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Article: Yeast goes viral: probing SARS-CoV-2 biology using

Ho, Brandon / Loll-Krippleber, Raphael / Brown, Grant W

2022 Volume 9, Issue 4, Page(s) 80–83

Abstract: The budding ... ...

Abstract	The budding yeast
Language	English
Publishing date	2022-03-21
Publishing country	Austria
Document type	Journal Article ; Comment
ZDB-ID	2814756-X
ISSN	2311-2638
ISSN	2311-2638
DOI	10.15698/mic2022.04.774
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Article ; Online: Genetic screens in Saccharomyces cerevisiae identify a role for 40S ribosome recycling factors Tma20 and Tma22 in nonsense-mediated decay.

Pacheco, Miguel / D'Orazio, Karole N / Lessen, Laura N / Veltri, Anthony J / Neiman, Zachary / Loll-Krippleber, Raphael / Brown, Grant W / Green, Rachel

G3 (Bethesda, Md.)

2024 Volume 14, Issue 3

Abstract: The decay of messenger RNA with a premature termination codon by nonsense-mediated decay (NMD) is an important regulatory pathway for eukaryotes and an essential pathway in mammals. NMD is typically triggered by the ribosome terminating at a stop codon ... ...

Abstract	The decay of messenger RNA with a premature termination codon by nonsense-mediated decay (NMD) is an important regulatory pathway for eukaryotes and an essential pathway in mammals. NMD is typically triggered by the ribosome terminating at a stop codon that is aberrantly distant from the poly-A tail. Here, we use a fluorescence screen to identify factors involved in NMD in Saccharomyces cerevisiae. In addition to the known NMD factors, including the entire UPF family (UPF1, UPF2, and UPF3), as well as NMD4 and EBS1, we identify factors known to function in posttermination recycling and characterize their contribution to NMD. These observations in S. cerevisiae expand on data in mammals indicating that the 60S recycling factor ABCE1 is important for NMD by showing that perturbations in factors implicated in 40S recycling also correlate with a loss of NMD.
MeSH term(s)	Animals ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; RNA Helicases/metabolism ; Nonsense Mediated mRNA Decay ; Ribosomes/genetics ; Ribosomes/metabolism ; RNA, Messenger/genetics ; Mammals/genetics
Chemical Substances	RNA Helicases (EC 3.6.4.13) ; RNA, Messenger
Language	English
Publishing date	2024-01-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkad295
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Article ; Online: Complex mutation profiles in mismatch repair and ribonucleotide reductase mutants reveal novel repair substrate specificity of MutS homolog (MSH) complexes.

Lamb, Natalie A / Bard, Jonathan E / Loll-Krippleber, Raphael / Brown, Grant W / Surtees, Jennifer A

Genetics

2022 Volume 221, Issue 4

Abstract: Determining mutation signatures is standard for understanding the etiology of human tumors and informing cancer treatment. Multiple determinants of DNA replication fidelity prevent mutagenesis that leads to carcinogenesis, including the regulation of ... ...

Abstract	Determining mutation signatures is standard for understanding the etiology of human tumors and informing cancer treatment. Multiple determinants of DNA replication fidelity prevent mutagenesis that leads to carcinogenesis, including the regulation of free deoxyribonucleoside triphosphate pools by ribonucleotide reductase and repair of replication errors by the mismatch repair system. We identified genetic interactions between rnr1 alleles that skew and/or elevate deoxyribonucleoside triphosphate levels and mismatch repair gene deletions. These defects indicate that the rnr1 alleles lead to increased mutation loads that are normally acted upon by mismatch repair. We then utilized a targeted deep-sequencing approach to determine mutational profiles associated with mismatch repair pathway defects. By combining rnr1 and msh mutations to alter and/or increase deoxyribonucleoside triphosphate levels and alter the mutational load, we uncovered previously unreported specificities of Msh2-Msh3 and Msh2-Msh6. Msh2-Msh3 is uniquely able to direct the repair of G/C single-base deletions in GC runs, while Msh2-Msh6 specifically directs the repair of substitutions that occur at G/C dinucleotides. We also identified broader sequence contexts that influence variant profiles in different genetic backgrounds. Finally, we observed that the mutation profiles in double mutants were not necessarily an additive relationship of mutation profiles in single mutants. Our results have implications for interpreting mutation signatures from human tumors, particularly when mismatch repair is defective.
MeSH term(s)	Humans ; Deoxyribonucleosides ; DNA Mismatch Repair ; DNA Repair ; DNA-Binding Proteins/metabolism ; Mutation ; MutS Homolog 2 Protein/genetics ; MutS Homolog 2 Protein/metabolism ; MutS Proteins/genetics ; MutS Proteins/metabolism ; Ribonucleotide Reductases/genetics ; Ribonucleotide Reductases/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Substrate Specificity
Chemical Substances	Deoxyribonucleosides ; DNA-Binding Proteins ; MutS Homolog 2 Protein (EC 3.6.1.3) ; MutS Proteins (EC 3.6.1.3) ; Ribonucleotide Reductases (EC 1.17.4.-) ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2022-06-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1093/genetics/iyac092
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Article ; Online: Mec1-independent activation of the Rad53 checkpoint kinase revealed by quantitative analysis of protein localization dynamics.

Ho, Brandon / Sanford, Ethan J / Loll-Krippleber, Raphael / Torres, Nikko P / Smolka, Marcus B / Brown, Grant W

eLife

2023 Volume 12

Abstract: The replication checkpoint is essential for accurate DNA replication and repair, and maintenance of genomic integrity when a cell is challenged with genotoxic stress. Several studies have defined the complement of proteins that change subcellular ... ...

Abstract	The replication checkpoint is essential for accurate DNA replication and repair, and maintenance of genomic integrity when a cell is challenged with genotoxic stress. Several studies have defined the complement of proteins that change subcellular location in the budding yeast
MeSH term(s)	Protein Serine-Threonine Kinases/metabolism ; Cell Cycle Proteins/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Intracellular Signaling Peptides and Proteins/metabolism ; Checkpoint Kinase 2/genetics ; Checkpoint Kinase 2/metabolism ; Saccharomyces cerevisiae/metabolism ; Phosphorylation ; DNA Damage ; Methyl Methanesulfonate/pharmacology ; DNA Replication
Chemical Substances	Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Cell Cycle Proteins ; Saccharomyces cerevisiae Proteins ; Intracellular Signaling Peptides and Proteins ; Checkpoint Kinase 2 (EC 2.7.1.11) ; Methyl Methanesulfonate (AT5C31J09G)
Language	English
Publishing date	2023-06-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.82483
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Article: A conserved function of corepressors is to nucleate assembly of the transcriptional preinitiation complex.

Leydon, Alexander R / Downing, Benjamin / Sanchez, Janet Solano / Loll-Krippleber, Raphael / Belliveau, Nathan M / Rodriguez-Mias, Ricard A / Bauer, Andrew / Watson, Isabella J / Bae, Lena / Villén, Judit / Brown, Grant W / Nemhauser, Jennifer L

bioRxiv : the preprint server for biology

2024

Abstract: The plant corepressor TPL is recruited to diverse chromatin contexts, yet its mechanism of repression remains unclear. Previously, we have leveraged the fact that TPL retains its function in a synthetic transcriptional circuit in the yeast ... ...

Abstract	The plant corepressor TPL is recruited to diverse chromatin contexts, yet its mechanism of repression remains unclear. Previously, we have leveraged the fact that TPL retains its function in a synthetic transcriptional circuit in the yeast model
Language	English
Publishing date	2024-04-01
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.01.587599
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Article ; Online: Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation.

Veltri, Anthony J / D'Orazio, Karole N / Lessen, Laura N / Loll-Krippleber, Raphael / Brown, Grant W / Green, Rachel

eLife

2022 Volume 11

Abstract: Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay ( ... ...

Abstract	Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully designed reporter mRNAs to perform genetic screens and functional assays in
MeSH term(s)	Codon/metabolism ; Protein Biosynthesis ; RNA Stability/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factors/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Vesicular Transport Proteins
Chemical Substances	Codon ; Hel2 protein, S cerevisiae (EC 2.3.2.27) ; NOT5 protein, S cerevisiae ; RNA, Messenger ; Saccharomyces cerevisiae Proteins ; SMY2 protein, S cerevisiae ; Transcription Factors ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Vesicular Transport Proteins ; Myr1 protein, S cerevisiae
Language	English
Publishing date	2022-07-27
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.76038
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Article ; Online: P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance.

Loll-Krippleber, Raphael / Brown, Grant W

Nature communications

2017 Volume 8, Issue 1, Page(s) 558

Abstract: mRNA-processing (P-) bodies are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, ... ...

Abstract	mRNA-processing (P-) bodies are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment. The key P-body protein Lsm1 controls the abundance of HHT1, ACF4, ARL3, TMA16, RRS1 and YOX1 mRNAs to prevent their toxic accumulation during replication stress. Accumulation of YOX1 mRNA causes aberrant downregulation of a network of genes critical for DNA replication stress resistance and leads to toxic acetaldehyde accumulation. Our data reveal the scope and the targets of regulation by P-body proteins during the DNA replication stress response.P-bodies form in response to stress and act as sites of mRNA storage and degradation. Here the authors identify the mRNA targets of P-bodies during DNA replication stress, and show that P-body proteins act to prevent toxic accumulation of these target transcripts.
MeSH term(s)	ADP-Ribosylation Factors/genetics ; Cell Cycle Proteins/genetics ; Cytoplasmic Granules/metabolism ; DNA Replication/genetics ; Enzyme Inhibitors/pharmacology ; Gene Expression Regulation ; Homeodomain Proteins/genetics ; Hydroxyurea/pharmacology ; Nuclear Proteins/genetics ; RNA Cap-Binding Proteins/genetics ; RNA, Messenger/metabolism ; Repressor Proteins/genetics ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/genetics ; Stress, Physiological/genetics
Chemical Substances	Cell Cycle Proteins ; Enzyme Inhibitors ; Homeodomain Proteins ; LSM1 protein, S cerevisiae ; Nuclear Proteins ; RNA Cap-Binding Proteins ; RNA, Messenger ; RRS1 protein, S cerevisiae ; Repressor Proteins ; Saccharomyces cerevisiae Proteins ; Yox1 protein, S cerevisiae ; ADP-Ribosylation Factors (EC 3.6.5.2) ; ARL3 protein, S cerevisiae (EC 3.6.5.2) ; Hydroxyurea (X6Q56QN5QC)
Language	English
Publishing date	2017-09-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2041-1723
ISSN (online)	2041-1723
DOI	10.1038/s41467-017-00632-2
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Article ; Online: Genetic background and mistranslation frequency determine the impact of mistranslating tRNASerUGG.

Berg, Matthew D / Zhu, Yanrui / Loll-Krippleber, Raphaël / San Luis, Bryan-Joseph / Genereaux, Julie / Boone, Charles / Villén, Judit / Brown, Grant W / Brandl, Christopher J

G3 (Bethesda, Md.)

2022 Volume 12, Issue 7

Abstract: Transfer RNA variants increase the frequency of mistranslation, the misincorporation of an amino acid not specified by the "standard" genetic code, to frequencies approaching 10% in yeast and bacteria. Cells cope with these variants by having multiple ... ...

Abstract	Transfer RNA variants increase the frequency of mistranslation, the misincorporation of an amino acid not specified by the "standard" genetic code, to frequencies approaching 10% in yeast and bacteria. Cells cope with these variants by having multiple copies of each tRNA isodecoder and through pathways that deal with proteotoxic stress. In this study, we define the genetic interactions of the gene encoding tRNASerUGG,G26A, which mistranslates serine at proline codons. Using a collection of yeast temperature-sensitive alleles, we identify negative synthetic genetic interactions between the mistranslating tRNA and 109 alleles representing 91 genes, with nearly half of the genes having roles in RNA processing or protein folding and turnover. By regulating tRNA expression, we then compare the strength of the negative genetic interaction for a subset of identified alleles under differing amounts of mistranslation. The frequency of mistranslation correlated with the impact on cell growth for all strains analyzed; however, there were notable differences in the extent of the synthetic interaction at different frequencies of mistranslation depending on the genetic background. For many of the strains, the extent of the negative interaction with tRNASerUGG,G26A was proportional to the frequency of mistranslation or only observed at intermediate or high frequencies. For others, the synthetic interaction was approximately equivalent at all frequencies of mistranslation. As humans contain similar mistranslating tRNAs, these results are important when analyzing the impact of tRNA variants on disease, where both the individual's genetic background and the expression of the mistranslating tRNA variant need to be considered.
MeSH term(s)	Codon/genetics ; Genetic Background ; Humans ; Protein Biosynthesis ; RNA, Transfer/genetics ; Saccharomyces cerevisiae/genetics
Chemical Substances	Codon ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2022-05-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkac125
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Article ; Online: Chemical-Genetic Interactions with the Proline Analog L-Azetidine-2-Carboxylic Acid in

Berg, Matthew D / Zhu, Yanrui / Isaacson, Joshua / Genereaux, Julie / Loll-Krippleber, Raphaël / Brown, Grant W / Brandl, Christopher J

G3 (Bethesda, Md.)

2020 Volume 10, Issue 12, Page(s) 4335–4345

Abstract: Non-proteinogenic amino acids, such as the proline analog L-azetidine-2-carboxylic acid (AZC), are detrimental to cells because they are mis-incorporated into proteins and lead to proteotoxic stress. Our goal was to identify genes that show chemical- ... ...

Abstract	Non-proteinogenic amino acids, such as the proline analog L-azetidine-2-carboxylic acid (AZC), are detrimental to cells because they are mis-incorporated into proteins and lead to proteotoxic stress. Our goal was to identify genes that show chemical-genetic interactions with AZC in
MeSH term(s)	Azetidinecarboxylic Acid/toxicity ; Gonadotropin-Releasing Hormone/analogs & derivatives ; Proline ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics
Chemical Substances	LHRH, Ac-Nal(1)-Cpa(2)-Pal(3,6)-Arg(5)-Ala(10)- ; Saccharomyces cerevisiae Proteins ; Gonadotropin-Releasing Hormone (33515-09-2) ; Azetidinecarboxylic Acid (5GZ3E0L9ZU) ; Proline (9DLQ4CIU6V)
Language	English
Publishing date	2020-12-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1534/g3.120.401876
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Article ; Online: Mistranslating tRNA identifies a deleterious S213P mutation in the

Zhu, Yanrui / Berg, Matthew D / Yang, Phoebe / Loll-Krippleber, Raphaël / Brown, Grant W / Brandl, Christopher J

Biochemistry and cell biology = Biochimie et biologie cellulaire

2020 Volume 98, Issue 5, Page(s) 624–630

Abstract: Mistranslation occurs when an amino acid not specified by the standard genetic code is incorporated during translation. Since the ribosome does not read the amino acid, tRNA variants aminoacylated with a non-cognate amino acid or containing a non-cognate ...

Abstract	Mistranslation occurs when an amino acid not specified by the standard genetic code is incorporated during translation. Since the ribosome does not read the amino acid, tRNA variants aminoacylated with a non-cognate amino acid or containing a non-cognate anticodon dramatically increase the frequency of mistranslation. In a systematic genetic analysis, we identified a suppression interaction between tRNA
MeSH term(s)	Acetyltransferases/genetics ; Alleles ; Mutation ; Nuclear Proteins/genetics ; Proline/genetics ; RNA, Transfer/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Serine/genetics
Chemical Substances	Nuclear Proteins ; Saccharomyces cerevisiae Proteins ; Serine (452VLY9402) ; RNA, Transfer (9014-25-9) ; Proline (9DLQ4CIU6V) ; Acetyltransferases (EC 2.3.1.-) ; ECO1 protein, S cerevisiae (EC 2.3.1.-)
Language	English
Publishing date	2020-05-30
Publishing country	Canada
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	54104-7
ISSN	1208-6002 ; 0829-8211
ISSN (online)	1208-6002
ISSN	0829-8211
DOI	10.1139/bcb-2020-0151
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