Ex situ preservation of genetic resources is an essential strategy for the conservation of plant ... more Ex situ preservation of genetic resources is an essential strategy for the conservation of plant biodiversity. In this regard, seed storage is the most convenient and efficient way of preserving germplasm for future plant breeding efforts. A better understanding of the molecular changes that occur during seed desiccation and aging is necessary to improve conservation protocols, as well as real-time methods for monitoring seed quality. In the present study, we assessed changes in the level of genomic 5-methylcytosine (5mC) in seeds of Populus nigra L. by 2D-TLC. Epigenetic changes were characterized in response to several seed storage regimes. Our results demonstrate that P. nigra seeds represent an intermediate type of post-harvest behavior, falling between recalcitrant and orthodox seeds. This was also true for the epigenetic response of P. nigra seeds to external factors. A crucial question is whether aging in seeds is initiated by a decline in the level of 5mC, or if epigenetic c...
We have cloned and sequenced glutamate-tRNA synthetase (GluRS) and glutaminyl-tRNA synthetase (Gl... more We have cloned and sequenced glutamate-tRNA synthetase (GluRS) and glutaminyl-tRNA synthetase (GlnRS) from Arabidopsis thaliana. They have conservative motifs found in all known GlxRS genes. For Lupinus luteus we found only one gene of GlxRS. At the moment we do not know exactly, whether it corresponds to GlnRS or GluRS.
Squalene monooxygenase catalyzes the epoxidation of C-C double bond of squalene to yield 2,3-oxid... more Squalene monooxygenase catalyzes the epoxidation of C-C double bond of squalene to yield 2,3-oxidosqualene, the key step of sterol biosynthesis pathways in eukaryotes. Sterols are essential compounds of these organisms and squalene epoxidation is an important regulatory point in their synthesis. Squalene monooxygenase downregulation in vertebrates and fungi decreases synthesis of cholesterol and ergosterol, respectively, which makes squalene monooxygenase a potent and attractive target of hypercholesterolemia and antifungal therapies. Currently some fungal squalene monooxygenase inhibitors (terbinafine, naftifine, butenafine) are in clinical use, whereas mammalian enzymes’ inhibitors are still under investigation. Research on new squalene monooxygenase inhibitors is important due to the prevalence of hypercholesterolemia and the lack of both sufficient and safe remedies. In this paper we (i) review data on activity and the structure of squalene monooxygenase, (ii) present its inhibi...
Noncoding RNAs (ncRNA) are ubiquitous regulatory factors affecting gene expression in all organis... more Noncoding RNAs (ncRNA) are ubiquitous regulatory factors affecting gene expression in all organisms. In eukaryotes ncRNAs have been shown to operate on virtually every level of transmission of genetic information. They are implicated in processes that are crucial for the correct growth and development of multicellular organisms. Changes in their expression are often related to stress conditions or associated with diseases or developmental disorders.
Appreciation is growing for the importance of RNA and its interacting proteins across biology. Th... more 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. ...
The level of 5-methylcytosine (m5C) in DNA has been observed to change in plants in response to b... more The level of 5-methylcytosine (m5C) in DNA has been observed to change in plants in response to biotic and abiotic stress factors. Little information has been reported on alterations in DNA methylation in orthodox tree seeds in response to storage conditions. In the current study, epigenetic integrity was analyzed in seeds of Pyrus communis L. in response to conventional and cryogenic storage. The results indicate that conventional storage under optimal conditions resulted in a significant increase in m5C. In contrast, a decrease in m5C level after cryostorage at high water content (WC) was observed, not only in seeds but also in 3-month-old seedlings which were smaller than seedlings obtained from seeds cryostored at optimal WC. This shows that non-optimal cryostorage conditions increase epigenetic instability in seeds and seedlings. Optimal procedures for germplasm conservation are very important for germplasm banking since they have serious implications for the quality of stored ...
Transfer RNAs (tRNAs) represent a major class of RNA molecules for which primary, secondary, and ... more Transfer RNAs (tRNAs) represent a major class of RNA molecules for which primary, secondary, and tertiary structures are known.
Neoplasms arising from glial cells make up the most common group of primary brain tumors. The cli... more Neoplasms arising from glial cells make up the most common group of primary brain tumors. The clinical outcome, especially the survival rates of the patients with brain tumours depend on tumour grade expressing its malignancy. A prognosis for glioblastomas (WHO IV) is very poor, but for astrocytomas (WHO I and II) it is relatively favourable. For oligodendrogliomas a longer survival time than for glioblastomas is observed. There is evidence that oxidative stress and reactive oxygen species (ROS) are crucial in the etiology and progression of a number of human diseases, including neoplasms. An oxidative damage of DNA, lipids and proteins is caused mainly with hydroxyl radical (*OH), the most reactive ROS species and may be seriously deleterious. In addition to all four basic nucleotides: adenosine (A), guanosine (G), tymidine (T) and cytosine (C), 5-methylcytosine (m5C) is a rare but normal component of cellular DNA and occurs mainly within a sequence of a structural gene or in regul...
W 2021 roku mija 100 lat od poznania kwasu rybonukleinowego oraz 60 lat od odkrycia informacyjneg... more W 2021 roku mija 100 lat od poznania kwasu rybonukleinowego oraz 60 lat od odkrycia informacyjnego (messenger) RNA i kodu genetycznego. Z okazji tego wyjątkowego jubileuszu pragniemy przypomnieć najważniejsze wydarzenia w historii kwasów nukleinowych, które doprowadziły do powyższych odkryć. Wspomniany początek nowej ery w nauce spowodowany izolacją nukleiny, a następnie kwasu rybonukleinowego, którego składniki i właściwości były stopniowo poznawane, często przez mało znanych badaczy. Wyróżnienie RNA i DNA oraz analiza ich występowania w komórkach pozwoliły sformułować pierwsze wnioski dotyczące funkcji tych molekuł. Konkluzje dotyczące proporcji zasad azotowych w DNA doprowadziły do poznania struktury podwójnej helisy, wywołując lawinę pytań o istotę przekazywania informacji genetycznej. Odpowiedzi zaczęły nasuwać się wraz z odkryciem mRNA, a poznanie pierwszej trójki nukleotydów kodującej fenyloalaninę rozpoczęło wyścig o rozszyfrowanie kodu genetycznego. Powyższe odkrycia stanow...
RNA-based tools are frequently used to modulate gene expression in living cells. However, the sta... more RNA-based tools are frequently used to modulate gene expression in living cells. However, the stability and effectiveness of such RNA-based tools is limited by cellular nuclease activity. One way to increase RNA’s resistance to nucleases is to replace its D-ribose backbone with L-ribose isomers. This modification changes chirality of an entire RNA molecule to L-form giving it more chance of survival when introduced into cells. Recently, we have described the activity of left-handed hammerhead ribozyme (L-Rz, L-HH) that can specifically hydrolyse RNA with the opposite chirality at a predetermined location. To understand the structural background of the RNA specific cleavage in a heterochiral complex, we used circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy as well as performed molecular modelling and dynamics simulations of homo- and heterochiral RNA complexes. The active ribozyme-target heterochiral complex showed a mixed chirality as well as low field imino...
Cellular senescence is a tumor-suppressive mechanism blocking cell proliferation in response to s... more Cellular senescence is a tumor-suppressive mechanism blocking cell proliferation in response to stress. However, recent evidence suggests that senescent tumor cells can re-enter the cell cycle to become cancer stem cells, leading to relapse after cancer chemotherapy treatment. Understanding how the senescence reprogramming process is a precursor to cancer stem cell formation is of great medical importance. To study the interplay between senescence, stemness, and cancer, we applied a stem cell medium (SCM) to human embryonic fibroblasts (MRC5 and WI-38) and cancer cell lines (A549 and 293T). MRC5 and WI-38 cells treated with SCM showed symptoms of oxidative stress and became senescent. Transcriptome analysis over a time course of SCM-induced senescence, revealed a developmental process overlapping with the upregulation of genes for growth arrest and the senescence-associated secretory phenotype (SASP). We demonstrate that histone demethylases jumonji domain-containing protein D3 (Jmj...
The ribosome is a macromolecular assembly that is responsible for protein biosynthesis in all org... more The ribosome is a macromolecular assembly that is responsible for protein biosynthesis in all organisms. It is composed of two-subunit, ribonucleoprotein particles that translate the genetic material into an encoded polypeptides. The small subunit is the site of codon-anticodon interaction between the messenger RNA (mRNA) and transfer RNA (tRNA) substrates, and the large subunit catalyses peptide bond formation. The peptidyltransferase activity is fulfilled by 23S rRNA, which means that ribosome is a ribozyme. 5S rRNA is a conserved component of the large ribosomal subunit that is thought to enhance protein synthesis by stabilizing ribosome structure. This paper shortly summarises new results obtained on the structure and function of 5S rRNA.
Cytokininy stanowią jedną z grup hormonów roślinnych, które odgrywają ważną rolę we wzroście i ro... more Cytokininy stanowią jedną z grup hormonów roślinnych, które odgrywają ważną rolę we wzroście i rozwoju roślin. Wykazują różne efekty działania, szczególnie stymulują syntezę białek i uczestniczą w kontroli cyklu komórkowego. Pierwszą odkrytą cytokininą była N6-furfuryloadenina (kinetyna). Jest ona uważana za silny inhibitor procesów utleniania białek i kwasów nukleinowych w warunkach in vitro oraz in vivo. Zarówno kinetyna, jak i jej rybozyd (N6-furfuryloadenozyna, rybozyd kinetyny) jako naturalne związki występują w mleku kokosowym w stężeniu nanomolarnym. Rybozyd kinetyny selektywnie hamuje proliferację komórek nowotworowych oraz indukuje ich apoptozę. W tym artykule skupiono się na występowaniu rybozydu kinetyny, a przede wszystkim na jego metabolizmie oraz aktywności biologicznej.
This mini‐review describes the interaction between small molecules and RNA, in addition to its ap... more This mini‐review describes the interaction between small molecules and RNA, in addition to its application either in treating RNA‐associated diseases or detecting target molecules. In the case of RNA‐associated disease treatment, the designed small molecules interact with RNA sites, forming adducts and providing successful therapeutic strategies over oligonucleotides. On the other hand, synthetically designed RNA moieties (aptamers) interact with target molecules like toxins, drugs, hormones; these interactions are useful in the detection, quantification or separation of these target moieties.
Ex situ preservation of genetic resources is an essential strategy for the conservation of plant ... more Ex situ preservation of genetic resources is an essential strategy for the conservation of plant biodiversity. In this regard, seed storage is the most convenient and efficient way of preserving germplasm for future plant breeding efforts. A better understanding of the molecular changes that occur during seed desiccation and aging is necessary to improve conservation protocols, as well as real-time methods for monitoring seed quality. In the present study, we assessed changes in the level of genomic 5-methylcytosine (5mC) in seeds of Populus nigra L. by 2D-TLC. Epigenetic changes were characterized in response to several seed storage regimes. Our results demonstrate that P. nigra seeds represent an intermediate type of post-harvest behavior, falling between recalcitrant and orthodox seeds. This was also true for the epigenetic response of P. nigra seeds to external factors. A crucial question is whether aging in seeds is initiated by a decline in the level of 5mC, or if epigenetic c...
We have cloned and sequenced glutamate-tRNA synthetase (GluRS) and glutaminyl-tRNA synthetase (Gl... more We have cloned and sequenced glutamate-tRNA synthetase (GluRS) and glutaminyl-tRNA synthetase (GlnRS) from Arabidopsis thaliana. They have conservative motifs found in all known GlxRS genes. For Lupinus luteus we found only one gene of GlxRS. At the moment we do not know exactly, whether it corresponds to GlnRS or GluRS.
Squalene monooxygenase catalyzes the epoxidation of C-C double bond of squalene to yield 2,3-oxid... more Squalene monooxygenase catalyzes the epoxidation of C-C double bond of squalene to yield 2,3-oxidosqualene, the key step of sterol biosynthesis pathways in eukaryotes. Sterols are essential compounds of these organisms and squalene epoxidation is an important regulatory point in their synthesis. Squalene monooxygenase downregulation in vertebrates and fungi decreases synthesis of cholesterol and ergosterol, respectively, which makes squalene monooxygenase a potent and attractive target of hypercholesterolemia and antifungal therapies. Currently some fungal squalene monooxygenase inhibitors (terbinafine, naftifine, butenafine) are in clinical use, whereas mammalian enzymes’ inhibitors are still under investigation. Research on new squalene monooxygenase inhibitors is important due to the prevalence of hypercholesterolemia and the lack of both sufficient and safe remedies. In this paper we (i) review data on activity and the structure of squalene monooxygenase, (ii) present its inhibi...
Noncoding RNAs (ncRNA) are ubiquitous regulatory factors affecting gene expression in all organis... more Noncoding RNAs (ncRNA) are ubiquitous regulatory factors affecting gene expression in all organisms. In eukaryotes ncRNAs have been shown to operate on virtually every level of transmission of genetic information. They are implicated in processes that are crucial for the correct growth and development of multicellular organisms. Changes in their expression are often related to stress conditions or associated with diseases or developmental disorders.
Appreciation is growing for the importance of RNA and its interacting proteins across biology. Th... more 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. ...
The level of 5-methylcytosine (m5C) in DNA has been observed to change in plants in response to b... more The level of 5-methylcytosine (m5C) in DNA has been observed to change in plants in response to biotic and abiotic stress factors. Little information has been reported on alterations in DNA methylation in orthodox tree seeds in response to storage conditions. In the current study, epigenetic integrity was analyzed in seeds of Pyrus communis L. in response to conventional and cryogenic storage. The results indicate that conventional storage under optimal conditions resulted in a significant increase in m5C. In contrast, a decrease in m5C level after cryostorage at high water content (WC) was observed, not only in seeds but also in 3-month-old seedlings which were smaller than seedlings obtained from seeds cryostored at optimal WC. This shows that non-optimal cryostorage conditions increase epigenetic instability in seeds and seedlings. Optimal procedures for germplasm conservation are very important for germplasm banking since they have serious implications for the quality of stored ...
Transfer RNAs (tRNAs) represent a major class of RNA molecules for which primary, secondary, and ... more Transfer RNAs (tRNAs) represent a major class of RNA molecules for which primary, secondary, and tertiary structures are known.
Neoplasms arising from glial cells make up the most common group of primary brain tumors. The cli... more Neoplasms arising from glial cells make up the most common group of primary brain tumors. The clinical outcome, especially the survival rates of the patients with brain tumours depend on tumour grade expressing its malignancy. A prognosis for glioblastomas (WHO IV) is very poor, but for astrocytomas (WHO I and II) it is relatively favourable. For oligodendrogliomas a longer survival time than for glioblastomas is observed. There is evidence that oxidative stress and reactive oxygen species (ROS) are crucial in the etiology and progression of a number of human diseases, including neoplasms. An oxidative damage of DNA, lipids and proteins is caused mainly with hydroxyl radical (*OH), the most reactive ROS species and may be seriously deleterious. In addition to all four basic nucleotides: adenosine (A), guanosine (G), tymidine (T) and cytosine (C), 5-methylcytosine (m5C) is a rare but normal component of cellular DNA and occurs mainly within a sequence of a structural gene or in regul...
W 2021 roku mija 100 lat od poznania kwasu rybonukleinowego oraz 60 lat od odkrycia informacyjneg... more W 2021 roku mija 100 lat od poznania kwasu rybonukleinowego oraz 60 lat od odkrycia informacyjnego (messenger) RNA i kodu genetycznego. Z okazji tego wyjątkowego jubileuszu pragniemy przypomnieć najważniejsze wydarzenia w historii kwasów nukleinowych, które doprowadziły do powyższych odkryć. Wspomniany początek nowej ery w nauce spowodowany izolacją nukleiny, a następnie kwasu rybonukleinowego, którego składniki i właściwości były stopniowo poznawane, często przez mało znanych badaczy. Wyróżnienie RNA i DNA oraz analiza ich występowania w komórkach pozwoliły sformułować pierwsze wnioski dotyczące funkcji tych molekuł. Konkluzje dotyczące proporcji zasad azotowych w DNA doprowadziły do poznania struktury podwójnej helisy, wywołując lawinę pytań o istotę przekazywania informacji genetycznej. Odpowiedzi zaczęły nasuwać się wraz z odkryciem mRNA, a poznanie pierwszej trójki nukleotydów kodującej fenyloalaninę rozpoczęło wyścig o rozszyfrowanie kodu genetycznego. Powyższe odkrycia stanow...
RNA-based tools are frequently used to modulate gene expression in living cells. However, the sta... more RNA-based tools are frequently used to modulate gene expression in living cells. However, the stability and effectiveness of such RNA-based tools is limited by cellular nuclease activity. One way to increase RNA’s resistance to nucleases is to replace its D-ribose backbone with L-ribose isomers. This modification changes chirality of an entire RNA molecule to L-form giving it more chance of survival when introduced into cells. Recently, we have described the activity of left-handed hammerhead ribozyme (L-Rz, L-HH) that can specifically hydrolyse RNA with the opposite chirality at a predetermined location. To understand the structural background of the RNA specific cleavage in a heterochiral complex, we used circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy as well as performed molecular modelling and dynamics simulations of homo- and heterochiral RNA complexes. The active ribozyme-target heterochiral complex showed a mixed chirality as well as low field imino...
Cellular senescence is a tumor-suppressive mechanism blocking cell proliferation in response to s... more Cellular senescence is a tumor-suppressive mechanism blocking cell proliferation in response to stress. However, recent evidence suggests that senescent tumor cells can re-enter the cell cycle to become cancer stem cells, leading to relapse after cancer chemotherapy treatment. Understanding how the senescence reprogramming process is a precursor to cancer stem cell formation is of great medical importance. To study the interplay between senescence, stemness, and cancer, we applied a stem cell medium (SCM) to human embryonic fibroblasts (MRC5 and WI-38) and cancer cell lines (A549 and 293T). MRC5 and WI-38 cells treated with SCM showed symptoms of oxidative stress and became senescent. Transcriptome analysis over a time course of SCM-induced senescence, revealed a developmental process overlapping with the upregulation of genes for growth arrest and the senescence-associated secretory phenotype (SASP). We demonstrate that histone demethylases jumonji domain-containing protein D3 (Jmj...
The ribosome is a macromolecular assembly that is responsible for protein biosynthesis in all org... more The ribosome is a macromolecular assembly that is responsible for protein biosynthesis in all organisms. It is composed of two-subunit, ribonucleoprotein particles that translate the genetic material into an encoded polypeptides. The small subunit is the site of codon-anticodon interaction between the messenger RNA (mRNA) and transfer RNA (tRNA) substrates, and the large subunit catalyses peptide bond formation. The peptidyltransferase activity is fulfilled by 23S rRNA, which means that ribosome is a ribozyme. 5S rRNA is a conserved component of the large ribosomal subunit that is thought to enhance protein synthesis by stabilizing ribosome structure. This paper shortly summarises new results obtained on the structure and function of 5S rRNA.
Cytokininy stanowią jedną z grup hormonów roślinnych, które odgrywają ważną rolę we wzroście i ro... more Cytokininy stanowią jedną z grup hormonów roślinnych, które odgrywają ważną rolę we wzroście i rozwoju roślin. Wykazują różne efekty działania, szczególnie stymulują syntezę białek i uczestniczą w kontroli cyklu komórkowego. Pierwszą odkrytą cytokininą była N6-furfuryloadenina (kinetyna). Jest ona uważana za silny inhibitor procesów utleniania białek i kwasów nukleinowych w warunkach in vitro oraz in vivo. Zarówno kinetyna, jak i jej rybozyd (N6-furfuryloadenozyna, rybozyd kinetyny) jako naturalne związki występują w mleku kokosowym w stężeniu nanomolarnym. Rybozyd kinetyny selektywnie hamuje proliferację komórek nowotworowych oraz indukuje ich apoptozę. W tym artykule skupiono się na występowaniu rybozydu kinetyny, a przede wszystkim na jego metabolizmie oraz aktywności biologicznej.
This mini‐review describes the interaction between small molecules and RNA, in addition to its ap... more This mini‐review describes the interaction between small molecules and RNA, in addition to its application either in treating RNA‐associated diseases or detecting target molecules. In the case of RNA‐associated disease treatment, the designed small molecules interact with RNA sites, forming adducts and providing successful therapeutic strategies over oligonucleotides. On the other hand, synthetically designed RNA moieties (aptamers) interact with target molecules like toxins, drugs, hormones; these interactions are useful in the detection, quantification or separation of these target moieties.
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