LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 7 of total 7

Search options

  1. Article ; Online: DNA polymerases in the mitochondria: A critical review of the evidence.

    Krasich, Rachel / Copeland, William C

    Frontiers in bioscience (Landmark edition)

    2017  Volume 22, Issue 4, Page(s) 692–709

    Abstract: Since 1970, the DNA polymerase gamma (PolG) has been known to be the DNA polymerase responsible for replication and repair of mitochondrial DNA, and until recently it was generally accepted that this was the only polymerase present in mitochondria. ... ...

    Abstract Since 1970, the DNA polymerase gamma (PolG) has been known to be the DNA polymerase responsible for replication and repair of mitochondrial DNA, and until recently it was generally accepted that this was the only polymerase present in mitochondria. However, recent data has challenged that opinion, as several polymerases are now proposed to have activity in mitochondria. To date, their exact role of these other DNA polymerases is unclear and the amount of evidence supporting their role in mitochondria varies greatly. Further complicating matters, no universally accepted standards have been set for definitive proof of the mitochondrial localization of a protein. To gain an appreciation of these newly proposed DNA polymerases in the mitochondria, we review the evidence and standards needed to establish the role of a polymerase in the mitochondria. Employing PolG as an example, we established a list of criteria necessary to verify the existence and function of new mitochondrial proteins. We then apply this criteria towards several other putative mitochondrial polymerases. While there is still a lot left to be done in this exciting new direction, it is clear that PolG is not acting alone in mitochondria, opening new doors for potential replication and repair mechanisms.
    MeSH term(s) Animals ; DNA Polymerase beta/genetics ; DNA Polymerase beta/metabolism ; DNA Polymerase gamma/genetics ; DNA Polymerase gamma/metabolism ; DNA Primase/genetics ; DNA Primase/metabolism ; DNA, Mitochondrial/genetics ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Humans ; Mitochondria/enzymology ; Mitochondria/genetics ; Mitochondrial Diseases/enzymology ; Mitochondrial Diseases/genetics ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Multifunctional Enzymes/genetics ; Multifunctional Enzymes/metabolism ; Mutation ; DNA Polymerase theta
    Chemical Substances DNA, Mitochondrial ; DNA-Binding Proteins ; Mitochondrial Proteins ; Multifunctional Enzymes ; DNA Primase (EC 2.7.7.-) ; DNA polymerase zeta (EC 2.7.7.-) ; PrimPol protein, human (EC 2.7.7.-) ; DNA Polymerase beta (EC 2.7.7.7) ; DNA Polymerase gamma (EC 2.7.7.7) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; POLG protein, human (EC 2.7.7.7) ; REV3L protein, human (EC 2.7.7.7) ; Rad30 protein (EC 2.7.7.7)
    Language English
    Publishing date 2017-01-01
    Publishing country Singapore
    Document type Journal Article ; Review
    ZDB-ID 2704569-9
    ISSN 2768-6698 ; 2768-6698
    ISSN (online) 2768-6698
    ISSN 2768-6698
    DOI 10.2741/4510
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Functions that protect Escherichia coli from DNA-protein crosslinks.

    Krasich, Rachel / Wu, Sunny Yang / Kuo, H Kenny / Kreuzer, Kenneth N

    DNA repair

    2015  Volume 28, Page(s) 48–59

    Abstract: Pathways for tolerating and repairing DNA-protein crosslinks (DPCs) are poorly defined. We used transposon mutagenesis and candidate gene approaches to identify DPC-hypersensitive Escherichia coli mutants. DPCs were induced by azacytidine (aza-C) ... ...

    Abstract Pathways for tolerating and repairing DNA-protein crosslinks (DPCs) are poorly defined. We used transposon mutagenesis and candidate gene approaches to identify DPC-hypersensitive Escherichia coli mutants. DPCs were induced by azacytidine (aza-C) treatment in cells overexpressing cytosine methyltransferase; hypersensitivity was verified to depend on methyltransferase expression. We isolated hypersensitive mutants that were uncovered in previous studies (recA, recBC, recG, and uvrD), hypersensitive mutants that apparently activate phage Mu Gam expression, and novel hypersensitive mutants in genes involved in DNA metabolism, cell division, and tRNA modification (dinG, ftsK, xerD, dnaJ, hflC, miaA, mnmE, mnmG, and ssrA). Inactivation of SbcCD, which can cleave DNA at protein-DNA complexes, did not cause hypersensitivity. We previously showed that tmRNA pathway defects cause aza-C hypersensitivity, implying that DPCs block coupled transcription/translation complexes. Here, we show that mutants in tRNA modification functions miaA, mnmE and mnmG cause defects in aza-C-induced tmRNA tagging, explaining their hypersensitivity. In order for tmRNA to access a stalled ribosome, the mRNA must be cleaved or released from RNA polymerase. Mutational inactivation of functions involved in mRNA processing and RNA polymerase elongation/release (RNase II, RNaseD, RNase PH, RNase LS, Rep, HepA, GreA, GreB) did not cause aza-C hypersensitivity; the mechanism of tmRNA access remains unclear.
    MeSH term(s) Azacitidine/toxicity ; DNA Damage ; DNA Repair ; Escherichia coli/drug effects ; Escherichia coli/genetics ; Escherichia coli/physiology ; Escherichia coli Proteins/genetics ; RNA, Bacterial/metabolism ; Transcription, Genetic/drug effects
    Chemical Substances Escherichia coli Proteins ; RNA, Bacterial ; tmRNA ; Azacitidine (M801H13NRU)
    Language English
    Publishing date 2015-04
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2015.01.016
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Importance of the tmRNA system for cell survival when transcription is blocked by DNA-protein cross-links.

    Kuo, H Kenny / Krasich, Rachel / Bhagwat, Ashok S / Kreuzer, Kenneth N

    Molecular microbiology

    2010  Volume 78, Issue 3, Page(s) 686–700

    Abstract: Anticancer drug 5-azacytidine (aza-C) induces DNA-protein cross-links (DPCs) between cytosine methyltransferase and DNA as the drug inhibits methylation. We found that mutants defective in the tmRNA translational quality control system are hypersensitive ...

    Abstract Anticancer drug 5-azacytidine (aza-C) induces DNA-protein cross-links (DPCs) between cytosine methyltransferase and DNA as the drug inhibits methylation. We found that mutants defective in the tmRNA translational quality control system are hypersensitive to aza-C. Hypersensitivity requires expression of active methyltransferase, indicating the importance of DPC formation. Furthermore, the tmRNA pathway is activated upon aza-C treatment in cells expressing methyltransferase, resulting in increased levels of SsrA tagged proteins. These results argue that the tmRNA pathway clears stalled ribosome-mRNA complexes generated after transcriptional blockage by aza-C-induced DPCs. In support, an ssrA mutant is also hypersensitive to streptolydigin, which blocks RNA polymerase elongation by a different mechanism. The tmRNA pathway is thought to act only on ribosomes containing a 3' RNA end near the A site, and the known pathway for releasing RNA 3' ends from a blocked polymerase involves Mfd helicase. However, an mfd knockout mutant is not hypersensitive to either aza-C-induced DPC formation or streptolydigin, indicating that Mfd is not involved. Transcription termination factor Rho is also likely not involved, because the Rho-specific inhibitor bicyclomycin failed to show synergism with either aza-C or streptolydigin. Based on these findings, we discuss models for how E. coli processes transcription/translation complexes blocked at DPCs.
    MeSH term(s) Azacitidine/pharmacology ; Cross-Linking Reagents/pharmacology ; DNA, Bacterial/chemistry ; DNA, Bacterial/genetics ; Escherichia coli/cytology ; Escherichia coli/drug effects ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Microbial Viability/drug effects ; Protein Biosynthesis/drug effects ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; Transcription, Genetic/drug effects
    Chemical Substances Cross-Linking Reagents ; DNA, Bacterial ; Escherichia coli Proteins ; RNA, Bacterial ; tmRNA ; Azacitidine (M801H13NRU)
    Language English
    Publishing date 2010-09-16
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 619315-8
    ISSN 1365-2958 ; 0950-382X
    ISSN (online) 1365-2958
    ISSN 0950-382X
    DOI 10.1111/j.1365-2958.2010.07355.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article ; Online: Complementation of aprataxin deficiency by base excision repair enzymes in mitochondrial extracts.

    Çaglayan, Melike / Prasad, Rajendra / Krasich, Rachel / Longley, Matthew J / Kadoda, Kei / Tsuda, Masataka / Sasanuma, Hiroyuki / Takeda, Shunichi / Tano, Keizo / Copeland, William C / Wilson, Samuel H

    Nucleic acids research

    2017  Volume 45, Issue 17, Page(s) 10079–10088

    Abstract: Mitochondrial aprataxin (APTX) protects the mitochondrial genome from the consequence of ligase failure by removing the abortive ligation product, i.e. the 5'-adenylate (5'-AMP) group, during DNA replication and repair. In the absence of APTX activity, ... ...

    Abstract Mitochondrial aprataxin (APTX) protects the mitochondrial genome from the consequence of ligase failure by removing the abortive ligation product, i.e. the 5'-adenylate (5'-AMP) group, during DNA replication and repair. In the absence of APTX activity, blocked base excision repair (BER) intermediates containing the 5'-AMP or 5'-adenylated-deoxyribose phosphate (5'-AMP-dRP) lesions may accumulate. In the current study, we examined DNA polymerase (pol) γ and pol β as possible complementing enzymes in the case of APTX deficiency. The activities of pol β lyase and FEN1 nucleotide excision were able to remove the 5'-AMP-dRP group in mitochondrial extracts from APTX-/- cells. However, the lyase activity of purified pol γ was weak against the 5'-AMP-dRP block in a model BER substrate, and this activity was not able to complement APTX deficiency in mitochondrial extracts from APTX-/-Pol β-/- cells. FEN1 also failed to provide excision of the 5'-adenylated BER intermediate in mitochondrial extracts. These results illustrate the potential role of pol β in complementing APTX deficiency in mitochondria.
    Language English
    Publishing date 2017-09-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkx654
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article: Importance of the tmRNA system for cell survival when transcription is blocked by DNA-protein cross‐links

    Kuo, H. Kenny / Krasich, Rachel / Bhagwat, Ashok S / Kreuzer, Kenneth N

    Molecular microbiology. 2010 Nov., v. 78, no. 3

    2010  

    Abstract: Anticancer drug 5‐azacytidine (aza‐C) induces DNA-protein cross‐links (DPCs) between cytosine methyltransferase and DNA as the drug inhibits methylation. We found that mutants defective in the tmRNA translational quality control system are hypersensitive ...

    Abstract Anticancer drug 5‐azacytidine (aza‐C) induces DNA-protein cross‐links (DPCs) between cytosine methyltransferase and DNA as the drug inhibits methylation. We found that mutants defective in the tmRNA translational quality control system are hypersensitive to aza‐C. Hypersensitivity requires expression of active methyltransferase, indicating the importance of DPC formation. Furthermore, the tmRNA pathway is activated upon aza‐C treatment in cells expressing methyltransferase, resulting in increased levels of SsrA tagged proteins. These results argue that the tmRNA pathway clears stalled ribosome‐mRNA complexes generated after transcriptional blockage by aza‐C‐induced DPCs. In support, an ssrA mutant is also hypersensitive to streptolydigin, which blocks RNA polymerase elongation by a different mechanism. The tmRNA pathway is thought to act only on ribosomes containing a 3′ RNA end near the A site, and the known pathway for releasing RNA 3′ ends from a blocked polymerase involves Mfd helicase. However, an mfd knockout mutant is not hypersensitive to either aza‐C‐induced DPC formation or streptolydigin, indicating that Mfd is not involved. Transcription termination factor Rho is also likely not involved, because the Rho‐specific inhibitor bicyclomycin failed to show synergism with either aza‐C or streptolydigin. Based on these findings, we discuss models for how E. coli processes transcription/translation complexes blocked at DPCs.
    Language English
    Dates of publication 2010-11
    Size p. 686-700.
    Publishing place Blackwell Publishing Ltd
    Document type Article
    ZDB-ID 619315-8
    ISSN 1365-2958 ; 0950-382X
    ISSN (online) 1365-2958
    ISSN 0950-382X
    DOI 10.1111/j.1365-2958.2010.07355.x
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  6. Article ; Online: DNA polymerase β: A missing link of the base excision repair machinery in mammalian mitochondria.

    Prasad, Rajendra / Çağlayan, Melike / Dai, Da-Peng / Nadalutti, Cristina A / Zhao, Ming-Lang / Gassman, Natalie R / Janoshazi, Agnes K / Stefanick, Donna F / Horton, Julie K / Krasich, Rachel / Longley, Matthew J / Copeland, William C / Griffith, Jack D / Wilson, Samuel H

    DNA repair

    2017  Volume 60, Page(s) 77–88

    Abstract: Mitochondrial genome integrity is fundamental to mammalian cell viability. Since mitochondrial DNA is constantly under attack from oxygen radicals released during ATP production, DNA repair is vital in removing oxidatively generated lesions in ... ...

    Abstract Mitochondrial genome integrity is fundamental to mammalian cell viability. Since mitochondrial DNA is constantly under attack from oxygen radicals released during ATP production, DNA repair is vital in removing oxidatively generated lesions in mitochondrial DNA, but the presence of a strong base excision repair system has not been demonstrated. Here, we addressed the presence of such a system in mammalian mitochondria involving the primary base lesion repair enzyme DNA polymerase (pol) β. Pol β was localized to mammalian mitochondria by electron microscopic-immunogold staining, immunofluorescence co-localization and biochemical experiments. Extracts from purified mitochondria exhibited base excision repair activity that was dependent on pol β. Mitochondria from pol β-deficient mouse fibroblasts had compromised DNA repair and showed elevated levels of superoxide radicals after hydrogen peroxide treatment. Mitochondria in pol β-deficient fibroblasts displayed altered morphology by electron microscopy. These results indicate that mammalian mitochondria contain an efficient base lesion repair system mediated in part by pol β and thus pol β plays a role in preserving mitochondrial genome stability.
    MeSH term(s) Animals ; DNA Damage ; DNA Polymerase beta/genetics ; DNA Polymerase beta/metabolism ; DNA Repair ; DNA, Mitochondrial/drug effects ; DNA, Mitochondrial/metabolism ; Fibroblasts/enzymology ; Fibroblasts/metabolism ; Gene Knockout Techniques ; HEK293 Cells ; HeLa Cells ; Humans ; Hydrogen Peroxide/toxicity ; Mice ; Mitochondria/enzymology ; Mitochondria/genetics ; Mitochondria/pathology ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Oxidative Stress/drug effects ; Superoxides/analysis ; Superoxides/metabolism
    Chemical Substances DNA, Mitochondrial ; Mitochondrial Proteins ; Superoxides (11062-77-4) ; Hydrogen Peroxide (BBX060AN9V) ; DNA Polymerase beta (EC 2.7.7.7) ; DNA polymerase beta, mouse (EC 2.7.7.7) ; POLB protein, human (EC 2.7.7.7)
    Language English
    Publishing date 2017-10-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2017.10.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article: Redefining endothelial progenitor cells via clonal analysis and hematopoietic stem/progenitor cell principals.

    Yoder, Mervin C / Mead, Laura E / Prater, Daniel / Krier, Theresa R / Mroueh, Karim N / Li, Fang / Krasich, Rachel / Temm, Constance J / Prchal, Josef T / Ingram, David A

    Blood

    2006  Volume 109, Issue 5, Page(s) 1801–1809

    Abstract: The limited vessel-forming capacity of infused endothelial progenitor cells (EPCs) into patients with cardiovascular dysfunction may be related to a misunderstanding of the biologic potential of the cells. EPCs are generally identified by cell surface ... ...

    Abstract The limited vessel-forming capacity of infused endothelial progenitor cells (EPCs) into patients with cardiovascular dysfunction may be related to a misunderstanding of the biologic potential of the cells. EPCs are generally identified by cell surface antigen expression or counting in a commercially available kit that identifies "endothelial cell colony-forming units" (CFU-ECs). However, the origin, proliferative potential, and differentiation capacity of CFU-ECs is controversial. In contrast, other EPCs with blood vessel-forming ability, termed endothelial colony-forming cells (ECFCs), have been isolated from human peripheral blood. We compared the function of CFU-ECs and ECFCs and determined that CFU-ECs are derived from the hematopoietic system using progenitor assays, and analysis of donor cells from polycythemia vera patients harboring a Janus kinase 2 V617F mutation in hematopoietic stem cell clones. Further, CFU-ECs possess myeloid progenitor cell activity, differentiate into phagocytic macrophages, and fail to form perfused vessels in vivo. In contrast, ECFCs are clonally distinct from CFU-ECs, display robust proliferative potential, and form perfused vessels in vivo. Thus, these studies establish that CFU-ECs are not EPCs and the role of these cells in angiogenesis must be re-examined prior to further clinical trials, whereas ECFCs may serve as a potential therapy for vascular regeneration.
    MeSH term(s) Adult ; Animals ; Antigens/metabolism ; Biomarkers ; Cell Differentiation ; Cell Transplantation ; Cells, Cultured ; Clone Cells/cytology ; Colony-Forming Units Assay ; Endothelial Cells/cytology ; Endothelial Cells/metabolism ; Female ; Hematopoietic System/cytology ; Humans ; Janus Kinase 2/genetics ; Janus Kinase 2/metabolism ; Macrophages/cytology ; Male ; Mice ; Middle Aged ; Monocytes/cytology ; Mutation/genetics ; Stem Cells/cytology
    Chemical Substances Antigens ; Biomarkers ; Janus Kinase 2 (EC 2.7.10.2)
    Language English
    Publishing date 2006-10-19
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 80069-7
    ISSN 1528-0020 ; 0006-4971
    ISSN (online) 1528-0020
    ISSN 0006-4971
    DOI 10.1182/blood-2006-08-043471
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top