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  • 1
    Electronic Resource
    Electronic Resource
    Separation of Different Conformations of Plant Mitochondrial DNA Molecules by Field Inversion Gel Electrophoresis (1998)
    Springer
    Plant molecular biology reporter 16 (1998), S. 219-229 
    Details
    ISSN: 1572-9818
    Keywords: field inversion gel electrophoresis ; genome structure ; plant mitochondrial DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Mitochondrial (mt) DNA structure in higher plants is still unclear as to the circularity or linearity of the genome. We have developed a system to electrophoretically separate distinct populations of mtDNA, with some populations enriched for networked linear and circular DNA molecules. Using field inversion gel electrophoresis (FIGE) and electron microscopy (EM), we have identified four distinct populations of mtDNA from two Brassica species. Using FIGE, two slow migrating mtDNA populations ran faster than a 66 kbp Escherichia coli circular plasmid marker, while these same populations comigrated in the compression zone in contour-clamped homogeneous electrophoretic field (CHEF) gels. A fast-migrating mtDNA population was also resolved by FIGE as a diffuse band between 20 to 70 kbp when compared with linear lambda (λ) markers. FIGE resolved the 66 kbp circular marker into several multimers, while CHEF resolved only open-circular monomers and linears. In agreement with FIGE results, EM analysis indicated the two slow migrating mtDNA populations contained circular (both supercoiled and relaxed circles) and free linear molecules of 10-60 kbp, and networked linear molecules of 45–140 kbp total size that may represent recombination intermediates. The fast migrating population consisted of 10–50 kbp linear molecules. Well-bound mtDNA showed only long linear molecules of 40–150 kbp with no detection of circles or complex/rosette molecules. This report shows that FIGE has clear advantages over CHEF for separating large DNA molecules with different conformations, and may be very useful for studies to characterize genome structure in complex systems such as plant mitochondria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1007512108373
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  • 2
    Electronic Resource
    Electronic Resource
    A 7.5-kbp region of the maize (T cytoplasm) mitochondrial genome contains a chloroplast-like trnI (CAT) pseudo gene and many short segments homologous to chloroplast and other known genes (1997)
    Springer
    Current genetics 32 (1997), S. 125-131 
    Details
    ISSN: 1432-0983
    Keywords: Key words mtDNA ; Promiscuous DNA ; Maize cmsT ; Organelle genomes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The DNA sequence of a 7.5-kbp region from the maize cmsT mt genome was determined. Nucleotide-sequence analysis of this region reveals the presence of a ct-like trnI (CAT) gene, orf31 and orf48 which are respectively homologous to the trnI (CAT) gene in the maize and rice chloroplast genomes, and to orf28 and orf64 in the rice chloroplast genome. Northern-blot analysis indicates that the ct-like trnI (CAT) gene is likely to be a pseudo gene in the maize cmsT mt genome because it is not transcribed. A nucleotide-sequence homology search of this 7.5-kbp region reveals several short segments homologous to portions of chloroplast (ct), mitochondrial (mt) and other known genes. These segments range from 17 bp to 187 bp in length with homology from 71 to 100%. These observations also suggest that the transfer of DNA fragments from the ct genome to the mt genome may have occurred at different times during the evolution of the maize mt genome, and that multiple recombination events and rearrangements in both mt and ct genomes have occurred after the transfer of DNA fragments from the ct to the mt genome. A few segments were identified by their homology to be portions of genes from sources other than the ct genome. While it is known that large fragments of ctDNA have been transferred to maize mt genomes, this is the first report of the presence of numerous short ctDNA, or other foreign DNA segments, in the maize cmsT mt genome. These segments may provide valuable information regarding the evolution of plant mt genomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002940050256
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  • 3
    Electronic Resource
    Electronic Resource
    Characterization of replication origins flanking the 23S rRNA gene in tobacco chloroplast DNA (1996)
    Springer
    Plant molecular biology 32 (1996), S. 693-706 
    Details
    ISSN: 1573-5028
    Keywords: chloroplast DNA replication ; D-loops ; primer extension ; tobacco
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Using 5′ end-labeled nascent strands of tobacco chloroplast DNA (ctDNA) as a probe, replication displacement loop (D-loop) regions were identified. The strongest hybridization was observed with restriction fragments containing the rRNA genes from the inverted repeat region. Two-dimensional gel analysis of various digests of tobacco ctDNA suggested that a replication origin is located near each end of the 7.1 kb BamHI fragment containing part of the rRNA operon. Analysis of in vitro replication products indicated that templates from either of the origin regions supported replication, while the vector alone or ctDNA clones from other regions of the genome did not support in vitro replication. Sequences from both sides of the BamHI site in the rRNA spacer region were required for optimal in vitro DNA replication activity. Primer extension was used for the first time to identify the start site of DNA synthesis for the D-loop in the rRNA spacer region. The major 5′ end of the D-loop was localized to the base of a stem-loop structure which contains the rRNA spacer BamHI site. Primer extension products were insensitive to both alkali and RNase treatment, suggesting that RNA primers had already been removed from the 5′ end of nascent DNA. Location of an origin in the rRNA spacer region of ctDNA from tobacco, pea and Oenothera suggests that ctDNA replication origins may be conserved in higher plants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00020210
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  • 4
    Electronic Resource
    Electronic Resource
    Pea chloroplast topoisomerase I: purification, characterization, and role in replication (1988)
    Springer
    Plant molecular biology 11 (1988), S. 3-14 
    Details
    ISSN: 1573-5028
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A DNA-relaxing enzyme was purified 5 000-fold to homogeneity from isolated chloroplasts of Pisum sativum. The enzyme consists of a single polypeptide of 112 kDa. The enzyme was able to relax negatively supercoiled DNA in the absence of ATP. It is resistant to nalidixic acid and novobiocin, and causes a unit change in the linkage number of supercoiled DNA. The enzyme shows optimum activity at 37°C with 50 mM KCl and 10 mM MgCl2. From these properties, the enzyme can be classified as a prokaryotic type I topoisomerase. Using a partiall purified pea chloroplast DNA polymerase fraction devoid of topoisomerase I activity for in vitro replication on clones containing the pea chloroplast DNA origins of replication, a 2–6-fold stimulation of replication activity was obtained when the purified topoisomerase I was added to the reaction at 70–100 mM KCl. However, when the same reaction was carried out at 125 mM KCl, which does not affect DNA polymerase activity on calf thymus DNA but is completely inhibitory for topoisomerase I activity, a 4-fold drop in activity resulted. Novobiocin, an inhibitor of topoisomerase II, was not found to inhibit the in vitro replication of chloroplast DNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00016009
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  • 5
    Electronic Resource
    Electronic Resource
    Pea chloroplast DNA primase: characterization and role in initiation of replication (1991)
    Springer
    Plant molecular biology 16 (1991), S. 1019-1034 
    Details
    ISSN: 1573-5028
    Keywords: chloroplasts ; DNA primase ; DNA replication ; Pisum sativum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A DNA primase activity was isolated from pea chloroplasts and examined for its role in replication. The DNA primase activity was separated from the majority of the chloroplast RNA polymerase activity by linear salt gradient elution from a DEAE-cellulose column, and the two enzyme activities were separately purified through heparin-Sepharose columns. The primase activity was not inhibited by tagetitoxin, a specific inhibitor of chloroplast RNA polymerase, or by polyclonal antibodies prepared against purified pea chloroplast RNA polymerase, while the RNA polymerase activity was inhibited completely by either tagetitoxin or the polyclonal antibodies. The DNA primase activity was capable of priming DNA replication on single-stranded templates including poly(dT), poly(dC), M13mp19, and M13mp19_+ 2.1, which contains the AT-rich pea chloroplast origin of replication. The RNA polymerase fraction was incapable of supporting incorporation of 3H-TTP in in vitro replication reactions using any of these single-stranded DNA templates. Glycerol gradient analysis indicated that the pea chloroplast DNA primase (115–120 kDa) separated from the pea chloroplast DNA polymerase (90 kDa), but is much smaller than chloroplast RNA polymerase. Because of these differences in size, template specificity, sensitivity to inhibitors, and elution characteristics, it is clear that the pea chloroplast DNA primase is an distinct enzyme form RNA polymerase. In vitro replication activity using the DNA primase fraction required all four rNTPs for optimum activity. The chloroplast DNA primase was capable of priming DNA replication activity on any single-stranded M13 template, but shows a strong preference for M13mp19+2.1. Primers synthesized using M13mp19+2.1 are resistant to DNase I, and range in size from 4 to about 60 nucleotides.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00016074
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