@article{AdamlaIgnatova2015,
  author    = {Adamla, Frauke and Ignatova, Zoya},
  title     = {Somatic expression of unc-54 and vha-6 mRNAs declines but not pan-neuronal rgef-1 and unc-119 expression in aging Caenorhabditis elegans},
  series = {Scientific reports},
  volume    = {5},
  journal   = {Scientific reports},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/srep10692},
  pages     = {10},
  year      = {2015},
  abstract  = {Aging is a highly controlled biological process characterized by a progressive deterioration of various cellular activities. One of several hallmarks of aging describes a link to transcriptional alteration, suggesting that it may impact the steady-state mRNA levels. We analyzed the mRNA steady-state levels of polyCAG-encoding transgenes and endogenous genes under the control of well-characterized promoters for intestinal (vha-6), muscular (unc-54, unc-15) and pan-neuronal (rgef-1, unc-119) expression in the nematode Caenorhabditis elegans. We find that there is not a uniform change in transcriptional profile in aging, but rather a tissue-specific difference in the mRNA levels of these genes. While levels of mRNA in the intestine (vha-6) and muscular (unc-54, unc-15) cells decline with age, pan-neuronal tissue shows more stable mRNA expression (rgef-1, unc-119) which even slightly increases with the age of the animals. Our data on the variations in the mRNA abundance from exemplary cases of endogenous and transgenic gene expression contribute to the emerging evidence for tissue-specific variations in the aging process.},
  language  = {en}
}
@article{AvcilarKucukgozeBartholomaeusVarelaetal.2016,
  author    = {Avcilar-Kucukgoze, Irem and Bartholom{\"a}us, Alexander and Varela, Juan A. Cordero and Kaml, Robert Franz-Xaver and Neubauer, Peter and Budisa, Nediljko and Ignatova, Zoya},
  title     = {Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli},
  series = {Nucleic acids research},
  volume    = {44},
  journal   = {Nucleic acids research},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0305-1048},
  doi       = {10.1093/nar/gkw697},
  pages     = {8324 -- 8334},
  year      = {2016},
  abstract  = {Translation is a central cellular process and is optimized for speed and fidelity. The speed of translation of a single codon depends on the concentration of aminoacyl-tRNAs. Here, we used microarray-based approaches to analyze the charging levels of tRNAs in Escherichia coli growing at different growth rates. Strikingly, we observed a non-uniform aminoacylation of tRNAs in complex media. In contrast, in minimal medium, the level of aminoacyl-tRNAs is more uniform and rises to approximately 60\%. Particularly, the charging level of tRNA(Ser), tRNA(Cys), tRNA(Thr) and tRNA(His) is below 50\% in complex medium and their aminoacylation levels mirror the degree that amino acids inhibit growth when individually added to minimal medium. Serine is among the most toxic amino acids for bacteria and tRNAs(Ser) exhibit the lowest charging levels, below 10\%, at high growth rate although intracellular serine concentration is plentiful. As a result some serine codons are among the most slowly translated codons. A large fraction of the serine is most likely degraded by L-serine-deaminase, which competes with the seryl-tRNA-synthetase that charges the tRNAs(Ser). These results indicate that the level of aminoacylation in complex media might be a competition between charging for translation and degradation of amino acids that inhibit growth.},
  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}
}
@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}
}
@article{BorwankarRoethleinZhangetal.2011,
  author    = {Borwankar, Tejas and Roethlein, Christoph and Zhang, Gong and Techen, Anne and Dosche, Carsten and Ignatova, Zoya},
  title     = {Natural osmolytes remodel the aggregation pathway of mutant huntingtin exon 1},
  series = {Biochemistry},
  volume    = {50},
  journal   = {Biochemistry},
  number    = {12},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {0006-2960},
  doi       = {10.1021/bi1018368},
  pages     = {2048 -- 2060},
  year      = {2011},
  abstract  = {In response to stress small organic compounds termed osmolytes are ubiquitously accumulated in all cell types to regulate the intracellular solvent quality and to counteract the deleterious effect on the stability and function of cellular proteins. Given the evidence that destabilization of the native state of a protein either by mutation or by environmental changes triggers the aggregation in the neurodegenerative pathologies, the modulation of the intracellular solute composition with osmolytes is an attractive strategy to stabilize an aggregating protein. Here we report the effect of three natural osmolytes on the in vivo and in vitro aggregation landscape of huntingtin exon 1 implicated in the Huntington's disease. Trimethylamine N-oxide (TMAO) and proline redirect amyloid fibrillogenesis of the pathological huntingtin exon 1 to nonamyloidogenic amorphous assemblies via two dissimilar molecular mechanisms. TMAO causes a rapid formation of bulky amorphous aggregates with minimally exposed surface area, whereas proline solubilizes the monomer and suppresses the accumulation of early transient aggregates. Conversely, glycine betaine enhances fibrillization in a fashion reminiscent of the genesis of functional amyloids. Strikingly, none of the natural osmolytes can completely abrogate the aggregate formation; however, they redirect the amyloidogenesis into alternative, nontoxic aggregate species. Our study reveals new insights into the complex interactions of osmoprotectants with polyQaggregates.},
  language  = {en}
}
@article{CzechFedyuninZhangetal.2010,
  author    = {Czech, Andreas and Fedyunin, Ivan and Zhang, Gong and Ignatova, Zoya},
  title     = {Silent mutations in sight : co-variations in tRNA abundance as a key to unravel consequences of silent mutations},
  issn      = {1742-206X},
  doi       = {10.1039/C004796c},
  year      = {2010},
  abstract  = {Mutations that alter the amino acid sequence are known to potentially exert deleterious effects on protein function, whereas substitutions of nucleotides without amino acid change are assumed to be neutral for the protein's functionality. However, cumulative evidence suggests that synonymous substitutions might also induce phenotypic variability by affecting splicing accuracy, translation fidelity, and conformation and function of proteins. tRNA isoacceptors mediate the translation of codons to amino acids, and asymmetric tRNA abundance causes variations in the rate of translation of each single triplet. Consequently, the effect of a silent point mutation in the coding region could be significant due to differential abundances of the cognate tRNA(s), emphasizing the importance of precise assessment of tRNA composition. Here, we provide an overview of the methods used to quantitatively determine the concentrations of tRNA species and discuss synonymous mutations in the context of tRNA composition of the cell, thus providing a new twist on the detrimental impact of the silent mutations.},
  language  = {en}
}
@article{CzechWendeMoerletal.2013,
  author    = {Czech, Andreas and Wende, Sandra and Moerl, Mario and Pan, Tao and Ignatova, Zoya},
  title     = {Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress},
  series = {PLoS Genetics : a peer-reviewed, open-access journal},
  volume    = {9},
  journal   = {PLoS Genetics : a peer-reviewed, open-access journal},
  number    = {8},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1553-7404},
  doi       = {10.1371/journal.pgen.1003767},
  pages     = {9},
  year      = {2013},
  abstract  = {Stress-induced changes of gene expression are crucial for survival of eukaryotic cells. Regulation at the level of translation provides the necessary plasticity for immediate changes of cellular activities and protein levels. In this study, we demonstrate that exposure to oxidative stress results in a quick repression of translation by deactivation of the aminoacylends of all transfer-RNA (tRNA). An oxidative-stress activated nuclease, angiogenin, cleaves first within the conserved single-stranded 3'-CCA termini of all tRNAs, thereby blocking their use in translation. This CCA deactivation is reversible and quickly repairable by the CCA-adding enzyme [ATP(CTP): tRNA nucleotidyltransferase]. Through this mechanism the eukaryotic cell dynamically represses and reactivates translation at low metabolic costs.},
  language  = {en}
}
@article{DelCampoBartholomaeusFedyuninetal.2015,
  author    = {Del Campo, Cristian and Bartholom{\"a}us, Alexander and Fedyunin, Ivan and Ignatova, Zoya},
  title     = {Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function},
  series = {PLoS Genetics : a peer-reviewed, open-access journal},
  volume    = {11},
  journal   = {PLoS Genetics : a peer-reviewed, open-access journal},
  number    = {10},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1553-7404},
  doi       = {10.1371/journal.pgen.1005613},
  pages     = {23},
  year      = {2015},
  abstract  = {Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation.},
  language  = {en}
}
@article{FedyuninLehnhardtBoehmeretal.2012,
  author    = {Fedyunin, Ivan and Lehnhardt, Lothar and B{\"o}hmer, Nadine and Kaufmann, Paul and Zhang, Gong and Ignatova, Zoya},
  title     = {tRNA concentration fine tunes protein solubility},
  series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences},
  volume    = {586},
  journal   = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences},
  number    = {19},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0014-5793},
  doi       = {10.1016/j.febslet.2012.07.012},
  pages     = {3336 -- 3340},
  year      = {2012},
  abstract  = {Clusters of codons pairing to low-abundance tRNAs synchronize the translation with co-translational folding of single domains in multidomain proteins. Although proven with some examples, the impact of the ribosomal speed on the folding and solubility on a global, cell-wide level remains elusive. Here we show that upregulation of three low-abundance tRNAs in Escherichia coil increased the aggregation propensity of several cellular proteins as a result of an accelerated elongation rate. Intriguingly, alterations in the concentration of the natural tRNA pool compromised the solubility of various chaperones consequently rendering the solubility of some chaperone-dependent proteins.},
  language  = {en}
}
@inproceedings{FerrolinoZhuravlevaIgnatovaetal.2012,
  author    = {Ferrolino, Mylene and Zhuravleva, Anastasia and Ignatova, Zoya and Gierasch, Lila},
  title     = {Exploring In vitro and in vivo aggregation of a beta-Clam protein},
  series = {Protein science : a publication of the Protein Society},
  volume    = {21},
  booktitle = {Protein science : a publication of the Protein Society},
  number    = {2},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0961-8368},
  pages     = {89 -- 89},
  year      = {2012},
  language  = {en}
}