@article{BuehningVallerianiLeimkuehler2017,
  author    = {B{\"u}hning, Martin and Valleriani, Angelo and Leimk{\"u}hler, Silke},
  title     = {The role of SufS is restricted to Fe-S cluster biosynthesis in escherichia coli},
  series = {Biochemistry},
  volume    = {56},
  journal   = {Biochemistry},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {0006-2960},
  doi       = {10.1021/acs.biochem.7b00040},
  pages     = {1987 -- 2000},
  year      = {2017},
  abstract  = {In Escherichia coli, two different systems that are important for the coordinate formation of Fe-S clusters have been identified, namely, the ISC and SUF systems. The ISC system is the housekeeping Fe-S machinery, which provides Fe-S clusters for numerous cellular proteins. The IscS protein of this system was additionally revealed to be the primary sulfur donor for several sulfur-containing molecules with important biological functions, among which are the molybdenum cofactor (Moco) and thiolated nucleosides in tRNA. Here, we show that deletion of central components of the ISC system in addition to IscS leads to an overall decrease in Fe-S cluster enzyme and molybdoenzyme activity in addition to a decrease in the number of Fe-S-dependent thiomodifications of tRNA, based on the fact that some proteins involved in Moco biosynthesis and tRNA thiolation are Fe-S-dependent. Complementation of the ISC deficient strains with the suf operon restored the activity of Fe-S-containing proteins, including the MoaA protein, which is involved in the conversion of 5′GTP to cyclic pyranopterin monophosphate in the fist step of Moco biosynthesis. While both systems share a high degree of similarity, we show that the function of their respective l-cysteine desulfurase IscS or SufS is specific for each cellular pathway. It is revealed that SufS cannot play the role of IscS in sulfur transfer for the formation of 2-thiouridine, 4-thiouridine, or the dithiolene group of molybdopterin, being unable to interact with TusA or ThiI. The results demonstrate that the role of the SUF system is exclusively restricted to Fe-S cluster assembly in the cell.},
  language  = {en}
}
@article{BroekerRoskeVallerianietal.2019,
  author    = {Broeker, Nina K. and Roske, Yvette and Valleriani, Angelo and Stephan, Mareike Sophia and Andres, Dorothee and Koetz, Joachim and Heinemann, Udo and Barbirz, Stefanie},
  title     = {Time-resolved DNA release from an O-antigen-specific Salmonella bacteriophage with a contractile tail},
  series = {The journal of biological chemistry},
  volume    = {294},
  journal   = {The journal of biological chemistry},
  number    = {31},
  publisher = {American Society for Biochemistry and Molecular Biology},
  address   = {Bethesda},
  issn      = {1083-351X},
  doi       = {10.1074/jbc.RA119.008133},
  pages     = {11751 -- 11761},
  year      = {2019},
  abstract  = {Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 angstrom resolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an E15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches.},
  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{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{VallerianiIgnatovaNagaretal.2010,
  author    = {Valleriani, Angelo and Ignatova, Zoya and Nagar, Apoorva and Lipowsky, Reinhard},
  title     = {Turnover of messenger RNA : polysome statistics beyond the steady state},
  issn      = {0295-5075},
  doi       = {10.1209/0295-5075/89/58003},
  year      = {2010},
  abstract  = {The interplay between turnover or degradation and ribosome loading of messenger RNA (mRNA) is studied theoretically using a stochastic model that is motivated by recent experimental results. Random mRNA degradation affects the statistics of polysomes, i.e., the statistics of the number of ribosomes per mRNA as extracted from cells. Since ribosome loading of newly created mRNA chains requires some time to reach steady state, a fraction of the extracted mRNA/ ribosome complexes does not represent steady state conditions. As a consequence, the mean ribosome density obtained from the extracted complexes is found to be inversely proportional to the mRNA length. On the other hand, the ribosome density profile shows an exponential decrease along the mRNA for prokaryotes and becomes uniform in eukaryotic cells. Copyright (C) EPLA, 2010},
  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}
}