@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{ZhangFedyuninKirchneretal.2012, author = {Zhang, Gong and Fedyunin, Ivan and Kirchner, Sebastian and Xiao, Chuanle and Valleriani, Angelo and Ignatova, Zoya}, title = {FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads}, series = {Nucleic acids research}, volume = {40}, journal = {Nucleic acids research}, number = {11}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gks196}, pages = {11}, year = {2012}, abstract = {The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith-Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets.}, language = {en} } @article{ZhangFedyuninMiekleyetal.2010, author = {Zhang, Gong and Fedyunin, Ivan and Miekley, Oskar and Valleriani, Angelo and Moura, Alessandro and Ignatova, Zoya}, title = {Global and local depletion of ternary complex limits translational elongation}, issn = {0305-1048}, doi = {10.1093/Nar/Gkq196}, year = {2010}, abstract = {The translation of genetic information according to the sequence of the mRNA template occurs with high accuracy and fidelity. Critical events in each single step of translation are selection of transfer RNA (tRNA), codon reading and tRNA-regeneration for a new cycle. We developed a model that accurately describes the dynamics of single elongation steps, thus providing a systematic insight into the sensitivity of the mRNA translation rate to dynamic environmental conditions. Alterations in the concentration of the aminoacylated tRNA can transiently stall the ribosomes during translation which results, as suggested by the model, in two outcomes: either stress-induced change in the tRNA availability triggers the premature termination of the translation and ribosomal dissociation, or extensive demand for one tRNA species results in a competition between frameshift to an aberrant open-reading frame and ribosomal drop-off. Using the bacterial Escherichia coli system, we experimentally draw parallels between these two possible mechanisms.}, 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{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{FedyuninLehnhardtBoehmeretal.2012, author = {Fedyunin, Ivan and Lehnhardt, Lothar and B{\"o}hmer, Nadine and Kaufmann, Paul and Zhang, Gong and Ignatov, Zoya}, title = {tRNA concentration fine tunes protein solubility}, year = {2012}, 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} }