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.

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 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.

scholarly journals ON INVERTED REPEAT SEQUENCES IN CHROMOSOMAL DNA

Genetics ◽  
1976 ◽  
Vol 82 (1) ◽  
pp. 139-140
Author(s):  
Bruce Wallace ◽  
Thomas L Kass
Keyword(s):  
Inverted Repeat ◽  
Transcription Termination ◽  
The Other ◽  
Complementary Strand ◽  
Chromosomal Dna ◽  
Repeat Sequences

ABSTRACT It is suggested that chromosomal DNA should contain a class of palindromic reverse repeats, comparable in number to that of genes themselves, which are formed as follows: (1) a transcription-termination signal that follows the gene plus (on the complementary strand and located as near to the "anti-gene" as possible); (2) a second termination signal which actively prevents the accidental transcription of the anti-gene. Thus, the adjacent termination-anti-termination region of one strand would complement the anti-termination-termination region of the other.

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 Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis saxicola and C. tomentella

2020 ◽  
Author(s):  
fengming Ren ◽  
Liqiang Wang ◽  
Ying Li ◽  
Wei Zhuo ◽  
Zhichao Xu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Duplication ◽  
Inverted Repeat ◽  
Nadh Dehydrogenase ◽  
Single Copy ◽  
High Variability ◽  
The Other ◽  
Evolutionary Relationships ◽  
Cp Genome

Abstract Backgroud: Corydalis DC., the largest genus of Papaveraceae, is recognized as one of the most taxonomically challenging plant taxa. However, no complete chloroplast (cp) genome for this genus has been reported to date. Results: We sequenced four complete cp genomes of two affinities Corydalis saxicola and C. tomentellav of the genus Corydalis, compared these cp genomes with each other and others from Papaveraceae, and analyzed the phylogenetic relationships based on the sequences of common CDS. The cp genomes are 189,029 to 190,247 bp in length, possessing a quadripartite structure and with two highly expanded inverted repeat (IR) regions (length: 41,955 to 42,350 bp). Comparison between the cp genomes of C. tomentella, C. saxicola and Papaveraceae species revealed high variability in genome sizes, genome structures, gene content, and gene arrangements. Five NADH dehydrogenase-like genes with psaC, rpl32, ccsA and trnL-UAG normally located in the SSC region have migrated to IRs resulting in IR expansion and gene duplication. An up to 9 kb inversion involving five genes (rpl23, ycf2, ycf15, trnI-CAU and trnL-CAA) was found within IR regions. In addition, the accD gene was found to be absent. The ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. Phylogenetic analysis showed that genus Corydalis is quite distantly related to the other genera of Papaveraceae, supporting for recent advocacy to establish a separate Fumariaceae family. Conclusions: Our results provide a useful resource for classification of this taxonomically complicated genus, and will be valuable for understanding Papaveraceae evolutionary relationships.

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 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.

scholarly journals The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yan-Yan Guo ◽  
Jia-Xing Yang ◽  
Ming-Zhu Bai ◽  
Guo-Qiang Zhang ◽  
Zhong-Jian Liu
Keyword(s):  
Gene Order ◽  
Inverted Repeat ◽  
Single Copy ◽  
Gene Content ◽  
Comparative Genomic ◽  
Substitution Rates ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Ideal System ◽  
Small Single Copy

Abstract Background Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. Results Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 – 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum. The plastomes of Paphiopedilum have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates. Conclusions We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.

A mammalian origin of bidirectional DNA replication within the Chinese hamster RPS14 locus

1994 ◽  
Vol 14 (9) ◽  
pp. 5628-5635
Author(s):  
E S Tasheva ◽  
D J Roufa
Keyword(s):  
Dna Replication ◽  
Chinese Hamster ◽  
Housekeeping Gene ◽  
Single Copy ◽  
The Other ◽  
Replication Origins ◽  
Chromosomal Replication ◽  
Dna Binding Sites ◽  
Sequence Encoding ◽  
Copy Dna

Two complementary experimental approaches have been used to identify a chromosomal origin of bidirectional DNA replication within or immediately downstream of the Chinese hamster ribosomal protein S14 gene (RPS14). The replication origin, designated oriS14, maps within a 1.6- to 2.0-kbp region of RPS14 that includes the gene's third and fourth introns, exons IV plus V, and approximately 500 bp of proximal downstream flanking DNA. The nucleic acid sequence encoding oriS14 closely resembles the other mammalian chromosomal replication origins whose primary structures are known. It contains DNA binding sites for a large number of transcription factors, replication proteins, and mammalian oncogenes as well as several dinucleotide repeat motifs, an AT-rich region, and a sequence that is likely to bend the DNA. In contrast to the other well-characterized mammalian replication origins, which are autosomal and therefore carried as two copies per somatic cell, oriS14 is encoded by single-copy DNA within a hemizygous segment of chromosome 2q in CHO-K1 cells. Also, other known mammalian replication origins are situated in nontranscribed, intergenic DNA, whereas the DNA sequence encoding oriS14 substantially overlaps the transcribed portion of a constitutively expressed housekeeping gene.

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