Chloroplasts

Analysis of the Plastid Genome Sequence During Maize Seedling Development

Shoot development in maize progresses from small, non-pigmented meristematic cells to expanded cells in the green leaf. During this transition, large plastid DNA (ptDNA) molecules in proplastids become fragmented in the photosynthetically-active chloroplasts. The genome sequences were determined for ptDNA obtained from Zea mays B73 plastids isolated from four tissues: base of the stalk (the meristem region); fully-developed first green leaf; first three leaves from light-grown seedlings; and first three leaves from dark-grown (etiolated) seedlings. These genome sequences were then compared to the Z. mays B73 plastid reference genome sequence that was previously obtained from green leaves. The assembled plastid genome was identical among these four tissues to the reference genome. Furthermore, there was no difference among these tissues in the sequence at and around the previously documented 27 RNA editing sites. There were, however, more sequence variants (insertions/deletions and single-nucleotide polymorphisms) for leaves grown in the dark than in the light. These variants were tightly clustered into two areas within the inverted repeat regions of the plastid genome. We propose a model for how these variant clusters could be generated by replication-transcription conflict.

Isolation, quantification, and analysis of chloroplast DNA

Many areas of chloroplast research require methods that can assess the quality and quantity of chloroplast DNA (cpDNA). The study of chloroplast functions that depend on the proper maintenance and expression of the chloroplast genome, understanding cpDNA replication and repair, and the development of technologies for chloroplast transformation are just some of the disciplines that require the isolation of high-quality cpDNA. Arabidopsis thaliana offers several advantages for studying these processes because of the sizeable collection of mutants and natural varieties (accessions) available from stock centers and a broad community of researchers that has developed many other genetic resources. Several approaches for the isolation and quantification of cpDNA have been developed, but little consideration has been given to the strengths and weaknesses and the type of information obtained by each method, especially with respect to A. thaliana. Here, we provide protocols for obtaining high-quality cpDNA for PCR and other applications, and we evaluate several different isolation and analytical methods in order to build a robust framework for the study of cpDNA with this model organism.

The loss of DNA from chloroplasts as leaves mature: fact or artefact?

In this review, the controversy regarding the preservation or degradation of chloroplast DNA (cpDNA) as chloroplasts develop their photosynthetic capacity and leaves reach maturity is addressed. A constant amount of cpDNA during maturity might be expected in order to support photosynthesis over the lifespan of the leaf. Nevertheless, a decline in cpDNA during leaf development was found for all seven plant species investigated. Initial measurements showed that Arabidopsis was similar to the other seven. The controversy arose with two recent studies concluding that the amount of cpDNA remains constant as Arabidopsis leaves mature. These authors proposed that the observation of Arabidopsis chloroplasts with undetectable levels of DNA was an artefact, although the most recent data support the original findings. If the amount of cpDNA remains constant, then Arabidopsis is atypical and would not serve as a good model for chloroplast development. It is shown that the apparently contradictory data may be attributed to methodology and the choice of leaves to be compared. Thus, it is concluded that the controversy can be resolved, Arabidopsis can serve as a representative model, and cpDNA degradation is a common event in chloroplast development.