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De March M. Crystal structure of the 3'→5' exonuclease from Methanocaldococcus jannaschii. Biochem Biophys Res Commun 2024; 712-713:149893. [PMID: 38657529 DOI: 10.1016/j.bbrc.2024.149893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
RecJ exonucleases are members of the DHH phosphodiesterase family ancestors of eukaryotic Cdc45, the key component of the CMG (Cdc45-MCM-GINS) complex at the replication fork. They are involved in DNA replication and repair, RNA maturation and Okazaki fragment degradation. Bacterial RecJs resect 5'-end ssDNA. Conversely, archaeal RecJs are more versatile being able to hydrolyse in both directions and acting on ssDNA as well as on RNA. In Methanocaldococcus jannaschii two RecJs were previously characterized: RecJ1 is a 5'→3' DNA exonuclease, MjaRecJ2 works only on 3'-end DNA/RNA with a preference for RNA. Here, I present the crystal structure of MjaRecJ2, solved at a resolution of 2.8 Å, compare it with the other RecJ structures, in particular the 5'→3' TkoGAN and the bidirectional PfuRecJ, and discuss its characteristics in light of the more recent knowledge on RecJs. This work adds new structural data that might improve the knowledge of these class of proteins.
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Affiliation(s)
- Matteo De March
- Structural Biology Laboratory, Elettra Sincrotrone Trieste S.c.p.A., 34149, Trieste, Italy; Department of Environmental and Biological Sciences, University of Nova Gorica, SI-5000, Nova Gorica, Slovenia.
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2
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Bhattacharya S, Agarwal A, Muniyappa K. Deciphering the Substrate Specificity Reveals that CRISPR-Cas12a Is a Bifunctional Enzyme with Both Endo- and Exonuclease Activities. J Mol Biol 2024; 436:168550. [PMID: 38575054 DOI: 10.1016/j.jmb.2024.168550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
The class 2 CRISPR-Cas9 and CRISPR-Cas12a systems, originally described as adaptive immune systems of bacteria and archaea, have emerged as versatile tools for genome-editing, with applications in biotechnology and medicine. However, significantly less is known about their substrate specificity, but such knowledge may provide instructive insights into their off-target cleavage and previously unrecognized mechanism of action. Here, we document that the Acidaminococcus sp. Cas12a (AsCas12a) binds preferentially, and independently of crRNA, to a suite of branched DNA structures, such as the Holliday junction (HJ), replication fork and D-loops, compared with single- or double-stranded DNA, and promotes their degradation. Further, our study revealed that AsCas12a binds to the HJ, specifically at the crossover region, protects it from DNase I cleavage and renders a pair of thymine residues in the HJ homologous core hypersensitive to KMnO4 oxidation, suggesting DNA melting and/or distortion. Notably, these structural changes enabled AsCas12a to resolve HJ into nonligatable intermediates, and subsequently their complete degradation. We further demonstrate that crRNA impedes HJ cleavage by AsCas12a, and that of Lachnospiraceae bacterium Cas12a, without affecting their DNA-binding ability. We identified a separation-of-function variant, which uncouples DNA-binding and DNA cleavage activities of AsCas12a. Importantly, we found robust evidence that AsCas12a endonuclease also has 3'-to-5' and 5'-to-3' exonuclease activity, and that these two activities synergistically promote degradation of DNA, yielding di- and mononucleotides. Collectively, this study significantly advances knowledge about the substrate specificity of AsCas12a and provides important insights into the degradation of different types of DNA substrates.
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Affiliation(s)
- Supreet Bhattacharya
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Ankit Agarwal
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India.
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Louvat C, Deymier S, Nguyen XN, Labaronne E, Noy K, Cariou M, Corbin A, Mateo M, Ricci EP, Fiorini F, Cimarelli A. Stable structures or PABP1 loading protects cellular and viral RNAs against ISG20-mediated decay. Life Sci Alliance 2024; 7:e202302233. [PMID: 38418089 PMCID: PMC10902665 DOI: 10.26508/lsa.202302233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024] Open
Abstract
ISG20 is an IFN-induced 3'-5' RNA exonuclease that acts as a broad antiviral factor. At present, the features that expose RNA to ISG20 remain unclear, although recent studies have pointed to the modulatory role of epitranscriptomic modifications in the susceptibility of target RNAs to ISG20. These findings raise the question as to how cellular RNAs, on which these modifications are abundant, cope with ISG20. To obtain an unbiased perspective on this topic, we used RNA-seq and biochemical assays to identify elements that regulate the behavior of RNAs against ISG20. RNA-seq analyses not only indicate a general preservation of the cell transcriptome, but they also highlight a small, but detectable, decrease in the levels of histone mRNAs. Contrarily to all other cellular ones, histone mRNAs are non-polyadenylated and possess a short stem-loop at their 3' end, prompting us to examine the relationship between these features and ISG20 degradation. The results we have obtained indicate that poly(A)-binding protein loading on the RNA 3' tail provides a primal protection against ISG20, easily explaining the overall protection of cellular mRNAs observed by RNA-seq. Terminal stem-loop RNA structures have been associated with ISG20 protection before. Here, we re-examined this question and found that the balance between resistance and susceptibility to ISG20 depends on their thermodynamic stability. These results shed new light on the complex interplay that regulates the susceptibility of different classes of viruses against ISG20.
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Affiliation(s)
- Camille Louvat
- Molecular Microbiology and Structural Biochemistry, MMSB-IBCP, UMR 5086 CNRS University of Lyon, Lyon, France
| | - Séverine Deymier
- https://ror.org/059sz6q14 Centre International de Recherche en Infectiologie(CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieure de Lyon, Lyon, France
| | - Xuan-Nhi Nguyen
- https://ror.org/059sz6q14 Centre International de Recherche en Infectiologie(CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieure de Lyon, Lyon, France
| | - Emmanuel Labaronne
- Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm, U1293, Lyon, France
| | - Kodie Noy
- https://ror.org/059sz6q14 Centre International de Recherche en Infectiologie(CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieure de Lyon, Lyon, France
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
| | - Marie Cariou
- https://ror.org/059sz6q14 Centre International de Recherche en Infectiologie(CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieure de Lyon, Lyon, France
| | - Antoine Corbin
- https://ror.org/059sz6q14 Centre International de Recherche en Infectiologie(CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieure de Lyon, Lyon, France
| | - Mathieu Mateo
- https://ror.org/059sz6q14 Centre International de Recherche en Infectiologie(CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieure de Lyon, Lyon, France
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm, U1293, Lyon, France
| | - Francesca Fiorini
- Molecular Microbiology and Structural Biochemistry, MMSB-IBCP, UMR 5086 CNRS University of Lyon, Lyon, France
| | - Andrea Cimarelli
- https://ror.org/059sz6q14 Centre International de Recherche en Infectiologie(CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieure de Lyon, Lyon, France
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Yoon JH, Sellamuthu K, Prakash L, Prakash S. WRN exonuclease imparts high fidelity on translesion synthesis by Y family DNA polymerases. Genes Dev 2024; 38:213-232. [PMID: 38503516 PMCID: PMC11065173 DOI: 10.1101/gad.351410.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024]
Abstract
Purified translesion synthesis (TLS) DNA polymerases (Pols) replicate through DNA lesions with a low fidelity; however, TLS operates in a predominantly error-free manner in normal human cells. To explain this incongruity, here we determine whether Y family Pols, which play an eminent role in replication through a diversity of DNA lesions, are incorporated into a multiprotein ensemble and whether the intrinsically high error rate of the TLS Pol is ameliorated by the components in the ensemble. To this end, we provide evidence for an indispensable role of Werner syndrome protein (WRN) and WRN-interacting protein 1 (WRNIP1) in Rev1-dependent TLS by Y family Polη, Polι, or Polκ and show that WRN, WRNIP1, and Rev1 assemble together with Y family Pols in response to DNA damage. Importantly, we identify a crucial role of WRN's 3' → 5' exonuclease activity in imparting high fidelity on TLS by Y family Pols in human cells, as the Y family Pols that accomplish TLS in an error-free manner manifest high mutagenicity in the absence of WRN's exonuclease function. Thus, by enforcing high fidelity on TLS Pols, TLS mechanisms have been adapted to safeguard against genome instability and tumorigenesis.
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Affiliation(s)
- Jung-Hoon Yoon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Karthi Sellamuthu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, USA
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Wang J, Zhang Z, Cai Y, Lu J, Zhang H, Pang J, Wu H, Liang Z. A Comprehensive Study of Heterogeneous Mismatch Repair Expression in Solid Tumors Reveals Different Immunohistochemical Patterns and Distinct Genetic Mechanisms. Am J Surg Pathol 2024; 48:417-425. [PMID: 37997470 DOI: 10.1097/pas.0000000000002158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
OBJECTIVE Immunohistochemistry is routinely performed to detect mismatch repair deficiency in solid tumors. Heterogeneous MMR expression (MMR-het) has been reported occasionally but not systemically studied. METHODS In this study, we depicted MMR-het patterns of 40 tumors of different anatomical sites and analyzed MMR genetic alterations and tumor mutational burdens (TMB) through comprehensive genomic profiling. RESULTS The MMR-het patterns were classified into 4 subgroups: "single-loss" (3 cases), "MLH1/PMS2 double-loss" (16 cases), "MSH2/MSH6 double-loss" (8 cases), and "triple/tetra-loss" (13 cases). Seventeen MMR-het cases exhibited histological heterogeneity, in which MMR protein loss was generally confined to either poorly differentiated or well-differentiated tumor areas. All "single-loss" tumors had MMR somatic mutations and coexisting POLE exonuclease domain mutations. "MLH1/PMS2 double-loss" tumors unexceptionally harbored MLH1 hypermethylation without MMR germline mutations. In the "MSH2/MSH6 double-loss" subgroup, 4 cases had MSH2/MSH6 germline mutations, while another 4 cases had multiple MSH2/MSH6 somatic mutations. Additional POLE exonuclease domain mutations were identified in 2 cases. Tumors in the "triple/tetra-loss" subgroup generally had MLH1 abnormalities (8 MLH1 hypermethylation, 4 MLH1 germline mutation, 1 MLH1 double somatic mutations), and coexistent somatic mutations on MSH2/MSH6 . Thirty-one cases (83.8%) were TMB-H, and all POLE -mutated cases exhibited ultra-high TMB (111.4 to 524.2 mut/Mb). CONCLUSION Our findings highlighted the importance of accurately interpreting heterogeneous MMR protein staining patterns for developing a more efficient personalized genetic investigation strategy.
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Affiliation(s)
- Jing Wang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Diseases, Molecular Pathology Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Ma Y, Wang J, He X, Liu Y, Zhen S, An L, Yang Q, Niu F, Wang H, An B, Tai X, Yan Z, Wu C, Yang X, Liu X. Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA. Nucleic Acids Res 2024; 52:1878-1895. [PMID: 38153123 PMCID: PMC10899777 DOI: 10.1093/nar/gkad1210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/03/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023] Open
Abstract
The exonuclease ISG20L2 has been initially characterized for its role in the mammalian 5.8S rRNA 3' end maturation, specifically in the cleavage of ITS2 of 12S precursor ribosomal RNA (pre-rRNA). Here, we show that human ISG20L2 is also involved in 18S pre-rRNA maturation through removing the ITS1 region, and contributes to ribosomal biogenesis and cell proliferation. Furthermore, we determined the crystal structure of the ISG20L2 nuclease domain at 2.9 Å resolution. It exhibits the typical αβα fold of the DEDD 3'-5' exonuclease with a catalytic pocket located in the hollow near the center. The catalytic residues Asp183, Glu185, Asp267, His322 and Asp327 constitute the DEDDh motif in ISG20L2. The active pocket represents conformational flexibility in the absence of an RNA substrate. Using structural superposition and mutagenesis assay, we mapped RNA substrate binding residues in ISG20L2. Finally, cellular assays revealed that ISG20L2 is aberrantly up-regulated in colon adenocarcinoma and promotes colon cancer cell proliferation through regulating ribosome biogenesis. Together, these results reveal that ISG20L2 is a new enzymatic member for 18S pre-rRNA maturation, provide insights into the mechanism of ISG20L2 underlying pre-rRNA processing, and suggest that ISG20L2 is a potential therapeutic target for colon adenocarcinoma.
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Affiliation(s)
- Yinliang Ma
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Jiaxu Wang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
- College of Life Sciences, State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453002 Henan, China
| | - Xingyi He
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Yuhang Liu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Shuo Zhen
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Lina An
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Qian Yang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Fumin Niu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Hong Wang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Boran An
- Affiliated Hospital of Hebei University, Hebei University, Baoding 071002 Hebei, China
| | - Xinyue Tai
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Zhenzhen Yan
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Chen Wu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Xiaoyun Yang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Xiuhua Liu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
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Sahoo A, Das G, Ghosh A, Shivappa Bagale S, Kumar Choudhary N, Harikrishna S, Sinha S, Gore KR. N 3-Methyluridine and 2'-O-Alkyl/2'-Fluoro-N 3-methyluridine functionalized nucleic acids improve nuclease resistance while maintaining duplex geometry. Bioorg Med Chem 2024; 100:117616. [PMID: 38295488 DOI: 10.1016/j.bmc.2024.117616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/16/2024] [Accepted: 01/26/2024] [Indexed: 02/02/2024]
Abstract
Herein, we report the synthesis of 2'-O-alkyl/2'-fluoro-N3-methyluridine (2'-O-alkyl/2'-F-m3U) phosphoramidites and their incorporation in DNA and RNA oligonucleotides. The duplex binding affinity and base discrimination studies showed that all 2'-O-alkyl/2'-F-m3U modifications significantly decreased the thermal stability and base-pairing discrimination ability. Serum stability study of dT20 with 2'-O-alkyl-m3U modification exhibited excellent nuclease resistance when incubated with 3'-exonucleases (SVPD) or 5'-exonucleases (PDE-II) as compared to m3U, 2'-F, 2'-OMe modified oligonucleotides. MD simulation studies with RNA tetradecamer duplexes illustrated that the m3U and 2'-O-methyl-m3U modifications reduce the duplex stabilities by disrupting the Watson-Crick hydrogen bonding and base-stacking interactions. Further molecular modelling investigations demonstrated that the 2'-O-propyl-m3U modification exhibits steric interactions with amino acid residues in the active site of 3'- and 5'-exonuclease, leading to enhanced stability. These combined data indicate that the 2'-modified-m3U nucleotides can be used as a promising tool to enhance the stability, silencing efficiency, and drug-like properties of antisense/siRNA-based therapeutics.
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Affiliation(s)
- Avijit Sahoo
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | | | - Nishant Kumar Choudhary
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - S Harikrishna
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, United States
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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Xie S, Liang S, Tian L, Ding G, He M, Li H, Yang H. Electrochemical aptasensor based on DNA-templated copper nanoparticles and RecJf exonuclease-assisted target recycling for lipopolysaccharide detection. Anal Methods 2024; 16:396-402. [PMID: 38131415 DOI: 10.1039/d3ay01638b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
An electrochemical aptasensor for detecting lipopolysaccharides (LPS) was fabricated based on DNA-templated copper nanoparticles (DNA-CuNPs) and RecJf exonuclease-assisted target recycling. The DNA-CuNPs were synthesized on a double-stranded DNA template generated through the hybridization of the LPS aptamer and its complementary chain (cDNA). In the absence of LPS, the CuNPs were synthesized on DNA double-strands, and a strong readout corresponding to the CuNPs was achieved at 0.10 V (vs. SCE). In the presence of LPS, the fabricated aptamer could detach from the DNA double-strand to form a complex with LPS, disrupting the template for the synthesis of CuNPs on the electrode. Meanwhile, RecJf exonuclease could hydrolyze the cDNA together with this single-stranded aptamer, releasing the LPS for the next round of aptamer binding, thereby enabling target recycling amplification. As a result, the electrochemical signal decreased and could be used to indicate the LPS content. The fabricated electrochemical aptasensor exhibited an extensive dynamic working range of 0.01 pg mL-1 to 100 ng mL-1, and its detection limit was 6.8 fg mL-1. The aptasensor also exhibited high selectivity and excellent reproducibility. Moreover, the proposed aptasensor could be used in practical applications for the detection of LPS in human serum samples.
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Affiliation(s)
- Shunbi Xie
- Chongqing Key Laboratory of Environmental Materials and Remediation Technologies, College of Chemistry & Environmental Engineering (Chongqing University of Arts and Sciences), Chongqing 402160, P. R. China.
| | - Shuting Liang
- Chongqing Key Laboratory of Environmental Materials and Remediation Technologies, College of Chemistry & Environmental Engineering (Chongqing University of Arts and Sciences), Chongqing 402160, P. R. China.
| | - Liangliang Tian
- School of Electronic Information and Electrical Engineering (Chongqing University of Arts and Sciences), Chongqing 402160, P. R. China
| | - Ge Ding
- Chongqing Key Laboratory of Environmental Materials and Remediation Technologies, College of Chemistry & Environmental Engineering (Chongqing University of Arts and Sciences), Chongqing 402160, P. R. China.
| | - Meiting He
- Chongqing Key Laboratory of Environmental Materials and Remediation Technologies, College of Chemistry & Environmental Engineering (Chongqing University of Arts and Sciences), Chongqing 402160, P. R. China.
| | - Haojie Li
- Chongqing Key Laboratory of Environmental Materials and Remediation Technologies, College of Chemistry & Environmental Engineering (Chongqing University of Arts and Sciences), Chongqing 402160, P. R. China.
| | - Heshan Yang
- Chongqing Key Laboratory of Environmental Materials and Remediation Technologies, College of Chemistry & Environmental Engineering (Chongqing University of Arts and Sciences), Chongqing 402160, P. R. China.
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Bowles IE, Jackman JE. A tRNA-specific function for tRNA methyltransferase Trm10 is associated with a new tRNA quality control mechanism in Saccharomyces cerevisiae. RNA 2024; 30:171-187. [PMID: 38071471 PMCID: PMC10798241 DOI: 10.1261/rna.079861.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/28/2023] [Indexed: 01/18/2024]
Abstract
In Saccharomyces cerevisiae, a single homolog of the tRNA methyltransferase Trm10 performs m1G9 modification on 13 different tRNAs. Here we provide evidence that the m1G9 modification catalyzed by S. cerevisiae Trm10 plays a biologically important role for one of these tRNA substrates, tRNATrp Overexpression of tRNATrp (and not any of 38 other elongator tRNAs) rescues growth hypersensitivity of the trm10Δ strain in the presence of the antitumor drug 5-fluorouracil (5FU). Mature tRNATrp is depleted in trm10Δ cells, and its levels are further decreased upon growth in 5FU, while another Trm10 substrate (tRNAGly) is not affected under these conditions. Thus, m1G9 in S. cerevisiae is another example of a tRNA modification that is present on multiple tRNAs but is only essential for the biological function of one of those species. In addition to the effects of m1G9 on mature tRNATrp, precursor tRNATrp species accumulate in the same strains, an effect that is due to at least two distinct mechanisms. The levels of mature tRNATrp are rescued in the trm10Δmet22Δ strain, consistent with the known role of Met22 in tRNA quality control, where deletion of met22 causes inhibition of 5'-3' exonucleases that catalyze tRNA decay. However, none of the known Met22-associated exonucleases appear to be responsible for the decay of hypomodified tRNATrp, based on the inability of mutants of each enzyme to rescue the growth of the trm10Δ strain in the presence of 5FU. Thus, the surveillance of tRNATrp appears to constitute a distinct tRNA quality control pathway in S. cerevisiae.
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Affiliation(s)
- Isobel E Bowles
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Ohio State Biochemistry Program, Columbus, Ohio 43210, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Ohio State Biochemistry Program, Columbus, Ohio 43210, USA
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10
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Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D. Structural basis for DNA proofreading. Nat Commun 2023; 14:8501. [PMID: 38151585 PMCID: PMC10752894 DOI: 10.1038/s41467-023-44198-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
DNA polymerase (DNAP) can correct errors in DNA during replication by proofreading, a process critical for cell viability. However, the mechanism by which an erroneously incorporated base translocates from the polymerase to the exonuclease site and the corrected DNA terminus returns has remained elusive. Here, we present an ensemble of nine high-resolution structures representing human mitochondrial DNA polymerase Gamma, Polγ, captured during consecutive proofreading steps. The structures reveal key events, including mismatched base recognition, its dissociation from the polymerase site, forward translocation of DNAP, alterations in DNA trajectory, repositioning and refolding of elements for primer separation, DNAP backtracking, and displacement of the mismatched base into the exonuclease site. Altogether, our findings suggest a conserved 'bolt-action' mechanism of proofreading based on iterative cycles of DNAP translocation without dissociation from the DNA, facilitating primer transfer between catalytic sites. Functional assays and mutagenesis corroborate this mechanism, connecting pathogenic mutations to crucial structural elements in proofreading steps.
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Affiliation(s)
- Gina Buchel
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Ashok R Nayak
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Karl Herbine
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Azadeh Sarfallah
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Viktoriia O Sokolova
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Angelica Zamudio-Ochoa
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Dmitry Temiakov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA.
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11
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Betancurt-Anzola L, Martínez-Carranza M, Delarue M, Zatopek KM, Gardner AF, Sauguet L. Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. Nat Commun 2023; 14:8306. [PMID: 38097591 PMCID: PMC10721889 DOI: 10.1038/s41467-023-44125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.
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Affiliation(s)
- Leonardo Betancurt-Anzola
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA
- New England Biolabs France, 5 Rue Henri Auguste Desbruères, 91000, Évry-Courcouronnes, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Kelly M Zatopek
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Andrew F Gardner
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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12
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Crevel G, Kearsey S, Cotterill S. A simple bypass assay for DNA polymerases shows that cancer-associated hypermutating variants exhibit differences in vitro. FEBS J 2023; 290:5744-5758. [PMID: 37592814 PMCID: PMC10953417 DOI: 10.1111/febs.16936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/13/2023] [Accepted: 08/16/2023] [Indexed: 08/19/2023]
Abstract
Errors made by DNA polymerases contribute to both natural variation and, in extreme cases, genome instability and its associated diseases. Recently, the importance of polymerase misincorporation in disease has been highlighted by the identification of cancer-associated polymerase variants with mutations in the exonuclease domain. A subgroup of these variants have a hypermutation phenotype in tumours, and when modelled in yeast, they show mutation rates in excess of that seen with polymerase with simple loss of proofreading activity. We have developed a bypass assay to rapidly determine the tendency of a polymerase to misincorporate in vitro. We have used the assay to compare misincorporation by wild-type, exonuclease-defective and two hypermutating human DNA polymerase ε variants, P286R and V411L. The assay clearly distinguished between the misincorporation rates of wild-type, exonuclease dead and P286R polymerases. However, the V411L polymerase showed misincorporation rate comparable to the exonuclease dead enzyme rather than P286R, suggesting that there may be some differences in the way that these variants cause hypermutation. Using this assay, misincorporation opposite a templated C nucleotide was consistently higher than for other nucleotides, and this caused predominantly C-to-T transitions. This is consistent with the observation that C-to-T transitions are commonly seen in DNA polymerase ε mutant tumours.
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13
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Zanin O, Eastham M, Winczura K, Ashe M, Martinez-Nunez RT, Hebenstreit D, Grzechnik P. Ceg1 depletion reveals mechanisms governing degradation of non-capped RNAs in Saccharomyces cerevisiae. Commun Biol 2023; 6:1112. [PMID: 37919390 PMCID: PMC10622555 DOI: 10.1038/s42003-023-05495-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023] Open
Abstract
Most functional eukaryotic mRNAs contain a 5' 7-methylguanosine (m7G) cap. Although capping is essential for many biological processes including mRNA processing, export and translation, the fate of uncapped transcripts has not been studied extensively. Here, we employed fast nuclear depletion of the capping enzymes in Saccharomyces cerevisiae to uncover the turnover of the transcripts that failed to be capped. We show that although the degradation of cap-deficient mRNA is dominant, the levels of hundreds of non-capped mRNAs increase upon depletion of the capping enzymes. Overall, the abundance of non-capped mRNAs is inversely correlated to the expression levels, altogether resembling the effects observed in cells lacking the cytoplasmic 5'-3' exonuclease Xrn1 and indicating differential degradation fates of non-capped mRNAs. The inactivation of the nuclear 5'-3' exonuclease Rat1 does not rescue the non-capped mRNA levels indicating that Rat1 is not involved in their degradation and consequently, the lack of the capping does not affect the distribution of RNA Polymerase II on the chromatin. Our data indicate that the cap presence is essential to initiate the Xrn1-dependent degradation of mRNAs underpinning the role of 5' cap in the Xrn1-dependent buffering of the cellular mRNA levels.
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Affiliation(s)
- Onofrio Zanin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- School of Immunology & Microbial Sciences, King's College London, Guy's Campus, London, SE1 9RT, UK
| | - Matthew Eastham
- Division of Molecular and Cellular Function, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Kinga Winczura
- Division of Molecular and Cellular Function, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Mark Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Rocio T Martinez-Nunez
- School of Immunology & Microbial Sciences, King's College London, Guy's Campus, London, SE1 9RT, UK
| | | | - Pawel Grzechnik
- Division of Molecular and Cellular Function, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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14
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Zhu J, Liu S, Fang J, Cui Z, Wang B, Wang Y, Liu L, Wang Q, Cao X. Enzymolysis-based RNA pull-down identifies YTHDC2 as an inhibitor of antiviral innate response. Cell Rep 2023; 42:113192. [PMID: 37776518 DOI: 10.1016/j.celrep.2023.113192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 06/06/2023] [Accepted: 09/15/2023] [Indexed: 10/02/2023] Open
Abstract
The innate immune response must be terminated in a timely manner at the late stage of infection to prevent unwanted inflammation. The role of m6A-modified RNAs and their binding partners in this process is not well known. Here, we develop an enzymolysis-based RNA pull-down (eRP) method that utilizes the immunoglobulin G-degrading enzyme of Streptococcus pyogenes (IdeS) to fish out m6A-modified RNA-associated proteins. We apply eRP to capture the methylated single-stranded RNA (ssRNA) probe-associated proteins and identify YT521-B homology domain-containing 2 (YTHDC2) as the m6A-modified interferon β (IFN-β) mRNA-binding protein. YTHDC2, induced in macrophages at the late stage of virus infection, recruits IFN-stimulated exonuclease ISG20 (IFN-stimulated exonuclease gene 20) to degrade IFN-β mRNA, consequently inhibiting antiviral innate immune response. In vitro and in vivo deficiency of YTHDC2 increases IFN-β production at the late stage of viral infection. Our findings establish an eRP method to effectively identify RNA-protein interactions and add mechanistic insight to the termination of innate response for maintaining homeostasis.
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Affiliation(s)
- Jun Zhu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shuo Liu
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jiali Fang
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zenghui Cui
- Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Bingjing Wang
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yuzhou Wang
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lin Liu
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Qingqing Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xuetao Cao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China; Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; Chinese Academy of Medical Sciences Oxford Institute, Chinese Academy of Medical Sciences, Beijing 100005, China.
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15
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Kaushal V, Klim J, Skoneczna A, Kurlandzka A, Enkhbaatar T, Kaczanowski S, Zielenkiewicz U. Apoptotic Factors Are Evolutionarily Conserved Since Mitochondrial Domestication. Genome Biol Evol 2023; 15:evad154. [PMID: 37616576 PMCID: PMC10565124 DOI: 10.1093/gbe/evad154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/18/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
The mechanisms initiating apoptotic programmed cell death in diverse eukaryotes are very similar. Basically, the mitochondrial permeability transition activates apoptotic proteases, DNases, and flavoproteins such as apoptosis-inducing factors (AIFs). According to the hypothesis of the endosymbiotic origin of apoptosis, these mechanisms evolved during mitochondrial domestication. Various phylogenetic analyses, including ours, have suggested that apoptotic factors were eubacterial protomitochondrial toxins used for killing protoeukaryotic hosts. Here, we tested whether the function of yeast Saccharomyces cerevisiae apoptotic proteases (metacaspases Mca1 and Nma111), DNase Nuc1, and flavoprotein Ndi1 can be substituted with orthologs from remotely related eukaryotes such as plants, protists, and eubacteria. We found that orthologs of remotely related eukaryotic and even eubacterial proteins can initiate apoptosis in yeast when triggered by chemical stresses. This observation suggests that apoptotic mechanisms have been maintained since mitochondrial domestication, which occurred approximately 1,800 Mya. Additionally, it supports the hypothesis that some of these apoptotic factors could be modified eubacterial toxins.
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Affiliation(s)
- Vandana Kaushal
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Joanna Klim
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Anna Kurlandzka
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Szymon Kaczanowski
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Urszula Zielenkiewicz
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warszawa, Poland
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16
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Lu X, Gu X, Li Y, Wu Y, Wang Q, Yu W, Chen Q. Biochemical characterization of RNase R 2'-O-methylation sensitivity. Biochimie 2023; 212:106-113. [PMID: 37105299 DOI: 10.1016/j.biochi.2023.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 04/02/2023] [Accepted: 04/24/2023] [Indexed: 04/29/2023]
Abstract
RNase R is a member of the RNA exonuclease family that digests RNA in the 3'-5' direction. Previous studies have identified RNase R from Mycoplasma genitalium (MgR) as the only RNA exonuclease that is sensitive to 2'-O-methylation (Nm) modification. However, the mechanism underlying this characteristic is not well understood. In this study, we aimed to explore the molecular mechanism of RNase R Nm sensitivity using an improved assay that can better evaluate Nm sensitivity. By comparing the sequences of five wild-type RNase R variants from Mycoplasma, we identified the importance of loop 18 in Nm sensitivity. Furthermore, we demonstrated the critical roles of L283, T278, and T279 within loop18. Our findings deepen the understanding of the molecular mechanism of why MgR is sensitive to Nm and provide a potential direction of protein engineering for applications.
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Affiliation(s)
- Xiaolan Lu
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, 210093, China; Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Xiangwen Gu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Yong Li
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Yifan Wu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Qiang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Wenkui Yu
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, 210093, China
| | - Qihan Chen
- Medical School of Nanjing University, Nanjing, Jiangsu, 210093, China.
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17
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Jia H, Dantuluri S, Margulies S, Smith V, Lever R, Allers T, Koh J, Chen S, Maupin-Furlow JA. RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii. mBio 2023; 14:e0085223. [PMID: 37458473 PMCID: PMC10470531 DOI: 10.1128/mbio.00852-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
Nucleases are strictly regulated and often localized in the cell to avoid the uncontrolled degradation of DNA and RNA. Here, a new type of nuclease complex, composed of RecJ3, RecJ4, and aRNase J, was identified through its ATP-dependent association with the ubiquitin-like SAMP1 and AAA-ATPase Cdc48a. The complex was discovered in Haloferax volcanii, an archaeon lacking an RNA exosome. Genetic analysis revealed aRNase J to be essential and RecJ3, RecJ4, and Cdc48a to function in the recovery from DNA damage including genotoxic agents that generate double-strand breaks. The RecJ3:RecJ4:aRNase J complex (isolated in 2:2:1 stoichiometry) functioned primarily as a 3'-5' exonuclease in hydrolyzing RNA and ssDNA, with the mechanism non-processive for ssDNA. aRNase J could also be purified as a homodimer that catalyzed endoribonuclease activity and, thus, was not restricted to the 5'-3' exonuclease activity typical of aRNase J homologs. Moreover, RecJ3 and RecJ4 could be purified as a 560-kDa subcomplex in equimolar subunit ratio with nuclease activities mirroring the full RecJ3/4-aRNase J complex. These findings prompted reconstitution assays that suggested RecJ3/4 could suppress, alter, and/or outcompete the nuclease activities of aRNase J. Based on the phenotypic results, this control mechanism of aRNase J by RecJ3/4 is not necessary for cell growth but instead appears important for DNA repair. IMPORTANCE Nucleases are critical for various cellular processes including DNA replication and repair. Here, a dynamic type of nuclease complex is newly identified in the archaeon Haloferax volcanii, which is missing the canonical RNA exosome. The complex, composed of RecJ3, RecJ4, and aRNase J, functions primarily as a 3'-5' exonuclease and was discovered through its ATP-dependent association with the ubiquitin-like SAMP1 and Cdc48a. aRNase J alone forms a homodimer that has endonuclease function and, thus, is not restricted to 5'-3' exonuclease activity typical of other aRNase J enzymes. RecJ3/4 appears to suppress, alter, and/or outcompete the nuclease activities of aRNase J. While aRNase J is essential for growth, RecJ3/4, Cdc48a, and SAMPs are important for recovery against DNA damage. These biological distinctions may correlate with the regulated nuclease activity of aRNase J in the RecJ3/4-aRNaseJ complex.
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Affiliation(s)
- Huiyong Jia
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Swathi Dantuluri
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Shae Margulies
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rebecca Lever
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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18
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Brambati A, Sacco O, Porcella S, Heyza J, Kareh M, Schmidt JC, Sfeir A. RHINO directs MMEJ to repair DNA breaks in mitosis. Science 2023; 381:653-660. [PMID: 37440612 PMCID: PMC10561558 DOI: 10.1126/science.adh3694] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023]
Abstract
Nonhomologous end-joining (NHEJ) and homologous recombination (HR) are the primary pathways for repairing DNA double-strand breaks (DSBs) during interphase, whereas microhomology-mediated end-joining (MMEJ) has been regarded as a backup mechanism. Through CRISPR-Cas9-based synthetic lethal screens in cancer cells, we identified subunits of the 9-1-1 complex (RAD9A-RAD1-HUS1) and its interacting partner, RHINO, as crucial MMEJ factors. We uncovered an unexpected function for RHINO in restricting MMEJ to mitosis. RHINO accumulates in M phase, undergoes Polo-like kinase 1 (PLK1) phosphorylation, and interacts with polymerase θ (Polθ), enabling its recruitment to DSBs for subsequent repair. Additionally, we provide evidence that MMEJ activity in mitosis repairs persistent DSBs that originate in S phase. Our findings offer insights into the synthetic lethal relationship between the genes POLQ and BRCA1 and BRAC2 and the synergistic effect of Polθ and poly(ADP-ribose) polymerase (PARP) inhibitors.
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Affiliation(s)
- Alessandra Brambati
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Olivia Sacco
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Sarina Porcella
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Joshua Heyza
- Institute for Quantitative Health Sciences and Engineering, Michigan State University; East Lansing, MI, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University; East Lansing, MI, USA
| | - Mike Kareh
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Jens C. Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State University; East Lansing, MI, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University; East Lansing, MI, USA
| | - Agnel Sfeir
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
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19
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Xu X, An H, Wu C, Sang R, Wu L, Lou Y, Yang X, Xi Y. HR repair pathway plays a crucial role in maintaining neural stem cell fate under irradiation stress. Life Sci Alliance 2023; 6:e202201802. [PMID: 37197982 PMCID: PMC10192720 DOI: 10.26508/lsa.202201802] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
Environmental stress can cause mutation or genomic instability in stem cells which, in some cases, leads to tumorigenesis. Mechanisms to monitor and eliminate these mutant stem cells remain elusive. Here, using the Drosophila larval brain as a model, we show that X-ray irradiation (IR) at the early larval stage leads to accumulation of nuclear Prospero (Pros), resulting in premature differentiation of neural stem cells (neuroblasts, NBs). Through NB-specific RNAi screenings, we determined that it is the Mre11-Rad50-Nbs1 complex and the homologous recombination (HR) repair pathway, rather than non-homologous end-joining pathway that plays, a dominant role in the maintenance of NBs under IR stress. The DNA damage sensor ATR/mei-41 is shown to act to prevent IR-induced nuclear Pros in a WRNexo-dependent manner. The accumulation of nuclear Pros in NBs under IR stress, leads to NB cell fate termination, rather than resulting in mutant cell proliferation. Our study reveals an emerging mechanism for the HR repair pathway in maintaining neural stem cell fate under irradiation stress.
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Affiliation(s)
- Xiao Xu
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huanping An
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Clinical Molecular Biology of Hanzhong City, Hanzhong Vocational and Technique College, Hanzhong, China
| | - Cheng Wu
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
| | - Rong Sang
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
| | - Litao Wu
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuhan Lou
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohang Yang
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
- Joint Institute of Genetics and Genomic Medicine, Between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, China
| | - Yongmei Xi
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
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20
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Li Q, Ding Y, Zhang Y. Capture the in vivo intact RNA structurome by CAP-STRUCTURE-seq. Methods Enzymol 2023; 691:127-152. [PMID: 37914443 DOI: 10.1016/bs.mie.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
RNA decay serves as a crucial mechanism for maintaining cellular homeostasis and regulating gene expression. Large-scale analyses indicate that altered rates of decay contribute significantly to changes in mRNA levels, with up to half of these changes attributed to decay. The regulation of RNA decay is, at least in part, through structured RNA elements, especially in the non-coding regions of the mRNAs. The development of next-generation sequencing, and in vivo chemical probing techniques has allowed for unprecedented understanding of RNA folding in vivo and genome-wide. To explore the RNA structure elements that are responsible for RNA cleavage, we need to capture the RNA structure before cleavage. In this method, we introduce a new experimental procedure called CAP-STRUCTURE-seq, a modified STRUCTURE-Seq approach combining with the enrichment of in intact mRNAs by the use of terminator exonuclease treatment (5'-Phosphate-Dependent Exonuclease) that digests RNA containing 5-monophosphate ends. This approach is designed to investigate the RNA structure for these intact RNAs, providing a means to study the impact of RNA structure on RNA decay in greater detail. This method can provide insights into the function of RNA structure in RNA decay and help advance our understanding of biological processes.
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Affiliation(s)
- Qianqian Li
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, P.R. China; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.
| | - Yueying Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.
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21
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Ran XB, Ding LW, Sun QY, Yang H, Said JW, Zhentang L, Madan V, Dakle P, Xiao JF, Loh X, Li Y, Xu L, Xiang XQ, Wang LZ, Goh BC, Lin DC, Chng WJ, Tan SY, Jha S, Koeffler HP. Targeting RNA Exonuclease XRN1 Potentiates Efficacy of Cancer Immunotherapy. Cancer Res 2023; 83:922-938. [PMID: 36638333 DOI: 10.1158/0008-5472.can-21-3052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/29/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Despite the remarkable clinical responses achieved with immune checkpoint blockade therapy, the response rate is relatively low and only a subset of patients can benefit from the treatment. Aberrant RNA accumulation can mediate IFN signaling and stimulate an immune response, suggesting that targeting RNA decay machinery might sensitize tumor cells to immunotherapy. With this in mind, we identified an RNA exoribonuclease, XRN1, as a potential therapeutic target to suppress RNA decay and stimulate antitumor immunity. Silencing of XRN1 suppressed tumor growth in syngeneic immunocompetent mice and potentiated immunotherapy efficacy, while silencing of XRN1 alone did not affect tumor growth in immunodeficient mice. Mechanistically, XRN1 depletion activated IFN signaling and the viral defense pathway; both pathways play determinant roles in regulating immune evasion. Aberrant RNA-sensing signaling proteins (RIG-I/MAVS) mediated the expression of IFN genes, as depletion of each of them blunted the elevation of antiviral/IFN signaling in XRN1-silenced cells. Analysis of pan-cancer CRISPR-screening data indicated that IFN signaling triggered by XRN1 silencing is a common phenomenon, suggesting that the effect of XRN1 silencing may be extended to multiple types of cancers. Overall, XRN1 depletion triggers aberrant RNA-mediated IFN signaling, highlighting the importance of the aberrant RNA-sensing pathway in regulating immune responses. These findings provide the molecular rationale for developing XRN1 inhibitors and exploring their potential clinical application in combination with cancer immunotherapy. SIGNIFICANCE Targeting XRN1 activates an intracellular innate immune response mediated by RNA-sensing signaling and potentiates cancer immunotherapy efficacy, suggesting inhibition of RNA decay machinery as a novel strategy for cancer treatment.
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Affiliation(s)
- Xue-Bin Ran
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Qiao-Yang Sun
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jonathan W Said
- Santa Monica-University of California, Los Angeles Medical Center, California, Los Angeles
| | - Lao Zhentang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
| | - Xinyi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ying Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- College of life Science, Zhejiang University, Hangzhou, China
| | - Xiao-Qiang Xiang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai, China
| | - Ling-Zhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - De-Chen Lin
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Soo-Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University, Singapore, Singapore
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
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22
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Rocque MJ, Leipart V, Kumar Singh A, Mur P, Olsen MF, Engebretsen LF, Martin-Ramos E, Aligué R, Sætrom P, Valle L, Drabløs F, Otterlei M, Sjursen W. Characterization of POLE c.1373A > T p.(Tyr458Phe), causing high cancer risk. Mol Genet Genomics 2023; 298:555-566. [PMID: 36856825 PMCID: PMC10133059 DOI: 10.1007/s00438-023-02000-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023]
Abstract
The cancer syndrome polymerase proofreading-associated polyposis results from germline mutations in the POLE and POLD1 genes. Mutations in the exonuclease domain of these genes are associated with hyper- and ultra-mutated tumors with a predominance of base substitutions resulting from faulty proofreading during DNA replication. When a new variant is identified by gene testing of POLE and POLD1, it is important to verify whether the variant is associated with PPAP or not, to guide genetic counseling of mutation carriers. In 2015, we reported the likely pathogenic (class 4) germline POLE c.1373A > T p.(Tyr458Phe) variant and we have now characterized this variant to verify that it is a class 5 pathogenic variant. For this purpose, we investigated (1) mutator phenotype in tumors from two carriers, (2) mutation frequency in cell-based mutagenesis assays, and (3) structural consequences based on protein modeling. Whole-exome sequencing of two tumors identified an ultra-mutator phenotype with a predominance of base substitutions, the majority of which are C > T. A SupF mutagenesis assay revealed increased mutation frequency in cells overexpressing the variant of interest as well as in isogenic cells encoding the variant. Moreover, exonuclease repair yeast-based assay supported defect in proofreading activity. Lastly, we present a homology model of human POLE to demonstrate structural consequences leading to pathogenic impact of the p.(Tyr458Phe) mutation. The three lines of evidence, taken together with updated co-segregation and previously published data, allow the germline variant POLE c.1373A > T p.(Tyr458Phe) to be reclassified as a class 5 variant. That means the variant is associated with PPAP.
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Affiliation(s)
- Mariève J Rocque
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Vilde Leipart
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
| | - Ashish Kumar Singh
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maren F Olsen
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Lars F Engebretsen
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Edgar Martin-Ramos
- Department of Biomedical Sciences, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Rosa Aligué
- Department of Biomedical Sciences, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Department of Computer and Information Science, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Bioinformatics Core Facility-BioCore, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway.
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway.
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23
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Abstract
DNA replication is complex and highly regulated, and DNA replication errors can lead to human diseases such as cancer. DNA polymerase ε (polε) is a key player in DNA replication and contains a large subunit called POLE, which possesses both a DNA polymerase domain and a 3'-5' exonuclease domain (EXO). Mutations at the EXO domain and other missense mutations on POLE with unknown significance have been detected in a variety of human cancers. Based on cancer genome databases, Meng and colleagues (pp. 74-79) previously identified several missense mutations in POPS (pol2 family-specific catalytic core peripheral subdomain), and mutations at the conserved residues of yeast Pol2 (pol2-REL) showed reduced DNA synthesis and growth. In this issue of Genes & Development, Meng and colleagues (pp. 74-79) found unexpectedly that mutations at the EXO domain rescue the growth defects of pol2-REL. They further discovered that EXO-mediated polymerase backtracking impedes forward movement of the enzyme when POPS is defective, revealing a novel interplay between the EXO domain and POPS of Pol2 for efficient DNA synthesis. Additional molecular insight into this interplay will likely inform the impact of cancer-associated mutations found in both the EXO domain and POPS on tumorigenesis and uncover future novel therapeutic strategies.
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Affiliation(s)
- Matthew Gallitto
- Institute for Cancer Genetics, Department of Pediatrics, Department of Genetics and Development, Irving Cancer Research Center, Columbia University, New York, New York 10032, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics, Department of Genetics and Development, Irving Cancer Research Center, Columbia University, New York, New York 10032, USA
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24
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Meng X, Claussin C, Regan-Mochrie G, Whitehouse I, Zhao X. Balancing act of a leading strand DNA polymerase-specific domain and its exonuclease domain promotes genome-wide sister replication fork symmetry. Genes Dev 2023; 37:74-79. [PMID: 36702483 PMCID: PMC10069448 DOI: 10.1101/gad.350054.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/19/2022] [Indexed: 01/28/2023]
Abstract
Pol2 is the leading-strand DNA polymerase in budding yeast. Here we describe an antagonism between its conserved POPS (Pol2 family-specific catalytic core peripheral subdomain) and exonuclease domain and the importance of this antagonism in genome replication. We show that multiple defects caused by POPS mutations, including impaired growth and DNA synthesis, genome instability, and reliance on other genome maintenance factors, were rescued by exonuclease inactivation. Single-molecule data revealed that the rescue stemmed from allowing sister replication forks to progress at equal rates. Our data suggest that balanced activity of Pol2's POPS and exonuclease domains is vital for genome replication and stability.
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Affiliation(s)
- Xiangzhou Meng
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Clémence Claussin
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Gemma Regan-Mochrie
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA;
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA;
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25
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Cao K, Zhang Y, Yao Q, Peng Y, Pan Q, Jiao Q, Ren K, Sun F, Zhang Q, Guo R, Zhang J, Chen T. Hypericin blocks the function of HSV-1 alkaline nuclease and suppresses viral replication. J Ethnopharmacol 2022; 296:115524. [PMID: 35811028 DOI: 10.1016/j.jep.2022.115524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/23/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Hypericum perforatum L. has a long history in many countries of being used as a herbal medicine. It is also widely used in Chinese herbal medicine for the treatment of infections. Hypericin, a main component extracted from Hypericum perforatum L., has attracted the attention of many researchers for its remarkable antiviral, antitumor and antidepressant effects. AIM OF THE STUDY To find plant molecules that inhibit the alkaline nuclease (AN) of herpes simplex virus type 1 (HSV-1) and suppress viral replication. MATERIALS AND METHODS Bioinformatics methods were used to determine which compounds from a variety of natural compounds in our laboratory interact with AN. By this means we predicted that hypericin may interact with AN and suppress HSV-1 replication. Experiments were then carried out to verify whether hypericin inhibits the bioactivity of AN. The Pichia pastoris expression system was used to obtain recombinant AN. The exonuclease and endonuclease activity of AN treated with hypericin were tested by electrophoresis. Immunohistochemical staining of the HSV-1 nucleocapsids was used to find out whether hypericin inhibits the intracellular function of AN. Real-time PCR and western blotting analysis were performed to test viral gene expression and viral protein synthesis. The extent of viral replication inhibited by hypericin was determined by a plaque assay and a time of addition assay. RESULTS Recombinant AN was obtained by Pichia pastoris expression system. The exonuclease and endonuclease activity of recombinant AN were inhibited by hypericin in the electrophoresis assay. Hypericin showed no inhibitory effect on BeyoZonase™ Super Nuclease or DNase I. T5 Exonuclease activity was inhibited partially by10 μM hypericin, and was completely suppressed by 50 μM hypericin. Hind Ⅲ was inhibited by hypericin at concentrations greater than 100 μM, but EcoR I, BamH I, and Sal I were not inhibited by hypericin. HSV-1 nucleocapsids gathered in the nucleus when the viruses were treated with hypericin. Plaque formation was significantly reduced by hypericin (EC50 against HSV-1 F is 2.59 ± 0.08 μM and EC50 against HSV-1 SM44 is 2.94 ± 0.10 μM). UL12, ICP27, ICP8, gD, and UL53 gene expression (P < 0.01, 4.0 μM hypericin treated group vs control group) and ICP4 (P < 0.05, 6.0 μM hypericin treated group vs control group), ICP8 and gD (P < 0.05, 2.0 μM hypericin treated group vs control group) protein synthesis were inhibited by hypericin. In the time of addition assay, HSV-1 was suppressed by hypericin in the early stages of viral replication. Hypericin exhibits potent virucidal activity against HSV-1 and inhibits the adsorption and penetration of HSV-1. CONCLUSION Hypericin inhibits the bioactivity of AN and suppresses HSV-1 replication. The data revealed a novel mechanism of the antiherpetic effect of hypericin.
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Affiliation(s)
- Kang Cao
- Department of Pathogen Biology, Chengdu Medical College, Chengdu, China
| | - Yan Zhang
- Department of Pathogen Biology, Chengdu Medical College, Chengdu, China; Department of Pathology, Fourth People's Hospital of Zhenjiang City, Zhenjiang, China
| | - Qian Yao
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, China
| | - Yanjuan Peng
- Department of Pharmacology, Chengdu Medical College, Chengdu, China
| | - Qu Pan
- Department of Pathogen Biology, Chengdu Medical College, Chengdu, China
| | - Qiuxia Jiao
- Department of Pathogen Biology, Chengdu Medical College, Chengdu, China
| | - Ke Ren
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Fenghui Sun
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Qian Zhang
- Department of Nursing, The Second People's Hospital of Xindu District, Chengdu, China
| | - Ran Guo
- Grade 2019 of Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Jiali Zhang
- Grade 2019 of Clinical Medicine, Chengdu Medical College, Chengdu, China
| | - Tian Chen
- Department of Pathogen Biology, Chengdu Medical College, Chengdu, China.
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26
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Zhou ZX, Kunkel TA. Extrinsic proofreading. DNA Repair (Amst) 2022; 117:103369. [PMID: 35850061 PMCID: PMC9561950 DOI: 10.1016/j.dnarep.2022.103369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/24/2022]
Abstract
The high fidelity of replication of the nuclear DNA genome in eukaryotes involves three processes. Correct rather than incorrect dNTPs are almost always incorporated by the three major replicases, DNA polymerases α, δ and ε. When an incorrect base is occasionally inserted, the latter Pols δ and ε also have a 3 ´ to 5 ´ exonuclease activity that can remove the mismatch to allow correct DNA synthesis to proceed. Lastly, rare mismatches that escape proofreading activity and are present in newly replicated DNA can be removed by DNA mismatch repair. In this review, we consider evidence supporting the hypothesis that the second mechanism, proofreading, can operate in two different ways. Primer terminal mismatches made by either Pol δ or Pol ε can be 'intrinsically' proofread. This mechanism occurs by direct transfer of a misinserted base made at the polymerase active site to the exonuclease active site that is located a short distance away. Intrinsic proofreading allows mismatch excision without intervening enzyme dissociation. Alternatively, considerable evidence suggests that mismatches made by any of the three replicases can also be proofread by 'extrinsic' proofreading by Pol δ. Extrinsic proofreading occurs when a mismatch made by any of the three replicases is initially abandoned, thereby allowing the exonuclease active site of Pol δ to bind directly to and remove the mismatch before replication continues. Here we review the evidence that extrinsic proofreading significantly enhances the fidelity of nuclear DNA replication, and we then briefly consider the implications of this process for evolution and disease.
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Affiliation(s)
- Zhi-Xiong Zhou
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.
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27
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Manils J, Marruecos L, Soler C. Exonucleases: Degrading DNA to Deal with Genome Damage, Cell Death, Inflammation and Cancer. Cells 2022; 11:cells11142157. [PMID: 35883600 PMCID: PMC9316158 DOI: 10.3390/cells11142157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 01/27/2023] Open
Abstract
Although DNA degradation might seem an unwanted event, it is essential in many cellular processes that are key to maintaining genomic stability and cell and organism homeostasis. The capacity to cut out nucleotides one at a time from the end of a DNA chain is present in enzymes called exonucleases. Exonuclease activity might come from enzymes with multiple other functions or specialized enzymes only dedicated to this function. Exonucleases are involved in central pathways of cell biology such as DNA replication, repair, and death, as well as tuning the immune response. Of note, malfunctioning of these enzymes is associated with immune disorders and cancer. In this review, we will dissect the impact of DNA degradation on the DNA damage response and its links with inflammation and cancer.
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Affiliation(s)
- Joan Manils
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Spain;
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
| | - Laura Marruecos
- Breast Cancer Laboratory, Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Concepció Soler
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Correspondence:
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28
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Omkar S, Wani TH, Zheng B, Mitchem MM, Truman AW. The APE2 Exonuclease Is a Client of the Hsp70–Hsp90 Axis in Yeast and Mammalian Cells. Biomolecules 2022; 12:biom12070864. [PMID: 35883419 PMCID: PMC9312491 DOI: 10.3390/biom12070864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/18/2022] [Accepted: 06/18/2022] [Indexed: 12/10/2022] Open
Abstract
Molecular chaperones such as Hsp70 and Hsp90 help fold and activate proteins in important signal transduction pathways that include DNA damage response (DDR). Previous studies have suggested that the levels of the mammalian APE2 exonuclease, a protein critical for DNA repair, may be dependent on chaperone activity. In this study, we demonstrate that the budding yeast Apn2 exonuclease interacts with molecular chaperones Ssa1 and Hsp82 and the co-chaperone Ydj1. Although Apn2 does not display a binding preference for any specific cytosolic Hsp70 or Hsp90 paralog, Ssa1 is unable to support Apn2 stability when present as the sole Ssa in the cell. Demonstrating conservation of this mechanism, the exonuclease APE2 also binds to Hsp70 and Hsp90 in mammalian cells. Inhibition of chaperone function via specific small molecule inhibitors results in a rapid loss of APE2 in a range of cancer cell lines. Taken together, these data identify APE2 and Apn2 as clients of the chaperone system in yeast and mammalian cells and suggest that chaperone inhibition may form the basis of novel anticancer therapies that target APE2-mediated processes.
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29
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Brown JM, De Ornellas S, Parisi E, Schermelleh L, Buckle VJ. RASER-FISH: non-denaturing fluorescence in situ hybridization for preservation of three-dimensional interphase chromatin structure. Nat Protoc 2022; 17:1306-1331. [PMID: 35379945 DOI: 10.1038/s41596-022-00685-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/10/2022] [Indexed: 11/09/2022]
Abstract
DNA fluorescence in situ hybridization (FISH) has been a central technique in advancing our understanding of how chromatin is organized within the nucleus. With the increasing resolution offered by super-resolution microscopy, the optimal maintenance of chromatin structure within the nucleus is essential for accuracy in measurements and interpretation of data. However, standard 3D-FISH requires potentially destructive heat denaturation in the presence of chaotropic agents such as formamide to allow access to the DNA strands for labeled FISH probes. To avoid the need to heat-denature, we developed Resolution After Single-strand Exonuclease Resection (RASER)-FISH, which uses exonuclease digestion to generate single-stranded target DNA for efficient probe binding over a 2 d process. Furthermore, RASER-FISH is easily combined with immunostaining of nuclear proteins or the detection of RNAs. Here, we provide detailed procedures for RASER-FISH in mammalian cultured cells to detect single loci, chromatin tracks and topologically associating domains with conventional and super-resolution 3D structured illumination microscopy. Moreover, we provide a validation and characterization of our method, demonstrating excellent preservation of chromatin structure and nuclear integrity, together with improved hybridization efficiency, compared with classic 3D-FISH protocols.
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Affiliation(s)
- Jill M Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Sara De Ornellas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Eva Parisi
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
- School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Lothar Schermelleh
- Micron Oxford Advanced Bioimaging Unit, Department of Biochemistry, Oxford University, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK.
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30
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Hurtig JE, van Hoof A. Yeast Dxo1 is required for 25S rRNA maturation and acts as a transcriptome-wide distributive exonuclease. RNA 2022; 28:657-667. [PMID: 35140172 PMCID: PMC9014881 DOI: 10.1261/rna.078952.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/24/2022] [Indexed: 05/03/2023]
Abstract
The Dxo1/Rai1/DXO family of decapping and exonuclease enzymes can catalyze the in vitro removal of chemically diverse 5' ends from RNA. Specifically, these enzymes act poorly on RNAs with a canonical 7mGpppN cap, but instead prefer RNAs with a triphosphate, monophosphate, hydroxyl, or nonconventional cap. In each case, these enzymes generate an RNA with a 5' monophosphate, which is then thought to be further degraded by Rat1/Xrn1 5' exoribonucleases. For most Dxo1/Rai1/DXO family members, it is not known which of these activities is most important in vivo. Here we describe the in vivo function of the poorly characterized cytoplasmic family member, yeast Dxo1. Using RNA-seq of 5' monophosphate ends, we show that Dxo1 can act as a distributive exonuclease, removing a few nucleotides from endonuclease or decapping products. We also show that Dxo1 is required for the final 5' end processing of 25S rRNA, and that this is the primary role of Dxo1. While Dxo1/Rai1/DXO members were expected to act upstream of Rat1/Xrn1, this order is reversed in 25S rRNA processing, with Dxo1 acting downstream from Rat1. Such a hand-off from a processive to a distributive exonuclease may be a general phenomenon in the precise maturation of RNA ends.
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Affiliation(s)
- Jennifer E Hurtig
- Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Ambro van Hoof
- Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030, USA
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Domingo E, García-Crespo C, Lobo-Vega R, Perales C. Mutation Rates, Mutation Frequencies, and Proofreading-Repair Activities in RNA Virus Genetics. Viruses 2021; 13:1882. [PMID: 34578463 PMCID: PMC8473064 DOI: 10.3390/v13091882] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/06/2021] [Accepted: 09/17/2021] [Indexed: 12/29/2022] Open
Abstract
The error rate displayed during template copying to produce viral RNA progeny is a biologically relevant parameter of the replication complexes of viruses. It has consequences for virus-host interactions, and it represents the first step in the diversification of viruses in nature. Measurements during infections and with purified viral polymerases indicate that mutation rates for RNA viruses are in the range of 10-3 to 10-6 copying errors per nucleotide incorporated into the nascent RNA product. Although viruses are thought to exploit high error rates for adaptation to changing environments, some of them possess misincorporation correcting activities. One of them is a proofreading-repair 3' to 5' exonuclease present in coronaviruses that may decrease the error rate during replication. Here we review experimental evidence and models of information maintenance that explain why elevated mutation rates have been preserved during the evolution of RNA (and some DNA) viruses. The models also offer an interpretation of why error correction mechanisms have evolved to maintain the stability of genetic information carried out by large viral RNA genomes such as the coronaviruses.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Rebeca Lobo-Vega
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain;
| | - Celia Perales
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain;
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Auth M, Nyikó T, Auber A, Silhavy D. The role of RST1 and RIPR proteins in plant RNA quality control systems. Plant Mol Biol 2021; 106:271-284. [PMID: 33864582 PMCID: PMC8116306 DOI: 10.1007/s11103-021-01145-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/22/2021] [Indexed: 05/03/2023]
Abstract
To keep mRNA homeostasis, the RNA degradation, quality control and silencing systems should act in balance in plants. Degradation of normal mRNA starts with deadenylation, then deadenylated transcripts are degraded by the SKI-exosome 3'-5' and/or XRN4 5'-3' exonucleases. RNA quality control systems identify and decay different aberrant transcripts. RNA silencing degrades double-stranded transcripts and homologous mRNAs. It also targets aberrant and silencing prone transcripts. The SKI-exosome is essential for mRNA homeostasis, it functions in normal mRNA degradation and different RNA quality control systems, and in its absence silencing targets normal transcripts. It is highly conserved in eukaryotes, thus recent reports that the plant SKI-exosome is associated with RST1 and RIPR proteins and that, they are required for SKI-exosome-mediated decay of silencing prone transcripts were unexpected. To clarify whether RST1 and RIPR are essential for all SKI-exosome functions or only for the elimination of silencing prone transcripts, degradation of different reporter transcripts was studied in RST1 and RIPR inactivated Nicotiana benthamiana plants. As RST1 and RIPR, like the SKI-exosome, were essential for Non-stop and No-go decay quality control systems, and for RNA silencing- and minimum ORF-mediated decay, we propose that RST1 and RIPR are essential components of plant SKI-exosome supercomplex.
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Affiliation(s)
- Mariann Auth
- Biological Research Centre, Institute of Plant Biology, ELKH, Temesvári krt 62, 6726, Szeged, Hungary
- Agricultural Biotechnology Institute, Department of Genetics, NARIC, Gödöllő, Hungary
| | - Tünde Nyikó
- Agricultural Biotechnology Institute, Department of Genetics, NARIC, Gödöllő, Hungary
| | - Andor Auber
- Agricultural Biotechnology Institute, Department of Genetics, NARIC, Gödöllő, Hungary
| | - Dániel Silhavy
- Biological Research Centre, Institute of Plant Biology, ELKH, Temesvári krt 62, 6726, Szeged, Hungary.
- Agricultural Biotechnology Institute, Department of Genetics, NARIC, Gödöllő, Hungary.
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Kishimoto Y, Nakagawa O, Fujii A, Yoshioka K, Nagata T, Yokota T, Hari Y, Obika S. 2',4'-BNA/LNA with 9-(2-Aminoethoxy)-1,3-diaza-2-oxophenoxazine Efficiently Forms Duplexes and Has Enhanced Enzymatic Resistance*. Chemistry 2021; 27:2427-2438. [PMID: 33280173 PMCID: PMC7898338 DOI: 10.1002/chem.202003982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 11/28/2022]
Abstract
Artificial nucleic acids are widely used in various technologies, such as nucleic acid therapeutics and DNA nanotechnologies requiring excellent duplex-forming abilities and enhanced nuclease resistance. 2'-O,4'-C-Methylene-bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA) with 1,3-diaza-2-oxophenoxazine (BNAP (BH )) was previously reported. Herein, a novel BH analogue, 2',4'-BNA/LNA with 9-(2-aminoethoxy)-1,3-diaza-2-oxophenoxazine (G-clamp), named BNAP-AEO (BAEO ), was designed. The BAEO nucleoside was successfully synthesized and incorporated into oligodeoxynucleotides (ODNs). ODNs containing BAEO possessed up to 104 -, 152-, and 11-fold higher binding affinities for complementary (c) RNA than those of ODNs containing 2'-deoxycytidine (C), 2',4'-BNA/LNA with 5-methylcytosine (L), or 2'-deoxyribonucleoside with G-clamp (PAEO ), respectively. Moreover, duplexes formed by ODN bearing BAEO with cDNA and cRNA were thermally stable, even under molecular crowding conditions induced by the addition of polyethylene glycol. Furthermore, ODN bearing BAEO was more resistant to 3'-exonuclease than ODNs with phosphorothioate linkages.
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Faculty of Pharmaceutical SciencesTokushima Bunri University180 Nishihamahoji, Yamashiro-choTokushima770-8514Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
| | - Kotaro Yoshioka
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Tetsuya Nagata
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Takanori Yokota
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical SciencesTokushima Bunri University180 Nishihamahoji, Yamashiro-choTokushima770-8514Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
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Pham KM, Suter SR, Lu SS, Beal PA. Ester modification at the 3' end of anti-microRNA oligonucleotides increases potency of microRNA inhibition. Bioorg Med Chem 2021; 29:115894. [PMID: 33290908 PMCID: PMC8610567 DOI: 10.1016/j.bmc.2020.115894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that play a fundamental role in gene regulation. Deregulation of miRNA expression has a strong correlation with disease and antisense oligonucleotides that bind and inhibit miRNAs associated with disease have therapeutic potential. Current research on the chemical modification of anti-miRNA oligonucleotides (anti-miRs) is focused on alterations of the phosphodiester-ribose backbone to improve nuclease resistance and binding affinity to miRNA strands. Here we describe a structure-guided approach for modification of the 3'-end of anti-miRs by screening for modifications compatible with a nucleotide-binding pocket present on human Argonaute2 (hAgo2). We computationally screened a library of 190 triazole-modified nucleoside analogs for complementarity to the t1A-binding pocket of hAgo2. Seventeen top scoring triazoles were then incorporated into the 3' end of anti-miR21 and potency was evaluated for each in a cell-based assay for anti-miR activity. Four triazole-modified anti-miRs showed higher potency than anti-miR21 bearing a 3' adenosine. In particular, a triazole-modified nucleoside bearing an ester substituent imparted a nine-fold and five-fold increase in activity for both anti-miR21 and anti-miR122 at 300 and 5 nM, respectively. The ester group was shown to be critical as a similar carboxylic acid and amide were inactive. Furthermore, anti-miR 3' end modification with triazole-modified nucleoside analogs improved resistance to snake venom phosphodiesterase, a 3'-exonuclease. Thus, the modifications described here are good candidates for improvement of anti-miR activity.
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Affiliation(s)
- Kevin M Pham
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, United States
| | - Scott R Suter
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, United States
| | - Shannon S Lu
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, United States
| | - Peter A Beal
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, United States.
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35
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Wong N, John S, Nussenzweig A, Canela A. END-seq: An Unbiased, High-Resolution, and Genome-Wide Approach to Map DNA Double-Strand Breaks and Resection in Human Cells. Methods Mol Biol 2021; 2153:9-31. [PMID: 32840769 DOI: 10.1007/978-1-0716-0644-5_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA double-strand breaks (DSBs) represent the most toxic form of DNA damage and can arise in either physiological or pathological conditions. If left unrepaired, these DSBs can lead to genome instability which serves as a major driver to tumorigenesis and other pathologies. Consequently, localizing DSBs and understanding the dynamics of break formation and the repair process are of great interest for dissecting underlying mechanisms and in the development of targeted therapies. Here, we describe END-seq, a highly sensitive next-generation sequencing technique for quantitatively mapping DNA double-strand breaks (DSB) at nucleotide resolution across the genome in an unbiased manner. END-seq is based on the direct ligation of a sequencing adapter to the ends of DSBs and provides information about DNA processing (end resection) at DSBs, a critical determinant in the selection of repair pathways. The absence of cell fixation and the use of agarose for embedding cells and exonucleases for blunting the ends of DSBs are key advances that contribute to the technique's increased sensitivity and robustness over previously established methods. Overall, END-seq has provided a major technical advance for mapping DSBs and has also helped inform the biology of complex biological processes including genome organization, replication fork collapse and chromosome fragility, off-target identification of RAG recombinase and gene-editing nucleases, and DNA end resection at sites of DSBs.
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Affiliation(s)
- Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sam John
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
| | - Andrés Canela
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
- The Hakubi Center for Advanced Research and Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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36
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Zabolotnaya E, Mela I, Henderson RM, Robinson NP. Turning the Mre11/Rad50 DNA repair complex on its head: lessons from SMC protein hinges, dynamic coiled-coil movements and DNA loop-extrusion? Biochem Soc Trans 2020; 48:2359-2376. [PMID: 33300987 PMCID: PMC7752040 DOI: 10.1042/bst20170168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
The bacterial SbcC/SbcD DNA repair proteins were identified over a quarter of a century ago. Following the subsequent identification of the homologous Mre11/Rad50 complex in the eukaryotes and archaea, it has become clear that this conserved chromosomal processing machinery is central to DNA repair pathways and the maintenance of genomic stability in all forms of life. A number of experimental studies have explored this intriguing genome surveillance machinery, yielding significant insights and providing conceptual advances towards our understanding of how this complex operates to mediate DNA repair. However, the inherent complexity and dynamic nature of this chromosome-manipulating machinery continue to obfuscate experimental interrogations, and details regarding the precise mechanisms that underpin the critical repair events remain unanswered. This review will summarize our current understanding of the dramatic structural changes that occur in Mre11/Rad50 complex to mediate chromosomal tethering and accomplish the associated DNA processing events. In addition, undetermined mechanistic aspects of the DNA enzymatic pathways driven by this vital yet enigmatic chromosomal surveillance and repair apparatus will be discussed. In particular, novel and putative models of DNA damage recognition will be considered and comparisons will be made between the modes of action of the Rad50 protein and other related ATPases of the overarching SMC superfamily.
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Affiliation(s)
| | - Ioanna Mela
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, U.K
| | | | - Nicholas P. Robinson
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, U.K
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Dodd T, Botto M, Paul F, Fernandez-Leiro R, Lamers MH, Ivanov I. Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path. Nat Commun 2020; 11:5379. [PMID: 33097731 PMCID: PMC7584608 DOI: 10.1038/s41467-020-19165-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/02/2020] [Indexed: 12/27/2022] Open
Abstract
Proofreading by replicative DNA polymerases is a fundamental mechanism ensuring DNA replication fidelity. In proofreading, mis-incorporated nucleotides are excised through the 3'-5' exonuclease activity of the DNA polymerase holoenzyme. The exonuclease site is distal from the polymerization site, imposing stringent structural and kinetic requirements for efficient primer strand transfer. Yet, the molecular mechanism of this transfer is not known. Here we employ molecular simulations using recent cryo-EM structures and biochemical analyses to delineate an optimal free energy path connecting the polymerization and exonuclease states of E. coli replicative DNA polymerase Pol III. We identify structures for all intermediates, in which the transitioning primer strand is stabilized by conserved Pol III residues along the fingers, thumb and exonuclease domains. We demonstrate switching kinetics on a tens of milliseconds timescale and unveil a complete pol-to-exo switching mechanism, validated by targeted mutational experiments.
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Affiliation(s)
- Thomas Dodd
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Margherita Botto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Fabian Paul
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL, USA
| | | | - Meindert H Lamers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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Jockusch S, Tao C, Li X, Chien M, Kumar S, Morozova I, Kalachikov S, Russo JJ, Ju J. Sofosbuvir terminated RNA is more resistant to SARS-CoV-2 proofreader than RNA terminated by Remdesivir. Sci Rep 2020; 10:16577. [PMID: 33024223 PMCID: PMC7538426 DOI: 10.1038/s41598-020-73641-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2 is responsible for COVID-19, resulting in the largest pandemic in over a hundred years. After examining the molecular structures and activities of hepatitis C viral inhibitors and comparing hepatitis C virus and coronavirus replication, we previously postulated that the FDA-approved hepatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) might inhibit SARS-CoV-2. We subsequently demonstrated that Sofosbuvir triphosphate is incorporated by the relatively low fidelity SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases (RdRps), serving as an immediate polymerase reaction terminator, but not by a host-like high fidelity DNA polymerase. Other investigators have since demonstrated the ability of Sofosbuvir to inhibit SARS-CoV-2 replication in lung and brain cells; additionally, COVID-19 clinical trials with EPCLUSA and with Sofosbuvir plus Daclatasvir have been initiated in several countries. SARS-CoV-2 has an exonuclease-based proofreader to maintain the viral genome integrity. Any effective antiviral targeting the SARS-CoV-2 RdRp must display a certain level of resistance to this proofreading activity. We report here that Sofosbuvir terminated RNA resists removal by the exonuclease to a substantially higher extent than RNA terminated by Remdesivir, another drug being used as a COVID-19 therapeutic. These results offer a molecular basis supporting the current use of Sofosbuvir in combination with other drugs in COVID-19 clinical trials.
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Affiliation(s)
- Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Irina Morozova
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Sergey Kalachikov
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA.
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Huang F, Tanaka H, Knudsen BS, Rutgers JK. Mutant POLQ and POLZ/REV3L DNA polymerases may contribute to the favorable survival of patients with tumors with POLE mutations outside the exonuclease domain. BMC Med Genet 2020; 21:167. [PMID: 32838755 PMCID: PMC7446057 DOI: 10.1186/s12881-020-01089-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Mutations in the exonuclease domain of POLE, a DNA polymerase associated with DNA replication and repair, lead to cancers with ultra-high mutation rates. Most studies focus on intestinal and uterine cancers with POLE mutations. These cancers exhibit a significant immune cell infiltrate and favorable prognosis. We questioned whether loss of function of other DNA polymerases can cooperate to POLE to generate the ultramutator phenotype. METHODS We used cases and data from 15 cancer types in The Cancer Genome Atlas to investigate mutation frequencies of 14 different DNA polymerases. We tested whether tumor mutation burden, patient outcome (disease-free survival) and immune cell infiltration measured by ESTIMATE can be attributed to mutations in POLQ and POLZ/REV3L. RESULTS Thirty six percent of colorectal, stomach and endometrial cancers with POLE mutations carried additional mutations in POLQ (E/Q), POLZ/REV3L (E/Z) or both DNA polymerases (E/Z/Q). The mutation burden in these tumors was significantly greater compared to POLE-only (E) mutant tumors (p < 0.001). In addition, E/Q, E/Z, and E/Q/Z mutant tumors possessed an increased frequency of mutations in the POLE exonuclease domain (p = 0.013). Colorectal, stomach and endometrial E/Q, E/Z, and E/Q/Z mutant tumors within TCGA demonstrated 100% disease-free survival, even if the POLE mutations occurred outside the exonuclease domain (p = 0.003). However, immune scores in these tumors were related to microsatellite instability (MSI) and not POLE mutation status. This suggests that the host immune response may not be the sole mechanism for prolonged disease-free survival of ultramutated tumors in this cohort. CONCLUSION Results in this study demonstrate that mutations in POLQ and REV3L in POLE mutant tumors should undergo further investigation to determine whether POLQ and REV3L mutations contribute to the ultramutator phenotype and favorable outcome of patients with POLE mutant tumors.
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Affiliation(s)
- Fangjin Huang
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Hisashi Tanaka
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Samuel Oschin Cancer Research Institute (SOCCI), Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Beatrice S Knudsen
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Samuel Oschin Cancer Research Institute (SOCCI), Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Department of Pathology, University of Utah, Salt Lake City, UT, 84112, USA.
| | - Joanne K Rutgers
- Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
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40
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Pan S, Li KE, Huang W, Zhong H, Wu H, Wang Y, Zhang H, Cai Z, Guo H, Chen X, Xia Y. Arabidopsis DXO1 possesses deNADding and exonuclease activities and its mutation affects defense-related and photosynthetic gene expression. J Integr Plant Biol 2020; 62:967-983. [PMID: 31449356 PMCID: PMC8034840 DOI: 10.1111/jipb.12867] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/23/2019] [Indexed: 05/26/2023]
Abstract
RNA capping and decapping tightly coordinate with transcription, translation, and RNA decay to regulate gene expression. Proteins in the DXO/Rai1 family have been implicated in mRNA decapping and decay, and mammalian DXO was recently found to also function as a decapping enzyme for NAD+ -capped RNAs (NAD-RNA). The Arabidopsis genome contains a single gene encoding a DXO/Rai1 protein, AtDXO1. Here we show that AtDXO1 possesses both NAD-RNA decapping activity and 5'-3' exonuclease activity but does not hydrolyze the m7 G cap. The atdxo1 mutation increased the stability of NAD-RNAs and led to pleiotropic phenotypes, including severe growth retardation, pale color, and multiple developmental defects. Transcriptome profiling analysis showed that the atdxo1 mutation resulted in upregulation of defense-related genes but downregulation of photosynthesis-related genes. The autoimmunity phenotype of the mutant could be suppressed by either eds1 or npr1 mutation. However, the various phenotypes associated with the atdxo1 mutant could be complemented by an enzymatically inactive AtDXO1. The atdxo1 mutation apparently enhances post-transcriptional gene silencing by elevating levels of siRNAs. Our study indicates that AtDXO1 regulates gene expression in various biological and physiological processes through its pleiotropic molecular functions in mediating RNA processing and decay.
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Affiliation(s)
- Shuying Pan
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Kai-en Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Wei Huang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Huan Zhong
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Huihui Wu
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuan Wang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - He Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Hongwei Guo
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
- State Key Laboratory of Agricultural Biotechnology, School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
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Boeckemeier L, Kraehenbuehl R, Keszthelyi A, Gasasira MU, Vernon EG, Beardmore R, Vågbø CB, Chaplin D, Gollins S, Krokan HE, Lambert SAE, Paizs B, Hartsuiker E. Mre11 exonuclease activity removes the chain-terminating nucleoside analog gemcitabine from the nascent strand during DNA replication. Sci Adv 2020; 6:eaaz4126. [PMID: 32523988 PMCID: PMC7259961 DOI: 10.1126/sciadv.aaz4126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
The Mre11 nuclease is involved in early responses to DNA damage, often mediated by its role in DNA end processing. MRE11 mutations and aberrant expression are associated with carcinogenesis and cancer treatment outcomes. While, in recent years, progress has been made in understanding the role of Mre11 nuclease activities in DNA double-strand break repair, their role during replication has remained elusive. The nucleoside analog gemcitabine, widely used in cancer therapy, acts as a replication chain terminator; for a cell to survive treatment, gemcitabine needs to be removed from replicating DNA. Activities responsible for this removal have, so far, not been identified. We show that Mre11 3' to 5' exonuclease activity removes gemcitabine from nascent DNA during replication. This contributes to replication progression and gemcitabine resistance. We thus uncovered a replication-supporting role for Mre11 exonuclease activity, which is distinct from its previously reported detrimental role in uncontrolled resection in recombination-deficient cells.
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Affiliation(s)
- L. Boeckemeier
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - R. Kraehenbuehl
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - A. Keszthelyi
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - M. U. Gasasira
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - E. G. Vernon
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - R. Beardmore
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - C. B. Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - D. Chaplin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - S. Gollins
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - H. E. Krokan
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - S. A. E. Lambert
- Institut Curie, Paris-Saclay University, UMR3348, F-91450 Orsay, France
| | - B. Paizs
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - E. Hartsuiker
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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Imam H, Kim GW, Mir SA, Khan M, Siddiqui A. Interferon-stimulated gene 20 (ISG20) selectively degrades N6-methyladenosine modified Hepatitis B Virus transcripts. PLoS Pathog 2020; 16:e1008338. [PMID: 32059034 PMCID: PMC7046284 DOI: 10.1371/journal.ppat.1008338] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/27/2020] [Accepted: 01/20/2020] [Indexed: 12/24/2022] Open
Abstract
Interferon (IFN) stimulates a whole repertoire of cellular genes, collectively referred to as ISGs (Interferon-stimulated genes). ISG20, a 3´-5´ exonuclease enzyme, has been previously shown to bind and degrade hepatitis B Virus (HBV) transcripts. Here, we show that the N6-methyladenosine (m6A)-modified HBV transcripts are selectively recognized and processed for degradation by ISG20. Moreover, this effect of ISG20 is critically regulated by m6A reader protein, YTHDF2 (YTH-domain family 2). Previously, we identified a unique m6A site within HBV transcripts and confirmed that methylation at nucleotide A1907 regulates HBV lifecycle. In this report, we now show that the methylation at A1907 is a critical regulator of IFN-α mediated decay of HBV RNA. We observed that the HBV RNAs become less sensitive to ISG20 mediated degradation when methyltransferase enzymes or m6A reader protein YTHDF2 are silenced in HBV expressing cells. By using an enzymatically inactive form ISG20D94G, we further demonstrated that ISG20 forms a complex with m6A modified HBV RNA and YTHDF2 protein. Due to terminal redundancy, HBV genomic nucleotide A1907 position is acquired twice by pregenomic RNA (pgRNA) during transcription and therefore the sites of methylation are encoded within 5´ and 3´ epsilon stem loops. We generated HBV mutants that lack m6A site at either one (5´ or 3´) or both the termini (5´& 3´). Using these mutants, we demonstrated that m6A modified HBV RNAs are subjected to ISG20-mediated decay and propose sequence of events, in which ISG20 binds with YTHDF2 and recognizes m6A-modified HBV transcripts to carry out the ribonuclease activity. This is the first study, which identifies a hitherto unknown role of m6A modification of RNA in IFN-α induced viral RNA degradation and proposes a new role of YTHDF2 protein as a cofactor required for IFN-α mediated viral RNA degradation. Hepatitis B Virus (HBV) is a DNA virus but replicates through a transitional pregenomic RNA (pgRNA). Interferon stimulated antiviral RNase, ISG20 selectively binds to the lower epsilon stem loop of HBV RNA and causes their degradation. Surprisingly this ISG20 binding site is chemically modified by N6-methyladenosine addition to A1907 residue, which resides in the lower region of the epsilon stem loop. This single m6A site occurs twice due to terminal redundancy of sequences in the pgRNA. We demonstrated herein that IFN-α-induced ISG20 can selectively degrade m6A modified HBV RNA. Using a combined strategy of silencing cellular methyltransferases, m6A binding protein YTHDF2 and the m6A sites mutants, we show that HBV transcripts are resistant to either IFN-α treatment or ectopically introduced ISG20 mediated degradation. YTHDF2 is an m6A binding protein which makes the HBV RNAs less stable. YTHDF2 protein forms a complex with IFN-α stimulated ISG20 and executes the nuclease digestion of the recruited m6A modified transcripts. Absence of cellular m6A machinery (methyltransferases or m6A reader proteins) makes the HBV RNA unresponsive to ISG20 mediated decay. This study provides molecular explanation of IFN-α mediated degradation of m6A modified HBV RNAs.
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Affiliation(s)
- Hasan Imam
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Geon-Woo Kim
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Saiful Anam Mir
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Mohsin Khan
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
- * E-mail: (MK); (AS)
| | - Aleem Siddiqui
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
- * E-mail: (MK); (AS)
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Abstract
Phage-display technology offers robust methods for isolating antibody (Ab) molecules with specificity for different target antigens. Recent advancements couple Ab selections with in silico strategies, such as predictive computational models or next-generation sequencing metadata analysis of Ab selections. These advancements result in enhanced Ab clonal diversities with potential for enlarged epitope coverage of the target antigen. A current limitation however, is that de novo Ab sequences must undergo DNA gene synthesis, and subsequent expression as Ab proteins for downstream validations. Due to the high costs and time for commercially generating large sets of DNA genes, we report a high-throughput platform for the synthesis of in silico derived Ab clones. As a proof of concept we demonstrate the simultaneous synthesis of 96 unique Abs with varied lengths and complementary determining region compositions. Each of the 96 Ab clones undergoes a one-step enzymatic assembly of distinct DNA fragments that combine into a circularized Fab expression plasmid. This strategy allows for the rapid and efficient synthesis of 96 DNA constructs in a 3 day window, and exhibits high percentage fidelity-greater than 93%. Accordingly, the synthesis of Ab DNA constructs as Fab expression plasmids allow for rapid execution of downstream Ab protein validations, with potential for implementation into high-throughput Ab protein characterization pipelines. Altogether, the platform presented here proves rapid and also cost-effective, which is important for labs with limited resources, since it utilizes standard laboratory equipment and molecular reagents.
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Affiliation(s)
- Eugenio Gallo
- Department of Molecular Genetics, Charles Best Institute, University of Toronto, 112 College Street, 112 College Street, Room 70, Toronto, ON, M5G 1L6, Canada.
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Yoganand KN, Muralidharan M, Nimkar S, Anand B. Fidelity of prespacer capture and processing is governed by the PAM-mediated interactions of Cas1-2 adaptation complex in CRISPR-Cas type I-E system. J Biol Chem 2019; 294:20039-20053. [PMID: 31748409 PMCID: PMC6937570 DOI: 10.1074/jbc.ra119.009438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes deploy CRISPR-Cas-based RNA-guided adaptive immunity to fend off mobile genetic elements such as phages and plasmids. During CRISPR adaptation, which is the first stage of CRISPR immunity, the Cas1-2 integrase complex captures invader-derived prespacer DNA and specifically integrates it at the leader-repeat junction as spacers. For this integration, several variants of CRISPR-Cas systems use Cas4 as an indispensable nuclease for selectively processing the protospacer adjacent motif (PAM) containing prespacers to a defined length. Surprisingly, however, a few CRISPR-Cas systems, such as type I-E, are bereft of Cas4. Despite the absence of Cas4, how the prespacers show impeccable conservation for length and PAM selection in type I-E remains intriguing. Here, using in vivo and in vitro integration assays, deep sequencing, and exonuclease footprinting, we show that Cas1-2/I-E-via the type I-E-specific extended C-terminal tail of Cas1-displays intrinsic affinity for PAM containing prespacers of variable length in Escherichia coli Although Cas1-2/I-E does not prune the prespacers, its binding protects the prespacer boundaries from exonuclease action. This ensures the pruning of exposed ends by exonucleases to aptly sized substrates for integration into the CRISPR locus. In summary, our work reveals that in a few CRISPR-Cas variants, such as type I-E, the specificity of PAM selection resides with Cas1-2, whereas the prespacer processing is co-opted by cellular non-Cas exonucleases, thereby offsetting the need for Cas4.
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Affiliation(s)
- Kakimani Nagarajan Yoganand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Manasasri Muralidharan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Siddharth Nimkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Baskaran Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
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45
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Wu CC, Lin JL, Yang-Yen HF, Yuan HS. A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication. Nucleic Acids Res 2019; 47:5405-5419. [PMID: 30949702 PMCID: PMC6547421 DOI: 10.1093/nar/gkz241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/13/2019] [Accepted: 03/25/2019] [Indexed: 01/01/2023] Open
Abstract
Replication of sufficient mitochondrial DNA (mtDNA) is essential for maintaining mitochondrial functions in mammalian cells. During mtDNA replication, RNA primers must be removed before the nascent circular DNA strands rejoin. This process involves mitochondrial RNase H1, which removes most of the RNA primers but leaves two ribonucleotides attached to the 5′ end of nascent DNA. A subsequent 5′-exonuclease is required to remove the residual ribonucleotides, however, it remains unknown if any mitochondrial 5′-exonuclease could remove two RNA nucleotides from a hybrid duplex DNA. Here, we report that human mitochondrial Exonuclease G (ExoG) may participate in this particular process by efficiently cleaving at RNA–DNA junctions to remove the 5′-end RNA dinucleotide in an RNA/DNA hybrid duplex. Crystal structures of human ExoG bound respectively with DNA, RNA/DNA hybrid and RNA–DNA chimeric duplexes uncover the underlying structural mechanism of how ExoG specifically recognizes and cleaves at RNA–DNA junctions of a hybrid duplex with an A-form conformation. This study hence establishes the molecular basis of ExoG functioning as a unique 5′-exonuclease to mediate the flap-independent RNA primer removal process during mtDNA replication to maintain mitochondrial genome integrity.
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Affiliation(s)
- Chyuan-Chuan Wu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Jason L J Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Hsin-Fang Yang-Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, ROC
- To whom correspondence should be addressed. Tel: +886 2 27884151;
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Zheng J, Peng X, Wang Y, Bao T, Wen W, Zhang X, Wang S. An exonuclease-assisted triple-amplified electrochemical aptasensor for mucin 1 detection based on strand displacement reaction and enzyme catalytic strategy. Anal Chim Acta 2019; 1086:75-81. [PMID: 31561796 DOI: 10.1016/j.aca.2019.08.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/07/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022]
Abstract
The development of some sensitive methods for MUC1 is critical for preclinical diagnosis of tumors. In this experiment, we built a triple-amplified electrochemical aptasensor to achieve sensitive detection of MUC1, which was based on exonuclease III (Exo III)-assisted with strand displacement reaction and enzyme catalytic strategy. Firstly, with the help of Exo III, MUC1 and aptamer could be recycled during the cycle I, the single stranded DNA-1 (S-1) was produced during the process and was introduced to the hybride reaction on the electrode. Secondly, during the cycle II, strand displacement reaction was triggered on the electrode with the adding of hairpin DNA-2 (H-2). Thirdly, after the gold nanoparticles (AuNPs)-DNA-enzyme conjugates hybrided with the H-2 on the electrode, the AuNPs-DNA-enzyme conjugates could act as signal probe to produce electrochemical catalytic signal. We used the fabricated triple-amplified electrochemical aptasensor that could detect MUC1 from 0.1 pg mL-1 to 10 ng mL-1 with the detection limit of 0.04 pg mL-1 under the optimized experimental conditions. The constructed triple-amplified electrochemical aptasensor could be applied in real samples determination. Besides, the strategy can be applied to detect other proteins for health monitoring.
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Affiliation(s)
- Jiaxin Zheng
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Xiaolun Peng
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Yijia Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Ting Bao
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Wei Wen
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China.
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Kotlajich MV, Xia J, Zhai Y, Lin HY, Bradley CC, Shen X, Mei Q, Wang AZ, Lynn EJ, Shee C, Chen LT, Li L, Miller KM, Herman C, Hastings PJ, Rosenberg SM. Fluorescent fusions of the N protein of phage Mu label DNA damage in living cells. DNA Repair (Amst) 2018; 72:86-92. [PMID: 30268364 PMCID: PMC6287932 DOI: 10.1016/j.dnarep.2018.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 09/09/2018] [Accepted: 09/10/2018] [Indexed: 01/06/2023]
Abstract
The N protein of phage Mu was indicated from studies in Escherichia coli to hold linear Mu chromosomes in a circular conformation by non-covalent association, and thus suggested potentially to bind DNA double-stranded ends. Because of its role in association with linear Mu DNA, we tested whether fluorescent-protein fusions to N might provide a useful tool for labeling DNA damage including double-strand break (DSB) ends in single cells. We compared N-GFP with a biochemically well documented DSB-end binding protein, the Gam protein of phage Mu, also fused to GFP. We find that N-GFP produced in live E. coli forms foci in response to DNA damage induced by radiomimetic drug phleomycin, indicating that it labels damaged DNA. N-GFP also labels specific DSBs created enzymatically by I-SceI double-strand endonuclease, and by X-rays, with the numbers of foci corresponding with the numbers of DSBs generated, indicating DSB labeling. However, whereas N-GFP forms about half as many foci as GamGFP with phleomycin, its labeling of I-SceI- and X-ray-induced DSBs is far less efficient than that of GamGFP. The data imply that N-GFP binds and labels DNA damage including DSBs, but may additionally label phleomycin-induced non-DSB damage, with which DSB-specific GamGFP does not interact. The data indicate that N-GFP labels DNA damage, and may be useful for general, not DSB-specific, DNA-damage detection.
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Affiliation(s)
- Matthew V Kotlajich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jun Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yin Zhai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hsin-Yu Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Catherine C Bradley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA; Robert and Janice McNair Foundation/McNair Medical Institute M.D./Ph.D. Scholars Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xi Shen
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Qian Mei
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA; Systems, Synthetic and Physical Biology Program, Rice University, Houston, Texas 77030, USA
| | - Anthony Z Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erica J Lynn
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Chandan Shee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Li-Tzu Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kyle M Miller
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA; Systems, Synthetic and Physical Biology Program, Rice University, Houston, Texas 77030, USA.
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Takami T, Ohnishi N, Kurita Y, Iwamura S, Ohnishi M, Kusaba M, Mimura T, Sakamoto W. Organelle DNA degradation contributes to the efficient use of phosphate in seed plants. Nat Plants 2018; 4:1044-1055. [PMID: 30420711 DOI: 10.1038/s41477-018-0291-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/27/2018] [Indexed: 06/09/2023]
Abstract
Mitochondria and chloroplasts (plastids) both harbour extranuclear DNA that originates from the ancestral endosymbiotic bacteria. These organelle DNAs (orgDNAs) encode limited genetic information but are highly abundant, with multiple copies in vegetative tissues, such as mature leaves. Abundant orgDNA constitutes a substantial pool of organic phosphate along with RNA in chloroplasts, which could potentially contribute to phosphate recycling when it is degraded and relocated. However, whether orgDNA is degraded nucleolytically in leaves remains unclear. In this study, we revealed the prevailing mechanism in which organelle exonuclease DPD1 degrades abundant orgDNA during leaf senescence. The DPD1 degradation system is conserved in seed plants and, more remarkably, we found that it was correlated with the efficient use of phosphate when plants were exposed to nutrient-deficient conditions. The loss of DPD1 compromised both the relocation of phosphorus to upper tissues and the response to phosphate starvation, resulting in reduced plant fitness. Our findings highlighted that DNA is also an internal phosphate-rich reservoir retained in organelles since their endosymbiotic origin.
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Affiliation(s)
- Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Norikazu Ohnishi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Yuko Kurita
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Shoko Iwamura
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Miwa Ohnishi
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Makoto Kusaba
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.
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Saathoff JH, Käshammer L, Lammens K, Byrne RT, Hopfner KP. The bacterial Mre11-Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions. Nucleic Acids Res 2018; 46:11303-11314. [PMID: 30277537 PMCID: PMC6265447 DOI: 10.1093/nar/gky878] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022] Open
Abstract
The Mre11-Rad50 complex is a DNA double-strand break sensor that cleaves blocked DNA ends and hairpins by an ATP-dependent endo/exonuclease activity for subsequent repair. For that, Mre11-Rad50 complexes, including the Escherichia coli homolog SbcCD, can endonucleolytically cleave one or both strands near a protein block and process free DNA ends via a 3'-5' exonuclease, but a unified basis for these distinct activities is lacking. Here we analyzed DNA binding, ATPase and nuclease reactions on different DNA substrates. SbcCD clips terminal bases of both strands of the DNA end in the presence of ATPγS. It introduces a DNA double-strand break around 20-25 bp from a blocked end after multiple rounds of ATP hydrolysis in a reaction that correlates with local DNA meltability. Interestingly, we find that nuclease reactions on opposing strands are chemically distinct, leaving a 5' phosphate on one strand, but a 3' phosphate on the other strand. Collectively, our results identify an unexpected chemical variability of the nuclease, indicating that the complex is oriented at a free DNA end and facing a block with opposite polarity. This suggests a unified model for ATP-dependent endo- and exonuclease reactions at internal DNA near a block and at free DNA ends.
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Affiliation(s)
- Jan-Hinnerk Saathoff
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Lisa Käshammer
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Katja Lammens
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Robert Thomas Byrne
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Center for Integrated Protein Science, Munich, Germany
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Abstract
DNA synthesis, carried out by DNA polymerases, requires balancing speed and accuracy for faithful replication of the genome. High fidelity DNA polymerases contain a 3'-5' exonuclease domain that can remove misincorporated nucleotides on the 3' end of the primer strand, a process called proofreading. The E. coli replicative polymerase, DNA polymerase III, has spatially separated (∼55 Å apart) polymerase and exonuclease subunits. Here, we report on the dynamics of E. coli DNA polymerase III proofreading in the presence of its processivity factor, the β2-sliding clamp, at varying base pair termini using single-molecule FRET. We find that the binding kinetics do not depend on the base identity at the termini, indicating a tolerance for DNA mismatches. Further, our single-molecule data and MD simulations show two previously unobserved features: (1) DNA Polymerase III is a highly dynamic protein that adopts multiple conformational states while bound to DNA with matched or mismatched ends, and (2) an exonuclease-deficient DNA polymerase III has reduced conformational flexibility. Overall, our single-molecule experiments provide high time-resolution insight into a mechanism that ensures high fidelity DNA replication to maintain genome integrity.
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Affiliation(s)
- Hailey L Gahlon
- Department of Medicine, Molecular Virology, Imperial College London, Du Cane Road, London W12 0NN, UK.
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