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Evolution of linear chromosomes and multipartite genomes in yeast mitochondria.

Valach M, Farkas Z, Fricova D, Kovac J, Brejova B, Vinar T, Pfeiffer I, Kucsera J, Tomaska L, Lang BF, Nosek J - Nucleic Acids Res. (2011)

Bottom Line: Our survey revealed a puzzling variability of genome architecture, including circular- and linear-mapping and multipartite linear forms.We propose that the arrangement of large inverted repeats identified in these genomes plays a crucial role in alterations of their molecular architectures.We suggest that molecular transactions generating linear mitochondrial DNA molecules with defined telomeric structures may parallel the evolutionary emergence of linear chromosomes and multipartite genomes in general and may provide clues for the origin of telomeres and pathways implicated in their maintenance.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Comenius University, Mlynska dolina CH-1, 842 15 Bratislava, Slovak republic.

ABSTRACT
Mitochondrial genome diversity in closely related species provides an excellent platform for investigation of chromosome architecture and its evolution by means of comparative genomics. In this study, we determined the complete mitochondrial DNA sequences of eight Candida species and analyzed their molecular architectures. Our survey revealed a puzzling variability of genome architecture, including circular- and linear-mapping and multipartite linear forms. We propose that the arrangement of large inverted repeats identified in these genomes plays a crucial role in alterations of their molecular architectures. In specific arrangements, the inverted repeats appear to function as resolution elements, allowing genome conversion among different topologies, eventually leading to genome fragmentation into multiple linear DNA molecules. We suggest that molecular transactions generating linear mitochondrial DNA molecules with defined telomeric structures may parallel the evolutionary emergence of linear chromosomes and multipartite genomes in general and may provide clues for the origin of telomeres and pathways implicated in their maintenance.

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Circular- and linear-mapping genome isomers in mitochondria of C. viswanathii. (A) The mtDNA samples were digested with BamHI (lane 1) or Eco91I (lane 2) and separated in 1% (w/v) agarose gel. The Southern blot was hybridized with radioactively labeled oligonucleotide probe Oligo-32 derived from the large palindrome (shown as dashed arrows). The solid arrows show positions of the palindrome and the presumed terminal fragments of resolved linear molecules capped with t-hairpins. Scheme shows presumed circular- (I) and linear-mapping (II) genome isomers. (B) Isolated mtDNA was treated or untreated with BAL-31 nuclease (0.2 U for 5 min). The mtDNA was then extracted from the reaction, digested with BamHI or Eco91I endonuclease, and electrophoretically separated. Note that the fragments containing presumed t-hairpins were sensitive to BAL-31 nuclease (indicated by asterisk).
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Figure 3: Circular- and linear-mapping genome isomers in mitochondria of C. viswanathii. (A) The mtDNA samples were digested with BamHI (lane 1) or Eco91I (lane 2) and separated in 1% (w/v) agarose gel. The Southern blot was hybridized with radioactively labeled oligonucleotide probe Oligo-32 derived from the large palindrome (shown as dashed arrows). The solid arrows show positions of the palindrome and the presumed terminal fragments of resolved linear molecules capped with t-hairpins. Scheme shows presumed circular- (I) and linear-mapping (II) genome isomers. (B) Isolated mtDNA was treated or untreated with BAL-31 nuclease (0.2 U for 5 min). The mtDNA was then extracted from the reaction, digested with BamHI or Eco91I endonuclease, and electrophoretically separated. Note that the fragments containing presumed t-hairpins were sensitive to BAL-31 nuclease (indicated by asterisk).

Mentions: Physical mapping uncovered genome isomers also in mitochondria of C. viswanathii. However, in this case we observed two BamHI (∼7 and ∼3.5 kb) and Eco91I (∼5 and ∼2.5 kb) bands, with sizes corresponding to a monomer (lower faint band) and a dimer (upper band). Southern hybridization indicates that the two fragments have the same sequence (Figure 3A), and that the ratio between them varied in different preparations (data not shown). In this case, the complete mtDNA sequence of C. viswanathii contains LIRs arranged as a large palindrome (see below), suggesting that the palindrome (represented by the upper band) could be resolved into the smaller fragment (the lower band), i.e. a linear mtDNA with defined terminal sequences/structures. To support this idea we treated isolated mtDNA with BAL-31 nuclease prior to restriction enzyme analysis. This experiment demonstrated that the lower faint band was the only mtDNA fragment sensitive to BAL-31 nuclease activity (Figure 3B). On the other hand, this fragment seems to be refractory to both exonuclease III and T4 polynucleotide kinase (data not shown). This indicates that the termini of resolved linear mtDNA molecules are protected by a special arrangement. We presume that, similar to species from the genera Williopsis and Pichia (44), the linear mtDNA molecules terminate with single-stranded covalently closed telomeric hairpins (t-hairpins). In contrast, we did not identify genome isomers in C. jiufengensis, which lacks LIRs.Figure 3.


Evolution of linear chromosomes and multipartite genomes in yeast mitochondria.

Valach M, Farkas Z, Fricova D, Kovac J, Brejova B, Vinar T, Pfeiffer I, Kucsera J, Tomaska L, Lang BF, Nosek J - Nucleic Acids Res. (2011)

Circular- and linear-mapping genome isomers in mitochondria of C. viswanathii. (A) The mtDNA samples were digested with BamHI (lane 1) or Eco91I (lane 2) and separated in 1% (w/v) agarose gel. The Southern blot was hybridized with radioactively labeled oligonucleotide probe Oligo-32 derived from the large palindrome (shown as dashed arrows). The solid arrows show positions of the palindrome and the presumed terminal fragments of resolved linear molecules capped with t-hairpins. Scheme shows presumed circular- (I) and linear-mapping (II) genome isomers. (B) Isolated mtDNA was treated or untreated with BAL-31 nuclease (0.2 U for 5 min). The mtDNA was then extracted from the reaction, digested with BamHI or Eco91I endonuclease, and electrophoretically separated. Note that the fragments containing presumed t-hairpins were sensitive to BAL-31 nuclease (indicated by asterisk).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
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Figure 3: Circular- and linear-mapping genome isomers in mitochondria of C. viswanathii. (A) The mtDNA samples were digested with BamHI (lane 1) or Eco91I (lane 2) and separated in 1% (w/v) agarose gel. The Southern blot was hybridized with radioactively labeled oligonucleotide probe Oligo-32 derived from the large palindrome (shown as dashed arrows). The solid arrows show positions of the palindrome and the presumed terminal fragments of resolved linear molecules capped with t-hairpins. Scheme shows presumed circular- (I) and linear-mapping (II) genome isomers. (B) Isolated mtDNA was treated or untreated with BAL-31 nuclease (0.2 U for 5 min). The mtDNA was then extracted from the reaction, digested with BamHI or Eco91I endonuclease, and electrophoretically separated. Note that the fragments containing presumed t-hairpins were sensitive to BAL-31 nuclease (indicated by asterisk).
Mentions: Physical mapping uncovered genome isomers also in mitochondria of C. viswanathii. However, in this case we observed two BamHI (∼7 and ∼3.5 kb) and Eco91I (∼5 and ∼2.5 kb) bands, with sizes corresponding to a monomer (lower faint band) and a dimer (upper band). Southern hybridization indicates that the two fragments have the same sequence (Figure 3A), and that the ratio between them varied in different preparations (data not shown). In this case, the complete mtDNA sequence of C. viswanathii contains LIRs arranged as a large palindrome (see below), suggesting that the palindrome (represented by the upper band) could be resolved into the smaller fragment (the lower band), i.e. a linear mtDNA with defined terminal sequences/structures. To support this idea we treated isolated mtDNA with BAL-31 nuclease prior to restriction enzyme analysis. This experiment demonstrated that the lower faint band was the only mtDNA fragment sensitive to BAL-31 nuclease activity (Figure 3B). On the other hand, this fragment seems to be refractory to both exonuclease III and T4 polynucleotide kinase (data not shown). This indicates that the termini of resolved linear mtDNA molecules are protected by a special arrangement. We presume that, similar to species from the genera Williopsis and Pichia (44), the linear mtDNA molecules terminate with single-stranded covalently closed telomeric hairpins (t-hairpins). In contrast, we did not identify genome isomers in C. jiufengensis, which lacks LIRs.Figure 3.

Bottom Line: Our survey revealed a puzzling variability of genome architecture, including circular- and linear-mapping and multipartite linear forms.We propose that the arrangement of large inverted repeats identified in these genomes plays a crucial role in alterations of their molecular architectures.We suggest that molecular transactions generating linear mitochondrial DNA molecules with defined telomeric structures may parallel the evolutionary emergence of linear chromosomes and multipartite genomes in general and may provide clues for the origin of telomeres and pathways implicated in their maintenance.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Comenius University, Mlynska dolina CH-1, 842 15 Bratislava, Slovak republic.

ABSTRACT
Mitochondrial genome diversity in closely related species provides an excellent platform for investigation of chromosome architecture and its evolution by means of comparative genomics. In this study, we determined the complete mitochondrial DNA sequences of eight Candida species and analyzed their molecular architectures. Our survey revealed a puzzling variability of genome architecture, including circular- and linear-mapping and multipartite linear forms. We propose that the arrangement of large inverted repeats identified in these genomes plays a crucial role in alterations of their molecular architectures. In specific arrangements, the inverted repeats appear to function as resolution elements, allowing genome conversion among different topologies, eventually leading to genome fragmentation into multiple linear DNA molecules. We suggest that molecular transactions generating linear mitochondrial DNA molecules with defined telomeric structures may parallel the evolutionary emergence of linear chromosomes and multipartite genomes in general and may provide clues for the origin of telomeres and pathways implicated in their maintenance.

Show MeSH
Related in: MedlinePlus