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Identification Of A Novel Human Mitochondrial Endo-/exonuclease Ddk1/c20orf72 Necessary For Maintenance Of Proper 7S DNA Levels

Roman J Szczesny, Monika S. Hejnowicz, Kamil Steczkiewicz, A. Muszewska, Lukasz S Borowski, K. Ginalski, A. Dziembowski
Published 2013 · Biology, Medicine

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Although the human mitochondrial genome has been investigated for several decades, the proteins responsible for its replication and expression, especially nucleolytic enzymes, are poorly described. Here, we characterized a novel putative PD-(D/E)XK nuclease encoded by the human C20orf72 gene named Ddk1 for its predicted catalytic residues. We show that Ddk1 is a mitochondrially localized metal-dependent DNase lacking detectable ribonuclease activity. Ddk1 degrades DNA mainly in a 3′–5′ direction with a strong preference for single-stranded DNA. Interestingly, Ddk1 requires free ends for its activity and does not degrade circular substrates. In addition, when a chimeric RNA–DNA substrate is provided, Ddk1 can slide over the RNA fragment and digest DNA endonucleolytically. Although the levels of the mitochondrial DNA are unchanged on RNAi-mediated depletion of Ddk1, the mitochondrial single-stranded DNA molecule (7S DNA) accumulates. On the other hand, overexperssion of Ddk1 decreases the levels of 7S DNA, suggesting an important role of the protein in 7S DNA regulation. We propose a structural model of Ddk1 and discuss its similarity to other PD-(D/E)XK superfamily members.
This paper references
10.1016/S1097-2765(00)80267-1
Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
A. Hickman (2000)
The 2-5A/RNase L/RNase L inhibitor (RLI) [correction of (RNI)] pathway regulates mitochondrial mRNAs stability in interferon alpha-treated H9 cells.
F. Le Roy (2001)
10.1042/BST20120022
The mystery of mitochondrial RNases.
F. Bruni (2012)
10.1093/bioinformatics/bth444
CLANS: a Java application for visualizing protein families based on pairwise similarity
T. Frickey (2004)
10.1038/nmeth1010
Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
M. Li (2007)
10.1074/jbc.M110.215715
APOPTOSIS INDUCED BY PERSISTENT SINGLE-STRAND BREAKS IN THE MITOCHONDRIAL GENOME: CRITICAL ROLE OF EXOG (5’ EXO/ENDONUCLEASE) IN THEIR REPAIR
Anne W. Tann (2011)
10.1093/nar/gkp903
Human mitochondrial RNA turnover caught in flagranti: involvement of hSuv3p helicase in RNA surveillance
Roman J Szczesny (2010)
10.1042/BC20060108
Down‐regulation of human RNA/DNA helicase SUV3 induces apoptosis by a caspase‐ and AIF‐dependent pathway
Roman J Szczesny (2007)
10.1093/nar/gkn175
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
J. Orlowski (2008)
10.1093/nar/gkl070
Biochemical analysis of human Dna2
Taro Masuda-Sasa (2006)
10.1074/jbc.M111.243071
Characterization of the Endonuclease and ATP-dependent Flap Endo/Exonuclease of Dna2*
Barbara K. Fortini (2011)
10.1113/eph8802514
Replication and Transcription of Mammalian Mitochondrial Dna
P. Fernández-Silva (2003)
10.1093/nar/gks382
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily
Kamil Steczkiewicz (2012)
10.1093/nar/gkn1020
The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome
C. Schneider (2009)
10.1093/NAR/28.18.3417
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
L. Aravind (2000)
10.1038/sj.emboj.7601392
Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand
T. Yasukawa (2006)
10.1038/35083620
Endonuclease G is an apoptotic DNase when released from mitochondria
L. Li (2001)
10.1016/j.molcel.2008.09.024
Human DNA2 is a mitochondrial nuclease/helicase for efficient processing of DNA replication and repair intermediates.
L. Zheng (2008)
10.1093/nar/gkl703
Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells
J. Pohjoismäki (2006)
10.1074/jbc.M108461200
Action of Recombinant Human Apoptotic Endonuclease G on Naked DNA and Chromatin Substrates
P. Widłak (2001)
10.1093/nar/gkq493
Differential regulation of full-length genome and a single-stranded 7S DNA along the cell cycle in human mitochondria
Anita Antes (2010)
10.1016/j.dnarep.2008.01.002
Mitochondrial base excision repair of uracil and AP sites takes place by single-nucleotide insertion and long-patch DNA synthesis.
M. Akbari (2008)
10.1080/10409230390259382
The Protein Components and Mechanism of Eukaryotic Okazaki Fragment Maturation
Hui-I Kao (2003)
10.1158/0008-5472.CAN-03-1101
Energy Substrate Modulates Mitochondrial Structure and Oxidative Capacity in Cancer Cells
R. Rossignol (2004)
10.1093/nar/gkr470
PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria
J. Rorbach (2011)
Crystal structure of E. coli RecE protein reveals a toroidal tetramer for processing double-stranded DNA
J. Zhang (2009)
10.1016/j.bbagrm.2011.11.005
Mitochondrial DNA nucleoid structure.
D. Bogenhagen (2012)
10.1093/nar/gkp1055
Dna2 is a structure-specific nuclease, with affinity for 5′-flap intermediates
J. Stewart (2010)
10.1002/j.1460-2075.1994.tb06373.x
The characterization of a mammalian DNA structure‐specific endonuclease.
J. Harrington (1994)
10.1128/MCB.00457-08
Removal of Oxidative DNA Damage via FEN1-Dependent Long-Patch Base Excision Repair in Human Cell Mitochondria
P. Liu (2008)
Crystal
J. Zhang (2009)
10.1038/nature02988
Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks
M. Singleton (2004)
10.1074/jbc.M409231200
Dna2p Helicase/Nuclease Is a Tracking Protein, Like FEN1, for Flap Cleavage during Okazaki Fragment Maturation*
Hui-I Kao (2004)
10.1016/J.TIG.2005.11.007
Bacteriophage origins of mitochondrial replication and transcription proteins.
T. Shutt (2006)
10.1093/nar/gkp614
The accessory subunit of mitochondrial DNA polymerase γ determines the DNA content of mitochondrial nucleoids in human cultured cells
M. Di Re (2009)
10.1016/0022-2836(78)90269-3
Mechanism of mitochondrial DNA replication in mouse L-cells: kinetics of synthesis and turnover of the initiation sequence.
D. Bogenhagen (1978)
Structure and function of the 5
S Xiang (2009)
10.4161/rna.8.4.15393
Involvement of human ELAC2 gene product in 3' end processing of mitochondrial tRNAs
Lien K Brzezniak (2011)
10.1093/bioinformatics/btl002
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
Annette Höglund (2006)
10.1038/sj.cdd.4402130
Regulation of mitochondrial mRNA stability by RNase L is translation-dependent and controls IFNα-induced apoptosis
F. L. Roy (2007)
10.1016/S0092-8674(00)80688-1
Coupled Leading- and Lagging-Strand Synthesis of Mammalian Mitochondrial DNA
I. Holt (2000)
10.1038/nsmb1184
A single subunit, Dis3, is essentially responsible for yeast exosome core activity
A. Dziembowski (2007)
10.1016/j.bbamcr.2010.04.008
Mitochondrial single-stranded DNA binding protein is required for maintenance of mitochondrial DNA and 7S DNA but is not required for mitochondrial nucleoid organisation.
Heini Ruhanen (2010)
10.1016/S0167-4781(99)00015-9
Mitochondrial DNA replication in human T lymphocytes is regulated primarily at the H-strand termination site.
Y. Kai (1999)
10.1074/JBC.270.51.30377
Calf 5′ to 3′ Exo/Endonuclease Must Slide from a 5′ End of the Substrate to Perform Structure-specific Cleavage (*)
R. S. Murante (1995)
10.1093/NAR/9.20.5411
Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA.
M. W. Walberg (1981)
10.1128/MCB.01321-09
Yeast Exonuclease 5 Is Essential for Mitochondrial Genome Maintenance
P. Burgers (2010)
10.1093/nar/gkm1169
EXOG, a novel paralog of Endonuclease G in higher eukaryotes
I. Cymerman (2008)
10.1074/jbc.M806174200
Native R-loops Persist throughout the Mouse Mitochondrial DNA Genome*S⃞
T. Brown (2008)
10.1007/s10495-005-0410-9
Regulation of the human apoptotic DNase/RNase Endonuclease G: involvement of Hsp70 and ATP
M. Kalinowska (2005)
10.1093/HMG/DDH342
Twinkle helicase is essential for mtDNA maintenance and regulates mtDNA copy number.
H. Tyynismaa (2004)
10.1016/S0092-8674(02)01075-9
Biased Incorporation of Ribonucleotides on the Mitochondrial L-Strand Accounts for Apparent Strand-Asymmetric DNA Replication
M. Y. Yang (2002)
10.1093/jmcb/mjq048
Okazaki fragment maturation: nucleases take centre stage.
Li Zheng (2011)
10.1016/j.str.2009.03.008
Crystal structure of E. coli RecE protein reveals a toroidal tetramer for processing double-stranded DNA breaks.
Jinjin Zhang (2009)
10.1073/pnas.1103467108
Crystal structures of λ exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity
Jinjin Zhang (2011)
10.1093/nar/gks388
Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1
Jason W. Gloor (2012)
10.1074/jbc.M803491200
Long Patch Base Excision Repair in Mammalian Mitochondrial Genomes*
B. Szczesny (2008)
10.1016/J.TIM.2005.08.012
Viral proteins functioning in organelles: a cryptic origin?
J. Filée (2005)
10.1074/JBC.M306766200
Mitochondrial pH Monitored by a New Engineered Green Fluorescent Protein Mutant*
M. C. Abad (2004)
10.1038/nprot.2007.131
Locating proteins in the cell using TargetP, SignalP and related tools
Olof Emanuelsson (2007)
10.1016/j.jmb.2010.02.029
Mammalian mitochondrial DNA replication intermediates are essentially duplex but contain extensive tracts of RNA/DNA hybrid.
J. Pohjoismäki (2010)
10.1093/nar/gkm215
Expression of catalytic mutants of the mtDNA helicase Twinkle and polymerase POLG causes distinct replication stalling phenotypes
S. Wanrooij (2007)
10.1073/PNAS.75.2.735
Human mitochondrial DNA: analysis of 7S DNA from the origin of replication.
W. Brown (1978)
10.1093/bioinformatics/btg008
PCMA: fast and accurate multiple sequence alignment based on profile consistency
J. Pei (2003)
10.1093/emboj/17.5.1526
Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases
C. Ban (1998)
Dna 2 is a structure-specific nuclease , with affinity for 5 0-flap intermediates
J. Stewart (2009)
10.1038/290457A0
Sequence and organization of the human mitochondrial genome
S. Anderson (1981)
10.1093/nar/gks1130
Human mitochondrial RNA decay mediated by PNPase–hSuv3 complex takes place in distinct foci
Lukasz S Borowski (2013)
10.1093/nar/gkq1282
Human 2′-phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover
J. Poulsen (2011)
10.1007/978-1-60327-355-8_24
Assays of the helicase, ATPase, and exoribonuclease activities of the yeast mitochondrial degradosome.
Michał Małecki (2010)
10.1093/nar/gkl102
Isolation of human Dna2 endonuclease and characterization of its enzymatic properties
J. Kim (2006)
10.1073/PNAS.75.2.677
Displacement-loop replication initiation sequence in animal mitochondrial DNA exists as a family of discrete lengths.
A. Gillum (1978)
10.1016/j.bbabio.2012.08.001
Loss, replacement and gain of proteins at the origin of the mitochondria.
M. Huynen (2013)
10.1093/nar/gkr1013
PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update
X. Wang (2012)
10.1016/j.tibs.2009.03.007
Mitochondrial DNA replication and repair: all a flap.
I. Holt (2009)
10.1093/nar/gkv947
Nucleic Acids Research
K. Otto (2015)
10.1038/emboj.2010.121
The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L
Rafał Tomecki (2010)
10.1111/j.1742-4658.2009.07374.x
Crystal structure of the shutoff and exonuclease protein from the oncogenic Kaposi’s sarcoma‐associated herpesvirus
Sue-Li Dahlroth (2009)
10.1074/jbc.M107482200
The 2–5A/RNase L/RNase L Inhibitor (RNI) Pathway Regulates Mitochondrial mRNAs Stability in Interferon α-treated H9 Cells*
F. Le Roy (2001)
10.1093/bioinformatics/btg124
3D-Jury: A Simple Approach to Improve Protein Structure Predictions
K. Ginalski (2003)
Mechanism of replication of human mitochondrial DNA. Localization of the 5' ends of nascent daughter strands.
D. Tapper (1981)
10.1111/J.1432-1033.1996.00779.X
Computational method to predict mitochondrially imported proteins and their targeting sequences.
M. G. Claros (1996)
10.1002/prot.10548
Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment
K. Ginalski (2003)
10.1016/j.cell.2008.09.013
RNase P without RNA: Identification and Functional Reconstitution of the Human Mitochondrial tRNA Processing Enzyme
J. Holzmann (2008)
Gapped BLAST and PSI-BLAST: A new
D. Lipman (1997)
10.1016/0092-8674(82)90049-6
Replication of animal mitochondrial DNA
D. Clayton (1982)
10.1038/90058
Human mitochondrial DNA deletions associated with mutations in the gene encoding Twinkle, a phage T7 gene 4-like protein localized in mitochondria
J. N. Spelbrink (2001)
10.1128/MCB.01834-08
Human Dna2 Is a Nuclear and Mitochondrial DNA Maintenance Protein
Julien P. Duxin (2009)
10.1038/nature07731
Structure and function of the 5’→3’ exoribonuclease Rat1 and its activating partner Rai1
S. Xiang (2009)
10.1093/NAR/29.17.3657
Mechanism of mammalian mitochondrial DNA replication: import of mitochondrial transcription factor A into isolated mitochondria stimulates 7S DNA synthesis.
S. Gensler (2001)
10.1016/j.pep.2010.04.001
Production and characterization of recombinant protein preparations of Endonuclease G-homologs from yeast, C. elegans and humans.
Jana Kieper (2010)
Pulse-labeled components in the replication of mitochondrial deoxyribonucleic acid.
D. Robberson (1973)
10.1083/jcb.200609158
The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization
J. He (2007)
10.1038/nature07480
Endonucleolytic RNA cleavage by a eukaryotic exosome
A. Lebreton (2008)
10.1128/MCB.17.4.2136
A yeast replicative helicase, Dna2 helicase, interacts with yeast FEN-1 nuclease in carrying out its essential function.
M. Budd (1997)
10.1016/S0092-8674(00)80287-1
Another Bridge between Kingdoms: tRNA Splicing in Archaea and Eukaryotes
M. Belfort (1997)
10.1006/JMBI.1993.1626
Comparative protein modelling by satisfaction of spatial restraints.
A. S̆ali (1993)



This paper is referenced by
10.1016/j.dnarep.2015.07.003
Primer removal during mammalian mitochondrial DNA replication.
J. Uhler (2015)
10.1016/j.exger.2014.03.027
In D-loop: 40years of mitochondrial 7S DNA
T. Nicholls (2014)
Derivation of the human cell cycle transcriptional signature
Bruno Giotti (2017)
10.1016/j.dnarep.2014.03.010
Mitochondrial genome maintenance in health and disease.
W. Copeland (2014)
10.1093/nar/gky708
A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL
Ali Al-Behadili (2018)
10.1111/bph.12469
Next‐generation sequencing for mitochondrial disorders
C. J. Carroll (2014)
10.1101/2020.04.28.066605
Using Expansion Microscopy to visualize and characterize the morphology of mitochondrial cristae
T. Kunz (2020)
10.1016/bs.enz.2019.08.004
Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response.
Linlin Zhao (2019)
10.1128/JVI.02306-13
Mitochondrial Nucleases ENDOG and EXOG Participate in Mitochondrial DNA Depletion Initiated by Herpes Simplex Virus 1 UL12.5
Brett A Duguay (2013)
10.1093/nar/gkz542
Quantitative proteomics revealed C6orf203/MTRES1 as a factor preventing stress-induced transcription deficiency in human mitochondria
Anna V. Kotrys (2019)
10.1038/s41598-019-45244-6
Replication fork rescue in mammalian mitochondria
R. Torregrosa-Muñumer (2019)
10.1016/j.molcel.2019.09.010
Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria
Thomas J. Nicholls (2019)
10.3233/JND-140041
Adult-onset Mendelian PEO Associated with Mitochondrial Disease.
E. Sommerville (2014)
10.1093/nar/gkz241
A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication
Chyuan-Chuan Wu (2019)
10.1016/bs.enz.2016.03.006
Animal Mitochondrial DNA Replication.
G. Ciesielski (2016)
Identifying new genes in mitochondrial disease
E. Sommerville (2017)
10.1038/s41467-018-05007-9
Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria
Zbigniew Pietras (2018)
10.1093/nar/gkw468
MGME1 processes flaps into ligatable nicks in concert with DNA polymerase γ during mtDNA replication
J. Uhler (2016)
10.1093/hmg/ddu336
Linear mtDNA fragments and unusual mtDNA rearrangements associated with pathological deficiency of MGME1 exonuclease
T. Nicholls (2014)
Initiation of Mammalian Mitochondrial DNA Replication
Elisabeth Jemt (2014)
10.1371/journal.pone.0176795
Selective mitochondrial DNA degradation following double-strand breaks
Amandine Moretton (2017)
10.2210/PDB5ZKI/PDB
A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication.
Chyuan-Chuan Wu (2019)
10.1038/ncomms8303
The exonuclease activity of DNA polymerase γ is required for ligation during mitochondrial DNA replication
B. Macao (2015)
10.1371/journal.pgen.1006628
Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA
Anna-Karin Berglund (2017)
10.1371/journal.pone.0116726
Whole Cell Formaldehyde Cross-Linking Simplifies Purification of Mitochondrial Nucleoids and Associated Proteins Involved in Mitochondrial Gene Expression
Nina Rajala (2015)
10.1111/febs.13981
Human mitochondrial nucleases
F. Bruni (2017)
10.1093/nar/gkw649
Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs
Anna Łabno (2016)
10.1038/s41467-018-03552-x
Mice lacking the mitochondrial exonuclease MGME1 accumulate mtDNA deletions without developing progeria
S. Matic (2018)
10.1093/nar/gky855
Structural insights into DNA degradation by human mitochondrial nuclease MGME1
Chun Yang (2018)
10.3390/ijms18071562
DNA2—An Important Player in DNA Damage Response or Just Another DNA Maintenance Protein?
E. Pawlowska (2017)
10.1016/j.arr.2016.04.006
Role of the mitochondrial DNA replication machinery in mitochondrial DNA mutagenesis, aging and age-related diseases
Karen L. DeBalsi (2017)
10.1007/s11010-015-2532-x
Mitochondrial DNA maintenance: an appraisal
A. T. Akhmedov (2015)
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