Jan Barciszewski

Institute of Bioorganic Chemistry Polish Academy of Science, Posen, Greater Poland Voivodeship, Poland

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Publications (261)733.31 Total impact

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    ABSTRACT: The depletion of stem cell pools and the accumulation of senescent cells in animal tissues are linked to aging. Planarians are invertebrate flatworms and are unusual in that their stem cells, called neoblasts, are constantly replacing old and dying cells. By eliminating neoblasts in worms via irradiation, the biological principles of aging are exposed in the absence of wound healing and regeneration, making planaria a powerful tool for aging research.
    No preview · Article · Dec 2015
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    ABSTRACT: Transfer RNAs (tRNAs) represent a major class of RNA molecules. Their primary function is to help decode a messenger RNA (mRNA) sequence in order to synthesize protein and thus ensures the precise translation of genetic information that is imprinted in DNA. The discovery of tRNA in the late 1950's provided critical insight into a genetic machinery when little was known about the central dogma of molecular biology. In 1965, Robert Holley determined the first nucleotide sequence of alanine transfer RNA (tRNA(Ala)) which earned him the 1968 Nobel Prize in Physiology or Medicine. Today, tRNA is one of the best described and characterized biological molecules. Here we review some of the key historical events in tRNA research which led to breakthrough discoveries and new developments in molecular biology.
    No preview · Article · Nov 2015 · Molecular BioSystems
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    ABSTRACT: Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA–protein interactions and molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across three domains of life. Here, we give an overview of new developments in the database and associated web tools since 2002, including updates to database content, curation processes and user web interfaces.
    Preview · Article · Oct 2015 · Nucleic Acids Research
  • Patrick M. Perrigue · Volker A. Erdmann · Jan Barciszewski
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    ABSTRACT: Rich's biggest discoveries were left-handed Z-DNA, the tertiary structure of tRNA, and that DNA and RNA strands could pair up. His discoveries provided the groundwork for our understanding of nucleic acid structure and consequently the development of the fields of molecular biology, biotechnology, and nanotechnology.
    No preview · Article · Oct 2015 · Trends in Biochemical Sciences
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    ABSTRACT: Despite great progress in the treatment of AIDS, the Human Immunodeficiency Virus type I (HIV-1) remains one of the major concerns as a human pathogen. One of the therapeutic strategies against viral infections is the application of catalytic ribonucleic acids (ribozymes) that can significantly reduce expression of a target gene by site-specific hydrolysis of its mRNA. In this paper we report a study on the activity of several variants of hammerhead ribozymes targeting a conserved region within mRNA encoding HIV-1 envelope glycoprotein gp41. Based on the data from in vitro assays and gene silencing in the cultured cells, we propose a new hammerhead ribozyme targeting the gp41-encoding sequence that can be potentially used as a therapeutic agent in AIDS treatment. Moreover, we demonstrate that the hydrolytic activity of the ribozyme in the intracellular environment can not be inferred solely from the results of the in vitro experiments. Copyright 2015 The Author(s).
    No preview · Article · Jul 2015 · Biochemical Journal
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    ABSTRACT: Methylation at position 5 of cytosine (Cyt) at the CpG sequences leading to formation of 5-methyl-cytosine (m(5)Cyt) is an important element of epigenetic regulation of gene expression. Modification of the normal methylation pattern, unique to each organism, leads to the development of pathological processes and diseases, including cancer. Therefore, quantification of the DNA methylation and analysis of changes in the methylation pattern is very important from a practical point of view and can be used for diagnostic purposes, as well as monitoring of the treatment progress. In this paper we present a new method for quantification of 5-methyl-2'deoxycytidine (m(5)C) in the DNA. The technique is based on conversion of m(5)C into fluorescent 3,N(4)-etheno-5-methyl-2'deoxycytidine (εm(5)C) and its identification by reversed-phase high-performance liquid chromatography (RP-HPLC). The assay was used to evaluate m(5)C concentration in DNA of calf thymus and peripheral blood of cows bred under different conditions. This approach can be applied for measuring of 5-methylcytosine in cellular DNA from different cells and tissues.
    No preview · Article · Jun 2015 · Acta biochimica Polonica
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    Full-text · Article · Jun 2015 · ACS Chemical Biology
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    ABSTRACT: Background and aims: Epigenetic regulation plays an important role in the management of plant growth, development and response to stress factors, and several reports have indicated that DNA methylation plays a critical role in seed development and viability. This study examines changes in 5-methylcytosine (m(5)C) levels in the DNA of seeds during ageing, a process that has important implications for plant conservation and agriculture. Methods: Changes in the global level of m(5)C were measured in mature seeds of oak, Quercus robur. The extent of DNA methylation was measured using a protocol based on two-dimensional thin-layer chromatography. Viability of seeds was determined by germination and seedling emergence tests. Key results: An ageing-related decrease in total m(5)C during storage of recalcitrant seeds was highly and significantly correlated with a decrease in seed viability, as reflected by a reduction in germination (r = 0·8880) and seedling emergence (r = 0·8269). Conclusions: The decrease in viability during ageing of Q. robur seeds is highly correlated with a global decline in the amount of m(5)C in genomic DNA, and it is possible that this may represent a typical response to ageing and senescence in recalcitrant seeds. Potential mechanisms that drive changes in genomic DNA methylation during ageing are discussed, together with their implications for seed viability.
    Full-text · Article · May 2015 · Annals of Botany
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    ABSTRACT: Malignant gliomas represent the most devastating group of brain tumors in adults, among which glioblastoma multiforme (GBM) exhibits the highest malignancy rate. Despite combined modality treatment, GBM recurs and is invariably fatal. A further insight into the molecular background of gliomagenesis is required to improve patient outcomes. The primary aim of this study was to gain broad information on the miRNA expression pattern in malignant gliomas, mainly GBM. We investigated the global miRNA profile of malignant glioma tissues with miRNA microarrays, deep sequencing and meta-analysis. We selected miRNAs that were most frequently deregulated in glioblastoma tissues, as well as in peritumoral areas, in comparison with normal human brain. We identified candidate miRNAs associated with the progression from glioma grade III to glioma grade IV. The meta-analysis of miRNA profiling studies in GBM tissues summarizes the past and recent advances in the investigation of the miRNA signature in GBM versus noncancerous human brain and provides a comprehensive overview. We propose a list of 35 miRNAs whose expression is most frequently deregulated in GBM patients and of 30 miRNA candidates recognized as novel GBM biomarkers. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
    Full-text · Article · Mar 2015 · Molecular oncology
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    ABSTRACT: Genetic transformation of mitochondria in multicellular eukaryotes has remained inaccessible, hindering fundamental investigations and applications to gene therapy or biotechnology. In this context, we have developed a strategy to target nuclear transgene-encoded RNAs into mitochondria in plants. We describe here mitochondrial targeting of trans-cleaving ribozymes destined to knockdown organelle RNAs for regulation studies and inverse genetics and biotechnological purposes. The design and functional assessment of chimeric RNAs combining the ribozyme and the mitochondrial shuttle are detailed, followed by all procedures to prepare constructs for in vivo expression, generate stable plant transformants, and establish target RNA knockdown in mitochondria.
    No preview · Article · Jan 2015 · Methods in molecular biology (Clifton, N.J.)
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    ABSTRACT: The generally accepted model of the miRNA-guided RNA down-regulation suggests that mature miRNA targets mRNA in a nucleotide sequence-specific manner. However, we have shown that the nucleotide sequence of miRNA is not the only determinant of miRNA specificity. Using specific nucleases, T1, V1 and S1 as well as NMR, UV/Vis and CD spectroscopies, we found that miR-21, miR-93 and miR-296 can adopt hairpin and/or homoduplex structures. The secondary structure of those miRNAs in solution is a function of RNA concentration and ionic conditions. Additionally, we have shown that a formation of miRNA hairpin is facilitated by cellular environment.Looking for functional consequences of this observation, we have perceived that structure of these miRNAs resemble RNA aptamers, short oligonucleotides forming a stable 3D structures with a high affinity and specificity for their targets. We compared structures of anti-tenascin C (anti-Tn-C) aptamers, which inhibit brain tumor glioblastoma multiforme (GBM, WHO IV) and selected miRNA. A strong overexpression of miR-21, miR-93 as well Tn-C in GBM may imply some connections between them. The structural similarity of these miRNA hairpins and anti-Tn-C aptamers indicates that miRNAs may function also beyond RISC and are even more sophisticated regulators, that it was previously expected. We think that the knowledge of the miRNA structure may give a new insight into miRNA-dependent gene regulation mechanism and be a step forward in the understanding their function and involvement in cancerogenesis. This may improve design process of anti-miRNA therapeutics.
    Full-text · Article · Nov 2014 · PLoS ONE
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    ABSTRACT: 5-methylcytosine, an abundant epigenetic mark, plays an important role in the regulation of plant growth and development, but there is little information about stress-induced changes in DNA methylation in seeds. In the present study, changes in a global level of m5C were measured in orthodox seeds of Acer platanoides L. during seed desiccation from a WC of 1.04 to 0.05–0.06 g H2O·g−1 dry mass (g·g−1). Changes in the level of DNA methylation were measured using 2D TLC – based method. Quality of desiccated seeds was examined by germination and seedling emergence tests. Global m5C content (R2) increase was observed in embryonic axes isolated from seeds collected at a high WC of 1.04 g·g−1 after their desiccation to significantly lower WC of 0.17 and 0.19 g·g−1. Further desiccation of these seeds to a WC of 0.06 g·g−1, however, resulted in a significant DNA demethylation to R2 = 11.52–12.22%. Similar m5C decrease was observed in seeds which undergo maturation drying on the tree and had four times lower initial WC of 0.27 g· g−1 at the time of harvest, as they were dried to a WC of 0.05 g·g−1. These data confirm that desiccation induces changes in seed m5C levels. Results were validated by seed lots derived from tree different A. platanoides provenances. It is plausible that sine wave-like alterations in m5C amount may represent a specific response of orthodox seeds to drying and play a relevant role in desiccation tolerance in seeds.
    Full-text · Article · Oct 2014 · Plant Physiology and Biochemistry
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    Jan Barciszewski · Volker A. Erdmann · Eric G. Moss
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    ABSTRACT: Appreciation is growing for the importance of RNA and its interacting proteins across biology. These molecules function not only in basic cellular processes and the flow of genetic information, but in controlling gene expression, quality control, cell health and development. Yet a full understanding of the signficance of these molecules is only emerging. Genome sequencing has identified numerous RNA-binding proteins whose biological functions are not yet known, as well as many mysterious non-coding RNAs. Importantly, RNA itself is becoming increasingly relevant to disease and its treatment.
    Preview · Article · Oct 2014 · RNA Biology
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    ABSTRACT: The Cu(I) catalyzed Huisgen 1,3-dipolar azide-alkyne cycloaddition (CuAAC) was applied for a nucleoside-peptide bioconjugation. Systemin (Sys), an 18-aa plant signaling peptide naturally produced in response to wounding or pathogen attack, was chemically synthesized as its N-propynoic acid functionalized analog (Prp-Sys) using the SPPS. Next, CuAAC was applied to conjugate Prp-Sys with 3′-azido-2′,3′-dideoxythymidine (AZT), a model cargo molecule. 1,4-Linked 1,2,3-triazole AZT-Sys conjugate was designed to characterize the spreading properties and ability to translocate of cargo molecules of systemin. CuAAC allowed the synthesis of the conjugate in a chemoselective and regioselective manner, with high purity and yield. The presence of Cu(I) ions generated in situ drove the CuAAC reaction to completion within a few minutes without any by-products. Under typical separation conditions of phosphate ‘buffer’ at low pH and uncoated fused bare-silica capillary, an increasing peak intensity assigned to triazole-linked AZT-Sys conjugate was observed using capillary electrophoresis (CE) during CuAAC. CE analysis showed that systemin peptides are stable in tomato leaf extract for up to a few hours. CE-ESI-MS revealed that the native Sys and its conjugate with AZT are translocated through the tomato stem and can be directly detected in stem exudates. The results show potential application of systemin as a transporter of low molecular weight cargo molecules in tomato plant and of CE method to characterize a behavior of plant peptides and its analogs. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.
    Full-text · Article · Sep 2014 · Journal of Peptide Science
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    ABSTRACT: Plants respond to environmental changes by modifying gene expression. One of the mechanisms regulating gene expression is methylation of cytosine to 5-methylcytosine (m(5)C) which modulates gene expression by changing chromatin structure. Methylation/demethylation processes affect genes that are controlled upon environmental stresses. Here, on account of the regulatory role of m(5)C, we evaluate the content of m(5)C in DNA from normal and wound-damaged maize leaves. Wounding leads to a transient decrease of the global DNA methylation level ca 20-30% 1 h after the treatment followed by a return to the initial level within the next hours. Similar results were obtained using of radio-labeled nucleotides separated by Thin Layer Chromatography (TLC) or using m(5)C-specific Enzyme-Linked Immunosorbent Assay (ELISA). Wounding induced in maize leaves a two-step oxidative stress, an early one just after wounding and the second two hours later. It coincides with the transient changes of the cytosine methylation level. In the stress-inducible maize calcium-dependent protein kinase ZmCPK11 gene wounding transiently reduced methylation of cytosines 100 and 126 in the first exon.
    No preview · Article · Jun 2014 · Plant Physiology and Biochemistry
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    ABSTRACT: Pedunculate oak (Quercus robur) is an ecologically and economically important forest tree species which produces seeds that are classified as recalcitrant. Thus, cryopreservation of seed meristems is a method for long-term preservation of this germplasm in gene banks. During cryopreservation, many factors, such as desiccation, cryoprotection and cooling/rewarming, can induce stress in the frozen meristems. In this study, in vitro survival and the global DNA methylation level of plumules after cryoprotection, desiccation and cryostorage was evaluated. Results indicated that both desiccation and storage in liquid nitrogen have negligible influence on DNA methylation status of Q. robur plumules. These findings support the cryopreservation of plumules as an appropriate method for conservation of Q. robur germplasm.
    Full-text · Article · Apr 2014 · Plant Cell Tissue and Organ Culture
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    ABSTRACT: With the discovery of small non-coding RNA (ncRNA) molecules as regulators for cellular processes, it became intriguing to develop technologies by which these regulators can be applied in molecular biology and molecular medicine. The application of ncRNAs has significantly increased our knowledge about the regulation and functions of a number of proteins in the cell. It is surprising that similar successes in applying these small ncRNAs in biotechnology and molecular medicine have so far been very limited. The reasons for these observations may lie in the high complexity in which these RNA regulators function in the cells and problems with their delivery, stability and specificity. Recently, we have described mirror-image hammerhead ribozymes and DNAzymes (Spiegelzymes®) which can sequence-specifically hydrolyse mirror-image nucleic acids, such as our mirror-image aptamers (Spiegelmers) discovered earlier. In this paper, we show for the first time that Spiegelzymes are capable of recognising complementary enantiomeric substrates (D-nucleic acids), and that they efficiently hydrolyse them at submillimolar magnesium concentrations and at physiologically relevant conditions. The Spiegelzymes are very stable in human sera, and do not require any protein factors for their function. They have the additional advantages of being non-toxic and non-immunogenic. The Spiegelzymes can be used for RNA silencing and also as therapeutic and diagnostic tools in medicine. We performed extensive three-dimensional molecular modelling experiments with mirror-image hammerhead ribozymes and DNAzymes interacting with D-RNA targets. We propose a model in which L/D-double helix structures can be formed by natural Watson-Crick base pairs, but where the nucleosides of one of the two strands will occur in an anticlinal conformation. Interestingly enough, the duplexes (L-RNA/D-RNA and L-DNA/D-RNA) in these models can show either right- or left-handedness. This is a very new observation, suggesting that molecular symmetry of enantiomeric nucleic acids is broken down.
    Full-text · Article · Jan 2014 · PLoS ONE
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    Marta M Gabryelska · Jan Barciszewski
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    ABSTRACT: One of the key questions of biology is the nature and mechanisms of gene function. It has been 60 years since proposing the right-handed model of DNA double helix in 1953. This discovery was honored with Nobel Prize in 1962 and become a breakthrough in knowing and understanding mechanisms of heredity and genetic code. Since that time a great deal of data have been gathered considering functions, structure and DNA application. It became the basis of modern molecular biology, chemical biology and biotechnology. Today we know, that double helix is characterized by its dynamics and plasticity, which depend on its nucleotide sequence. Chromatin structure and DNA mediated charge transport have a crucial role in understanding mechanisms of its damage and repair. Progress in epigenetics allowed to identify new DNA bases, such as 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine. Design of new catalytic nucleic acids and the nanotechnology field of DNA origami reveal its application potential.
    Full-text · Article · Dec 2013 · Postepy biochemii
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    ABSTRACT: The effects of storage and deep desiccation on structural changes of DNA in orthodox seeds are poorly characterized. In this study we analyzed the 5-methylcytosine (m(5)C) global content of DNA isolated from seeds of common pear (Pyrus communis L.) that had been subjected to extreme desiccation, and the seedlings derived from these seeds. Germination and seedling emergence tests were applied to determine seed viability after their desiccation. In parallel, analysis of the global content of m(5)C in dried seeds and DNA of seedlings obtained from such seeds was performed with a 2D TLC method. Desiccation of fresh seeds to 5.3% moisture content (mc) resulted in a slight reduction of DNA methylation, whereas severe desiccation down to 2-3% mc increased DNA methylation. Strong desiccation of seeds resulted in the subsequent generation of seedlings of shorter height. A 1-year period of seed storage induced a significant increase in the level of DNA methylation in seeds. It is possible that alterations in the m(5)C content of DNA in strongly desiccated pear seeds reflect a reaction of desiccation-tolerant (orthodox) seeds to severe desiccation. Epigenetic changes were observed not only in severely desiccated seeds but also in 3-month old seedlings obtained from these seeds. With regard to seed storage practices, epigenetic assessment could be used by gene banks for early detection of structural changes in the DNA of stored seeds.
    Full-text · Article · Aug 2013 · PLoS ONE
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    ABSTRACT: Hammerhead ribozyme is the smallest naturally occurring catalytic RNA. It is a perfect model for structure-function relation studies. Initially, it was identified as an autocatalytic part of viroid and virusoid genomic RNA. It exists within the genomes of many organisms including human, which makes it the most common autocatalytic motif in the nature. After 25 years of intensive research, there are a lot of data considering its structure, conformational dynamics and an influence of tertiary stabilizing motifs on its stability and properties. Structure of the hammerhead ribozyme is a system of elements that influence each other. The knowledge of ribozyme architecture is outstandingly interesting in the context of rules and logic of design, construction and application of such molecules as spatial molecular constructions. Presence of additional structural motifs distinguishes extended hammerhead ribozyme from the minimal one. Hammerhead ribozyme recognizes complementary RNA and catalyses transesterification after the 5'-NUH-3' sequence. Reaction efficiency depends on an arrangement of atoms of the catalytic core presence of metal ions and other intracellular factors. Innovative and potentially better derivatives of the hammerhead ribozyme are objects of extensive research in the field of molecular medicine.
    No preview · Article · Jul 2013 · Postepy biochemii

Publication Stats

3k Citations
733.31 Total Impact Points

Institutions

  • 1981-2015
    • Institute of Bioorganic Chemistry Polish Academy of Science
      Posen, Greater Poland Voivodeship, Poland
  • 1978-2014
    • Polish Academy of Sciences
      • Institute of Organic Chemistry
      Cracovia, Lesser Poland Voivodeship, Poland
  • 1992-2013
    • Instytut Historii Polskiej Akademii Nauk
      Posen, Greater Poland Voivodeship, Poland
  • 2010
    • Gdansk University of Technology
      Danzig, Pomeranian Voivodeship, Poland
    • Poznan University of Medical Sciences
      • Department of Neurosurgery and Neurotraumatology
      Posen, Greater Poland Voivodeship, Poland
  • 1999-2008
    • Freie Universität Berlin
      • Institute of Chemistry and Biochemistry
      Berlin, Land Berlin, Germany
  • 2004
    • University of Gdansk
      Danzig, Pomeranian Voivodeship, Poland
  • 2003
    • Instytut Chemii Fizycznej PAN
      Warszawa, Masovian Voivodeship, Poland
  • 2001
    • University of Wroclaw
      • Faculty of Chemistry
      Vrotslav, Lower Silesian Voivodeship, Poland
  • 1997
    • Medical University of Gdansk
      • Department of Pharmacology
      Gdańsk, Pomeranian Voivodeship, Poland