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  1. Article ; Online: Rare A360T Mutation Alters GSK3β(Ser9) Binding in the Cytosolic Loop of Presenilin 1, Influencing β-Catenin Nuclear Localization and Pro-Death Gene Expression in Alzheimer's Disease Case.

    Wężyk, Michalina / Berdyński, Mariusz / Figarski, Adam / Skrzypczak, Magdalena / Ginalski, Krzysztof / Zboch, Marzena / Winkel, Izabela / Żekanowski, Cezary

    International journal of molecular sciences

    2023  Volume 24, Issue 23

    Abstract: Presenilin 1 (PS1) forms, via its large cytosolic loop, a trimeric complex with N-cadherin and β-catenin, which is a key component of Wnt signaling. PS1 undergoes phosphorylation at 353 and 357 serines upon enhanced activity and elevated levels of the ... ...

    Abstract Presenilin 1 (PS1) forms, via its large cytosolic loop, a trimeric complex with N-cadherin and β-catenin, which is a key component of Wnt signaling. PS1 undergoes phosphorylation at 353 and 357 serines upon enhanced activity and elevated levels of the GSK3β isoform. PS1 mutations surrounding these serines may alter the stability of the β-catenin complex. Such mutations are found in some cases of familial early-onset Alzheimer's disease (fEOAD), but their functional impact remains obscure. One of such variants of PS1, the A360T substitution, is located close to GSK3β-targeted serine residues. This variant was recently demonstrated in the French population, but more detail is needed to understand its biological effects. To assess the significance of this variant, we employed functional studies using a fibroblast cell line from an Alzheimer's disease case (a female proband) carrying the A360T mutation. Based on functional transcriptomic, cellular, and biochemical assays, we demonstrated atypically impaired β-catenin/GSK3β signaling in the A360T patient's fibroblasts. In detail, this was characterized by a decreased level of active cytosolic β-catenin and bound by PS1, an increased level of nuclear β-catenin, an increased level of inhibited GSK3β phosphorylated on Ser9, and enhanced interaction of GSK3β(Ser9) with PS1. Based on the transcriptomic profile of the A360T fibroblasts, we proposed a dysregulated transcriptional activity of β-catenin, exemplified by increased expression of various cyclin-dependent kinases and cyclins, such as cyclin D1, potentially inducing neurons' cell cycle re-entry followed by apoptosis. The A360T cells did not exhibit significant amyloid pathology. Therefore, cell death in this PS1 cytosolic loop mutation may be attributed to impaired β-catenin/GSK3β signaling rather than amyloid deposition per se. We further estimated the biological and clinical relevance of the A360T variant by whole exome sequencing (WES). WES was performed on DNA from the blood of an A360T female proband, as well as an unrelated male patient carrying the A360T mutation and his mutation-free daughter (both unavailable for the derivation of the fibroblast cell lines). WES confirmed the highest-priority AD causality of the A360T variant in PS1 and also profiled the pathways and processes involved in the A360T case, highlighting the greatest importance of altered Wnt signaling.
    MeSH term(s) Female ; Male ; Humans ; beta Catenin/genetics ; Alzheimer Disease/genetics ; Glycogen Synthase Kinase 3 beta/genetics ; Trans-Activators/genetics ; Presenilin-1/genetics ; Mutation ; Gene Expression
    Chemical Substances beta Catenin ; Glycogen Synthase Kinase 3 beta (EC 2.7.11.1) ; Trans-Activators ; Presenilin-1
    Language English
    Publishing date 2023-11-30
    Publishing country Switzerland
    Document type Case Reports
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms242316999
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Rare A360T Mutation Alters GSK3β(Ser9) Binding in the Cytosolic Loop of Presenilin 1, Influencing β-Catenin Nuclear Localization and Pro-Death Gene Expression in Alzheimer’s Disease Case

    Michalina Wężyk / Mariusz Berdyński / Adam Figarski / Magdalena Skrzypczak / Krzysztof Ginalski / Marzena Zboch / Izabela Winkel / Cezary Żekanowski

    International Journal of Molecular Sciences, Vol 24, Iss 23, p

    2023  Volume 16999

    Abstract: Presenilin 1 (PS1) forms, via its large cytosolic loop, a trimeric complex with N-cadherin and β-catenin, which is a key component of Wnt signaling. PS1 undergoes phosphorylation at 353 and 357 serines upon enhanced activity and elevated levels of the ... ...

    Abstract Presenilin 1 (PS1) forms, via its large cytosolic loop, a trimeric complex with N-cadherin and β-catenin, which is a key component of Wnt signaling. PS1 undergoes phosphorylation at 353 and 357 serines upon enhanced activity and elevated levels of the GSK3β isoform. PS1 mutations surrounding these serines may alter the stability of the β-catenin complex. Such mutations are found in some cases of familial early-onset Alzheimer’s disease (fEOAD), but their functional impact remains obscure. One of such variants of PS1, the A360T substitution, is located close to GSK3β-targeted serine residues. This variant was recently demonstrated in the French population, but more detail is needed to understand its biological effects. To assess the significance of this variant, we employed functional studies using a fibroblast cell line from an Alzheimer’s disease case (a female proband) carrying the A360T mutation. Based on functional transcriptomic, cellular, and biochemical assays, we demonstrated atypically impaired β-catenin/GSK3β signaling in the A360T patient’s fibroblasts. In detail, this was characterized by a decreased level of active cytosolic β-catenin and bound by PS1, an increased level of nuclear β-catenin, an increased level of inhibited GSK3β phosphorylated on Ser9, and enhanced interaction of GSK3β(Ser9) with PS1. Based on the transcriptomic profile of the A360T fibroblasts, we proposed a dysregulated transcriptional activity of β-catenin, exemplified by increased expression of various cyclin-dependent kinases and cyclins, such as cyclin D1, potentially inducing neurons’ cell cycle re-entry followed by apoptosis. The A360T cells did not exhibit significant amyloid pathology. Therefore, cell death in this PS1 cytosolic loop mutation may be attributed to impaired β-catenin/GSK3β signaling rather than amyloid deposition per se. We further estimated the biological and clinical relevance of the A360T variant by whole exome sequencing (WES). WES was performed on DNA from the blood of an A360T female proband, as well ...
    Keywords Alzheimer’s disease ; β-catenin/GSK3β ; PS1 cytosolic loop mutation ; non-amyloidogenic pathology ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 572
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution.

    Mourad, Raphaël / Ginalski, Krzysztof / Legube, Gaëlle / Cuvier, Olivier

    Genome biology

    2018  Volume 19, Issue 1, Page(s) 34

    Abstract: Double-strand breaks (DSBs) result from the attack of both DNA strands by multiple sources, including radiation and chemicals. DSBs can cause the abnormal chromosomal rearrangements associated with cancer. Recent techniques allow the genome-wide mapping ... ...

    Abstract Double-strand breaks (DSBs) result from the attack of both DNA strands by multiple sources, including radiation and chemicals. DSBs can cause the abnormal chromosomal rearrangements associated with cancer. Recent techniques allow the genome-wide mapping of DSBs at high resolution, enabling the comprehensive study of their origins. However, these techniques are costly and challenging. Hence, we devise a computational approach to predict DSBs using the epigenomic and chromatin context, for which public data are readily available from the ENCODE project. We achieve excellent prediction accuracy at high resolution. We identify chromatin accessibility, activity, and long-range contacts as the best predictors.
    MeSH term(s) Cell Line ; Chromatin/metabolism ; DNA/chemistry ; DNA Breaks, Double-Stranded ; Epigenesis, Genetic ; Histone Code ; Humans ; Nucleotide Motifs
    Chemical Substances Chromatin ; DNA (9007-49-2)
    Language English
    Publishing date 2018-03-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/s13059-018-1411-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Biochemical and structural bioinformatics studies of fungal CutA nucleotidyltransferases explain their unusual specificity toward CTP and increased tendency for cytidine incorporation at the 3'-terminal positions of synthesized tails.

    Kobyłecki, Kamil / Kuchta, Krzysztof / Dziembowski, Andrzej / Ginalski, Krzysztof / Tomecki, Rafał

    RNA (New York, N.Y.)

    2017  Volume 23, Issue 12, Page(s) 1902–1926

    Abstract: Noncanonical RNA nucleotidyltransferases (NTases), including poly(A), poly(U) polymerases (PAPs/PUPs), and C/U-adding enzymes, modify 3'-ends of different transcripts affecting their functionality and stability. They contain PAP/OAS1 substrate-binding ... ...

    Abstract Noncanonical RNA nucleotidyltransferases (NTases), including poly(A), poly(U) polymerases (PAPs/PUPs), and C/U-adding enzymes, modify 3'-ends of different transcripts affecting their functionality and stability. They contain PAP/OAS1 substrate-binding domain (SBD) with inserted NTase domain.
    Language English
    Publishing date 2017-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.061010.117
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Transposable elements contribute to fungal genes and impact fungal lifestyle.

    Muszewska, Anna / Steczkiewicz, Kamil / Stepniewska-Dziubinska, Marta / Ginalski, Krzysztof

    Scientific reports

    2019  Volume 9, Issue 1, Page(s) 4307

    Abstract: The last decade brought a still growing experimental evidence of mobilome impact on host's gene expression. We systematically analysed genomic location of transposable elements (TEs) in 625 publicly available fungal genomes from the NCBI database in ... ...

    Abstract The last decade brought a still growing experimental evidence of mobilome impact on host's gene expression. We systematically analysed genomic location of transposable elements (TEs) in 625 publicly available fungal genomes from the NCBI database in order to explore their potential roles in genome evolution and correlation with species' lifestyle. We found that non-autonomous TEs and remnant copies are evenly distributed across genomes. In consequence, they also massively overlap with regions annotated as genes, which suggests a great contribution of TE-derived sequences to host's coding genome. Younger and potentially active TEs cluster with one another away from genic regions. This non-randomness is a sign of either selection against insertion of TEs in gene proximity or target site preference among some types of TEs. Proteins encoded by genes with old transposable elements insertions have significantly less repeat and protein-protein interaction motifs but are richer in enzymatic domains. However, genes only proximal to TEs do not display any functional enrichment. Our findings show that adaptive cases of TE insertion remain a marginal phenomenon, and the overwhelming majority of TEs are evolving neutrally. Eventually, animal-related and pathogenic fungi have more TEs inserted into genes than fungi with other lifestyles. This is the first systematic, kingdom-wide study concerning mobile elements and their genomic neighbourhood. The obtained results should inspire further research concerning the roles TEs played in evolution and how they shape the life we know today.
    MeSH term(s) DNA Transposable Elements/genetics ; Enzymes/genetics ; Evolution, Molecular ; Fungi/genetics ; Genes, Fungal/genetics ; Genome, Fungal/genetics ; Life Style ; Protein Interaction Domains and Motifs/genetics
    Chemical Substances DNA Transposable Elements ; Enzymes
    Language English
    Publishing date 2019-03-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-019-40965-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: High-resolution, ultrasensitive and quantitative DNA double-strand break labeling in eukaryotic cells using i-BLESS.

    Biernacka, Anna / Skrzypczak, Magdalena / Zhu, Yingjie / Pasero, Philippe / Rowicka, Maga / Ginalski, Krzysztof

    Nature protocols

    2020  Volume 16, Issue 2, Page(s) 1034–1061

    Abstract: DNA double-strand breaks (DSBs) are implicated in various physiological processes, such as class-switch recombination or crossing-over during meiosis, but also present a threat to genome stability. Extensive evidence shows that DSBs are a primary source ... ...

    Abstract DNA double-strand breaks (DSBs) are implicated in various physiological processes, such as class-switch recombination or crossing-over during meiosis, but also present a threat to genome stability. Extensive evidence shows that DSBs are a primary source of chromosome translocations or deletions, making them a major cause of genomic instability, a driving force of many diseases of civilization, such as cancer. Therefore, there is a great need for a precise, sensitive, and universal method for DSB detection, to enable both the study of their mechanisms of formation and repair as well as to explore their therapeutic potential. We provide a detailed protocol for our recently developed ultrasensitive and genome-wide DSB detection method: immobilized direct in situ breaks labeling, enrichment on streptavidin and next-generation sequencing (i-BLESS), which relies on the encapsulation of cells in agarose beads and labeling breaks directly and specifically with biotinylated linkers. i-BLESS labels DSBs with single-nucleotide resolution, allows detection of ultrarare breaks, takes 5 d to complete, and can be applied to samples from any organism, as long as a sufficient amount of starting material can be obtained. We also describe how to combine i-BLESS with our qDSB-Seq approach to enable the measurement of absolute DSB frequencies per cell and their precise genomic coordinates at the same time. Such normalization using qDSB-Seq is especially useful for the evaluation of spontaneous DSB levels and the estimation of DNA damage induced rather uniformly in the genome (e.g., by irradiation or radiomimetic chemotherapeutics).
    MeSH term(s) DNA/chemistry ; DNA/genetics ; DNA Breaks, Double-Stranded ; DNA Repair/genetics ; DNA Replication/genetics ; Eukaryotic Cells ; Genomic Instability/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Meiosis/genetics ; Primed In Situ Labeling/methods
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2020-12-21
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/s41596-020-00448-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Comparative modeling for protein structure prediction.

    Ginalski, Krzysztof

    Current opinion in structural biology

    2006  Volume 16, Issue 2, Page(s) 172–177

    Abstract: With the progression of structural genomics projects, comparative modeling remains an increasingly important method of choice. It helps to bridge the gap between the available sequence and structure information by providing reliable and accurate protein ... ...

    Abstract With the progression of structural genomics projects, comparative modeling remains an increasingly important method of choice. It helps to bridge the gap between the available sequence and structure information by providing reliable and accurate protein models. Comparative modeling based on more than 30% sequence identity is now approaching its natural template-based limits and further improvements require the development of effective refinement techniques capable of driving models toward native structure. For difficult targets, for which the most significant progress in recent years has been observed, optimal template selection and alignment accuracy are still the major problems.
    MeSH term(s) Algorithms ; Escherichia coli Proteins/chemistry ; Membrane Proteins/chemistry ; Models, Molecular ; Nitroreductases/chemistry ; Proteins/chemistry ; Sequence Analysis, Protein ; Structural Homology, Protein ; Thermotoga maritima/enzymology
    Chemical Substances Escherichia coli Proteins ; Membrane Proteins ; Proteins ; tonB protein, E coli ; Nitroreductases (EC 1.7.-)
    Language English
    Publishing date 2006-04
    Publishing country England
    Document type Comparative Study ; Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 0959-440X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2006.02.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Systematic classification of the His-Me finger superfamily.

    Jablonska, Jagoda / Matelska, Dorota / Steczkiewicz, Kamil / Ginalski, Krzysztof

    Nucleic acids research

    2017  Volume 45, Issue 20, Page(s) 11479–11494

    Abstract: The His-Me finger endonucleases, also known as HNH or ββα-metal endonucleases, form a large and diverse protein superfamily. The His-Me finger domain can be found in proteins that play an essential role in cells, including genome maintenance, intron ... ...

    Abstract The His-Me finger endonucleases, also known as HNH or ββα-metal endonucleases, form a large and diverse protein superfamily. The His-Me finger domain can be found in proteins that play an essential role in cells, including genome maintenance, intron homing, host defense and target offense. Its overall structural compactness and non-specificity make it a perfectly-tailored pathogenic module that participates on both sides of inter- and intra-organismal competition. An extremely low sequence similarity across the superfamily makes it difficult to identify and classify new His-Me fingers. Using state-of-the-art distant homology detection methods, we provide an updated and systematic classification of His-Me finger proteins. In this work, we identified over 100 000 proteins and clustered them into 38 groups, of which three groups are new and cannot be found in any existing public domain database of protein families. Based on an analysis of sequences, structures, domain architectures, and genomic contexts, we provide a careful functional annotation of the poorly characterized members of this superfamily. Our results may inspire further experimental investigations that should address the predicted activity and clarify the potential substrates, to provide more detailed insights into the fundamental biological roles of these proteins.
    Language English
    Publishing date 2017-11-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkx924
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Comprehensive classification of the PIN domain-like superfamily.

    Matelska, Dorota / Steczkiewicz, Kamil / Ginalski, Krzysztof

    Nucleic acids research

    2017  Volume 45, Issue 12, Page(s) 6995–7020

    Abstract: PIN-like domains constitute a widespread superfamily of nucleases, diverse in terms of the reaction mechanism, substrate specificity, biological function and taxonomic distribution. Proteins with PIN-like domains are involved in central cellular ... ...

    Abstract PIN-like domains constitute a widespread superfamily of nucleases, diverse in terms of the reaction mechanism, substrate specificity, biological function and taxonomic distribution. Proteins with PIN-like domains are involved in central cellular processes, such as DNA replication and repair, mRNA degradation, transcription regulation and ncRNA maturation. In this work, we identify and classify the most complete set of PIN-like domains to provide the first comprehensive analysis of sequence-structure-function relationships within the whole PIN domain-like superfamily. Transitive sequence searches using highly sensitive methods for remote homology detection led to the identification of several new families, including representatives of Pfam (DUF1308, DUF4935) and CDD (COG2454), and 23 other families not classified in the public domain databases. Further sequence clustering revealed relationships between individual sequence clusters and showed heterogeneity within some families, suggesting a possible functional divergence. With five structural groups, 70 defined clusters, over 100,000 proteins, and broad biological functions, the PIN domain-like superfamily constitutes one of the largest and most diverse nuclease superfamilies. Detailed analyses of sequences and structures, domain architectures, and genomic contexts allowed us to predict biological function of several new families, including new toxin-antitoxin components, proteins involved in tRNA/rRNA maturation and transcription/translation regulation.
    MeSH term(s) Amino Acid Sequence ; Bacteria/enzymology ; Bacteria/genetics ; Bacteriophages/enzymology ; Bacteriophages/genetics ; Binding Sites ; Biocatalysis ; Crystallography, X-Ray ; Deoxyribonucleases/chemistry ; Deoxyribonucleases/classification ; Deoxyribonucleases/genetics ; Deoxyribonucleases/metabolism ; Fungi/enzymology ; Fungi/genetics ; Humans ; Kinetics ; Models, Molecular ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Domains ; Protein Structure, Tertiary ; Ribonucleases/chemistry ; Ribonucleases/classification ; Ribonucleases/genetics ; Ribonucleases/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity
    Chemical Substances Deoxyribonucleases (EC 3.1.-) ; Ribonucleases (EC 3.1.-)
    Language English
    Publishing date 2017-07-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkx494
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution

    Raphaël Mourad / Krzysztof Ginalski / Gaëlle Legube / Olivier Cuvier

    Genome Biology, Vol 19, Iss 1, Pp 1-

    2018  Volume 14

    Abstract: Abstract Double-strand breaks (DSBs) result from the attack of both DNA strands by multiple sources, including radiation and chemicals. DSBs can cause the abnormal chromosomal rearrangements associated with cancer. Recent techniques allow the genome-wide ...

    Abstract Abstract Double-strand breaks (DSBs) result from the attack of both DNA strands by multiple sources, including radiation and chemicals. DSBs can cause the abnormal chromosomal rearrangements associated with cancer. Recent techniques allow the genome-wide mapping of DSBs at high resolution, enabling the comprehensive study of their origins. However, these techniques are costly and challenging. Hence, we devise a computational approach to predict DSBs using the epigenomic and chromatin context, for which public data are readily available from the ENCODE project. We achieve excellent prediction accuracy at high resolution. We identify chromatin accessibility, activity, and long-range contacts as the best predictors.
    Keywords Double-strand breaks ; Epigenetics ; Chromatin ; Machine learning ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Language English
    Publishing date 2018-03-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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