}, language = {en} } @article{SaffertAdamlaSchiewecketal.2016, author = {Saffert, Paul and Adamla, Frauke and Schieweck, Rico and Atkins, John F. and Ignatova, Zoya}, title = {An Expanded CAG Repeat in Huntingtin Causes+1 Frameshifting}, series = {The journal of biological chemistry}, volume = {291}, journal = {The journal of biological chemistry}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M116.744326}, pages = {18505 -- 18513}, year = {2016}, abstract = {Maintenance of triplet decoding is crucial for the expression of functional protein because deviations either into the -1 or +1 reading frames are often non-functional. We report here that expression of huntingtin (Htt) exon 1 with expanded CAG repeats, implicated in Huntington pathology, undergoes a sporadic +1 frameshift to generate from the CAG repeat a trans-frame AGC repeat-encoded product. This +1 recoding is exclusively detected in pathological Htt variants, i.e. those with expanded repeats with more than 35 consecutive CAG codons. An atypical +1 shift site, UUC C at the 5 end of CAG repeats, which has some resemblance to the influenza A virus shift site, triggers the +1 frameshifting and is enhanced by the increased propensity of the expanded CAG repeats to form a stem-loop structure. The +1 trans-frame-encoded product can directly influence the aggregation of the parental Htt exon 1.}, language = {en} } @article{GorochowskiAycilarKucukgozeBovenbergetal.2016, author = {Gorochowski, Thomas E. and Aycilar-Kucukgoze, Irem and Bovenberg, Roel A. L. and Roubos, Johannes A. and Ignatova, Zoya}, title = {A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes}, series = {ACS synthetic biology}, volume = {5}, journal = {ACS synthetic biology}, publisher = {American Chemical Society}, address = {Washington}, issn = {2161-5063}, doi = {10.1021/acssynbio.6b00040}, pages = {710 -- 720}, year = {2016}, abstract = {Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here, we develop a minimal model of ribosome allocation dynamics capturing the demands on translation when expressing a synthetic construct together with endogenous genes required for the maintenance of cell physiology. Critically, it contains three key variables related to design parameters of the synthetic construct covering transcript abundance, translation initiation rate, and elongation time. We show that model-predicted changes in ribosome allocation closely match experimental shifts in synthetic protein expression rate and cellular growth. Intriguingly, the model is also able to accurately infer transcript levels and translation times after further exposure to additional ambient stress. Our results demonstrate that a simple model of resource allocation faithfully captures the redistribution of protein synthesis resources when faced with the burden of synthetic gene expression and environmental stress. The tractable nature of the model makes it a versatile tool for exploring the guiding principles of efficient heterologous expression and the indirect interactions that can arise between synthetic circuits and their host chassis because of competition for shared translational resources.}, language = {en} } @article{BartholomaeusFedyuninFeistetal.2016, author = {Bartholom{\"a}us, Alexander and Fedyunin, Ivan and Feist, Peter and Sin, Celine and Zhang, Gong and Valleriani, Angelo and Ignatova, Zoya}, title = {Bacteria differently regulate mRNA abundance to specifically respond to various stresses}, series = {Geology}, volume = {374}, journal = {Geology}, publisher = {Royal Society}, address = {London}, issn = {1364-503X}, doi = {10.1098/rsta.2015.0069}, pages = {16}, year = {2016}, abstract = {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.}, language = {en} }