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Article ; Online: Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells.

Pollpeter, Darja / Sobala, Andrew / Malim, Michael H

Journal of visualized experiments : JoVE

2019 , Issue 143

Abstract: Monitoring of nucleic acid intermediates during virus replication provides insights into the effects and mechanisms of action of antiviral compounds and host cell proteins on viral DNA synthesis. Here we address the lack of a cell-based, high-coverage, ... ...

Abstract	Monitoring of nucleic acid intermediates during virus replication provides insights into the effects and mechanisms of action of antiviral compounds and host cell proteins on viral DNA synthesis. Here we address the lack of a cell-based, high-coverage, and high-resolution assay that is capable of defining retroviral reverse transcription intermediates within the physiological context of virus infection. The described method captures the 3'-termini of nascent complementary DNA (cDNA) molecules within HIV-1 infected cells at single nucleotide resolution. The protocol involves harvesting of whole cell DNA, targeted enrichment of viral DNA via hybrid capture, adaptor ligation, size fractionation by gel purification, PCR amplification, deep sequencing, and data analysis. A key step is the efficient and unbiased ligation of adaptor molecules to open 3'-DNA termini. Application of the described method determines the abundance of reverse transcripts of each particular length in a given sample. It also provides information about the (internal) sequence variation in reverse transcripts and thereby any potential mutations. In general, the assay is suitable for any questions relating to DNA 3'-extension, provided that the template sequence is known.
MeSH term(s)	DNA, Viral/genetics ; HEK293 Cells ; HIV Infections/virology ; HIV-1/genetics ; Humans ; Oligonucleotides/metabolism ; Reverse Transcription/genetics ; Virus Replication/genetics
Chemical Substances	DNA, Viral ; Oligonucleotides
Language	English
Publishing date	2019-01-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/58715
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Author Correction: MX2-mediated innate immunity against HIV-1 is regulated by serine phosphorylation.

Betancor, Gilberto / Jimenez-Guardeño, Jose M / Lynham, Steven / Antrobus, Robin / Khan, Hataf / Sobala, Andrew / Dicks, Matthew D J / Malim, Michael H

Nature microbiology

2021 Volume 6, Issue 9, Page(s) 1211

Language	English
Publishing date	2021-08-13
Publishing country	England
Document type	Published Erratum
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-021-00960-6
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Article ; Online: MX2-mediated innate immunity against HIV-1 is regulated by serine phosphorylation.

Betancor, Gilberto / Jimenez-Guardeño, Jose M / Lynham, Steven / Antrobus, Robin / Khan, Hataf / Sobala, Andrew / Dicks, Matthew D J / Malim, Michael H

Nature microbiology

2021 Volume 6, Issue 8, Page(s) 1031–1042

Abstract: The antiviral cytokine interferon activates expression of interferon-stimulated genes to establish an antiviral state. Myxovirus resistance 2 (MX2, also known as MxB) is an interferon-stimulated gene that inhibits the nuclear import of HIV-1 and ... ...

Abstract	The antiviral cytokine interferon activates expression of interferon-stimulated genes to establish an antiviral state. Myxovirus resistance 2 (MX2, also known as MxB) is an interferon-stimulated gene that inhibits the nuclear import of HIV-1 and interacts with the viral capsid and cellular nuclear transport machinery. Here, we identified the myosin light chain phosphatase (MLCP) subunits myosin phosphatase target subunit 1 (MYPT1) and protein phosphatase 1 catalytic subunit-β (PPP1CB) as positively-acting regulators of MX2, interacting with its amino-terminal domain. We demonstrated that serine phosphorylation of the N-terminal domain at positions 14, 17 and 18 suppresses MX2 antiviral function, prevents interactions with the HIV-1 capsid and nuclear transport factors, and is reversed by MLCP. Notably, serine phosphorylation of the N-terminal domain also impedes MX2-mediated inhibition of nuclear import of cellular karyophilic cargo. We also found that interferon treatment reduces levels of phosphorylation at these serine residues and outline a homeostatic regulatory mechanism in which repression of MX2 by phosphorylation, together with MLCP-mediated dephosphorylation, balances the deleterious effects of MX2 on normal cell function with innate immunity against HIV-1.
MeSH term(s)	Amino Acid Motifs ; HIV Infections/genetics ; HIV Infections/immunology ; HIV Infections/virology ; HIV-1/genetics ; HIV-1/immunology ; HIV-1/physiology ; HeLa Cells ; Humans ; Immunity, Innate ; Myosin-Light-Chain Phosphatase/genetics ; Myosin-Light-Chain Phosphatase/immunology ; Myosin-Light-Chain Phosphatase/metabolism ; Myxovirus Resistance Proteins/chemistry ; Myxovirus Resistance Proteins/genetics ; Myxovirus Resistance Proteins/immunology ; Phosphorylation ; Protein Domains ; Protein Phosphatase 1/genetics ; Protein Phosphatase 1/immunology ; Serine/metabolism
Chemical Substances	MX2 protein, human ; Myxovirus Resistance Proteins ; Serine (452VLY9402) ; PPP1CB protein, human (EC 3.1.3.16) ; Protein Phosphatase 1 (EC 3.1.3.16) ; Myosin-Light-Chain Phosphatase (EC 3.1.3.53) ; PPP1R12A protein, human (EC 3.1.3.53)
Language	English
Publishing date	2021-07-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-021-00937-5
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Article ; Online: Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells.

Sobala, Andrew / Hutvagner, Gyorgy

RNA biology

2013 Volume 10, Issue 4, Page(s) 553–563

Abstract: Recently, it has been shown that tRNA molecules can be processed into small RNAs that are derived from both the 5' and 3' termini. To date, the function of these tRNA fragments (tRFs) derived from the 5' end of tRNA has not been investigated in depth. We ...

Abstract	Recently, it has been shown that tRNA molecules can be processed into small RNAs that are derived from both the 5' and 3' termini. To date, the function of these tRNA fragments (tRFs) derived from the 5' end of tRNA has not been investigated in depth. We present evidence that conserved residues in tRNA, present in all 5' tRFs, can inhibit the process of protein translation without the need for complementary target sites in the mRNA. These results implicate 5' tRFs in a new mechanism of gene regulation by small RNAs in human cells.
MeSH term(s)	Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; Gene Expression Regulation ; Genes, Reporter ; HeLa Cells ; Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Protein Biosynthesis ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Small Untranslated/chemistry ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/metabolism ; RNA, Transfer/chemistry ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Transfection
Chemical Substances	Argonaute Proteins ; MicroRNAs ; RNA, Messenger ; RNA, Small Untranslated ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2013-04-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1555-8584
ISSN (online)	1555-8584
DOI	10.4161/rna.24285
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Article: Determining 3'-termini and sequences of nascent single-stranded viral dna molecules during hiv-1 reverse transcription in infected cells

Pollpeter, Darja / Sobala, Andrew / Malim, Michael H

Journal of visualized experiments. 2019 Jan. 30, , no. 143

2019

Abstract	Monitoring of nucleic acid intermediates during virus replication provides insights into the effects and mechanisms of action of antiviral compounds and host cell proteins on viral DNA synthesis. Here we address the lack of a cell-based, high-coverage, and high-resolution assay that is capable of defining retroviral reverse transcription intermediates within the physiological context of virus infection. The described method captures the 3'-termini of nascent complementary DNA (cDNA) molecules within HIV-1 infected cells at single nucleotide resolution. The protocol involves harvesting of whole cell DNA, targeted enrichment of viral DNA via hybrid capture, adaptor ligation, size fractionation by gel purification, PCR amplification, deep sequencing, and data analysis. A key step is the efficient and unbiased ligation of adaptor molecules to open 3'-DNA termini. Application of the described method determines the abundance of reverse transcripts of each particular length in a given sample. It also provides information about the (internal) sequence variation in reverse transcripts and thereby any potential mutations. In general, the assay is suitable for any questions relating to DNA 3'-extension, provided that the template sequence is known.
Keywords	DNA replication ; HIV infections ; Human immunodeficiency virus 1 ; antiviral agents ; complementary DNA ; fractionation ; gels ; harvesting ; high-throughput nucleotide sequencing ; hybrid capture methods ; mechanism of action ; messenger RNA ; monitoring ; mutation ; polymerase chain reaction ; proteins ; reverse transcription ; sequence diversity ; virus replication ; viruses
Language	English
Dates of publication	2019-0130
Size	p. e58715.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/58715
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Article ; Online: tRNA-Derived RNA Fragments Associate with Human Multisynthetase Complex (MSC) and Modulate Ribosomal Protein Translation.

Keam, Simon P / Sobala, Andrew / Ten Have, Sara / Hutvagner, Gyorgy

Journal of proteome research

2017 Volume 16, Issue 2, Page(s) 413–420

Abstract: The functionality of small RNAs from abundant species of "housekeeping" noncoding RNAs (e.g., rRNA, tRNA, snRNA, snoRNA, etc.) remains a highly studied topic. The current state of research on short RNAs derived from transfer RNA (tRNA), called tRNA- ... ...

Abstract	The functionality of small RNAs from abundant species of "housekeeping" noncoding RNAs (e.g., rRNA, tRNA, snRNA, snoRNA, etc.) remains a highly studied topic. The current state of research on short RNAs derived from transfer RNA (tRNA), called tRNA-derived fragments (tRFs), has been restricted largely to expression studies and limited functional studies. 5' tRFs are known translational inhibitors in mammalian cells, yet little is known about their functionality. Here we report on the first experimental evidence of the tRF protein interactome, identifying the mammalian multisynthetase complex as the primary interactor of the 5' tRF Gln19. We also present proteome-wide SILAC evidence that 5' tRFs increase ribosomal and poly(A)-binding protein translation.
MeSH term(s)	Base Sequence ; Computational Biology ; Immunoprecipitation ; Isotope Labeling ; Ligases/genetics ; Ligases/metabolism ; Multienzyme Complexes/genetics ; Multienzyme Complexes/metabolism ; Poly A/genetics ; Poly A/metabolism ; Protein Biosynthesis ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism
Chemical Substances	Multienzyme Complexes ; RNA, Untranslated ; RNA-Binding Proteins ; Poly A (24937-83-5) ; RNA, Transfer (9014-25-9) ; Ligases (EC 6.-)
Language	English
Publishing date	2017-02-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.6b00267
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Article ; Online: Transfer RNA-derived fragments: origins, processing, and functions.

Sobala, Andrew / Hutvagner, Gyorgy

Wiley interdisciplinary reviews. RNA

2011 Volume 2, Issue 6, Page(s) 853–862

Abstract: Deep sequencing approaches have revealed multiple types of small RNAs with known and unknown functions. In this review we focus on a recently identified group of small RNAs that are derived from transfer RNAs (tRNAs), tRNA fragments (tRFs). We review the ...

Abstract	Deep sequencing approaches have revealed multiple types of small RNAs with known and unknown functions. In this review we focus on a recently identified group of small RNAs that are derived from transfer RNAs (tRNAs), tRNA fragments (tRFs). We review the mechanism of their processing and their functions in mammalian cells, and highlight points of possible cross-talk between tRFs and the canonical small RNA pathway characterized by small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi-interacting RNAs (piRNAs). We also propose a nomenclature that is based on their processing characteristics.
MeSH term(s)	Animals ; Argonaute Proteins/metabolism ; Humans ; MicroRNAs/metabolism ; Models, Biological ; RNA Processing, Post-Transcriptional ; RNA, Small Interfering/metabolism ; RNA, Small Untranslated/metabolism ; RNA, Transfer/metabolism
Chemical Substances	Argonaute Proteins ; MicroRNAs ; RNA, Small Interfering ; RNA, Small Untranslated ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2011-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2634714-3
ISSN	1757-7012 ; 1757-7004
ISSN (online)	1757-7012
ISSN	1757-7004
DOI	10.1002/wrna.96
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Article ; Online: Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host-glycosylation target.

Sobala, Łukasz F / Fernandes, Pearl Z / Hakki, Zalihe / Thompson, Andrew J / Howe, Jonathon D / Hill, Michelle / Zitzmann, Nicole / Davies, Scott / Stamataki, Zania / Butters, Terry D / Alonzi, Dominic S / Williams, Spencer J / Davies, Gideon J

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 47, Page(s) 29595–29601

Abstract: Mammalian protein N-linked glycosylation is critical for glycoprotein folding, quality control, trafficking, recognition, and function. N-linked glycans are synthesized from ... ...

Abstract	Mammalian protein N-linked glycosylation is critical for glycoprotein folding, quality control, trafficking, recognition, and function. N-linked glycans are synthesized from Glc
MeSH term(s)	Animals ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Bovine Virus Diarrhea-Mucosal Disease/drug therapy ; Cattle ; Cell Line ; Dengue Virus/drug effects ; Dogs ; Glucosidases/metabolism ; Glycosylation/drug effects ; Humans ; Madin Darby Canine Kidney Cells ; Mannosidases/chemistry ; Mannosidases/pharmacology ; Polysaccharides/metabolism ; Secretory Pathway/drug effects
Chemical Substances	Antiviral Agents ; Polysaccharides ; Glucosidases (EC 3.2.1.-) ; Mannosidases (EC 3.2.1.-)
Language	English
Publishing date	2020-11-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2013620117
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Article: An Epoxide Intermediate in Glycosidase Catalysis.

ACS central science

2020 Volume 6, Issue 5, Page(s) 760–770

Abstract: Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or ... ...

Abstract	Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or neighboring-group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational, and kinetic evidence for neighboring-group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99
Language	English
Publishing date	2020-04-16
Publishing country	United States
Document type	Journal Article
ISSN	2374-7943
ISSN	2374-7943
DOI	10.1021/acscentsci.0c00111
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Article ; Online: Four exons of the serotonin receptor 4 gene are associated with multiple distant branch points.

Hallegger, Martina / Sobala, Andrew / Smith, Christopher W J

RNA (New York, N.Y.)

2010 Volume 16, Issue 4, Page(s) 839–851

Abstract: Splicing of vertebrate introns involves recognition of three consensus elements at the 3' end. The branch point (BP) and polypyrimidine tract (PPT) are usually located within 40 nucleotides (nt) of the 3' splice site (3' ss), AG, but can be much more ... ...

Abstract	Splicing of vertebrate introns involves recognition of three consensus elements at the 3' end. The branch point (BP) and polypyrimidine tract (PPT) are usually located within 40 nucleotides (nt) of the 3' splice site (3' ss), AG, but can be much more distant. A characteristic of the region between distant BPs (dBPs) and the 3' ss is the absence of intervening AG dinucleotides, leading to its designation as the "AG exclusion zone" (AGEZ). The human HTR4 gene, which encodes serotonin receptor 4 and has been associated with schizophrenia, bipolar disease, and gastrointestinal disorders, has four exons with extensive AGEZs. We have mapped the BPs for HTR4 exons 3, 4, 5, and g generated by in vitro splicing, and validated them by mutagenesis in exon-trapping vectors. All exons used dBPs up to 273 nt upstream of the exon. Strikingly, exons 4 and 5 used combinations of both distant and conventionally located BPs, suggesting that successful splicing of these exons can occur by distinct pathways. Our results emphasize the importance for single nucleotide polymorphism resequencing projects to take account of potential dBPs, as the extended AGEZs are vulnerable to mutations that could affect splicing itself or regulation of alternative splicing.
MeSH term(s)	Base Sequence ; Conserved Sequence ; Exons/genetics ; HeLa Cells ; Humans ; Molecular Sequence Data ; Polymorphism, Single Nucleotide ; RNA Splicing ; Receptors, Serotonin, 5-HT4/genetics ; Receptors, Serotonin, 5-HT4/metabolism
Chemical Substances	Receptors, Serotonin, 5-HT4 (158165-40-3)
Language	English
Publishing date	2010-03-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.2013110
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