Linear molecules of tobacco ptDNA end at known replication origins and additional loci

Abstract

Higher plant plastid DNA (ptDNA) is generally described as a double-stranded circular molecule of the size of the monomer of the plastid genome. Also, the substrates and products of ptDNA replication are generally assumed to be circular molecules. Linear or partly linear ptDNA molecules were detected in our present study using pulsed-field gel electrophoresis and Southern blotting of ptDNA restricted with 'single cutter' restriction enzymes. These linear DNA molecules show discrete end points which were mapped using appropriate probes. One possible explanation of discrete ends would be that they represent origins of replication. Indeed, some of the mapped ends correlate well with the known origins of replication of tobacco plastids, i.e. both of the oriA sequences and--less pronouncedly--with the oriB elements. Other ends correspond to replication origins that were described for Oenothera hookeri, Zea mays, Glycine max and Chlamydomonas reinhardtii, respectively, while some of the mapped ends were not described previously and might therefore represent additional origins of replication.

The Structure of Chloroplast DNA Molecules and the Effects of Light on the Amount of Chloroplast DNA during Development in Medicago truncatula

“…For M. truncatula, we found this profile in lane 1 of Figure 1A and for cpDNA representing three other stages of leaf development (Shaver et al 2006), as well as for pea (Pisum sativum), another species without an IR, at one stage of seedling development (Bendich and Smith, 1990). The subgenomic restriction fragments for M. truncatula and tobacco (Scharff and Koop, 2006) were less prominent than those for maize. This difference can be attributed to a larger size of the concatemers and branched forms giving a higher ratio of monomersized fragments to end fragments in M. truncatula and tobacco than in maize.…”

“…1A, lane 4, and C; Table I). Taken as pairs, the fragments can be summed to the approximate size of the genome (as done previously for maize [Oldenburg and Bendich, 2004b] and tobacco [Nicotiana tabacum; Scharff and Koop, 2006]) in three ways: p2 (109 kb) and a predicted fragment of 15 kb, p3 (97 kb) and a predicted fragment of 27 kb, and a pair of p4 fragments (66 kb; Fig. 1C; Table I).…”

“…The ends of linear cpDNA molecules have been mapped for the IR-containing maize (Oldenburg and Bendich, 2004b) and tobacco (Scharff and Koop, 2006) and now for M. truncatula that has no IR. For all three species, ends are located at positions near regions homologous to tobacco oriA (homologous to Oenothera oriB) and Oenothera oriA (Fig.…”

“…For M. truncatula, we mapped an additional end (Fig. 1C, map d) near gene psbK that corresponds to ends found in tobacco (Scharff and Koop, 2006) and two ends (Fig. 1C, maps b and f) that so far appear to be unique to M. truncatula.…”

Effects of Reduced Chloroplast Gene Copy Number on Chloroplast Gene Expression in Maize

“…It seems likely that these trends are related to genomic features that influence DNA replication or maintenance (for review, see Day and Madesis, 2007). For example, origins of replication (Kunnimalaiyaan and Nielsen, 1997;Wang et al, 2002;Wang et al, 2003) and ends of linear plastid DNA molecules (Oldenburg and Bendich, 2004b;Scharff and Koop, 2006) map near the junction of the inverted repeat and small single copy region in various angiosperms. The disproportionate loss of DNA from the small single-copy region in w2-mum2 mutants may be related to these features.…”