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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
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)
The mystery of mitochondrial RNases.
F. Bruni (2012)
CLANS: a Java application for visualizing protein families based on pairwise similarity
T. Frickey (2004)
Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
M. Li (2007)
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)
Human mitochondrial RNA turnover caught in flagranti: involvement of hSuv3p helicase in RNA surveillance
Roman J Szczesny (2010)
Down‐regulation of human RNA/DNA helicase SUV3 induces apoptosis by a caspase‐ and AIF‐dependent pathway
Roman J Szczesny (2007)
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
J. Orlowski (2008)
Biochemical analysis of human Dna2
Taro Masuda-Sasa (2006)
Characterization of the Endonuclease and ATP-dependent Flap Endo/Exonuclease of Dna2*
Barbara K. Fortini (2011)
Replication and Transcription of Mammalian Mitochondrial Dna
P. Fernández-Silva (2003)
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily
Kamil Steczkiewicz (2012)
The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome
C. Schneider (2009)
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
L. Aravind (2000)
Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand
T. Yasukawa (2006)
Endonuclease G is an apoptotic DNase when released from mitochondria
L. Li (2001)
Human DNA2 is a mitochondrial nuclease/helicase for efficient processing of DNA replication and repair intermediates.
L. Zheng (2008)
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)
Action of Recombinant Human Apoptotic Endonuclease G on Naked DNA and Chromatin Substrates
P. Widłak (2001)
Differential regulation of full-length genome and a single-stranded 7S DNA along the cell cycle in human mitochondria
Anita Antes (2010)
Mitochondrial base excision repair of uracil and AP sites takes place by single-nucleotide insertion and long-patch DNA synthesis.
M. Akbari (2008)
The Protein Components and Mechanism of Eukaryotic Okazaki Fragment Maturation
Hui-I Kao (2003)
Energy Substrate Modulates Mitochondrial Structure and Oxidative Capacity in Cancer Cells
R. Rossignol (2004)
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)
Mitochondrial DNA nucleoid structure.
D. Bogenhagen (2012)
Dna2 is a structure-specific nuclease, with affinity for 5′-flap intermediates
J. Stewart (2010)
The characterization of a mammalian DNA structure‐specific endonuclease.
J. Harrington (1994)
Removal of Oxidative DNA Damage via FEN1-Dependent Long-Patch Base Excision Repair in Human Cell Mitochondria
P. Liu (2008)
J. Zhang (2009)
Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks
M. Singleton (2004)
Dna2p Helicase/Nuclease Is a Tracking Protein, Like FEN1, for Flap Cleavage during Okazaki Fragment Maturation*
Hui-I Kao (2004)
Bacteriophage origins of mitochondrial replication and transcription proteins.
T. Shutt (2006)
The accessory subunit of mitochondrial DNA polymerase γ determines the DNA content of mitochondrial nucleoids in human cultured cells
M. Di Re (2009)
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)
Involvement of human ELAC2 gene product in 3' end processing of mitochondrial tRNAs
Lien K Brzezniak (2011)
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
Annette Höglund (2006)
Regulation of mitochondrial mRNA stability by RNase L is translation-dependent and controls IFNα-induced apoptosis
F. L. Roy (2007)
Coupled Leading- and Lagging-Strand Synthesis of Mammalian Mitochondrial DNA
I. Holt (2000)
A single subunit, Dis3, is essentially responsible for yeast exosome core activity
A. Dziembowski (2007)
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)
Mitochondrial DNA replication in human T lymphocytes is regulated primarily at the H-strand termination site.
Y. Kai (1999)
Calf 5′ to 3′ Exo/Endonuclease Must Slide from a 5′ End of the Substrate to Perform Structure-specific Cleavage (*)
R. S. Murante (1995)
Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA.
M. W. Walberg (1981)
Yeast Exonuclease 5 Is Essential for Mitochondrial Genome Maintenance
P. Burgers (2010)
EXOG, a novel paralog of Endonuclease G in higher eukaryotes
I. Cymerman (2008)
Native R-loops Persist throughout the Mouse Mitochondrial DNA Genome*S⃞
T. Brown (2008)
Regulation of the human apoptotic DNase/RNase Endonuclease G: involvement of Hsp70 and ATP
M. Kalinowska (2005)
Twinkle helicase is essential for mtDNA maintenance and regulates mtDNA copy number.
H. Tyynismaa (2004)
Biased Incorporation of Ribonucleotides on the Mitochondrial L-Strand Accounts for Apparent Strand-Asymmetric DNA Replication
M. Y. Yang (2002)
Okazaki fragment maturation: nucleases take centre stage.
Li Zheng (2011)
Crystal structure of E. coli RecE protein reveals a toroidal tetramer for processing double-stranded DNA breaks.
Jinjin Zhang (2009)
Crystal structures of λ exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity
Jinjin Zhang (2011)
Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1
Jason W. Gloor (2012)
Long Patch Base Excision Repair in Mammalian Mitochondrial Genomes*
B. Szczesny (2008)
Viral proteins functioning in organelles: a cryptic origin?
J. Filée (2005)
Mitochondrial pH Monitored by a New Engineered Green Fluorescent Protein Mutant*
M. C. Abad (2004)
Locating proteins in the cell using TargetP, SignalP and related tools
Olof Emanuelsson (2007)
Mammalian mitochondrial DNA replication intermediates are essentially duplex but contain extensive tracts of RNA/DNA hybrid.
J. Pohjoismäki (2010)
Expression of catalytic mutants of the mtDNA helicase Twinkle and polymerase POLG causes distinct replication stalling phenotypes
S. Wanrooij (2007)
Human mitochondrial DNA: analysis of 7S DNA from the origin of replication.
W. Brown (1978)
PCMA: fast and accurate multiple sequence alignment based on profile consistency
J. Pei (2003)
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)
Sequence and organization of the human mitochondrial genome
S. Anderson (1981)
Human mitochondrial RNA decay mediated by PNPase–hSuv3 complex takes place in distinct foci
Lukasz S Borowski (2013)
Human 2′-phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover
J. Poulsen (2011)
Assays of the helicase, ATPase, and exoribonuclease activities of the yeast mitochondrial degradosome.
Michał Małecki (2010)
Isolation of human Dna2 endonuclease and characterization of its enzymatic properties
J. Kim (2006)
Displacement-loop replication initiation sequence in animal mitochondrial DNA exists as a family of discrete lengths.
A. Gillum (1978)
Loss, replacement and gain of proteins at the origin of the mitochondria.
M. Huynen (2013)
PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update
X. Wang (2012)
Mitochondrial DNA replication and repair: all a flap.
I. Holt (2009)
Nucleic Acids Research
K. Otto (2015)
The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L
Rafał Tomecki (2010)
Crystal structure of the shutoff and exonuclease protein from the oncogenic Kaposi’s sarcoma‐associated herpesvirus
Sue-Li Dahlroth (2009)
The 2–5A/RNase L/RNase L Inhibitor (RNI) Pathway Regulates Mitochondrial mRNAs Stability in Interferon α-treated H9 Cells*
F. Le Roy (2001)
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)
Computational method to predict mitochondrially imported proteins and their targeting sequences.
M. G. Claros (1996)
Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment
K. Ginalski (2003)
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)
Replication of animal mitochondrial DNA
D. Clayton (1982)
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)
Human Dna2 Is a Nuclear and Mitochondrial DNA Maintenance Protein
Julien P. Duxin (2009)
Structure and function of the 5’→3’ exoribonuclease Rat1 and its activating partner Rai1
S. Xiang (2009)
Mechanism of mammalian mitochondrial DNA replication: import of mitochondrial transcription factor A into isolated mitochondria stimulates 7S DNA synthesis.
S. Gensler (2001)
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)
The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization
J. He (2007)
Endonucleolytic RNA cleavage by a eukaryotic exosome
A. Lebreton (2008)
A yeast replicative helicase, Dna2 helicase, interacts with yeast FEN-1 nuclease in carrying out its essential function.
M. Budd (1997)
Another Bridge between Kingdoms: tRNA Splicing in Archaea and Eukaryotes
M. Belfort (1997)
Comparative protein modelling by satisfaction of spatial restraints.
A. S̆ali (1993)
This paper is referenced by
Primer removal during mammalian mitochondrial DNA replication.
J. Uhler (2015)
In D-loop: 40years of mitochondrial 7S DNA
T. Nicholls (2014)
Derivation of the human cell cycle transcriptional signature
Bruno Giotti (2017)
Mitochondrial genome maintenance in health and disease.
W. Copeland (2014)
A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL
Ali Al-Behadili (2018)
Next‐generation sequencing for mitochondrial disorders
C. J. Carroll (2014)
Using Expansion Microscopy to visualize and characterize the morphology of mitochondrial cristae
T. Kunz (2020)
Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response.
Linlin Zhao (2019)
Mitochondrial Nucleases ENDOG and EXOG Participate in Mitochondrial DNA Depletion Initiated by Herpes Simplex Virus 1 UL12.5
Brett A Duguay (2013)
Quantitative proteomics revealed C6orf203/MTRES1 as a factor preventing stress-induced transcription deficiency in human mitochondria
Anna V. Kotrys (2019)
Replication fork rescue in mammalian mitochondria
R. Torregrosa-Muñumer (2019)
Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria
Thomas J. Nicholls (2019)
Adult-onset Mendelian PEO Associated with Mitochondrial Disease.
E. Sommerville (2014)
A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication
Chyuan-Chuan Wu (2019)
Animal Mitochondrial DNA Replication.
G. Ciesielski (2016)
Identifying new genes in mitochondrial disease
E. Sommerville (2017)
Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria
Zbigniew Pietras (2018)
MGME1 processes flaps into ligatable nicks in concert with DNA polymerase γ during mtDNA replication
J. Uhler (2016)
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)
Selective mitochondrial DNA degradation following double-strand breaks
Amandine Moretton (2017)
A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication.
Chyuan-Chuan Wu (2019)
The exonuclease activity of DNA polymerase γ is required for ligation during mitochondrial DNA replication
B. Macao (2015)
Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA
Anna-Karin Berglund (2017)
Whole Cell Formaldehyde Cross-Linking Simplifies Purification of Mitochondrial Nucleoids and Associated Proteins Involved in Mitochondrial Gene Expression
Nina Rajala (2015)
Human mitochondrial nucleases
F. Bruni (2017)
Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs
Anna Łabno (2016)
Mice lacking the mitochondrial exonuclease MGME1 accumulate mtDNA deletions without developing progeria
S. Matic (2018)
Structural insights into DNA degradation by human mitochondrial nuclease MGME1
Chun Yang (2018)
DNA2—An Important Player in DNA Damage Response or Just Another DNA Maintenance Protein?
E. Pawlowska (2017)
Role of the mitochondrial DNA replication machinery in mitochondrial DNA mutagenesis, aging and age-related diseases
Karen L. DeBalsi (2017)
Mitochondrial DNA maintenance: an appraisal
A. T. Akhmedov (2015)See more