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Article ; Online: In silico protein interaction screening uncovers DONSON's role in replication initiation.

Lim, Yang / Tamayo-Orrego, Lukas / Schmid, Ernst / Tarnauskaite, Zygimante / Kochenova, Olga V / Gruar, Rhian / Muramatsu, Sachiko / Lynch, Luke / Schlie, Aitana Verdu / Carroll, Paula L / Chistol, Gheorghe / Reijns, Martin A M / Kanemaki, Masato T / Jackson, Andrew P / Walter, Johannes C

Science (New York, N.Y.)

2023 Volume 381, Issue 6664, Page(s) eadi3448

Abstract: CDC45-MCM2-7-GINS (CMG) helicase assembly is the central event in eukaryotic replication initiation. In yeast, a multi-subunit "pre-loading complex" (pre-LC) accompanies GINS to chromatin-bound MCM2-7, leading to CMG formation. Here, we report that ... ...

Abstract	CDC45-MCM2-7-GINS (CMG) helicase assembly is the central event in eukaryotic replication initiation. In yeast, a multi-subunit "pre-loading complex" (pre-LC) accompanies GINS to chromatin-bound MCM2-7, leading to CMG formation. Here, we report that DONSON, a metazoan protein mutated in microcephalic primordial dwarfism, is required for CMG assembly in vertebrates. Using AlphaFold to screen for protein-protein interactions followed by experimental validation, we show that DONSON scaffolds a vertebrate pre-LC containing GINS, TOPBP1, and DNA pol ε. Our evidence suggests that DONSON docks the pre-LC onto MCM2-7, delivering GINS to its binding site in CMG. A patient-derived DONSON mutation compromises CMG assembly and recapitulates microcephalic dwarfism in mice. These results unify our understanding of eukaryotic replication initiation, implicate defective CMG assembly in microcephalic dwarfism, and illustrate how in silico protein-protein interaction screening accelerates mechanistic discovery.
MeSH term(s)	Animals ; Humans ; Mice ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; DNA Replication ; DNA-Binding Proteins/metabolism ; Minichromosome Maintenance Proteins/genetics ; Minichromosome Maintenance Proteins/metabolism ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins ; Protein Interaction Mapping/methods ; Computer Simulation ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Dwarfism/genetics ; Microcephaly/genetics ; Xenopus laevis
Chemical Substances	Cell Cycle Proteins ; DNA-Binding Proteins ; Minichromosome Maintenance Proteins (EC 3.6.4.12) ; Saccharomyces cerevisiae Proteins ; Nuclear Proteins ; DONSON protein, human
Language	English
Publishing date	2023-09-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.adi3448
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Article ; Online: User acceptability of saliva and gargle samples for identifying COVID-19 positive high-risk workers and household contacts.

McLennan, Kirsty / Barton, Ellen / Lang, Christie / Adams, Ian R / McAllister, Gina / Reijns, Martin A M / Templeton, Kate / Johannessen, Ingólfur / Leckie, Alastair / Gilbert, Nick

Diagnostic microbiology and infectious disease

2022 Volume 104, Issue 1, Page(s) 115732

Abstract: Throughout the COVID-19 pandemic nasopharyngeal or nose and/or throat swabs (NTS) have been the primary approach for collecting patient samples for the subsequent detection of viral RNA. However, this procedure, if undertaken correctly, can be unpleasant ...

Abstract	Throughout the COVID-19 pandemic nasopharyngeal or nose and/or throat swabs (NTS) have been the primary approach for collecting patient samples for the subsequent detection of viral RNA. However, this procedure, if undertaken correctly, can be unpleasant and therefore deters individuals from providing high quality samples. To overcome these limitations other modes of sample collection have been explored. In a cohort of frontline health care workers we have compared saliva and gargle samples to gold-standard NTS. 93% of individuals preferred providing saliva or gargle samples, with little sex-dependent variation. Viral titers collected in samples were analyzed using standard methods and showed that gargle and saliva were similarly comparable for identifying COVID-19 positive individuals compared to NTS (92% sensitivity; 98% specificity). We suggest that gargle and saliva collection are viable alternatives to NTS swabs and may encourage testing to provide better disease diagnosis and population surveillance.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing ; Humans ; Mouthwashes ; Nasopharynx ; Pandemics ; RNA, Viral/genetics ; SARS-CoV-2 ; Saliva ; Specimen Handling/methods
Chemical Substances	Mouthwashes ; RNA, Viral
Language	English
Publishing date	2022-05-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2022.115732
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Article ; Online: Ribonuclease H2 in health and disease.

Reijns, Martin A M / Jackson, Andrew P

Biochemical Society transactions

2014 Volume 42, Issue 4, Page(s) 717–725

Abstract: Innate immune sensing of nucleic acids provides resistance against viral infection and is important in the aetiology of autoimmune diseases. AGS (Aicardi-Goutières syndrome) is a monogenic autoinflammatory disorder mimicking in utero viral infection of ... ...

Abstract	Innate immune sensing of nucleic acids provides resistance against viral infection and is important in the aetiology of autoimmune diseases. AGS (Aicardi-Goutières syndrome) is a monogenic autoinflammatory disorder mimicking in utero viral infection of the brain. Phenotypically and immunologically, it also exhibits similarities to SLE (systemic lupus erythaematosus). Three of the six genes identified to date encode components of the ribonuclease H2 complex. As all six encode enzymes involved in nucleic acid metabolism, it is thought that pathogenesis involves the accumulation of nucleic acids to stimulate an inappropriate innate immune response. Given that AGS is a monogenic disorder with a defined molecular basis, we use it as a model for common autoimmune disease to investigate cellular processes and molecular pathways responsible for nucleic-acid-mediated autoimmunity. These investigations have also provided fundamental insights into the biological roles of the RNase H2 endonuclease enzyme. In the present article, we describe how human RNase H2 and its role in AGS were first identified, and give an overview of subsequent structural, biochemical, cellular and developmental studies of this enzyme. These investigations have culminated in establishing this enzyme as a key genome-surveillance enzyme required for mammalian genome stability.
MeSH term(s)	Autoimmune Diseases of the Nervous System/enzymology ; Autoimmune Diseases of the Nervous System/genetics ; Autoimmune Diseases of the Nervous System/metabolism ; Genomic Instability/genetics ; Genomic Instability/physiology ; Humans ; Inflammation/enzymology ; Inflammation/genetics ; Inflammation/metabolism ; Nervous System Malformations/enzymology ; Nervous System Malformations/genetics ; Nervous System Malformations/metabolism ; Ribonuclease H/genetics ; Ribonuclease H/metabolism
Chemical Substances	ribonuclease HII (EC 3.1.26.-) ; Ribonuclease H (EC 3.1.26.4)
Language	English
Publishing date	2014-07-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20140079
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Article ; Online: Genome-wide mapping of embedded ribonucleotides and other noncanonical nucleotides using emRiboSeq and EndoSeq.

Ding, James / Taylor, Martin S / Jackson, Andrew P / Reijns, Martin A M

Nature protocols

2015 Volume 10, Issue 9, Page(s) 1433–1444

Abstract: Ribonucleotides are the most common noncanonical nucleotides incorporated into the genome of replicating cells. They are efficiently removed by ribonucleotide excision repair initiated by RNase H2 cleavage. In the absence of RNase H2, such embedded ... ...

Abstract	Ribonucleotides are the most common noncanonical nucleotides incorporated into the genome of replicating cells. They are efficiently removed by ribonucleotide excision repair initiated by RNase H2 cleavage. In the absence of RNase H2, such embedded ribonucleotides can be used to track DNA polymerase activity in vivo. To determine their precise location in Saccharomyces cerevisiae, we developed embedded ribonucleotide sequencing (emRiboSeq), which uses recombinant RNase H2 to selectively create ligatable 3'-hydroxyl groups, in contrast to alternative methods that use alkaline hydrolysis. EmRiboSeq allows reproducible, strand-specific and potentially quantitative detection of embedded ribonucleotides at single-nucleotide resolution. For the genome-wide mapping of other noncanonical bases, RNase H2 can be replaced with specific nicking endonucleases in this protocol; we term this method endonuclease sequencing (EndoSeq). With the protocol taking <5 d to complete, these methods allow the in vivo study of DNA replication and repair, including the identification of replication origins and termination regions.
MeSH term(s)	Chromosome Mapping ; Genomics/methods ; Ribonuclease H/metabolism ; Saccharomyces cerevisiae ; Sequence Analysis/methods
Chemical Substances	ribonuclease HII (EC 3.1.26.-) ; Ribonuclease H (EC 3.1.26.4)
Language	English
Publishing date	2015-08-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/nprot.2015.099
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Article ; Online: Novel Escherichia coli active site dnaE alleles with altered base and sugar selectivity.

Vaisman, Alexandra / Łazowski, Krystian / Reijns, Martin A M / Walsh, Erin / McDonald, John P / Moreno, Kristiniana C / Quiros, Dominic R / Schmidt, Marlen / Kranz, Harald / Yang, Wei / Makiela-Dzbenska, Karolina / Woodgate, Roger

Molecular microbiology

2021 Volume 116, Issue 3, Page(s) 909–925

Abstract: The Escherichia coli dnaE gene encodes the α-catalytic subunit (pol IIIα) of DNA polymerase III, the cell's main replicase. Like all high-fidelity DNA polymerases, pol III possesses stringent base and sugar discrimination. The latter is mediated by a so- ... ...

Abstract	The Escherichia coli dnaE gene encodes the α-catalytic subunit (pol IIIα) of DNA polymerase III, the cell's main replicase. Like all high-fidelity DNA polymerases, pol III possesses stringent base and sugar discrimination. The latter is mediated by a so-called "steric gate" residue in the active site of the polymerase that physically clashes with the 2'-OH of an incoming ribonucleotide. Our structural modeling data suggest that H760 is the steric gate residue in E.coli pol IIIα. To understand how H760 and the adjacent S759 residue help maintain genome stability, we generated DNA fragments in which the codons for H760 or S759 were systematically changed to the other nineteen naturally occurring amino acids and attempted to clone them into a plasmid expressing pol III core (α-θ-ε subunits). Of the possible 38 mutants, only nine were successfully sub-cloned: three with substitutions at H760 and 6 with substitutions at S759. Three of the plasmid-encoded alleles, S759C, S759N, and S759T, exhibited mild to moderate mutator activity and were moved onto the chromosome for further characterization. These studies revealed altered phenotypes regarding deoxyribonucleotide base selectivity and ribonucleotide discrimination. We believe that these are the first dnaE mutants with such phenotypes to be reported in the literature.
MeSH term(s)	Alleles ; Amino Acid Substitution ; Catalytic Domain ; DNA/chemistry ; DNA/metabolism ; DNA Mismatch Repair ; DNA Polymerase III/chemistry ; DNA Polymerase III/genetics ; DNA Polymerase III/metabolism ; DNA Replication ; Deoxyribonucleotides/chemistry ; Escherichia coli/chemistry ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Genomic Instability ; Models, Molecular ; Mutation ; Phenotype ; Ribonucleotides/chemistry
Chemical Substances	Deoxyribonucleotides ; Escherichia coli Proteins ; Ribonucleotides ; DNA (9007-49-2) ; DNA polymerase III, alpha subunit (EC 2.7.7.-) ; DNA Polymerase III (EC 2.7.7.7)
Language	English
Publishing date	2021-07-31
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/mmi.14779
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Article ; Online: User acceptability of saliva and gargle samples for identifying COVID-19 positive high-risk workers

McLennan, Kirsty / Barton, Ellen / Lang, Christie / Adams, Ian R / McAllister, Gina / Reijns, Martin / Templeton, Kate / Johannessen, Ingolfur / Leckie, Alastair / Gilbert, Nick

medRxiv

Abstract: Throughout the COVID-19 pandemic nasopharyngeal or nose/throat swabs (NTS) have been the primary approach for collecting patient samples for the subsequent detection of viral RNA. However, this procedure, if undertaken correctly, can be unpleasant and ... ...

Abstract	Throughout the COVID-19 pandemic nasopharyngeal or nose/throat swabs (NTS) have been the primary approach for collecting patient samples for the subsequent detection of viral RNA. However, this procedure, if undertaken correctly, can be unpleasant and therefore deters individuals from providing high quality samples. To overcome these limitations other modes of sample collection have been explored. In a cohort of frontline healthcare workers we have compared saliva and gargle samples to gold-standard NTS. 93% of individuals preferred providing saliva or gargle samples, with little sex-dependent variation. Viral titres collected in samples were analysed using standard methods and showed that gargle and saliva were similarly comparable for identifying COVID-19 positive individuals compared to NTS (92% sensitivity; 98% specificity). We suggest that gargle and saliva collection are viable alternatives to NTS swabs and may encourage testing to provide better disease diagnosis and population surveillance.
Keywords	covid19
Language	English
Publishing date	2022-01-30
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2022.01.28.22270033
Database	COVID19

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Article ; Online: DNA damage contributes to neurotoxic inflammation in Aicardi-Goutières syndrome astrocytes.

Giordano, Anna Maria Sole / Luciani, Marco / Gatto, Francesca / Abou Alezz, Monah / Beghè, Chiara / Della Volpe, Lucrezia / Migliara, Alessandro / Valsoni, Sara / Genua, Marco / Dzieciatkowska, Monika / Frati, Giacomo / Tahraoui-Bories, Julie / Giliani, Silvia Clara / Orcesi, Simona / Fazzi, Elisa / Ostuni, Renato / D'Alessandro, Angelo / Di Micco, Raffaella / Merelli, Ivan /

Lombardo, Angelo / Reijns, Martin A M / Gromak, Natalia / Gritti, Angela / Kajaste-Rudnitski, Anna

The Journal of experimental medicine

2022 Volume 219, Issue 4

Abstract: Aberrant induction of type I IFN is a hallmark of the inherited encephalopathy Aicardi-Goutières syndrome (AGS), but the mechanisms triggering disease in the human central nervous system (CNS) remain elusive. Here, we generated human models of AGS using ... ...

Abstract	Aberrant induction of type I IFN is a hallmark of the inherited encephalopathy Aicardi-Goutières syndrome (AGS), but the mechanisms triggering disease in the human central nervous system (CNS) remain elusive. Here, we generated human models of AGS using genetically modified and patient-derived pluripotent stem cells harboring TREX1 or RNASEH2B loss-of-function alleles. Genome-wide transcriptomic analysis reveals that spontaneous proinflammatory activation in AGS astrocytes initiates signaling cascades impacting multiple CNS cell subsets analyzed at the single-cell level. We identify accumulating DNA damage, with elevated R-loop and micronuclei formation, as a driver of STING- and NLRP3-related inflammatory responses leading to the secretion of neurotoxic mediators. Importantly, pharmacological inhibition of proapoptotic or inflammatory cascades in AGS astrocytes prevents neurotoxicity without apparent impact on their increased type I IFN responses. Together, our work identifies DNA damage as a major driver of neurotoxic inflammation in AGS astrocytes, suggests a role for AGS gene products in R-loop homeostasis, and identifies common denominators of disease that can be targeted to prevent astrocyte-mediated neurotoxicity in AGS.
MeSH term(s)	Astrocytes/metabolism ; Autoimmune Diseases of the Nervous System/genetics ; DNA Damage ; Humans ; Inflammation/genetics ; Inflammation/metabolism ; Nervous System Malformations/genetics
Language	English
Publishing date	2022-03-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218343-2
ISSN	1540-9538 ; 0022-1007
ISSN (online)	1540-9538
ISSN	0022-1007
DOI	10.1084/jem.20211121
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Article ; Online: Publisher Correction: Signatures of TOP1 transcription-associated mutagenesis in cancer and germline.

Nature

2022 Volume 605, Issue 7910, Page(s) E7

Language	English
Publishing date	2022-05-01
Publishing country	England
Document type	Published Erratum
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-022-04812-z
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Article ; Online: Signatures of TOP1 transcription-associated mutagenesis in cancer and germline.

Nature

2022 Volume 602, Issue 7898, Page(s) 623–631

Abstract: The mutational landscape is shaped by many processes. Genic regions are vulnerable to mutation but are preferentially protected by transcription-coupled ... ...

Abstract	The mutational landscape is shaped by many processes. Genic regions are vulnerable to mutation but are preferentially protected by transcription-coupled repair
MeSH term(s)	Animals ; DNA Repair/genetics ; DNA Topoisomerases, Type I/metabolism ; Germ Cells/metabolism ; Humans ; Mutagenesis/genetics ; Mutation ; Neoplasms/genetics ; Ribonucleotides/genetics
Chemical Substances	Ribonucleotides ; DNA Topoisomerases, Type I (EC 5.99.1.2) ; TOP1 protein, human (EC 5.99.1.2)
Language	English
Publishing date	2022-02-09
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-022-04403-y
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Article ; Online: Analysis of Lsm1p and Lsm8p domains in the cellular localization of Lsm complexes in budding yeast.

Reijns, Martin A M / Auchynnikava, Tatsiana / Beggs, Jean D

The FEBS journal

2009 Volume 276, Issue 13, Page(s) 3602–3617

Abstract: In eukaryotes, two heteroheptameric Sm-like (Lsm) complexes that differ by a single subunit localize to different cellular compartments and have distinct functions in RNA metabolism. The cytoplasmic Lsm1-7p complex promotes mRNA decapping and localizes ... ...

Abstract	In eukaryotes, two heteroheptameric Sm-like (Lsm) complexes that differ by a single subunit localize to different cellular compartments and have distinct functions in RNA metabolism. The cytoplasmic Lsm1-7p complex promotes mRNA decapping and localizes to processing bodies, whereas the Lsm2-8p complex takes part in a variety of nuclear RNA processing events. The structural features that determine their different functions and localizations are not known. Here, we analyse a range of mutant and hybrid Lsm1 and Lsm8 proteins, shedding light on the relative importance of their various domains in determining their localization and ability to support growth. Although no single domain is either essential or sufficient for cellular localization, the Lsm1p N-terminus may act as part of a nuclear exclusion signal for Lsm1-7p, and the shorter Lsm8p N-terminus contributes to nuclear accumulation of Lsm2-8p. The C-terminal regions seem to play a secondary role in determining localization, with little or no contribution coming from the central Sm domains. The essential Lsm8 protein is remarkably resistant to mutation in terms of supporting viability, whereas Lsm1p appears more sensitive. These findings contribute to our understanding of how two very similar protein complexes can have different properties.
MeSH term(s)	Amino Acid Sequence ; Cell Survival ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Structure, Tertiary ; RNA Cap-Binding Proteins/genetics ; RNA Cap-Binding Proteins/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Small Nuclear/genetics ; RNA, Small Nuclear/metabolism ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Ribonucleoproteins, Small Nuclear/genetics ; Ribonucleoproteins, Small Nuclear/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Alignment
Chemical Substances	LSM1 protein, S cerevisiae ; Lsm8 protein, S cerevisiae ; RNA Cap-Binding Proteins ; RNA, Messenger ; RNA, Small Nuclear ; Recombinant Fusion Proteins ; Ribonucleoproteins, Small Nuclear ; Saccharomyces cerevisiae Proteins ; U6 small nuclear RNA
Language	English
Publishing date	2009-05-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/j.1742-4658.2009.07080.x
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