scholarly journals Comparative analysis of mitochondrial genomes in different species reveals the evolution of G-quadruplexes

2021 ◽  
Author(s):  
Hiroshi Sugiyama ◽  
Vinodh Sahayasheela ◽  
Zutao Yu ◽  
Ganesh Pandian
Keyword(s):  
Gene Expression ◽  
Mitochondrial Dna ◽  
Comparative Analysis ◽  
Lower Order ◽  
Genome Stability ◽  
Mitochondrial Genomes ◽  
Cellular Functions ◽  
Higher Eukaryotes ◽  
Heavy Strand ◽  
Light Strand

Abstract G-quadruplexes (G4s) are noncanonical structures that can form in the genomes of a range of organisms and are known to play various roles in cellular function. G4s can also form in mitochondrial DNA (mtDNA) because of their high guanine content, and these G4s may play roles in regulating gene expression, DNA replication, and genome stability. However, little is known regarding the evolution and dissemination of G4s in mitochondria. Here we analyzed the potential G4-forming sequences in mtDNA of 16 species from various families and demonstrated that the heavy strand of mtDNA of higher-order organisms contained higher levels of G4 regions than that of lower-order organisms. Analysis of the codons in the light strand revealed enrichment of guanine/cytosine-rich regions in higher eukaryotes and of adenine/thymidine-rich regions in lower-order organisms. Our study showed the diversity of G4s in species ranging from lower to higher orders. In particular, mammals such as humans, chimpanzees, and monkeys display a greater number of G4s than lower-order organisms. These potentially play a role in a range of cellular functions and assist in the evolution of higher organisms.

Replication-competent human mitochondrial DNA lacking the heavy-strand promoter region

1991 ◽  
Vol 11 (3) ◽  
pp. 1631-1637
Author(s):  
C T Moraes ◽  
F Andreetta ◽  
E Bonilla ◽  
S Shanske ◽  
S DiMauro ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Promoter Region ◽  
Direct Repeat ◽  
Progressive External Ophthalmoplegia ◽  
Mitochondrial Transcription Factor ◽  
Mtdna Deletion ◽  
Heavy Strand ◽  
Light Strand

We identified two patients with progressive external ophthalmoplegia, a mitochondrial disease, who harbored a population of partially deleted mitochondrial DNA (mtDNA) with unusual properties. These molecules were deleted from mtDNA positions 548 to 4,442 and encompassed not only rRNA sequences but the heavy-strand promoter region as well. A 13-bp direct repeat was found flanking the breakpoint precisely, with the repeat at positions 535 to 547 located within the binding site for mitochondrial transcription factor 1 (mtTF1). This is the second mtDNA deletion involving a 13-bp direct repeat reported but is at least 10 times less frequent in the patient population than the former one. In situ hybridization studies showed that transcripts under the control of the light-strand promoter were abundant in muscle fibers with abnormal proliferation of mitochondria, while transcripts directed by the heavy-strand promoter, whether of genes residing inside or outside the deleted region, were not. The efficient transcription from the light-strand promoter implies that the major heavy-and light-strand promoters, although physically close, are functionally independent, confirming previous in vitro studies.

scholarly journals Identification of primary transcriptional start sites of mouse mitochondrial DNA: accurate in vitro initiation of both heavy- and light-strand transcripts.

1986 ◽  
Vol 6 (5) ◽  
pp. 1446-1453 ◽  
Author(s):  
D D Chang ◽  
D A Clayton
Keyword(s):  
Mitochondrial Dna ◽  
Transcriptional Control ◽  
Spatial Relationship ◽  
S1 Nuclease ◽  
Loop Region ◽  
Loop Sequence ◽  
Transcriptional Start Sites ◽  
Heavy Strand ◽  
Light Strand

The major transcriptional control sequences of vertebrate mitochondrial DNA lie within the displacement loop region. Transcription events initiating in the displacement loop sequence of the mouse genome were identified by 5' end mapping of primary transcripts by S1 nuclease protection and primer extension techniques. Light-strand transcription initiates at a single site, 165 nucleotides upstream of the major heavy-strand origin of replication. Transcription of the heavy strand occurs at two distinct sites, 5 and 13 nucleotides upstream of the gene for phenylalanyl-tRNA, the first heavy-strand-encoded gene. This spatial relationship of the two transcriptional start sites with each other and with the origin of heavy-strand replication and the gene for tRNAPhe is quite similar to that for human mitochondrial DNA. The predominant form of primary heavy-strand transcript in mouse is a short, ca. 75-nucleotide, RNA containing the sequences of tRNAPhe and a few additional nucleotides at the 5' end of tRNAPhe, suggesting that the processing of tRNA involves independent cleavages at the 5' and 3' ends of tRNA sequences.

scholarly journals Mitochondrial DNA structure and expression in specialized subtypes of mammalian striated muscle.

1990 ◽  
Vol 10 (11) ◽  
pp. 5671-5678 ◽  
Author(s):  
B H Annex ◽  
R S Williams
Keyword(s):  
Mitochondrial Dna ◽  
Copy Number ◽  
Striated Muscle ◽  
Dna Structure ◽  
Triplex Dna ◽  
Mtdna Copy Number ◽  
Loop Region ◽  
D Loop ◽  
Heavy Strand ◽  
Light Strand

Mitochondrial DNA (mt DNA) in cells of vertebrate organisms can assume an unusual triplex DNA structure known as the displacement loop (D loop). This triplex DNA structure forms when a partially replicated heavy strand of mtDNA (7S mtDNA) remains annealed to the light strand, displacing the native heavy strand in this region. The D-loop region contains the promoters for both heavy- and light-strand transcription as well as the origin of heavy-strand replication. However, the distribution of triplex and duplex forms of mtDNA in relation to respiratory activity of mammalian tissues has not been systematically characterized, and the functional significance of the D-loop structure is unknown. In comparisons of specialized muscle subtypes within the same species and of the same muscle subtype in different species, the relative proportion of D-loop versus duplex forms of mtDNA in striated muscle tissues of several mammalian species demonstrated marked variation, ranging from 1% in glycolytic fast skeletal fibers of the rabbit to 65% in the mouse heart. There was a consistent and direct correlation between the ratio of triplex to duplex forms of mtDNA and the capacity of these tissues for oxidative metabolism. The proportion of D-loop forms likewise correlated directly with mtDNA copy number, mtRNA abundance, and the specific activity of the mtDNA (gamma) polymerase. The D-loop form of mtDNA does not appear to be transcribed at greater efficiency than the duplex form, since the ratio of mtDNA copy number to mtRNA was unrelated to the proportion of triplex mtDNA genomes. However, tissues with a preponderance of D-loop forms tended to express greater levels of cytochrome b mRNA relative to mitochondrial rRNA transcripts, suggesting that the triplex structure may be associated with variations in partial versus full-length transcription of the heavy strand.

scholarly journals Identification of initiation sites for heavy-strand and light-strand transcription in human mitochondrial DNA.

1982 ◽  
Vol 79 (23) ◽  
pp. 7195-7199 ◽  
Author(s):  
J. Montoya ◽  
T. Christianson ◽  
D. Levens ◽  
M. Rabinowitz ◽  
G. Attardi
Keyword(s):  
Mitochondrial Dna ◽  
Human Mitochondrial Dna ◽  
Heavy Strand ◽  
Light Strand

scholarly journals Replication-competent human mitochondrial DNA lacking the heavy-strand promoter region.

1991 ◽  
Vol 11 (3) ◽  
pp. 1631-1637 ◽  
Author(s):  
C T Moraes ◽  
F Andreetta ◽  
E Bonilla ◽  
S Shanske ◽  
S DiMauro ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Promoter Region ◽  
Direct Repeat ◽  
Progressive External Ophthalmoplegia ◽  
Mitochondrial Transcription Factor ◽  
Mtdna Deletion ◽  
Heavy Strand ◽  
Light Strand

We identified two patients with progressive external ophthalmoplegia, a mitochondrial disease, who harbored a population of partially deleted mitochondrial DNA (mtDNA) with unusual properties. These molecules were deleted from mtDNA positions 548 to 4,442 and encompassed not only rRNA sequences but the heavy-strand promoter region as well. A 13-bp direct repeat was found flanking the breakpoint precisely, with the repeat at positions 535 to 547 located within the binding site for mitochondrial transcription factor 1 (mtTF1). This is the second mtDNA deletion involving a 13-bp direct repeat reported but is at least 10 times less frequent in the patient population than the former one. In situ hybridization studies showed that transcripts under the control of the light-strand promoter were abundant in muscle fibers with abnormal proliferation of mitochondria, while transcripts directed by the heavy-strand promoter, whether of genes residing inside or outside the deleted region, were not. The efficient transcription from the light-strand promoter implies that the major heavy-and light-strand promoters, although physically close, are functionally independent, confirming previous in vitro studies.

Identification of primary transcriptional start sites of mouse mitochondrial DNA: accurate in vitro initiation of both heavy- and light-strand transcripts

1986 ◽  
Vol 6 (5) ◽  
pp. 1446-1453
Author(s):  
D D Chang ◽  
D A Clayton
Keyword(s):  
Mitochondrial Dna ◽  
Transcriptional Control ◽  
Spatial Relationship ◽  
S1 Nuclease ◽  
Loop Region ◽  
Loop Sequence ◽  
Transcriptional Start Sites ◽  
Heavy Strand ◽  
Light Strand

The major transcriptional control sequences of vertebrate mitochondrial DNA lie within the displacement loop region. Transcription events initiating in the displacement loop sequence of the mouse genome were identified by 5' end mapping of primary transcripts by S1 nuclease protection and primer extension techniques. Light-strand transcription initiates at a single site, 165 nucleotides upstream of the major heavy-strand origin of replication. Transcription of the heavy strand occurs at two distinct sites, 5 and 13 nucleotides upstream of the gene for phenylalanyl-tRNA, the first heavy-strand-encoded gene. This spatial relationship of the two transcriptional start sites with each other and with the origin of heavy-strand replication and the gene for tRNAPhe is quite similar to that for human mitochondrial DNA. The predominant form of primary heavy-strand transcript in mouse is a short, ca. 75-nucleotide, RNA containing the sequences of tRNAPhe and a few additional nucleotides at the 5' end of tRNAPhe, suggesting that the processing of tRNA involves independent cleavages at the 5' and 3' ends of tRNA sequences.

scholarly journals Fluorescent in situ hybridization of mitochondrial DNA and RNA.

2010 ◽  
Vol 57 (4) ◽  
Author(s):  
Lukáš Alán ◽  
Jaroslav Zelenka ◽  
Jan Ježek ◽  
Andrea Dlasková ◽  
Petr Ježek
Keyword(s):  
Mitochondrial Dna ◽  
Fluorescent In Situ Hybridization ◽  
Molecular Beacon ◽  
Rnase A ◽  
Dna And Rna ◽  
D Loop ◽  
Heavy Strand ◽  
Light Strand ◽  
Mitochondrial Reticulum

To reveal nucleic acid localization in mitochondria, we designed molecular beacon fluorescent probes against: i) the light strand complementary to ND5 mitochondrial DNA (mtDNA) gene (annealing also to corresponding mRNA); ii) displacement (D) loop 7S DNA (annealing also to parallel heavy strand mtDNA and corresponding light strand transcript); iii) the proximal D-loop heavy strand displaced by the light strand promoter minor RNA. Confocal microscopy demonstrated ND5 probe spreading (less for other probes) in mitochondrial reticulum tubules but upon RNase A treatment all probes contoured mtDNA nucleoid localization. DNase I spread the signal over mitochondrial tubules. Future applications are discussed.

Mitochondrial DNA structure and expression in specialized subtypes of mammalian striated muscle

1990 ◽  
Vol 10 (11) ◽  
pp. 5671-5678
Author(s):  
B H Annex ◽  
R S Williams
Keyword(s):  
Mitochondrial Dna ◽  
Copy Number ◽  
Striated Muscle ◽  
Dna Structure ◽  
Triplex Dna ◽  
Mtdna Copy Number ◽  
Loop Region ◽  
D Loop ◽  
Heavy Strand ◽  
Light Strand

Mitochondrial DNA (mt DNA) in cells of vertebrate organisms can assume an unusual triplex DNA structure known as the displacement loop (D loop). This triplex DNA structure forms when a partially replicated heavy strand of mtDNA (7S mtDNA) remains annealed to the light strand, displacing the native heavy strand in this region. The D-loop region contains the promoters for both heavy- and light-strand transcription as well as the origin of heavy-strand replication. However, the distribution of triplex and duplex forms of mtDNA in relation to respiratory activity of mammalian tissues has not been systematically characterized, and the functional significance of the D-loop structure is unknown. In comparisons of specialized muscle subtypes within the same species and of the same muscle subtype in different species, the relative proportion of D-loop versus duplex forms of mtDNA in striated muscle tissues of several mammalian species demonstrated marked variation, ranging from 1% in glycolytic fast skeletal fibers of the rabbit to 65% in the mouse heart. There was a consistent and direct correlation between the ratio of triplex to duplex forms of mtDNA and the capacity of these tissues for oxidative metabolism. The proportion of D-loop forms likewise correlated directly with mtDNA copy number, mtRNA abundance, and the specific activity of the mtDNA (gamma) polymerase. The D-loop form of mtDNA does not appear to be transcribed at greater efficiency than the duplex form, since the ratio of mtDNA copy number to mtRNA was unrelated to the proportion of triplex mtDNA genomes. However, tissues with a preponderance of D-loop forms tended to express greater levels of cytochrome b mRNA relative to mitochondrial rRNA transcripts, suggesting that the triplex structure may be associated with variations in partial versus full-length transcription of the heavy strand.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

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