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Article ; Online: Poly(ADP-ribose) in Condensates: The PARtnership of Phase Separation and Site-Specific Interactions.

Alemasova, Elizaveta E / Lavrik, Olga I

International journal of molecular sciences

2022 Volume 23, Issue 22

Abstract: Biomolecular condensates are nonmembrane cellular compartments whose formation in many cases involves phase separation (PS). Despite much research interest in this mechanism of macromolecular self-organization, the concept of PS as applied to a live cell ...

Abstract	Biomolecular condensates are nonmembrane cellular compartments whose formation in many cases involves phase separation (PS). Despite much research interest in this mechanism of macromolecular self-organization, the concept of PS as applied to a live cell faces certain challenges. In this review, we discuss a basic model of PS and the role of site-specific interactions and percolation in cellular PS-related events. Using a multivalent poly(ADP-ribose) molecule as an example, which has high PS-driving potential due to its structural features, we consider how site-specific interactions and network formation are involved in the formation of phase-separated cellular condensates.
MeSH term(s)	Poly Adenosine Diphosphate Ribose ; Macromolecular Substances
Chemical Substances	Poly Adenosine Diphosphate Ribose (26656-46-2) ; Macromolecular Substances
Language	English
Publishing date	2022-11-15
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/ijms232214075
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Article ; Online: A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates.

Alemasova, Elizaveta E / Lavrik, Olga I

Nucleic acids research

2022 Volume 50, Issue 19, Page(s) 10817–10838

Abstract: Condensates are biomolecular assemblies that concentrate biomolecules without the help of membranes. They are morphologically highly versatile and may emerge via distinct mechanisms. Nucleic acids-DNA, RNA and poly(ADP-ribose) (PAR) play special roles in ...

Abstract	Condensates are biomolecular assemblies that concentrate biomolecules without the help of membranes. They are morphologically highly versatile and may emerge via distinct mechanisms. Nucleic acids-DNA, RNA and poly(ADP-ribose) (PAR) play special roles in the process of condensate organization. These polymeric scaffolds provide multiple specific and nonspecific interactions during nucleation and 'development' of macromolecular assemblages. In this review, we focus on condensates formed with PAR. We discuss to what extent the literature supports the phase separation origin of these structures. Special attention is paid to similarities and differences between PAR and RNA in the process of dynamic restructuring of condensates during their functioning.
MeSH term(s)	Poly Adenosine Diphosphate Ribose ; RNA/genetics ; RNA/chemistry ; Biomolecular Condensates ; Macromolecular Substances ; Nucleic Acids
Chemical Substances	Poly Adenosine Diphosphate Ribose (26656-46-2) ; RNA (63231-63-0) ; Macromolecular Substances ; Nucleic Acids
Language	English
Publishing date	2022-10-01
Publishing country	England
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't
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/gkac866
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Article ; Online: Role of YB-1 in Regulation of Poly(ADP-Ribosylation) Catalyzed by Poly(ADP-Ribose) Polymerases.

Alemasova, Elizaveta E / Naumenko, Konstantin N / Sukhanova, Maria V / Lavrik, Olga I

Biochemistry. Biokhimiia

2022 Volume 87, Issue Suppl 1, Page(s) S32–S0

Abstract: Poly(ADP-ribosyl)ation is a post-translational modification of proteins that performs an essential regulatory function in the cellular response to DNA damage. The key enzyme synthesizing poly(ADP-ribose) (PAR) in the cells is poly(ADP-ribose) polymerase ... ...

Abstract	Poly(ADP-ribosyl)ation is a post-translational modification of proteins that performs an essential regulatory function in the cellular response to DNA damage. The key enzyme synthesizing poly(ADP-ribose) (PAR) in the cells is poly(ADP-ribose) polymerase 1 (PARP1). Understanding the mechanisms of the PARP1 activity regulation within the cells is necessary for development of the PARP1-targeted antitumor therapy. This review is devoted to the studies of the role of the RNA-binding protein YB-1 in the PARP1-catalyzed PARylation. The mechanisms of PARP1 activity stimulation by YB-1 protein can possibly be extended to other RNA-binding proteins involved in the maintenance of the genome stability.
MeSH term(s)	Catalysis ; DNA Damage ; Poly ADP Ribosylation ; Poly Adenosine Diphosphate Ribose ; Poly(ADP-ribose) Polymerases/metabolism ; Proteins/metabolism
Chemical Substances	Proteins ; Poly Adenosine Diphosphate Ribose (26656-46-2) ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30)
Language	English
Publishing date	2022-05-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1109-5
ISSN	1608-3040 ; 0006-2979 ; 0320-9717
ISSN (online)	1608-3040
ISSN	0006-2979 ; 0320-9717
DOI	10.1134/S0006297922140048
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Article ; Online: Poly(ADP-ribosyl)ation by PARP1: reaction mechanism and regulatory proteins.

Alemasova, Elizaveta E / Lavrik, Olga I

Nucleic acids research

2019 Volume 47, Issue 8, Page(s) 3811–3827

Abstract: Poly(ADP-ribosyl)ation (PARylation) is posttranslational modification of proteins by linear or branched chains of ADP-ribose units, originating from NAD+. The central enzyme for PAR production in cells and the main target of poly(ADP-ribosyl)ation during ...

Abstract	Poly(ADP-ribosyl)ation (PARylation) is posttranslational modification of proteins by linear or branched chains of ADP-ribose units, originating from NAD+. The central enzyme for PAR production in cells and the main target of poly(ADP-ribosyl)ation during DNA damage is poly(ADP-ribose) polymerase 1 (PARP1). PARP1 ability to function as a catalytic and acceptor protein simultaneously made a considerable contribution to accumulation of contradictory data. This topic is directly related to other questions, such as the stoichiometry of PARP1 molecules in auto-modification reaction, direction of the chain growth during PAR elongation and functional coupling of PARP1 with PARylation targets. Besides DNA damage necessary for the folding of catalytically active PARP1, other mechanisms appear to be required for the relevant intensity and specificity of PARylation reaction. Indeed, in recent years, PARP research has been enriched by the discovery of novel PARP1 interaction partners modulating its enzymatic activity. Understanding the details of PARP1 catalytic mechanism and its regulation is especially important in light of PARP-targeted therapy and may significantly aid to PARP inhibitors drug design. In this review we summarize old and up-to-date literature to clarify several points concerning PARylation mechanism and discuss different ways for regulation of PAR synthesis by accessory proteins reported thus far.
MeSH term(s)	Adenosine Diphosphate Ribose/metabolism ; Animals ; Catalytic Domain ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Damage ; DNA Repair ; Humans ; Isoenzymes/genetics ; Isoenzymes/metabolism ; Poly (ADP-Ribose) Polymerase-1/chemistry ; Poly (ADP-Ribose) Polymerase-1/genetics ; Poly (ADP-Ribose) Polymerase-1/metabolism ; Poly ADP Ribosylation ; Poly Adenosine Diphosphate Ribose/biosynthesis ; Protein Binding ; Protein Folding ; Protein Multimerization ; Protein Processing, Post-Translational
Chemical Substances	Isoenzymes ; Adenosine Diphosphate Ribose (20762-30-5) ; Poly Adenosine Diphosphate Ribose (26656-46-2) ; DNA (9007-49-2) ; PARP1 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30)
Language	English
Publishing date	2019-02-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
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/gkz120
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Article: At the Interface of Three Nucleic Acids: The Role of RNA-Binding Proteins and Poly(ADP-ribose) in DNA Repair.

Alemasova, E E / Lavrik, O I

Acta naturae

2015 Volume 9, Issue 2, Page(s) 4–16

Abstract: RNA-binding proteins (RBPs) regulate RNA metabolism, from synthesis to decay. When bound to RNA, RBPs act as guardians of the genome integrity at different levels, from DNA damage prevention to the post-transcriptional regulation of gene expression. ... ...

Abstract	RNA-binding proteins (RBPs) regulate RNA metabolism, from synthesis to decay. When bound to RNA, RBPs act as guardians of the genome integrity at different levels, from DNA damage prevention to the post-transcriptional regulation of gene expression. Recently, RBPs have been shown to participate in DNA repair. This fact is of special interest as DNA repair pathways do not generally involve RNA. DNA damage in higher organisms triggers the formation of the RNA-like polymer - poly(ADP-ribose) (PAR). Nucleic acid-like properties allow PAR to recruit DNA- and RNA-binding proteins to the site of DNA damage. It is suggested that poly(ADP-ribose) and RBPs not only modulate the activities of DNA repair factors, but that they also play an important role in the formation of transient repairosome complexes in the nucleus. Cytoplasmic biomolecules are subjected to similar sorting during the formation of RNA assemblages by functionally related mRNAs and promiscuous RBPs. The Y-box-binding protein 1 (YB-1) is the major component of cytoplasmic RNA granules. Although YB-1 is a classic RNA-binding protein, it is now regarded as a non-canonical factor of DNA repair.
Language	English
Publishing date	2015-12-07
Publishing country	Russia (Federation)
Document type	Journal Article
ISSN	2075-8251
ISSN	2075-8251
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Article ; Online: Y-Box-Binding Protein 1 Stimulates Abasic Site Cleavage.

Alemasova, E E / Naumenko, K N / Moor, N A / Lavrik, O I

Biochemistry. Biokhimiia

2017 Volume 82, Issue 12, Page(s) 1521–1528

Abstract: Apurinic/apyrimidinic (AP) sites are among the most frequent DNA lesions. The first step in the AP site repair involves the magnesium-dependent enzyme AP endonuclease 1 (APE1) that catalyzes hydrolytic cleavage of the DNA phosphodiester bond at the 5' ... ...

Abstract	Apurinic/apyrimidinic (AP) sites are among the most frequent DNA lesions. The first step in the AP site repair involves the magnesium-dependent enzyme AP endonuclease 1 (APE1) that catalyzes hydrolytic cleavage of the DNA phosphodiester bond at the 5' side of the AP site, thereby generating a single-strand DNA break flanked by the 3'-OH and 5'-deoxyribose phosphate (dRP) groups. Increased APE1 activity in cancer cells might correlate with tumor chemoresistance to DNA-damaging treatment. It has been previously shown that the multifunctional oncoprotein Y-box-binding protein 1 (YB-1) interacts with APE1 and inhibits APE1-catalyzed hydrolysis of AP sites in single-stranded DNAs. In this work, we demonstrated that YB-1 stabilizes the APE1 complex with double-stranded DNAs containing the AP sites and stimulates cleavage of these AP sites at low magnesium concentrations.
MeSH term(s)	Binding Sites ; DNA Cleavage ; DNA Repair ; DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; Humans ; Hydrolysis ; Kinetics ; Magnesium/chemistry ; Magnesium/metabolism ; Mutagenesis ; Oligonucleotides/metabolism ; Protein Binding ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/chemistry ; Recombinant Proteins/isolation & purification ; Y-Box-Binding Protein 1/genetics ; Y-Box-Binding Protein 1/metabolism
Chemical Substances	Oligonucleotides ; Recombinant Proteins ; Y-Box-Binding Protein 1 ; APEX1 protein, human (EC 4.2.99.18) ; DNA-(Apurinic or Apyrimidinic Site) Lyase (EC 4.2.99.18) ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2017-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	1109-5
ISSN	1608-3040 ; 0006-2979 ; 0320-9717
ISSN (online)	1608-3040
ISSN	0006-2979 ; 0320-9717
DOI	10.1134/S0006297917120112
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Article ; Online: Regulation of Poly(ADP-Ribose) Polymerase 1 Activity by Y-Box-Binding Protein 1.

Naumenko, Konstantin N / Sukhanova, Mariya V / Hamon, Loic / Kurgina, Tatyana A / Alemasova, Elizaveta E / Kutuzov, Mikhail M / Pastré, David / Lavrik, Olga I

Biomolecules

2020 Volume 10, Issue 9

Abstract: Y-box-binding protein 1 (YB-1) is a multifunctional positively charged protein that interacts with DNA or RNA and poly(ADP-ribose) (PAR). YB-1 is poly(ADP-ribosyl)ated and stimulates poly(ADP-ribose) polymerase 1 (PARP1) activity. Here, we studied the ... ...

Abstract	Y-box-binding protein 1 (YB-1) is a multifunctional positively charged protein that interacts with DNA or RNA and poly(ADP-ribose) (PAR). YB-1 is poly(ADP-ribosyl)ated and stimulates poly(ADP-ribose) polymerase 1 (PARP1) activity. Here, we studied the mechanism of YB-1-dependent PAR synthesis by PARP1 in vitro using biochemical and atomic force microscopy assays. PAR synthesis activity of PARP1 is known to be facilitated by co-factors such as Mg
MeSH term(s)	DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Damage ; Fluorescence Polarization ; HeLa Cells ; Humans ; Magnesium/metabolism ; Microscopy, Atomic Force ; Nucleic Acid Conformation ; Nucleosomes/genetics ; Nucleosomes/metabolism ; Poly (ADP-Ribose) Polymerase-1/chemistry ; Poly (ADP-Ribose) Polymerase-1/genetics ; Poly (ADP-Ribose) Polymerase-1/metabolism ; Poly Adenosine Diphosphate Ribose/metabolism ; Protein Binding ; Protein Multimerization ; Protein Processing, Post-Translational ; Y-Box-Binding Protein 1/chemistry ; Y-Box-Binding Protein 1/genetics ; Y-Box-Binding Protein 1/metabolism
Chemical Substances	Nucleosomes ; Y-Box-Binding Protein 1 ; Poly Adenosine Diphosphate Ribose (26656-46-2) ; DNA (9007-49-2) ; PARP1 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30) ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2020-09-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom10091325
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Article ; Online: The multifunctional protein YB-1 potentiates PARP1 activity and decreases the efficiency of PARP1 inhibitors.

Alemasova, Elizaveta E / Naumenko, Konstantin N / Kurgina, Tatyana A / Anarbaev, Rashid O / Lavrik, Olga I

Oncotarget

2018 Volume 9, Issue 34, Page(s) 23349–23365

Abstract: Y-box-binding protein 1 (YB-1) is a multifunctional cellular factor overexpressed in tumors resistant to chemotherapy. An intrinsically disordered structure together with a high positive charge peculiar to YB-1 allows this protein to function in almost ... ...

Abstract	Y-box-binding protein 1 (YB-1) is a multifunctional cellular factor overexpressed in tumors resistant to chemotherapy. An intrinsically disordered structure together with a high positive charge peculiar to YB-1 allows this protein to function in almost all cellular events related to nucleic acids including RNA, DNA and poly(ADP-ribose) (PAR). In the present study we show that YB-1 acts as a potent poly(ADP-ribose) polymerase 1 (PARP1) cofactor that can reduce the efficiency of PARP1 inhibitors. Similarly to that of histones or polyamines, stimulatory effect of YB-1 on the activity of PARP1 was significantly higher than the activator potential of Mg
Language	English
Publishing date	2018-05-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.25158
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Article: Y-box-binding protein 1 as a non-canonical factor of base excision repair.

Alemasova, Elizaveta E / Moor, Nina A / Naumenko, Konstantin N / Kutuzov, Mikhail M / Sukhanova, Maria V / Pestryakov, Pavel E / Lavrik, Olga I

Biochimica et biophysica acta

2016 Volume 1864, Issue 12, Page(s) 1631–1640

Abstract: Base excision repair (BER) is a flagship DNA repair system responsible for maintaining genome integrity. Apart from basal enzymes, this system involves several accessory factors essential for coordination and regulation of DNA processing during substrate ...

Abstract	Base excision repair (BER) is a flagship DNA repair system responsible for maintaining genome integrity. Apart from basal enzymes, this system involves several accessory factors essential for coordination and regulation of DNA processing during substrate channeling. Y-box-binding protein 1 (YB-1), a multifunctional factor that can interact with DNA, RNA, poly(ADP-ribose) and plenty of proteins including DNA repair enzymes, is increasingly considered as a non-canonical protein of BER. Here we provide quantitative characterization of YB-1 physical interactions with key BER factors such as PARP1, PARP2, APE1, NEIL1 and pol β and comparison of the full-length YB-1 and its C-terminally truncated nuclear form in regard to their binding affinities for BER proteins. Data on functional interactions reveal strong stimulation of PARP1 autopoly(ADP-ribosyl)ation and inhibition of poly(ADP-ribose) degradation by PARG in the presence of YB-1. Moreover, YB-1 is shown to stimulate AP lyase activity of NEIL1 and to inhibit dRP lyase activity of pol β on model DNA duplex structure. We also demonstrate for the first time YB-1 poly(ADP-ribosyl)ation in the presence of RNA.
MeSH term(s)	Animals ; DNA Damage ; DNA Glycosylases/metabolism ; DNA Polymerase beta/metabolism ; DNA Repair/physiology ; DNA-(Apurinic or Apyrimidinic Site) Lyase/chemistry ; DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; Humans ; Mice ; Peptide Fragments/chemistry ; Peptide Fragments/genetics ; Peptide Fragments/metabolism ; Poly (ADP-Ribose) Polymerase-1/genetics ; Poly (ADP-Ribose) Polymerase-1/metabolism ; Poly(ADP-ribose) Polymerases/genetics ; Poly(ADP-ribose) Polymerases/metabolism ; Protein Interaction Domains and Motifs ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Spectrometry, Fluorescence ; Y-Box-Binding Protein 1/chemistry ; Y-Box-Binding Protein 1/genetics ; Y-Box-Binding Protein 1/metabolism
Chemical Substances	Peptide Fragments ; Recombinant Proteins ; Y-Box-Binding Protein 1 ; YBX1 protein, human ; PARP1 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30) ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30) ; Parp2 protein, mouse (EC 2.4.2.30.) ; DNA Polymerase beta (EC 2.7.7.-) ; POLB protein, human (EC 2.7.7.7) ; DNA Glycosylases (EC 3.2.2.-) ; NEIL1 protein, human (EC 3.2.2.-) ; APEX1 protein, human (EC 4.2.99.18) ; DNA-(Apurinic or Apyrimidinic Site) Lyase (EC 4.2.99.18)
Language	English
Publishing date	2016-08-18
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbapap.2016.08.012
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Article: Y-box-binding protein 1 as a non-canonical factor of base excision repair

Alemasova, Elizaveta E / Konstantin N. Naumenko / Maria V. Sukhanova / Mikhail M. Kutuzov / Nina A. Moor / Olga I. Lavrik / Pavel E. Pestryakov

Biochimica et biophysica acta. 2016 Dec., v. 1864, no. 12

2016

Abstract	Base excision repair (BER) is a flagship DNA repair system responsible for maintaining genome integrity. Apart from basal enzymes, this system involves several accessory factors essential for coordination and regulation of DNA processing during substrate channeling. Y-box-binding protein 1 (YB-1), a multifunctional factor that can interact with DNA, RNA, poly(ADP-ribose) and plenty of proteins including DNA repair enzymes, is increasingly considered as a non-canonical protein of BER. Here we provide quantitative characterization of YB-1 physical interactions with key BER factors such as PARP1, PARP2, APE1, NEIL1 and pol β and comparison of the full-length YB-1 and its C-terminally truncated nuclear form in regard to their binding affinities for BER proteins. Data on functional interactions reveal strong stimulation of PARP1 autopoly(ADP-ribosyl)ation and inhibition of poly(ADP-ribose) degradation by PARG in the presence of YB-1. Moreover, YB-1 is shown to stimulate AP lyase activity of NEIL1 and to inhibit dRP lyase activity of pol β on model DNA duplex structure. We also demonstrate for the first time YB-1 poly(ADP-ribosyl)ation in the presence of RNA.
Keywords	binding capacity ; DNA ; DNA repair ; enzymes ; genome ; proteins ; RNA
Language	English
Dates of publication	2016-12
Size	p. 1631-1640.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2918798-9
ISSN	1878-1454 ; 1570-9639
ISSN (online)	1878-1454
ISSN	1570-9639
DOI	10.1016/j.bbapap.2016.08.012
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