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  1. Article ; Online: METTL16, Methyltransferase-Like Protein 16: Current Insights into Structure and Function.

    Ruszkowska, Agnieszka

    International journal of molecular sciences

    2021  Volume 22, Issue 4

    Abstract: Methyltransferase-like protein 16 (METTL16) is a human RNA methyltransferase that installs ... ...

    Abstract Methyltransferase-like protein 16 (METTL16) is a human RNA methyltransferase that installs m
    MeSH term(s) Binding Sites ; Humans ; Methylation ; Methyltransferases/chemistry ; Methyltransferases/metabolism ; Neoplasms/enzymology ; Neoplasms/genetics ; Nucleic Acid Conformation ; Protein Domains ; RNA/metabolism ; RNA, Long Noncoding/chemistry ; RNA, Long Noncoding/metabolism
    Chemical Substances MALAT1 long non-coding RNA, human ; RNA, Long Noncoding ; RNA (63231-63-0) ; METTL16 protein, human (EC 2.1.1.-) ; Methyltransferases (EC 2.1.1.-)
    Language English
    Publishing date 2021-02-22
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22042176
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  2. Article: New aspects of DNA recognition by group II WRKY transcription factor revealed by structural and functional study of AtWRKY18 DNA binding domain

    Grzechowiak, Marta / Ruszkowska, Agnieszka / Sliwiak, Joanna / Urbanowicz, Anna / Jaskolski, Mariusz / Ruszkowski, Milosz

    International journal of biological macromolecules. 2022 July 31, v. 213

    2022  

    Abstract: WRKY transcription factors (TFs) constitute one of the largest families of plant TFs. Based on the organization of domains and motifs, WRKY TFs are divided into three Groups (I-III). The WRKY subgroup IIa includes three representatives in A. thaliana, ... ...

    Abstract WRKY transcription factors (TFs) constitute one of the largest families of plant TFs. Based on the organization of domains and motifs, WRKY TFs are divided into three Groups (I-III). The WRKY subgroup IIa includes three representatives in A. thaliana, AtWRKY18, AtWRKY40, and AtWRKY60, that participate in biotic and abiotic stress responses. Here we present crystal structures of the DNA binding domain (DBD) of AtWRKY18 alone and in the complex with a DNA duplex containing the WRKY-recognition sequence, W-box. Subgroup IIa WRKY TFs are known to form homo and heterodimers. Our data suggest that the dimerization interface of the full-length AtWRKY18 involves contacts between the DBD subunits. DNA binding experiments and structural analysis point out novel aspects of DNA recognition by WRKY TFs. In particular, AtWRKY18-DBD preferentially binds an overlapping tandem of W-boxes accompanied by a quasi-W-box motif. The binding of DNA deforms the B-type double helix, which suggests that the DNA fragment must be prone to form a specific structure. This can explain why despite the short W-box consensus, WRKY TFs can precisely control gene expression. Finally, this first experimental structure of a Group II WRKY TF allowed us to compare Group I-III representatives.
    Keywords DNA ; DNA fragmentation ; abiotic stress ; dimerization ; gene expression ; transcription factors
    Language English
    Dates of publication 2022-0731
    Size p. 589-601.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2022.05.186
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  3. Article: Structural Insights Into the 5'UG/3'GU Wobble Tandem in Complex With Ba

    Ruszkowska, Agnieszka / Zheng, Ya Ying / Mao, Song / Ruszkowski, Milosz / Sheng, Jia

    Frontiers in molecular biosciences

    2022  Volume 8, Page(s) 762786

    Abstract: G•U wobble base pair frequently occurs in RNA structures. The unique chemical, thermodynamic, and structural properties of the G•U pair are widely exploited in RNA biology. In several RNA molecules, the G•U pair plays key roles in folding, ribozyme ... ...

    Abstract G•U wobble base pair frequently occurs in RNA structures. The unique chemical, thermodynamic, and structural properties of the G•U pair are widely exploited in RNA biology. In several RNA molecules, the G•U pair plays key roles in folding, ribozyme catalysis, and interactions with proteins. G•U may occur as a single pair or in tandem motifs with different geometries, electrostatics, and thermodynamics, further extending its biological functions. The metal binding affinity, which is essential for RNA folding, catalysis, and other interactions, differs with respect to the tandem motif type due to the different electrostatic potentials of the major grooves. In this work, we present the crystal structure of an RNA 8-mer duplex r[UCGUGCGA]
    Language English
    Publishing date 2022-01-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.762786
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  4. Article ; Online: New aspects of DNA recognition by group II WRKY transcription factor revealed by structural and functional study of AtWRKY18 DNA binding domain.

    Grzechowiak, Marta / Ruszkowska, Agnieszka / Sliwiak, Joanna / Urbanowicz, Anna / Jaskolski, Mariusz / Ruszkowski, Milosz

    International journal of biological macromolecules

    2022  Volume 213, Page(s) 589–601

    Abstract: WRKY transcription factors (TFs) constitute one of the largest families of plant TFs. Based on the organization of domains and motifs, WRKY TFs are divided into three Groups (I-III). The WRKY subgroup IIa includes three representatives in A. thaliana, ... ...

    Abstract WRKY transcription factors (TFs) constitute one of the largest families of plant TFs. Based on the organization of domains and motifs, WRKY TFs are divided into three Groups (I-III). The WRKY subgroup IIa includes three representatives in A. thaliana, AtWRKY18, AtWRKY40, and AtWRKY60, that participate in biotic and abiotic stress responses. Here we present crystal structures of the DNA binding domain (DBD) of AtWRKY18 alone and in the complex with a DNA duplex containing the WRKY-recognition sequence, W-box. Subgroup IIa WRKY TFs are known to form homo and heterodimers. Our data suggest that the dimerization interface of the full-length AtWRKY18 involves contacts between the DBD subunits. DNA binding experiments and structural analysis point out novel aspects of DNA recognition by WRKY TFs. In particular, AtWRKY18-DBD preferentially binds an overlapping tandem of W-boxes accompanied by a quasi-W-box motif. The binding of DNA deforms the B-type double helix, which suggests that the DNA fragment must be prone to form a specific structure. This can explain why despite the short W-box consensus, WRKY TFs can precisely control gene expression. Finally, this first experimental structure of a Group II WRKY TF allowed us to compare Group I-III representatives.
    MeSH term(s) DNA/genetics ; Gene Expression Regulation, Plant ; Phylogeny ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Protein Domains ; Stress, Physiological ; Transcription Factors/metabolism
    Chemical Substances Plant Proteins ; Transcription Factors ; DNA (9007-49-2)
    Language English
    Publishing date 2022-06-02
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2022.05.186
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: In vivo secondary structural analysis of Influenza A virus genomic RNA.

    Mirska, Barbara / Woźniak, Tomasz / Lorent, Dagny / Ruszkowska, Agnieszka / Peterson, Jake M / Moss, Walter N / Mathews, David H / Kierzek, Ryszard / Kierzek, Elzbieta

    Cellular and molecular life sciences : CMLS

    2023  Volume 80, Issue 5, Page(s) 136

    Abstract: Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA- ... ...

    Abstract Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA-targeting antivirals. Chemical RNA mapping using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) coupled with Mutational Profiling (MaP) allows for the thorough examination of secondary structures in low-abundance RNAs in their biological context. So far, the method has been used for analyzing the RNA secondary structures of several viruses including SARS-CoV-2 in virio and in cellulo. Here, we used SHAPE-MaP and dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) for genome-wide secondary structure analysis of viral RNA (vRNA) of the pandemic influenza A/California/04/2009 (H1N1) strain in both in virio and in cellulo environments. Experimental data allowed the prediction of the secondary structures of all eight vRNA segments in virio and, for the first time, the structures of vRNA5, 7, and 8 in cellulo. We conducted a comprehensive structural analysis of the proposed vRNA structures to reveal the motifs predicted with the highest accuracy. We also performed a base-pairs conservation analysis of the predicted vRNA structures and revealed many highly conserved vRNA motifs among the IAVs. The structural motifs presented herein are potential candidates for new IAV antiviral strategies.
    MeSH term(s) Humans ; Influenza A Virus, H1N1 Subtype/genetics ; COVID-19 ; SARS-CoV-2/genetics ; Influenza A virus/genetics ; RNA, Viral/genetics ; Genomics
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2023-05-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1358415-7
    ISSN 1420-9071 ; 1420-682X
    ISSN (online) 1420-9071
    ISSN 1420-682X
    DOI 10.1007/s00018-023-04764-1
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  6. Article: Secondary Structure of Subgenomic RNA M of SARS-CoV-2

    Soszynska-Jozwiak, Marta / Ruszkowska, Agnieszka / Kierzek, Ryszard / O’Leary, Collin A. / Moss, Walter N. / Kierzek, Elzbieta

    Viruses. 2022 Feb. 04, v. 14, no. 2

    2022  

    Abstract: SARS-CoV-2 belongs to the Coronavirinae family. Like other coronaviruses, SARS-CoV-2 is enveloped and possesses a positive-sense, single-stranded RNA genome of ~30 kb. Genomic RNA is used as the template for replication and transcription. During these ... ...

    Abstract SARS-CoV-2 belongs to the Coronavirinae family. Like other coronaviruses, SARS-CoV-2 is enveloped and possesses a positive-sense, single-stranded RNA genome of ~30 kb. Genomic RNA is used as the template for replication and transcription. During these processes, positive-sense genomic RNA (gRNA) and subgenomic RNAs (sgRNAs) are created. Several studies presented the importance of the genomic RNA secondary structure in SARS-CoV-2 replication. However, the structure of sgRNAs has remained largely unsolved so far. In this study, we probed the sgRNA M model of SARS-CoV-2 in vitro. The presented model molecule includes 5′UTR and a coding sequence of gene M. This is the first experimentally informed secondary structure model of sgRNA M, which presents features likely to be important in sgRNA M function. The knowledge of sgRNA M structure provides insights to better understand virus biology and could be used for designing new therapeutics.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; genes ; genomics ; models ; therapeutics ; viruses
    Language English
    Dates of publication 2022-0204
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14020322
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  7. Article: Chloroplastic Serine Hydroxymethyltransferase From

    Ruszkowski, Milosz / Sekula, Bartosz / Ruszkowska, Agnieszka / Dauter, Zbigniew

    Frontiers in plant science

    2018  Volume 9, Page(s) 584

    Abstract: Serine hydroxymethyltransferase (SHMT, EC 2.1.2.1) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme which catalyzes the reversible serine-to-glycine conversion in either a tetrahydrofolate-dependent or -independent manner. The enzyme is also ... ...

    Abstract Serine hydroxymethyltransferase (SHMT, EC 2.1.2.1) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme which catalyzes the reversible serine-to-glycine conversion in either a tetrahydrofolate-dependent or -independent manner. The enzyme is also responsible for the tetrahydrofolate-independent cleavage of other β-hydroxy amino acids. In addition to being an essential player in the serine homeostasis, SHMT action is the main source of activated one-carbon units, which links SHMT activity with the control of cell proliferation. In plants, studies of SHMT enzymes are more complicated than of those of, e.g., bacterial or mammalian origins because plant genomes encode multiple SHMT isozymes that are targeted to different subcellular compartments: cytosol, mitochondria, plastids, and nucleus. Here we report crystal structures of chloroplast-targeted SHMT from
    Language English
    Publishing date 2018-05-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2018.00584
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  8. Article ; Online: Secondary Structure of Subgenomic RNA M of SARS-CoV-2.

    Soszynska-Jozwiak, Marta / Ruszkowska, Agnieszka / Kierzek, Ryszard / O'Leary, Collin A / Moss, Walter N / Kierzek, Elzbieta

    Viruses

    2022  Volume 14, Issue 2

    Abstract: SARS-CoV-2 belongs to ... ...

    Abstract SARS-CoV-2 belongs to the
    MeSH term(s) 5' Untranslated Regions ; COVID-19/virology ; Genome, Viral ; Genomics ; Humans ; Open Reading Frames ; RNA, Viral/chemistry ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Transcription, Genetic
    Chemical Substances 5' Untranslated Regions ; RNA, Viral
    Language English
    Publishing date 2022-02-04
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14020322
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  9. Article ; Online: Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples.

    Ruszkowska, Agnieszka / Ruszkowski, Milosz / Hulewicz, Jacob P / Dauter, Zbigniew / Brown, Jessica A

    Nucleic acids research

    2020  Volume 48, Issue 18, Page(s) 10614

    Language English
    Publishing date 2020-10-06
    Publishing country England
    Document type Journal Article ; Published Erratum
    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/gkaa770
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  10. Article ; Online: The experience of adult children of mothers with intellectual disability: A qualitative retrospective study from Poland.

    Wołowicz-Ruszkowska, Agnieszka / McConnell, David

    Journal of applied research in intellectual disabilities : JARID

    2017  Volume 30, Issue 3, Page(s) 482–491

    Abstract: Background: Little is known about the experience of growing up with a mother with intellectual disability. The aim of this study was to explore this experience from the perspective of adult children.: Method: In-depth interviews with 23 adult ... ...

    Abstract Background: Little is known about the experience of growing up with a mother with intellectual disability. The aim of this study was to explore this experience from the perspective of adult children.
    Method: In-depth interviews with 23 adult children brought up by mothers with moderate-to-severe intellectual disability. The interview data were analysed using grounded theory methods.
    Results: The childhood experiences of the interviewees and the role their mothers played in their upbringing varied, depending in part on the involvement of extended family. It was the stigma of maternal intellectual disability, rather than their mother's functional limitations, that posed the greatest challenge.
    Conclusion: Interviewees characterized their mothers and childhoods as different, yet ordinary. Understanding the social context, including but not limited to the availability of informal support, is critical to understanding the experience of children growing up with mothers with intellectual disability.
    MeSH term(s) Adult ; Adult Children/psychology ; Child of Impaired Parents/psychology ; Female ; Humans ; Intellectual Disability/psychology ; Male ; Mothers/psychology ; Poland ; Qualitative Research ; Young Adult
    Language English
    Publishing date 2017-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 1326222-1
    ISSN 1468-3148 ; 0952-9608 ; 1360-2322
    ISSN (online) 1468-3148
    ISSN 0952-9608 ; 1360-2322
    DOI 10.1111/jar.12322
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