Online citations, reference lists, and bibliographies.
← Back to Search

GC Skew And Mitochondrial Origins Of Replication.

Abdullah H. Sahyoun, M. Bernt, P. Stadler, K. Tout
Published 2014 · Biology, Medicine

Cite This
Download PDF
Analyze on Scholarcy
The comprehensive understanding of mitochondrial genome evolution requires a detailed mechanistic picture of mitogenomic replication. Despite many previous efforts it has remained a non-trivial problem to determine the origins of replication and trace their fate across rearrangements of the gene order even in the small genomes of animal mitochondria. We elaborate here on the observation that the GC skew is correlated with the distance from the replication origins. This effect has been explained as a consequence of the standard model of mitochondrial DNA replication, i.e. the strand displacement model. According to this model chemical damage accumulates proportional to the duration that DNA is exposed in single-stranded form during replication (Dssh) which depends on the relative position with respect to the replication origins. Based on this model we developed a computational method to infer the positions of both the heavy strand and the light strand origin from nucleotide skew data. In a comprehensive survey of deuterostome mitochondria we infer conserved replication origins for the vast majority of vertebrates and cephalochordates. Deviations from the consensus picture are presumably associated with genome rearrangements.
This paper references
Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures.
J. Pütz (2007)
Skewed oligomers and origins of replication.
S. Salzberg (1998)
Database resources of the National Center for Biotechnology
D. L. Wheeler (2003)
Replication of animal mitochondrial DNA
D. Clayton (1982)
Major patterns of higher
S. M. Shirai (2003)
Inverted replication of 950 vertebrate mitochondria
M. M. Fonseca (2008)
The main regulatory region 1062 of mammalian mitochondrial DNA : structure - function model and 1063 evolutionary pattern
S. L. Salzberg (1991)
The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences
M. Miya (2005)
Rearrangements of mitochondrial transfer RNA genes in marsupials
S. Pääbo (2005)
Origins of Mitochondria and Plastids
M. Gray (2012)
Complete sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome: early establishment of the vertebrate genome organization.
W. J. Lee (1995)
The mitochondrial
O. raelsson (2007)
A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny.
M. Bernt (2013)
Animal mitochondrial genomes.
J. Boore (1999)
Analyzing genomes with cumulative skew diagrams.
A. Grigoriev (1998)
R: A language and environment for statistical computing.
R. Team (2014)
The complete mitochondrial genome of bighead croaker, Collichthys niveatus (Perciformes, Sciaenidae): structure of control region and phylogenetic considerations
Tian-jun Xu (2010)
Evolution of the Mitochondrial Genome in Cephalochordata as Inferred from Complete Nucleotide Sequences from Two Epigonichthys Species
M. Nohara (2004)
The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): unusual features of its control region and the phylogenetic position of the Sciaenidae.
Z. Cui (2009)
Both the conserved stem-loop and divergent 5'-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication.
J. Hixson (1986)
Replicating animal mitochon - 996 drial DNA
E. A. McKinney
Human mitochondrial DNA replication.
I. Holt (2012)
The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deu
J. Boore (2000)
, 1049 a database of mammalian mitochondrial tRNA primary and sec - 1050 ondary structures
A. Reyes (2012)
Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes
N. Perna (2004)
The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis
Marleen Perseke (2007)
Mammalian Mitochondrial DNA Replicates Bidirectionally from an Initiation Zone*
Mark Bowmaker (2003)
Mitochondrial Genome Evolution
M. Bernt (2013)
Mitochondrial DNA replication proceeds via a ‘bootlace’ mechanism involving the incorporation of processed transcripts
A. Reyes (2013)
Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes
N. Perna (1995)
MITOS: improved de novo metazoan mitochondrial genome annotation.
M. Bernt (2013)
Complete sequence, gene arrangement, and genetic code of mitochondrial DNA of the cephalochordate Branchiostoma floridae (Amphioxus)
J. Boore (1999)
Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids.
M. Picardeau (2000)
Intrastrand parity rules of DNA base composition and usage biases of synonymous codons
N. Sueoka (2004)
The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes
S. Bourlat (2008)
Complete sequence of the amphioxus (Branchiostoma lanceolatum) mitochondrial genome: relations to vertebrates
N. Spruyt (1998)
Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements.
D. Lavrov (2005)
The complete nucleotide sequence of theRattus norvegicus mitochondrial genome: Cryptic signals revealed by comparative analysis between vertebrates
G. Gadaleta (2007)
An algorithm to
H. Markov (1997)
Inverted replication of vertebrate mitochondria.
M. Fonseca (2008)
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree
M. Bernt (2008)
Complete mitochondrial DNA of the hagfish, Eptatretus burgeri: the comparative analysis of mitochondrial DNA sequences strongly supports the cyclostome monophyly.
C. Delarbre (2002)
Strand asymmetry in human mitochondrial DNA mutations.
M. Tanaka (1994)
Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand
T. Yasukawa (2006)
The enigmatic mitochondrial genome of Rhab - 1034 dopleura compacta ( Pterobranchia ) reveals insights into selection 1035 of an e ffi cient tRNA system and supports monophyly of Ambu - 1036 lacraria
M. Perseke (2011)
Evolution of mitochondrial gene orders in echinoderms.
Marleen Perseke (2008)
atabase resources of the National Center for Biotechnology Information: update
D. L. Wheeler (2004)
Is blood protein amide nitrogen a source of urinary ammonia ? 3. On the question of synthesis of protein amides from ammonia.
E. F. Williams (1932)
The complete mitochondrial genome of Scutigerella causeyae (Myriapoda: Symphyla) and the phylogenetic position of Symphyla.
L. Podsiadlowski (2007)
Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): a mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae.
Jiao Cheng (2012)
Replicating animal mitochondrial DNA
Emily A. McKinney (2013)
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
J. Thompson (1994)
Precise sequence assignment of replication origin in the control region of chick mitochondrial DNA relative to 5′ and 3′ D-loop ends, secondary structure, DNA synthesis, and protein binding
M. M. Nass (2004)
The 1098 complete mitochondrial genome of bighead croaker , Collichthys 1099 niveatus ( Perciformes , Sciaenidae ) : structure of control region and 1100 phylogenetic considerations
T. Yasukawa (2006)
Asymmetrical di - 1055 rectional mutation pressure in the mitochondrial genome of mam - 1056 mals
A. Reyes (1998)
A method for computing an inventory of metazoan mitochondrial gene order rearrangements
Matthias Bernt (2011)
Big trees from little genomes: mitochondrial gene order as a phylogenetic tool.
J. Boore (1998)
Mamit -
J. Pütz
Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications.
E. Sbisà (1997)
Coupled Leading- and Lagging-Strand Synthesis of Mammalian Mitochondrial DNA
I. Holt (2000)
Genetic aspects of mitochondrial genome evolution.
M. Bernt (2013)
The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell
Thomas Junier (2010)
Strand asymmetry in human mitochon - 1089 drial DNA mutations
J. D. Thompson (1994)
Possible multiple origins of replication in primate mitochondria: Alternative role of tRNA sequences.
H. Seligmann (2006)
Requirements and standards for organelle genome databases.
J. Boore (2006)
Complete mitochondrial genome of the rock bream Oplegnathus fasciatus (Perciformes, Oplegnathidae) with phylogenetic considerations.
D. Oh (2007)
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
K. Pruitt (2012)
Strand asymmetries in DNA evo - 952 lution
M. P. Francino (1997)
Mitochondrial DNA Replication
K. Keshav (1998)
Transcription and replication of mitochondrial DNA.
D. Clayton (2000)
Asymmetrical directional mutation pressure in the mitochondrial genome of mammals.
A. Reyes (1998)
A phylogeny of the temperate seabasses (Moronidae) characterized by a translocation of the mt-nd6 gene.
E. Williams (2012)
Mapping of control elements in the displacement loop region of bovine mitochondrial DNA.
T. King (1987)
Hypervariability of ascidian mitochondrial gene order: exposing the myth of deuterostome organelle genome stability.
C. Gissi (2010)
Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences.
M. Miya (2003)
Noise‐reduction filtering for accurate detection of replication termini in bacterial genomes
K. Arakawa (2007)
Replication and transcription of vertebrate mitochondrial DNA.
D. Clayton (1991)
Mechanism of mitochondrial DNA replication in mouse L-cells: localization and sequence of the light-strand origin of replication.
P. Martens (1979)
Intrastrand parity rules of DNA base composition and usage biases of synonymous codons
N. Sueoka (2005)
The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria
Marleen Perseke (2011)
Strand asymmetries in DNA evolution.
M. P. Francino (1997)
The main regulatory region of mammalian mitochondrial DNA: Structure-function model and evolutionary pattern
C. Saccone (2005)
39 Mitochondrial DNA Replication
D. Clayton (1996)
Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers.
Y. Kumazawa (1995)
The complete nucleotide sequence of the rat 18S ribosomal RNA gene and comparison with the respective yeast and frog genes.
R. Torczynski (1983)
Sequence and organization of the human mitochondrial genome
S. Anderson (1981)

This paper is referenced by
iterb-PPse: Identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC
Yongxian Fan (2020)
Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses
Yu-Ting Cai (2020)
Is there a mutation gradient along vertebrate mitochondrial genome mediated by genome replication?
X. Xia (2019)
Complete mitochondrial genome of Anadara vellicata (Bivalvia: Arcidae): A unique gene order and large atypical non-coding region.
Shao'e Sun (2015)
The complete mitochondrial genome of the Caulerpa lentillifera (Ulvophyceae, Chlorophyta): Sequence, genome content, organization structure and phylogenetic consideration.
Fengrong Zheng (2018)
The Inversion of the Control Region in Three Mitogenomes Provides Further Evidence for an Asymmetric Model of Vertebrate mtDNA Replication
M. Fonseca (2014)
Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae).
L. Ding (2019)
Dynamics of small autocatalytic reaction network IV : Inhomogeneous replicator equations
M. Chadha (2016)
Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications
Li-fang Xiao (2019)
The chloroplast genome sequence of the green macroalga Caulerpa okamurae (Ulvophyceae, Chlorophyta): Its structural features, organization and phylogenetic analysis.
Fengrong Zheng (2020)
The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis
Sree Rohit Raj Kolora (2017)
iterb-PPse: Identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC
Yongxian Fan (2020)
The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata
M. T. Aguado (2015)
Evolutionary history of inversions in the direction of architecture-driven mutational pressures in crustacean mitochondrial genomes
D. Zhang (2020)
Mitochondrial genome sequencing of a vermivorous cone snail Conus quercinus supports the correlative analysis between phylogenetic relationships and dietary types of Conus species
B. Gao (2018)
Phylogenetics and comparative analysis of the mitochondrial genomes of three violet‐ringed octopuses
Y. Tang (2019)
Semantic Scholar Logo Some data provided by SemanticScholar