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Current Genetics

, Volume 62, Issue 2, pp 431–442 | Cite as

The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication

  • Delene J. Oldenburg
  • Arnold J. BendichEmail author
Original Article

Abstract

The structure of a chromosomal DNA molecule may influence the way in which it is replicated and inherited. For decades plastid DNA (ptDNA) was believed to be circular, with breakage invoked to explain linear forms found upon extraction from the cell. Recent evidence indicates that ptDNA in vivo consists of linear molecules with discrete termini, although these ends were not characterized. We report the sequences of two terminal regions, End1 and End2, for maize (Zea mays L.) ptDNA. We describe structural features of these terminal regions and similarities found in other plant ptDNAs. The terminal sequences are within inverted repeat regions (leading to four genomic isomers) and adjacent to origins of replication. Conceptually, stem-loop structures may be formed following melting of the double-stranded DNA ends. Exonuclease digestion indicates that the ends in maize are unobstructed, but tobacco (Nicotiana tabacum L.) ends may have a 5′-protein. If the terminal structure of ptDNA molecules influences the retention of ptDNA, the unprotected molecular ends in mature leaves of maize may be more susceptible to degradation in vivo than the protected ends in tobacco. The terminal sequences and cumulative GC skew profiles are nearly identical for maize, wheat (Triticum aestivum L.) and rice (Oryza sativa L.), with less similarity among other plants. The linear structure is now confirmed for maize ptDNA and inferred for other plants and suggests a virus-like recombination-dependent replication mechanism for ptDNA. Plastid transformation vectors containing the terminal sequences may increase the chances of success in generating transplastomic cereals.

Keywords

GC skew Herpes simplex virus Chloroplast DNA Recombination-dependent replication Telomeres 

Abbreviations

DB

Dilution buffer

HSB

High salt buffer

HSV

Herpes simplex virus

IR

Inverted repeat

LSC

Long single copy

mtDNA

Mitochondrial DNA

OBP

Origin binding protein

ori

Origin of replication

PFGE

Pulsed-field gel electrophoresis

PK

Proteinase K

ptDNA

Plastid DNA

RDR

Recombination-dependent replication

SSBP

Single-strand binding protein

SSC

Short single copy

SSA

Single-strand annealing

Notes

Acknowledgments

This research was funded by the Junat Fund (a private charitable fund).

Compliance with ethical standards

Conflict of interest

The authors DO and AB are co-inventers for the patent application: “Plastid Transformation Using Linear DNA Vectors”; application nos. PCT/US2013/030775, WO2014/065857A1. The linear vectors described in this patent are based on the terminal ptDNA sequences reported in this manuscript.

Supplementary material

294_2015_548_MOESM1_ESM.pdf (1.3 mb)
Supplementary material 1 (PDF 1370 kb) Online Resource 1: Comparisons of maize ptDNA end sequences to sequences from other ptDNAs; sequence alignments and amount of similarity are shown
294_2015_548_MOESM2_ESM.pdf (366 kb)
Supplementary material 2 (PDF 365 kb) Online Resource 2: GC skew plots of the plastid genomes from several land plants and the protist Euglena gracilis and viral genome of herpes simplex
294_2015_548_MOESM3_ESM.pdf (855 kb)
Supplementary material 3 (PDF 855 kb) Online Resource 3: Exonuclease digestion and PFGE of maize and tobacco ptDNAs
294_2015_548_MOESM4_ESM.pdf (382 kb)
Supplementary material 4 (PDF 383 kb) Online Resource 4: Secondary structure prediction of the terminal sequences from maize, rice, and wheat

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Department of BiologyUniversity of WashingtonSeattleUSA

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