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  1. Article ; Online: CDK signaling via nonconventional CDK phosphorylation sites.

    Valk, Ervin / Örd, Mihkel / Faustova, Ilona / Loog, Mart

    Molecular biology of the cell

    2023  Volume 34, Issue 12, Page(s) pe5

    Abstract: Since the discovery of cyclin-dependent kinases (CDKs), it has been perceived as a dogma that CDK signaling in the cell cycle is mediated via targeting the CDK consensus sites: the optimal and the minimal motifs S/T-P-x-K/R and S/T-P, respectively. ... ...

    Abstract Since the discovery of cyclin-dependent kinases (CDKs), it has been perceived as a dogma that CDK signaling in the cell cycle is mediated via targeting the CDK consensus sites: the optimal and the minimal motifs S/T-P-x-K/R and S/T-P, respectively. However, more recent evidence suggests that often the CDK phosphorylation events of regulatory importance are mediated via nonconventional CDK sites that lack the required +1Pro of the consensus site motif. In these cases, the loss of specificity seems to be compensated via distant docking interactions facilitated by 1) phosphorylated priming sites binding to phospho-adaptor Cks1 and/or 2) cyclin-specific docking interactions via Short Linear Motifs (SLiMs) in substrates. This
    MeSH term(s) Phosphorylation ; Saccharomyces cerevisiae Proteins/metabolism ; Cyclin-Dependent Kinases/metabolism ; Signal Transduction ; Cyclins/metabolism
    Chemical Substances Saccharomyces cerevisiae Proteins ; Cyclin-Dependent Kinases (EC 2.7.11.22) ; Cyclins
    Language English
    Publishing date 2023-10-31
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1098979-1
    ISSN 1939-4586 ; 1059-1524
    ISSN (online) 1939-4586
    ISSN 1059-1524
    DOI 10.1091/mbc.E22-06-0196
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  2. Article ; Online: Detection of Multisite Phosphorylation of Intrinsically Disordered Proteins Using Phos-tag SDS-PAGE.

    Örd, Mihkel / Loog, Mart

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2141, Page(s) 779–792

    Abstract: ... Phos- ... ...

    Abstract Phos-tag
    MeSH term(s) Acrylamide ; Acrylamides ; Autoradiography/methods ; Blotting, Western/methods ; Buffers ; Electrophoresis, Polyacrylamide Gel/instrumentation ; Electrophoresis, Polyacrylamide Gel/methods ; Gels ; Intrinsically Disordered Proteins/analysis ; Intrinsically Disordered Proteins/chemistry ; Manganese ; Molecular Weight ; Phosphoproteins/analysis ; Phosphoproteins/chemistry ; Phosphorylation ; Protein Processing, Post-Translational ; Rosaniline Dyes ; Saccharomyces cerevisiae Proteins/analysis ; Saccharomyces cerevisiae Proteins/chemistry ; Staining and Labeling/methods ; Zinc
    Chemical Substances Acrylamides ; Buffers ; Gels ; Intrinsically Disordered Proteins ; Phosphoproteins ; Rosaniline Dyes ; Saccharomyces cerevisiae Proteins ; Acrylamide (20R035KLCI) ; Manganese (42Z2K6ZL8P) ; N,N'-methylenebisacrylamide (EDK4RIE19C) ; Zinc (J41CSQ7QDS) ; coomassie Brilliant Blue (M1ZRX790SI)
    Language English
    Publishing date 2020-07-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0524-0_40
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  3. Article ; Online: How the cell cycle clock ticks.

    Örd, Mihkel / Loog, Mart

    Molecular biology of the cell

    2019  Volume 30, Issue 2, Page(s) 169–172

    Abstract: Eukaryotic cell division has been studied thoroughly and is understood in great mechanistic detail. Paradoxically, however, we lack an understanding of its core control process, in which the master regulator of the cell cycle, cyclin-dependent kinase ( ... ...

    Abstract Eukaryotic cell division has been studied thoroughly and is understood in great mechanistic detail. Paradoxically, however, we lack an understanding of its core control process, in which the master regulator of the cell cycle, cyclin-dependent kinase (CDK), temporally coordinates an array of complex molecular events. The core elements of the CDK control system are conserved in eukaryotic cells, which contain multiple cyclin-CDK forms that have poorly defined and partially overlapping responsibilities in the cell cycle. However, a single CDK can drive all events of cell division in both mammalian and yeast cells, and in fission yeast a single mitotic cyclin can drive the cell cycle without major problems. But how can the same CDK induce different events when activated at different times during the cell cycle? This question, which has bewildered cell cycle researchers for decades, now has a sufficiently clear mechanistic answer. This Perspective aims to provide a synthesis of recent data to facilitate a better understanding of this central cellular control system.
    MeSH term(s) Cell Cycle ; Cyclin-Dependent Kinases/metabolism ; Cyclins/metabolism ; Models, Biological ; Phosphorylation ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/metabolism ; Substrate Specificity
    Chemical Substances Cyclins ; Cyclin-Dependent Kinases (EC 2.7.11.22)
    Language English
    Publishing date 2019-05-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1098979-1
    ISSN 1939-4586 ; 1059-1524
    ISSN (online) 1939-4586
    ISSN 1059-1524
    DOI 10.1091/mbc.E18-05-0272
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  4. Article ; Online: The sequence at Spike S1/S2 site enables cleavage by furin and phospho-regulation in SARS-CoV2 but not in SARS-CoV1 or MERS-CoV.

    Örd, Mihkel / Faustova, Ilona / Loog, Mart

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 16944

    Abstract: The Spike protein of the novel coronavirus SARS-CoV2 contains an ... ...

    Abstract The Spike protein of the novel coronavirus SARS-CoV2 contains an insertion
    MeSH term(s) Amino Acid Motifs/genetics ; Amino Acid Sequence ; Betacoronavirus/genetics ; Furin/metabolism ; Middle East Respiratory Syndrome Coronavirus/genetics ; Phosphorylation ; Proteolysis ; SARS Virus/genetics ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Virus Internalization
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Furin (EC 3.4.21.75)
    Keywords covid19
    Language English
    Publishing date 2020-10-09
    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/s41598-020-74101-0
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  5. Article ; Online: Docking to a Basic Helix Promotes Specific Phosphorylation by G1-Cdk1.

    Faustova, Ilona / Möll, Kaidi / Valk, Ervin / Loog, Mart / Örd, Mihkel

    International journal of molecular sciences

    2021  Volume 22, Issue 17

    Abstract: Cyclins are the activators of cyclin-dependent kinase (CDK) complex, but they also act as docking scaffolds for different short linear motifs (SLiMs) in CDK substrates and inhibitors. According to the unified model of CDK function, the cell cycle is ... ...

    Abstract Cyclins are the activators of cyclin-dependent kinase (CDK) complex, but they also act as docking scaffolds for different short linear motifs (SLiMs) in CDK substrates and inhibitors. According to the unified model of CDK function, the cell cycle is coordinated by CDK both via general CDK activity thresholds and cyclin-specific substrate docking. Recently, it was found that the G1-cyclins of
    MeSH term(s) Amino Acid Motifs ; CDC2 Protein Kinase/chemistry ; CDC2 Protein Kinase/genetics ; CDC2 Protein Kinase/metabolism ; Multienzyme Complexes/chemistry ; Multienzyme Complexes/genetics ; Multienzyme Complexes/metabolism ; Phosphorylation ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances Multienzyme Complexes ; Saccharomyces cerevisiae Proteins ; CDC2 Protein Kinase (EC 2.7.11.22)
    Language English
    Publishing date 2021-09-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22179514
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  6. Article ; Online: The sequence at Spike S1/S2 site enables cleavage by furin and phospho-regulation in SARS-CoV2 but not in SARS-CoV1 or MERS-CoV

    Mihkel Örd / Ilona Faustova / Mart Loog

    Scientific Reports, Vol 10, Iss 1, Pp 1-

    2020  Volume 10

    Abstract: Abstract The Spike protein of the novel coronavirus SARS-CoV2 contains an insertion 680SPRRAR↓SV687 forming a cleavage motif RxxR for furin-like enzymes at the boundary of S1/S2 subunits. Cleavage at S1/S2 is important for efficient viral entry into ... ...

    Abstract Abstract The Spike protein of the novel coronavirus SARS-CoV2 contains an insertion 680SPRRAR↓SV687 forming a cleavage motif RxxR for furin-like enzymes at the boundary of S1/S2 subunits. Cleavage at S1/S2 is important for efficient viral entry into target cells. The insertion is absent in other CoV-s of the same clade, including SARS-CoV1 that caused the 2003 outbreak. However, an analogous cleavage motif was present at S1/S2 of the Spike protein of the more distant Middle East Respiratory Syndrome coronavirus MERS-CoV. We show that a crucial third arginine at the left middle position, comprising a motif RRxR is required for furin recognition in vitro, while the general motif RxxR in common with MERS-CoV is not sufficient for cleavage. Further, we describe a surprising finding that the two serines at the edges of the insert SPRRAR↓SV can be efficiently phosphorylated by proline-directed and basophilic protein kinases. Both phosphorylations switch off furin’s ability to cleave the site. Although phospho-regulation of secreted proteins is still poorly understood, further studies, supported by a recent report of ten in vivo phosphorylated sites in the Spike protein of SARS-CoV2, could potentially uncover important novel regulatory mechanisms for SARS-CoV2.
    Keywords Medicine ; R ; Science ; Q ; covid19
    Subject code 572
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Docking to a Basic Helix Promotes Specific Phosphorylation by G1-Cdk1

    Ilona Faustova / Kaidi Möll / Ervin Valk / Mart Loog / Mihkel Örd

    International Journal of Molecular Sciences, Vol 22, Iss 9514, p

    2021  Volume 9514

    Abstract: Cyclins are the activators of cyclin-dependent kinase (CDK) complex, but they also act as docking scaffolds for different short linear motifs (SLiMs) in CDK substrates and inhibitors. According to the unified model of CDK function, the cell cycle is ... ...

    Abstract Cyclins are the activators of cyclin-dependent kinase (CDK) complex, but they also act as docking scaffolds for different short linear motifs (SLiMs) in CDK substrates and inhibitors. According to the unified model of CDK function, the cell cycle is coordinated by CDK both via general CDK activity thresholds and cyclin-specific substrate docking. Recently, it was found that the G1-cyclins of S. cerevisiae have a specific function in promoting polarization and growth of the buds, making the G1 cyclins essential for cell survival. Thus, while a uniform CDK specificity of a single cyclin can be sufficient to drive the cell cycle in some cells, such as in fission yeast, cyclin specificity can be essential in other organisms. However, the known G1-CDK specific LP docking motif, was not responsible for this essential function, indicating that G1-CDKs use yet other unknown docking mechanisms. Here we report a discovery of a G1 cyclin-specific (Cln1,2) lysine-arginine-rich helical docking motif (the K/R motif) in G1-CDK targets involved in the mating pathway (Ste7), transcription (Xbp1), bud morphogenesis (Bud2) and spindle pole body (Spc29, Spc42, Spc110, Sli15) function of S. cerevisiae . We also show that the docking efficiency of K/R motif can be regulated by basophilic kinases such as protein kinase A. Our results further widen the list of cyclin specificity mechanisms and may explain the recently demonstrated unique essential function of G1 cyclins in budding yeast.
    Keywords cyclin specificity ; cyclin-dependent kinase ; SLiM ; kinase specificity ; phosphorylation ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 571
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Multisite phosphorylation by Cdk1 initiates delayed negative feedback to control mitotic transcription.

    Asfaha, Jonathan B / Örd, Mihkel / Carlson, Christopher R / Faustova, Ilona / Loog, Mart / Morgan, David O

    Current biology : CB

    2021  Volume 32, Issue 1, Page(s) 256–263.e4

    Abstract: Cell-cycle progression is driven by the phosphorylation of cyclin-dependent kinase (Cdk) substrates. ...

    Abstract Cell-cycle progression is driven by the phosphorylation of cyclin-dependent kinase (Cdk) substrates.
    MeSH term(s) CDC2 Protein Kinase/genetics ; CDC2 Protein Kinase/metabolism ; Cell Cycle Proteins/metabolism ; Cyclin B/genetics ; Cyclin B/metabolism ; Cyclins/genetics ; Feedback ; Mitosis ; Phosphorylation ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factors/metabolism
    Chemical Substances Cell Cycle Proteins ; Cyclin B ; Cyclins ; Saccharomyces cerevisiae Proteins ; Transcription Factors ; CDC2 Protein Kinase (EC 2.7.11.22)
    Language English
    Publishing date 2021-11-23
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2021.11.001
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  9. Article ; Online: A synthetic biology approach reveals diverse and dynamic CDK response profiles via multisite phosphorylation of NLS-NES modules.

    Faustova, Ilona / Örd, Mihkel / Kiselev, Viacheslav / Fedorenko, Dmytro / Borovko, Irina / Macs, Dags / Pääbo, Kaur / Lõoke, Marko / Loog, Mart

    Science advances

    2022  Volume 8, Issue 33, Page(s) eabp8992

    Abstract: The complexity of multisite phosphorylation mechanisms in regulating nuclear localization signals (NLSs) and nuclear export signals (NESs) is not understood, and its potential has not been used in synthetic biology. The nucleocytoplasmic shuttling of ... ...

    Abstract The complexity of multisite phosphorylation mechanisms in regulating nuclear localization signals (NLSs) and nuclear export signals (NESs) is not understood, and its potential has not been used in synthetic biology. The nucleocytoplasmic shuttling of many proteins is regulated by cyclin-dependent kinases (CDKs) that rely on multisite phosphorylation patterns and short linear motifs (SLiMs) to dynamically control proteins in the cell cycle. We studied the role of motif patterns in nucleocytoplasmic shuttling using sensors based on the CDK targets Dna2, Psy4, and Mcm2/3 of
    Language English
    Publishing date 2022-08-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.abp8992
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  10. Article ; Online: Cdc6 is sequentially regulated by PP2A-Cdc55, Cdc14, and Sic1 for origin licensing in

    Philip, Jasmin / Örd, Mihkel / Silva, Andriele / Singh, Shaneen / Diffley, John Fx / Remus, Dirk / Loog, Mart / Ikui, Amy E

    eLife

    2022  Volume 11

    Abstract: Cdc6, a subunit of the pre-replicative complex (pre-RC), contains multiple regulatory cyclin-dependent kinase (Cdk1) consensus sites, SP or TP motifs. ... ...

    Abstract Cdc6, a subunit of the pre-replicative complex (pre-RC), contains multiple regulatory cyclin-dependent kinase (Cdk1) consensus sites, SP or TP motifs. In
    MeSH term(s) Cell Cycle Proteins/metabolism ; Cyclin-Dependent Kinase Inhibitor Proteins/metabolism ; DNA Replication/physiology ; Mitosis ; Phosphorylation ; Protein Phosphatase 2/metabolism ; Protein Tyrosine Phosphatases/metabolism ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances CDC14 protein, S cerevisiae ; CDC55 protein, S cerevisiae ; CDC6 protein, S cerevisiae ; Cell Cycle Proteins ; Cyclin-Dependent Kinase Inhibitor Proteins ; SIC1 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; Protein Phosphatase 2 (EC 3.1.3.16) ; Protein Tyrosine Phosphatases (EC 3.1.3.48)
    Language English
    Publishing date 2022-02-10
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.74437
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