Mfd Affects Global Transcription and the Physiology of Stressed Bacillus subtilis Cells

For several decades, Mfd has been studied as the bacterial transcription-coupled repair factor. However, recent observations indicate that this factor influences cell functions beyond DNA repair. Our lab recently described a role for Mfd in disulfide stress that was independent of its function in nucleotide excision repair and base excision repair. Because reports showed that Mfd influenced transcription of single genes, we investigated the global differences in transcription in wild-type and mfd mutant growth-limited cells in the presence and absence of diamide. Surprisingly, we found 1,997 genes differentially expressed in Mfd– cells in the absence of diamide. Using gene knockouts, we investigated the effect of genetic interactions between Mfd and the genes in its regulon on the response to disulfide stress. Interestingly, we found that Mfd interactions were complex and identified additive, epistatic, and suppressor effects in the response to disulfide stress. Pathway enrichment analysis of our RNASeq assay indicated that major biological functions, including translation, endospore formation, pyrimidine metabolism, and motility, were affected by the loss of Mfd. Further, our RNASeq findings correlated with phenotypic changes in growth in minimal media, motility, and sensitivity to antibiotics that target the cell envelope, transcription, and DNA replication. Our results suggest that Mfd has profound effects on the modulation of the transcriptome and on bacterial physiology, particularly in cells experiencing nutritional and oxidative stress.

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Mfd affects global transcription and the physiology of stressed Bacillus subtilis cells

10.1101/2020.11.27.401687 ◽

2020 ◽

Author(s):

Holly Anne Martin ◽

Anitha Sundararajan ◽

Tatiana Ermi ◽

Robert Heron ◽

Jason Gonzales ◽

...

Keyword(s):

Excision Repair ◽

Cell Envelope ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Bacterial Physiology ◽

Cell Functions ◽

Bacterial Transcription ◽

Nucleotide Excision ◽

Repair Factor ◽

Base Excision

AbstractFor several decades, Mfd has been studied as the bacterial transcription-coupled repair factor. However, recent observations indicate that this factor influences cell functions beyond DNA repair. Our lab recently described a role for Mfd in disulfide stress that was independent of its function in nucleotide excision repair and base excision repair. Because reports showed that Mfd influenced transcription of single genes, we investigated the global differences in transcription in wild-type and mfd mutant growth-limited cells in the presence and absence of diamide. Surprisingly, we found 1,997 genes differentially expressed in Mfd- cells in the absence of diamide. Using gene knockouts, we investigated the effect of genetic interactions between Mfd and the genes in its regulon on the response to disulfide stress. Interestingly, we found that Mfd interactions were complex and identified additive, epistatic, and suppressor effects in the response to disulfide stress. Pathway enrichment analysis of our RNASeq assay indicated that major biological functions, including translation, endospore formation, pyrimidine metabolism, and motility, were affected by the loss of Mfd. Further, our RNASeq findings correlated with phenotypic changes in growth in minimal media, motility, and sensitivity to antibiotics that target the cell envelope, transcription, and DNA replication. Our results suggest that Mfd has profound effects on the modulation of the transcriptome and on bacterial physiology, particularly in cells experiencing nutritional and oxidative stress.

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Dissection of the Molecular Defects Caused by Pathogenic Mutations in the DNA Repair Factor XPC

Molecular and Cellular Biology ◽

10.1128/mcb.00781-08 ◽

2008 ◽

Vol 28 (23) ◽

pp. 7225-7235 ◽

Cited By ~ 63

Author(s):

Bruno M. Bernardes de Jesus ◽

Magnar Bjørås ◽

Frédéric Coin ◽

Jean Marc Egly

Keyword(s):

Amino Acid ◽

Excision Repair ◽

Biochemical Properties ◽

Molecular Defects ◽

Damage Sensing ◽

Stop Mutation ◽

Nucleotide Excision ◽

Repair Factor ◽

Base Excision ◽

Repair Defect

ABSTRACT XPC is responsible for DNA damage sensing in nucleotide excision repair (NER). Mutations in XPC lead to a defect in NER and to xeroderma pigmentosum (XP-C). Here, we analyzed the biochemical properties behind mutations found within three patients: one amino acid substitution (P334H, XP1MI, and GM02096), one amino acid incorporation in a conserved domain (697insVal, XP8BE, and GM02249), and a stop mutation (R579St, XP67TMA, and GM14867). Using these mutants, we demonstrated that HR23B stabilizes XPC on DNA and protects it from degradation. XPC recruits the transcription/repair factor TFIIH and stimulates its XPB ATPase activity to initiate damaged DNA opening. In an effort to understand the severity of XP-C phenotypes, we also demonstrated that single mutations in XPC perturb other repair processes, such as base excision repair (e.g., the P334H mutation prevents the stimulation of Ogg1 glycosylase because it thwarts the interaction between XPC and Ogg1), thereby leading to a deeper understanding of the molecular repair defect of the XP-C patients.

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Nucleotide excision repair–initiating proteins bind to oxidative DNA lesions in vivo

The Journal of Cell Biology ◽

10.1083/jcb.201205149 ◽

2012 ◽

Vol 199 (7) ◽

pp. 1037-1046 ◽

Cited By ~ 67

Author(s):

Hervé Menoni ◽

Jan H.J. Hoeijmakers ◽

Wim Vermeulen

Keyword(s):

Nucleotide Excision Repair ◽

Oxidative Dna Damage ◽

Excision Repair ◽

Dna Lesions ◽

Dna Damages ◽

Nucleotide Excision ◽

Repair Factor ◽

Base Excision ◽

Group B

Base excision repair (BER) is the main repair pathway to eliminate abundant oxidative DNA lesions such as 8-oxo-7,8-dihydroguanine. Recent data suggest that the key transcription-coupled nucleotide excision repair factor (TC-NER) Cockayne syndrome group B (CSB) and the global genome NER-initiating factor XPC are implicated in the protection of cells against oxidative DNA damages. Our novel live-cell imaging approach revealed a strong and very rapid recruitment of XPC and CSB to sites of oxidative DNA lesions in living cells. The absence of detectable accumulation of downstream NER factors at the site of local oxidative DNA damage provide the first in vivo indication of the involvement of CSB and XPC in the repair of oxidative DNA lesions independent of the remainder of the NER reaction. Interestingly, CSB exhibited different and transcription-dependent kinetics in the two compartments studied (nucleolus and nucleoplasm), suggesting a direct transcription-dependent involvement of CSB in the repair of oxidative lesions associated with different RNA polymerases but not involving other NER proteins.

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miR-27b-3p a Negative Regulator of DSB-DNA Repair

Genes ◽

10.3390/genes12091333 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1333

Author(s):

Ricardo I. Peraza-Vega ◽

Mahara Valverde ◽

Emilio Rojas

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Excision Repair ◽

Enrichment Analysis ◽

Dna Lesions ◽

Negative Regulator ◽

Pathway Enrichment Analysis ◽

Cellular Processes ◽

Repair Mechanisms ◽

Base Excision

Understanding the regulation of DNA repair mechanisms is of utmost importance to identify altered cellular processes that lead to diseases such as cancer through genomic instability. In this sense, miRNAs have shown a crucial role. Specifically, miR-27b-3 biogenesis has been shown to be induced in response to DNA damage, suggesting that this microRNA has a role in DNA repair. In this work, we show that the overexpression of miR-27b-3p reduces the ability of cells to repair DNA lesions, mainly double-stranded breaks (DSB), and causes the deregulation of genes involved in homologous recombination repair (HRR), base excision repair (BER), and the cell cycle. DNA damage was induced in BALB/c-3T3 cells, which overexpress miR-27b-3p, using xenobiotic agents with specific mechanisms of action that challenge different repair mechanisms to determine their reparative capacity. In addition, we evaluated the expression of 84 DNA damage signaling and repair genes and performed pathway enrichment analysis to identify altered cellular processes. Taken together, our results indicate that miR-27b-3p acts as a negative regulator of DNA repair when overexpressed.

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DNA base excision repair and nucleotide excision repair proteins in malignant salivary gland tumors

Archives of Oral Biology ◽

10.1016/j.archoralbio.2020.104987 ◽

2021 ◽

Vol 121 ◽

pp. 104987

Author(s):

Fernanda Aragão Felix ◽

Leorik Pereira da Silva ◽

Maria Luiza Diniz de Sousa Lopes ◽

Ana Paula Veras Sobral ◽

Roseana de Almeida Freitas ◽

...

Keyword(s):

Salivary Gland ◽

Nucleotide Excision Repair ◽

Base Excision Repair ◽

Excision Repair ◽

Salivary Gland Tumors ◽

Dna Base Excision Repair ◽

Dna Base ◽

Nucleotide Excision ◽

Base Excision ◽

Malignant Salivary Gland Tumors

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Abasic Sites in the Transcribed Strand of Yeast DNA Are Removed by Transcription-Coupled Nucleotide Excision Repair

Molecular and Cellular Biology ◽

10.1128/mcb.00308-10 ◽

2010 ◽

Vol 30 (13) ◽

pp. 3206-3215 ◽

Cited By ~ 45

Author(s):

Nayun Kim ◽

Sue Jinks-Robertson

Keyword(s):

Nucleotide Excision Repair ◽

Excision Repair ◽

Genome Integrity ◽

Genetic Studies ◽

Abasic Sites ◽

Dna And Rna ◽

Nucleotide Excision ◽

Ap Sites ◽

Base Excision ◽

Ap Site

ABSTRACT Abasic (AP) sites are potent blocks to DNA and RNA polymerases, and their repair is essential for maintaining genome integrity. Although AP sites are efficiently dealt with through the base excision repair (BER) pathway, genetic studies suggest that repair also can occur via nucleotide excision repair (NER). The involvement of NER in AP-site removal has been puzzling, however, as this pathway is thought to target only bulky lesions. Here, we examine the repair of AP sites generated when uracil is removed from a highly transcribed gene in yeast. Because uracil is incorporated instead of thymine under these conditions, the position of the resulting AP site is known. Results demonstrate that only AP sites on the transcribed strand are efficient substrates for NER, suggesting the recruitment of the NER machinery by an AP-blocked RNA polymerase. Such transcription-coupled NER of AP sites may explain previously suggested links between the BER pathway and transcription.

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