‘Empty’ minicircles and petB/atpA and psbD/psbE (cytb₅₅₉ α) genes in tandem in Amphidinium carterae plastid DNA1

Abstract

Amphidinium carterae minicircle chloroplast DNA was separated from total DNA by centrifugation through a sucrose/NaCl gradient. Sequences of minicircles with psbA and 23S rRNA contained a common region of 67 bp. Primers designed from this generated numerous polymerase chain reaction products of 1.5^2.6 kb. These contained psaA and psaB as one gene/circle, and petB/atpA and psbD/psbE as two genes/ circle.`Empty' minicircles of 1.7^2.5 kb containing no identifiable genes or parts of genes were more abundant than genecontaining circles. From 15 minicircles a minimum common region of 48 bp was identified, with little identity to that from other dinoflagellate minicircles. ß 2001 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.

5 The origin of the dinoflagellate plastid

“…Uchida (1988) showed that peridinin dinoflagellates have a divergent ferredoxin and later found that dinoflagellate psbA sequences are also extremely divergent from other algae (Takishita and Uchida 1999). Using density gradient centrifugation Zhang (1999) and later Barbrook and Howe (2000) as well as Hiller (2001), and Bachvaroff (unpublished) have separated circular, or plasmid-like DNAs from peridinin dinoflagellates. These minicircles encode one or sometimes two genes, although partial or incomplete genes have also been found (Hiller 2001).…”

“…Using density gradient centrifugation Zhang (1999) and later Barbrook and Howe (2000) as well as Hiller (2001), and Bachvaroff (unpublished) have separated circular, or plasmid-like DNAs from peridinin dinoflagellates. These minicircles encode one or sometimes two genes, although partial or incomplete genes have also been found (Hiller 2001). The messenger RNA for psbA is located in the plastid and therefore it is likely that the minicircles are also in the plastid (Takishita et al 2003).…”

“…The typical, peridinin plastid is pigmented with chlorophylls a, c and peridinin, is surrounded by three unit membranes, and has thylakoids stacked in groups of three (Van den Hoek et al 1995). Among the distinctive properties of the peridinin plastid are a chloroplast genome that is thought to consist entirely of singlegene minicircles (Zhang et al 1999;Barbrook and Howe 2000;Hiller 2001), a water soluble light-harvesting complex composed of a chlorophyll a/c and peridinin binding protein, and reliance upon a nuclear-encoded form II rubisco of a type known elsewhere only from anoxygenic photosynthetic bacteria (Morse et al 1995;Rowan et al 1996).…”

“…However, the position of the dinoflagellate plastid in particular is unclear using typically plastid-encoded genes . Dinoflagellates appear to have an extremely reduced plastid coding potential, and about eleven protein-coding genes that would normally be found in the chloroplast genome are found on single or double gene minicircles (Zhang et al 1999;Barbrook and Howe 2000;Hiller 2001). Apparently many of the remaining genes have been transferred to the dinoflagellate nucleus ).…”

Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium

“…Unigenic DNA minicircles of 2-3 kbp that encode plastid gene functions have been found in a number of different peridinin-containing dinoflagellates, including species of Heterocapsa (Zhang et al, 1999(Zhang et al, , 2002, Amphidinium operculatum (Barbrook & Howe, 2000;Barbrook et al, 2001), Amphidinium carterae (Hiller, 2001) and Protoceratium reticulatum (Zhang et al, 2002). The non-coding regions of the minicircles are highly divergent across dinoflagellate genera, except that short stretches of a single nucleotide are frequent.…”