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  1. AU="Palani, Sowmiya"
  2. AU="Manfred Frick"
  3. AU="Jensen, Leonard"
  4. AU="Pakhomov, Evgeny A."
  5. AU="Subramanyam, Chithirala Bala"
  6. AU=Petrek J A
  7. AU="Thomson-Baker, B"
  8. AU=Shahidi Shahrzad
  9. AU="Taylor, Holly A"
  10. AU="Yeong Jeong Jeon"
  11. AU="Bueno-Cavanillas, Aurora"
  12. AU="Kavčič, Tina"
  13. AU="Arias-Jiménez, José Luís"
  14. AU="Tünçok, Ekin"
  15. AU="Roberto Toro"
  16. AU="Bharti Sahu"
  17. AU="Soo-Yeon Choi"
  18. AU="Nono, Sandra"
  19. AU="Diepens, Robin J W"
  20. AU="Baselga-Garriga, Clara"

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  1. Artikel ; Online: Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes.

    Palani, Sowmiya / Machida, Yuka / Alvey, Julia R / Mishra, Vandana / Welter, Allison L / Cui, Gaofeng / Bragantini, Benoît / Botuyan, Maria Victoria / Cong, Anh T Q / Mer, Georges / Schellenberg, Matthew J / Machida, Yuichi J

    Nature communications

    2024  Band 15, Heft 1, Seite(n) 2064

    Abstract: FAM111A, a serine protease, plays roles in DNA replication and antiviral defense. Missense mutations in the catalytic domain cause hyper-autocleavage and are associated with genetic disorders with developmental defects. Despite the enzyme's biological ... ...

    Abstract FAM111A, a serine protease, plays roles in DNA replication and antiviral defense. Missense mutations in the catalytic domain cause hyper-autocleavage and are associated with genetic disorders with developmental defects. Despite the enzyme's biological significance, the molecular architecture of the FAM111A serine protease domain (SPD) is unknown. Here, we show that FAM111A is a dimerization-dependent protease containing a narrow, recessed active site that cleaves substrates with a chymotrypsin-like specificity. X-ray crystal structures and mutagenesis studies reveal that FAM111A dimerizes via the N-terminal helix within the SPD. This dimerization induces an activation cascade from the dimerization sensor loop to the oxyanion hole through disorder-to-order transitions. Dimerization is essential for proteolytic activity in vitro and for facilitating DNA replication at DNA-protein crosslink obstacles in cells, while it is dispensable for autocleavage. These findings underscore the role of dimerization in FAM111A's function and highlight the distinction in its dimerization dependency between substrate cleavage and autocleavage.
    Mesh-Begriff(e) Dimerization ; Serine Endopeptidases/metabolism ; Proteolysis ; Serine Proteases ; DNA Replication ; Serine
    Chemische Substanzen Serine Endopeptidases (EC 3.4.21.-) ; Serine Proteases (EC 3.4.-) ; Serine (452VLY9402)
    Sprache Englisch
    Erscheinungsdatum 2024-03-07
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-46207-w
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex.

    Shukla, Prakash K / Bissell, Jesse E / Kumar, Sanjit / Pokhrel, Srijana / Palani, Sowmiya / Radmall, Kaitlin S / Obidi, Onyeka / Parnell, Timothy J / Brasch, Julia / Shrieve, Dennis C / Chandrasekharan, Mahesh B

    Nucleic acids research

    2023  Band 51, Heft 5, Seite(n) 2117–2136

    Abstract: The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a ... ...

    Abstract The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 'backside'. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6-Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6-Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6-Bre1 interaction through a novel interface that is important for their biochemical and biological responses.
    Mesh-Begriff(e) Humans ; Chromatin/genetics ; Chromatin/metabolism ; Histones/genetics ; Histones/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Ubiquitin/metabolism ; Ubiquitin-Conjugating Enzymes/genetics ; Ubiquitin-Conjugating Enzymes/metabolism
    Chemische Substanzen Bre1 protein, S cerevisiae ; Chromatin ; Histones ; RAD6 protein, S cerevisiae (EC 2.3.2.23) ; Saccharomyces cerevisiae Proteins ; Ubiquitin ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23)
    Sprache Englisch
    Erscheinungsdatum 2023-01-29
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    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/gkad012
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: FAM111A protects replication forks from protein obstacles via its trypsin-like domain.

    Kojima, Yusuke / Machida, Yuka / Palani, Sowmiya / Caulfield, Thomas R / Radisky, Evette S / Kaufmann, Scott H / Machida, Yuichi J

    Nature communications

    2020  Band 11, Heft 1, Seite(n) 1318

    Abstract: Persistent protein obstacles on genomic DNA, such as DNA-protein crosslinks (DPCs) and tight nucleoprotein complexes, can block replication forks. DPCs can be removed by the proteolytic activities of the metalloprotease SPRTN or the proteasome in a ... ...

    Abstract Persistent protein obstacles on genomic DNA, such as DNA-protein crosslinks (DPCs) and tight nucleoprotein complexes, can block replication forks. DPCs can be removed by the proteolytic activities of the metalloprotease SPRTN or the proteasome in a replication-coupled manner; however, additional proteolytic mechanisms may exist to cope with the diversity of protein obstacles. Here, we show that FAM111A, a PCNA-interacting protein, plays an important role in mitigating the effect of protein obstacles on replication forks. This function of FAM111A requires an intact trypsin-like protease domain, the PCNA interaction, and the DNA-binding domain that is necessary for protease activity in vivo. FAM111A, but not SPRTN, protects replication forks from stalling at poly(ADP-ribose) polymerase 1 (PARP1)-DNA complexes trapped by PARP inhibitors, thereby promoting cell survival after drug treatment. Altogether, our findings reveal a role of FAM111A in overcoming protein obstacles to replication forks, shedding light on cellular responses to anti-cancer therapies.
    Mesh-Begriff(e) Camptothecin/pharmacology ; Cell Cycle Checkpoints/drug effects ; Cell Line, Tumor ; DNA Damage ; DNA Replication ; DNA Topoisomerases, Type I/metabolism ; DNA, Single-Stranded/metabolism ; Humans ; Mutation/genetics ; Poly(ADP-ribose) Polymerase Inhibitors/pharmacology ; Poly(ADP-ribose) Polymerases/metabolism ; Protein Binding/drug effects ; Protein Domains ; Receptors, Virus/chemistry ; Receptors, Virus/genetics ; Receptors, Virus/metabolism ; Trypsin/chemistry
    Chemische Substanzen DNA, Single-Stranded ; FAM111A protein, human ; Poly(ADP-ribose) Polymerase Inhibitors ; Receptors, Virus ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30) ; Trypsin (EC 3.4.21.4) ; DNA Topoisomerases, Type I (EC 5.99.1.2) ; Camptothecin (XT3Z54Z28A)
    Sprache Englisch
    Erscheinungsdatum 2020-03-12
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-15170-7
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Gradient nanocomposite hydrogels for interface tissue engineering.

    Cross, Lauren M / Shah, Kunal / Palani, Sowmiya / Peak, Charles W / Gaharwar, Akhilesh K

    Nanomedicine : nanotechnology, biology, and medicine

    2017  Band 14, Heft 7, Seite(n) 2465–2474

    Abstract: Two-dimensional (2D) nanomaterials are an emerging class of materials with unique physical and chemical properties due to their high surface area and disc-like shape. Recently, these 2D nanomaterials have been investigated for a range of biomedical ... ...

    Abstract Two-dimensional (2D) nanomaterials are an emerging class of materials with unique physical and chemical properties due to their high surface area and disc-like shape. Recently, these 2D nanomaterials have been investigated for a range of biomedical applications including tissue engineering, therapeutic delivery and bioimaging, due to their ability to physically reinforce polymeric networks. Here, we present a facile fabrication of a gradient scaffold with two natural polymers (gelatin methacryloyl (GelMA) and methacrylated kappa carrageenan (MκCA)) reinforced with 2D nanosilicates to mimic the native tissue interface. The addition of nanosilicates results in shear-thinning characteristics of prepolymer solution and increases the mechanical stiffness of crosslinked gradient structure. A gradient in mechanical properties, microstructures and cell adhesion characteristics was obtained using a microengineered flow channel. The gradient structure can be used to understand cell-matrix interactions and to design gradient scaffolds for mimicking tissue interfaces.
    Mesh-Begriff(e) Cell Adhesion ; Cells, Cultured ; Humans ; Hydrogels/chemistry ; Mesenchymal Stem Cells/cytology ; Nanocomposites/chemistry ; Polymers/chemistry ; Rheology ; Silicates/chemistry ; Tissue Engineering ; Tissue Scaffolds
    Chemische Substanzen Hydrogels ; Polymers ; Silicates
    Sprache Englisch
    Erscheinungsdatum 2017-05-26
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2183417-9
    ISSN 1549-9642 ; 1549-9634
    ISSN (online) 1549-9642
    ISSN 1549-9634
    DOI 10.1016/j.nano.2017.02.022
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription.

    Sdano, Matthew A / Fulcher, James M / Palani, Sowmiya / Chandrasekharan, Mahesh B / Parnell, Timothy J / Whitby, Frank G / Formosa, Tim / Hill, Christopher P

    eLife

    2017  Band 6

    Abstract: We determined that the tandem SH2 domain ... ...

    Abstract We determined that the tandem SH2 domain of
    Mesh-Begriff(e) Crystallography, X-Ray ; Histone Chaperones/chemistry ; Histone Chaperones/metabolism ; Models, Molecular ; Phosphorylation ; Protein Binding ; Protein Conformation ; Protein Processing, Post-Translational ; RNA Polymerase II/chemistry ; RNA Polymerase II/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription, Genetic ; Transcriptional Elongation Factors/chemistry ; Transcriptional Elongation Factors/metabolism
    Chemische Substanzen Histone Chaperones ; SPT6 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; Transcriptional Elongation Factors ; RNA Polymerase II (EC 2.7.7.-) ; RPB1 protein, S cerevisiae (EC 2.7.7.-)
    Sprache Englisch
    Erscheinungsdatum 2017-08-16
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.28723
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription.

    Ramakrishnan, Saravanan / Pokhrel, Srijana / Palani, Sowmiya / Pflueger, Christian / Parnell, Timothy J / Cairns, Bradley R / Bhaskara, Srividya / Chandrasekharan, Mahesh B

    Nature communications

    2016  Band 7, Seite(n) 11949

    Abstract: Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic roles in transcription and chromatin dynamics remain poorly understood. We investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase ...

    Abstract Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic roles in transcription and chromatin dynamics remain poorly understood. We investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Here, we show that Set1 and Jhd2 predominantly co-regulate genome-wide transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal turnover and occupancy during transcriptional co-regulation. Moreover, we find a genome-wide co-regulation of chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study puts forth a model wherein combined actions of Set1 and Jhd2 via modulating H3K4 methylation-demethylation together control chromatin dynamics during various facets of transcriptional regulation.
    Mesh-Begriff(e) Chromatin Assembly and Disassembly ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Histone-Lysine N-Methyltransferase/genetics ; Histone-Lysine N-Methyltransferase/metabolism ; Histones/genetics ; Histones/metabolism ; Jumonji Domain-Containing Histone Demethylases/genetics ; Jumonji Domain-Containing Histone Demethylases/metabolism ; Methylation ; Models, Genetic ; Multigene Family ; Nucleosomes/chemistry ; Nucleosomes/metabolism ; Protein Processing, Post-Translational ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription, Genetic
    Chemische Substanzen Histones ; Nucleosomes ; Saccharomyces cerevisiae Proteins ; JHD2 protein, S cerevisiae (EC 1.14.11.-) ; Jumonji Domain-Containing Histone Demethylases (EC 1.14.11.-) ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; SET1 protein, S cerevisiae (EC 2.1.1.43)
    Sprache Englisch
    Erscheinungsdatum 2016-06-21
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/ncomms11949
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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