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Article ; Online: microRNAs in action: biogenesis, function and regulation.

Shang, Renfu / Lee, Seungjae / Senavirathne, Gayan / Lai, Eric C

2023 Volume 24, Issue 12, Page(s) 816–833

Abstract: Ever since microRNAs (miRNAs) were first recognized as an extensive gene family >20 years ago, a broad community of researchers was drawn to investigate the universe of small regulatory RNAs. Although core features of miRNA biogenesis and function were ... ...

Abstract	Ever since microRNAs (miRNAs) were first recognized as an extensive gene family >20 years ago, a broad community of researchers was drawn to investigate the universe of small regulatory RNAs. Although core features of miRNA biogenesis and function were revealed early on, recent years continue to uncover fundamental information on the structural and molecular dynamics of core miRNA machinery, how miRNA substrates and targets are selected from the transcriptome, new avenues for multilevel regulation of miRNA biogenesis and mechanisms for miRNA turnover. Many of these latest insights were enabled by recent technological advances, including massively parallel assays, cryogenic electron microscopy, single-molecule imaging and CRISPR-Cas9 screening. Here, we summarize the current understanding of miRNA biogenesis, function and regulation, and outline challenges to address in the future.
MeSH term(s)	MicroRNAs/genetics ; Transcriptome
Chemical Substances	MicroRNAs
Language	English
Publishing date	2023-06-28
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2035157-4
ISSN	1471-0064 ; 1471-0056
ISSN (online)	1471-0064
ISSN	1471-0056
DOI	10.1038/s41576-023-00611-y
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Zs.A 5474: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: DNA strand breaks and gaps target retroviral intasome binding and integration.

Senavirathne, Gayan / London, James / Gardner, Anne / Fishel, Richard / Yoder, Kristine E

Nature communications

2023 Volume 14, Issue 1, Page(s) 7072

Abstract: Retrovirus integration into a host genome is essential for productive infections. The integration strand transfer reaction is catalyzed by a nucleoprotein complex (Intasome) containing the viral integrase (IN) and the reverse transcribed (RT) copy DNA ( ... ...

Abstract	Retrovirus integration into a host genome is essential for productive infections. The integration strand transfer reaction is catalyzed by a nucleoprotein complex (Intasome) containing the viral integrase (IN) and the reverse transcribed (RT) copy DNA (cDNA). Previous studies suggested that DNA target-site recognition limits intasome integration. Using single molecule Förster resonance energy transfer (smFRET), we show prototype foamy virus (PFV) intasomes specifically bind to DNA strand breaks and gaps. These break and gap DNA discontinuities mimic oxidative base excision repair (BER) lesion-processing intermediates that have been shown to affect retrovirus integration in vivo. The increased DNA binding events targeted strand transfer to the break/gap site without inducing substantial intasome conformational changes. The major oxidative BER substrate 8-oxo-guanine as well as a G/T mismatch or +T nucleotide insertion that typically introduce a bend or localized flexibility into the DNA, did not increase intasome binding or targeted integration. These results identify DNA breaks or gaps as modulators of dynamic intasome-target DNA interactions that encourage site-directed integration.
MeSH term(s)	DNA, Viral/metabolism ; Integrases/metabolism ; Retroviridae/genetics ; Retroviridae/metabolism ; Spumavirus/genetics ; Spumavirus/metabolism ; DNA, Complementary ; Virus Integration
Chemical Substances	DNA, Viral ; Integrases (EC 2.7.7.-) ; DNA, Complementary
Language	English
Publishing date	2023-11-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-42641-4
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Article ; Online: Expression and Purification of Nuclease-Free Oxygen Scavenger Protocatechuate 3,4-Dioxygenase.

Messer, Ryan K / Lopez, Miguel A / Senavirathne, Gayan / Yoder, Kristine E

Journal of visualized experiments : JoVE

2019 , Issue 153

Abstract: Single molecule (SM) microscopy is used in the study of dynamic molecular interactions of fluorophore labeled biomolecules in real time. However, fluorophores are prone to loss of signal via photobleaching by dissolved oxygen (O2). To prevent ... ...

Abstract	Single molecule (SM) microscopy is used in the study of dynamic molecular interactions of fluorophore labeled biomolecules in real time. However, fluorophores are prone to loss of signal via photobleaching by dissolved oxygen (O2). To prevent photobleaching and extend the fluorophore lifetime, oxygen scavenging systems (OSS) are employed to reduce O2. Commercially available OSS may be contaminated by nucleases that damage or degrade nucleic acids, confounding interpretation of experimental results. Here we detail a protocol for the expression and purification of highly active Pseudomonas putida protocatechuate-3,4-dioxygenase (PCD) with no detectable nuclease contamination. PCD can efficiently remove reactive O2 species by conversion of the substrate protocatechuic acid (PCA) to 3-carboxy-cis,cis-muconic acid. This method can be used in any aqueous system where O2 plays a detrimental role in data acquisition. This method is effective in producing highly active, nuclease free PCD in comparison with commercially available PCD.
MeSH term(s)	Oxygen/metabolism ; Photobleaching ; Protocatechuate-3,4-Dioxygenase/isolation & purification ; Protocatechuate-3,4-Dioxygenase/metabolism ; Pseudomonas putida/enzymology ; Substrate Specificity
Chemical Substances	Protocatechuate-3,4-Dioxygenase (EC 1.13.11.3) ; Oxygen (S88TT14065)
Language	English
Publishing date	2019-11-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/59599
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Article: Expression and purification of nuclease-free oxygen scavenger protocatechuate 3,4-dioxygenase

Messer, Ryan K / Lopez Jr., Miguel A / Senavirathne, Gayan / Yoder, Kristine E

Journal of visualized experiments. 2019 Nov. 08, , no. 153

2019

Abstract	Single molecule (SM) microscopy is used in the study of dynamic molecular interactions of fluorophore labeled biomolecules in real time. However, fluorophores are prone to loss of signal via photobleaching by dissolved oxygen (O2). To prevent photobleaching and extend the fluorophore lifetime, oxygen scavenging systems (OSS) are employed to reduce O2. Commercially available OSS may be contaminated by nucleases that damage or degrade nucleic acids, confounding interpretation of experimental results. Here we detail a protocol for the expression and purification of highly active Pseudomonas putida protocatechuate-3,4-dioxygenase (PCD) with no detectable nuclease contamination. PCD can efficiently remove reactive O2 species by conversion of the substrate protocatechuic acid (PCA) to 3-carboxy-cis,cis-muconic acid. This method can be used in any aqueous system where O2 plays a detrimental role in data acquisition. This method is effective in producing highly active, nuclease free PCD in comparison with commercially available PCD.
Keywords	data collection ; dissolved oxygen ; fluorescent dyes ; microscopy ; nucleases ; nucleic acids ; oxygen ; photobleaching ; protocatechuic acid ; Pseudomonas putida
Language	English
Dates of publication	2019-1108
Size	p. e59599.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/59599
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Article: Expression and purification of nuclease-free protocatechuate 3,4-dioxygenase for prolonged single-molecule fluorescence imaging

Senavirathne, Gayan / Lopez, Miguel A / Messer, Ryan / Fishel, Richard / Yoder, Kristine E

Analytical biochemistry. 2018 Sept. 01, v. 556

2018

Abstract: Single-molecule (SM) microscopy is a powerful tool capable of visualizing individual molecules and events in real time. SM imaging may rely on proteins or nucleic acids labelled with a fluorophore. Unfortunately photobleaching of fluorophores leads to ... ...

Abstract	Single-molecule (SM) microscopy is a powerful tool capable of visualizing individual molecules and events in real time. SM imaging may rely on proteins or nucleic acids labelled with a fluorophore. Unfortunately photobleaching of fluorophores leads to irreversible loss of signal, impacting the collection of data from SM experiments. Trace amounts of dissolved oxygen (O2) are the main cause of photobleaching. Oxygen scavenging systems (OSS) have been developed that decrease dissolved O2. Commercial OSS enzyme preparations are frequently contaminated with nucleases that damage nucleic acid substrates. In this protocol, we purify highly active Pseudomonas putida protocatechuate 3,4-dioxygenase (PCD) without nuclease contaminations. Quantitation of Cy3 photostability revealed that PCD with its substrate protocatechuic acid (PCA) increased the fluorophore half-life 100-fold. This low cost purification method of recombinant PCD yields an enzyme superior to commercially available OSS that is effectively free of nuclease activity.
Keywords	Pseudomonas putida ; data collection ; dissolved oxygen ; enzyme activity ; fluorescence ; fluorescent dyes ; half life ; image analysis ; microscopy ; nucleases ; nucleic acids ; oxygen ; photobleaching ; photostability ; proteins ; protocatechuic acid ; protocols ; purification methods
Language	English
Dates of publication	2018-0901
Size	p. 78-84.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2018.06.016
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Expression and purification of nuclease-free protocatechuate 3,4-dioxygenase for prolonged single-molecule fluorescence imaging.

Senavirathne, Gayan / Lopez, Miguel A / Messer, Ryan / Fishel, Richard / Yoder, Kristine E

Analytical biochemistry

2018 Volume 556, Page(s) 78–84

Abstract	Single-molecule (SM) microscopy is a powerful tool capable of visualizing individual molecules and events in real time. SM imaging may rely on proteins or nucleic acids labelled with a fluorophore. Unfortunately photobleaching of fluorophores leads to irreversible loss of signal, impacting the collection of data from SM experiments. Trace amounts of dissolved oxygen (O
MeSH term(s)	Bacterial Proteins/biosynthesis ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/isolation & purification ; Deoxyribonucleases ; Enzyme Stability ; Gene Expression ; Hydroxybenzoates/chemistry ; Optical Imaging ; Oxygen/chemistry ; Protocatechuate-3,4-Dioxygenase/biosynthesis ; Protocatechuate-3,4-Dioxygenase/chemistry ; Protocatechuate-3,4-Dioxygenase/genetics ; Protocatechuate-3,4-Dioxygenase/isolation & purification ; Pseudomonas putida/enzymology ; Pseudomonas putida/genetics ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/isolation & purification
Chemical Substances	Bacterial Proteins ; Hydroxybenzoates ; Recombinant Proteins ; protocatechuic acid (36R5QJ8L4B) ; Protocatechuate-3,4-Dioxygenase (EC 1.13.11.3) ; Deoxyribonucleases (EC 3.1.-) ; Oxygen (S88TT14065)
Language	English
Publishing date	2018-06-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2018.06.016
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 389: Show issues

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Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Prototype foamy virus intasome aggregation is mediated by outer protein domains and prevented by protocatechuic acid.

Jones, Nathan D / Mackler, Randi M / Lopez, Miguel A / Baltierra-Jasso, Laura E / Altman, Matthew P / Senavirathne, Gayan / Yoder, Kristine E

Scientific reports

2019 Volume 9, Issue 1, Page(s) 132

Abstract: The integrase (IN) enzyme of retrovirus prototype foamy virus (PFV) consists of four domains: amino terminal extension (NED), amino terminus (NTD), catalytic core (CCD), and carboxyl terminus domains (CTD). A tetramer of PFV IN with two viral DNA ends ... ...

Abstract	The integrase (IN) enzyme of retrovirus prototype foamy virus (PFV) consists of four domains: amino terminal extension (NED), amino terminus (NTD), catalytic core (CCD), and carboxyl terminus domains (CTD). A tetramer of PFV IN with two viral DNA ends forms the functional intasome. Two inner monomers are catalytically active while the CCDs of the two outer monomers appear to play only structural roles. The NED, NTD, and CTD of the outer monomers are disordered in intasome structures. Truncation mutants reveal that integration to a supercoiled plasmid increases without the outer monomer CTDs present. Deletion of the outer CTDs enhances the lifetime of the intasome compared to full length (FL) IN or deletion of the outer monomer NTDs. High ionic strength buffer or several additives, particularly protocatechuic acid (PCA), enhance the integration of FL intasomes by preventing aggregation. These data confirm previous studies suggesting the disordered outer domains of PFV intasomes are not required for intasome assembly or integration. Instead, the outer CTDs contribute to aggregation of PFV intasomes which may be inhibited by high ionic strength buffer or the small molecule PCA.
MeSH term(s)	Buffers ; Hydroxybenzoates/pharmacology ; Integrases/chemistry ; Integrases/metabolism ; Osmolar Concentration ; Protein Aggregates/drug effects ; Protein Domains/physiology ; Protein Multimerization/drug effects ; Spumavirus/enzymology ; Viral Proteins/chemistry ; Viral Proteins/metabolism
Chemical Substances	Buffers ; Hydroxybenzoates ; Protein Aggregates ; Viral Proteins ; protocatechuic acid (36R5QJ8L4B) ; Integrases (EC 2.7.7.-)
Language	English
Publishing date	2019-01-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-36725-1
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Article ; Online: Retroviral prototype foamy virus intasome binding to a nucleosome target does not determine integration efficiency.

Kotlar, Randi M / Jones, Nathan D / Senavirathne, Gayan / Gardner, Anne M / Messer, Ryan K / Tan, Yow Yong / Rabe, Anthony J / Fishel, Richard / Yoder, Kristine E

The Journal of biological chemistry

2021 Volume 296, Page(s) 100550

Abstract: Retroviral integrases must navigate host DNA packaged as chromatin during integration of the viral genome. Prototype foamy virus (PFV) integrase (IN) forms a tetramer bound to two viral DNA (vDNA) ends in a complex termed an intasome. PFV IN consists of ... ...

Abstract	Retroviral integrases must navigate host DNA packaged as chromatin during integration of the viral genome. Prototype foamy virus (PFV) integrase (IN) forms a tetramer bound to two viral DNA (vDNA) ends in a complex termed an intasome. PFV IN consists of four domains: the amino terminal extension domain (NED), amino terminal domain (NTD), catalytic core domain (CCD), and carboxyl terminal domain (CTD). The domains of the two inner IN protomers have been visualized, as well as the CCDs of the two outer IN protomers. However, the roles of the amino and carboxyl terminal domains of the PFV intasome outer subunits during integration to a nucleosome target substrate are not clear. We used the well-characterized 601 nucleosome to assay integration activity as well as intasome binding. PFV intasome integration to 601 nucleosomes occurs in clusters at four independent sites. We find that the outer protomer NED and NTD domains have no significant effects on integration efficiency, site selection, or binding. The CTDs of the outer PFV intasome subunits dramatically affect nucleosome binding but have little effect on total integration efficiency. The outer PFV IN CTDs did significantly alter the integration efficiency at one site. Histone tails also significantly affect intasome binding, but have little impact on PFV integration efficiency or site selection. These results indicate that binding to nucleosomes does not correlate with integration efficiency and suggests most intasome-binding events are unproductive.
MeSH term(s)	Catalytic Domain ; Chromatin/genetics ; Chromatin/metabolism ; DNA, Viral/genetics ; DNA, Viral/metabolism ; Genome, Viral ; Histones/metabolism ; Humans ; Integrases/genetics ; Integrases/metabolism ; Nucleosomes/metabolism ; Protein Multimerization ; Spumavirus/genetics ; Spumavirus/growth & development ; Spumavirus/metabolism ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Virus Integration
Chemical Substances	Chromatin ; DNA, Viral ; Histones ; Nucleosomes ; Viral Proteins ; Integrases (EC 2.7.7.-)
Language	English
Publishing date	2021-03-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2021.100550
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Article ; Online: Dynamic unwrapping of nucleosomes by HsRAD51 that includes sliding and rotational motion of histone octamers.

Senavirathne, Gayan / Mahto, Santosh K / Hanne, Jeungphill / O'Brian, Daniel / Fishel, Richard

Nucleic acids research

2016 Volume 45, Issue 2, Page(s) 685–698

Abstract: Wrapping of genomic DNA into nucleosomes poses thermodynamic and kinetic barriers to biological processes such as replication, transcription, repair and recombination. Previous biochemical studies have demonstrated that in the presence of adenosine ... ...

Abstract	Wrapping of genomic DNA into nucleosomes poses thermodynamic and kinetic barriers to biological processes such as replication, transcription, repair and recombination. Previous biochemical studies have demonstrated that in the presence of adenosine triphosphate (ATP) the human RAD51 (HsRAD51) recombinase can form a nucleoprotein filament (NPF) on double-stranded DNA (dsDNA) that is capable of unwrapping the nucleosomal DNA from the histone octamer (HO). Here, we have used single molecule Förster Resonance Energy Transfer (smFRET) to examine the real time nucleosome dynamics in the presence of the HsRAD51 NPF. We show that oligomerization of HsRAD51 leads to stepwise, but stochastic unwrapping of the DNA from the HO in the presence of ATP. The highly reversible dynamics observed in single-molecule trajectories suggests an antagonistic mechanism between HsRAD51 binding and rewrapping of the DNA around the HO. These stochastic dynamics were independent of the nucleosomal DNA sequence or the asymmetry created by the presence of a linker DNA. We also observed sliding and rotational oscillations of the HO with respect to the nucleosomal DNA. These studies underline the dynamic nature of even tightly associated protein-DNA complexes such as nucleosomes.
MeSH term(s)	Adenosine Triphosphate/metabolism ; DNA/genetics ; DNA/metabolism ; DNA Replication ; Histones/chemistry ; Histones/metabolism ; Humans ; Hydrolysis ; Models, Biological ; Nucleoproteins/metabolism ; Nucleosomes/metabolism ; Protein Binding ; Protein Multimerization ; Rad51 Recombinase/metabolism
Chemical Substances	Histones ; Nucleoproteins ; Nucleosomes ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; Rad51 Recombinase (EC 2.7.7.-)
Language	English
Publishing date	2016-10-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
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/gkw920
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Article ; Online: Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution.

Senavirathne, Gayan / Bertram, Jeffrey G / Jaszczur, Malgorzata / Chaurasiya, Kathy R / Pham, Phuong / Mak, Chi H / Goodman, Myron F / Rueda, David

Nature communications

2015 Volume 6, Page(s) 10209

Abstract: Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. ... ...

Abstract	Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of stalled bubbles. AID scans randomly when constrained in an 8 nt model bubble. When unconstrained on single-stranded (ss) DNA, AID moves in random bidirectional short slides/hops over the entire molecule while remaining bound for ∼ 5 min. Our analysis distinguishes dynamic scanning from static ssDNA creasing. That AID alone can track along with RNAP during transcription and scan within stalled transcription bubbles suggests a mechanism by which AID can initiate SHM and CSR when properly regulated, yet when unregulated can access non-Ig genes and cause cancer.
MeSH term(s)	Animals ; Antibody Diversity/genetics ; Antibody Diversity/immunology ; B-Lymphocytes/immunology ; B-Lymphocytes/metabolism ; Cytidine Deaminase/immunology ; Cytidine Deaminase/metabolism ; DNA/metabolism ; DNA, Single-Stranded/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli ; Fluorescence Resonance Energy Transfer ; Immunoglobulin Class Switching/genetics ; Immunoglobulin Class Switching/immunology ; Sf9 Cells ; Somatic Hypermutation, Immunoglobulin/genetics ; Somatic Hypermutation, Immunoglobulin/immunology ; Spodoptera ; Transcription, Genetic/genetics ; Transcription, Genetic/immunology ; Viral Proteins/metabolism
Chemical Substances	DNA, Single-Stranded ; Viral Proteins ; DNA (9007-49-2) ; bacteriophage T7 RNA polymerase (EC 2.7.7.-) ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; AICDA (activation-induced cytidine deaminase) (EC 3.5.4.-) ; Cytidine Deaminase (EC 3.5.4.5)
Language	English
Publishing date	2015-12-18
Publishing country	England
Document type	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	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/ncomms10209
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