DNA sequence organization in the water mold Achlya

Abstract

Experiments are described that characterize the organization of DNA sequences in the water mold Achlya bisexualis . These experiments demonstrate that repetitive and single copy sequences in the Achlya genome are arranged in a long-period interspersion pattern. Estimates of the spacing intervals between repetitive and single copy DNA indicate, however, that the interspersion pattern in Achlya is longer than has been previously reported in other eukaryotes. These data and measurements of structural gene expression in Achlya [Timberlake, W.E., Shumard, D. S. & Goldberg, R. B. (1977) Cell 10, 623-632] make it difficult to propose a regulatory function for repeated DNA in this eukaryote.

Electron microscopy of Achlya deoxyribonucleic acid sequence organization.

“…No singlestranded loops were observed within these duplex regions, indicating the absence of detectable regions of base mispairing. This conclusion is supported by melting profiles of reassociated repetitive DNA which showed a Tm of only 3°C lower than that of similar-sized native DNA (13 observed are presented in Table 1, and electron micrographs of representative molecules are shown in Fig. 3A (21), and such molecules often appear in electron microscope spreads of longer Cot fractions (e.g., 3,19).…”

“…This conclusion is strengthened by the absence of any complexes or aggregates of short multiple forks in this population. Short, clustered, permuted repeats (e.g., R1R4R2R7R4) or short repeats interspersed with single-copy sequences should readily form such forked and multiple-forked structures when reannealed at the fragment lengths used here (3 (13). With the exception of inverted repeats, these DNA sequences appear to be organized in precisely paired arrays and are not interspersed with other sequences of significantly different repetition frequency at the largest fragment lengths examined.…”

“…2C and D because they also represented the random sizes of stems and loops contained in the foldback fraction as a whole. In addition, Hudspeth et al (13) observed only a very small increase in DNA binding to hydroxyapatite at a Cot of 10-5 over a >30-fold range of DNA fragment sizes. Taken together, these results predict that inverted repeats are spaced at large intervals within the genome.…”

“…The average patterns of DNA sequence organization in the fimgus Achlya have been studied by Hudspeth et al (13) using reassociation kinetics. They demonstrated that ca.…”

“…These are (i) short-period interspersion in which 0.2-to 0.4-kilobase pair (kbp) repetitive sequences are interspersed among single-copy sequences at intervals of<3 kbp (e.g., Xenopus, sea urchin) and (ii) long-period interspersion in which repetitive sequences averaging 6 kbp are contiguous with single-copy sequences of >10 kbp in length (e.g., Drosophila). Reassociation analysis of the nuclear DNA ofAspergillus (23), Neurospora (16), Saccharomyces (12), Phycomyces (11), Schizophillum (6), and Achlya (13) has shown that these organisms have very small genomes (<0.05 pg) and contain only limited amounts of repetitive DNA, most of which may be ribosomal DNA (rDNA). The repetitive DNA appears not to be interspersed with single-copy sequences at the longest DNA lengths studied (>10 kbp).…”