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Volumn 100, Issue 1, 2014, Pages 219-226

To be or not to be a nucleoid protein: A comparison of mass-spectrometry based approaches in the identification of potential mtDNA-nucleoid associated proteins

Author keywords

Mass spectrometry; Mitoribosome; mtDNA; Nucleoid; TFAM

Indexed keywords

MITOCHONDRIAL DNA; MITOCHONDRIAL TRANSCRIPTION FACTOR A; MITOCHONDRIAL TRANSCRIPTION FACTOR B; MITOCHONDRIAL TRANSCRIPTION FACTOR B2; NUCLEAR PROTEIN; NUCLEOID ASSOCIATED PROTEIN; RIBOSOME PROTEIN; UNCLASSIFIED DRUG;

EID: 84897075686     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2013.09.017     Document Type: Article
Times cited : (56)

References (70)
  • 1
    • 78651128209 scopus 로고
    • Intramitochondrial fibers with DNA characteristics. I. Fixation and electron staining reactions
    • M.M. Nass, S. Nass, Intramitochondrial fibers with DNA characteristics. I. Fixation and electron staining reactions, J. Cell Biol. 19 (1963) 593-611.
    • (1963) J. Cell Biol. , vol.19 , pp. 593-611
    • Nass, M.M.1    Nass, S.2
  • 4
    • 0022374832 scopus 로고
    • Characterization of DNA-protein complexes from the mitochondria of Xenopus laevis oocytes
    • DOI 10.1016/0014-4827(85)90163-6
    • M. Barat, D. Rickwood, C. Dufresne, J.C. Mounolou, Characterization of DNA-protein complexes from the mitochondria of Xenopus laevis oocytes, Exp. Cell Res. 157 (1985) 207-217. (Pubitemid 16205879)
    • (1985) Experimental Cell Research , vol.157 , Issue.1 , pp. 207-217
    • Barat, M.1    Rickwood, D.2    Dufresne, C.3    Mounolou, J.C.4
  • 5
    • 84864308607 scopus 로고    scopus 로고
    • Mitochondrial DNA nucleoid structure
    • D.F. Bogenhagen, Mitochondrial DNA nucleoid structure, Biochim. Biophys. Acta 1819 (2012) 914-920.
    • (2012) Biochim. Biophys. Acta , vol.1819 , pp. 914-920
    • Bogenhagen, D.F.1
  • 6
    • 0026054963 scopus 로고
    • Organization of multiple nucleoids and DNA molecules in mitochondria of a human cell
    • M. Satoh, T. Kuroiwa, Organization of multiple nucleoids and DNA molecules in mitochondria of a human cell, Exp. Cell Res. 196 (1991) 137-140. (Pubitemid 121006382)
    • (1991) Experimental Cell Research , vol.196 , Issue.1 , pp. 137-140
    • Satoh, M.1    Kuroiwa, T.2
  • 8
    • 0019888719 scopus 로고
    • Characterization of a rat liver mitochondrial DNA-protein complex. Replicative intermediates are protected against branch migrational loss
    • G.C. Van Tuyle, P.A. Pavco, Characterization of a rat liver mitochondrial DNA-protein complex. Replicative intermediates are protected against branch migrational loss, J. Biol. Chem. 256 (1981) 12772-12779.
    • (1981) J. Biol. Chem. , vol.256 , pp. 12772-12779
    • Van Tuyle, G.C.1    Pavco, P.A.2
  • 9
    • 0023046962 scopus 로고
    • Characterization of a Xenopus laevis mitochondrial protein with a high affinity for supercoiled DNA
    • B. Mignotte, M. Barat, Characterization of a Xenopus laevis mitochondrial protein with a high affinity for supercoiled DNA, Nucleic Acids Res. 14 (1986) 5969-5980.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 5969-5980
    • Mignotte, B.1    Barat, M.2
  • 12
    • 3242884720 scopus 로고    scopus 로고
    • Organization and dynamics of human mitochondrial DNA
    • DOI 10.1242/jcs.01134
    • F. Legros, F. Malka, P. Frachon, A. Lombes, M. Rojo, Organization and dynamics of human mitochondrial DNA, J. Cell Sci. 117 (2004) 2653-2662. (Pubitemid 38997249)
    • (2004) Journal of Cell Science , vol.117 , Issue.13 , pp. 2653-2662
    • Legros, F.1    Malka, F.2    Frachon, P.3    Lombes, A.4    Rojo, M.5
  • 13
    • 80051972817 scopus 로고    scopus 로고
    • Super-resolution microscopy reveals that mammalian mitochondrial nucleoids have a uniform size and frequently contain a single copy of mtDNA
    • C. Kukat, C.A. Wurm, H. Spahr, M. Falkenberg, N.G. Larsson, S. Jakobs, Super-resolution microscopy reveals that mammalian mitochondrial nucleoids have a uniform size and frequently contain a single copy of mtDNA, Proc. Natl. Acad. Sci. U. S. A. 108 (2011) 13534-13539.
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , pp. 13534-13539
    • Kukat, C.1    Wurm, C.A.2    Spahr, H.3    Falkenberg, M.4    Larsson, N.G.5    Jakobs, S.6
  • 14
    • 77950573964 scopus 로고    scopus 로고
    • Functional organization of mammalian mitochondrial DNA in nucleoids: History, recent developments, and future challenges
    • J.N. Spelbrink, Functional organization of mammalian mitochondrial DNA in nucleoids: history, recent developments, and future challenges, IUBMB Life 62 (2010) 19-32.
    • (2010) IUBMB Life , vol.62 , pp. 19-32
    • Spelbrink, J.N.1
  • 15
    • 79959450877 scopus 로고    scopus 로고
    • Mitochondrial DNA mutations in disease and aging
    • C.B. Park, N.-G. Larsson, Mitochondrial DNA mutations in disease and aging, J. Cell Biol. 193 (2011) 809-818.
    • (2011) J. Cell Biol. , vol.193 , pp. 809-818
    • Park, C.B.1    Larsson, N.-G.2
  • 16
  • 17
    • 83755205842 scopus 로고    scopus 로고
    • Defects in mitochondrial DNA replication and human disease
    • W.C. Copeland, Defects in mitochondrial DNA replication and human disease, Crit. Rev. Biochem. Mol. Biol. 47 (2012) 64-74.
    • (2012) Crit. Rev. Biochem. Mol. Biol. , vol.47 , pp. 64-74
    • Copeland, W.C.1
  • 20
    • 0015290162 scopus 로고
    • A new synthetic RNA-dependent DNA polymerase from human tissue culture cells (HeLa- fibro-blast- synthetic oligonucleotides-template-purified enzymes)
    • B. Fridlender, M. Fry, A. Bolden, A. Weissbach, A new synthetic RNA-dependent DNA polymerase from human tissue culture cells (HeLa- fibro-blast- synthetic oligonucleotides-template-purified enzymes), Proc. Natl. Acad. Sci. U. S. A. 69 (1972) 452-455.
    • (1972) Proc. Natl. Acad. Sci. U. S. A. , vol.69 , pp. 452-455
    • Fridlender, B.1    Fry, M.2    Bolden, A.3    Weissbach, A.4
  • 21
    • 0025124856 scopus 로고
    • Structural and functional studies of the rat mitochondrial single strand DNA binding protein P16
    • G.D. Hoke, P.A. Pavco, B.J. Ledwith, G.C. Van Tuyle, Structural and functional studies of the rat mitochondrial single strand DNA binding protein P16, Arch. Biochem. Biophys. 282 (1990) 116-124. (Pubitemid 20304893)
    • (1990) Archives of Biochemistry and Biophysics , vol.282 , Issue.1 , pp. 116-124
    • Hoke, G.D.1    Pavco, P.A.2    Ledwith, B.J.3    Van Tuyle, G.C.4
  • 22
  • 23
    • 84878835055 scopus 로고    scopus 로고
    • Mitochondrial DNA replication proceeds via a 'bootlace' mechanism involving the incorporation of processed transcripts
    • A. Reyes, L. Kazak, S.R. Wood, T. Yasukawa, H.T. Jacobs, I.J. Holt, Mitochondrial DNA replication proceeds via a 'bootlace' mechanism involving the incorporation of processed transcripts, Nucleic Acids Res. 41 (2013) 5837-5850.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 5837-5850
    • Reyes, A.1    Kazak, L.2    Wood, S.R.3    Yasukawa, T.4    Jacobs, H.T.5    Holt, I.J.6
  • 24
    • 33751088000 scopus 로고    scopus 로고
    • Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand
    • DOI 10.1038/sj.emboj.7601392, PII 7601392
    • T. Yasukawa, A. Reyes, T.J. Cluett, M.Y. Yang, M. Bowmaker, H.T. Jacobs, I.J. Holt, Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand, EMBO J. 25 (2006) 5358-5371. (Pubitemid 44764145)
    • (2006) EMBO Journal , vol.25 , Issue.22 , pp. 5358-5371
    • Yasukawa, T.1    Reyes, A.2    Cluett, T.J.3    Yang, M.-Y.4    Bowmaker, M.5    Jacobs, H.T.6    Holt, I.J.7
  • 25
    • 0037112343 scopus 로고    scopus 로고
    • Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric DNA replication
    • DOI 10.1016/S0092-8674(02)01075-9
    • M.Y. Yang, M. Bowmaker, A. Reyes, L. Vergani, P. Angeli, E. Gringeri, H.T. Jacobs, I.J. Holt, Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric DNA replication, Cell 111 (2002) 495-505. (Pubitemid 35356555)
    • (2002) Cell , vol.111 , Issue.4 , pp. 495-505
    • Yang, M.Y.1    Bowmaker, M.2    Reyes, A.3    Vergani, L.4    Angeli, P.5    Gringeri, E.6    Jacobs, H.T.7    Holt, I.J.8
  • 27
    • 0345354684 scopus 로고    scopus 로고
    • Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice
    • DOI 10.1016/S1097-2765(03)00088-1
    • S.M. Cerritelli, E.G. Frolova, C. Feng, A. Grinberg, P.E. Love, R.J. Crouch, Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice, Mol. Cell 11 (2003) 807-815. (Pubitemid 36385132)
    • (2003) Molecular Cell , vol.11 , Issue.3 , pp. 807-815
    • Cerritelli, S.M.1    Frolova, E.G.2    Feng, C.3    Grinberg, A.4    Love, P.E.5    Crouch, R.J.6
  • 29
    • 0029070402 scopus 로고
    • Addition of a 29 residue carboxyl-terminal tail converts a simple HMG box-containing protein into a transcriptional activator
    • D.J. Dairaghi, G.S. Shadel, D.A. Clayton, Addition of a 29 residue carboxyl-terminal tail converts a simple HMG box-containing protein into a transcriptional activator, J. Mol. Biol. 249 (1995) 11-28.
    • (1995) J. Mol. Biol. , vol.249 , pp. 11-28
    • Dairaghi, D.J.1    Shadel, G.S.2    Clayton, D.A.3
  • 31
    • 0024365289 scopus 로고
    • Termination of transcription in human mitochondria: Identification and purification of a DNA binding protein factor that promotes termination
    • DOI 10.1016/0092-8674(89)90853-2
    • B. Kruse, N. Narasimhan, G. Attardi, Termination of transcription in human mitochondria: identification and purification of a DNA binding protein factor that promotes termination, Cell 58 (1989) 391-397. (Pubitemid 19191420)
    • (1989) Cell , vol.58 , Issue.2 , pp. 391-397
    • Kruse, B.1    Narasimhan, N.2    Attardi, G.3
  • 36
    • 84869822219 scopus 로고    scopus 로고
    • LRPPRC/SLIRP suppresses PNPase-mediated mRNA decay and promotes polyadenylation in human mitochondria
    • T. Chujo, T. Ohira, Y. Sakaguchi, N. Goshima, N. Nomura, A. Nagao, T. Suzuki, LRPPRC/SLIRP suppresses PNPase-mediated mRNA decay and promotes polyadenylation in human mitochondria, Nucleic Acids Res. 40 (2012) 8033-8047.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 8033-8047
    • Chujo, T.1    Ohira, T.2    Sakaguchi, Y.3    Goshima, N.4    Nomura, N.5    Nagao, A.6    Suzuki, T.7
  • 37
    • 77950901962 scopus 로고    scopus 로고
    • LRPPRC and SLIRP interact in a ribonucleoprotein complex that regulates posttranscriptional gene expression in mitochondria
    • F. Sasarman, C. Brunel-Guitton, H. Antonicka, T. Wai, E.A. Shoubridge, L. Consortium, LRPPRC and SLIRP interact in a ribonucleoprotein complex that regulates posttranscriptional gene expression in mitochondria, Mol. Biol. Cell 21 (2010) 1315-1323.
    • (2010) Mol. Biol. Cell , vol.21 , pp. 1315-1323
    • Sasarman, F.1    Brunel-Guitton, C.2    Antonicka, H.3    Wai, T.4    Shoubridge, E.A.5    Consortium, L.6
  • 38
    • 41249098355 scopus 로고    scopus 로고
    • The layered structure of human mitochondrial DNA nucleoids
    • D.F. Bogenhagen, D. Rousseau, S. Burke, The layered structure of human mitochondrial DNA nucleoids, J. Biol. Chem. 283 (2008) 3665-3675.
    • (2008) J. Biol. Chem. , vol.283 , pp. 3665-3675
    • Bogenhagen, D.F.1    Rousseau, D.2    Burke, S.3
  • 39
    • 84866729278 scopus 로고    scopus 로고
    • Minimizing the damage: Repair pathways keep mitochondrial DNA intact
    • L. Kazak, A. Reyes, I.J. Holt, Minimizing the damage: repair pathways keep mitochondrial DNA intact, Nat. Rev. Mol. Cell. Biol. 13 (2012) 659-671.
    • (2012) Nat. Rev. Mol. Cell. Biol. , vol.13 , pp. 659-671
    • Kazak, L.1    Reyes, A.2    Holt, I.J.3
  • 41
    • 0024241304 scopus 로고
    • Mitochondrial endonuclease activities specific for apurinic/apyrimidinic sites in DNA from mouse cells
    • A.E. Tomkinson, R.T. Bonk, S. Linn, Mitochondrial endonuclease activities specific for apurinic/apyrimidinic sites in DNA from mouse cells, J. Biol. Chem. 263 (1988) 12532-12537. (Pubitemid 19000434)
    • (1988) Journal of Biological Chemistry , vol.263 , Issue.25 , pp. 12532-12537
    • Tomkinson, A.E.1    Bonk, R.T.2    Linn, S.3
  • 42
    • 0032960864 scopus 로고    scopus 로고
    • The human DNA ligase III gene encodes nuclear and mitochondrial proteins
    • U. Lakshmipathy, C. Campbell, The human DNA ligase III gene encodes nuclear and mitochondrial proteins, Mol. Cell. Biol. 19 (1999) 3869-3876. (Pubitemid 29193846)
    • (1999) Molecular and Cellular Biology , vol.19 , Issue.5 , pp. 3869-3876
    • Lakshmipathy, U.1    Campbell, C.2
  • 46
    • 79960729178 scopus 로고    scopus 로고
    • The regulation of mitochondrial morphology: Intricate mechanisms and dynamic machinery
    • C.S. Palmer, L.D. Osellame, D. Stojanovski, M.T. Ryan, The regulation of mitochondrial morphology: intricate mechanisms and dynamic machinery, Cell. Signal 23 (2011) 1534-1545.
    • (2011) Cell. Signal , vol.23 , pp. 1534-1545
    • Palmer, C.S.1    Osellame, L.D.2    Stojanovski, D.3    Ryan, M.T.4
  • 47
    • 57349100367 scopus 로고    scopus 로고
    • Mitofusin 2 tethers endoplasmic reticulum to mitochondria
    • O.M. de Brito, L. Scorrano, Mitofusin 2 tethers endoplasmic reticulum to mitochondria, Nature 456 (2008) 605-610.
    • (2008) Nature , vol.456 , pp. 605-610
    • De Brito, O.M.1    Scorrano, L.2
  • 48
    • 34547601410 scopus 로고    scopus 로고
    • Mitochondrial Fusion Protects against Neurodegeneration in the Cerebellum
    • DOI 10.1016/j.cell.2007.06.026, PII S0092867407007933
    • H. Chen, J.M. McCaffery, D.C. Chan, Mitochondrial fusion protects against neurodegeneration in the cerebellum, Cell 130 (2007) 548-562. (Pubitemid 47198302)
    • (2007) Cell , vol.130 , Issue.3 , pp. 548-562
    • Chen, H.1    McCaffery, J.M.2    Chan, D.C.3
  • 53
    • 33748746678 scopus 로고    scopus 로고
    • Human mitochondrial DNA nucleoids are linked to protein folding machinery and metabolic enzymes at the mitochondrial inner membrane
    • DOI 10.1074/jbc.M604501200
    • Y. Wang, D.F. Bogenhagen, Human mitochondrial DNA nucleoids are linked to protein folding machinery and metabolic enzymes at the mitochondrial inner membrane, J. Biol. Chem. 281 (2006) 25791-25802. (Pubitemid 44401967)
    • (2006) Journal of Biological Chemistry , vol.281 , Issue.35 , pp. 25791-25802
    • Wang, Y.1    Bogenhagen, D.F.2
  • 55
    • 2442558106 scopus 로고    scopus 로고
    • Protein components of mitochondrial DNA nucleoids in higher eukaryotes
    • D.F. Bogenhagen, Y. Wang, E.L. Shen, R. Kobayashi, Protein components of mitochondrial DNA nucleoids in higher eukaryotes, Mol. Cell. Proteomics 11 (2003) 1205-1216.
    • (2003) Mol. Cell. Proteomics , vol.11 , pp. 1205-1216
    • Bogenhagen, D.F.1    Wang, Y.2    Shen, E.L.3    Kobayashi, R.4
  • 58
    • 70449627527 scopus 로고    scopus 로고
    • Association of a novel mitochondrial protein M19 with mitochondrial nucleoids
    • M. Sumitani, K. Kasashima, E. Ohta, D. Kang, H. Endo, Association of a novel mitochondrial protein M19 with mitochondrial nucleoids, J. Biochem. 146 (2009) 725-732.
    • (2009) J. Biochem. , vol.146 , pp. 725-732
    • Sumitani, M.1    Kasashima, K.2    Ohta, E.3    Kang, D.4    Endo, H.5
  • 61
    • 84864454280 scopus 로고    scopus 로고
    • Human C4orf14 interacts with the mitochondrial nucleoid and is involved in the biogenesis of the small mitochondrial ribosomal subunit
    • J. He, H.M. Cooper, A. Reyes, M. Di Re, L. Kazak, S.R. Wood, C.C. Mao, I.M. Fearnley, J.E. Walker, I.J. Holt, Human C4orf14 interacts with the mitochondrial nucleoid and is involved in the biogenesis of the small mitochondrial ribosomal subunit, Nucleic Acids Res. 40 (2012) 6097-6108.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 6097-6108
    • He, J.1    Cooper, H.M.2    Reyes, A.3    Di Re, M.4    Kazak, L.5    Wood, S.R.6    Mao, C.C.7    Fearnley, I.M.8    Walker, J.E.9    Holt, I.J.10
  • 63
    • 33845629364 scopus 로고    scopus 로고
    • Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells
    • DOI 10.1093/nar/gkl703
    • J.L. Pohjoismaki, S. Wanrooij, A.K. Hyvarinen, S. Goffart, I.J. Holt, J.N. Spelbrink, H.T. Jacobs, Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells, Nucleic Acids Res. 34 (2006) 5815-5828. (Pubitemid 44941161)
    • (2006) Nucleic Acids Research , vol.34 , Issue.20 , pp. 5815-5828
    • Pohjoismaki, J.L.O.1    Wanrooij, S.2    Hyvarinen, A.K.3    Goffart, S.4    Holt, I.J.5    Spelbrink, J.N.6    Jacobs, H.T.7
  • 64
    • 1542677230 scopus 로고    scopus 로고
    • TWINKLE has 5′ > 3′ DNA helicase activity and is specifically stimulated by mitochondrial single-stranded DNA-binding protein
    • DOI 10.1074/jbc.M306981200
    • J.A. Korhonen, M. Gaspari, M. Falkenberg, TWINKLE Has 5'→3' DNA helicase activity and is specifically stimulated by mitochondrial single-stranded DNA-binding protein, J. Biol. Chem. 278 (2003) 48627-48632. (Pubitemid 41079501)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.49 , pp. 48627-48632
    • Korhonen, J.A.1    Gaspari, M.2    Falkenberg, M.3
  • 65
    • 3242705680 scopus 로고    scopus 로고
    • The functional organization of mitochondrial genomes in human cells
    • F.J. Iborra, H. Kimura, P.R. Cook, The functional organization of mitochondrial genomes in human cells, BMC Biol. 2 (2004) 9.
    • (2004) BMC Biol. , vol.2 , pp. 9
    • Iborra, F.J.1    Kimura, H.2    Cook, P.R.3
  • 67
    • 84875309966 scopus 로고    scopus 로고
    • The mitochondrial RNA-binding protein GRSF1 localizes to RNA granules and is required for posttranscriptional mitochondrial gene expression
    • H. Antonicka, F. Sasarman, T. Nishimura, V. Paupe, E.A. Shoubridge, The mitochondrial RNA-binding protein GRSF1 localizes to RNA granules and is required for posttranscriptional mitochondrial gene expression, Cell Metab. 17 (2013) 386-398.
    • (2013) Cell Metab. , vol.17 , pp. 386-398
    • Antonicka, H.1    Sasarman, F.2    Nishimura, T.3    Paupe, V.4    Shoubridge, E.A.5
  • 68
    • 54549088876 scopus 로고    scopus 로고
    • RNase P without RNA: Identification and functional reconstitution of the human mitochondrial tRNA processing enzyme
    • J. Holzmann, P. Frank, E. Loffler, K.L. Bennett, C. Gerner, W. Rossmanith, RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme, Cell 135 (2008) 462-474.
    • (2008) Cell , vol.135 , pp. 462-474
    • Holzmann, J.1    Frank, P.2    Loffler, E.3    Bennett, K.L.4    Gerner, C.5    Rossmanith, W.6


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