Inheritance of extrachromosomal rDNA in Physarum polycephalum.

Abstract

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.In some lower eucaryotic organisms, the multiple genes coding for rRNA are located on extrachromosomal DNA molecules. In the best studied of these systems, Tetrahymena species (ciliates) and Physarum polycephalum (an acellular slime mold), the extrachromosomal rDNAs are of a discrete size (about 20 and 60 kilobases [kb], respectively) and have a similar structure. The molecules are linear and are organized as palindromes, with two transcription units arranged in opposite orientations near the ends of the DNA, separated by a spacer region with a rotational symmetry axis in the middle (13, 21). In P. polycephalum rDNA this spacer is 20 kb in size and contains a complex series of directly repeated, inversely repeated, and unique sequences (8). Replication of P. polycephalum rDNA molecules (22) commences at one of four potential origins in the central spacer region and proceeds bidirectionally towards the ends of the linear molecules. In contrast to chromosomal DNA replication, rDNA replication takes place during most of the mitotic cycle, notjust in the S phase, and is unscheduled. That is, some rDNA molecules replicate once, some more than once, and some not at all, with the end result being that the total number of molecules after each mitosis is unchanged. The ends of the linear P. polycephalum rDNA molecules are heterogeneous in size, and near each end are located onenucleotide gaps on one strand at specific nucleotide seq...

Inheritance of extrachromosomal ribosomal DNA during the asexual life cycle of Dictyostelium discoideum: examination by use of DNA polymorphisms.

“…In Physarum polycephalum replication of rDNA palindromes occurs throughout the S and G2 cell cycle stages, and some, but not necessarily all, rDNA palindromes serve as replication templates (33). Similar changes to those observed in this work in the relative proportions of polymorphic rDNA palindromes and effects on rDNA inheritance were observed during the sexual cycle of Physarum polycephalum (6). In D. discoideum NC4-derived haploids, in which multiple rDNA forms exist, more than one rDNA gene must serve as a template.…”

“…exhibits levels of polymorphism between those observed in D. discoideum and T. thermophila (6). This degree of polymorphism correlates with the size of the palindromes: that ofD.…”

“…In Physarum polycephalum the situation is not clear. If there is a chromosomal copy, assumptions need to be made to explain the mode of inheritance of ribosomal DNA (rDNA) (6). In D. discoideum there is no firm evidence supporting the existence of a chromosomal copy of rDNA (13).…”

Immunoelectron microscopic localization of the nucleolar protein B-36 (fibrillarin) during the cell cycle of Physarum polycephalum

“…These 60-kb long linear DNA molecules which contain the 2 transcription units in opposite orientation ( [14]; this paper) are replicated as independent entities mostly during the G2 phase of the cell cycle [34]. No integrated copy has been found within the chromosomes, although the inheritance of rDNA genes through meiosis does not exclude the existence of such a molecule [11]. Clearly, Physarum is lacking a typical NOR, as the rRNA genes are not tandemly arranged within the genome.…”

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

“…The usability of a DNA marker gene depends on its ability to separate species by a distinction between intra‐ and interspecific divergence between sequences of the same and related species, the so‐called “barcoding gap” (Meyer & Paulay, ). Partial sequences of the 18S rRNA gene (SSU) have been suggested as universal eukaryotic DNA marker due to its multicopy and homologous nature (Hadziavdic et al., ; Pawlowski et al., ), which is also the case in myxomycetes (Ferris, Vogt, & Truitt, ; Torres‐Machorro, Hernández, Cevallos, & López‐Villaseñor, ). In accordance, SSU markers have been successfully used to assign sequences to known species of protists as recently demonstrated for ciliates (Bachy, Dolan, López‐García, Deschamps, & Moreira, ), alveolates (Medinger et al., ), marine cercozoans (Chantangsi & Leander, ) and euglyphid testate amoebae (Heger et al., ).…”