Inverted Repeat Sequences in Physarum polycephalum Nuclear Deoxyribonucleic Acid

1977 ◽  
Vol 5 (3) ◽  
pp. 678-679 ◽  
Author(s):  
PETER L. JACK ◽  
NORMAN HARDMAN
Keyword(s):  
Inverted Repeat ◽  
Physarum Polycephalum ◽  
Deoxyribonucleic Acid ◽  
Repeat Sequences ◽  
Nuclear Deoxyribonucleic Acid

Distribution of Inverted Repeat Sequences in Nuclear DNA from Physarum polycephalum

1979 ◽  
Vol 94 (1) ◽  
pp. 179-187 ◽  
Author(s):  
Norman HARDMAN ◽  
Peter L. JACK ◽  
J. P. BROWN ◽  
Alan MCLACHLAN
Keyword(s):  
Inverted Repeat ◽  
Physarum Polycephalum ◽  
Nuclear Dna ◽  
Repeat Sequences

scholarly journals Microbubbles in replicating nuclear deoxyribonucleic acid from Physarum polycephalum

1979 ◽  
Vol 183 (2) ◽  
pp. 477-480 ◽  
Author(s):  
D A F Gillespie ◽  
N Hardman
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Dna Synthesis ◽  
Physarum Polycephalum ◽  
Deoxyribonucleic Acid ◽  
Nuclear Dna ◽  
S Phase ◽  
Dna Structures ◽  
Nuclear Deoxyribonucleic Acid

Clusters of microbubbles, represent probable sites of newly initiated DNA synthesis, were identified in nuclear DNA from Physarum polycephalum by using the electron microscope. Their presence is associated specifically with S-phase. Each microbubble corresponds in size to a replicating segment of DNA about 100-5000 nucleotide residues in length. The DNA structures containing microbubbles are metastable, and revert to native DNA in the presence of moderate concentrations of formamide used to prepare samples for electron microscopy. It is suggested that each cluster of microbubbles may correspond to a unit of replication (a replicon) in Physarum DNA.

scholarly journals Inheritance of extrachromosomal rDNA in Physarum polycephalum.

1983 ◽  
Vol 3 (4) ◽  
pp. 635-642 ◽  
Author(s):  
P J Ferris ◽  
V M Vogt ◽  
C L Truitt
Keyword(s):  
Inverted Repeat ◽  
Physarum Polycephalum ◽  
Symmetry Axis ◽  
Single Copy ◽  
The Other ◽  
Cleavage Pattern ◽  
Extrachromosomal Dna ◽  
Repeat Sequences ◽  
Rdna Sequences ◽  
Restriction Endonuclease Cleavage

In the acellular slime mold Physarum polycephalum, the several hundred genes coding for rRNA are located on linear extrachromosomal DNA molecules of a discrete size, 60 kilobases. Each molecule contains two genes that are arranged in a palindromic fashion and separated by a central spacer region. We investigated how rDNA is inherited after meiosis. Two Physarum amoebal strains, each with an rDNA recognizable by its restriction endonuclease cleavage pattern, were mated, the resulting diploid plasmodium was induced to sporulate, and haploid progeny clones were isolated from the germinated spores. The type of rDNA in each was analyzed by blotting hybridization, with cloned rDNA sequences used as probes. This analysis showed that rDNA was inherited in an all-or-nothing fashion; that is, progeny clones contained one or the other parental rDNA type, but not both. However, the rDNA did not segregate in a simple Mendelian way; one rDNA type was inherited more frequently than the other. The same rDNA type was also in excess in the diploid plasmodium before meiosis, and the relative proportions of the two rDNAs changed after continued plasmodial growth. The proportion of the two rDNA types in the population of progeny clones reflected the proportion in the parent plasmodium before meoisis. The rDNAs in many of the progeny clones contained specific deletions of some of the inverted repeat sequences at the central palindromic symmetry axis. To explain the pattern of inheritance of Physarum rDNA, we postulate that a single copy of rDNA is inserted into each spore or is selectively replicated after meiosis.

scholarly journals Protein tightly bound near the termini of the Physarum extrachromosomal rDNA palindrome.

1981 ◽  
Vol 91 (1) ◽  
pp. 309-314 ◽  
Author(s):  
M K Cheung ◽  
D T Drivas ◽  
V C Littau ◽  
E M Johnson
Keyword(s):  
Molecular Weight ◽  
Organic Solvents ◽  
Ribosomal Rna ◽  
Inverted Repeat ◽  
Gel Electrophoresis ◽  
Physarum Polycephalum ◽  
Chromosomal Integration ◽  
Terminal Protein ◽  
Restriction Fragments ◽  
Repeat Sequences

The genes coding for ribosomal RNa in plasmodia of Physarum polycephalum are arranged palindromically on extrachromosomal rDNA molecules of 61 kb (kilobasepairs). Incubation of mildly extracted rDNA with the 125I Bolton-Hunter reagent results in incorporation of label not removed by SDS, CsCl, or various organic solvents. Labeled protein is preferentially associated with terminal rDNA restriction fragments, as detected after gel electrophoresis of the DNA. Antibody reaction with dinitrophenylated protein-rDNA complexes allows visualization of protein located from 1 to 2 kb from the termini, in a region containing multiple inverted repeat sequences and single-strand gaps. DNase I treatment of either rDNA or rDNA termini releases primarily two labeled protein bands of 5,000 and 13,000 daltons as well as less prominent bands of higher molecular weight. We discuss mechanisms for involvement of terminal protein in replication of 3' ends and chromosomal integration of the rDNA.

scholarly journals Sequence organization in nuclear deoxyribonucleic acid from Physarum polycephalum. Physical properties of foldback sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 105-113 ◽  
Author(s):  
P L Jack ◽  
N Hardman
Keyword(s):  
Inverted Repeat ◽  
Physarum Polycephalum ◽  
Nuclear Dna ◽  
Single Copy ◽  
Dna Molecules ◽  
Single Chain ◽  
Sequence Organization ◽  
Repeat Sequences ◽  
Salt Gradient ◽  
Average Size

An investigation was performed with the use of physical techniques, to determine the nature and organization of inverted repeat sequences in nuclear DNA fragments from Physarum polycephalum. From the average size of foldback duplexes (550 nucleotide pairs), and the foldback duplex yield as determined by treatment of DNA with S1 deoxyribonuclease followed by hydroxyapatite chromatography, it is estimated that there are at least 25000 foldback sequences in the Physarum genome. Foldback DNA molecules exhibit properties intermediate between single-stranded DNA and native duplexes on elution from hydroxyapatite with a salt gradient. In addition, thermal-elution chromatography of foldback DNA from hydroxyapatite crystals shows that foldback duplexes are less stable than native DNA. These properties can be explained on the basis that inverted repeat sequences are mismatched when in the foldback configuration. The results of experiments in which the binding of foldback DNA molecules to hydroxyapatite was determined, by using fragments of different single-chain size, agree with previous studies indicating that inverted repeat sequences are located, on average, every 7000 residues throughout the Physarum genome. The inverted repeats are derived from both the repetitive and single-copy components in Physarum nuclear DNA.

Inheritance of extrachromosomal rDNA in Physarum polycephalum

1983 ◽  
Vol 3 (4) ◽  
pp. 635-642
Author(s):  
P J Ferris ◽  
V M Vogt ◽  
C L Truitt
Keyword(s):  
Inverted Repeat ◽  
Physarum Polycephalum ◽  
Symmetry Axis ◽  
Single Copy ◽  
The Other ◽  
Cleavage Pattern ◽  
Extrachromosomal Dna ◽  
Repeat Sequences ◽  
Rdna Sequences ◽  
Restriction Endonuclease Cleavage

In the acellular slime mold Physarum polycephalum, the several hundred genes coding for rRNA are located on linear extrachromosomal DNA molecules of a discrete size, 60 kilobases. Each molecule contains two genes that are arranged in a palindromic fashion and separated by a central spacer region. We investigated how rDNA is inherited after meiosis. Two Physarum amoebal strains, each with an rDNA recognizable by its restriction endonuclease cleavage pattern, were mated, the resulting diploid plasmodium was induced to sporulate, and haploid progeny clones were isolated from the germinated spores. The type of rDNA in each was analyzed by blotting hybridization, with cloned rDNA sequences used as probes. This analysis showed that rDNA was inherited in an all-or-nothing fashion; that is, progeny clones contained one or the other parental rDNA type, but not both. However, the rDNA did not segregate in a simple Mendelian way; one rDNA type was inherited more frequently than the other. The same rDNA type was also in excess in the diploid plasmodium before meiosis, and the relative proportions of the two rDNAs changed after continued plasmodial growth. The proportion of the two rDNA types in the population of progeny clones reflected the proportion in the parent plasmodium before meoisis. The rDNAs in many of the progeny clones contained specific deletions of some of the inverted repeat sequences at the central palindromic symmetry axis. To explain the pattern of inheritance of Physarum rDNA, we postulate that a single copy of rDNA is inserted into each spore or is selectively replicated after meiosis.

scholarly journals Nuclear deoxyribonucleic acid polymerases of liver.

1975 ◽  
Vol 250 (20) ◽  
pp. 8179-8183
Author(s):  
WE Lynch ◽  
S Surrey ◽  
I Lieberman
Keyword(s):  
Deoxyribonucleic Acid ◽  
Nuclear Deoxyribonucleic Acid

scholarly journals Formation of Large Palindromic DNA by Homologous Recombination of Short Inverted Repeat Sequences in Saccharomyces cerevisiae

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1065-1075
Author(s):  
David K Butler ◽  
David Gillespie ◽  
Brandi Steele
Keyword(s):  
Homologous Recombination ◽  
Inverted Repeat ◽  
Excision Repair ◽  
Strand Break ◽  
Double Strand Break ◽  
Repeat Sequence ◽  
Inverted Repeat Sequence ◽  
Repeat Sequences ◽  
Dna Double Strand Break ◽  
Intermolecular Reaction

Abstract Large DNA palindromes form sporadically in many eukaryotic and prokaryotic genomes and are often associated with amplified genes. The presence of a short inverted repeat sequence near a DNA double-strand break has been implicated in the formation of large palindromes in a variety of organisms. Previously we have established that in Saccharomyces cerevisae a linear DNA palindrome is efficiently formed from a single-copy circular plasmid when a DNA double-strand break is introduced next to a short inverted repeat sequence. In this study we address whether the linear palindromes form by an intermolecular reaction (that is, a reaction between two identical fragments in a head-to-head arrangement) or by an unusual intramolecular reaction, as it apparently does in other examples of palindrome formation. Our evidence supports a model in which palindromes are primarily formed by an intermolecular reaction involving homologous recombination of short inverted repeat sequences. We have also extended our investigation into the requirement for DNA double-strand break repair genes in palindrome formation. We have found that a deletion of the RAD52 gene significantly reduces palindrome formation by intermolecular recombination and that deletions of two other genes in the RAD52-epistasis group (RAD51 and MRE11) have little or no effect on palindrome formation. In addition, palindrome formation is dramatically reduced by a deletion of the nucleotide excision repair gene RAD1.

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